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22nd International Congress on Irrigation and Drainage

14-20 September 2014, Gwangju Metropolitan City, Republic of Korea

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SYM (1) PAPER NO. 171


ASSESSMENTS OF SWAT FOR WATER QUALITY MODELING IN WATERSHED
CONTAINING PADDY FIELD: CASE STUDY IN UPPER KASHIMA RIVER, JAPAN
Hanhan A. Sofiyuddin1, Ryota Tsuchiya2, and Tasuku Kato3
ABSTRACT
Soil and Water Assessment Tool (SWAT) is very promising to simulate streamflow and
water quality in an agricultural watershed. Many studies have reported that it can give
acceptable result to assess non-point source pollution. In Kashima River, SWAT
application is expected to aid the planning process in mitigating non-point source
pollution, by means of environmental conservation scenario development. The
present study was conducted to investigate the applicability of SWAT in Kashima
River watershed. SWAT model was configured using ARC-SWAT 2009 and calibrated
using SUFI-2 method. Model evaluation was done by examining model structure and
interpreting calibration results using the information gathered from the field and
literatures. This study showed that SWAT can model streamflow well regardless of its
inappropriate model structure to represent the hydrological process in paddy fields.
However, nitrogen simulation was not satisfactory. This is mainly due to complicated
processes in ponded storage, water movement into the soil, ground water flow and
denitrification.

1Master student in Department of International


Environment and Agricultural Sciences, Faculty of
Agriculture, Tokyo University of Agriculture and
Technology, Japan; Research and development staff
in Irrigation Experimental Station, Research Center
for Water Resources, Research and Development
Agency, Ministry of Public Works, Indonesia. E-mail:
hanhan.ahmad@gmail.com.
2Master student in Department of International
Environment and Agricultural Sciences, Faculty of
Agriculture, Tokyo University of Agriculture and
Technology, Japan.
3Associate Professor in Department of International
Environment and Agricultural Sciences, Faculty of
Agriculture, Tokyo University of Agriculture and
Technology, Japan.
1

22nd International Congress on Irrigation and Drainage


14-20 September 2014, Gwangju Metropolitan City, Republic of Korea

R58.1.10
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Keywords: SWAT, paddy field, streamflow, total nitrogen, evaluation, Japan.

1.

Introduction

Soil and Water Assessment Tool (SWAT) is a very promising model for hydrologic and
water quality simulation in an agricultural watershed. SWAT is a basin scale timecontinuous model that operates on a daily time step and is designed to predict water,
sediment, nutrients, pesticides dynamics, and the impact of agricultural management
practices on them. The model is physically based, computationally efficient, capable
of continuous simulation over long time periods and proved by many researches to
give reasonable performance in assessing non-point source pollution (Gassman et
al., 2007). Furthermore, SWAT is an open source model thus it is continuously tested
and developed by many researchers around the world. SWAT can give valuable
insight regarding approach to solve water resources and non-point sources pollution
issues. For examples, SWAT was used to develop Total Maximum Daily Load (Kang
et al., 2006), evaluate Best Management Practices scenario (Dechmi and Skhiri,
2013), assess the impact of land use (Volk et al., 2009), assess the impact of climate
change (Ficklin et al., 2009, Somura et al., 2009), and so on.
On its application for paddy fields land use, there are some differences in the
validation results among researches. Some have successfully validated SWAT in
watersheds containing paddy fields (Somura et al., 2012; Luo et al., 2011). In other
researches, SWAT showed some limitation that may produce significant error. Thus,
modified version of SWAT model is more preferable (Kim et al., 2003; Xie and Cui,
2011; Sakaguchi et al., 2014). The difference of validation results is related to the
watershed characteristic and the issues being considered. Paddy fields have distinct
features of water and pollutant dynamics compared to other agricultural land use.
Thus, paddy fields affect differently to runoff (Hayase, 1999) and also pollutant
balances (Feng et al. 2004; Takeda et al., 1997). Water quality dynamics in paddy
fields is more complex because it is influenced not only by hydrological process but
also biochemical interaction (Kato et al., 2011).
In our study area, Kashima River watershed, land use is dominated by agriculture and
growing paddy is one of the agricultural activities. Paddy fields are located along the
river and use the river both as a source of water for irrigation as well as as a sink for
drainage effluent discharge. Under such condition, paddy fields have the opportunity
to enhance the water quality (Ichino and Kasuya, 1998) and hence, proper irrigation
management in paddy fields area can mitigate non-point source pollution from other
agricultural areas, especially total nitrogen.
SWAT application is expected to give insight into the non-point source pollution and
its mitigation possibilities. As the first step towards applying SWAT to watersheds
containing paddy fields, this study is aimed to understand the performance and
applicability of SWAT for paddy fields hydrological process that consists of both
surface and ground water processes. The parameters considered in this study were
streamflow and total nitrogen. These parameters are evaluated by uncertainty
analysis.

2.
2.1

Method
Study Area

The study was conducted for the upper part of Kashima river watershed (Figure 1) in
Chiba Prefecture, Japan. Major land use in study area is agriculture, comprising
upland (38.1%) and paddy field (9.2%). River conveys drainage water from upstream

22nd International Congress on Irrigation and Drainage


14-20 September 2014, Gwangju Metropolitan City, Republic of Korea

R58.1.10
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agricultural area that is used for paddy irrigation. The area mainly consists of 2 soil
types with relatively high permeability, i.e. Humic Andosols and Gley Soil.

Figure 1. Study location (Upper Kashima River watershed)


The river flows into Inbanuma Lake, which has serious water quality problem due to
mixing with river water polluted by inflows from agricultural lands and habitated areas.
Monthly average value of COD (9.6-14.0 mg/l), total nitrogen (1.9-3.1 mg/l) and total
phosphorous (0.11-0.14 mg/l) is more than two times greater than the maximum
allowable value (Chiba Prefecture Government, 2010). Compared to other lakes in
Japan, Inbanuma Lake is considered to have the worst water quality (Inbanuma Lake
Water Quality Council, 2011).
2.2.

SWAT model

SWAT is a semi lumped hydrological model. Spatial heterogeneity is simplified by


dividing watershed into sub-watersheds. Each sub-watershed is further discretised
into Hydrological Response Unit (HRU). Watershed and sub-watershed are generated
based on Digital Elevation Model (DEM). HRU are generated by overlaying land use,
soil and slope data. Each HRU in sub-watersheds has specific combination of land
use, soil and slope category. Calculation of hydrological component is conducted in
each HRU. Afterwards, the outflow of each HRU is accumulated and routed as
streamflow. SWAT model framework was documented in details by Neitsch et al.
(2011).
By default, HRU simulation is based on the Soil Conservation Service Curve Number
(SCS CN) procedure to divide rainfall into surface runoff and infiltration (Neitsch et al.,
2011). This is an empirical procedure that calculates runoff based on rainfall-runoff
relationships from small rural watershed. Runoff is calculated by equation:
(R day I a )2
Qsurf
(R day I a S)
...............................................................................
1000

S 25 .4
10
CN

................................................................................

where Qsurf is the runoff (mm), Rday is rainfall (mm), Ia is initial abstractions (mm), S is
retention parameter (mm) and CN is curve number of the day, representing the
overall watershed response characteristics to rainfall.

22nd International Congress on Irrigation and Drainage


14-20 September 2014, Gwangju Metropolitan City, Republic of Korea

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Nitrogen processes is modelled in each HRU. In surface layer, nitrogen is estimated


separately in several forms which dynamically changed i.e. organic Nitrogen, NO 3-N,
and NH4-N. Along with water movement, those N are discharged from surface layer.
In soil layers and ground water, N discharges are assumed inorganic forms i.e. NO 3N. Schematically, modelled nitrogen process is represented in Figure 2.

Figure 2. Modelled nitrogen processes in SWAT (Neitsch et al., 2009)


To model the paddy field, Neitsch et al. (2011) recommend the use of pothole module.
Originally, pothole module was developed in SWAT model to accommodate physical
process in depression area. Runoff generated in HRU is flowing to the lowest portion
of the potholes rather than directly contributing to the flow in the river. Storage
dynamics in paddy field could be better represented by using this option.
Furthermore, pothole module enables the simulation of nitrogen decaying process in
ponded water.
2.3.

Model Parameterisation

Model input file was generated using ARC-SWAT 2009 with following data:
a. Digital Elevation Model (50 m mesh) by Geographical Survey Institute, Japan
b. Land use (100 m mesh) by Ministry of Land, Infrastructure, Transport and
Tourism, Japan
c. Soil map by Japan Soil Association with soil vertical data by Eguchi et al. (2011)
d. Weather data by Japan Metrological Agency (Automated Meteorological Data
Acquisition System)
e. Management data (irrigation, fertilizer rate, cropping season, etc) from local
authorities
Watershed divided into 13 sub-watersheds and total 188 HRUs that have different
properties of slope, land use, and soil types.
2.4.

Model Calibration and Evaluation

The model was calibrated using SUFI-2 method with SWAT-CUP software. This
method is capable in considering all uncertainty sources, such as uncertainty in
driving variables (e.g., rainfall), conceptual model, parameters, and measured data
(Abbaspour, 2014).
SUFI-2 started with some initial range of parameter value. Simulation was then
conducted based on parameter generated by the Latin Hypercube Sampling within
the initial range. At the end of each calibration round, SUFI-2 generates new
parameter range that can give better model performance. The calibration is repeated
until simulation results good performance, adjudged through p-factor, r-factor and
4

22nd International Congress on Irrigation and Drainage


14-20 September 2014, Gwangju Metropolitan City, Republic of Korea

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goodness of fit criterion. Details of the algorithm are available in Abbaspour et al.
(2004).
p-factor is the percentage of measured data bracketed by the 95% prediction
uncertainty (95PPU). When all measured data are bracketed in 95PPU band, p-factor
will be 100%. The r-factor is the average thickness of the 95PPU band divided by the
standard deviation of the measured data. p-factor range between 0 and 100% and rfactor ranges between 0 and infinity. A p-factor of 1 and r-factor of 0 means that
simulation exactly corresponds to measured data. Calibration is considered
successful if r-factor is less than 1 while maintaining high enough p-factor (more than
80% for high quality data or more than 50% for low quality data) and best simulation
has satisfactory goodness of fit (Abbaspour et al., 2007).
This study uses goodness of fit criterion proposed by Moriasi et al. (2007). RSR (root
mean square error to observation standard deviation ratio) is the measure of
magnitude of the error that defined as root mean square error divided by standard
deviation of observation data. NSE (Nash Sutcliffe model efficiency) is the measure of
how well the observed and simulated data fits 1:1 line. NSE ranges between - to 1.
NSE less than 0 means that average value of observed data is the better predictor
than simulation result while NSE equal to 1 means that the simulated and the
observed data are exactly equal. PBIAS (per cent bias) is the measure of tendency of
simulated data to overestimate or underestimate the observed value. Positive value
indicates model underestimation while negative value indicates model overestimation.
Generally, model simulation can be judged satisfactory if RSR 0.7, NSE > 0.5 and
PBIAS 25% for streamflow and PBIAS 75% for nitrogen (Moriasi et al., 2007).
The model was evaluated by examining model structure and interpreting calibration
results. Using the information from field and literatures, model structure and
simulation process were examined to evaluate the applicability of the model.
Additionally, model diagnostic analysis was conducted by analysing model
performance in different time periods and flow regimes. Time period considered in this
study are irrigation and non-irrigation period. Flow regime was separated into 3 types
by adapting method in Wagener et al. (1999), i.e. FD, FQ and FS. The time steps with
non-zero rainfalls, lagged by the time of concentration for the catchment, were
classified as rainfall driven flow (FD). The remaining time steps with streamflow lower
than a certain threshold value (mean of the logarithms) were classified as non-rainfall
driven slow (FS) and the rest are classified as non-rainfall driven quick (FQ). The
goodness of fit in each period or flow regime was plotted in a box-plot to determine in
which period the model performs poorly (Guse et al., 2013).

3.
3.1

Result and Discussion


Paddy Field Characteristic in Kashima River

In the study area, the river conveys polluted drainage water from agricultural fields.
Paddy field that lies along the river side uses river water for irrigation and the river for
drainage. To some extent, this system allows paddy field to perform water purification
function. The irrigation water is retained in the ponded storage for a quite long time so
that the biochemical processes can reduce its nutrient content. Thus during drainage,
paddy field contributes less polluted water to the river. Measurement conducted in
2012 and 2013 showed that nitrogen content in drainage water was generally lower
than concentration in the river (Figure 3).

22nd International Congress on Irrigation and Drainage


14-20 September 2014, Gwangju Metropolitan City, Republic of Korea

R58.1.10
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Figure 3. Total nitrogen measurement in 2012 and 2013


Purification characteristic depends on several factors. Generally in Japan, paddy
fields can contribute to purification if pollutant concentration in irrigation water is
above 2 mg/L (Misawa et al., 1999). Thus, the purification is very likely since the
concentration in Kashima River is generally above 5 mg/L. Another factor is the
retention time in paddy field. Retention time of more than 5-7 days is preferable for
the purification to occur (Takeda et al., 1996, Feng et al., 2004). However, the
retention time is a function of storage and water input (irrigation or precipitation).
Thus, proper irrigation management is needed.
Currently, water pumped from river or deep aquifer is used for irrigation. Based on
data from local irrigation office, gross irrigation for about one third of paddy field in
study area is described in Figure 4. River is a major source of irrigation that
comprises around 75% of total irrigation and maximum 45% of river outflow. Thus due
to its significant amount, paddy field irrigation can affect greatly to streamflow. This
emphasizes the importance of water management in paddy field to maintain
streamflow as well as its water quality.
Streamflow
Irrigation from river
Irrigation from deep aquifer

Figure 4. Monthly river outflow and irrigation


3.2

SWAT Model Calibration and Evaluation

Calibration was conducted using SUFI-2 method until p-value more than 50% and rfactor less than 1. The results are in Table 1, Figure 5, and Figure 6. Streamflow can
be simulated well by both methods. Both models can bracket more than 70% of the
data with r-factor less than 1. The resulting best simulation performance also give
quite good performance with RSR less than 0.7, NSE more than 0.5 and PBIAS less
than 10%. On the contrary, TN simulation shows not satisfactory results for both
methods.
Table 1. Performance of the model after calibration
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22nd International Congress on Irrigation and Drainage


14-20 September 2014, Gwangju Metropolitan City, Republic of Korea
`

Model
SWAT with
SCS-CN
SWAT with
Pothole

Best Simulation

Output

p-factor
(%)

r-factor

Q
TN
Q

72
45
87

TN

52

RSR

NSE

PBIAS
(%)

0.60
0.84
0.96

0.67
1.03
0.69

0.54
-0.07
0.52

-8.7
-2.1
-4.8

0.79

1.06

-0.12

6.6

Figure 5. Calibrated model (SWAT with SCS CN)

Figure 6. Calibrated model (SWAT with pothole module)


Theoretically, there is some differences in the assumption between the modelled
process in SWAT and commonly modelling approaches in paddy field (Figure 7).

Figure 7. Schematic representation of simulated process in SCS CN (left), pothole


module (middle) and paddy field (right)

22nd International Congress on Irrigation and Drainage


14-20 September 2014, Gwangju Metropolitan City, Republic of Korea

R58.1.10
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SCS CN method was originally developed to model upland agricultural system. Using
this method, runoff is generated directly as a fraction of rainfall that does not infiltrate
to the soil. Thus, this method does not consider surface storage (ponded water),
which is an important component to model runoff in paddy field. Many other modelling
approaches configure paddy field differently from other land use and explicitly
simulated the process in ponded water situation, as in Hayase (1999) and Khepar et
al. (2000). Runoff from paddy field is commonly modelled as overflow which varied
with the outlet height and initial ponding depth (Kim et al., 2003).
To model ponded water, pothole module is available in SWAT. However, there is also
some different assumptions that can lead to model structural error. This module is
originally developed to model closed depression area in young glacial till plains (Du et
al., 2005). In pothole module, storage is assumed cone shaped so surface area is not
constant. This can lead to underestimation of evapotranspiration since in paddy field
the storage is almost cuboids with constant surface storage (Xie and Cui, 2011).
Another different assumption is in seepage into the soil profile and hydrological
process during non-ponding period as described by Sakaguchi et al. (2014).
However, these differences in model structures would not have significant effect on
streamflow simulation. By arranging parameters during calibration process, quite
satisfactory results were obtained. Resulting calibrated model also have quite good
performance.
Different from streamflow simulation, total nitrogen simulation seems more sensitive
to physical representation of the model. 95PPU can bracket only less than 60% of the
observed data when r-factor less than 1 and best simulation was not having a
satisfactory performance. One possible cause is due to not representative simulation
in low-flow period. Figure 8 shows temporal RSR of both models. Generally both
models can only represent streamflow in non-irrigation period and rainfall driven flow
(FD). Poorest model performance was obtained at slow non-driven flow (FS). Since
total nitrogen transport is mainly by ground water flow, it is obvious that poor
performance of streamflow simulation during low flow period (FQ and FS) can lead to
poor performance of overall total nitrogen simulation. Another possible cause is due
to simulated denitrification and nutrient leaching process. Model structure differences
are resulting in non-representative simulation of water movement in the soil. Thus,
simulation of those processes is impaired. Furthermore, Kato et al. (2011) suggested
that improved nutrient cycling algorithm is needed to model paddy field, especially the
denitrification process in them.

22nd International Congress on Irrigation and Drainage


14-20 September 2014, Gwangju Metropolitan City, Republic of Korea

R58.1.10
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Figure 8. Temporal performance (RSR) for streamflow simulation of SWAT with SCS
CN (left) and SWAT with pothole (right). Dashed line is RSR at 0.7 indicating
threshold for satisfactory model performance

4.

Conclusion

In Kashima River Watershed, paddy fields play important role in determining


streamflow and water quality. Thus, proper water management in paddy fields is very
important. SWAT is a promising model to work on this idea by means of
environmental conservation scenario development. However, there is some
inappropriate model structure in SWAT to model paddy fields that hampers the
application of SWAT in this watershed.
This study showed that SWAT can represent streamflow quite well regardless of its
inappropriate model structure in representing the hydrological process in paddy fields.
However, nitrogen simulation was quite sensitive to physical representation of the
model so the result was not satisfactory. Thus, model improvement is needed,
especially in the process of surface storage, water movement into the soil, ground
water flow and denitrification. Further study is required to apply and evaluate the
modification ideas.

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