Modeling Pollution Dispersi

Environmental Modelling & Software 17 (2002) 363385
www.elsevier.com/locate/envsoft
Review
Modelling pollution dispersion, the ecosystem and water quality in

coastal waters: a review
I.D. James *
Proudman Oceanographic Laboratory, Bidston Observatory, Birkenhead CH43 7RA, UK
Received 10 May 2001; received in revised form 29 July 2001; accepted 11 October 2001
Abstract
This review is intended as a comprehensive but concise summary of present capabilities in coastal pollutant, ecosystem and water
quality modelling. It reflects the recent rapid developments in multidisciplinary modelling in shelf seas.
The behaviour of conservative pollutants that act as passive tracers is contrasted with those that have more complex behaviours,
including oil spills. The importance of sediment modelling is emphasised, since contaminants commonly exist in both a dissolved
and a particulate state, or adhere to sediments.
Recently developed ecological models can have great complexity, reflecting the complexity of the real ecosystem. These models
are now being linked to physical models of coastal waters and run with the same resolution. This has become possible only recently
because of increases in computer power, particularly the availability of parallel systems at reasonable cost.
The main advances in physical modelling are likely to come through greater understanding of turbulence and other sub-gridscale processes as well as increased resolution.
In the coastal seas there is often a lack of oceanographic data, which is even greater for the many biological and chemical
variables than it is for physical variables. This is probably the single most important factor limiting the progress of operational
water quality models. 2002 Elsevier Science Ltd. All rights reserved.
Keywords: Coastal; Pollutant; Ecological; Water quality; Modelling; Multidisciplinary; Review
Contents
1.
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364
2. Modelling pollutants in coastal waters

2.1. Pollutants as passive tracers . . . .
2.2. Sediment and SPM . . . . . . . . .
2.3. Metals . . . . . . . . . . . . . . . . .
2.4. Oil spills . . . . . . . . . . . . . . . .
2.5. Chemicals and toxins . . . . . . . .
3.
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365
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Ecosystem modelling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
4. Physical modelling . . . . . . .
4.1. Diffusion and dispersion .
4.1.1. Vertical diffusivity . . .
4.1.2. Retinoic acid syndrome:
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a report of
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two casesLateral dispersion
* Tel.: +44-151-653-1533; fax: +44-151-653-6269.

E-mail address: idj@pol.ac.uk (I.D. James).
1364-8152/02/$ - see front matter 2002 Elsevier Science Ltd. All rights reserved.
PII: S 1 3 6 4 - 8 1 5 2 ( 0 1 ) 0 0 0 8 0 - 9
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374
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375
364
I.D. James / Environmental Modelling & Software 17 (2002) 363385
4.1.3. Quasi-two-dimensional turbulence

4.1.4. Lagrangian chaos . . . . . . . . . .
4.1.5. Numerical diffusion . . . . . . . .
4.2. Further requirements for the physical
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376
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5.
A model system for coastal water quality applications . . . . . . . . . . . . . . . . . . . . . . . . 379
6.
Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
1. Introduction
A general review paper covering the modelling of pollution, the ecosystem and water quality in coastal waters,
and the prospects for making this modelling operational,
is timely for at least two reasons. One is the increase in
such multidisciplinary modelling in the last decade, and
the need for an introductory review for those modellers
who previously were limited to a single discipline. The
other is the increase in computer power, involving the
use of parallel processing, which has made it possible
for the first time to run linked physical and ecological
models on the same high resolution. Multidisciplinary
modelling is therefore coming of age, and moving to the
stage where it is feasible to contemplate running a model
operationally to provide real-time predictions of water
quality in coastal waters.
The intention here has been to cover this very wide
and active field comprehensively but concisely to give
an accurate picture of present capabilities. To explore
individual topics in greater depth the reader is referred
to the bibliography.
This subject is essentially multidisciplinary: to attempt
to understand the whole system demands knowledge of
disciplines ranging over ecology, biogeochemistry, toxicology, sedimentology and fluid dynamics, while modelling the system involves numerical analysis and, for
complex simulation models, coding techniques for highperformance computers such as massively parallel
machines. The total coastal system is extremely complicated and includes many variables and processes including highly non-linear interactions. Most modelling to
date has therefore tackled only part of the system, or
very simplified systems, in order to make progress and
gain insight. Only recently have high-resolution hydrodynamic models and complex ecological models been
combined. The effectiveness of such deterministic models for making useful predictions about the ecosystem is
not yet completely proven and can still be controversial:
Nuttle (2000) argues in favour of the more traditional
empirical approach.
In this paper the view is taken that it is the physical
system and the physical conditions that are fundamental
and set the stage for the chemical and biological systems. While there can be some influence of these on the
physics (for example, the effect on penetrating solar
radiation of a surface plankton bloom), in general a good

representation of the physics can be achieved in a model
without considering biology and chemistry. Conversely,
the physical conditions, which include currents, tides,
waves, turbulence, light, temperature, salinity, bed
materials and suspended particles, determine the transport and dispersion of all suspended and dissolved
material in the sea, including contaminants and nutrients,
and affect all biological activity from the transport of
larvae and bacteria and the growth of phytoplankton to
the behaviour of fish. Therefore it is a necessary condition for any model of an estuary or coastal region to
be used to help understand the present conditions and to
make useful predictions that the physics is properly represented.
Of course, no physical model can give information on
physical variables on all space and time scales: these
have to be appropriate to the problem in hand. For
example, a simulation of the spring phytoplankton bloom
in the North Sea can be achieved with a fairly coarse
horizontal resolution, so long as the vertical resolution
and reproduction of tidal mixing in the water column are
sufficient to represent the onset of stratification, but the
details of horizontal patchiness in phytoplankton and
zooplankton require much higher horizontal resolution
to include eddies and the details of stirring and mixing.
Several physical processes which are sub-grid-scale
and which cannot be resolved by the physical model
have to be parameterised; that is, described by variables which represent them more or less adequately. One
of these is eddy viscosity, which describes the effect
of turbulence as if it behaved in the same way as an
increased molecular viscosity. A detailed model of turbulence and sediment dynamics near the sea bed would
be needed to reproduce the processes seen in experiments that can release material from the sea bed into the
water column, but this is often parameterised in a simple
resuspension term.
Despite the fundamental nature of the physical model
and the apparent simplicity of the physics in comparison
with the complexity of an ecosystem model or contaminant behaviour, it should not be assumed that the physics
is solved, easy to model or even well understood. It
involves non-linear equations which can lead to chaotic
or turbulent flow, a wide range of scales, and includes
difficult problems such as the behaviour of suspended

particles of various shapes and sizes in fluid flow. For
prediction purposes, it is also critically dependent on the
boundary conditions that drive it. For example, a twodimensional model for sea level which resolves tides and
surges and which has been well tested over many years
is still dependent on accurate meteorological data for
giving good surge forecasts. Such surge models are the
archetype for successful operational application of
numerical modelling to coastal processes. Some reasons
for their success are that they deal with relatively simple,
almost linear processes, long waves that are easily
resolved and energy dissipation that can be successfully
represented by a simple bottom friction term. The history
of surge modelling is the paradigm for the progress of
all coastal modelling: the original empirical methods
based on statistical relationships between surge level and
meteorological and other variables have been replaced
by deterministic numerical models based on the equations of motion, which are time-stepped forward from
an initial state. Now this paradigm is being followed for
very much more complicated processes, and while
results may not be so reliable or accurate as for storm
surges, much progress has been made in recent years, as
this review will make clear. It is worth bearing in mind
that numerical surge modelling is still being refined after
a development period of nearly 40 years, and that
meteorological agencies can and do still keep the statistical methods available as a check on the results. For models of much more complex systems it is even more
important to use the models in conjunction with complementary information, possibly from empirical models.
If the analogy with surge modelling is correct, we are
at present in the initial stages of deterministic water
quality and ecosystem modelling in the coastal zone,
now made feasible by advances in computer power, with
many decades of development ahead.
The following two sections review pollutant and ecosystem modelling. Then follows a section on modelling
the physics which underpins the pollutant and ecosystem
models. Then an outline is given of the requirements
for a possible complete model system that would be a
prototype for an operational water quality capability.
2. Modelling pollutants in coastal waters

A pollutant may be defined as any substance that
reduces the water quality. It may or may not result from
human activity. It may have a well-defined source (such
as an oil spill) or a diffuse source (such as radioactivity
from the atmosphere or antifouling paints). It may be
dissolved in the water, be attached to particles, exist as
particles, float, or be mainly in benthic sediments or
mud. Some pollutants may be partitioned (divided)
between several different phases (for example, metals
365
may exist in solution or as particulates). Some undergo

chemical reactions during dispersion in the sea; radioactivity decays with time. Oil may behave in several ways
depending on its type and the prevailing conditions: it
can evaporate, spread out in a thin slick, become
attached to sediments and form emulsions. The undesirability of a pollutant may be measured by its biological
effect: it may be toxic; nutrients from fertilisers in river
discharges may cause excessive plant blooms
(eutrophication), killing animal life by deprivation of
oxygen as the algae in the bloom decompose; it may
simply be aesthetically displeasing to humans. Distinction is sometimes made between contamination, defined
as any artificial increase above a background level, and
pollution, which implies harm to living things (for
example, Chapman, 1995), but this is not a distinction
made in the dictionary, nor is it universally accepted by
ecologists (Taylor, 1993), since the level of contamination that causes harm is not always easily identified.
The variety of pollutant behaviours means that each
pollutant must have its own algorithm (that is, rule for
calculation) to describe its modelled behaviour. This
may take the form of either a time-stepping concentration equation or a particle-tracking routine. The concentration equations are suitable for a widely dispersed
substance, but care must be taken over the numerical
advection scheme used: more on this will be found in
Section 4. Advection merely describes the motion of a
substance with the water velocity, as a passive tracer.
Although this is a simple concept, simple numerical
advection schemes can cause either excessive diffusion
or rippling near sharp gradients. This is not a problem
with particle tracking, which is a natural method to use
with point sources, but once the substance is dispersed
a large number of particles may need to be used to retain
enough in each grid box to represent the concentration
there.
The advectiondiffusion equation
C
C
C
K
ui
t
xi xi ijxj
(1)
is the core of any equations determining pollutant concentration C. Kij is the diffusivity tensor: usually for
shelf seas it is assumed that Kij 0 if i j and that
K11 K22 KH, a horizontal diffusivity, and K33
KV, a vertical diffusivity. This equation alone would
describe a passive tracer. The diffusion part represents
tracer motion on scales too small for the model to represent. If the flow is laminar, i.e. if there is no turbulence,
the diffusion is on the molecular scale, with a thermal
diffusivity of the order of 1.4 107 m2 s1 in pure
water. In coastal waters, the flow is almost always turbulent and the effective diffusivity is several orders of magnitude greater. Diffusion due to sub-grid-scale processes
in a model is often described by eddy diffusivity, often
determined by a turbulent energy equation, which,
366
although much greater, nevertheless behaves like molecular diffusion: fluxes are always down-gradient and
sharp changes are always smoothed out. This does not
necessarily represent the real processes of mixing that
may be taking place, and in reality there may be stirring
of material into thin filaments of high concentration that
are ultimately diffused on the molecular scale. The distinction could be important if the highest local concentration of a pollutant is important, rather than the average
within a model grid box. The ability of a model to predict concentrations from the advectiondiffusion equation is always limited by the resolution of the model as
well as the representation of sub-grid-scale mixing in the
diffusion term. This will be discussed further in Section
4. In a particle-tracking model, where advection is
straightforward, diffusion must be represented by random motion of the particles, determined by the value of
eddy diffusivity. However, convergence in the largescale velocity field can lead to narrow filaments of particles that would not be so well resolved by a concentration equation.
In addition to the advectiondiffusion equation are the
terms that describe the way the pollutant behaviour differs from a passive tracer. These must also be represented in a particle-tracking model, possibly by a
change in the properties of each particle. For a dissolved
radioactive substance, this may simply be a decay of the
radioactivity with time. For a sediment, or other particulate matter, there may be a fall velocity. For large particles, there may be other differences between the particle velocity and the water velocity. For sediments there
may need to be terms representing deposition and resuspension at the sea bed, cohesion and flocculation. There
can be terms representing interaction, whether chemical
or biological, with other variables. The algorithm for
each individual pollutant variable needs to be derived
from a clear understanding of how that pollutant behaves
in coastal waters.
In the following subsections the simplest pollutants,
which behave most like passive tracers, are treated first,
and then pollutants with more complex behaviours are
described.
2.1. Pollutants as passive tracers
A passive tracer is subject simply to advection and
diffusion and sources and sinks, possibly including
exchange across the sea surface and sea bed. The water
movement is independent of the tracer concentration, so
can be calculated separately. Quantities behaving in this
way include some dissolved metals (Prandle et al., 1993;
Charnock et al., 1994). Sources may typically include
rivers and the atmosphere; sinks for dissolved metals
may include adsorption on to particulates. The latter process is greater for some metals, for example lead, than
for others and for these the behaviour is less like a sim-
ple tracer. Nevertheless, Prandle et al. (1993) calculated

the distributions of salinity and metals in the southern
North Sea on the basis of residual flows from a twodimensional model and river and atmospheric sources.
This process is most straightforward for conservative
quantities, where there is no significant source or sink
term apart from perhaps a river input. In the case of
salinity, its influence on density cannot usually be neglected when calculating currents, and certainly not near
river outflows, so it is not simply a passive tracer.
One pollutant that approximates closely to a tracer is
a dissolved radioactive substance with a long half-life.
Radioactive decay adds only an exponential decay term
to the concentration predicted from the advectiondiffusion equation. In fact, over a long period radioactive
substances have been useful for testing models of the
long-term circulation of shelf seas. Prandle (1984) used
residual currents from a two-dimensional shelf model to
simulate the transport of 137Cs from Sellafield in this
way. Recent discharges of technetium, which has a very
long half-life (2.13 105 years), from Sellafield
(Leonard et al., 1997) and Cap de la Hague have provided more tracer information. Dahlgaard (1995), in an
overview of the EU MAST-52 project, discusses radioactive tracers as a tool in coastal oceanography.
The relative importance of advection and diffusion in
the dispersion of a tracer may be represented by the
Pe clet number Pe UL / K, where K is (horizontal)
diffusivity, U the velocity and L a length scale. Prandle
et al. (1993) estimate that for the southern North Sea,
and this may be typical for tidal shelf seas in general,
advection dominates diffusion for a conservative tracer
on space scales O(10 km). This underlines the importance of accurate numerical advection methods in pollutant models as well as the need for a realistic representation of the mean circulation.
However, the less conservative the quantity of interest
is and the more it responds to local sources and sinks, the
less it can be regarded simply as a tracer. Temperature is
an example of a physical variable of this kind; over
much of the shelf a good simulation of the annual temperature cycle can be achieved by one-dimensional models of the water column, knowing heat input at the surface and vertical mixing due to tidal currents. Here, the
critical factor is the specification of the vertical diffusion. Except near coastal plumes and strong persistent
residual currents, advection is of secondary importance.
As for salinity, temperature cannot be a passive tracer
since it affects the water density and hence currents,
particularly near fronts and plumes.
The general conclusion is that for a pollutant to
behave as a tracer, it must be conservative and have
well-defined non-local sources and sinks. Pollutants that
approximate most closely to this are dissolved radioactive substances with long half-lives, metals with low
values of partition coefficients (representing the ratio of
particulate to dissolved phases) and low uptake by particles, and very fine particles with low settling velocities.
Most pollutants, however, do not behave like simple tracers and much of the emphasis in the following sections
is on the additional terms beyond advection and diffusion that are needed to model them.
2.2. Sediment and SPM
Here, SPM stands for suspended particulate matter,
while sediment also includes those particles which lie on
or near the sea bed. Coarse material with grain size
larger than about 0.1 mm generally moves only as bed
load except during exceptional storms. Sediment may be
cohesive (particles, more often fine ones, may stick
together) or non-cohesive. The modelling of sediment
and SPM is important not just for its own sake but
because pollutants may exist in a particulate phase or
adhere to or be adsorbed on to particles and because
particulates are an important part of ecological and water
quality models. For example, nutrients and detritus can
exist as particles, and SPM in turbid waters reduces
light levels.
The main additional terms in the equation for SPM
concentration are those that account for sinking, erosion
and deposition at the sea bed. Sinking is represented by
a fall velocity, which can be an addition to the vertical
advection in the model. The fall velocity varies according to the size of the particle, so a model needs to have
separate SPM variables for a range of particle sizes.
Sediment is deposited on and eroded from a separate
benthic layer. This layer in turn can be modelled in
detail, including the effects of bioturbation. Erosion may
be supposed to occur if the bed stress is greater than a
critical value, and then increases as the stress increases,
while deposition occurs if bed stress is less than another
critical value. For particles of finite size and density different from the water, the assumption that they behave
as a passive tracer with the addition of a fall velocity is
of course a simplification of their complete dynamics
(Maxey, 1990). The interaction of particles in suspension
is also often neglected in SPM transport models.
Results shown by Holt and James (1999) for SPM
from coastal sources in the southern North Sea show
how the addition of the extra sinking, erosion and deposition terms can result in a considerable difference from
the dispersion predicted for a passive tracer. SPM transport can depend strongly on the sequence and timing of
erosion and deposition together with the variable winddriven circulation. The bed stress, which is a critical
quantity in the model formulae, is strongly influenced
by storms (partly through enhancement due to waves in
shallow areas) as well as tidal currents, varying through
the spring-neap cycle.
As an alternative to the concentration equations a particle-tracking method can be used (Puls and Su n-
367
dermann, 1990; Pohlmann and Puls, 1994; Su ndermann,

1993). For both methods, the calculation increases as the
number of particle types and sizes increases. If the SPM
is passive, the hydrodynamic equations are unaffected
by the SPM concentrations. In this case, calculating the
residual flow and tidal currents once means they can be
used several times in different SPM runs (Su ndermann,
1993). The total flow, not residual only, is needed to
calculate the bed stress at any time. When concentration
of SPM is very high, however, it affects the apparent
density of the water and very turbid water may flow as
a density current (Simpson, 1987). Self-stratification of
the boundary layer by resuspended fine sediment during
storms may limit further resuspension (Jago et al., 1993).
The need for separate equations for each SPM fraction
is an example of the increase in the number of variables
and calculation load necessary for water quality modelling when compared with the hydrodynamic model
alone. Ideally, SPM modelling also has a requirement
for high resolution in the vertical to cover stratification
and boundary layers and in the horizontal to resolve turbidity fronts and plumes.
The requirement for wave information in shallow
areas to provide an enhanced bed stress (Grant and
Madsen, 1979) suggests also that, if this effect is to be
included accurately, a wave model needs to be run simultaneously. Some of the effect of enhanced bed stress
can, however, be represented by a simplified assumption
of wave activity (Jones and Davies, 1998).
Some effects not included in the Holt and James
(1999) model that are more difficult to parameterise are
those of flocculation, which increases the effective particle size and affects the fall velocity; biology, which
may change cohesiveness, affect resuspension and alter
the bed sediments by bioturbation; and trawling and
dredging, which can be significant in many areas. Willows et al. (1998) consider the modelling of biological
effects on the erosion of intertidal sediments.
The parameterisations in the SPM equations are themselves only simplifications of detailed processes at the
sea bed and in the turbulent bottom boundary layer.
These include bursting phenomena and the effect of bed
forms, including rippling of the bed. Detailed measurements of sediment resuspension (for example, Williams
et al., 1998) show many complex processes that are only
approximately accounted for in the shelf-wide models.
The application of models to coastal morphodynamics
(change of bathymetry due to sediment movement) often
requires high resolution so as to include banks, channels
and the effect of structures. Near beaches, longshore currents driven by waves are important. Bedload, which
may be due to ripple movement, needs to be taken into
account. Despite the complexity of the problem, model
packages are available for the prediction of changes in
coastal morphology (for example, DELFT 3D-MOR
from WL|Delft Hydraulics). These changes may need to
368
be taken into account if a water quality model is used

to predict the consequences of new structures or dredging and dumping. Areas of tidal flats such as Morecambe
Bay can have very variable bathymetry because of the
movement of channels, which is very difficult or impossible to predict. However, for many water quality applications, even involving sediment transport, changes in
bathymetry may be neglected.
2.3. Metals
As noted above, metals can exist in both dissolved
and particulate forms. The partition coefficient Kd (Balls,
1988) is defined as the ratio of metal concentration in
particulates (mg/kg) to the dissolved concentration
(mg/l). The concept of partition coefficient is heavily
used in modelling, but is essentially a simplification of
complex underlying processes. If Kd is known, assuming
equilibrium existing between the dissolved and particulate phases, a knowledge of the total metal concentration
and the SPM concentration in a model grid box determines the fraction in solution. The greater the concentration of SPM for a given Kd, the greater the percentage
of metal that is particle-bound. Burton et al. (1993) give
curves demonstrating this for four trace metals (Mn, Pb,
Cu and Cd) in the Thames estuary. These curves show
also that Kd is not a constant for a given metal and that
it varies between metals: it is much larger for lead than
for copper. For copper, the dissolved fraction dominates
for all but the highest concentrations of SPM. Lead is
much more readily adsorbed on to particles and so may
be quickly removed from the dissolved phase. This is an
example of particle scavenging. Part of the variation
in Kd can be attributed to particle type: biological particles such as plankton may have high values for some
metals (Huthnance et al., 1993).
The dissolved fraction of a metal may be modelled as
a tracer, while the particulate fraction may be modelled
in the same way as SPM. If Kd were known and a constant and if there were a state of equilibrium, it would
be simple to calculate an instantaneous transfer between
the phases as indicated above. However, this is complicated by variations in Kd and finite transfer times
between dissolved and particulate phases (Turner et al.,
1992). If significant, these transfer time scales must
appear in source and sink terms in the separate equations
for dissolved and particulate metal concentrations.
Because Kd is relatively small for Cd and Cu, Prandle
et al. (1993) had some success in modelling these as
tracers, given various coastal, boundary and atmospheric
sources. For metals with a greater particle affinity such
as lead, significant amounts may be stored in sea bed
sediments and benthic recycling, as these sediments are
resuspended in the water column, may be an important
source.
Tappin et al. (1997) have presented a transport model
(NOSTRADAMUS) for metals (Cd, Cu, Ni, Pb, Zn) in

the southern North Sea. The currents are based on a twodimensional 35 km hydrodynamic model (from the Proudman Oceanographic Laboratory). Exchange between
dissolved and particulate phases is driven by distribution
coefficients Kd taken from observations and changing
seasonally. Part of this change is due to changes in particle type. Sediment is divided between organic and inorganic, so a biological transport model is included. Estimated uncertainties in the inputs of metals are
highlighted, but these apparently make relatively little
difference to the results.
The modelling of metal concentration in coastal waters is therefore feasible now, the main uncertainties lying
in inputs and partition coefficients. However, fundamental progress beyond the use of Kd awaits improved understanding of the spatio-temporal variation of the rates at
which biogeochemical transfer processes take place. A
move to three-dimensional models of higher resolution
is likely to improve results, particularly in regions stratified by temperature or salinity, as in coastal plumes that
may be carrying metals from rivers.
2.4. Oil spills
Oil spills are an area of pollution modelling that has
attracted a great deal of attention because of the immediate and catastrophic results of major accidents. Because
of the emphasis on accidental spills, it is also an area
where operational modelling is needed to provide realtime predictions of the movement and fate of the oil. For
this to be effective, a high-resolution model of the area
at risk needs to be already set up, or needs to be easily
set up as part of a relocatable model system.
There have been several review papers summarising
the extensive literature on oil-spill modelling, including
Spaulding (1988), ASCE (1996) and Reed et al. (1999).
Here the main features will be outlined as far as they
affect algorithms for oil transport in the models.
Oil has a range of physical and chemical properties
that need to be considered when setting up a model.
These properties may vary considerably between different types of oil. For a particular spill, the oil type must
be specified. The values of viscosity, volatility and density, for example, affect the rate of spreading, evaporation and dispersion in the water column.
As for the other pollutants, oil is subject to advection
and diffusion. As it is less dense than water, much of
the oil travels in a surface slick, which is affected by
wind, waves and the surface current in the water. Many
spill models assume an empirically based wind- and
wave-induced (Stokes drift) component for the drift of
a slick, which may be added together and are typically
around 3.5% of the wind speed. Both Elliott (1986) and
Reed et al. (1994) suggest the angle between the wind
and this wind-driven component is small, effectively
zero. As the wind increases, oil droplets are dispersed

into the water column and the water current at depth
becomes a significant factor. Although Proctor et al.
(1994a,b) use a two-dimensional numerical model to
hindcast tide and surge currents for the Braer and Gulf
oil spills, the vertical variation in wind-driven currents in particular is important and a three-dimensional model of currents would have advantages, but it
needs to resolve strong current gradients near the sea
surface and preferably include wavecurrent interactions. The importance of the advection of oil dispersed
through the water column was shown in the Braer spill
off the Shetlands (Turrell, 1994): a southward transport
did not follow the wind direction.
Vertical diffusion of oil can be calculated by vertical
diffusivity in the water column, modified by the buoyancy of the oil droplets. Elliott (1986) uses a random
walk technique in the vertical as well as the horizontal
direction. Horizontal diffusion is often calculated by a
random walk, which is appropriate for particle tracking,
which is clearly preferable to concentration equations for
modelling oil spills. The properties of the particles may
change due to the effects of other processes acting on
the oil. The spill may be represented by a number of
parcels or droplets, which may have a size distribution
(Elliott, 1986), or individual spillets may represent a
spill that is released over a period of time or over a
wider area.
Some near-surface transport effects, such as those
induced by Langmuir circulation (Faller and Auer,
1988), are commonly neglected in models, but may have
important effects on dispersion of oil. Additional complexity is introduced if there is ice present (see, for
example, Yapa and Weerasuriya, 1997), and the
reliability of predictions is limited by the ability of seaice modelling at the appropriate scale (Reed et al., 1999).
Spreading is important in the early stages of an oil
spill. This describes the increase in area of the oil slick
under the forces of gravity, viscosity and surface tension,
and is distinct from any expansion of the slick due to
turbulent diffusion. The spreading formulae now
described as classical (Reed et al., 1999) are reviewed
by Hoult (1972). Eventually spreading will cease at
some terminal thickness, and the time taken to reach this
state depends on the properties of the oil. Most spreading
may be expected to take place in a matter of hours to
days after a spill. In practice, the slick may break up
into patches. Shear spreading, caused by the dispersion
into the water column and resurfacing of oil droplets
after being moved apart by vertical shear in the horizontal currents (Elliott et al., 1986), is likely to describe the
main physics of spreading once the initial gravitational
spreading has ceased.
Evaporation of oil is another important process that
needs to be included: in the first few days between 10%
and 75% of the mass may evaporate depending on
369
whether the oil is heavy or light. The most commonly

used equations describing evaporation are those of Stiver
and Mackay (1984). The oil may be considered as consisting of a number of different fractions, the evaporation
of each fraction being considered separately. An alternative approach (Proctor et al., 1994b), in a model based
on the tracking of droplets, is to introduce an evaporation
time scale l1, giving the probability p 1elt of a
droplet being removed within a time step t. A similar
use of a time scale can also describe other decay processes, such as biodegradation. Further weathering
effects, including photochemical oxidation, can change
the character of the oil and cause decay.
Dispersion of the oil into the water column follows
the breakup of the slick into small droplets and the
spread and diffusion of these droplets in the vertical.
Although the oil may be less dense than water, in certain
conditions turbulence and breaking waves may mix the
oil well below the surface. Oil dispersed below the surface is not subject to evaporation, but the processes of
biodegradation and dissolution (transfer to a dissolved
phase) are enhanced. Usually much less than 1% of the
oil spilled will dissolve, so this process is often neglected. Once oil droplets are dispersed below the surface
they are subject to advection and diffusion by the fluid
flow, plus buoyancy (or rise velocity) and the possibility of adsorption on to SPM or the sea bed. The
methods of Delvigne and Sweeney (1988) are often used
to estimate the oil mass entrained into the water column
per unit area and unit time. Vertical dispersion followed
by resurfacing, by the process of shear spreading noted
above, tends to result in the elongation of the slick in
the wind direction.
Water-in-oil emulsions or mousses sometimes form
when chemical conditions are right and there is enough
mixing energy. Algorithms for emulsification have been
formulated by Mackay et al. (1980a,b). Compared with
the original oil, the emulsion has a much greater volume,
is denser and more solid, and has a very much larger
viscosity. Evaporation and spreading are much reduced.
Of particular concern in relation to oil spills in the
coastal zone is the stranding of oil at the shoreline. Many
models can predict the motion of oil until it reaches the
shore but cannot include beach and surf-zone processes.
One exception is COZOIL (Reed et al., 1989), which
includes such processes as a wave-induced longshore
current. Some simplifying concepts that have been used
to describe shoreline deposition are the holding
capacity of the shoreline type, removal rates and
half-life values. On many coasts, tide levels and the
possibility of a tidal cycle of deposition on the shore
are important.
The number and complexity of processes involved in
the oil spill problem are clearly very great. This brief
review has already touched on advection, diffusion,
spreading, evaporation, biodegradation, dispersion,
370
weathering, photochemical oxidation, emulsification,

adsorption on to sediment, interactions with ice and
shoreline stranding. The prediction of the biological
impact is a further step beyond the types of model discussed here. Models must introduce major simplifications and may neglect some processes, but nevertheless they have become broadly successful in simulating
oil-spill trajectories. Among many applications that demonstrate this are hindcasts of the Braer spill off Shetland
(Proctor et al., 1994a; Spaulding et al., 1994) and the
Gulf War spill (Proctor et al., 1994b).
2.5. Chemicals and toxins
The previous section on oil spills shows that for an
individual pollutant several complex behaviours specific
to that substance may need to be included in a model.
The very many chemical contaminants released to the
coastal environment through river and outfall discharges
and via the atmosphere may therefore need to be considered individually. Some may be represented as passive tracers but many have complex and sometimes
poorly understood physico-chemical speciation, which
controls phase partitioning. Thermodynamic partition
coefficients used to model particulatewater exchange of
compounds can be inaccurate owing to the heterogeneity
of sorbants, which can alter the kinetics of partition to
such an extent that equilibrium is never attained. However, the partitioning between dissolved and particulate
phases and the possible scavenging of chemical pollutants by sediment and organic particles are of critical
importance. Some pollutants may become bound to sediments and are released from the sea bed to the water
column through bioturbation, resuspension in storms,
fishing and dredging. Several of these processes have
already been discussed in relation to metals: they can in
principle be modelled, but with large uncertainties over
partition coefficients and over the realism of the representation of sediment and SPM. For example, there
may in reality be efficient scavenging by organisms or
large flocculated organic material not included in the
model. As in the case of oil, chemical processes such
as oxidation and reduction, the effects of sunlight and
reactions with other substances present in the water may
need to be considered.
Estimates of the bioavailability and toxicity of chemical pollutants are needed to make predictions about their
ecological impact. To date this has not been included in
the complex predictive ecosystem models to be discussed in Section 3, and would be extremely ambitious.
To the uncertainties involved in the prediction of contaminant concentration must be added the poorly understood mechanisms of uptake of a complex cocktail of
chemicals by aquatic organisms, the resulting toxic
responses and the effect of bioaccumulation in the food
chain. Progress has been made on simulating responses
to contaminants at a cellular level (for example, Moore

and Willows, 1998), but the aim of scaling up such models to whole animals and embedding them in an ecosystem model is some way from realisation. Ecotoxicology
is a relatively new term for the study of the ecological
effects of toxins, integrating ecology and toxicology
(Chapman, 1995). This considers rather more complex,
subtle and long-term effects of the harm caused by pollution than the crude concepts of the lethal dose and the
LC50 test (the concentration required to kill 50% of a
test species within a set time). Environmental Quality
Standards, which are set by national governments and
the EU, give what are regarded as safe levels based on
a range of biological assay tests. The standard is sometimes expressed as a PNEC (predicted no effect
concentration) level. There are uncertainties related to
the interpretation of the biological tests, to the effects of
a mixture of contaminants and to long-term ecological
consequences, but it remains the first-order aim of water
quality models to predict concentrations and make conclusions about safety based on these available quality
standards.
The ability of coastal models to predict these concentrations is still limited. For example, Stolwijk et al.
(1998) compared five water quality models of the North
Sea, one of the most heavily modelled shelf-sea areas in
the world. It was claimed in this paper that it was the
first time that water quality models of the North Sea had
been reviewed and compared with field data. Five substances were selected for comparison: cadmium, PCB153, two PAHs (polycyclic aromatic hydrocarbons),
namely fluoranthene and benzo[a]pyrene, and atrazine (a
pesticide), but only cadmium was common to all five
models. These were from BSH (Hamburg),
NORWECOM from IMR (Bergen) (Skogen et al., 1995),
NOSTRADAMUS (Tappin et al., 1997) and SCREMOTOX and ZeeBOS-TOX from WL|Delft Hydraulics.
They vary in the processes represented in the pollutant
transport simulations. The BSH model could only represent
passive
conservative
substances.
In
NORWECOM, Cd and atrazine were modelled as dissolved passive tracers (neglecting adsorption to particulate matter). An equilibrium model based on the octanol
water partition coefficient was used to calculate the distribution of PCB-153 and PAH between the dissolved
and particulate phase. NOSTRADAMUS was run for
metals only (as described in Section 2.3), so results for
Cd only were considered in this comparison. SCREMOTOX is a model with limited physics, a steady-state
residual flow only, but includes among the chemical processes adsorption/desorption to inorganic silt and POC
(particulate organic carbon), volatilisation, degradation
and sedimentation/resuspension. ZeeBOS-TOX has
more physics, from a two-dimensional hydrodynamic
model, while there can be adsorption to POC, DOC
(dissolved organic carbon) and inorganic matter, sedi-
mentation and resuspension, volatilisation and degradation. Pollutants such as heavy metals can adsorb to
inorganic suspended matter, while others such as organic
micropollutants can adsorb to POC or DOC, calculated
using equilibrium sorption equations involving Kd and
Kpoc. The intercomparison, which showed a considerable
deviation of the modelled from the measured values for
Cd (usually model values were lower), led to the conclusion that there was a lack of quality-controlled field
data to calibrate and validate the models.
This lack of data is likely to limit the testability of
the most sophisticated models, and not only are monitoring data needed for the interior of the model for testing
purposes, but input data are also required to give boundary conditions. In the intercomparison above (Stolwijk
et al., 1998) the substances chosen were some for which
adequate boundary data and field data as well as process
knowledge were thought to be available. For other substances there are even fewer data, and therefore there
is even less chance of accurate predictions, even if the
understanding of their behaviour is good and simulated
well by the models.
3. Ecosystem modelling
An ecosystem may be defined as a connected group
of organisms together with their environment. More
particularly, it involves a natural unit of living and nonliving components that interact to form a system in
which an interchange of materials and energy takes
place. Ecosystem or ecological modelling must describe
the interactions between all elements of the ecosystem
in either a deterministic or an empirical manner. Despite
some remaining controversy over the effectiveness and
usefulness of the deterministic numerical models (Nuttle,
2000), which follow the time-stepping approach of the
hydrodynamic models but may be much more complex
as shown below, these are the types of model that will
be discussed here.
All ecological models involve some form of simplification since it is not feasible to include every organism
individually or indeed every species. Many models
aggregate these biological components and abstract them
into functional groups or compartments. For example,
all phytoplankton may be considered together and within
this group associated state variables such as carbon and
nitrogen may be defined. These functional groups represent the main functional roles of production (e.g.
phytoplankton), consumption (e.g. zooplankton, fish)
and decomposition (bacteria). Individual organisms
within a functional group are assumed to be identical
and physiological processes and population dynamics
are described in terms of fluxes of carbon and nutrients
between functional groups and between organic and
inorganic material. Functional groups may be subdivided
371
into size classes to create a food web. A review of functional group models may be found in Totterdell (1993).
However, the functional group models have limitations
when it comes to representing the larger, long-lived
organisms in the higher trophic levels. For example,
biomass increase here may be by growth of individuals
rather than by increased numbers of identically sized
organisms. Other approaches such as structured population models and individual-based models can then be
used. Structured population models are appropriate for
considering cohorts of particular species with multi-stage
development, and can be coupled with spatially resolved
models (e.g. Bryant et al., 1997). Individual-based models track individuals through time and consider their
interaction with the environment. Although this technique has been used with the larger animals such as wading birds (Wolff, 1994), a similarly Lagrangian approach
has been applied to plankton (Woods and Barkmann,
1994). Multi-species models may be constructed from a
combination of hydrodynamic, functional group, structured population and individual-based models.
Functional group models are commonly used to simulate phytoplankton and nutrient cycling. Phytoplankton,
which is responsible for most marine primary productivity, consists of microscopic floating plants (algae)
and bacteria (cyanobacteria, or blue-green algae) which
by photosynthesis use sunlight to convert dissolved inorganic substances to organic material: in a simplified form
this is represented by
6CO2 6H2OC6H12O6 6O2
(2)
This process also requires nutrients: these are mainly
nitrogen, as the ions nitrate (NO

3 ), nitrite (NO2 ) or
ammonium (NH4 ), phosphorus, as phosphate (PO

4 ),
and silicate (SiO2). If any of these nutrients is not available, growth of phytoplankton may be limited. The
larger phytoplankton, which may be captured in nets,
occur mainly in two groups: diatoms, which are silicatedependent and are often the dominant type in temperate
and high latitudes, and dinoflagellates. However, the
smaller phytoplankton below 20 m in size, namely nanoplankton (2 to 20 m) and picoplankton (0.2 to 2 m),
make a considerable contribution to total photosynthesis.
Zooplankton are the small drifting animals which feed
on phytoplankton and other animals. Copepods are often
the dominant larger zooplankton. The zooplankton in
turn provide food for larger animals such as fish, and
also break down some of the organic material into its
inorganic components: this process is known as remineralisation. Detritus consists of both inorganic and nonliving organic particles resulting from excretion and
death of plankton, and tends to sink to the sea bed. The
microbial loop describes the process by which dissolved organic matter is scavenged by bacteria, which
are then grazed by single-celled animals, which provide
food for larger zooplankton. This can be an important
372
part of the food chain in terms of energy transfer in certain circumstances. The small zooplankton also consume
the small phytoplankton, extending the microbial loop
to the microbial food web.
The complexity of the biological system means that
there is less consensus on the basic equations describing
it than for the physical system. Models have been constructed with varying levels of detail. One of the simplest
is the early model of Riley (1946), in which phytoplankton biomass is represented by a single variable P, and
its rate of change is given by
dP / dt P(PhRG),
(3)
where Ph is photosynthetic rate, R is respiration and G

is grazing by zooplankton. Quantities determining the
value of terms on the right-hand side, such as nutrient
(phosphate), temperature, depth of mixed layer, transparency and quantity of zooplankton, were given (as
monthly means). P, as given by the above equation, was
then found to agree well with the observed population.
Fasham et al. (1990), in a model of the oceanic mixed
layer, extended this concept from the one variable P to
seven compartments (phytoplankton, zooplankton, bacteria, nitrate, ammonium, dissolved organic nitrogen and
detritus), each of which has an ordinary differential equation giving its rate of change. The right-hand sides of
the equations include intercompartmental exchanges.
In the shelf seas, a key component of ecological modelling has been the linking with physical models. As discussed above in connection with tracers, the relative
importance of diffusion, horizontal advection and local
forcing can vary with the location and scales of the processes concerned. In areas where advection is relatively
unimportant but local sources for example, resuspension of material that may contain nutrients from the sea
bed have a major influence, a one-dimensional model
such as SEDBIOL (Smith and Tett, 2000) can reproduce
seasonal cycles and give estimates of annual production.
This model includes a Mellor and Yamada level 2 turbulence closure scheme to determine values of vertical
eddy diffusivity and it also includes a sediment resuspension model that takes particles from a finite fluff
layer on top of the sea bed. It has eight state variables
in the biological sub-model; microplankton carbon and
nitrogen, detrital carbon and nitrogen, concentrations of
dissolved nitrate, ammonium and oxygen, and zooplankton nitrogen. Each of these has source and sink terms
that are added to the advectiondiffusion equation for
each variable (the advection in the one-dimensional
model being entirely due to fall velocity). Chlorophyll
is derived from microplankton carbon and nitrogen so is
not a state variable. Physical driving terms include solar
radiation, tidal pressure gradients and wind stress.
Other one-dimensional models have had some success
in reproducing primary production in areas such as the
central North Sea (Radach and Moll, 1993; but this is
based on an upper-layer model that does not include tidal

stirring, and also has a single nutrient, phosphate). However, a three-dimensional model is necessary where horizontal advection is significant and inputs are non-local,
for example where nutrients are introduced by river runoff. Several of the biological models have now been
linked to three-dimensional hydrodynamic models, or at
least have included estimates of horizontal transports,
with horizontal resolution of varying scales. The SEDBIOL model has been linked with the Belgian MUROFI
shelf-sea model (described in Ruddick et al., 1995) to
form COHERENS (Luyten et al., 2000). A development
of the Radach and Moll (1993) model has been combined with the Hamburg three-dimensional model
(Pohlmann, 1996; Moll 1997, 1998; Skogen and Moll,
2000) to form ECOHAM1. The Princeton Ocean Model
(POM; Blumberg and Mellor, 1987) provides the physical module for NORWECOM (the Norwegian Ecological Model System), described by Skogen et al. (1995).
The biological module in NORWECOM contains as
prognostic variables inorganic nitrogen, phosphorus and
silicate, two types of phytoplankton (diatoms and
flagellates) and detritus, as well as light and turbidity.
These biological modules all contain considerable
simplifications, and the choices clearly differ; several
have just one type of phytoplankton and some have just
one nutrient. A deliberately more complex ecosystem
model in terms of numbers of variables is ERSEM (the
European Regional Seas Ecosystem Model), which
attempts to include all significant processes necessary to
produce a realistic representation of the cycling of carbon and nutrients in the European shelf seas (Baretta et
al., 1995). ERSEM includes several kinds of phytoplankton, a microbial loop and explicit mesozooplankton. It
incorporates a benthic submodel, which describes the
complex processes within the seabed including bioturbation: these have an important effect on the exchange
of nutrients between the sea bed and the water column.
Benthic processes are of course also important for contaminants, but this was not the focus for ERSEM. The
EU-funded ERSEM programme ran in two parts:
ERSEM-I from 1990 to 1993 (Baretta-Bekker, 1995) and
ERSEM-II, which included many detail developments,
from 1993 to 1996 (Baretta-Bekker and Baretta, 1997).
In ERSEM-I the model had been applied to a very
coarse box model of the North Sea. In the horizontal,
these were the ICES boxes (10 covered the whole North
Sea) and in the vertical there was either one box or two,
where thermal stratification occurs, making 15 boxes in
all. Transport between boxes was estimated from the
Hamburg three-dimensional circulation model (Lenhart
et al., 1995). The reason for such a coarse box approach
was the complexity of the biological model combined
with the limitations of computer power at the time. A
few years later, in ERSEM-II, the North Sea model had
been refined to 130 boxes, the horizontal resolution
being 1 1. It had also been applied to a 4.5 km resolution grid, with hydrodynamics from a two-dimensional
model, around the Humber estuary, with 359 biologically active cells (Allen, 1997).
The enormous computational demand of a biological
model such as ERSEM, in comparison with the hydrodynamic model alone (there are some 100 extra variables,
around 30 to 40 of which need to be advected and
diffused), requires the power of a massively parallel
computing system if it is to be run with the resolution
in both space and time of a typical three-dimensional
shelf-sea physical model. This has now been achieved
in the coupling of ERSEM with the POL3DB model
(Allen et al., 2002). This hydrodynamic model is
described by Holt and James (2001), and includes scoordinates in the vertical, to maintain a resolved upper
mixed layer across the shelf edge in a terrain-following
coordinate system, and an advanced piecewise parabolic
advection scheme (see Section 4). Despite the computational demands of using this scheme with many variables, the performance of parallel systems means that
the calculation of annual cycles in three dimensions with
ERSEM on a shelf-wide grid with 12 km horizontal resolution and 20 levels in the vertical is readily achieved,
and higher resolutions are feasible. The parallel scheme
is based on domain decomposition in the horizontal, with
the use of the MPI (Message Passing Interface) standard
for communication between processors (Proctor et al.,
1999). The POL3DB model has been developed with the
assistance of funding from the UK Met. Office, and an
earlier version is running operationally there (from June
2000), so in principle the physical variables for the
coupled model are available operationally. All of the
elements for an operational shelf-wide ecosystem model
would be present if the necessary inputs and boundary
conditions for the ecological variables were also available in real time.
As the resolution of models increases and they
become eddy-resolving, they will be able to address
problems such as the observed patchiness of phytoplankton (Powell and Okubo, 1994; Abraham, 1998). The resolution required for an eddy-resolving model in shelf
seas is the order of 1 km or better (see Section 4).
As was remarked in the previous section, the ecological models have not generally included any direct effect
of contaminants such as oil or toxic chemicals. However,
an important aspect of water quality they have been used
to study is that of eutrophication, the effect of excess
nutrient supply, which may come from sewage outflow
or agricultural fertilisers in river run-off. The resulting
excess plant and phytoplankton growth is followed by
decay, in which bacteria use dissolved oxygen in the
water. These bacteria also decompose organic matter that
may be in the original outflow; sewage is a particularly
large source of this in coastal and estuarine waters. The
capacity of a volume of water to consume oxygen is
373
known as its biological oxygen demand (BOD). If this

is too high, oxygen will be depleted and animals including fish will die. The concentration of dissolved oxygen
(DO) is often taken as a key measure of the health of
the aquatic ecosystem. For example, measurements of
DO show the considerable recent improvements in the
water quality of the Mersey estuary, a large part of this
being a result of the ending of untreated sewage outflows: the BOD load has been reduced from over 300
t/day in 1972 to around 50 t/day in 2000 (Jones, 2000).
One of the main challenges for an operational ecosystem model would be to predict the timing and extent of
blooms of plankton, not only the normal spring and autumn blooms but also those due to an excess of nutrients,
which may result in rapidly growing toxic algal blooms
and red tides. Hindcasts of the spring bloom have been
successfully demonstrated in models (Ruardij et al.,
1997; Allen et al., 1998). At a longer time scale, one of
the uses of the model would be to predict the improvement in water quality to be expected by a reduction in
discharges. This would involve running the model to
give an environmental assessment, in which the
detailed meteorological input is unimportant, rather than
to give a prediction of conditions over the next few days.
This type of assessment has been made with several ecological models, for example scenarios of the effect on
the North Sea of reductions in the nutrient transport in
rivers, using ERSEM (Lenhart et al., 1997).
ERSEM has also been used in models of fish populations in combination with structured population models, including a larval stage. Fish are predators for zooplankton and zoobenthos, while fish excretion and
mortality can be returned to ERSEM from the fish model
as dissolved and particulate organic matter (Bryant et al.,
1995; Heath et al., 1997). Humans of course enter the
picture here as predators for fish as well as producers of
sewage and contaminants. Such models can be a step
towards an ecological modelling approach to fisheries
management which includes the potential impact of the
physical environment on fish populations. This complexity goes well beyond that of traditional fishery models (for example, Beverton and Holt, 1957) and could
form the basis of more accurate predictions to guide
fisheries policy in the future.
The complexity of biological models with their many
variables and parameters raises the question of how they
may be compared with measurements and hence validated and improved. Some data sets for a selection of
variables are obtainable from individual experiments and
more extensively for relatively well-monitored seas; for
example, climatological cycles of nutrients and chlorophyll in the North Sea (Radach and Pa tsch, 1997). These
data sets can be used for a straightforward comparison
with model data (for example, Moll, 1998). But it is not
always clear whether a poor fit with data is due to the
model structure or to the selection of model parameters,
374
as pointed out by Vallino (2000), and as we have noted

above there are many models with somewhat different
structures aimed at describing the same phenomenon,
such as phytoplankton growth, and it would be useful to
have some way of deciding which is superior. Vallino
(2000) describes the use of mesocosm experiments and
data assimilation for parameter estimation. A mesocosm
is an enclosed experimental ecosystem which, being
generally well-mixed, can reduce the number of
dimensions to that of time only, allows controlled
experiments to explore several regions of state space,
and allows intensive sampling. If parameter uncertainty
can be reduced, then model comparisons can concentrate
on differences in structure. However, model results may
still lack robustness through sensitivity to parameter
values, which may not in reality be constant. Mesocosms
cannot include all of the processes found in the open
sea, where there is a need for comprehensive data sets
including estimates of fluxes across the open system
boundaries. If such a data set were available, data assimilation may be able to determine whether the model is
able to fit it well by adjustment of parameters, and if not
it may be concluded that there is some structural
deficiency in the model. Spitz et al. (1998) applied data
assimilation to the Fasham et al. (1990) mixed layer
model and concluded in this way that some of the
assumptions needed to be carefully reconsidered. In most
circumstances, though, the use of data assimilation will
be limited by the availability of data.
4. Physical modelling
As stated in the Introduction, a good representation of
the physics is the necessary basis for a water quality
model. Physical modelling will not be reviewed comprehensively here; an overview of coastal models may be
found in Greatbatch and Mellor (1999). We concentrate
first on the modelling of diffusion and dispersion and
then outline some further topics that are important for a
physical model underpinning a water quality model.
4.1. Diffusion and dispersion
While present physical models may be expected to
give reasonable results for sea level, currents, temperature and salinity at medium (10 km) resolution, given
good boundary forcing information, it is not completely
clear that they are able to predict accurately the dispersion of pollutants. One of the main reasons for this is the
central importance of the advectiondiffusion equation,
which involves turbulence, which is generally unresolved in these models and remains a challenging problem in itself. So we review here the physical processes
of dispersion of material in the sea and the ability of
present models to reproduce them. It was noted in Sec-
tion 2 that diffusivity on a molecular scale, which will

always be unresolved by the models, is very much less
than the effective diffusivity in a turbulent flow on the
model grid scale but that the use of an effective eddy
diffusivity implies neglect of the details of the stirring
due to turbulence, which is ultimately followed by molecular diffusion.
4.1.1. Vertical diffusivity
In the coastal ocean, the disparity between horizontal
and vertical scales means that horizontal and vertical diffusion are usually considered separately and have very
different values. There is an extensive literature on the
parameterisation of vertical eddy viscosity and diffusivity, reviewed by Davies et al. (1995), and this will not
be covered again in detail here. Most shelf-sea models
use some form of turbulence closure scheme, whether
based on equations for turbulence energy and dissipation
(k, ) or for turbulence energy q2 2k and q2l, where l
is a length scale known as the mixing length, to determine vertical eddy viscosity and diffusivity. Many models use a turbulence energy equation but have an
algebraic form for mixing length. Some ocean models,
however, involve large eddy simulation (LES), in
which there is sufficient resolution to include explicitly
the most energetic turbulent eddies: this implies a vertical and horizontal resolution of the order of metres in
the upper ocean (Large and Gent, 1999; Wang, 2001)
but still requires parameterisation of the effect of smaller
eddies, and the resolution needed is prohibitive for widearea models. This approach has been very useful for the
study of Langmuir circulation and convection cells, both
of which are neglected in the usual turbulence energy
approach and which may be strong generators of mixing
in the surface layers (Skyllingstad and Denbo, 1995;
Wang et al., 1998).
The LES models do not indicate a simple parameterisation of Langmuir circulation or convection, which,
together with the effects of internal waves, can explain
some of the shortcomings of the turbulence energy closure schemes particularly in stratified flow. In the most
commonly used schemes, vertical diffusivity often
defaults to an arbitrary minimum value in a strongly
stratified region such as the thermocline, which then
determines cross-thermocline exchange. Convection
caused by surface cooling, when handled by instantaneous stabilisation of unstable density profiles or by
large values of mixing given directly by the turbulence
energy schemes, is still not always enough to explain
observed deepening of the surface mixed layer. Wind
waves also introduce effects that are not explicitly
included in the turbulence energy equations, whether
through wave breaking and wave-induced shear in the
upper layers (Craig and Banner, 1994) or additional
wave-induced bed stress in shallow water (Grant and
Madsen, 1979). Internal waves induce additional mixing
both by increasing shear across the thermocline (as do

inertial currents, but they may be resolved by the model)
and by breaking (Woods, 1968; Thorpe, 1994).
Models have problems in satisfactorily reproducing
mixing due to these processes, which are unresolved on
the model grid and are difficult to parameterise. Mellor
(1989) suggested an extra term in the turbulent energy
equation to account for the extra shear due to long
internal waves, but this does not account for the breaking
of short internal waves. Burchard et al. (1998) show that
both the k and the q2q2l models require modification
through the inclusion of an internal wave parameterisation to predict correctly the observed levels of turbulent
dissipation: this was done through setting a minimum
value of k and also applying a limiting condition to
(or l). Kantha and Clayson (1994) use results from LES
simulations to try to improve terms in the MellorYamada closure scheme, applied to the surface mixed layer,
while Large and Gent (1999) use LES and observations
to validate vertical mixing in an equatorial ocean model.
4.1.2. Lateral dispersion
Mixing in the vertical is not entirely detached from
mixing in the horizontal; in fact there are at least two
ways in which lateral dispersion is determined by vertical mixing. One is boundary mixing in the deep ocean,
the other is shear dispersion, which is particularly effective in shelf seas with strong currents, including tidal
currents. Boundary mixing in the ocean, reviewed by
Garrett et al. (1993), refers to mixing near the sloping
sea bed, at continental slopes or on shelves, which produces water that can spread preferentially along isopycnals into deeper water. This has been suggested
(Munk, 1966) as a source of the mixing required to
explain the overall heat balance in ocean basins. This
paper has been updated by Munk and Wunsch (1998),
who propose that the mixing required to maintain the
abyssal stratification against global upwelling associated
with deep water formation is concentrated in only a
small portion of the oceans, and is driven mainly by
wind and tides.
Dispersion from the shelf or slope into the deep ocean
may take place along isopycnal surfaces once mixing on
the shelf or in the boundary layer on the slope has
occurred, so it is determined by this mixing. It may
firstly include cascading down the slope for shelf water
that is denser than oceanic water at the same depth. Gent
and McWilliams (1990) introduced a parameterisation of
eddy-induced isopycnal mixing that can be used in noneddy-resolving ocean models. Diapycnal (crossisopycnal) mixing in the deep ocean is relatively
inhibited by buoyancy forces and low levels of turbulence away from the surface and sea bed. This behaviour
is a challenge to ocean models in which the vertical
coordinate is not based on isopycnals (as it is in the
MICOM model: Paiva et al., 1999 describe a recent
375
eddy-resolving application of this isopycnal coordinate

model to the North Atlantic) but on horizontal surfaces
(z-levels) or terrain-following systems (s- or scoordinates). Then the numerical scheme may introduce
false diapycnal mixing because of its tendency to mix
in the horizontal or along coordinate surfaces rather than
along isopycnals. In s-coordinates, where the coordinate
surfaces are not horizontal, an imposed horizontal diffusivity may induce spurious vertical diffusivity (Mellor
and Blumberg, 1985; Stelling and van Kester, 1994), but
even if the numerical formulation is suitable for bottom
boundary layers and minimises artificial vertical diffusion, a truly horizontal diffusivity in the ocean interior
will still give incorrect diapycnal mixing. However, on
the shelf the advantages of isopycnal coordinates are no
longer evident because of the prevalence of tide- and
wind-mixed layers and the large areas of vertically wellmixed water.
Shear dispersion, which we have met before in Section 2.4, occurs when vertical diffusion and a vertical
shear in the horizontal current occur together: it is therefore significant in the shelf seas, where there may be
strong, vertically sheared, wind-driven and tidal currents.
An initially vertical column of any substance is stretched
horizontally by the shear in the currents; vertical mixing
will then have the net effect of distributing this substance
over a wider region horizontally, which is a similar
effect to horizontal diffusion, except that it occurs in the
current direction (Bowden 1965, 1983). This occurs in
an oscillatory tidal flow as well as in a steady current.
Shear dispersion would occur in a three-dimensional
model even with no imposed horizontal diffusivity, but
would not be reproduced in a two-dimensional model,
which of course includes no effects of vertical shear. A
two-dimensional model would need an imposed diffusion coefficient to achieve the same result. The effect
can be increased by horizontal shear in the currents,
which strains the initial distribution further.
In this view of shear dispersion, horizontal currents
stretch or distort an initial patch of material by advection, while mixing is taken to occur by vertical diffusion.
This is an example of stirring increasing the rate of mixing, just as turbulent eddies themselves stir a substance
into thin sheets and filaments with a large surface area
over which molecular diffusivity can act effectively.
Classical results on dispersion were obtained by Richardson (1926), who proposed that the coefficient of eddy
diffusion should increase with length scale l as l4/3, from
observations in the atmosphere. This was deduced from
the rate of increase of distance between balloons. It
agrees with Kolmogorovs (1941) theory for the inertial
range of three-dimensional turbulence, in which kinetic
energy is transferred in a cascade from larger to smaller
scales, eventually to be dissipated at the smallest scales,
in the viscous range. If the rate of dissipation is and
wavenumber is k, this leads to a power spectrum
376
E(k) 2 / 3k5 / 3, and if a pair of particles is released a

distance l apart, the rate of increase of the square of their
distance apart varies as 1 / 3l4 / 3. Richardson and Stommel
(1948), in a paper beginning We have observed the
relative motion of two floating pieces of parsnip, suggested the 4/3 law of diffusivity applies also to horizontal diffusion in the sea. Applied to a patch of material
released at r 0 at time t 0 and spreading in the horizontal plane, an eddy diffusivity proportional to r4/3 leads
to a variance of the distribution varying as t3 and a central concentration at r 0 varying as t3: a constant
diffusivity would lead to a variance t and a central concentration t1, while a diffusivity r would lead to
variance t2 and central concentration t2 (Bowden,
1983). Some support for diffusivity obeying a power law
of 4/3, or near this value, is given by results from the
spreading of dye patches (Okubo 1971, 1974). However,
the apparent power law is affected by energy being put
in at intermediate scales, equivalent to a variation of .
Also, Zimmerman (1986) rejects the possibility of a
5/3 power law for the energy density in a shallow tidal
sea in the interval between 10 m (a scale set by the water
depth) and 10 km (a scale set by tidal excursion), in
which any real turbulence should be quasi-two-dimensional (see Section 4.1.3). In this range and in these conditions, vertical and then horizontal shear dispersion
should take over to spread a dye patch.
Both advection and diffusion can cause particles that
were initially close together to separate; however, advection is in principle reversible by reversing the velocity
field, but diffusion is not. Advection by eddies would
cause a patch of red dye to be sheared into thin red
streaks, while diffusion would result in a pink patch of
dyed water. The streakiness of a dispersing tracer in both
two- and three-dimensional turbulence is discussed by
Garrett (1983). In comparison with the deep ocean,
streakiness may be reduced in many areas of tidally
mixed shelf seas because of the magnitude of shear dispersion.
The difference between advective stirring by eddies
and diffusion may be significant for some polluting substances that do not mix well with water. In Section 2.4
on oil spills, it was noted that horizontal diffusion was
generally modelled by a random walk procedure applied
to particle tracking, which simulates the spreading of
particles while mixing with the water is not necessarily
implied. For a pollutant, the maximum concentration
may be important, and this is much higher within a
streak than in a diffused patch. If a model is based on
the concentration equations and so is unable to cover
scales smaller than the grid scale, the model concentration is the mean over a grid box, even if in reality
complete mixing over that volume has not occurred, and
the maximum concentration in streaks will not be reproduced. This is an example of artificial diffusion intro-
duced by the numerical method; more on this topic is

discussed below in Section 4.1.5.
4.1.3. Quasi-two-dimensional turbulence
As eddy scales become larger, in comparison with the
water depth or a stratification scale, the turbulence
becomes more two-dimensional. Because of the addition
of another constraint, the conservation of enstrophy (half
squared vorticity), two-dimensional turbulence behaves
in a quite different way from three-dimensional turbulence. As shown by Kraichnan (1967), if turbulence is
forced at a certain wavenumber, there will be an inverse
energy cascade to larger scales, or smaller wavenumber
k, in which E k5 / 3 as for the three-dimensional spectrum, and an enstrophy cascade to larger k, in which
E k3. In the case of freely decaying two-dimensional
turbulence the inverse cascade means that an initially
disordered flow becomes more ordered, into larger-scale
coherent vortex structures, that can be very stable. These
were modelled by McWilliams (1984). Similar results to
those for strictly two-dimensional turbulence are
obtained for geophysical flows: both rotation and stratification can make the flow more two-dimensional in
character. A consequence of the behaviour of geostrophic turbulence, i.e. turbulence in fluids that are near
to geostrophic and hydrostatic balance (Rhines, 1979),
and therefore typical of geophysical fluids, is the prevalence of long-lived mesoscale eddy motion in the deep
ocean and the smaller-scale eddies in the stratified
shelf seas.
Laboratory experiments by Linden et al. (1995) demonstrate the inverse energy cascade in a rotating stratified
fluid forced by an array of sources and sinks. The Rossby
deformation radius, which for the lowest baroclinic
mode is RD NH / f, where N is the buoyancy frequency, H the depth and f the Coriolis parameter, is a
key length scale: when this scale exceeds the size of the
tank the inverse cascade is seen to occur, but for smaller
values of RD baroclinic instability acts to reduce the size
of any flow structures that form on a scale larger than
RD. The inverse energy cascade is therefore modified by
a cascade to smaller scale due to baroclinic instability.
This result was also found by Griffiths and Hopfinger
(1984) in a laboratory experiment on turbulence generated by the instability of a front in a two-layer rotating
fluid. Narimousa et al. (1991) also show baroclinic instability at a front in a laboratory experiment and conclude
from the energy spectra that the dynamics is that of
quasi-two-dimensional turbulence, forced at the scale of
the most unstable frontal eddies. Numerical experiments
by Cushman-Roisin and Tang (1990) and Tang and
Cushman-Roisin (1992) were conducted in a reducedgravity model, for which RD (gh)1 / 2 / f, where g is
the reduced gravity and h the layer depth, and in a twolayer model, for which RD (gh)1 / 2 / f, where g
g(r2r1) / r2 and h h1h2 / (h1 h2), where upper-
and lower-layer depth and density are h1, r1 and h2, r2

respectively. They show in the reduced-gravity model,
for flow evolving from scales smaller than RD, that the
inverse energy cascade towards larger scales can halt at a
statistical equilibrium beyond RD, while energy at scales
larger than RD cascades to smaller scales and halts at a
scale just greater than RD. In the two-layer model, similar
results are obtained for flow evolving from scales
smaller than RD, but from larger scales baroclinic instability leads to quasi-geostrophic dynamics and, as
described by Rhines (1979), there can be eventual barotropisation of the flow, with a consequent resumption
of a cascade to larger scales as in two-dimensional turbulence.
These physical and numerical experiments suggest
that there should be significant energy in stratified waters
at around the Rossby radius scale. This is of the order
of a few kilometres in the stratified shelf seas, and that
is the scale of the most prominent eddies seen on satellite
AVHRR images, which have 1 km resolution. Among
processes generating eddies at or near this scale is baroclinic instability of frontal flow, and this is often clearly
shown on infrared images because of the temperature
contrasts at fronts.
Quasi-two-dimensional turbulence is likely to be suppressed by friction in the tidally well-mixed areas of the
shelf seas, where shear dispersion is important. However, these eddies could be a significant means of dispersion in the deeper stratified areas and near fronts. Not
only does the presence of eddies lead to strong shears,
adding to the effectiveness of shear dispersion, but
coherent eddy structures can trap material within them
and transport it with the eddy. Vortex pairs, consisting
of eddies of opposite sense of rotation, are commonly
found in developed two-dimensional turbulence, and are
particularly efficient at transporting material: their
motion is clearly visualised by dye in laboratory experiments because the dye is carried with them. Material
may also be transported effectively in filamentary structures between eddies.
Baroclinic instability can be an important mechanism
for transporting material from coastal currents, which
may be fed by rivers, into the open sea. The Norwegian
Coastal Current, which occurs in the relatively deep
water of the Norwegian Trench, and in an area of weak
tidal currents, develops prominent eddy structures
including vortex pairs (Johannessen et al., 1989). These
can be of the order of 50 km in diameter because of the
large value of RD there. Baroclinic instability can also
occur in a shallow tidal region such as the Rhine plume
(de Kok, 1997).
Horizontal dispersion by quasi-two-dimensional
eddies has not generally been included explicitly in shelf
models because of the need to resolve small scales at
least down to the Rossby radius scale. However, as parallel systems become more available and so computer
377
power increases, finer resolution of the full baroclinic

models is becoming feasible and coverage of the whole
northwest European continental shelf on a 1 km grid is
now possible, with higher resolution in some nested
areas. Reduced-gravity or two-layer models can also
provide insight into the processes and can be run at
extremely high horizontal resolution, but are less
realistic. Most numerical turbulence models (for
example, McWilliams, 1984) have used spectral
methods based on the vorticity equation, but these are
not necessarily readily applicable to shelf-sea problems.
From this discussion it is clear that eddy-resolving shelfsea models would include many processes leading to dispersion of material that are not well represented by a
horizontal eddy diffusivity.
4.1.4. Lagrangian chaos

It can be shown (Zimmerman, 1986; Pasmenter, 1988)
that turbulence is not necessary for dispersion: a deterministic Eulerian velocity field may result in Lagrangian chaos, in which particles initially close together may
move far apart. This is not necessarily surprising as the
equations for the advection of a particle can be considered as representing a non-linear dynamical system.
One example of such a deterministic velocity field is an
oscillating tide with superimposed eddies resembling
residual flow attached to bathymetric features. Lagrangian chaos may occur if the ratios of tidal excursion to
bathymetric scale and of residual current to tidal current
amplitude are large enough. For large tidal currents in
coastal areas with complex fine-scale bathymetry, this
suggests the interesting possibility that the path of an
individual particle is in principle unpredictable, even if
the Eulerian current field is known accurately.
This process is essentially different from stirring by
turbulent eddies. Ridderinkhof and Zimmerman (1992)
show chaotic stirring in a two-dimensional model of the
Wadden Sea. Some trajectories in Lagrangian chaos can
show coherent areas (islands) from which particles do
not escape: this can explain patchiness in the distributions, although patchiness can also arise from eddies
as noted in Section 3. Chaotic stirring does not result in
a Gaussian distribution and cannot be represented by a
diffusion coefficient. As pointed out by Zimmerman
(1986), each of the processes may dominate in different
regions. For example, tidal shear dispersion may be the
prevailing process in the open sea, while chaotic stirring
is important in a coastal bay with a complicated shoreline and bathymetry. A model with fine enough resolution should capture both processes: both resolution and
the treatment of advection will determine how well the
straining of any patch of material by either the tidal and
residual Eulerian currents or an explicitly resolved eddy
field is reproduced.
378
4.1.5. Numerical diffusion

Any numerical scheme applied to the advection equation for concentration of a substance may include nonphysical diffusion because of the finite size of the grid
boxes, but near sharp changes in value, or fronts, it may
also produce non-physical oscillations that can induce
negative values of concentration. James (1996) has considered several advection schemes applied to a threedimensional shelf-sea model. First-order upwind differencing is highly diffusive, with a diffusion coefficient
equal to (uxtu2) / 2, where u is the advection velocity and x and t the space and time steps. Centred
differencing (forward time, centred space) is unstable,
while the LaxWendroff scheme produces ripples near
a front. A TVD (total variation diminishing) scheme,
which is a combination of LaxWendroff and upwind
schemes that applies more of the upwind scheme near
sharp gradients, and a PPM (piecewise parabolic
method) scheme (Colella and Woodward, 1984), which
fits a parabola to the variable within a grid box and then
calculates fluxes using an upwind method, both have
positivity (ripple-free behaviour) and low numerical diffusion. The PPM scheme has less diffusion, but involves
more calculation. These schemes were demonstrated by
James (1996) in an eddy instability problem. The TVD
scheme has been used by Xing and Davies (1996) and
Davies and Xing (1999) in internal tide and plume models and the PPM scheme is used in the POL3DB model
(mentioned above in Section 3). Other TVD schemes
have been applied in ocean models by Pietrzak (1998).
Other advection schemes used in ocean models include
the QUICK and SHARP schemes of Leonard (1979,
1988) and the antidiffusive velocity scheme of Smolarkiewicz (1983, 1984).
Advection schemes based on particle tracking cannot
have the problem of oscillations and negative concentrations nor do they suffer from numerical diffusivity.
Dippner (1990) used a particle-tracking method to model
frontal circulation in coastal water, calculating the transport equation for density using dynamically active tracers. A disadvantage of this method may be the number
of particles needed to ensure grid boxes do not become
empty; alternatively, grid boxes may be reseeded with
particles during the calculation. This use of particle
tracking to simulate the advection of a continuous quantity throughout the model domain is different from the
more usual application of particle tracking to advection
of material introduced at a single point source. The accuracy of the particle-tracking method remains limited by
the grid size over which velocities are calculated and
over which particle properties are averaged to give density.
4.2. Further requirements for the physical model
We have seen that key requirements for a physical
model underpinning a water quality model, able to
advect and diffuse water quality variables, include a

positive numerical advection scheme with minimal
numerical diffusion and a diffusion scheme that reproduces realistically the effects of sub-grid-scale turbulence and quasi-two-dimensional eddies. These are not
trivial requirements and both continue to be active
research topics. The accurate reproduction of the largescale meteorologically and tidally driven flows, which
should be well resolved on the model grid scale, also
depends on the treatment of sub-grid-scale mixing, particularly the assumptions made about vertical eddy viscosity.
A lack of up-to-date bathymetry of the required resolution and accuracy often limits the possible accuracy of
model flows. This is important in coastal regions, where
high resolution is required, the bathymetry may be rapidly changing and surveys may be sparse. In intertidal
areas, a combination of remote sensing and models can
produce detailed bathymetric information (Flather et
al., 1998).
The dependence of the physical model on boundary
forcing means there is a requirement for boundary data
from meteorological models and wider-area ocean models, and there is a need for understanding of airsea interaction processes. Open boundary data can determine the
flow pattern within a limited-area model, as shown by
Xing and Davies (2001) for the Irish Sea, so a good
numerical scheme for the open boundary condition,
another continuing area of research, and the availability
of open boundary data from larger area models are critical requirements. The area of interest may be small relative to the whole system which determines flows there,
and may need to be treated at high resolution. Therefore
a nested system is often required, from a relatively
coarse ocean model to a fine-grid coastal model, or a
system with variable grid size within the same model,
such as the finite element model of Lynch et al. (1996).
A nested system may be one-way or two-way: in the
latter case there is feedback from the fine-grid nested
model to the coarse grid model. Fox and Maskell (1996),
in a nested model of the IcelandFaeroe front, found
improved results with a two-way model. A curvilinear
coordinate system can also be used to place high resolution in an area of interest: Spaulding et al. (1996) show
an application of such a model, with boundary-fitted
coordinates, in a system for use in monitoring and modelling oil spills, where the highest resolution is placed
in the coastal area where the oil spill has occurred. The
open boundary may be placed some distance away from
the area of interest, particularly in the finite element
models, which can have a large contrast between the size
of the largest and smallest elements. Other boundary
data include that from river inputs, which are often available only as flow data averaged over various periods.
River flow input is important for the physical model to
maintain the salinity balance and for density-driven cir-
culation in near-coastal regions. Since rivers are a major

source of pollutants and nutrients for the coastal system,
river input fluxes of these variables together with the
water flow rate are naturally of prime importance for a
coastal water quality model.
A further requirement is good meteorological data for
the surface boundary condition, which drives the currents through wind stress and changes the temperature
through heat fluxes and the salinity through precipitation
and evaporation. The surface boundary condition is also
critical for calculating the exchange of water quality
variables, which may be in gas or particle form, between
air and sea. Wind stress is usually derived from a formula dependent on wind speed only, although this neglects direct dependencies on waves (Geernaert et al.,
1986). Heat fluxes may be taken from bulk formulae,
given the necessary meteorological variables (Gill,
1982), but values given directly by numerical weather
prediction models can also be used successfully, as in
the version of POL3DB run at the UK Met. Office. One
of the more sensitive variables in the bulk formulae is
that of cloud cover, which can be taken from models or
satellite observations in the case of hindcasts. The type
of cloud as well as its extent also affects the heat flux.
Atmospheric pressure is important for sea level
(approximately represented by the inverse barometer
effect). The frequency of meteorological data required
is of the order of hourly, to reproduce the effects of
short-term events such as storms. In fact, the UK Met.
Office model mentioned above used hourly winds and
pressures and six-hourly heat fluxes from the atmospheric model. This use of frequent meteorological data
is necessary even if the aim is to reproduce a climatological result for transport or the ecosystem, since this may
be the consequence of a sequence of storm events, and
a correct result would not then be obtained with a
smoothed meteorological input from climatology.
Where wave effects are important, in the surface layer
and in shallow water, a wave prediction model may also
be a requirement at least to derive increased mixing due
to breaking waves, improved representation of surface
fluxes and wave-induced enhancement of bed stress.
Wave-driven residual flows such as Stokes drift and
longshore currents on beaches may be important in some
areas. Longshore currents are an effect of radiation
stress, the excess momentum transport in waves
(Longuet-Higgins, 1970). Where these flows are significant there would be an increased need for wave models,
although some oil-spill models (Section 2.4) include
Stokes drift with the directly wind-driven surface flow.
Most airsea interaction in coastal models has been
assumed to be one-way; that is, with the atmospheric
model affecting the coastal sea model with no feedback.
In that case, sea surface temperature effects in the atmospheric model may be obtained from a much coarser
model, or even from climatology. However, there is
379
growing evidence of some significant two-way coupling;

for example, sea surface temperature fronts can generate
low-level atmospheric fronts, which can in turn drive
coastal waters (Xie et al., 1999). Local weather conditions such as sea mist are clearly related to local coastal sea conditions. A coupled oceanatmosphere model
would be required to include these feedbacks.
5. A model system for coastal water quality

applications
Fig. 1 shows a concept diagram for a model system
that could form the basis of an operational water quality
model, summarising the inputs and outputs and the linking between the various parts. The core of such a model
system is a hydrodynamic model linked to models for
contaminants, sediment and the ecosystem. All possible
links and feedbacks between these component models
are shown here, although any feedback to the atmospheric model from the coastal model is neglected. We
have seen that the input data sets driving the model at
the surface, from river inflows and at the open boundary
are of key importance. For an operational model, it is
necessary to have real-time access to all these data
streams. The amount of real-time data for contaminants
and ecological variables, however, is likely to be limited.
As the models we have described step forward in time
from an initial state, the availability of initial conditions
Fig. 1. A concept diagram for an operational water quality model

system.
380
is also an issue. For some variables the initial conditions

may remain an influence for long periods; others may
be soon forgotten by the system. For example, the influence of initial temperature and salinity may be long-lasting, particularly in the ocean below the seasonal surface
layer, where the time scale for temperature changes may
be years, while currents on the shelf may be started at
zero but the tides are reproduced after just a few tidal
periods of boundary input. Average climatic conditions taken from observations may be a suitable initial
condition for some variables, for example temperature
and salinity and possibly nutrients.
If there are enough observations, data assimilation
may be used to bring the model results nearer to reality.
The extensive literature on data assimilation will not be
reviewed here (see Ghil and Malanotte-Rizzoli, 1991).
Recent applications to shelf seas include the assimilation
into models of temperatures from satellite AVHRR
measurements (Annan and Hargreaves, 1999) and coastal elevation data (Annan, 2001). The skill of a forecast
will depend both on the model and on the quality of the
initial conditions. Assimilation in an operational model
may be thought of as a way of combining models and
observations in an optimal way, with regular updates, to
give the best possible initial conditions, or representation
of the field of state variables, for the beginning of each
forecast period. It is dependent for its success on the
availability of suitable observations, but in this the coastal ocean is deficient in comparison with the atmosphere,
where assimilation of a large amount of data on scales
that resolve the main weather systems is an important
part of weather prediction. Also, because of the scales
involved (Rossby radii and long wave phase velocities
scale as depth1/2), the coastal seas can be considered as
less well sampled than the deep ocean by systems, such
as satellite altimetry, which produce data sets that can
be used for assimilation into ocean models.
A desirable attribute of a coastal ocean modelling system is that it should be easily relocatable to different
areas, since the high resolution needed for coastal applications means that each area of interest will either be
nested within a larger model or be an area of increased
resolution within a variable-grid (for example, finite
element) model. To relocate a coastal model to a new
area requires not only detailed bathymetry of the new
area, but also all the necessary initial and boundary conditions to run it. These could consist of interpolated
values from a coarser grid model covering the area if no
other information is available. Another desirable feature
of a model system is a user interface that makes this
relocation easy to accomplish without extensive reprogramming. An ideal user interface also makes model output easy to comprehend and analyse through use of
advanced visualisation techniques and standard data formats. A further preferred feature is for the model to be
easily relocatable to different machines so that it may
be run on whatever system is available and also take

advantage of any parallel system, such as a Cray T3E
or a Beowulf cluster.
Several organisations have developed, or are
developing, coastal water quality model systems with
some of the attributes described here. These include
ASA (Applied Science Associates), DHI (Danish
Hydraulics), HR Wallingford, HydroQual, MUMM
(Management Unit of the Mathematical Model of the
North Sea, Belgium; originators of the COHERENS
model), POL (Proudman Oceanographic Laboratory,
with the POLCOMS coastal ocean modelling system)
and WL|Delft Hydraulics. Up-to-date information on
these may be found on the web sites listed in Appendix
A. The evident extent of commercial as well as academic
interest in water quality modelling in the coastal area
reflects the growing importance of environmental protection legislation and the need for environmental assessments. This implies a need for running predictions based
on hypothetical scenarios and on the consequences of
proposed construction work or discharges as well as for
real-time predictions, which would be required in the
case of emergencies such as an accidental spill.
In the case of operational real-time modelling the need
for boundary conditions for a coastal model means that
it must ideally be linked to a wide-area, possibly global
operational system such as that proposed by GOOS
(Global
Ocean
Observing
System;
see
http://ioc.unesco.org/goos). Indeed, the requirements of
coastal ocean forecast systems are some of the drivers
for GODAE (the Global Ocean Data Assimilation
Experiment), one of the GOOS pilot projects. ESODAE
(the European Shelf Seas Ocean Data Assimilation and
Forecast Experiment) is a project which is intended to
run in conjunction with this and which is relevant to the
northwest European continental shelf, as is NOOS (the
Northwest Shelf Operational Oceanographic System).
As these systems develop there is a real prospect of
increasing availability of boundary model data together
with long-term monitoring for model comparisons and
validation. Such systems are, however, in the future, certainly as far as most water quality variables are concerned; one of the reasons for the success of tide and
storm surge models is the existence of long-term and
real-time monitoring of sea level from a network of
coastal tide gauges, and such a data set is not available
for the other physical, chemical and biological variables
we have been considering in this review.
6. Conclusions
1. Considerable advances have been made in recent
years in the elements needed for predicting coastal water
quality operationally, namely three-dimensional hydrodynamic shelf-sea models and ecological, pollutant and
sediment models. However, much more still needs to be

done to improve the models, and research remains very
active in each of these individual areas. There has also
been an increase in interdisciplinary modelling work
connecting these areas together. Fig. 2 is an outline of
progress in hydrodynamic and ecological modelling set
against a time scale and developments in computer
power. From this it can be deduced that there is a long
period of development before models become operational, and that the rate of increase in computer power
supporting the use of more complex models with higher
resolution shows no sign of slowing. For contaminant
modelling, it is not so easy to show progress on a single
diagram as this depends on the individual contaminant,
but generally it should follow progress in the hydrodynamic and sediment transport models.
2. Testing of models through model intercomparisons suggests that results may not yet be reliable. Stolwijk et al.s (1998) comparison of five water quality
models of the North Sea showed significant variation and
they concluded there was a lack of field data for calibration and validation. In the EU-funded programme
NOMADS, which compared the transport and dispersion
Fig. 2. An outline of progress since 1960 for hydrodynamic and ecological models, and computer power.
381
of tracers in several models of the same area in the North

Sea, considerable variation was found (Proctor, 1997).
Some of the variation could have been due to differences
in boundary and meteorological data. These results suggest that the rigorous testing of models, even for simple
conservative tracers, needs to be expanded, and some
estimate of error bars and sensitivity to input data needs
to be made, but to do this there has to be a large quantity
of relevant data readily available.
3. There has been a considerable amount of work
done on oil-spill modelling, driven by the need to predict
the consequences of accidental spills. Other pollutants
have not all had the same attention, partly because of
complex chemistry. The toxicity of a complex cocktail
of pollutants is not well understood, and not generally
included yet in ecological models. It is clear that sediment modelling is a key part of pollutant modelling,
because of the partitioning between dissolved and particulate fractions, scavenging of pollutants by particulate
matter, and resuspension of sediment carrying pollutants
from the sea bed.
4. There is still some controversy over the effectiveness of time-stepping deterministic ecological models, in
comparison with the more traditional empirical
approach. Ecological models even of the deterministic
kind also vary considerably in their complexity. While
a simple model involving one functional group for phytoplankton and one nutrient may succeed in reproducing
a spring bloom, in reality most phytoplankton populations are composed of several functional groups. If all
significant processes in the shelf-sea ecosystem are to be
included, even to simulate just the cycling of carbon and
nutrients, a model such as ERSEM with many more variables than a typical physical model is necessary. This
level of complexity not only increases the computational
load, it makes for difficulty in interpreting the results.
The consequences of changing a parameter are not
always clear in a deeply non-linear system with the order
of 100 variables. The limited amount of data for validation often corresponds to only a tiny part of the possible solution space. If there are sufficient data, assimilation may be used for parameter estimation and then it
would become possible to decide more easily which
model has the better functional structure. Confidence in
the results of the complex deterministic ecological models when used for predictions will only come after a considerable process of testing and validation.
5. The computational demands of high-resolution
and ecological models are becoming easier to satisfy,
thanks to the advent of massively parallel machines at
reasonable cost. The models described here are based on
spatial grids in the horizontal, which are ideal for dividing over many processors using domain decomposition.
Speedups of the order of hundreds over a single processor mean that a 1 km resolution ecological model
382
over the northwest European shelf is now looking feasible, which was not the case a decade ago.
6. Physical models are limited by our understanding
of turbulence and how to parameterise sub-grid-scale
processes generally. Quasi-two-dimensional eddies and
Langmuir circulation may have important effects on dispersion and mixing. Internal waves and convection
influence mixing across the thermocline and deepening
of the mixed layer. Improvements in understanding these
usually unresolved processes will improve the physical
models: with finer grids (as in large eddy simulations)
some may become resolved by the model. A model with
fine-scale bathymetry may resolve the non-linear effect
of chaotic stirring, which could be significant in some
coastal areas.
7. While we may expect continual improvement in
the model codes and in scientific understanding of the
underlying processes, and continuing increases in computer power at decreasing cost, leading to the feasibility
of calculations with ever more variables on ever finer
grids, the consequential demand for ever more data,
including bathymetric data, will not be easily satisfied.
This is because of the expense of data gathering and the
need for large international bodies to organise it and
make sure the data are readily available. For operational
modelling, the requirement to have data in real time is
added. This has not developed for the ocean as it has
for the atmosphere, and although GOOS is providing a
focus for the necessary developments it is probably
reasonable to conclude that the single most important
factor limiting the progress towards operational water
quality models is a lack of data.
Acknowledgements
This paper is based on a review funded by the Met.
Office under contract PB/B3197. I would like to thank
the referees, whose comments and suggestions have considerably improved the paper.
Appendix A
Web sites of some organisations modelling water
quality in coastal areas:
ASA (Applied Science Associates): www.appsci.com
DHI (Danish Hydraulics Institute): www.dhi.dk
HR Wallingford: www.hrwallingford.co.uk
HydroQual: www.hydroqual.com
MUMM (Management Unit of the Mathematical
Model of the North Sea, Belgium): www.mumm.ac.be
POL (Proudman Oceanographic Laboratory):
www.pol.ac.uk
WL|Delft Hydraulics: www.wldelft.nl

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Environmental Modelling & Software 17 (2002) 363385

Modelling pollution dispersion, the ecosystem and water quality in

2. Modelling pollutants in coastal waters

Ecosystem modelling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371

* Tel.: +44-151-653-1533; fax: +44-151-653-6269.

I.D. James / Environmental Modelling & Software 17 (2002) 363385

4.1.3. Quasi-two-dimensional turbulence

A model system for coastal water quality applications . . . . . . . . . . . . . . . . . . . . . . . . 379

radiation of a surface plankton bloom), in general a good

I.D. James / Environmental Modelling & Software 17 (2002) 363385

difficult problems such as the behaviour of suspended

2. Modelling pollutants in coastal waters

may exist in solution or as particulates). Some undergo

I.D. James / Environmental Modelling & Software 17 (2002) 363385

ple tracer. Nevertheless, Prandle et al. (1993) calculated

I.D. James / Environmental Modelling & Software 17 (2002) 363385

dermann, 1990; Pohlmann and Puls, 1994; Su ndermann,

I.D. James / Environmental Modelling & Software 17 (2002) 363385

be taken into account if a water quality model is used

(NOSTRADAMUS) for metals (Cd, Cu, Ni, Pb, Zn) in

I.D. James / Environmental Modelling & Software 17 (2002) 363385

zero. As the wind increases, oil droplets are dispersed

whether the oil is heavy or light. The most commonly

I.D. James / Environmental Modelling & Software 17 (2002) 363385

weathering, photochemical oxidation, emulsification,

to contaminants at a cellular level (for example, Moore

I.D. James / Environmental Modelling & Software 17 (2002) 363385

This process also requires nutrients: these are mainly

nitrogen, as the ions nitrate (NO

ammonium (NH4 ), phosphorus, as phosphate (PO

I.D. James / Environmental Modelling & Software 17 (2002) 363385

where Ph is photosynthetic rate, R is respiration and G

based on an upper-layer model that does not include tidal

I.D. James / Environmental Modelling & Software 17 (2002) 363385

known as its biological oxygen demand (BOD). If this

I.D. James / Environmental Modelling & Software 17 (2002) 363385

as pointed out by Vallino (2000), and as we have noted

tion 2 that diffusivity on a molecular scale, which will

I.D. James / Environmental Modelling & Software 17 (2002) 363385

both by increasing shear across the thermocline (as do

eddy-resolving application of this isopycnal coordinate

I.D. James / Environmental Modelling & Software 17 (2002) 363385

E(k) 2 / 3k5 / 3, and if a pair of particles is released a

duced by the numerical method; more on this topic is

I.D. James / Environmental Modelling & Software 17 (2002) 363385

and lower-layer depth and density are h1, r1 and h2, r2

power increases, finer resolution of the full baroclinic

4.1.4. Lagrangian chaos

I.D. James / Environmental Modelling & Software 17 (2002) 363385

4.1.5. Numerical diffusion

advect and diffuse water quality variables, include a

I.D. James / Environmental Modelling & Software 17 (2002) 363385

culation in near-coastal regions. Since rivers are a major

growing evidence of some significant two-way coupling;

5. A model system for coastal water quality

Fig. 1. A concept diagram for an operational water quality model

I.D. James / Environmental Modelling & Software 17 (2002) 363385

is also an issue. For some variables the initial conditions

be run on whatever system is available and also take

I.D. James / Environmental Modelling & Software 17 (2002) 363385

sediment models. However, much more still needs to be

of tracers in several models of the same area in the North

I.D. James / Environmental Modelling & Software 17 (2002) 363385

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