Defra Project WQ0112

UNDERSTANDING THE IMPACT OF FARMING ON AQUATIC

ECOSYSTEMS

Final Report 31 January 2008

Andrew Davey1
Mike Gardner1
Ian Johnson1
Stephen Nixon1
Michael Payne2
Holly Smith1

1
WRc plc, Frankland Road, Blagrove, Swindon, SN5 8YF
2
Michael Payne Environmental Consultants, Field Barn Farm, Boughton, Kings Lynn, PE33
9AH

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Table of contents

1 Introduction 1
1.1 Rationale 1
1.2 Aims and objectives 1
1.3 Scope of review 1
1.4 Approach 2
1.5 Trends in agricultural production and potential impacts on aquatic ecosystems 2

2 Impact of pollutants on aquatic ecosystems 4

2.1 Nitrate/nitrogen 4
2.2 Phosphorus 6
2.3 Ammonia 8
2.4 Soil sediment 10
2.5 Pesticides 12
2.6 Veterinary medicines 15
2.7 Faecal pathogens 16
2.8 Organic material 16
2.9 Endocrine disrupting chemicals 17
2.10 Other pollutants 19
2.11 Combined effects of different pressures 19

3 Indicators of pollution 21
3.1 Background 21
3.2 Species/biological quality elements indicative of the effects/impacts of farming 21
3.3 Monitoring under the Water Framework Directive 22
3.4 Use of biomarkers as early warning systems for farming-related activities 24
3.5 Summary 25

4 Understanding the impact of farming on aquatic ecosystems 26

4.1 Introduction 26
4.2 Knowledge of activities, pathways, processes, source apportionment and impacts 29
4.3 Quantification of scale and importance of impact 31
4.4 Improvement, development and implementation of cost-effective mitigation measures 32

5 Knowledge transfer plan 36

6 References 37

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1 Introduction
1.1 Rationale

The Water Framework Directive (WFD), which came into force on 22 December 2000, is a wide
ranging piece of European environmental legislation that sets objectives for protecting and enhancing
water quality and the status of aquatic ecosystems. Specifically, it aims to achieve “good chemical and
ecological status” in surface waters (rivers, lakes, transitional (estuarine) and coastal waters) by 2015,
where "good" represents a slight deviation from minimally impacted reference conditions. To achieve
this, the WFD makes provision for the establishment of River Basin Districts (RBDs) within which river
basin management plans will be implemented to target both point and diffuse sources of water
pollution.

Farming activities are major sources of pressures on the water environment. The development and
delivery of cost-effective measures to meet the objectives set out by the WFD requires an assessment
of the contribution that agricultural land management practices makes to pollutant losses to water. In
addition, the impact of those pollutants on the ecology of the receiving waters must be understood and
quantified. In 2002, Defra conducted a Strategic Review of diffuse water pollution from agriculture in
England, which assessed the environmental pressures and impacts exerted on water by agricultural
practices and critically appraised the success of existing policy instruments to control such pollution 1.
While some of the impacts of pollution are well documented (e.g. eutrophication), there is now a need
to pull together information on the effect of a wider range of pollutants across all types of aquatic
ecosystem.

This report summarises the main findings and conclusions from the study. It is accompanied by two
Annexes with more detailed background information on some of the key aspects: sources and
pathways of pollutants, and strategies to tackle agricultural water pollution are covered in Annex A,
and indicators of pollution are covered in Annex B.

1.2 Aims and objectives

The aim of this report is to explore and benchmark current knowledge and understanding of the effects
of farming on aquatic ecosystems in England and Wales and to identify future research needs. To
achieve that aim the Defra Tender document indicated that the desk study should address the
following points:

 The study should identify what data/information already exists, where it resides and how
readily available it is.
 It should focus on the impact of pollutants/contaminants, including sediments, at the aquatic
ecosystem level and on individual species, including vertebrates, invertebrates and algae etc.
 Existing knowledge on suitable indicator species for the effects of pollution/contamination,
including those that could act as early warning markers, should be collated and discussed.
 Knowledge on the sources and exposure pathways of potential pollutants, and the relative
contribution and effects of different farming management practices, should be discussed to
provide context and background for the study.
 Recommendations for future R&D on the effects of farming on aquatic ecosystems should be
proposed, and should focus in particular on research which could be used to identify cost-effective
mitigation approaches.
 A knowledge transfer plan should be included. It is important to identify clearly the outputs and
pathways to delivery from the proposed project.

1.3 Scope of review

Farming is defined as all agricultural and horticultural activities. Agriculture uses over 76% of the land
area of England and Wales and horticulture is undertaken on around 1% of the total agricultural land in
the UK.2 The main categories of pollutant arising from agricultural activities are: nitrate; ammonia;
phosphorus; soil sediment; pesticides; veterinary medicines; faecal pathogens; organic material;
endocrine disrupting chemicals; other hazardous substances such as heavy metals and hydrocarbons;
and hydromorphological pressures such as land drainage, flood defence and water abstraction.

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Hydromorphological pressures that directly impact ecosystems and indirectly affect water quality are
not discussed in detail in this review.

This report reviews the impact of agricultural pollution on all surface waters (rivers, lakes, transitional
and coastal waters). Groundwater provides base flow to many rivers and lakes and is an important
transport pathway for pollutants such as nitrates. The importance of groundwater in the achievement
of Good Ecological Status (GES) in dependent surface water bodies is recognised by the inclusion of
‘connection to groundwater’ as a quality element for the classification of the status of river and lake
water bodies. The role of groundwater in modifying water quality and ecology is therefore integrated
across all surface water body categories rather than considered separately.

Further details of the scope of the review are provided in Annex A.

1.4 Approach

The report collates and assimilates data and information from sources including: Defra research
projects (searched via Defra http://randd.defra.gov.uk/), Environment Agency technical reports and
science reports, UKTAG reports and guidance notes (searched via http://www.wfduk.org/) and WFD
Article 5 risk assessment reports and technical methods (available at http://www.environment-
agency.gov.uk/subjects/waterquality/955573/). In addition, a full CSA
(http://www.csa.com/csaillumina/login.php) search was conducted for relevant journal articles and
scientific reports using three keyword searches: (1) to search for information on the sources and
exposure pathways of pollutants we used the following terms: agriculture, pollution, water quality,
source, transport, pathway, diffuse pollution, run-off, agriculture, UK; (2) to search for information on
the impact of these pollutants on aquatic ecosystems we used the following terms: pollution, water
quality, impact, effect, stress, ecology/ecological, species, population, community, toxicity, river, lake,
estuary, coast, freshwater, marine, UK; (3) to search for information on indicators that are used to
assess the extent and intensity of pollution we used the following terms: (iii) pollution, water quality,
bioindicator/biological indicator, impact assessment, indicator species, index/metric, river, lake,
estuary, coast, freshwater, marine, UK.

A full reference list is provided in Section 6, where the availability of these documents is flagged.

1.5 Trends in agricultural production and potential impacts on aquatic ecosystems

Studies have been undertaken to assess how the reform of the EU’s Common Agriculture Policy and
other policies will impact on farming and water quality. Some of the main predicted changes and
projections to 2015 relevant to potential impacts on aquatic ecosystems include:

 Overall land use will not change markedly;3

 Changes in farming practices will help reduce levels of nitrate and phosphorus in surface and
ground waters;4
 The per hectare applications of fertiliser and sprays unlikely to change markedly; 5
 Extensification of grassland utilisation is likely to lead to reduced fertiliser applications; 6
 Marked reduction in livestock numbers;7
 Fewer larger herds of dairy cows – disappearance of mid-sized herds, focus of production will
be in the lowlands. Pressures of dairying will be concentrated in specific areas (more slurry to
be stored). 8. In some parts of country (South West) the size of herds is already increasing; 9
 Reductions in livestock numbers are likely to lead to reductions in levels of veterinary
medicines in water bodies in main livestock regions e.g. South West and West Midlands –
though intensification of dairying in parts of these regions may see an increase in localised
areas;10
 Fewer sheep will mean a reduction in sheep dip use;11 and
 Fewer cattle and sheep will reduce problems with poaching 12 and potential soil erosion;
 Outdoor pig sector to increase to escape from measures required under IPPC Directive for
installations for the intensive rearing of pigs (and poultry). 13

Climate change will have a significant effect on agriculture and potentially its impact on aquatic
ecosystems. Defra summarises the direct threats from climate change as prolonged and more
frequent droughts; changes in rainfall distribution; more storms and other extreme events; rising sea

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levels; increased and changing pest loads; increased risk of heat stress in livestock farming; and,
possible changes in soil water balance.14 Increasing temperatures and hence growing seasons may
also lead to new crops being grown. Other predicted impacts include: increased/change in range of
native/alien pest and disease problems15 (leading to the use of more or different pesticides); increased
use of irrigation16 (increased abstractions in some catchments); increased soil erosion (increased
sediment loads to water bodies); changed poaching/water logging risk in some areas (changes in
pollutants pathways and increased sediment load). Changes in intensity and seasonality of rainfall and
increased temperatures may change the fate and behaviour (and hence impact) of pesticides though
the overall effect may be very variable and difficult to predict. 17

The likely scale of the changes to agriculture that would be required to achieve good ecological status
(GES) for the WFD in terms of nitrate and phosphorus has been modelled. 18 The results predict that
the achievement of GES would require substantial changes in agricultural land use and management.
These might include identification of high risk areas where the risk of nutrient export is high, controls
on fertiliser use and livestock densities, and taking sensitive areas out of production. For example,
total nitrogen fertiliser usage and livestock numbers have declined in recent years and could be
expected to reduce agriculture’s contribution to water pollution. 19 However, other changes, such as the
continuing trend towards intensification, are likely to counteract this to some extent.

A more detailed description of sources and pathways of pollutants, and strategies to tackle agricultural
water pollution, is given in Annex A to this report.

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2 Impact of pollutants on aquatic ecosystems

This section reviews, for each of the ten pollutant categories listed in section 1.3, the key sources and
pathways, the magnitude of source and exposure pressure (including an assessment of the
proportional contribution from farming), the potential impact on aquatic ecosystems, and the current
extent and intensity of impact.

In assessing the extent and intensity of the impact of farming on aquatic ecosystems, the report draws
heavily on the results of the Environment Agency’s (EA) WFD Article 5 risk assessments, which
identify those water bodies at risk of failing to achieve the WFD objectives, such as the achievement of
good ecological and chemical status due to different categories of pressure. The risk assessments
give an indication of the potential impact of agriculture on the ecological status of water bodies.
However, water bodies were often identified as being at risk from more than one pressure making it
difficult to apportion the impact arising from agriculture from that arising from other activities and
sectors. Also some of the risk assessments were based on modelling rather than on direct evidence of
‘impact’ on ecological status. Therefore, even though the risk assessments identify the potential scale
of the impact of agriculture on ecological status, the actual impact may not have been fully quantified.
The UK Technical Advisory Group on the Water Framework Directive (UKTAG) has proposed
environmental standards for the implementation of the WFD and has assessed the implications of
applying them to existing monitoring data in terms of achievement of good ecological status. 20,21 These
results are also referred to in the text below as appropriate. The first full classification of ecological
status of water bodies will be available in December 2008 when draft River Basin Management Plans
will be published.

2.1 Nitrate/nitrogen
The principal farming activities leading to the pollution of water bodies by nitrate is the application of
inorganic fertilisers and animal manures to arable and pastoral land. Nitrate is highly soluble and is
readily leached from soils in water bodies via cracks and preferential (subsurface) pathways. 22 It can
also directly enter water bodies via run-off from land and through atmospheric deposition of NOx and
ammonia: the latter is rapidly oxidised when deposited on land. Nitrates lost from farmland may often
be accompanied by other agricultural pollutants which may compound the impact on ecology, for
instance nitrates lost from fertilisers and slurries applied to land are often accompanied by soil
sediment and organic matter. Unlike phosphorous, however, nitrate is unlikely to be incorporated with
soil sediments due to its high solubility.

At the national level (England and Wales) agriculture is the predominant source (60.6% in 2000/2001)
of the total nitrogen load to all surface waters, with 32.1% coming from sewage treatment works. 23
Total nitrogen loads to sea showed no clear trends between 1991 and 2003. 24 There are clear regional
differences with agricultural areas such as the South West and Anglian regions having the highest
nitrogen loads from agriculture while more populous areas such as the Thames region have a higher
proportion of nitrogen loads arising from sewage treatment works.

The EA’s WFD Article 5 risk assessments estimated that 37.9% of river water bodies (45.0% by
length), 19.9% of transitional water bodies (8.5% by area) and 13.1% of coastal water bodies (4.9% by
area) were at risk from diffuse nitrogen inputs.25 26 The risk assessment for rivers included nitrogen
inputs from agriculture and atmospheric deposition but did not consider any ecological effects of
nitrogen enrichment. For transitional and coastal waters, diffuse (riverine) inputs and direct discharges
were considered with no specific apportionment for agricultural inputs. No risk assessment was
undertaken for diffuse nitrogen in lakes.

As of 2007 there are 137 sensitive areas in England and Wales designated under the Urban Waste
Water Treatment Directive as being eutrophic or likely to become eutrophic in the near future without
action being taken. These sensitive areas are a mixture of rivers, lakes (reservoirs), harbours and
estuaries, and hence there will be a mixture of which nutrient will be most pertinent (nitrogen and/or
phosphorus) in terms of ecological impact and actions required. One of the criteria for the identification
of polluted waters under the Nitrates Directive is whether waters are eutrophic or will become
eutrophic in the near future without action being taken. As a result, a total of 55% of England was
designated as a Nitrate Vulnerable Zone (NVZ) in October 2002 though not all were necessarily

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designated because of the eutrophication criteria. Defra is currently reviewing and consulting on
increasing NVZs to 70% of England or applying the Action Programmes required under the Directive to
the whole of England. This latest review recognises that nitrogen may also play a role in the
eutrophication of freshwaters. There are also 12 problem or potential problem areas identified under
OSPAR's comprehensive procedure for the assessment of eutrophication. These are estuaries, bays
or harbours and correspond to areas designated under there UWWT and/or Nitrates Directive.

Nitrate concentrations are high in water draining from much of the agricultural land in England. 27 For
example in 2006, 28% of rivers had high concentrations of nitrate (greater than 30 mg l -1)28 with the
highest concentrations being found in the Midlands, Anglian and Thames regions, which have some of
the largest areas under intense agricultural production. Similarly, a review of nitrate concentrations in
rivers in England between 1999 and 2004 reported that the mean nitrate concentration varied
regionally from 15 mg l-1 in North West region to 39 mg l-1 in Anglian region.29 Typically, nitrate
concentrations are higher in lowland areas dominated by arable agriculture than in areas dominated
by pastoral farming30 and lower in wetter areas where high quantities of rainfall dilute the nitrate within
soils before being leached or washed into water courses. 31 Concentrations in drainage waters from
grassland systems are highly variable depending upon the intensity of stocking and management. 32
Nitrate concentrations are increased where manures are used, even under ‘best practice’.

The implications of the proposed WFD environmental standards for dissolved inorganic nitrogen have
been recently assessed.33 Of the 60 transitional and coastal water bodies with sufficient monitoring
data, 65% (by number) would be classified as less than good ecological status. There are 136
transitional and 99 coastal water bodies identified for the WFD, and hence this initial classification may
not be fully representative of all water bodies.

Nitrate occurs naturally in all surface waters but elevated concentrations of nitrate can cause
deterioration of ecological quality in three main ways: eutrophication, acidification and toxic effects.

Eutrophication: Nutrients (e.g. nitrogen and phosphorus) in the appropriate amounts (i.e. background
levels) are essential to maintain an adequate primary productivity, which in turn is essential to support
higher trophic levels and to maintain a healthy ecosystem structure and function. In general, excessive
nutrients of anthropogenic origin cause an increase in plant growth (eutrophication), which in still
waters causes increased phytoplankton biomass, often dominated by harmful or toxic species, leading
to increased turbidity and decreased light transparency. In rivers this may be seen as increased
attached algal growth or even excessive growth of higher plants. In estuaries and coastal waters,
excessive growth of opportunistic macroalgal species can result in the formation of dense algal mats,
which reduce light penetration to submerged communities and cover intertidal sediments. Sea grasses
may also experience severely retarded growth as a result of the growth of opportunistic macroalgal
species.34 These are examples of the direct effects of nutrient enrichment. As a consequence of
increased plant growth, there is an imbalance between the processes of plant/algal production and
consumption, followed by sedimentation of organic matter, stimulation of microbial decomposition and
oxygen consumption with depletion of bottom-water oxygen in stratified water bodies (indirect effects).
Thus, eutrophication causes not only nuisance increases in plant growth but also adverse changes in
species diversity as well as reduced suitability for human use and consumption.

In freshwaters, phosphorus is most likely to limit plant growth but some water bodies are limited by
nitrogen rather than phosphorus and are therefore vulnerable to nitrate-driven eutrophication.35 One
study, for example, found that phytoplankton growth was limited by nitrogen in one third of the 30
upland lakes studied.36 Nitrate /nitrogen rather than phosphorus is often the key limiting nutrient in
saline waters, although estuaries may be limited by phosphorous at their freshwater extreme. 37 There
are also many water body type-specific physical characteristics that influence the manifestation of
eutrophication. Such factors as water velocity, mixing characteristics, retention time, water
transparency and water temperature will fundamentally affect the response of any particular water
body to elevated nutrient concentrations. In the context of the WFD these factors are taken into
account in the quantification of type-specific reference conditions which equate to ‘natural’ undisturbed
ecological conditions and anchor the classification of ecological status against which the achievement
of good ecological status is judged.

Although macroalgal and toxic algal blooms are commonly associated with nutrient enrichment and
eutrophication, they can also occur naturally when, for example, stimulated by favourable

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meteorological conditions and physical processes such as advective heat transport. 38 The incidence of
naturally occurring algal blooms should be taken into account in the reference conditions of a water
body: an increase in the occurrence compared to reference conditions may indicate eutrophication
related bloom events. Under particular environmental conditions, the decay of algal blooms can lead to
a build up of bacteria which can release toxins that affect fish and lead to mass mortalities. A
significant example is the Hungerford fish mortality of 1998 when more than a million fish were killed. 39

Acidification: When the nitrate anion is leached from soils it may be accompanied by a hydrogen ion
or proton (H+) which may in some circumstances (such as in water bodies with low acid neutralising
capacity) contribute to the acidification of surface waters. 40 Acidification can exacerbate the loss of
macrophytes due to eutrophication and promote their replacement by filamentous green algae and
rushes which thrive in acidic conditions. Acidic conditions can also cause the proliferation of certain
macroinvertebrates that are more tolerant of low pH conditions (such as the mayfly Leptophlebia
vespertina), and a loss of those that are intolerant (such as the mayfly, Baetis rhodani).41 Few fish are
able to survive in highly acidic conditions; a pH of around 4.5 is fatal to most species. 42 Little is known
about how much acidification can be attributed to nitrates derived from agriculture. The contribution
that ammonia emissions from agricultural activities make to acidification is discussed under ammonia.

Toxic effects: Elevated nitrate concentrations can have direct toxic effects on certain freshwater
animals. Conversion of nitrate ions to nitrite ions in the body can cause respiratory problems in fish
and crayfish. Nitrates have also been implicated in the decline of amphibian populations as they can
cause impaired swimming ability and decreased body size in many species. It is thought that
freshwater organisms may be more sensitive to nitrate enrichment than those in coastal or estuarine
systems because nitrate is more toxic at low salinities.43

2.2 Phosphorus
The principal farming activities that lead to pollution of water bodies by phosphorus are the application
of inorganic fertilisers and animal manures to arable and pastoral land. Soil erosion by water and
overland flow are the principal pathways by which phosphorus enters water bodies. 44 Leaching and
subsurface flow, particularly via macropores or cracks, may also be important in some situations such
as on poorly permeable soils. The major point sources of phosphorus are from sewage treatment
works and industrial discharges. In many water bodies there may also be internal loads reflecting
historic external loads that are generated through a variety of chemical and biological processes acting
upon phosphorus stored within sediment and organic matter. The relative contributions of phosphorus
from external and internal sources are highly variable in both space and time. 45

The proportional loads of total phosphorus (TP) and soluble reactive phosphorus (SRP) to the waters
of Great Britain from agriculture have been estimated to be 23-28% and 19%, respectively. 46 The most
important source in both cases was households, which contributed 60.7% and 67.4% of TP and SRP,
respectively. There were regional differences in the proportions of TP loads contributed by agriculture
with the highest proportion of 62% occurring in the Western Wales RBD and 10% in the Thames RBD.
The total annual discharge (riverine and direct discharges) of orthophosphate to sea in England and
Wales between 1991 and 2003 was variable and showed no clear trends. 47 Riverine inputs, which
reflect both diffuse and point land-based sources, accounted for 40-75% of total inputs and were
highest in the southern North Sea and lowest in the Atlantic.

Emissions of phosphorus from sewage treatment works in rivers subject to both point and diffuse
sources of phosphorus are thought to pose a greater risk of eutrophication than emissions from
agriculture.48 This is because loads of soluble, and hence immediately bioavailable, phosphorus from
sewage treatment works enter the river continually throughout the year and are at minimum dilution
during the spring and summer when plant growth is high and most sensitive to phosphorus
concentrations in the water column. In contrast, the majority of the annual load of phosphorus from
agricultural land is attached to soil particles and not immediately bioavailable. It is delivered to rivers
and lakes during storm runoff events in autumn and winter, and a significant proportion of the load will
be immediately flushed out of the system by the high river flows. Some of this particulate phosphorus
may be deposited on the river bed and can enhance plant growth in subsequent growing seasons
either directly via root uptake or indirectly via desorption and diffusion into the water column. In slow-
flowing rivers accumulated sediment may therefore provide an instream reservoir of phosphorus that
may mask the effect of any changes in point source discharges. In general, however, the lower
bioavailability of phosphorus from diffuse sources means that point sources can provide the most

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significant risk of eutrophication in rivers, even in rural areas with high agricultural phosphorus
losses.49

However, it has also been demonstrated that intensively managed grassland can also be a significant
source of dissolved reactive phosphorus in some catchments from the surface applications of
manures, accumulation of soil phosphorus and the creation of bypass flow pathways that encourage
the loss of P from soil to water50.

The EA’s WFD Article 5 risk assessments estimated that 47.4% (out of 5858) of river water bodies
(50.3% by length), and 36.8% (out of 432) lake water bodies (40.2% by area) were at risk from diffuse
phosphorus (agricultural) inputs.51 Other diffuse sources such as septic tanks were not considered.
Under the UWWTD, 108 rivers, 4 canals, 8 lakes and10 reservoirs in England and Wales have been
designated as Sensitive Areas (eutrophic). This means that they are eutrophic or may become
eutrophic in the near future if preventative action is not taken. Lakes and rivers can be designated as
sensitive areas only if they show elevated phosphorus concentrations and evidence of change in
response parameters including diatoms and macrophytes (for rivers and lakes), chlorophyll-a and
water clarity (for lakes).52

Eutrophication due to elevated phosphorus concentrations is a serious and widespread problem in

rivers in England and Wales. In pristine rivers concentrations of SRP are very low – typically <30μg l -1.
In 2006, 55.3% of rivers in England and 10.7% of rivers in Wales had concentrations of phosphate
>100 μg l-1.53 Higher levels were generally found in the lowlands of central and east England and in
southern England and in rivers flowing through areas dominated by arable farming. However as this
assessment is only based on dissolved inorganic phosphorus (SRP) the figures do not provide a
profile of total phosphorus losses from agriculture, where a large part of the component will be in
particulate, as opposed to soluble, form.54

Although phosphorus concentrations >100 μg l-1 are considered to be indicative of existing or future
eutrophication problems, the sensitivity of rivers to eutrophication depends upon water chemistry and
hydrology. Calcareous (hard water) catchments are less sensitive to phosphorus enrichment than non-
calcareous (soft water) catchments. Furthermore, rivers in lowland areas are at greater risk of
eutrophication because deposition of sediment leads to the accumulation of a reservoir of instream
particulate phosphorus and high retention time facilitates uptake of phosphorus by diatoms and plants.

Lakes have been defined as eutrophic if they have mean phosphate concentrations in excess of 35 μg
l-1, mean chlorophyll-a concentrations greater than 2.5μg l-1 and a mean Secchi disk water
transparency of less than 6 m.55 Lakes tend to become naturally more eutrophic with (geologic) time
and as lakes naturally show a wide variation in trophic status, high phosphorus concentrations alone
are not indicative of anthropogenic eutrophication. Until the EA’s WFD monitoring programmes was
made operational in December 2006, there was no comprehensive monitoring scheme for lake water
quality in England and Wales and few data are currently available to make a national assessment of
lake trophic status. However, a review of research studies on 129 lakes in England and Wales found
that 69% of the lakes had total phosphorus concentrations greater than 100 μg l -1 P.56 In a study for
English Nature of 102 SSSI sites which were suspected of being eutrophic, 84% showed symptoms. 57
These studies suggest that a majority of lakes in England and Wales are nutrient enriched to some
extent.

More recently, the UK Technical Advisory Group (UKTAG) on the WFD proposed new standards for
phosphorus concentrations in rivers and lakes. These standards are type specific and would equate to
the achievement of good ecological status in terms of phosphorus. An assessment of the implications
of these new standards estimated that 63.3% of river water bodies and 67% of lake water bodies in
England and 12.8% of rivers and 80% of lakes in Wales would be reported as worse than Good Status
with at least 50% confidence for rivers and 95% confidence for lakes. 58 This preliminary classification
is in respect of all sources of phosphorus and not just that due to agricultural sources. It should also be
noted that UKTAG has expressed some concern on the validity of data used to classify lakes.

Although nitrogen (nitrate) is thought to be the key limiting nutrient in saline waters, phosphorus can
also contribute towards eutrophication. Estuaries, in particular, may be limited by phosphorus at their
freshwater extreme, grading through to nitrogen limitation at their seaward end. However, high
suspended sediments and turbidity in estuaries commonly means that light rather than nutrients often

7
limits algal growth. The WFD Article 5 risk assessments did not address diffuse phosphorus in
transitional or coastal waters.

The main impact and effect of enrichment of freshwater water bodies by phosphorus is eutrophication.
Eutrophication has already been described in the section on nitrate.

2.3 Ammonia
Major sources of ammonia include livestock farming such as pig and poultry farms. Other sources of
ammonia emissions include direct volatilisation from mineral fertilisers, animal manures, agricultural
crops and a wide range of non-agricultural sources including sewage, catalytic converters, wild
animals, seabirds and industrial processes.59

Ammonia can enter water bodies via a number of pathways including atmospheric deposition, run-off
from land, leaching and direct excretions from animals. Ammonia deposited from air to land is rapidly
oxidised to nitrate. Ammonia is the least stable form of nitrogen in water and is easily transformed to
nitrate in oxygenated waters. It is also readily converted to nitrate and nitrite in soils where it is applied
in fertilisers. As a result a small proportion of the nitrogen that is lost to water bodies is in the form of
ammonia. Deposition of ammonia can lead to terrestrial and aquatic eutrophication and acidification.

The source of ammonia and the pathway by which it reaches the water body can have an important
bearing on the degree of ecological effect. The greatest ecological impact will occur where livestock
have direct access to water and are able to defecate directly into streams, rivers and lakes. As this
direct input of ammonia will be highly concentrated it will be unlikely to be converted to nitrate quickly.
Leakages of slurry pits and farmyard manure storage facilities also pose a significant risk if there has
been insufficient storage time before the spillage to allow the conversion of ammonia to nitrate. By
comparison, the concentrations of ammonia in discharges from sewage treatment works are generally
low following treatment and are quickly converted to nitrate. Losses of ammonia from farmland will be
lower where slow movement of ammonia through cracks and spaces in soils promotes conversion to
nitrate and the adsorption and retention of ammonia in the soil. Consequently, ammonia contained in
organic material and slurries applied as fertiliser is more likely to be converted to nitrate before being
leached from the soil.

Ammonia losses from farmland are also dependent on the season and meteorological conditions at
the time of application of fertilisers and manures. For example, there is a greater risk of volatilisation of
ammonia from fertilisers and loss to the atmosphere during the summer months. If heavy rains follow
application of fertilisers to fields then a large percentage will be lost to watercourses as surface run-off
and is likely to be accompanied by sediment and other organic material.

It has been estimated that the UK released 263.4 kt of ammonia to air, water and soil in 2005 and that
agriculture accounted for 80% of emissions60 with cattle alone accounting for 44% of the total. 61 These
emissions arise from livestock housing, the storage, treatment and application of all types of animal
manures and the use of inorganic fertilisers. Ammonia emissions are highest in western England and
East Anglia, where the dominant sources of ammonia are cattle, pigs and poultry. Emissions are
lowest in upland areas of northern England and Wales. There has been a steady decline in
atmospheric ammonia emissions from agriculture since the early 1990s largely due to declining
livestock numbers and the use of nitrogen based fertiliser. Predictions indicate that this decline will
continue due to the influence of the Common Agriculture Policy (CAP) reform and IPPC Directive
regulations on both livestock numbers and management practices. 62 However, it is predicted that
atmospheric ammonia emissions will be the largest contributor to acidification, eutrophication and
secondary particulate matter at the European level by 2020 partly reflecting the success of European
polices to reduce SO2 and NOx emissions.63 Atmospheric ammonia emissions are affected by a large
number of factors that make the interpretation of experimental data difficult and emission estimates
uncertain64.

The total annual discharge of ammonia to sea from riverine and direct discharges in England and
Wales has declined steadily from 65 kt yr-1 in 1991 to around 40 kt yr-1 in 2003.65 Sewage discharges
contribute the majority of ammonia to UK coastal waters. Riverine inputs, which reflect both diffuse
and point land-based sources, have also shown a slight decline and continue to account for around
20% of total inputs. Atmospheric deposition of nitrogen (including ammonia) to surface water bodies
(excluding marine waters) has been estimated to be only a small proportion (~0.4%) of the total load. 66

8
However, in lakes with large surface areas compared with their total catchments and marine waters,
atmospheric deposition of nitrogen can constitute a significant part of the total inputs. 67 For example it
has been estimated that atmospheric deposition accounts for 25% of total nitrogen inputs into the
Baltic Sea.

The EA’s WFD Article 5 risk assessment only included point source discharges (e.g. sewage treatment
works and industrial discharges) of ammonia to rivers, transitional and coastal waters and did not
assess the risk of diffuse sources of ammonia. In terms of the effects of atmospheric emissions, the
EA risk assessments indicated that 21% (of 432) of lakes (16.4% by area) and 2.9% of river water
bodies (2.9% by length) are at risk from acidification: the assessment included the deposition of
ammonia with NOx and sulphate.

In 2005, the average concentration of ammonia in UK waters was 0.12 mg l -1 N, with the highest
concentrations being found in the North West (0.43 mg l -1 N) and North East (0.20 mg l-1 N) regions
and the lowest concentrations in the South West (0.07 mg l -1 N) and Welsh (0.04 mg l-1 N) regions.68

Ammonia occurs naturally in surface waters but at elevated concentrations it can become toxic to
aquatic organisms: the un-ionised form (NH3) is very toxic to aquatic life whilst the ionised form is
virtually non-toxic (NH4+).69 Current environmental quality standards (EQSs, expressed as annual
average concentrations) for the protection of freshwater and saltwater fish are 0.015 mg l -1 NH3-N and
0.021 mg l-1 NH3-N, respectively indicating that saltwater fish generally have a higher tolerance to
ammonia than freshwater fish. Standards for total ammonia (expressed as 90%ile concentrations)
have also been proposed for the classification of ecological status under the WFD: these are 0.3 mg
N/l and 0.6 mg N/l for the boundary between good and moderate ecological status for upland and low
alkalinity rivers, and lowland and high alkalinity rivers, respectively. 70 These proposed WFD standards
have been established in terms of effects on macroinvertebrate communities. No standards have been
proposed for lakes, transitional and coastal waters.

At low concentrations (<0.1 mg l-1 NH3) ammonia irritates the gills of some fish species, leading to skin
and gill hyperplasia which leaves the gills vulnerable to parasitic infection and disease. A study in
which rainbow trout were subjected to prolonged exposure of ammonia at low levels showed a
reduced success in egg hatching, reduced growth rates and morphological changes as well as
pathological changes in the gills, liver and kidneys.71

At higher concentrations, (>0.1 mg l-1 NH3) ammonia damages the skin, gills, eyes and internal organs
of fish.72 Negative physiological effects can result in reduced feeding activity and reduced body size. 73
Elevated levels of ammonia in the environment can impair ammonia excretion in fish or cause a net
uptake resulting in elevated concentrations in the body. This causes convulsions and eventually death.

Ammonia can be lethal to fish at concentrations less than 1 mg l -1. Freshwater coarse fish are less
sensitive to ammonia than salmonids; coarse species typically have an LC 50 (lethal concentrations for
50% mortality) of 0.3-2.5 mg l-1 whereas salmonids have an LC50 in the range 0.06-0.91 mg l-1.
However, a small number of species, such as the weather loach and mudskipper, can tolerate high
concentrations of ammonia.74 Atlantic salmon are amongst the species most susceptible to high
ammonia concentrations whilst species such as inland silverside and red drum are able to tolerate
higher concentrations.

Ammonia is also toxic to invertebrates, with toxicity being greatest during the early life stages and the
effects similar to those found in fish as mentioned above, and to Nitrosomonas and Nitrobacter
bacteria, where it inhibits the nitrification process which converts ammonia to less toxic nitrate. 75

Evidence is now emerging that nitrogen (NO x and ammonia) deposition in upland areas may be having
an eutrophication effect on UK upland waters76, and nitrate-driven eutrophication may be occurring in
some freshwater bodies.77 Further work is required on how nitrogen is affecting eutrophication in
upland lakes in the UK.78

The UKTAG’s preliminary assessment of the implications of the proposed standards for ammonia for
implementation of the WFD indicates that 17.3% of river water bodies in England (by length) and 2.7%
(by length) in Wales would be less than good ecological status. 79 This assessment was based on

9
measured levels of ammonia in rivers as part of the EA’s GQA scheme and would reflect the impact of
ammonia from all sources.

The effects of ammonia in transitional and coastal waters are similar to those observed in freshwaters,
but often exacerbated by high salinities and warm temperatures. The toxicity of ammonia can be
further increased by interactions with other chemical pollutants such as copper, cyanide, phenol, zinc
and chlorine. In well aerated waters, however, ammonia is converted to less toxic nitrate. Ammonia is
also toxic to crustaceans, but to a lesser extent than fish. Prawns are particularly sensitive, whereas
eastern oyster are particularly tolerant. At a lower trophic level, growth of algae is retarded when
exposed to concentrations of ammonia greater than 0.24 mg l -1 over 10 days.80

2.4 Soil sediment

The main mechanisms by which sediment is lost from farming activities are the erosion of river banks
and surface run-off and sub-surface pathways from fields. Loss of soil from river banks is a natural
process, but it can be accelerated where livestock have direct access to watercourses and loosen
sediment by trampling and de-stabilising the river bank. Poaching of soils is also a problem especially
during the winter months when soils are wet increasing their susceptibility to surface run-off.
Compared to other sources, surface run-off from fields has the potential for a greater impact on
aquatic ecosystems due to the associated pollutants, particularly phosphorus and pesticides, that can
be lost with it.

Soil is eroded by a variety of mechanisms and transported via numerous pathways. Susceptibility of
soils to erosion has a high spatial variability as a result of varying climatic conditions and soil
properties and, therefore, the intensity of the impact is highly variable, depending on the hydrodynamic
and ecological characteristics of the receiving water body. Losses of soil from farmland will not
necessarily be reflected in adjacent watercourses because sediment is transported and deposited
downstream. This increases the spatial extent of the impact and may displace the impact from the
immediate vicinity of the farmland. Furthermore, the sequential nature in which different sized fractions
of sediment are deposited as the river loses its capacity to transport sediment also means that the
intensity of the impact may vary spatially along the river, with the greatest impact being found in
lowland streams.

Erosion of soil sediment is estimated to result in losses ranging from 0.1 to 20 tonnes ha -1 yr-1,
depending upon soil characteristics, topography and land use. 81 Losses are greatest from arable
farmland, with the most vulnerable areas being the sandy soils in the southwest and southeast of
England, East Anglia, the Midlands and the chalky soils of the South Downs. Areas of farmland kept
for grazing and rearing of livestock situated adjacent to water courses have also proved problematic
due to trampling of river banks and soils, with much of this type of farming activity being concentrated
in north east and south west England. Highly susceptible land uses include late-sown winter cereal,
potatoes, sugar beet, field vegetables and outdoor pigs. 82 Preliminary source apportionment work
shows that 75% of sediment input into rivers can be attributed to agriculture. 83

Many studies on soil loss to water have concentrated on episodic and significant events (e.g. heavy
rain) of soil loss rather than on the smaller more cumulative processes and tended to focus on where
soil loss is present rather than where it is absent.84

The EA’s Article 5 risk assessment estimated that 21.0% of river water bodies (22.8% by length) were
at risk from sediment delivery from agricultural activities. The risk was calculated from models that
included only run-off from arable land but not field drains and eroding river banks. 85 Point sources such
as mines, quarries and gravel extraction sites were also omitted. No risk assessments were
undertaken for sediment in lakes, transitional and coastal waters.

The EA also reports that many chalk streams (approximately 101 out of 161) suffer from so-called
‘chalk stream malaise’. This is caused by a combination of silt smothering gravels and high phosphate
inputs, and exacerbated by low river flows. It is also thought that local geology and hydrological
conditions can worsen the impacts of any silt present in chalk streams by, for example, leading to river
bed concretion.86 In addition, in 2004 half of the 62 principal salmon rivers in England and Wales with
salmon action plans were at risk of missing their egg deposition targets, with siltation of spawning
gravels a major factor.87 However, there appears to be no representative assessment of the
geographic scale or the quantification of the potential problem of siltation in salmonid rivers. For

10
example, it appears that there is no information on how representative the 62 principal salmon rivers
are of the 34,500 km of rivers designated (salmonid or cyprinid) under the Freshwater Fish Directive
and the 51,183 km of river assessed for Article 5 of the WFD. Not all of these rivers would naturally
support salmonids.

There is limited data on levels of sediment deposition/siltation in fresh water bodies: a report from the
Life in UK Rivers project lists current data sources for rivers. 88 The available data does not provide a
representative assessment of siltation levels in rivers in England and Wales, and it has not been
possible to establish simple links between siltation and suspended solids concentrations/loads, and
siltation and land use. Suspended solids are monitored under the Freshwater Fish Directive which sets
a guideline standard of 25 mg l-1 for designated salmonid and cyprinid fishery waters. This standard is
exceeded in some rivers across the country, but particularly in central England, the Welsh borders and
south east England.89 The Harmonised Monitoring Scheme also includes the measurement of
suspended sediments at some of the 230 sites monitored, which are mainly located at the tidal limits
of major rivers or at the points of confluence of significant tributaries. 90

A study of the provenance of interstitial sediments in salmonid spawning gravels in 18 rivers in

England and Wales found that the vast majority of sediment was derived from surface run-off, although
there was large regional variation. For example, in the River Dee 98% of interstitial sediments were
derived from surface run-off and just 2% from bank erosion. 91 In southwest England, bank erosion is
thought to be the main source of fine sediment in spawning gravels whereas in southern England
surface soil erosion is more important. This difference reflects differences in agricultural activities in
the two areas: livestock farming (with animals poaching river channel margins) in the former and
mainly arable farming (with more stable river channels) in the latter. 92 93 A further survey looked at
siltation within artificial redds (spawning gravels) at 43 sites across 19 catchments in England and
Wales.94 It was thought that the silt (<0.85 mm particle size) accumulating at two of the sites could
adversely affect salmonid reproduction. It was hoped that the results from this survey could be
extrapolated to other rivers across England and Wales to obtain a more representative assessment.

The UKTAG has not proposed any standards for suspended sediment that would lead a water body to
be classified as less than good ecological status partly because the current Freshwater Fish Directive
annual average suspended standard of 25 mg/l was considered to be inappropriate and because of
the lack of suitable data to develop an alternative standard 95.

Sediment is constantly introduced into waterbodies through the natural processes of erosion and
runoff. Aquatic communities are adapted to cope with these natural levels of input and sediment
provides a habitat for many organisms. In the context of the WFD this would equate to ‘reference
conditions’ where natural levels of settled and suspended sediment would lead to typical plant and
animal communities that would be different for different types of water body. The detrimental effects of
increased loadings of sediment to water bodies resulting from human activities can affect all trophic
levels of the ecosystem.

In suspension, sediment can:

 Reduce primary production by increasing water turbidity. In marine waters there may be a
resultant reduction in growth rates, aerial coverage and depth of colonisation of macrophytes and
macroalgae. Macrophytes may be replaced by floating algae with resultant changes in fish and
invertebrate communities.96
 Alter water pH.
 Increase water temperatures by increasing heat absorption. Fish such as salmon and trout require
temperatures of between 5 and 15ºC for normal growth and maybe vulnerable to increases in
temperature.97
 Clog the gills of fish and crayfish, which impairs respiratory function and damages internal organs,
98
and overload the feeding appendages of filter-feeding organisms such as mussels, thereby
interfering with their digestive and respiratory systems.99
 Destroy the protective mucous covering the eyes and scales of fish, which makes them more
susceptible to disease and infection.100
 Be vectors of pollutants (organic matter, nutrients, chemical and microbial) that can, for example,
secondarily affect filter feeding animals.101 As a result, high suspended sediment can cause a shift
from filter-feeding organisms to deposit-feeding organisms.

11
When deposited, sediment can:
 Suppress growth of plants by reducing light penetration to, and oxygen uptake by, submerged
aquatic plants and causing instability for rooted plants such as brook water crowfoot. 102
 Blanket or smother benthic invertebrate habitats. Overall, sedimentation and turbidity has been
found to be inversely related to invertebrate densities and biomass 103 with, for example,
caddisfly104, mayfly and stonefly105 larvae being adversely affected by deposition of silt and
smothering and burial by fine sediments. Marine species which reside in burrows are particularly
vulnerable to smothering. Sediment boring species (e.g. the bivalve Pholas dactylus or burrowing
species such as the polychaete worm Polydora ciliata) are unlikely to recover from smothering due
to clogging of their burrows but may be able to tolerate high concentrations of sediment in
suspension.106
 Reduce the suitability of hard substrata as a habitat for colonising organisms, such as mussels
and oysters and other biofouling organisms. 107 Species of macroalgae such as Laminaria digitata,
which possess a holdfast for attachment to rocks, may be unable to establish themselves where
there is excessive deposition of fine cohesive sediments.
 Blanket spawning gravels of fish species such as Atlantic salmon108 109, sea trout, allis and twaite
shad and reduce egg and larvae survival rates.110
 Modify the morphology and hydrodynamic conditions of (river) waterbodies by reducing the speed
and turbulence of flow, thereby further reducing its ability to assimilate other pollutants.
 Have secondary effects on benthic organisms and on organisms with benthic stages of their life
cycles via pollutants associated with sediment.

Research is currently underway to link agricultural land use to the biodiversity of benthic invertebrates.
Preliminary results from the EU-Life funded SOWAP (Soil and Water Protection) project, a study
looking at the impact of soil loss on aquatic ecology, show that catchments with intensively cultivated
land have a lower diversity of benthic organisms than those catchments with woodland or natural
grassland.111

2.5 Pesticides
Agriculture and horticulture use over 80% of all pesticides in England and Wales. 112 The quantity of
pesticides used by agriculture and horticulture has remained relatively stable over recent years though
the area that they are applied to has increased and the unit area rate of active ingredient application
decreased.113 There are other significant sources of pesticides such as herbicide use in urban areas
and on railways. For example, diuron is used only in the amenity sector (not in agriculture) and in 2005
there was a significant increase in the incidence of detection for diuron in water bodies.

Pesticides can enter water bodies through a combination of sources and pathways in a catchment
including114:

 run-off through field and urban drainage systems and leaching through soil;
 spills, spray drift and ‘over-spray’ of water courses;
 pollution incidents;
 direct discharges/inputs, disposal routes or via sewage treatment works.

There are critical or determining factors (such as pesticide chemical characteristics, climatic,
agronomic practices, topographic, soil, and subsoil variability) that control the environmental fate,
behaviour and pathways of a pesticide, and the subsequent risk posed to aquatic ecosystems. There
appears to be no information on the total loads or apportionment of pesticides in the surface waters of
England and Wales.

The EA’s WFD Article 5 risk assessment estimated that diffuse pesticide use (agricultural uses and
sheep dip) were putting 20.8% of river water bodies (20.4% by length) at risk of failing environmental
objectives, and 2.9% (7.4% by length) were at risk because of diffuse pesticide EQS failures. In terms
of point sources of pesticides, 0.3% of river water bodies were assessed to be at risk. No separate risk
assessments were undertaken for pesticides in lakes or transitional and coastal waters. It should be
noted that the risk assessment relied solely upon water quality data to assess the level of exposure
pressure and does not take into account ecological impacts that might occur through pesticide
contamination of sediments or via the food chain in biota.

12
The EA monitors over 250 different pesticides at about 2,500 sites across England and Wales. 115 The
great majority of the sites monitored are rivers rather than lakes, for which there is relatively little
information. The monitoring covers the pesticides that are used most frequently and in the greatest
quantities for both agricultural and amenity use. Data from 2006 shows that for nine indicator
pesticides (atrazine, chlorotoluron, 2-4-D, dichloroprop, diuron, isoproturon, MCPA, mecoprop and
simazine), 6.5% of freshwater samples had pesticide concentrations exceeding the 0.1 µg l -1 threshold
value (the Drinking Water Directive maximum allowable concentration standard for any individual
pesticide and hence not necessarily related to possible effects on aquatic organisms). Between 6%
and 8% of samples exceeded the threshold value each year from 1998 to 2006. These exceedances
were mainly due to the herbicides diuron, isoproturon and mecoprop. The changes between years
may be related to weather patterns at the time pesticides are applied since watercourses are more
vulnerable to pesticide contamination when application coincides with rainfall. The highest levels of
diuron were found in Thames and North East regions. In the case of Thames this was probably linked
to the more urban nature of this region and correspondingly greater and more frequent use of this
substance. Diuron will be taken off the UK market during 2008.

Sheep dip chemicals containing either cypermethrin or diazinon caused over a third of all EQS failures
in freshwaters in 2006.116 There were two main sources: sheep-dipping, especially in Wales and the
north of England, and effluents from the wool processing industries centred in Yorkshire. In 2006 there
were 64 failures of EQS standards for cypermethrin and 16 failures for diazinon in England and Wales,
compared with a total of 22 failures in 2005. This large increase is due to the increased monitoring
effort of the EA at targeted locations as part of its Pollution Reduction Programme for sheep dip.
Although cypermethrin was withdrawn from sale in February 2006, farmers were still able to use up
existing stocks. Lower numbers of EQS failures for sheep dip chemicals are expected in 2007.

In terms of serious pollution incidents, out of 49 category 1 (most serious) and 2 (significant) incidents
in the years 2000 to 2005, 43 were attributable to agricultural uses of pesticides. 117

The UKTAG has assessed current compliance with proposed WFD standards for pesticides using
monitoring data and face value concentrations.118 The results indicate that the following percentages of
freshwater monitoring sites (total sites in brackets after percentages) in England and Wales,
respectively, would fail the standards: 21% (316) and 19% (257 sites) for cypermethrin, 4% (485) and
8% (247) for diazinon, and 2.4% (619) and 0% (78) for mecoprop. The equivalent figures for salt water
sites in England were 6% (16) cypermethrin, 5% (88) diazinon and 3% mecoprop (73); there were no
data for Wales. As monitoring is often targeted where problems are expected, the proportion of failures
was considered to be not necessarily representative of all water bodies. It should also be noted that
pesticide use that could result in transient, but still damaging, contamination could be associated with
seasonal or episodic activities such as spraying with insecticides. Such activity might not have been
captured in the current monitoring programme in which sampling is relatively infrequent.

EA groundwater monitoring data from 2005119 showed that the most commonly detected pesticide was
the herbicide atrazine and its degradation products desethyl atrazine and desisopropyl atrazine.
Although the ecological effects of substances in groundwater are not directly considered in the WFD,
the achievement of good chemical status of groundwater includes the requirement that associated
surface water bodies are able to meet the surface water EQSs or do not suffer any significant
diminution of ecological or chemical quality. There is some evidence of improving groundwater quality
and a general decline in pesticide concentrations in the Thames region over the last ten years.

Current monitoring of transitional and coastal waters for pesticides is carried out as part of the UK
marine monitoring programme. The most recent summary of environmental monitoring data for UK
estuarine and coastal waters120 concluded that in UK estuaries the concentrations of metals and
organic substances rarely exceeded the standards set under the EU Dangerous Substances Directive.
No median values exceeded any EQS for the period 1999 to 2001. In addition, estuarine biological
water quality measured by toxicity to oyster embryo-larval development was generally very good. The
oyster embryo larval test is a robust measure of the biological water quality of discrete water samples.
This information indicates that risks from agricultural pesticides to the ecological quality of transitional
and coastal waters are likely to be low. However, in 2006 there were 25 EQS failures for tributyl tin
(TBT) in marine waters compared with 54 in 2005 and 50 in 2004.121 Problems in the marine
environment often occur close to docks and boat yards, such as in the Thames and Mersey estuaries.
However, TBT use is not usually associated with farming.

13
The impact of agricultural pesticides on different elements of an aquatic ecosystem will be dependent
on the mode of action of the substance(s) involved and, therefore, the taxonomic group(s) which are
most susceptible to the substance at typical environmental concentrations. In the case of herbicides,
phytoplankton, phytobenthos, macrophytes and macroalgae would be expected to be the taxonomic
groups most affected by exposure in the receiving water. For insecticides and molluscicides,
invertebrates, crustaceans and molluscs would be expected to be those most likely to be affected by
exposure to these substances at typical environmental concentrations.

Otters are top predators and are seen as an important biological indicator of the health of rivers. The
main factor in the decline of the otter population in England during the 1950’s is believed to have been
the impact of organochlorine pesticides though degradation of river and riparian habitats in England,
mostly as a result of agricultural intensification, has also been a contributory factor since then. More
recently, otter numbers have increased in England and pollution is no longer generally believed to be
limiting fish populations sufficiently to constitute a barrier to the spread of otters in England. 122

EQSs are established for the protection against both long term, chronic effects and for short term,
direct and acute ecotoxic effects. If the EQS is exceeded in the receiving water, the severity of the
impact will be dependent on the magnitude and duration (hours, days or months) of the exceedance.
Where low concentrations of a chemical are released over a long period sub-lethal effects on growth,
development and reproduction in the most sensitive taxonomic groups may be observed whilst
releases of high concentrations over a short time scale may result in mortalities of indigenous
organisms.

It should be recognised, however, that even within the most sensitive taxonomic group not all the
species will respond in the same manner to a given concentration and there will be an order of
sensitivity. In reality this means that loss of the most sensitive species from a taxonomic group will
result in a change in the species composition of the community but will not necessarily result in a
change in biomass. This is because a slightly more tolerant species may increase its population to
take advantage of the available resources following the loss of the more sensitive species. The nature
of the change in species composition will be site-specific and will depend on a range of factors related
to the site (including habitat structure and water chemistry) as well as the pesticide involved and the
exposure concentration and duration.

The EU has currently identified 33 substances (or groups of substances) as Priority Substances under
the WFD of which 12 substances or groups are pesticides. EQSs will be established at the European
level for these substances in a Daughter Directive to the WFD. The EQSs will be expressed as Annual
Averages (AA) or Maximum Allowable Concentrations (MACs). The EQSs as AA concentrations are
designed to protect against sub-lethal effects of the substance resulting from long-term exposures
whereas the EQSs as MACs are designed to protect against transient short-term exposure at higher
concentrations which may result in mortality. These standards are also designed to protect against the
secondary poisoning of predators (e.g. birds and mammals) resulting from the consumption of aquatic
biota that has accumulated the chemical following exposure.

An aim of the WFD is the progressive reduction (or for certain of these substances the cessation or
phasing out) of discharges, emissions and losses of Priority Substances to surface waters. In the EU,
all pesticides are presently being reviewed to ensure that they satisfy modern standards for safety and
effectiveness. As a result some pesticides are being taken off the EU market, either for certain uses or
altogether. Atrazine and simazine have been withdrawn in 2007, diuron will be withdrawn around the
end of 2008 and isoproturon will be withdrawn in the UK in 2009.

EU Member States are required to establish national EQSs for other relevant pollutants not included in
the Priority Substance list. To that end, the UKTAG has identified 33 substances for early
consideration, partially chosen on the basis of those most often regulated for discharges to water
across the UK. So far, the UKTAG has evaluated 18 substances and the UKTAG Consultation Report
proposed new standards for nine of these substances including six pesticides. These substances are
all currently used in the UK for different agricultural applications with 2,4-D, linuron and mecoprop
being used as herbicides and cypermethrin, diazinon and dimethoate being used as insecticides.

14
2.6 Veterinary medicines
Veterinary medicines are used widely to treat disease and protect animal health. They include groups
of substances such as worming agents, antibiotics, antifungal agents and treatments for ectoparasites.
In 2003 the use of veterinary medicines in agriculture represented about 46% of the overall use by
market value, with cattle sheep and pig husbandry accounting for 38% and poultry rearing accounting
for 8%. The other 54% of the total use of veterinary medicines is associated with the treatment of
companion animals (pets).123 Most medicine residues from agricultural sources will be transported into
watercourses via direct inputs (e.g. defecation in rivers), surface run-off, contaminated soil transport
during storm events, and inputs derived from manure/slurry from intensive livestock rearing units.

There is no known information on the total loads and source apportionment of veterinary medicines in
surface waters of England and Wales. However, domestic sources are likely to predominate in urban
areas whereas water bodies in rural areas are more likely to be at risk from agricultural sources of
veterinary medicines where medicine use is concentrated more locally. Medicines in the excreta of
domestic pets might be removed at sewage treatment works before they reach a watercourse whereas
it is likely that a negligible proportion of agricultural slurry would receive treatment at a sewage
treatment works.

Some veterinary medicines are toxic to aquatic organisms. For example avermectins and sheep dip
chemicals are known to be toxic to organisms at low concentrations (ng l -1 to µg l-1). A number of
veterinary medicines also exhibit endocrine disrupting activity. The nature of the impact of veterinary
medicines will depend on the type of substance concerned; for example, ectoparasitides will exert their
principal effect on insects, whereas the predominant effect of worming agents is likely to be on
invertebrates and molluscs.

The EA’s Article 5 risk assessments did not consider veterinary medicines. However, the issue of
possible environmental impacts of veterinary medicine use in the UK has been addressed in a
sequence of research projects carried out by Defra and the Environment Agency. 124,125,126,127,128 These
had the aim of assessing risk and of prioritising the substances on which monitoring effort and
regulatory scrutiny should be concentrated. An initial priority list for further assessment contained 34
compounds from the antibacterial, ectoparasiticide and feed additive groups. For 13 of the
compounds, insufficient data were available for ranking purposes in either the terrestrial or aquatic
compartments. Using a ranking procedure based on modelling, 18 compounds (amoxicillin, apramycin,
bronopol, doramectin, enrofloxacin, eprinomectin, fenbendazole, florfenicol, ivermectin, lincomycin,
monensin, moxidectin, oxytetracycline, sulfadiazine, tiamulin, tilmicosin, trimethoprim, tylosin) were
identified as worth monitoring in the environment. The procedure identified the medicine treatment
scenarios that are most likely to cause harm and the environmental compartments that should be
monitored.

A monitoring study, based on the results of the ranking, was undertaken over a 11 month period in
2004 to determine concentrations in the UK environment of seven (doramectin, enrofloxacin,
ivermectin, lincomycin, oxytetracycline sulfadiazine trimethoprim) of the 18 compounds. Four river
sites were selected and targeted to: represent the highest ranked compounds and risk scenarios; have
characteristics that would enhance environmental contamination; and, focus on occasions when the
compounds were likely to be released to the environment. Overall the results from the study showed
that, in general, concentrations of these veterinary medicines were lower than Predicted No Effects
Concentrations (PNECs) and were likely to be below those that could affect aquatic and terrestrial
organisms. Given that estimates of concentrations in rivers did not raise undue concern and allowing
for the greater dilution available, the likelihood of impact in estuarine and marine waters is likely to be
low.

However, the study identified some areas where future work is warranted. These included:

 a more detailed assessment of the potential impacts of veterinary medicines on soil;

 investigations into the fate and effects of parasiticides in sediment;
 assessment of those compounds that could not be studied in the project due to insufficient data;
 further assessment of the potential impacts of the other 11 (of the 18) selected veterinary
medicines on the environment;
 monitoring of groundwater.

15
2.7 Faecal pathogens
The main pathways that faecal pathogens can be transferred to water bodies are: direct leakage to
drainage systems in farmyards; leakage of wastes from buildings and/or stores; run-off from animal
manure applications to land; and, direct inputs of faeces into water bodies. 129 The transfer of faecal
pathogens to water bodies is affected by, for example, soil type, soil water content, rainfall intensity,
temperature, topography and agricultural practices.

Faecal pathogens from agricultural activities are more of a human health issue rather than having
direct impacts on aquatic ecology, primarily because most pathogens are unable to survive for long
outside of their host. The EA’s WFD Article 5 risk assessment did not address the impact of faecal
pathogens in rivers, lakes or transitional and coastal waters.

Modelling of faecal indicator organisms (FIO) inputs into three problem areas (in terms of failing
Bathing Water Directive standards) estimated that diffuse agricultural sources contributed around 30%
to the total bathing season faecal coliform budget 130, although this average figure conceals significant
variations in the agricultural contribution to FIO pollution at high and low river flows. This load would
contribute to bathing water failures in these problem areas. Two of the three modelled problem areas
(North West and South West of England) were associated with flashy river flows and intensively
grazed livestock particularly of dairy cows.

2.8 Organic material

Organic material can enter water bodies by either point or diffuse sources with the main pathways
being: runoff and leaching from slurries and manures applied to land; leakages from slurry or silage
effluent stores; dirty water discharges from farm areas; use of dirty water for irrigation; and by direct
inputs (faeces) from animals. About 90 million tonnes of livestock manures are collected from housed
animals in England each year and spread to land.131 This represents around half of the material
deposited to land each year; the remainder is deposited directly by grazing livestock. There is no
known information on the total loads and source apportionment of organic material in surface waters of
England and Wales.

Inputs of organic material to water courses from agricultural sources are generally untreated and can
be acute in the case of leakage from, or catastrophic failure of, slurry pits and farmyard manure
storage facilities. By contrast, inputs from sewage treatment works are treated and tend to have low-
level chronic effects. Milk, silage effluent, pig slurry and cattle slurry have typical biochemical oxygen
demand (BOD) values of 100,000, 65,000, 25,000 and 17,000 mg l -1 of oxygen, respectively, all far
higher than that of raw domestic sewage (300 mg l -1).132

Organic material is often associated with other pollutants that can compound its impact on aquatic
ecology. Material derived from animal manures and slurries may contain faecal pathogens, ammonia
and residual nitrate, phosphate and veterinary medicines. Some types of manure may also contain
heavy metals such as from pigs and poultry which contain elevated levels of zinc and copper that may
accumulate in soils to later be leached into water courses having direct toxicity effects on the receiving
ecology.

The EA WFD Article 5 risk assessments for rivers and lakes did not consider point or diffuse sources
of organic material arising from agricultural activities. However, the risk of organic enrichment of
transitional and coastal waters was assessed. The assessment considered the contribution of organic
matter from riverine loads that would have included (but not quantified) inputs from farming. The
results indicated that 13.4% (by area) of transitional water bodies and 0.2% (by area) of coastal water
bodies were at risk: the ‘at risk’ water bodies were geographically spread around England and
Wales.133

The greatest impacts on ecology occur where direct inputs of organic material enter watercourses due
to storage failures, leakages etc. There were 55 such serious (category 1 and 2) water pollution
incidents involving organic materials in England and Wales in 2006. 134 Of these, slurry accounted for
75% of the incidents and other agricultural sources accounted for the remaining 25%.

BOD is used as an indicator of organic material and is measured in rivers across the UK as part of the
Harmonised Monitoring Scheme and in England and Wales for the chemical General Quality
Assessment (GQA) Scheme. The results from the HMS in 2005 indicated that the average BOD of

16
rivers in England and Wales was 1.6 mg l-1, with the highest values in the North West (2.4 mg l -1) and
North East (2.3 mg l-1) regions and the lowest values in the South West (1.2 mg l -1) and Welsh (0.9 mg
l-1) regions.135 BOD, dissolved oxygen and ammonia are used in the EA’s chemical GQA scheme for
rivers which is used as a general indicator of organic pollution of rivers. Data from 2006 indicate that
69.5% of rivers (by length) were of good quality in England and Wales with the highest quality
occurring in Wales (95% of rivers) and worst in Anglian region (47.4% of rivers). 136 The results also
indicate a general improvement of river quality since 1990. In terms of the proposed standards for
BOD for implementation of the WFD, 18.7% and 3.7% of river water bodies (by length) in England and
Wales, respectively, would be less than good ecological status, based on recent monitoring data. 137

Biodegradation of organic material produces a high BOD and results in deoxygenation of the water
column and sediment. Low dissolved oxygen levels can selectively remove the more pollution
sensitive invertebrate species such as stonefly nymphs while encouraging the productivity of pollution
tolerant organisms such as oligochaete worms (Tubificidae), midge larvae (Chironomidae) and
bloodworms. In heavily polluted waters, the establishment of monocultures can occur whereby tubificid
worms can become the dominant or sole species. The native white-clawed crayfish is particularly
vulnerable to high BOD, becoming stressed when oxygen levels fall to below 5 mg l -1, and is
vulnerable to spillages of materials with high BOD such as cattle slurry. 138 Decreased oxygen levels
can inhibit the passage of migratory fish such as Atlantic salmon and sea trout, as both these species
have a high oxygen requirement.139 Early life stages, in particular eggs, are highly sensitive to low
oxygen levels.

In addition to its deoxygenating effects, organic material can cause physical degradation of the aquatic
environment. The deposition and biodegradation of organic material on lake bottoms may produce a
thick, rich anoxic mud, reducing the suitability as a habitat for infaunal and benthic organisms.
Moreover the rich anoxic sediment may continue to provide a supply of nutrients to the water column
even if the source of pollution is reduced. Deposition of organic material on beds and banks can cause
de-stabilisation and reduce habitat suitability for rooted plants such as brook water crowfoot. 140

Organic wastes can also contain some solid material, which can increase turbidity and reduce light
penetration. Photosynthetic organisms such as algae and macrophytes may be eliminated at high
concentrations. Deposition of solid material in organic waste can occur on streambeds, altering the
substratum for the benthic communities and producing impacts similar to that of soil sediment.

The effects of organic material in transitional and coastal waters are similar to those observed in
freshwaters particularly in sediment deposition areas, although the capacity of transitional and coastal
waters to dilute and disperse organic material is generally much greater. Because of the associated
faecal pathogens, the effects of organic material in coastal waters are of more concern for human
health risks in bathing waters and due to the contamination of shellfish. However it is possible that the
deposition of organic material onto the beds of estuaries may alter the grain size distribution as a
result of flocculation, reducing habitat suitability for certain organisms. Deposition of organic material
onto hard rocky substrates will have an effect similar to that of soil sediment.

2.9 Endocrine disrupting chemicals

A range of chemicals have been shown to have the potential to adversely affect the endocrine systems
of invertebrates and vertebrates. These include natural hormones, synthetically produced hormones
and other man-made chemicals such as some pesticides and some plastic additives. The main
pathways that would potentially lead to impacts on aquatic ecosystems would, therefore, depend upon
the activities and uses associated with any particular endocrine disrupting chemical. The substances
that have been identified as presenting the greatest potential impact on freshwater ecosystems are
steroids, including the natural steroids (oestrone, oestradiol and oestriol) and the synthetic steroid
ethinyloestradiol. However it should be noted that although invertebrates represent approximately 95%
of all species, knowledge of the endocrinology of many taxonomic groups is limited and the vast
majority of research carried out to date has focused on chemical-induced effects on vertebrates.

Natural steroids from farming can enter water bodies by either point or diffuse sources with the main
pathways being: direct inputs (urine/faeces) from animals into water bodies; leakage and run-off from
slurry stores and from hard-standings in farm areas; and runoff from direct deposits of urine and
faeces on land, and run-off from slurries and manures applied to land. Run-off from land has been
considered to be the least significant pollution pathway for steroid hormones because of degradation

17
and adsorption of the substances in soil 141. Other chemicals associated with farming-related activities
(e.g. atrazine) have been shown to possess endocrine disrupting activity but these effects have been
considered in the derivation of EQSs.

Evidence from other European countries suggests that agriculture is the main source of oestrogens
excreted.142 In the Netherlands it has been estimated the total steroid oestrogen excretion by all
domestic animals and humans is 49.6 kg day-1, with farm animals accounting for 94% and humans for
6%. Among farm animals, pregnant cows and breeding female pigs contributed the greatest volume of
natural steroid oestrogens (22 and 10.6 kg day-1 respectively). The extent of the impact on steroids on
a particular receiving water body will obviously depend on the relative populations of humans and
animals in that catchment. In this context it also needs to be recognised that whilst releases of steroids
from humans will be treated at sewage treatment works before discharge to water bodies, releases
from farm animals can directly enter water bodies.

Most studies of hormones in rivers have focused on inputs from sewage treatment works, and their
consequences for endocrine disruption in fish. However, in areas where there is intensive livestock
rearing, excretion by farm animals can also contribute to the natural steroid oestrogen load in the
environment.143,144,145

The EA has carried out a critical evaluation of the numerous ecotoxicological studies that have been
undertaken for the natural steroids and the synthetic steroid ethinyloestradiol. 146 Based on this review,
a ‘tentative’ Proposed No Effects Concentrations (PNEC) value for the natural steroid 17β-oestradiol of
1.0 ng l-1 was proposed given that 17β-oestradiol can cause adverse effects in the 10-50 ng l -1 range
for a variety of species. No PNECs were proposed for oestrone and oestriol, which are know to be less
potent endocrine disrupters than oestradiol.

At present there is only limited data on the concentrations of agriculturally related endocrine disrupting
chemicals (excluding pesticides) in UK fresh and marine waters. A recent study conducted for Defra
investigated the extent of steroid hormone contamination in streams associated with livestock farms. 147
The majority of the 10 sites selected were streams running through dairy farms, although some
examples of beef, sheep and pigs were included. The sites were selected to represent worst case
conditions where, for example, small streams passed through intensive livestock farms, soil types and
topography were favourable to the transfer of substances and animals had access to the streams. An
experimental farm was also included, making 11 sites in total. Ninety-two percent of the monitoring
stations gave measurable oestrogenic activity, and on 8 of the 11 farms surveyed oestrogenic activity
exceeded at least once the PNEC for 17β-oestradiol in water. The data do not allow clear
discrimination between different livestock sources, but spreading of cattle slurry and run-off from
farmyards may be more important than direct excretion to farmland or streams. Overall, both the Yeast
Estrogen Screen (YES) bioassay and chemical analytical data were taken to indicate that fish in
headwater streams on or near some livestock farms may be at risk of endocrine disruption from
steroids (i.e. there would be exceedances of the PNEC). In terms of the likely contamination pathways,
it was noted that as long as good agricultural practice is followed then the risk to watercourses from
farming-related activities should be minimal and that humans are the primary source in UK rivers.
However, poor farming practice (e.g. direct excretion of livestock into unfenced streams, direct run-off
from slurry stores and farmyards) may lead to significant steroid hormone pollution. 148

Endocrine disrupting chemicals, whose effects may have been masked in the past by the presence of
gross pollution, are now recognised as having the potential to affect the viability of coarse fish
populations.149 The most evident effect is intersex in male fish. Typically males exhibit female-like
characteristics, possessing female oviducts and eggs within the testes. Such effects have been shown
to be permanent, progressive and can lead to reduced reproductive performance. Whilst initial
research programmes focused on a limited number of highly impacted sites receiving treated sewage
effluent150151, a more recent survey (2002/2003) was conducted to establish a more comprehensive view
of the spatial extent and severity of oestrogenic effects in wild fish (roach) in English and Welsh rivers
again primarily in relation to discharges of sewage effluent.152 A further objective of the latest survey was
to review predictions of impacts on fish at high, medium and low risk sites, based on predicted
oestrogenic activity of the sewage effluents. Intersex roach were found at 44 (86%) of the 51 sites
surveyed in 5 Agency regions. In addition, some roach populations where sewage treatment effluents
were low or absent showed no observable intersex effects. Further work is required to understand the

18
implication of endocrine disruption on the populations of roach and other fish populations in relation to all
potential sources (sewage treatment works effluent and farming).

2.10 Other pollutants

Phosphate fertilisers can contain cadmium and as such represent a cadmium input to arable soils,
where it is rapidly adsorbed by particulate matter, and potentially to adjacent water bodies. 153
Cadmium can also be found in trace quantities in manure, where it is probably associated with zinc
complements given to livestock, and again this represents a potential input to agricultural soils and
thereby to water. There appears to be no information on how important this potential agricultural
source of cadmium is in relation to the total load of cadmium in surface water bodies in England and
Wales though it has been estimated that between 1.4 to 6.5 g ha -1 yr-1 of cadmium can be input to
agricultural soils through the application of manure/compost. 154 Other estimates put the cadmium load
to UK soils as between 11.3 and 25 tonnes yr-1 155 and in 2005 the direct and riverine inputs of
cadmium to UK seas were calculated to be between 4.9 and 8 tonnes. 156

Oil and fuels are the most frequently reported type of pollutant of inland waters in England and Wales.
In 2006, there were 605 serious (category 1 and 2) water pollution incidents, of which oil and fuels
were implicated in 89 (14.7%).157 The proportion of these that originated from agricultural sources is
recorded but not publicly available.

2.11 Combined effects of different pressures

Although combined effects of different pressures are common in the aquatic environment, it is
important to recognise that it is difficult to interpret these impacts from information on individual
pressures. There are clearly many potential interactions in the environment, whereby the combined
effects could result in different effects or effects larger or smaller than those that might be expected on
the basis of the individual pressures. This is particularly evident for the combined effects of chemicals
(such as pesticide and veterinary medicines) and soil sediments or organic matter where the
bioavailability of the chemicals and their resulting toxicity to receiving water organisms is modified.

The problem of assessing the nature of combined effects is particularly problematic when these act in
opposing ways on particular biological elements. This is exemplified by the potential effects on the
biomass of aquatic plants in a water body of elevated concentrations of nitrate and/or phosphate and a
herbicide. Whilst the elevated nitrate and/or phosphate concentrations will tend to act to increase
aquatic plant biomass through eutrophication, the presence of the herbicide at sub-lethal
concentrations will tend to restrict the growth of aquatic plants. As a result no change in biomass may
be evident even though the two pressures are outside of “normal” conditions. Current knowledge on
the responses of aquatic biota to combined pressures from nutrients and priority substances has been
summarised by O’Toole and Irvine (2006)158.

These issues illustrate why it is necessary to use a series of indicators for a particular biological quality
element (e.g. phytoplankton, phytobenthos, macrophytes, macroalgae, angiosperms, benthic
invertebrates or fish) to assess potential impact. As described in section 3, a number of different
metrics (e.g. the abundance of particular species, overall diversity) may be used to estimate the status
of a quality element. Different metrics may be used to indicate the impact of different types of pressure
on the element159. In other cases, monitoring results for different metrics may be combined to give a
representative picture of the impact of a particular type of pressure (or range of pressures) on the
quality element. In terms of the use individual quality elements, tools are being developed for the
classification of ecological status that takes into account the response of the quality element to
different pressures160. For example, RIVPACs, the classification tool for river benthic invertebrates, is
being developed for the assessment of toxicity, acidification, hydrological, and perhaps morphological
pressures, as well as organic pollution pressure for which it was initially developed. For example,
using multiple metrics may be appropriate where none of the metrics on their own give a sufficiently
reliable indication that the quality element has been adversely impacted as a result of human activities.

The relationship between anthropogenic pressures and ecological status may vary according to the
sensitivity of river ecosystems and combinations of pressures. Agriculture and urbanisation are
considered the principal impairment sources in the literature but the relative influence of combined
pressures coming from agricultural or urban land use is not well established. 161 Nevertheless large
scale analysis comparing pressure-impact relationships across different spatial scales, countries and
ecoregions would still be necessary for the implementation of the WFD.

19
3 Indicators of pollution
3.1 Background
Potential indicators of pollution arising from farming range from sub-organism level determinands (e.g.
tissue analysis of persistent bioaccumulative substances in an appropriate species) through the
presence and abundance of key species, to indices which integrate information about the structure or
function of whole biological communities.

Several different types of ecological indicator exist and those chosen depend on their required role in
the assessment process. Ecological indicators can be divided into three classes 162:
1. early warning indicators that detect impending changes;
2. compliance indicators that detect changes in characteristics beyond acceptable limits;
3. diagnostic indicators that show the causes of deviations from “normal conditions”.

Indicators are commonly used to determine the impact of various pollutants and disturbances. The
indicator used for a defined part of the monitored system needs to be able to inform stakeholders
about the threat to a given element of the ecosystem. 163 The results should be unambiguous in their
response to pressures, although this may not always be possible given the complexity of the systems
being monitored.164 The validation process for indicators is also important, but unfortunately is rarely
fully implemented.165 The expression of the indicator should be directly related to changes in the
pressure so that the implications of changes in the indicator are evident. Furthermore there should be
an understanding of the variability in the relationship so that stakeholders can assign a level of
uncertainty to any management decisions that are based on the ecological indicator data.

It is unlikely that a single indicator will be indicative of a specific farming-related pressure. Instead a
series of indicators are likely to be needed from which the extent and magnitude of impacts of different
pressures can be elucidated.166 In addition, many water bodies will be subject to the same pressure
from a number of sources (e.g. nutrient enrichment from agriculture and sewage treatment works) and,
as a consequence, it will not always be straightforward to apportion the observed impacts to farming.

3.2 Species/biological quality elements indicative of the effects/impacts of farming

The pressures arising from farming and the subsequent impacts have been described in detail in
Section 2. The species/biological quality elements indicative of these pressures and impacts can be
summarised as follows:

Nutrient enrichment
The most sensitive indicators of the impact of the nutrients nitrate and phosphate on an aquatic
ecosystem are considered to be combinations of phytoplankton, phytobenthos and macrophytes in
rivers and lakes and phytoplankton, macroalgae and angiosperms in transitional and coastal
waters.167,168

Organic material enrichment

The available evidence indicates that benthic invertebrates are the most sensitive indicators of organic
material enrichment (e.g. elevated concentrations of BOD, ammonia and suspended solids) in all
receiving water types.169

Acidification
Acidification of freshwaters can result in a complete loss of fish species (the early life stages of trout
and salmon are particularly sensitive170) and changes in community structure and biodiversity in
general, particularly in terms of benthic invertebrates (e.g. reduction in sensitive species taxa such as
Ephemeroptera, Crustacean and Mollusca) and aquatic plants (e.g. diatoms) 171.

Pollutants
The impact of pollutants (e.g. pesticides, ammonia, veterinary medicines, endocrine disrupting
chemicals, heavy metals, oil) on different elements of an aquatic ecosystem will be dependent on the
mode of action of the substance(s) involved and, therefore, the taxonomic group(s) which are most

20
susceptible to the substance at typical environmental concentrations. In the case of herbicides,
phytoplankton, phytobenthos, macrophytes and macroalgae would be expected to be the taxonomic
groups most affected by exposure in the receiving water. For insecticides and molluscicides,
crustaceans and molluscs would be expected to be those most likely to be affected by exposure to
these substances at typical environmental concentrations. 172Fish are the taxonomic group most
sensitive to ammonia.

Habitat alteration
Habitat alteration resulting from sediment accumulation following soil erosion can potentially have
direct or indirect effects on all the biological quality elements resident in a water body. For example,
high suspended solids concentrations can affect the feeding and health of individual species either
indirectly through increased turbidity of the water (thereby inhibiting phytoplankton, phytobenthos,
macrophyte, macroalgal or angiosperm growth) or directly through clogging of gills of invertebrates
and fish. Siltation is a problem both with regard to access to suitable substrate – for example, for the
establishment of the freshwater pearl mussel (Margaritifera margaritifera) and water crowfoot
(Ranunculus spp.) plant communities – and with regard to egg and fry survival in Atlantic salmon
(Salmon salar), lamprey (Lampetra and Petromyzon spp.) and bullhead (Cottus gobio) populations.173

3.3 Monitoring under the Water Framework Directive

The WFD defines ecological status in terms of the status of biological, physicochemical and
hydromorphological quality elements reflecting the structure and functioning of aquatic ecosystems.
Chemical status relates to compliance with European EQSs established for a Priority List of
substances and for substances covered in other EU legislation. Surveillance monitoring for the WFD is
required for parameters indicative of all biological, hydromorphological and general physicochemical
quality elements, Priority List substances if discharged in the River Basin District and other pollutants if
discharged in significant quantities. Operational monitoring is required for parameters indicative of
those biological and hydromorphological quality elements most sensitive to the pressures to which the
water body is subject (i.e. those priority substances discharged into the water body and other
significant pollutants (including nutrients) that might cause failure of environmental objectives). Thus
water bodies identified as being at risk from farming activities and pressures (and hence included in
operational monitoring) will be monitored using parameters most indicative of that pressure. These
water bodies may also be included in surveillance monitoring, in which case all quality elements will
have to be monitored for.

The assessment and classification of the ecological status class of a water body will be based on the
monitoring results of the parameters included in surveillance and operational monitoring. In some
cases obtaining a reliable assessment of the conditions of a particular biological quality element may
require consideration of the monitoring results for several parameters indicative of that element. The
WFD gives the minimum quality elements that should be used in the assessment and classification of
the ecological status of each of the four water categories (rivers, lakes, transitional and coastal
waters). The results for several parameters or groups of parameters, each sensitive to a different
pressure or set of pressures, may be used in estimating the condition of the biological quality element.
Multi-metric indices may also be derived from measurement of individual parameters to assess
whether the quality element has been affected by the pressures to which the water body is subject.

As an example, the indicative parameters (metrics) based on measurements of composition and

abundance of benthic invertebrates could include: 174

 presence or absence of particular species or groups of species;

 overall richness or richness of particular taxonomic groups;
 relative number of taxa in particular taxonomic groups;
 abundance of particular species or groups of species;
 relative abundance of particular species or groups of species;
 overall diversity, or diversity within particular taxonomic groups;
 taxa could be selected and/or grouped by known sensitivity/tolerance, feeding type, habitat
preferences, etc.

The EA will be responsible for undertaking the monitoring required for the WFD in England and Wales.
To that end, the UKTAG has recommended appropriate quality elements for the monitoring of the

21
impacts of the pressures listed in Table 1. As has been pointed out, these pressures are associated
with, but are not exclusive to, farming. The recommended quality elements vary depending on the
nature of the pressure and the receiving water. The process of determining which parameters have the
best correlation with particular pressures and impacts is underway.

It should be recognised that not all of the elements which are relevant to farming-related pressures are
being fully addressed under the UK research programme. Phytoplankton in rivers is not being
considered since the turnover in the majority of UK rivers is too high to support a phytoplankton
community and this element has not historically been widely monitored. This quality element will be
monitored on a risk-based approach in those rivers where phytoplankton may be important.

Table 1 Biological quality elements likely to be used to assess pressures relevant to the impact of
farming activities
Pressure WFD biological quality elements for different receiving waters
Rivers Lakes Transitional Coastal waters
waters
Nutrient Phytobenthos Phytoplankton Phytoplankton Phytoplankton
enrichment Macrophytes Macrophytes Macroalgae Macroalgae
Phytobenthos Angiosperms Angiosperms
Benthic
invertebrates
Organic Benthic Benthic Phytoplankton Benthic
enrichment invertebrates invertebrates Benthic invertebrates
(Profundal invertebrates
invertebrates) Fish
Acidification Phytobenthos Phytobenthos Not applicable Not applicable
Benthic Benthic
invertebrates invertebrates
(fish)
Pollutants Benthic Benthic Macroalgae Macroalgae
invertebrates invertebrates Benthic Benthic
invertebrates invertebrates
Habitat (Macrophytes) (Phytoplankton) Angiosperms Angiosperms
alteration Fish (Macrophytes) Benthic Benthic
(Benthic invertebrates invertebrates
invertebrates) Fish
Fish
Notes: Elements in bold are likely to have the strongest sensitivity to the pressure
Elements in brackets require further work as more data is acquired
Elements underlined in italics recommended by CIS WG2.7175
Source: UKTAG 2005176

Details of the indicative metrics and methods proposed for the assessment and classification of water
bodies in England and Wales are given in Annex B to this report. The aim will be to have indicators,
metrics and methods that are responsive and suitably sensitive to changes in the pressures/effects
being monitored. At present a number of ecological indicators show statistical significant relationships
with pressures which are relevant to farming-related activities. However, in many instances there is a
high degree of variability associated with the relationships which limits their wide-scale application. It
has been reported that the variation between relationships for indicators of biological quality elements
and specific pressures was larger when they were derived from European wide datasets containing
information from many different sites. The quality of the relationships was improved by creating sub-
datasets for geographical regions and types of water bodies 177. Relationships may, therefore, have to
be water body type-specific rather than generic.

Detecting the impact of many of the farming related pollutants/pressure will rely on the selected quality
element being sensitive enough to the pressure, for example, siltation and endocrine disrupting effects
would expected to be detected by changes in fish populations. Statistically valid changes in the
metric/indicators must also be detectable over and above all sources of variability (natural and
anthropogenic) in water bodies.

Using this type of statistical assessment, it should be possible to determine the smallest change
detectable and to assess how that relates to changes in the pressure and impact and the degree of
early warning obtainable. Depending on what is an acceptable or desirable level of early warning,

22
some WFD methods may not be suitable for providing an early warning of impacts from some farming
activities. For example, intersex in fish would probably have to become very prevalent before it would
be detected by changes in the fish population metrics ‘composition, abundance, sensitive species and
age structure’ that will be used in the classification tools for the WFD. [Note: The relationship between
intersex in fish and fish populations and community structure has been identified as a gap in current
knowledge (section 2.9)]. Once the chemical(s) responsible for inducing intersex had been determined
then it would probably be subject to an EQS that would be aimed at reducing the risk of intersex
occurring.

In short, more sensitive and targeted indicators and methods may be required if early warning of some
farming induced impacts were to be required before they were detectable by a deterioration of
ecological status as defined by the WFD.

3.4 Use of biomarkers as early warning systems for farming-related activities

Biomarkers are broadly defined as a change in a biological response (ranging from molecular through
cellular and physiological responses) that can be related to exposure to, or toxic effects of,
environmental chemicals.178 In recent years, selected markers measured in indigenous aquatic
organisms have been shown to be sensitive indices or early warning signals of environmental
degradation caused by pollutants. These indices are typically those that can be measured with an
acceptable level of precision and accuracy, so that spatial and temporal trends can be monitored, and
that measure a response which can be linked with more traditional measures of effects on the
reproduction, development and growth of the organisms and the resulting effects on populations (i.e.
they are indicators of effect). Such biomarkers are more valuable as early warning tools that those
which are considered to be simply indicators of exposure to specific pollutants.

Table 2 provides an indication of the types of biomarkers that may be useful in measuring the effects
of pressures which result from farming-related activities, particularly pesticides and endocrine
disrupting chemicals.

With increasing activity in the fields of environmental genomics and proteomics, it is likely that
additional tools will become available that are linked mechanistically to effects in individuals. However,
irrespective of the tools developed, it will be necessary to use biomarkers as a tool within a broader
assessment framework and they may be best used in the coming years as mechanistic “signposts”
(e.g. to guide further monitoring) rather than as “traffic lights” in the environmental risk assessment of
pollutants.179,180

Table 2 Types of biomarkers that may be useful in measuring the effects of pressures which result
from farming related activities
Biomarker Description Type of chemical to
which biomarker
responds
Biochemical markers
Acetylchlolinesterase Inhibition of acetylcholinesterase activity in Organophosphorus
(AChE) exposed organisms pesticides
Phytochemical pattern Changes in different groups of compounds Herbicides
(e.g. amino acids, lipids and terpenes, phenolic
compounds) in exposed plants
Vitellogenin (VTG) Increased levels of the protein vitellogenin are Natural and synthetic
measured in exposed male fish steroids
Histological markers
Imposex Masculinisation of reproductive organs in Tributyltin
exposed clams and gastropods
Intersex Feminisation of reproductive organs in exposed Natural and synthetic
male fish steroids

3.5 Summary

23
1. A number of ecological indicators show statistical significant relationships with pressures which
are relevant to farming-related activities. However, in many instances there is a high degree of
variability associated with the relationships which limits their wide-scale application. Relationships
may, therefore, have to be water body type-specific rather than generic.
2. There is evidence that changes in abundance of certain key aquatic flora and/or fauna species
may be valuable in providing an early warning of the impacts of certain pressures associated with
farming-related activities. However, further research is needed to determine how applicable the
relationships would be across a particular water type (e.g. rivers, lakes, transitional and coastal
waters) and what procedure should be used to minimise the effects of potentially confounding
factors.
3. There may be a role for biomarkers in assessing the impacts of pressures resulting from farming-
related activities. However, irrespective of the tools developed, it will be necessary to use
biomarkers as a tool within a broader assessment framework.
4. It is unlikely that a single indicator can be used evaluate the impacts of specific pressures (e.g.
nutrient enrichment, organic enrichment, exposure to pesticides or veterinary medicines). Instead,
the outputs from a series of indicators will be needed.

24
4 Understanding the impact of farming on aquatic ecosystems
4.1 Introduction
The previous Sections of the report have described the current understanding and knowledge base on
the impact of farming on aquatic ecosystems in the context of current policy and practices. It is clear
that some farming activities and processes leading to impacts on aquatic ecosystems are better
understood than others. Control of these activities and processes should lead to improvements in the
status of some impacted water bodies. But as the more dominant pressures (e.g. point sources of
phosphorus and diffuse sources of nitrate) are reduced then the importance of other pressures (e.g.
veterinary medicines and endocrine disrupting chemicals) may be revealed and become more
important in terms of achieving good ecological status of some water bodies. There are significant
gaps in the current knowledge base which will have to filled if the impact of farming is to be better
understood, and more importantly identify what is required to achieve good ecological status in
impacted water bodies in as cost-effective way as possible.

Table 3 below summarises the main findings of Sections 2 and 3 in terms of the knowledge of how
farming may lead to impacts on aquatic ecosystems (e.g. activities, pathways, apportionment of loads,
processes, effects) and the quantification of scale and importance of the impact through information on
the significance (e.g. status of water bodies and proportion of water bodies affected) and the
geographic scale of the impact (e.g. local, regional, national). Both aspects have to be quantified in
order to fully understand the impact of farming on aquatic ecosystems.

Information on the status of water bodies and proportion of water bodies affected comes from several
available sources: results of the WFD Article 5 risk assessments, results of current monitoring
programmes, preliminary classification of the ecological status of waters according to the proposed
Environmental Standards for the implementation of the WFD, and recorded pollution incidents arising
from farming activities and sources. The aim is also to summarise knowledge gaps that must be filled
to improve understanding.

The significance of the gaps will also need to be assessed to define priorities for research and
development. Significance may relate to the potential severity of the effects of the different pollutants,
the scale (e.g. local, regional or national) of the farming activity leading to the impact, the size and
nature of the gap in current knowledge and the availability of existing cost effective mitigation
measures. Based on the evidence obtained from this review the most significant impacts arising from
farming are caused by phosphorus, nitrate, soil sediment, pesticides, organic matter and ammonia (in
decreasing order of the number of water bodies potentially impacted). However, it should be noted that
there is currently no representative overview of the significance of the potential impact from veterinary
medicines and non-regulated endocrine disrupting chemicals.

25
Table 3 Summary of knowledge of the how farming may lead to impacts, and on information for the quantification of scale and importance of the impact of
farming on aquatic ecosystems
Pollutant Knowledge of activities,
pathways, processes,
apportionment and impacts
Nitrate Pathways and processes relatively
well known. 60.6% of total nitrogen
load in E&W from agriculture.
Eutrophication: some further
research required. Acidification:
farming contribution unknown.
Toxicity: not fully assessed.
Phosphorus Pathways and processes relatively
well known.
23-28% of TP and 19% SRP loads
in GB from agriculture.
Eutrophication: some processes
(e.g. role of sediment bound P in
some rivers) not well quantified.
Ammonia Pathways and processes relatively
well known.
80% of emissions to air, water and
soil from agriculture.
Eutrophication: indirect effect, some
further research required.
Acidification – indirect effect.
Toxicity – direct effect.
Sediment Some processes and pathways not
fully quantified e.g. chronic releases
to water. 75% of sediment input to
rivers from agriculture.
Siltation and increased turbidity.
Pesticides Pathways and processes relatively
well known. No source
apportionment.
Toxic effects.
Quantification of scale and importance of impact
Water bodies at risk: Status of impacted water bodies Pollution incidents Geographic scale
WFD Article 5
37.9% river, 19.9% 28% rivers high nitrate concentrations Not relevant Highest
estuary, 13.1% coastal (all sources). concentrations tend to
WBs: sources: 39% of 60 estuaries/coastal WBs less be in arable areas
agriculture, atmospheric than good ecological status in E&W
deposition for rivers
47.4% river, 36.8% lake 63.3% river and 67% of lake WBs less Not relevant Higher concentrations
WBs: diffuse agriculture. than good ecological status in England: found in urban and
12.8% rivers and 80% lake WBs in arable areas
Wales: all sources.
2.9% rivers, 20.8% lakes, 17.3% of rivers in England and 2.7% in No information Acidification: Upland
acidification, atmospheric Wales predicted to be less than good areas. Highest water
deposition of emissions ecological status when applying concentrations in
(including ammonia) from proposed standards for WFD. This will North West
all sources. relate mainly to direct emissions of
ammonia to water bodies from point
and diffuse sources.
21% of river WBs at risk Salmonid reproduction affected by No information Regional differences,
from agriculture siltation at 2 of 43 sites. Up to 101 out NW, NE, Anglian,
of 161 chalk streams possibly affected Severn and South
by siltation. Half of 62 principal salmon East worst
rivers in E&W possibly affected. No
representative assessment of
suspended sediment or siltation levels
in rivers
20.8% river WBs at risk: Sheep dip chemicals caused third of 43 out of 49 significant Sheep dip failures
agriculture and sheep dip EQS failures, and cypermethrin pollution incidents from mainly Wales and
exceeds EQSs at 21% sites in England agricultural use north of England.
and 19% sites in Wales. Between 6 and
26
 Pollutant Knowledge of activities,
pathways, processes,
apportionment and impacts
Veterinary Pathways and processes not fully
medicines quantified.
No source apportionment.
Toxic effects.
Faecal Pathways and processes relatively
pathogens well known. No source
apportionment. No effects on
aquatic organisms found.
Organic Pathways and processes relatively
material well known. No source
apportionment.
Oxygen depletion, smothering.
Endocrine Pathways and processes not fully
disrupting quantified.
chemicals Hormone disruption (e.g. intersex in
fish, mainly roach). No information
on impact on other fish species and
invertebrates, and the implications
to fish populations as a whole.
Other Pathways and processes relatively
pollutants - oil well known. No source
apportionment. Toxic effects.
Quantification of scale and importance of impact
Water bodies at risk: Status of impacted water bodies Pollution incidents Geographic scale
WFD Article 5
8% of samples (taken at 2500 sites,
mainly rivers) exceeded 0.1 µg/l
between 1998 to 2006: mainly diuron
(mainly amenity use), isoproturon and
mecoprop. Monitoring not necessarily
representative of acute exposure
pathways or of all water bodies.
Not assessed Four sites representing worst case of No information No information, only
potential contamination generally had very limited case
concentrations below PNECs. studies undertaken.
Assessment of impact of other priority
medicines required. Information not
necessarily representative of all water
bodies.
Not assessed Contribution to failure of Bathing water Not relevant Problem (failing)
standards for example in two of three bathing waters
known 'problem areas'.
13.4% of estuaries, and 18.7% of rivers in England and 3.7% in 55 significant pollution Highest BOD in North
0.2% of coastal water Wales predicted to be less than good incidents in 2006: slurry England, worst quality
bodies at risk of organic ecological status when applying accounted for 75% of rivers from GQA in
enrichment (direct and proposed standards for WFD. incidents Anglian region.
riverine inputs)
Not assessed At eight of the 11 (worst-case) farms Not relevant Only Intensive
surveyed oestrogenic activity exceeded livestock farms and
at least once the PNEC for 17β- small streams
oestradiol in water. surveyed
Only limited data on concentrations of
agriculturally related EDC in fresh and
marine waters.
Not assessed No information Oil and fuel most Localised
important type of
pollution: 89 (14.7%) of
605 significant incidents
in 2006. Proportion from
agriculture not publicly
available.
27
4.2 Knowledge of activities, pathways, processes, source apportionment and impacts
The following Section summarises the main gaps in knowledge and the areas of further work relating
to activities, pathways, processes, source apportionment and impacts. Specific recommendations are
given as number paragraphs.

1. The processes of loss and the pathways to watercourses are reasonably well understood for
soluble nutrients such as nitrate. However there is less specific information about the details of
transport within any given catchment for less soluble pollutants and pollutants that are accumulated on
soil. This lack of information is in two main areas.

 For hydrophobic contaminants that are predominantly associated with sediment there is a
need for a better understanding of sediment transport and behaviour and of the processes by
which absorbed substances might be released.

 For less hydrophobic substances there is a need to obtain greater understanding of the
processes that control adsorption to suspended particulate matter in order that the
mechanisms of pollutant transport can be made clearer.

2. The quantities and proportion of some pollutants originating from agricultural activities that
become associated with sediment needs to be established. There is relatively good information for
phosphorous where it is estimated that approximately 60% of phosphorous is lost via absorption to
sediments. The case for other pollutants particularly organic material and pathogens is less well
quantified and understood.

3. More information is needed on the quantities of ammonia contained in fertilisers that is being
converted to nitrates/nitrites prior to being leached from soils and how much is actually lost as
ammonia.

4. Current monitoring of sources and pathways concentrates on those which are most evident
and easy to measure rather than smaller incidences which can have a cumulative effect such as those
relating to sediment. Monitoring should be extended to capture the smaller processes and enable an
assessment of the importance of such processes.

5. It is known that certain types of farming practices leave soils more susceptible to erosion than
others. Risk maps in terms of loss of sediment to water bodies could be drawn up at a national scale in
order to document these risks and in order to better direct mitigation measures.

6. In particular for pathogens, research is required into pathways (e.g. transport in soils via
vertical mechanisms and by-pass flow), pathogen survival and mitigation. This type of information
should improve the performance of current pathway models.

7. Better quantification is needed on losses of organic material from diffuse sources such as yard
washings and loss from manures applied as fertilisers. Moreover, soil sediment and some types of
organic material are often not treated as separate pollutants and needs to be addressed because of
their very different properties.

8. There is a lack of source apportionments for pollutants such as organic matter, soil sediment,
pesticides, veterinary medicines, faecal pathogens and endocrine disrupting chemicals. There also
needs be a better balance between the source-orientated approach and load-orientated approach for
a better apportionment of loads and understanding of likely impacts.

9. Further research is also needed on diffuse sources of nitrates to coastal waters taking into
account more recent issues such as fish farming and disposal of fish wastes.

10. The impacts of organic matter and ammonia on aquatic organisms are relatively well
understood as they have been monitored for many years, in particular in relation to the impact of
discharges from sewage treatment works and disposal of sewage sludge, and to assess the general
quality of rivers. Research has also been undertaken on the potential impacts of sediment on aquatic
organisms particular in terms of the silting of fish breeding gravels and their impact on dissolved
oxygen concentrations in the water column. The relative scale of the potential impact of sediment has
also been highlighted by the WFD Article 5 risk assessments.

28
11. The impact of nitrate on aquatic organisms has generally been considered in terms of the
indirect effects of eutrophication e.g. increased turbidity, oxygen demand arising from the degradation
of organic material etc. There is some evidence that some organisms may also be sensitive to nitrate
at concentrations not uncommon in freshwaters. Also nitrate and ammonia contribute to the
acidification of water bodies, particularly upland water bodies with low acid neutralising capacity. There
are well known effects on aquatic organisms arising from decreases in pH. There is also a lack of
information and data on some veterinary medicines that precludes detailed assessment of their
potential impact on aquatic organisms.

12. It is recommended that the potential toxicity of nitrate to freshwater organisms is further
investigated, and that the contribution of nitrate arising from agriculture to acidification is further
quantified.

13. There is a poor understanding of the relative importance of water and sediment sources of
phosphorus for vegetation (macrophyte) growth in both rivers and lakes 181. Thus the impact of
particulate sources of phosphorus or sediment-bound phosphorus on important diagnostic ecological
communities is less well understood, but it is likely that even in faster flowing river systems
phosphorus will impact on ecological status. Further research on these aspects is therefore required.

14. In terms of the impact of veterinary medicines on aquatic ecology there is a need for a more
detailed assessment of the potential impacts of veterinary medicines on soil in general and in
particular investigations into the fate and effects of parasiticides in sediment, and how that might affect
potential pathways to water bodies. There is also a lack of information and data on some compounds
that precludes detailed assessment of their potential impact on aquatic organisms. In particular, there
is a need to monitor for the presence of these compounds in groundwater.

15. Research over recent years has revealed the occurrence of male intersex fish in English rivers
mainly in relation to exposure to sewage effluents containing a number of feminising chemicals
including steroids but also, to a more limited extent, in relation to livestock farms as a potential source
of steroid hormones. It is recommended that surveys for intersex in roach and other potentially
sensitive fish species are extended to include a representative range of water body types and levels of
farming and other pressures to determine the geographic extent of intersex and whether farming is
potentially a significant source (compared to sewage effluents for example). In addition, further work is
required to understand the implications of endocrine disruption (from all sources) on the structure and
functioning of fish populations as a whole, and on other taxonomic groups (such as invertebrates) for
which there is very limited information.

16. The WFD requires that certain quality elements are used to monitor and assess the ecological
chemical status of water bodies. For most Member States the scope of the elements required went
beyond their existing national monitoring programmes and assessment schemes. There has been a
concerted effort at European and national levels to identify and fill these gaps. For example, the
European WFD Common Implementation Strategy Working Groups and the UK Technical Advisory
Group have identified gaps in knowledge and the need for further development. Some of those
relevant to the monitoring and assessment of the impact of agriculture are listed below: these are likely
to be subject of further research for European (under Framework 6 and 7 for example) organisations
as well as UK regulators.

 There is a general lack of knowledge on the combined effects on ecology of mixtures of toxic
substances in water that may individually be below EQSs concentrations.

 There is also a general lack of knowledge on the responses of aquatic ecosystems to combined
pressures.

 The relationships between nutrient concentrations and phytoplankton growth in rivers are not well
known. The concentration of nutrients may not be the only factor triggering algal blooms. Hence
the respective effects of nitrate and phosphorus, and their ratios and different forms on
phytoplankton biomass and assemblages need further investigation in large rivers.

 Further research is needed to investigate the occurrence of algal blooms in coastal waters
specifically in areas adjacent to agricultural catchments, and the extent to which the
nitrogen:phosphorus ratio and also silicate control algal blooms with an assessment of the
importance of nitrogen. This would need to be undertaken over a long time scale in order to
capture seasonal fluctuations and underlying trends in algal blooms.

29
 There is a lack of information on the responses of macrophytes to nutrient conditions in general
and in particular quantification of relationships that distinguish the effects of nutrients from the
effects of other variables, the response of macrophytes to nutrients in sediments, and lack of
robust quantitative relationships between water quality and macrophytes in coastal waters.

 There is an absence of quantitative relationships between phytobenthos and nutrients.

 There is lack of knowledge on the ecological impact of nitrogen conditions on some lakes and
rivers, particularly their potential to limit primary production.

 The responses to, and functional relationships between, phytoplankton, macrophytes and benthic
invertebrates in rivers and organic pollution from urban and agricultural run-off are not well known.

 The impacts of sediments in lakes need to be better understood and differentiated from natural
infilling processes.

 There is potentially scope to improve the responsiveness of certain biological indicators by

modifying the assessment procedure and focussing on particular sensitive elements of a given
index.

4.3 Quantification of scale and importance of impact

The WFD introduces the concept of risk-based monitoring and programmes have been established to
assess the status (ecological and chemical) of all water bodies subject to significant pressures such as
those arising from farming. This should lead to an improvement in the amount of information on the
status of water bodies in terms of water categories (e.g. lakes, estuaries and coastal waters) and
some pollutants (e.g. soil sediment and some veterinary medicines) not currently included in
established and routine monitoring programmes, and on the spatial and geographical significance of
any particular pressure/pollutants in terms of the water bodies affected. The following section
summarises the main gaps in knowledge and the areas of further work and makes recommendations
relating to quantification of the scale and importance of the impact of farming on aquatic ecosystems.

17. Episodic or seasonal farming activities may cause significant effects that are not detected by
monitoring programmes that employ infrequent spot sampling. Risk-based monitoring should therefore
be applied for assessing the impact of pesticides when the risk of an effect is the greatest (e.g. during
episodic or seasonal agricultural activities), and linked to the actual use of specific pesticides within
catchments. This will enable a more complete and representative overview of the impact of agricultural
pesticides on water bodies in England and Wales.

18. The monitoring of sediments in water bodies should reflect their potential impact on aquatic
ecosystems, in particular through siltation of fish spawning gravels.

19. Research over recent years has revealed a widespread occurrence of male intersex fish in
English rivers. This has now been linked with exposure to sewage effluents containing a number of
feminising chemicals including steroids. However certain water bodies may have elevated
concentrations of natural steroids arising from directly deposited animal urine and faeces or via other
pathways. Some targeted worst-case monitoring has been undertaken in relation to farming sources of
steroids, and these revealed some limited effects. Further monitoring surveys for intersex in roach and
other potentially sensitive fish species should be undertaken to include a representative range of water
body types and levels of farming and other pressures to determine the geographic extent of intersex
and whether farming is potentially a significant source (compared to sewage effluents for example). In
addition, further work is required to understand the implications of endocrine disruption (from all
sources) on the structure and functioning of fish populations as a whole, and on other taxonomic
groups (such as invertebrates) for which there is very limited information.

20. The monitoring of nitrate loadings and studies of nutrient loadings has concentrated largely on
the North Sea area where loadings are thought to be largest; therefore efforts should be made to
provide a more consistent coverage around UK waters.

21. A specific routine monitoring programme should be considered for monitoring the impact of
farming on a few selected representative catchments that are largely free from the effects of other
pressures and which would be intensively monitored. This type of monitoring could build on the

30
experience gained through the monitoring proposed to assess the effectiveness and outcomes of
England Catchment Sensitive Farming Delivery Initiative in the 40 priority catchments. 182 The
monitoring programme would also provide further valuable data and information for the calibration of
models that could be applied more generally.

22. A less intensive way of monitoring the impact of agriculture (for early warning information or
for general progress) would be to select those water bodies subject primarily to agricultural pressures
and which are included in the EA’s operational monitoring network (Note: It may not be necessary to
monitor all water bodies at risk or below good status because the WFD allows similar water bodies to
be grouped and a sub-set of the group to be representatively monitored).

23. There is a need to start undertaking larger and more comprehensive, perhaps catchment-
based, projects that deal with a range of pollutants and impacts. For example, it seems that the current
knowledge is not sufficient to give clear advice to decision makers on how to deal with complex
impacts of combined pressures across different spatial and temporal scales 183. A key issue is the
influence of scales when studying ecological processes. For example, there is evidence that human
actions at the landscape scale are a significant threat to the ecological integrity of river ecosystems,
impacting habitat, water quality, and the biota via numerous and complex pathways 184. It is also difficult
to distinguish between the influence of the local riparian zone, upstream riparian zone, basin or sub-
basin conditions and land use when studying causes for ecological degradation at a single site. 185
Large-scale analysis comparing relationships through different scales are therefore required. This
would require the study of pressure-impact relationships in geographically homogeneous areas with
respect of natural factors controlling aquatic ecosystems, and to identify the relative influence of
human and natural drivers on ecosystem responses.

24. For all pollutants the assessment of the effectiveness of mitigation of control measures needs
to be done regularly and over a long time scale as biological improvements may not be seen until long
after the source of the pollutant has been controlled.

4.4 Improvement, development and implementation of cost-effective mitigation measures

Information on the costs of a measure and its effectiveness in terms of emissions reduction is
contained in the User Manual on diffuse water pollution (subsequently referred to here as the User
Manual).186 The effectiveness information incorporates a considerable amount of expert judgment and
is often characterised by large ranges, while the costs are of a generic nature, more comparable to
those used for benchmarking farm operations contained in farm management costings publications.

The costs and effectiveness values for each measure contained in the User Manual relate specifically
to notional 'representative' Model Farm Systems for the main sectors, and are given for two main soil
types and a medium level of rainfall. The effectiveness of a measure in reducing pollution will however
be sensitive to a wider range of soil types and rainfall, as well as a number of site specific factors.
This is highlighted by Johnston and Dawson (2005), who reported that the relative importance of
different pathways will vary spatially and with time, both between and within catchments, and that
factors affecting phosphorus loss are field-specific. It is also reflected in a substantial research project
for English Nature and the Environment Agency. This concluded that different farms and different
locations will in general respond most effectively to a different local mix of changes in practice 187. A
similar view emerged from the Defra Phosphorus Cost Curve project which concluded that both cost
and effectiveness may vary considerably with location188.

The User Manual acknowledges that its standard Model Farming Systems cannot be extrapolated and
applied to the whole of a farming sector across farms of different sizes and in different regions. Also
that there may be appreciable differences between a model farm system within a sector and the
range of farms found within the sector, with corresponding differences in the applicability and
effectiveness of the mitigation methods reviewed. Modelling has been used to extend the
assessments in the User Manual to the regional scale according to three climatic (rainfall) categories
and two broad soil types (sandy loams and clay loams) as part of Defra’s consultation on diffuse
pollution.189

The assessment of the measures which are most cost effective can be complicated by the fact that
some pollutants are closely linked and measures often affect more than one pollutant, although
sometimes in conflicting ways. Measures which are effective for phosphorus, for example, are also
considered to be effective to varying degrees for sediment, organic pollution, BOD, and for those

31
pesticides attaching to soil particles. But applying manures in spring to help reduce nitrate loss for
example, may increase ammonia emissions.

The effectiveness of a measure will also depend on the extent to which measures are taken up by
farmers. This may be influenced by the mechanism used to deliver the measure (whether it is
supportive, economic or regulatory) and the receptiveness of farmers. A recent survey of farmer
attitudes carried out as part of the ECSFDI found that 81% of farmers do not believe they make a
significant contribution to pollution (Craig, pers.comm.). The effectiveness of mechanisms has been
addressed by Defra in its consultation on diffuse water pollution from agriculture, which found
regulation to be the most cost effective, albeit on the basis of certain specific assumptions (see
above).

The attributes contributing to effectiveness of a measure in closing the gap required to meet the
specified WFD objective are described briefly in the methodology developed for assessing the cost
effectiveness of measures for the UK's implementation of the WFD. 190 These are listed below, the first
four of which relate broadly to the efficacy of a measure, and the remainder to its uptake:

 Uncertainty of effectiveness;
 Characteristics of effects:
o Speed of effect,
o Durability of effect,
o Adaptability/reversibility of the measure (how easily it can be adapted to changes in
the requirement);
 Effort (the degree to which a measure is implemented);
 Practicability;
 Local acceptability;
 Motivation for implementation;
 Presence/absence of responsible organisation;
 Presence/absence of planning process.

The need for future research on measures for mitigating pollution therefore needs to be considered
against the background of the disciplined approach enshrined in this new cost effectiveness
methodology. The User Manual includes comments for some measures on their speed of effect where
the response time is particularly slow, but includes very little specific information. It also includes a
brief assessment for each measure on how easy it is to adopt, how it may impact on other farming
practices, problems with maximising effectiveness and possible resistance to uptake. Since it is based
on standard model farm systems, it does not contain sufficient information to allow assessment of cost
effectiveness across the range of situations which exists within farming sectors. It therefore increases
the uncertainty of effectiveness and so will score less well in this respect under the cost effectiveness
methodology.

Defra recognises that variability in soils (clay and sandy) and climate (rainfall) can cause different
measures to be the most cost effective in these different situations. 191 However, in the light of the
research findings cited above, this would not appear to have gone far enough in reflecting the
variability inherent in agriculture,

Much research has already been carried out to improve the understanding of factors influencing the
scale and other characteristics of nitrate loss, and to a considerable extent on phosphorus, although
gaps remain. This was acknowledged by Haygarth et al. (2005) who concluded that for P, there are
many areas where we lack knowledge192. Much less appears to be known about other pollutants.

In the light of the above, the following recommendations are made:

25. Effectiveness: To create a database of quantitative data on the effectiveness of measures for
the mitigation of various agricultural pollutants.

The data needs to reflect the range of variables which have a significant effect on the efficiency of
measures, such as soil type and condition, climate, topography and farm type. It should systematically
cover relevant attributes of effectiveness required for the WFD methodology, for example scale of
effect, timing and duration of effect. It also needs to cover the effects on other water pollutants, which
may be positive or negative. This would likely be a major undertaking, and prioritisation would be
needed.

32
There are relatively few data sets quantifying concentrations and loads of multiple pollutants for many
of the mitigation methods, as is recognised by IGER (IGER, pers. comm.). While the Defra project on
cracking clay soils (WQ0118) is looking at multiple pollutants from manures, it will be plot based and
so will not address scale effects. Also, it will be limited in the number of farming systems included and
will not address a number of the attributes of effectiveness detailed in the WFD methodology.

26. Scale: To investigate whether the most cost effective measures for different pollutants differ at
a field-by-field scale, and whether it would be feasible to predict the most cost effective measures at
this scale.

If the measures applied are not the most cost effective for a particular situation, this will increase the
costs unnecessarily and lead to misallocation of resources. It may also result in the objective for that
water body not being achieved. This recommendation would provide part of the information needed for
ensuring costs are not higher than necessary. Defra estimates the costs of implementing measures to
tackle diffuse water pollution from agriculture to meet WFD objectives at £140-200m p.a. (8-11% of
farm income for England in 2006). With costs of this order under consideration, the potential savings
from developing approaches and database to fine-tuning measures to achieve the most cost-effective
solution are likely to be substantial.

ADAS supports recommendations 25 and 26. It believes it would be feasible to predict the most cost
effective measures at a field scale, and that much of the information required to do this, for example
on slope, is available (Chambers, pers comm.).

27. Phosphorus emissions: As a priority, there is a need to identify and fill gaps in the existing
data on the effectiveness of agricultural measures for phosphorus in achieving ecological
improvement, as distinct from achieving reductions in total phosphorus as a chemical standard.

Environmental standards for the achievement of Good Ecological Status have been proposed on the
basis of soluble reactive phosphorus in rivers and total phosphorus in lakes. The achievement of the
standards will require consideration of all sources of phosphorus in the catchments of affected water
bodies.

It is widely believed that there are important differences in the ecological impact of phosphorus from
agriculture compared to other sources involving factors such as the chemical form of phosphorus,
particle sizes and behaviour, the timing of emissions and the extent to which these are effectively
removed from the water body before uptake by biota can occur. Agricultural phosphorus sources
generally have less soluble phosphate and emissions to water bodies are strongly biased towards
winter when temperatures are low and flows are high, which may reduce the impact relative to other
sources and so limit the scope for achieving improvements in status through agricultural measures
alone. There may also be differences between phosphorus derived from the respective agricultural
sources and transported through different pathways which could influence the ranking of measures for
cost-effectiveness. However, in some catchments it is likely that the achievement of good ecological
status will require measures to reduce emissions of phosphorus from both point and diffuse
(agricultural) sources.

28. Costs: To create a database of costs of environmental mitigation measures for agriculture
capturing significant differences, such as those between soil and enterprise types, regions, size and
structure of businesses and farming system employed.

Benchmark-type generic costs at national level as currently provided in the User Manual are unlikely to
be an adequate basis for deriving estimates of cost effectiveness. While the Manual goes some way to
differentiating costs by using broad geoclimatic categories (2 soil types and 3 levels of rainfall) and
certain enterprise types, it takes no account of other factors such as the varying size of enterprises
and it does not cover all sectors (e.g. sheep) nor all types of enterprise (e.g. layers). The costs data in
the User Manual also differ widely from other published sources in some respects, and so are open to
question. As with effectiveness, breaking down the ranges associated with the figures according to the
underlying factors would seem necessary. Costs for environmental mitigation measures regionally
differentiated according to production system used and scale of operation would seem more
appropriate than the current approach. A pilot project to assess the scope for finer resolution in cost
data is recommended.

29. Catchment studies: Approaches to reducing impacts from diffuse pollutants from agriculture
should be tested and developed at a catchment-scale in a small number of pilot catchments.

33
Information should be gathered on the dynamics and trade-offs in selecting measures for a wide range
of agricultural pollutants.

Catchment studies are required to assess and validate the performance of combinations of measures
in reducing ecological impacts, and to compare this with predicted effectiveness. Such studies could
help ascertain the extent to which improvements in cost effectiveness can be achieved by field-level
targeting, and the resources needed to achieve this.

34
5 Knowledge transfer plan

As a broad and timely review of the impact of farming on aquatic ecosystems, this report will be of
interest to a broad readership. The main target audience is Defra, but the findings will also be relevant
to stakeholders that have a statutory responsibility, commercial interest or professional role in the
management of water pollution in England and Wales. These include government agencies
(Environment Agency, Natural England), research funders and providers (e.g. NERC, BBSRC, Centre
for Ecology and Hydrology), private sector organisations (e.g. National Farmers Union, Water UK,
Country Land and Business Association, consultants) and non-governmental organisations (e.g.
Association of Rivers Trusts, RSPB, Salmon and Trout Association, Freshwater Biological
Association), as well as the broader farming community.

Table 4 identifies target outcomes for each stakeholder group and recommends appropriate pathways
to deliver relevant information and advice to intermediate and end users.

Table 4 Knowledge transfer plan

Target audience Target outcome Pathway to delivery

Defra Development of future R&D that Circulate report to key policymakers.
will identify cost-effective mitigation Hold seminar/workshop to discuss
approaches findings and prioritise future R&D.
Research funders and Alignment of R&D activity with Make report available via Defra
providers Defra research priorities website. Hold seminar/workshop to
discuss findings and prioritise future
R&D.
Private sector Broader understanding of the Make report available via Defra
organisations impact of farming on aquatic website. Publicise report via press
ecosystems release and conferences.
Non-governmental Broader understanding of the Make report available via Defra
organisations impact of farming on aquatic website. Publicise report via press
ecosystems release and conferences.
Farming community Enhanced awareness of Articles in trade magazines (e.g.
consequences of farming activities Farmers Weekly, Defra Farming
for aquatic ecosystems Link), and newsletters (e.g.
Defra/WAG CSF newsletter).

35
6 References

The availability of referenced documents is flagged as follows: (***) = in public domain and free, (**) =
in public domain but not free, (*) = not in public domain.

36
1
Defra (2002) Strategic review of diffuse water pollution from agriculture. Available at:
http://www.defra.gov.uk/environment/water/quality/diffuse/agri/reports/dwpa01.htm (***)
2
Defra (2007) Agriculture in the United Kingdom 2006. [Online] Available at:
(http://statistics.defra.gov.uk/esg/publications/auk/default.asp (***)
3
Cambridge University and the Scottish Agricultural College (2006) Business as Usual Projections of Agricultural
Activities for the Water Framework Directive: Phase 2. Report to Defra. (*)
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