Science of the Total Environment 603–604 (2017) 196–218

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Science of the Total Environment

journal homepage: www.elsevier.com/locate/scitotenv

Review

Modelling water and nutrient fluxes in the Danube River Basin

with SWAT
Anna Malagó ⁎, Faycal Bouraoui, Olga Vigiak, Bruna Grizzetti, Marco Pastori
European Commission, Joint Research Centre (JRC), Directorate D – Sustainable Resources, Ispra, VA, Italy

H I G H L I G H T S G R A P H I C A L A B S T R A C T

• A new SWAT model's calibration and

validation method for water quantity
and quality is provided.
• The approach includes prediction of
concentrations as affected by current
conservation measures.
• Modelled water and nutrient balances
can guide conservation management.
• Prediction of nutrient concentrations
increased the robustness of nutrient
fluxes estimations.

a r t i c l e i n f o a b s t r a c t

Article history: This study provides an innovative process-based modelling approach using the SWAT model and shows its appli-
Received 8 March 2017 cation to support the implementation of the European environmental policies in large river basins. The approach
Received in revised form 6 May 2017 involves several pioneering modelling aspects: the inclusion of current management practices; an innovative cal-
Accepted 26 May 2017
ibration and validation methodology of streamflow and water quality; a sequential calibration starting from crop
Available online 17 June 2017
yields, followed by streamflow and nutrients; and the use of concentrations instead of loads in the calibration.
Editor: Jay Gan The approach was applied in the Danube River Basin (800,000 km2), the second largest river basin in Europe,
that is under great nutrients pressure. The model was successfully calibrated and validated at multiple gauged
Keywords: stations for the period 1995–2009. About 70% and 61% of monthly streamflow stations reached satisfactory per-
Swat formances in the calibration and validation datasets respectively. N-NO3 monthly concentrations were in good
Danube agreement with the observations, albeit SWAT could not represent accurately the spatial variability of the deni-
Streamflow trification process. TN and TP concentrations were also well captured. Yet, local discrepancies were detected
Nutrient concentrations across the Basin. Baseflow and surface runoff were the main pathways of water pollution. The main sinks of TN
Nitrogen and phosphorus balances
and TP diffuse emissions were plant uptake which captured 58% of TN and 92% of TP sources, then soil retention
(35% of TN and 2% of TP), riparian filter strips (2% both for TN and TP) and river retention (2% of TN and 4% of TP).
Nitrates in the aquifer were estimated to be around 3% of TN sources. New reliable “state-of-the-art” knowledge
of water and nutrients fluxes in the Danube Basin were thus provided to be used for assessing the impact of best
management practices and for providing support to the implementation of the European Environmental
Directives.
© 2017 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license
(http://creativecommons.org/licenses/by/4.0/).

⁎ Corresponding author at: European Commission, Joint Research Centre (JRC), Directorate D – Sustainable Resources, Via E. Fermi 2749, Ispra I-21027, VA, Italy.
E-mail address: anna.malago@ec.europa.eu (A. Malagó).

http://dx.doi.org/10.1016/j.scitotenv.2017.05.242
0048-9697/© 2017 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218 197

Contents

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
2. Material and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
2.1. The study area and data collection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
2.2. The SWAT model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
2.3. Model set up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
2.4. The calibration and validation of the model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
2.4.1. Monitoring data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
2.4.2. Crop yields calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
2.4.3. Streamflow calibration and validation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
2.4.4. Nutrient calibration and evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
2.5. Assessment of model performance and analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
3. Results and discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
3.1. Calibration and validation of the model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
3.1.1. Crop yields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
3.1.2. Calibration and validation of streamflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
3.1.3. Nitrate-nitrogen calibration and evaluation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
3.1.4. Total nitrogen calibration and evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
3.1.5. Total phosphorus calibration and evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
3.2. Analysis of the water and nutrients fluxes per water management region . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
3.3. Analysis of the water and nutrients fluxes along the Danube River . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
3.4. The water and nutrient balances of the Danube River basin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
3.5. Usefulness of model predictions and future applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
3.6. Consideration about the nutrient pollution in the Danube River Basin and the end up in the Black Sea . . . . . . . . . . . . . . . . . . 214
4. Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Acknowledgement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Appendix A. Supplementary data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216

1. Introduction
In December 2000, the Water Framework Directive (WFD) of the Eu-
ropean Union (EU) was enforced (EC, 2000) to provide a new legislative
basis for water management, in terms of quantity and water chemical
and ecological quality in Europe. According to the WFD, one of the pur-
pose of EU Nitrates Directive (EC, 1991) and the Groundwater Directive
(EC, 2006) is to keep nitrates concentration below a threshold of
50 mg/L. In this context, computer modelling systems provide an im-
portant contribution to the process of integrated management and deci-
sion support, in particular for establishing action plans and to assess the
implementation of the measures and their impacts (Lindenschmidt et
al., 2007; Abbaspour et al., 2015). Large-scale hydrologic and water
quality models (H/WQ) are increasingly used for this purpose (Döll et
al., 2008). In particular, Ferrant et al. (2011) indicated that several
models have coupled hydrological and crop model to study the interac-
tion between agricultural practices and catchment physical characteris-
tics on the dynamic of nutrients in streams (i.e. Liu et al., 2005; Jha et al.,
2006). Without being exhaustive, the H/WQ models commonly used at
large-scale include SWAT (Arnold et al., 1998), WARMF (Herr and Chen,
2012), HSPF (Duda et al., 2012) and MIKE-SHE (Jaber and Shukla, 2012).
Bouraoui and Grizzetti (2014) provide a more detailed review of models
used in pollution assessment in Europe. The H/WQ have the capacity to
represent appropriately spatial-temporal heterogeneity through a
distributed or semi-distributed spatial discretization (Baffaut et al.,
2015). The Soil and Water Assessment Tool (SWAT) (Arnold et al.,
1998) has been extensively used for its modularity between quantity
and quality components, computational efficiency, ability to predict
long-term impacts as a continuous model (see for more details
Gassman et al., 2010; Abbaspour, 2008; Di Luzio et al., 2005). A signifi-
cant number of SWAT model applications has been reported ranging
from subbasin to continental scales addressing different environmental
issues (see overviews in Gassman et al., 2007, 2014; Krysanova and
Arnold, 2008; Douglas-Mankin et al., 2010; Tuppad et al., 2011;
Krysanova and Srinivasan, 2015; Krysanova and White, 2015 and the
most recent works of Haas et al., 2017 and Huang et al., 2017).
H/WQ models, such as SWAT, are particularly widely used in large
transboundary river basins where many challenges exist due to differ-
ent legislative frameworks and data availability across national bound-
aries (Chapman et al., 2016; Bloesch et al., 2012; Sommerwerk et al.,
2010).
The Danube River Basin with a total area of about 800,000 km2
shared by 80 million people in 19 countries is recognized as the world's
most international river basin. Management of water quantity and qual-
ity in the Danube Basin has been a top priority since decades (Liska,
2015). The Basin water management is coordinated by the International
Commission for the Protection of the Danube (ICPDR) that has recently
developed an updated Danube River Basin Management Plan (ICPDR,
2015) following the EU Water Framework Directive (EC, 2000) cycling
approach. According to the Plan assessment, 49% and 35% of total
25,582 km of rivers in the Basin are at risk of failure to achieve the
good ecological and chemical status by 2021 (ICPDR, 2015), mainly
due to the high organic and nutrient pollution from point sources (i.e.
wastewater treatment plant discharges) and diffuse sources (i.e. atmo-
spheric deposition, excessive fertilization, and tile drainage systems),
hazardous substances, and hydromorphological alterations. Further-
more, the rivers in the Basin are impacted by excessive water abstrac-
tions mainly for hydropower generation and irrigation use that can
significantly alter the streamflow and consequently reduce available
water resources.
To provide solutions to these issues, several H/WQ models were de-
veloped and applied in the Danube River Basin. Fehér and Muerth
(2015) provide an exhaustive inventory of hydrological models applied
in the Danube Basin giving details about models structure, spatial and
temporal scales, and aims of the applications. Pagliero et al. (2014) ap-
plied the Soil and Water Assessment Tool model (SWAT; Arnold et al.,
1998) to the Danube Basin delivering an accurate water resources as-
sessment. Based on this study, Karabulut et al. (2016) developed a
198 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218
framework for mapping indicators of water scarcity, water availability
and water use in the Danube Basin in the context of the ecosystem-
water-food-energy nexus. Nutrients assessments have been conducted
with the Modelling Nutrient Emissions into River Systems model
(MONERIS; Behrendt and Opitz, 2000; Venohr et al., 2011) and the re-
cent annual results of MONERIS for the period 2009–2012 were includ-
ed in the 2015 Danube River Basin Management Plan. Both water
quantity and quality aspects of the Black Sea Basin (2,300,000 km2) in-
cluding the Danube River Basin were simulated using SWAT model by
Rouholahnejad et al. (2014) and by Abbaspour et al. (2015). However,
they focused mainly on calibration aspects at large scale rather than
on water and nutrient balances of the Basin, which instead may offer
important guidelines for management.
All these model applications provided valuable information on
water and nutrient fluxes in the Basin but could be somehow limited
in the representation of hydrological and water quality processes,
since they failed to systematically address some drawbacks in water
and nutrient modelling. A major risk is the exclusive focus on reaching
very good fit between modelling results and observed water quantity
and quality data with the risk to obtain a good fit for “wrong” reasons
(Moriasi et al., 2015). For instance, good statistics can be obtained at
gauging stations even though point sources are underestimated and
the loads from agricultural lands are overestimated. This could result
in policy scenarios that overestimate the impact of conservation or
best management practices (BMPs) (Arnold et al., 2015). In addition,
often the models were set-up without including the current manage-
ment practices, irrigation, reservoirs, rivers and groundwater uses for
which information are rarely available (Döll et al., 2009) and thus usu-
ally neglected. Furthermore, many water quality and quantity models
are calibrated only at the final outlet of the watershed instead of using
multiple gauging stations (Arnold et al., 2012b; Pohlert et al., 2007;
Kuczera and Franks, 2002), or vice versa multiple gauging stations are
involved in the calibration albeit affected by anthropogenic activities
that the models are not able to represent (Pagliero et al., 2014). Finally,
it has been observed that the above mentioned studies used the calcu-
lated nutrients load to calibrate the models albeit realistic estimation
of loads is critical for accurate assessment of current water quality status
(Lloyd et al., 2016). Measurement and analytical errors of concentra-
tions are generally considered to be the smaller components of the
total uncertainty associated with load estimation (Rode and Suhr,
2007). This high uncertainty has important implications in the ability
to assess the effectiveness of management strategies which have to be
implemented to mitigate diffuse agricultural water pollution.
For these limitations, further efforts in modelling water quantity and
quality are necessary. Recently, the use of both soft and hard data
(Arnold et al., 2015) was found to be most useful in analysing topics
with missing data. Hard data are defined as long-term, measured time
series, typically at a gauging station within a watershed, whereas soft
data are defined as information on individual processes within a balance
that may not been directly measured (i.e. ancillary data simulation from
other models, GIS-map inspection, regional statistics and literature in-
formation). For instance, Yen et al. (2014) used soft data of denitrifica-
tion rate from subsurface tile flow to constrain SWAT parameters
related to denitrification process in a little Eagle Creek watershed
(248 km2, United States). Vigiak et al. (2015) instead used soil loss
rates measured on runoff plots from literature to calibrate the gross ero-
sion in the Upper Danube (132,000 km2). To improve the robustness of
calibration process, Pagliero et al. (2014) developed a step-wise calibra-
tion approach for streamflow based on a limited group of independent
gauged subbasins (headwaters) considered more appropriate to repre-
sent the natural condition of subbasins. Selected parameters underpin-
ning each hydrological process were systematically calibrated and then
transferred to ungauged subbasins trough a regionalization technique.
This approach was successfully applied in large regions, i.e. Danube
(Pagliero et al., 2014), Scandinavia, Iberian Peninsula, Upper Danube
and Crete Island (Malagó et al., 2015; Malagó et al., 2016; Malagó et
al., in press) decreasing the computation time for calibration at the
large scale and gaining good knowledge and insights of each hydrolog-
ical process.
The objective of this study was to develop a robust strategy of model
calibration and validation, inspired by the efforts done in recent afore-
mentioned studies, that addresses gaps observed in the international
literature, and to apply the approach to the Danube River Basin,
analysing in depth the hydrology and nutrients balance of this large
transboundary basin. More specifically, this work aimed at (i) develop-
ing a robust modelling of water quantity and quality using both hard
and soft data for the entire Danube Basin (800,000 km2) using SWAT;
(ii) assessing current water and nutrient fluxes accounting for conserva-
tion measures including agricultural and water practices that are pres-
ent across the Basin and that were not considered in previous studies
(i.e. in Pagliero et al., 2014); (iii) providing long term mean annual
water and nutrients balances for effective water management; and
(iv) identifying hot spots of nitrate contamination that breach European
drinking-water standards.
We start with briefly describing the Danube River Basin, and then in-
troducing the structure, algorithms and set up of the SWAT model for
the whole Danube. Next, we focus on water quantity and quality model-
ling approach, and in particular on the innovative aspects of the calibra-
tion and validation methodology. Then, we present water and nutrients
fluxes across the Basin identifying regions and processes for which the
model provides robust assessment, or conversely, where further inves-
tigations are necessary. Finally, hot spots of nitrate concentration in riv-
ers are identified in the Basins and discussed.
2. Material and methods
2.1. The study area and data collection
The Danube River Basin is the second largest river basin in Europe,
covering approximately 800,000 km2 of Central and South-Eastern Eu-
rope. In 2015, 19 countries were sharing the catchment, 14 of which
are called ‘Danube countries’ (ICPDR, 2009).
Due to its vast area and its topography ranging from lowlands to
mountains above 3000 m a.s.l., the Danube River Basin exhibits a pro-
nounced climatic variability. The western region is influenced by the
Atlantic climate, whereas the eastern region is characterized by a conti-
nental climate leading to lower precipitation and typically colder win-
ters. The mean annual precipitation for the whole Danube basin was
597 mm/y for the period 1980 to 2009, ranging from 220 mm/y near
the outlet of the river to 1510 mm/y in the Alps. The mean annual tem-
perature for the period was 9.7 °C, ranging from 0.8 to 13 °C.
Dominant land cover types in the Basin are agriculture (42%) and
forest (35%) (Karabulut et al., 2016). The rest of the basin is either cov-
ered by grasslands and heathlands (16%), urban areas (5%) and water
bodies (b 2%) (EEA, 2013). The irrigated area is around 9000 km2
(only ~1% of arable land), and the volume of irrigation is approximately
3000·106 m3 (Portmann et al., 2008).
The Danube River can be divided into four general sections, the
Upper, Middle, Lower Danube, and Delta (Habersack et al., 2013). With-
in these sections 15 water management regions were identified (DPR,
1999; Vogel and Pall, 2002; ICPDR, 2009) (Fig. 1). Table 1 provides spe-
cific information for each region.
2.2. The SWAT model
The Soil and Water Assessment Tool (SWAT; Arnold et al., 1998) was
used to simulate water quantity and quality fluxes in the Danube Basin.
SWAT is a process based, semi-distributed, basin-scale model that has
been widely used in many large basins around the world (Gassman et
al., 2014). There were two main reasons for selecting the SWAT model
for this research: it has a flexible structure that allows addressing differ-
ent water resource and pollution problems; and it is well documented
 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218 199

Fig. 1. Location of the Danube River Basin in Europe (background map) with the monitoring points (MP) involved in this study, and the 15 ICPDR water management regions (insert): 1 =
Upper Danube; 2 = Inn; 3 = Austrian Danube; 4 = Morava; 5 = Vah-Hron-Ipel; 6 = Pannonian Danube; 7 = Drava; 8 = Sava; 9 = Tisa;10 = Middle Danube; 11 = Velika Morava; 12 =
Bulgarian Danube; 13 = Romanian Danube; 14 = Siret-Prut; 15 = Delta-Liman. The letters A–B–C indicate the location of three stations for which time-series of simulated discharge and
nutrients in the rivers are provided in Fig. 4.

and is an open source code that can be adapted to specific applications
(Gassman et al., 2007).
The model operates at daily time step and its major components in-
clude weather, soil, hydrology, plant growth, nutrient cycles, and land
management (Gassman et al., 2007; Arnold et al., 2012a). In SWAT, a
watershed is divided into subbasins, which are further subdivided into
hydrologic response units (HRUs) that consist of unique combinations
of soil, land use/cover, and slope. The SWAT model structure comprises
two phases: a land phase solved at HRU level, and a stream phase solved
at reach level (Neitsch et al., 2011). In the land phase, the HRU water,
sediment and nutrients cycles into soil, and losses are aggregated at
the subbasin level. The movement of water, sediments, and nutrients
through the stream network to the watershed outlet are instead simu-
lated in the routing (stream) phase.
Table 2 summarizes the main water and nutrient processes and the
corresponding SWAT algorithms used in this study. Sediment processes
are presented in a companion paper (Vigiak et al., 2017).
2.3. Model set up
The SWAT model mainly requires input data related to topography,
land use, soil, climate, and land management. The Danube Basin was di-
vided into 4663 subbasins based on the 100 m pixel size Digital Eleva-
tion Model CCM2 DEM (Vogt et al., 2007). The land use was defined
using a map of 1 × 1 km for year 2000, built from the combination of
CAPRI (Britz, 2004), SAGE (Monfreda et al., 2008), HYDE 3 (Klein
Goldewijk and van Drecht, 2006) and GLC (Bartholome and Belward,
2005) databases. Crops were attributed to arable land subbasins accord-
ing to European statistics at NUTS2 level (administrative subdivision)
(EUROSTAT, 2013). Soil information was based on the 1 × 1 km Harmo-
nized World Soil Database (HWSD) (FAO, 2008), using top soil layer
data. Based on the combination of landuse, soils and slope, the Danube
Basin was discretized into 5181 HRUs with a median area of 129 km2.
The nutrient emissions from point sources were retrieved from the
UWWTD database (ICM, 2011) aggregated at subbasin level. This data-
base reports the collected annual discharged nutrients loads from urban
waste water treatment plants for the period 2007–2008 for the EU
Member State. The aggregated values at subbasin level were kept con-
stant for the whole simulation.
The climate data, including daily precipitation, temperature, solar ra-
diation, wind speed and relative humidity, were obtained from EFAS-
METEO at spatial resolution of 5 km × 5 km (Ntegeka et al., 2013) for
the period 1990–2009. To account for the increase in precipitation
with elevation that is typically observed in mountainous regions, four
elevation bands were implemented.
Reservoirs and lakes exceeding 20 km2 (Lehner and Döll, 2004; Vogt
et al., 2007) and hydropower plants of large generation capacity
(N10 MW; ICPDR, 2013) installed on the main rivers were also included
in the model. The total extended area of these water bodies was around
2170 km2, b 1% of entire Basin, and their volumes were set according to
Lehner and Döll (2004) and Vogt et al. (2007).
In this study land management data included agricultural practices
that were not considered in previous studies. The main crop manage-
ment operations consist of planting, fertilization, irrigation, tillage and
harvesting. The timing of management operations was implemented
through daily heat unit method (Arnold et al., 1998). In this study the
heat units for each crop were calculated by Bouraoui and Aloe (2007).
The application rates of manure and mineral fertilization was retrieved
from the CAPRI model (Britz, 2004) for the year 2000 and kept constant
through the simulation.
Irrigated cropland areas were identified using the MIRCA database
(Portmann et al., 2008). About 9200 km2 of the Basin are irrigated (1%
of entire Danube Basin), corresponding to a total of 290 HRUs. The
 200
Table 1
Overview of the main characteristics of the 15 ICPDR water management regions of Danube Basin (ID: identification number of each region). The overview includes the model discretization in terms of Hydrological Response Units (HRUs), the geo-
graphic characteristics and the current management practices included in SWAT set-up of the Basin. The reported percentages for each region were calculated excluding upstream area.

ID Name SWAT Regional characteristics Current management practices

implementation

A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218

HRUs Area Drain Area Average Average Long mean annual Cropland Forest Pasture Artificial Irrigated Conservation Cover Residue Terraces Riparian
(km2) (km2) elevation (m) slope (%) precipitation (mm)a (%) (%) (%) Drainage land tillage crops Management (%) strips
(%) (%) (%) (%) (%) (%)

1 Upper Danube 343 50,617 50,617 566 8 950 44 37 18 8 0 11 4 2 29 0.4

2 Inn 157 25,999 25,999 1132 28 1200 8 51 41 2 0 3 1 0 43 1.1
3 Austrian 142 25,187 101,803 621 18 1000 19 53 28 4 1 4 5 0 31 0.8
Danube
4 Morava 191 26,628 26,628 347 7 540 73 13 13 7 1 32 7 3 17 0.0
5 Vah-Hron-Ipel 210 30,587 30,587 385 11 720 39 40 21 19 3 8 1 3 32 0.0
6 Pannonian 415 58,486 217,504 175 4 790 74 12 12 26 1 12 3 5 35 0.1
Danube
7 Drava 242 39,679 39,679 600 16 860 21 47 32 4 0 1 2 1 35 0.6
8 Sava 601 100,102 100,102 460 14 915 32 48 20 5 0 4 1 1 35 0.5
9 Tisa 958 149,567 149,567 303 9 590 50 33 16 18 1 7 2 3 29 0.1
10 Middle 215 37,255 544,106 247 8 600 47 27 27 16 0 12 1 3 30 0.4
Danube
11 Velika Morava 214 37,702 37,702 574 16 790 48 30 22 1 0 4 0 3 37 0.3
12 Bulgarian 272 46,307 721,734 307 9 570 65 16 19 3 1 36 0 1 23 0.7
Danube
13 Romanian 562 93,619 272 7 570 59 17 23 1 5 4 1 2 20 0.1
Danube
14 Siret-Prut 412 68,012 68,012 339 10 560 40 27 33 0 1 5 1 2 25 0.4
15 Delta-Liman 96 13,917 803,663 49 3 710 72 0 27 9 0 5 3 2 100 0.1
Danube15 5030 803,663 803,663 425 11 530 47 31 22 9 1 9 2 2 35 0.3
a
Source: ESAF-meteo database (Ntegeka et al., 2013) considering the whole drained area of each region.
 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218 201

Table 2
Main simulated processes and related algorithms implemented using SWAT in this study.

Component Process Algorithms Reference

Hydrology Surface runoff SCS Curve Number method USDA Soil Conservation Service (1972)
Hydrology Lateral flow Kinetic storage method Neitsch et al. (2011); Malagó et al. (in press)
Hydrology Baseflow Baseflow recession constant; groundwater storage; re-evaporation Neitsch et al. (2011)
Hydrology Potential Evapotranspiration Penman-Monteith Monteith (1965), Penman (1956)
Hydrology Channel routing Variable storage routing method Williams (1969); Neitsch et al. (2011)
Hydrology Tile drainage flow Houghoudt and Kirkham drainage equations and drainage volume Moriasi et al. (2007a, 2013a, 2013b)
converted in water table depth using a variable water table factor
Plant Biomass and crop yields EPIC model equations Williams et al. (1984)
Growth
Quality Nitrogen and phosphorus Loading function; equations from Epic model, PAPRAN mineralization Neitsch et al. (2011); McElroy et al. (1976);
cycle model Williams and Hann (1978); Van Keulen (1981)
Quality Nitrate movement and soluble Exponential decay weighting function for transport in aquifer Neitsch et al. (2011); Venetis (1969); Sangrey et al.
phosphorus movement (1984)
Quality In stream nutrient-processes QUAL2E model Brown and Barnwell (1987)
Quality Nutrients in water bodies Nitrogen and phosphorus mass balance Chapra (1997)
Quality Riparian filters Empirical equations based on runoff reduction () White and Arnold (2009); Neitsch et al. (2011)
Quality Nitrogen and phosphorus in Equations function of tile flow (m3/d), concentration in solution in the Neitsch et al. (2011); Moriasi et al. (2013b)
tile drainage system layer containing the tile drain and the percolation coefficient
Quality Nitrogen and phosphorus build up/wash off approach Huber and Dickinson (1988)
from urban areas

SWAT auto-irrigation option, whereby irrigation is applied when the
soil moisture content drops below a threshold value, was used. Conven-
tional tillage was implemented on HRUs with annual crops setting the
plowing depth at 25 cm with biological mixing efficiency of 0.85 and
harrowing at 7 cm, with mixing efficiency of 0.3.
Current extent of best management practices such as conservation
tillage, cover crops and residue management in the Basin was based
on Eurostat (2010) data. Based on this information, conservation tillage
is applied in about 77,470 km2 in the Basin corresponding to 289 HRUs
of annual crops. Conservation tillage consisted of harrowing at 7 cm
with biological mixing efficiency of 0.4 since biological mixing can be
significant in systems where the soil is less disturbed (Arnold et al.,
2012b; Lam et al., 2011).
Cover crops extended over an estimated area of 15,013 km2, while
residue management is used in 18,400 km2. Implementation in SWAT
was set according to Arabi et al. (2007). The fraction of terraced pasture
and permanent crop land was based on presence of stone walls per farm
holding (Eurostat, 2010) using an approach similar to that applied by
Panagos et al. (2015). The extent of terraces was estimated at about
2565 km2 and they were modelled following SWAT recommendations
(Neitsch et al., 2011).
Riparian land was estimated using pan-European maps (Clerici et al.,
2013; Weissteiner et al., 2013). Riparian filters were applied to agricul-
tural HRUs following the method of White and Arnold (2009), as de-
scribed in Vigiak et al. (2016).
According to the global artificially drained agricultural areas
map (Feick et al., 2005), about 65,000 km2 (8% of the Basin)
were identified as artificially drained. As a result, tile drainage was
applied in 470 HRUs of flat cropland with poorly or moderately well
drained soils.
The daily nitrogen atmospheric deposition is computed by SWAT in
each subbasin based on the daily precipitation amount and the average
nitrogen concentration in precipitation. This average nitrogen concen-
tration was set at 1.8 mg/L accordingly to the EMEP data for the period
1995–2005 (EMEP, 2001).
Finally, the initial concentration of nitrates in the shallow aquifer
was based on measurements in bore holes (EU, 2013). Nutrient concen-
trations in reservoirs were based on concentrations measured in gaug-
ing stations located immediately downstream.
The simulation period was 1995–2009 (15 years), in addition to
5 years of warm-up to initialize model variables and allow processes
to reach a dynamic equilibrium (Daggupati et al., 2015).
2.4. The calibration and validation of the model
In line with recent guidelines for water quantity and quality model-
ling (Arnold et al., 2015; Baffaut et al., 2015; Daggupati et al., 2015), a
systematic calibration and validation (C/V) approach is proposed and
applied in the Danube River Basin. It includes a robust and reproducible
C/V strategy using both hard and soft data. The proposed C/V strategy is
a sequential approach since each step is influenced by the previous one
(Malagó et al., 2015). It involves four modules: (i) module 1, “crop
yield”, that involves the calibration of annual crop yields; (ii) module
2, “hydrology”, that focuses on the calibration/validation of streamflow
(and its components) and the extrapolation of streamflow to ungauged
subbasins; (iii) the module 3, “sediment”, that consists of the calibra-
tion/validation of gross erosion and annual sediment concentrations;
and finally (iv) the module 4, “nutrients”, that consists of the calibration
of denitrification process in the soil and the calibration/validation of
monthly concentrations of nitrate-nitrogen (N-NO3), total nitrogen
(TN) and total phosphorus (TP).
Modules 1, 2 and 4 of the C/V are described in detail in this paper,
while the sediment module is described in Vigiak et al. (2017).
The parameters selected for the calibration of each module were
based on a literature search (i.e. van Grievensen et al., 2006; Santhi et
al., 2001; Grizzetti et al., 2015; Me et al., 2015; Haas et al., 2015; Yen
et al., 2014; Cerro et al., 2012; Omani et al., 2012; Chu et al., 2004), the
main processes involved and a preliminary global sensitivity analyses,
performed using Latin Hypercube (LH) sampling methods using the
SWAT-CUP program (Abbaspour, 2007).
2.4.1. Monitoring data
An extensive database of streamflow and nutrient concentrations
(mg/L) in the Danube River Basin was assembled from several sources
(Table 3) covering the period 1995–2009 (15 years).
The streamflow dataset involved 708 monitoring points. It was the
richest in terms of spatial and temporal extent, whereas the nutrients
datasets consisted of 416 monitoring points for N-NO3, 260 of TN and
409 of TP, albeit the data collected reported both mineral and organic
forms of nitrogen and phosphorus. The sampling frequency was usually
once a month, and sometimes samples in large river cross sections were
taken at three or more locations (i.e. on the left, in the middle or on the
right bank of the river). In these cases, the average concentration of all
samples was retained. In addition, an extensive data quality check of
202 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218

Table 3
Streamflow and nutrients data collected in the Danube Basin (# = number; Data type: Q = streamflow (m3/s), N-NO3 = nitrogen nitrates (mg/L); TN = total nitrogen (mg/L), TP = total
phosphorus (mg/L); MP = monitoring points).

Acronym Data provider and owner Data type Time step #MP #data entries Period
extent

ATR Austrian Environment Agency (http://www.umweltbundesamt.at) Q Daily 151 824,723 1995 2009
N-NO3 Daily 106 10,913 1995 2009
TP Daily 106 10,817 1995 2009
BAFU Swiss Federal Office for the Environment (http://www.bafu.admin.ch/hydrologie/index.html?lang=en) Q Daily 1 5479 1995 2009
CZR Czech Hydrometeorological Institute (http://hydro.chmi.cz/ismnozstvi/) Q Monthly 16 983 2004 2009
EWA http://www.ewa-online.eu/ Q Daily 25 135,297 1995 2009
HUWQ Hungarian General Directorate of Water Management (http://www.ovf.hu/en/) Q Daily 118 587,525 1995 2009
BME (http://www.vkkt.bme.hu/munkatars/?mid=10) N-NO3 Daily 183 43,173 1995 2009
TN Daily 149 17,415 1995 2009
TP Daily 182 41,317 1995 2009
ICPDR International Commission for the Protection of the Danube River (http://www.icpdr.org/wq-db/) Q Daily 5 11,689 1995 2009
N-NO3 Daily 2 498 1996 2009
TN Daily 2 272 2000 2009
TP Daily 2 370 1996 2009
JRC JRC (European Commission, Joint Research Centre) database Q Daily 112 531,012 1995 2009
N-NO3 Daily 57 9870 1996 2009
TN Daily 43 3434 1995 2009
TP Daily 51 7916 1996 2009
LFU Bavarian Environment Agency (http://www.lfu.bayern.de/index.htm) Q Daily 103 556,640 1995 2009
SAVA International Sava River Basin Commission (http://www.savacommission.org/) Q Daily 45 94,791 1995 2009
RSEPA Serbian Environmental Protection Agency (http://www.sepa.gov.rs/index.php) N-NO3 Daily 13 1897 1996 2009
TN Daily 13 484 2002 2009
TP Daily 13 1136 1996 2009
SIRET University of Suceava, Romania (Radoane et al., 2013) Q Daily 32 173,493 1995 2009
SK Slovak University of Technology in Bratislava Q Daily 62 318,696 1995 2009
N-NO3 Daily 55 6753 1995 2009
TN Daily 53 2711 1995 2009
TP Daily 55 6589 1995 2009
SLV Slovenian Environment Agency (http://vode.arso.gov.si/) Q Daily 38 192,329 1995 2009

these measurements was performed to remove unrealistic values (due
to typing errors for instance) and correct for heterogeneous units. We
use the statistical software R (R Development Core Team, 2008) for cal-
culating the main descriptive statistics (25th and 75th percentiles, me-
dian and mean) for each variable and for automatically generating plots
of the time series of total nitrogen and nitrogen-nitrate (N-NO3), as well
as total phosphorus and phosphates (P-PO4) for each station. Using both
the descriptive statistics and the plots we identified the stations with in-
consistent observed nutrients values (i.e. anomalies in the units of mea-
surement and conversions). A manual correction of the anomalies was
then applied for each of the selected stations. Finally, the descriptive sta-
tistics and plots were regenerated to check the consistency of the
datasets.
Concentration at the Danube outlet was calculated as the average
concentration monitored in the three main arms of the Delta. Given
the heterogeneous spatial distribution of nutrient observations in the
Basin, the whole dataset of nutrient concentrations was used for calibra-
tion, whereas monthly loads were employed in the final evaluation of
the model. The loads were calculated using nutrients concentrations
and daily streamflow based on the flow weighted concentrations meth-
od proposed by Moatar and Meybeck (2005).
2.4.2. Crop yields calibration
SWAT simulated mean annual crop yields were compared with
those reported by EUROSTAT (EUROSTAT, 2013) for each Danube Coun-
try. To perform the comparison, the predicted crop yield was converted
to fresh weight yield by using a conversion table from the EPIC model
(Williams et al., 1984). The calibration was performed manually chang-
ing the crop harvest index (HVSTI), the optimal and minimum temper-
ature plant growth (T_OPT, T_BASE) (Table 4). The visual appraisal of
calibrated and simulated annual crop yields was used as criterion to de-
fine the near optimal parameter values.
2.4.3. Streamflow calibration and validation
The calibration of streamflow and its components was performed
using a step-wise approach that consists of a multi-variables
calibration of headwater subbasins and a regionalization of the calibrat-
ed parameters (Pagliero et al., 2014; Malagó et al., 2015; Malagó et al., in
press). The calibration of streamflow and its components focuses on a
limited group of independent gauged headwaters subbasins, since
they are more likely to represent natural hydrological behaviour
(Gudmundsson et al., 2012) and their streamflow components are
more representative than larger basins where streamflow is often influ-
enced by human activities (Döll et al., 2008).
The dataset of daily streamflow gauging stations was thus divided
into a calibration dataset and a validation dataset with different spatial
and temporal distribution: 264 stations with daily values for the period
1995–2006 were used for model calibration, while the validation
dataset comprised the remaining 444 stations for 1995–2009 plus the
264 calibration stations for the period 2007–2009.
The daily streamflow of the 264 headwater calibration subbasins
was divided into its main components (surface runoff SR, lateral flow
LF, and baseflow BF) using the SWAT filter (Lyne and Hollink, 1979).
The filter was applied twice, first it was applied to daily streamflow to
separate baseflow from quick flow, and then to the quick flow to sepa-
rate lateral flow from surface runoff. The streamflow components were
calibrated separately using the software SWAT-CUP and SUFI-2 method
(Abbaspour, 2007) in four sequential steps that focused on different hy-
drological processes: snow processes, surface runoff, lateral flow, and
baseflow. A fifth final step was also performed by calibrating all hydro-
logical parameters together using reduced ranges to account for any co-
variance of parameters belonging to different hydrological groups
(Malagó et al., in press).
The final sets of calibrated parameters of subbasins that reached
“acceptable performance” (Moriasi et al., 2007b) were transferred to
ungauged subbasins using a regionalization technique coupled with a
 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218 203

Table 4
Parameters involved in the calibration with their range before and after calibration. The values in the bracket represent the average of calibrated values. For each parameter the related
SWAT input file, the method of calibration (M = manual; SA = semi-automatic calibration using SUFI-2), and type of data used for calibration are reported.

Module Process Parameter and input Definition Unit Range Calibrated Range Data used in Calibration
file (average value) calibration method

Crop Plant growth HVSTI.crop Crop harvest index for optimal growing NA 0.02–2 0.04–2.5 (0.68) EUROSTAT M
yields conditions (2013)
o
Plant growth T_OPT.crop Optimal temperature for plant growth C 12.5–30 12.5–30 (22.6) EUROSTAT M
(2013)
o
Plant growth T_BASE.crop Minimum/base temperature for plant C 0–12 0 EUROSTAT M
growth (2013)
Water Baseflow ALPHA_BF.gw Baseflow alpha factor d 0–1 0.26–0.98 (0.73) Monthly SA
streamflow
Surface runoff CN2.mgt1 SCS runoff curve number for moisture NA −15–+15 e −15–+15 (10) Daily surface SA
condition II runoff
Surface runoff CH_N1.sub Manning's value for tributary channel NA 0.025 - 0.30 0.01–0.14 Daily surface SA
(0.096) runoff
Tile drainage flow DDRAIN.mgt1a Depth to subsurface tile mm 0–2000 300–900 (687) Monthly SA
streamflow
Tile drainage flow DEP_IMP.hrua Depth to impervious layer mm 0–6000 1050–6000 Monthly SA
(3100) streamflow
Lateral flow EPCO.hru Plant evaporation compensation factor NA 0.01–1 0.01–0.94 (0.44) Daily lateral SA
flow
Lateral flow ESCO.hru Soil evaporation compensation factor NA 0.01–1 0.03–0.99 (0.57) Daily lateral SA
flow
Tile drainage flow GDRAIN.mgt1a Drainage lag time hr 0–100 1–40 (20) Monthly SA
streamflow
Baseflow GW_DELAY.gw Groundwater delay d 0–500 0.75–498 (41) Monthly SA
streamflow
Baseflow GWQMN.gw Threshold depth of water in the shallow mm 0–1000 5.5–991 (618) Monthly SA
aquifer required for return flow to occur streamflow
Baseflow GW_REVAP.gw Groundwater ‘revap’ coefficient NA 0.02–2 0.02–0.19 (0.06) Monthly SA
streamflow
Snow proecess PLAPS.sub Precipitation laps rate mm/km 0–100 0.97–64.7 (24) Monthly SA
streamflow
Baseflow RCHRG_DP.gw Groundwater recharge to deep aquifer fr 0–1 0.005–0.93 Monthly SA
(0.09) streamflow
Baseflow REVAPMN.gw Threshold depth of water in the shallow mm 0–500 0.25–443 (196) Monthly SA
aquifer for revap to occur streamflow
o
Snow melt SFTMP.sno Snowfall temperature C −5–+5 −1.57–1.11 Monthly SA
(−0.84) streamflow
Snow melt SMFMN.sno Melt rate for snow on Dec 21 mm H2O 0–10 0.09–9.66 (5.10) Daily SA
°C− 1 d−1 streamflow
Snow melt SMFMX.sno Melt rate for snow on Jun 21 mm H2O 0–10 0.01–9.97 (4.36) Daily SA
°C− 1 d−1 streamflow
o
Snow melt SMTMP.sno Snowmelt base temperature C −5–+5 −0.17–2.53 Monthly SA
(0.60) streamflow
Lateral SOL_AWC.sol Available water capacity of the soil layer fr −25–+25 −25–+25 (10) Daily lateral SA
flow/Infiltration flow
Lateral SOL_K.sol Saturated hydraulic conductivity mm h−1 −25–+25 −25–+25 (16) Daily lateral SA
flow/Infiltration flow
Snow melt TIMP.sno Snow pack temperature lag factor 0.01–1 0.01–0.55 (0.18) Monthly SA
streamflow
Snow melt TLAPS.sub Temperature laps rate °C/km −10–0 −9.82 to −1.83 Monthly SA
(−5.37) streamflow
Tile drainage flow RE.hru/.sdr Effective radius of drains mm 5d–100 5–100 (52) Monthly SA
streamflow
Tile drainage flow SDRAIN.hru/.sdr Distance between two drain or tile tubes mm 7600–30,000 5060–27,700 Monthly SA
(16020) streamflow
Tile drainage flow DDRAIN_CO.hru/.sdr Drainage coefficient mm/day 10–51 6–50 (24) Monthly SA
streamflow
Tile drainage flow LATKSATF.hru/.sdr Multiplication factor to determine lateral NA 0.01–4 0.09–3.4 (1.22) Monthly SA
ksat from SWAT ksat input value streamflow
Nutrients Denitrification CDN.bsn Denitrification exponential rate NA 0–3 2.5 Velthof et al. M/SA
coefficient (2009)
Mineralization CMN.bsn Rate factor for humus mineralization of NA 0.0001–0.0003 0.000145 Monthly M/SA
active organic nitrogen concentration
Transport of ERORGN.hru Organic nitrogen enrichment ratio NA 0–5 0.05–4.5 (0.7) Monthly M/SA
nitrogen with concentration
sediment
Shallow aquifer HLIFE_NGW.gw Half-life of nitrate–nitrogen in the day−1 0–200 0–200 (116) Monthly M/SA
nitrates shallow aquifer concentration
Nitrogen NPERCO.bsn Nitrogen percolation coefficient NA 0–1 0.5 Monthly M/SA
percolation concentration
Nitrogen settling NSETLR1.lwq = Nitrogen settling rate m/year 1 - 150c 5.5–150 (30) Monthly M/SA
rate NSETLR2.lwqb concentration
Nitrogen uptake N_UPDIS.bsn Nitrogen uptake distribution parameter NA 1–31 28 Monthly M/SA
concentration

(continued on next page)

204 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218
Table 4 (continued)
Module Process Parameter and input Definition
file
Residue RSDCO.bsn Residue decomposition coefficient
Denitrification SDNCO.bsn Denitrification threshold water content
Transport of ERORGP.hru Organic phosphorus enrichment ratio
phosphorus with
sediment
Phosphorus settling PSETLR1.lwq = Phosphorus settling rate
rate PSETLR2.lwqb
a
Only in tile drained HRUs
b
The nitrogen and phosphorus settling rate didn't change during the year.
c
The range of settling rate of nutrients in reservoirs was set larger that the default accordingly with Panuska and Robertson (1999).
d
The lower limit of the RE was set to 5 mm to investigate all the possible range of values
e
CN2 was set to 30 in the HRUs with tile drain systems
classification procedure based on hydrologic similarity. The method is
described in detail in Malagó et al. (in press).
2.4.4. Nutrient calibration and evaluation
The calibration of sediments (Vigiak et al., 2017) was followed by the
calibration of nutrients which was based on concentrations rather than
loads (usually performed in other studies) to avoid uncertainty issues
related to loads estimation.
The mean soil denitrification (kg/ha/year) was calibrated for the
whole Basin. In this study the annual denitrification was constrained
using data obtained from the integrated assessment tool MITERRA-EU-
ROPE (Velthof et al., 2009; Oenema et al., 2007). The parameters CDN
(denitrification exponential coefficient) and SDNCO (denitrification
threshold water content, or the fraction of field capacity water content
above which denitrification is assumed to occur) were calibrated man-
ually to fit the MITERRA-EUROPE values.
TN and TP concentrations were calibrated adjusting the selected pa-
rameters reported in Table 4. The parameters were selected based on a
global sensitivity analysis that comprised parameters reported in litera-
ture (i.e. Arnold et al., 2012b; Me et al., 2015; Haas et al., 2015; Yen et al.,
2014; Cerro et al., 2012; Omani et al., 2012; Chu et al., 2004). Parameters
were sampled in a Latin hypercube sampling scheme of 1000 model
runs. The objective function was the root mean square error of the sim-
ulations divided by the standard deviation of the observations (RSR;
Moriasi et al., 2007b). The global parameter sensitivity was measured
by the value of the t-test (and associated probability level p-value) of
the regression coefficient of each parameter against the objective func-
tion, as well as using the visual appraisal of dot-plots (parameter values
vs RSR). The analysis was conducted for each water management re-
gion, where most data was available, i.e. Austrian Danube, Morava,
Vah-Hron-Ipel, Pannonian Danube, Drava, Sava and Tisa.
2.5. Assessment of model performance and analysis
To assess the model performances, for calibration and validation pe-
riods, both statistical and graphical techniques were used. The percent
bias (PBIAS) was used as performance measure with reference to its cor-
responding class of performance (“very good”, “good”, “satisfactory”
and “unsatisfactory”) based on recommendations of Moriasi et al.
(2007b). The PBIAS measures the tendency of the simulated data to be
higher or lower than the observations. Values close to 0 indicates a
lack of bias (neither underestimation nor overestimation). Positive
and negative values indicate an overestimation and underestimation
of the simulated data, respectively. In this study PBIAS values in the
range of ±25% for monthly streamflow and ±70% for monthly nutrient
concentrations and loads were considered acceptable (Moriasi et al.,
2007b). However, each class of performance was evaluated. The percent
bias was calculated using the R package “hydroGOF” (Zambrano-
Bigiarini, 2013).
Unit Range Calibrated Range Data used in Calibration
(average value) calibration method
NA 0.02–1 0.02 Monthly M/SA
concentration
NA 0–1 1 Velthof et al. M/SA
(2009)
NA 0–5 0–0.25 (0.1) Monthly M/SA
concentration
m/year 1–150c 9.5–150 (57) Monthly M/SA
concentration
Box and whisker plots, visual appraisal of time-series, and residuals
analysis (observation -simulation) for each water management region
were also performed (Harmel et al., 2014; Bieger et al., 2012). In addi-
tion, the simulated loads were assessed also considering the specific
loads (total loads divided by total drained area, ton/km2/y).
3. Results and discussion
3.1. Calibration and validation of the model
3.1.1. Crop yields
As a result of the calibration, the default base growth temperature of
each crop (T_BASE) was set to the minimum value. The optimal growth
temperature (T_OPT) was kept as default except for apple for which it
was decreased from 20 °C to 18 °C. The harvest index (HVSTI) was
also adjusted to match better the observed yields: it was increased for
permanent crops (apple and vineyard), corn silage, durum and spring
wheat, green beans, oats, sugar beet, sorghum hay and sunflower,
while it was decreased for barley and potatoes.
The comparison between the mean annual observed and simulated
crop yields for the period 1995–2009 is shown in Fig. 2. The predicted
mean annual crop yields compared well with the reported values, ex-
cept for corn silage and sugar beet for which a slight underestimation
can be noticed.
The annual variability of yields of dominant crops corn and spring
wheat was well captured in all countries across the Danube, except in
Austria (10% of the Basin), Ukraine (4% of the Basin), Slovenia (2% of
the Basin) and Moldova (2% of the Basin) probably due to the
misrepresenting of agricultural practices.
However, in the light of the simplification applied in the model setup
and the data available, the crop yield calibration was considered
satisfactory.
3.1.2. Calibration and validation of streamflow
For the calibration of streamflow 26 parameters were independently
changed at 264 gauged stations following the step-wise approach. Pa-
rameter sets of these stations were transposed in the different hydro-
logical regions. Four hydrological regions were defined based on
hydrological similarity (Malagó et al., 2015). In particular, the timing
of peak flow was adjusted changing the snow parameters: the mean
value of snowfall and snow melt temperature were set to − 0.84 °C
and 0.60 °C, respectively; the decrease of temperature with elevation
was estimated to be − 5.37 °C/km on average in the Basin. The snow
melt rates (SMFMN and SMFMX) were both 5 mm H2O/day °C on aver-
age. The calibration of surface runoff resulted in an increase of the curve
number (CN2) by about 10%, (except for artificially tile drained subba-
sins), and in a decrease of the Manning's value for tributary channel of
0.096 on average in the whole Danube. The lateral flow calibration
was particularly sensitive to the soil available water content
 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218 205

an increase of errors with the drainage area (see Supplementary mate-

rial for graphical details, Fig. S3). Visual appraisal of monthly streamflow
confirmed that monthly variations were well captured (see Supplemen-
tary material, Fig. S3).

3.1.3. Nitrate-nitrogen calibration and evaluation

Fig. 2. Box-and-whisker plots of SWAT annual crop yields of 20 simulated crops in the
Danube River Basin. Crops order (left to right) is based on decreasing land extent in the
Basin. Mean crop yield for 1995–2009 as observed (triangles) and simulated (circles)
are reported. (CORN: corn; SWHT: Spring Wheat; SGHY: Sorghum Hay; BARL: Spring
Barley; SUNF: Sunflower; CSIL: Corn Silage; CRRT: Carrot; POTA: Potato; OATS: Oats;
SGBT: Sugar Beet; SOYB: Soybean; GRBN: Green Beans; RYE: Rye; GRAP: Vineyard;
TOMA: Tomato; DWHT: Durum Wheat).
(SOL_AWC) and saturated hydraulic conductivity (SOL_K). Specifically,
across the Danube Basin the SOL_AWC was increased by 10% on aver-
age, while the hydraulic conductivity by 16%. The aquifer percolation co-
efficient (RCHRG_DP) and the baseflow recession factor (ALPHA_BF)
strongly influenced baseflow calculations across the Basin and their
values changed substantially from the Upper to the Lower Danube. In
the artificially tile drained subbasins, the depth of the impervious
layer (DEP_IMP) was very sensitive and resulted 3100 mm on average,
the depth of the subsurface tile (DDRAIN) resulted 690 mm, and the cal-
ibrated drainage lag time (GDRAIN) was 20 h on average in the whole
Danube. The range of variation of all calibrated parameters is reported
in Table 4.
Based on this final parametrization, the performance of SWAT model
in simulating streamflow resulted satisfactory both for calibration and
validation (Table 5). Specifically, the PBIAS% was acceptable
(PBIAS ≤ ±25%) for 70% and 61% of gauging stations in calibration and
validation, respectively, resulting good to very good for 48% and 44%
in the two datasets. The Interquartile Range (IQR) of monthly
streamflow showed good agreement between SWAT simulations and
observations (Table 6). The distribution of residuals (observations-sim-
ulations) was centred on zero and the IQR of residuals was [− 1.09;
5.05] m3/s in calibration and [− 2.64; 94.36] m3/s in validation with
The calibration of the nitrogen transformation processes resulted in
a nitrogen percolation coefficient (NPERCO) of 0.5, a denitrification ex-
ponential rate coefficient (CDN) of 2.5 and a denitrification threshold
water content (SDNCO) of 1 (Table 4). The half-life parameter of nitrate
in the shallow aquifer (HLIFE_NGW) was calibrated in each subbasin
with values in the range 0–200 day−1, resulting in 116 day−1 (mean
value) for the entire Danube. The initial nitrate concentration in the
shallow aquifer was increased by about 10% in all subbasins.
The mean annual denitrification was thus estimated for the whole
Basin around 19 kg/ha (Fig. 3), very close to the median value of
21 kg/ha obtained from the MITERRA-EUROPE results (Velthof et al.,
2009; Oenema et al., 2007). The denitrification decreased from Upper
to Lower Danube reflecting the distribution of precipitation since
lower precipitation leads to less soil saturation and thus less denitrifica-
tion. The highest values of mean annual denitrification were observed in
the Upper Danube (23 kg/ha), in the Morava (20 kg/ha) and in the
Pannonian Danube (21 kg/ha), whereas the lowest values were general-
ly simulated in the lower Danube, in particular in the Romanian Danube,
Siret Prut and Delta Liman.
The soft calibration of denitrification led to satisfactory predictions
of N-NO3 monthly concentration in 66% of gauging stations in the cali-
bration dataset (Table 5). Mean SWAT N-NO3 concentration was
2.56 mg/L, which compares well with the observed mean of 2.02 mg/L
(Table 6). The distribution of residuals was centred on zero with IQR
of [− 0.71; 3.05] mg/L. Yet, the highest model residuals occurred at
sites with smaller drainage areas, which are strongly affected by land
management. Residuals decreased with increasing drainage area, since
large basins better represent the “average” land management assumed
in the model.
Better performances were obtained in the evaluation dataset. The
PBIAS% calculated between the observed and simulated monthly loads
ranked from satisfactory to very good for about 73% of total gauging sta-
tions (Table 5). The IQR of simulated monthly loads [10.4; 1177] ton/
month were comparable to that calculated [5.24; 11,060] ton/month, al-
beit the 50th percentile was lower (27.6 ton/month) than that of obser-
vations (49.33 ton/month). The median value of monthly loads
residuals was 5.4 ton/month, i.e. about 10% of median observation

Table 5
Overview of calibration, validation, and evaluation datasets with percentage (%) of gauging stations that performed according to Moriasi et al. (2007b) PBIAS model performance classes.
The symbol # represents the number of gauging stations.

Dataseta Data Type # gauging stations # data entries (period) PBIAS performance class

Very good Good Satisfactory Unsatisfactory

(% of gauging stations)

C Q (m3/s) 264 37,074 36 12 22 30

(1995–2006)
V 708 126,375 33 11 17 39
(1995–2009)
C N-NO3 (mg/L) 340 36,120 23 17 26 34
(1995–2009)
E N-NO3 (ton/month) 202 21,666 26 15 33 27
(1995–2009)
C TN (mg/L) 191 34,380 38 12 24 27
(1995–2009)
E TN (ton/month) 121 5825 35 11 26 28
(1995–2009)
C TP (mg/L) 333 59,940 25 11 12 52
(1995–2009)
E TP (ton/month) 202 21,094 22 16 22 41
(1995–2009)
a
C = calibration; V = Validation; E = evaluation.
206 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218

Table 6
Overview of the main statistics of observed, simulated (SWAT) and residuals of monthly streamflow (m3/s), concentrations (mg/L) and loads (ton/month) of nutrients in each dataset.

Dataseta Data type # data entries Percentiles Mean

25th 50th 75th 95th

C Q (m3/s) 37,074 Observed 1.35 2.92 6.19 18.01 5.38

SWAT 1.02 2.88 6.41 19.05 5.41
Residuals −1.09 0.13 1.15 5.05 −0.02
V Q (m3/s) 126,375 Observed 2.3 7.58 36.84 1059.84 198.54
SWAT 2.18 8.08 38.38 912.53 190.21
Residuals −2.64 0.16 3.73 94.36 8.32
C N-NO3 (mg/L) 36,120 Observed 0.93 1.6 2.59 4.99 2.02
SWAT 0.65 1.26 2.43 10.39 2.56
Residuals −0.71 0.15 1.09 3.05 −0.38
E N-NO3 (ton/month) 21,666 Observed 11.3 49.33 354.6 11,773 1745
SWAT 5.24 27.61 255.10 11,060 1858
Residuals −11.8 5.4 54.89 1348 −61
C TN (mg/L) 34,380 Observed 1.77 2.62 3.93 10.60 3.72
SWAT 1.29 2.39 3.86 14.6 3.91
Residuals −1.20 0.02 1.28 5.94 −0.48
E TN (ton/month) 5825 Observed 19.0 134 1157 19,133 3144
SWAT 6.2 48 534 17,051 2436
Residuals −80 3.10 87 2482 −9.05
C TP (mg/L) 59,940 Observed 0.04 0.11 0.23 0.99 0.24
SWAT 0.04 0.10 0.23 1.09 0.25
Residuals −0.07 −0.009 0.06 0.66 0.002
E TP (ton/month) 21,094 Observed 0.57 2.87 24.67 734 123
SWAT 0.43 2.64 26.08 581 109
Residuals −3.04 −0.03 1.97 161 23.41
a
C = calibration, V = Validation; E = evaluation

(Table 6). These deviations may partially be explained by the uncertain-
ty related to the calculation of loads (Lloyd et al., 2016).
Simulated and observed monthly concentrations and loads for a
sample of stations are shown in Fig. 4 (see also the Supplementary
material).
3.1.4. Total nitrogen calibration and evaluation
TN concentrations were calibrated in 191 gauging stations changing
seven sensitive parameters (Table 4). First, the mineralization process
was adjusted reducing the default values of the rate factor of humus
mineralization of active organic nitrogen (CMN) to 0.000145 and the
rate coefficient for mineralization of the residue fresh organic nutrients
(RSDCO) to 0.2 in order to slow down the simulated kinetics; the
N_UPDIS was increased from the default value (20) to 28 for better con-
trolling the depth distribution of nitrogen uptake and thus the maxi-
mum amount of nitrate removed from the upper layers, as pointed
out in Haas et al. (2015). The enrichment ratio of organic nitrogen
(ERORGN) had a large impact on TN concentration and the median cal-
ibrated value was 0.7 for the whole Danube. The nitrogen settling rates
in reservoirs were kept constant during the year and their range was set
larger than the default values according to Panuska and Robertson
(1999), as for instance in the Sava River Basin, to better simulate the sig-
nificant retention of largest wetlands not implemented in SWAT (i.e.
two Ramsar sites, three important bird areas and the alluvial wetlands
in the Spacva –Bosut depression; Schneider-Jacoby, 2005).
As a result, the simulation of monthly TN concentration was satisfac-
tory to very good for 74% of total gauging stations (Table 5). The IQR,
median and mean of TN simulated concentrations were comparable to
observed statistics (Table 6). The residuals were centred on zero, with
median value of 0.02 mg/L and IQR of [− 1.20; 5.94] mg/L. However,
as for N-NO3 case, residuals tended to decrease with increasing drainage
area.
The monthly TN loads were satisfactory to very good for about 72%
of gauging stations. The IQR of observed and simulated loads were com-
parable, albeit the median and mean differed slightly (Table 6), with
SWAT simulations being lower than observed loads (Table 6). The dis-
tribution of residuals was centred on zero with median value of 3.1
ton/month and IQR of [−80; +87] ton/month.
Simulated and observed monthly TN concentration and loads are
shown in Fig. 4 for a subset of stations: the Drava at Dravaszabolcs,
Sava at Sremska Mitrovika and for the Danube Delta (see also the Sup-
plementary material for other graphical comparisons).

3.1.5. Total phosphorus calibration and evaluation

Fig. 3. Box and whisker plots of mean annual denitrification (kg/ha) simulated in the
period 1995–2009 in each ICPDR water management region. The grey dotted line
indicates mean annual denitrification simulated in the whole Basin; the grey continuous
lines indicate the 25th and 75th percentile of denitrification reported in literature
(Velthof et al., 2009).
Monthly TP concentrations were calibrated adjusting the organic
phosphorus enrichment ratio and the phosphorus settling rate in the
reservoirs. The median value of these parameters was respectively of
0.1 and 57 m/year in the whole Danube.
TP simulation was satisfactory simulated up to very good for about
48% of calibrated gauging stations. The IQR of observed and simulated
concentrations overlapped, with median of residuals well centred on
zero (Table 6). These findings were confirmed in the evaluation, with
about 60% of 202 the monitored stations reaching satisfactory results.
The highest percentage of unsatisfactory performance for TP in the
calibration dataset likely reflects the difficulty of SWAT of reproducing
high peak concentrations in events (Chu et al., 2004), which in turns
may lead to errors in sediment flux estimates and particulate P (e.g.
Me et al., 2015). The lower performance in simulating TP concentration
 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218 207

Fig. 4. Monthly time series of streamflow (Q), nitrogen nitrate (N-NO3), total nitrogen (TN) and phosphorus (TP) concentrations and monthly loads observed (black line) and simulated by
SWAT (grey line) at selected gauging stations across the Danube River Basin. The numbers in the title indicate the ICPDR water management region as reported in Table 1, whereas the
letters identify their location in Fig. 1. Graphs for all water management regions in the Danube Basin are reported in the supplementary materials (Fig. S8–S14).

may be linked to the local errors in simulating sediment fluxes as also
observed in Vigiak et al. (2017).
3.2. Analysis of the water and nutrients fluxes per water management
region
The mean observed average discharge of the Danube reaches ap-
proximately 2000 m3/s at the gauge Bratislava, 5500 m3/s at the gauge
Iron Gate, and 6500 m3/s at the Danube Delta at the Black Sea. The
main tributaries with the highest mean annual runoff are the rivers
Inn in the Upper Danube section, and Sava and Tisa in the Middle
Danube, leading to a significant increase of the mean annual streamflow
of the Danube at their confluences. The analysis of residuals (observed-
simulated) for each water management region allowed the identifica-
tion of local errors across the Danube. Streamflow residuals increased
with drainage area, with the highest residuals observed in the Middle
Danube, Bulgarian Danube and Delta-Liman (Fig. 5a and b).
Observed monthly N-NO3 concentrations did not vary considerably
between management regions (Fig. 5c). The long term average N-NO3
concentrations in the period 1995–2009 reached the highest values in
the Morava River Basin (mean value around 3 mg/L) and Pannonian
Danube region (mean value 2.8 mg/L). N-NO3 is the main component
of TN (about 70% of TN) and both N-NO3 and TN concentrations de-
crease with increasing river size. The largest IQR was predicted in the
Morava and Pannonian Danube, with average values typically observed
for intensively agricultural watersheds, while in the Danube Source and
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 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218
Inn River Basin the concentrations were lower. N-NO3 concentrations
were generally well captured in all water management regions, albeit
overestimations were observed in Morava, Pannonian, Middle Danube,
Siret Prut and Delta (Fig. 5d), whereas underestimations were detected
in the Austrian Danube, Vah-Hron-Ipel and Romanian Danube. Further-
more, SWAT could not simulate accurately the seasonal variation of N-
NO3 in the Inn River Basin, in the Upper Danube, and in the area be-
tween the Middle Danube and Delta-Liman. These findings highlighted
the need to improve the spatial representation of denitrification in large
river basins where its reliability is limited by setting the parameters at
watershed level. In fact, in the Upper Danube soil denitrification result-
ed excessive and the simulation of N-NO3 could be improved by de-
creasing the watershed parameter CDN from 2.5 to 0.6, whereas in the
Middle and Lower Danube soil denitrification CDN could be increased
to 3 (see VII section of the Supplementary material and Fig. S19). Fur-
thermore, the in-stream denitrification process is not simulated by
SWAT, limiting the accuracy of prediction. However, nitrate concentra-
tions were well captured in Drava, Prut and Siret River Basins.
Observed TN concentrations were the highest in the Morava and
Pannonian Danube, with median value of 3.20 and 2.38 mg/L, respec-
tively. At the Delta-Liman the long term average of TN concentration
was 2.3 mg/L. In the Upper Danube regional differences were noticeable,
with lowest TN concentrations observed in the Inn region whereas in
the Upper Danube and in the Morava they were among the highest of
the Basin (Fig. 5e). Conversely, TN varied little in the Lower Danube
(from Middle to Delta-Liman). SWAT model was able to capture well
these differences (Fig. 5f), albeit underestimations were observed in
regions with limited data (i.e. Morava). However, TN concentrations at
the outlets of the water management regions were all satisfactory (see
Supplementary material).
Conversely to N-NO3 and TN, TP concentrations differed between
water management regions, with highest values in predominantly
agricultural regions, i.e. in Morava, Vah-Hron-Ipel, Pannonian
Danube and Tisa (Table 1, Fig. 5g). The residuals were centred on
zero in all water management regions except in the Romanian
Danube, in which the median value of observed TP was similar to
Tisa, and in Pannonian Danube region where underestimations
were more frequent. Here the particulate P seems to be an important
component of the TP that is moved with sediments to river network
(Vigiak et al., 2017).
The observed specific loads (loads divided by drainage area), of
N-NO3 and TN vary considerably between the Upper Danube and
other regions. Higher N-NO3 specific loads are observed in the Upper
Danube and Austrian Danube (median value of 1 kg/ha/month and 0.6
kg/ha/month respectively), whereas in the other regions the median
value is approximately 0.25 kg/ha/month (Fig. 6a). Fig. 6b clearly
shows underestimations of specific loads in the Upper Danube and Aus-
trian Danube, and slight overestimations in the Middle and Bulgarian
Danube, as well as in the Danube Delta-Liman. In all other regions, the
residuals were centred on zero.
The highest TN specific loads were observed in the Upper
Danube and Austrian Danube with respectively median value of
2.4 kg/ha/month and 0.1 kg/ha/month, whereas the lowest values
were in the Morava, Middle Danube and Siret-Prut regions. In the other
regions, the median value was in the range of [0.3; 0.6] kg/ha/month.
This variability was well captured by SWAT since the residuals were
centred on zero in all water management regions (Fig. 6c and d), except
in the Upper Danube and Inn where the specific loads were respectively
underestimated and overestimated.
The TP specific loads were less variable than TN albeit high
values were observed in the Sava River Basin (median value of about
0.3 kg/ha/month). The SWAT simulations matched well the
Fig. 5. Left: distribution of observed values of streamflow and nutrients concentrations in each water management region. Right: SWAT simulations of residuals (observed–simulation).
The grey continuous lines indicate the median value of the whole dataset, the grey dotted lines indicate the interquartile range. The numbers of data entries are reported above each box
plot.
209
observations and the residuals were all centred on zero (Fig. 6e and f).
Yet, in the Pannonian region the underestimations of specific loads
were more frequent as seen also for concentrations.
3.3. Analysis of the water and nutrients fluxes along the Danube River
Fig. 7 shows the river Danube longitudinal profile of long term aver-
age monthly streamflow and in stream nutrients concentrations togeth-
er with the observations. The observations are represented using
bubbles with size proportional to the number of total observations in
the simulated period (1995–2009), thus larger the bubble, the more ob-
servations were available for that station.
The monthly streamflow of the Danube River was well simulated,
and in particular the sudden changes in correspondence with the con-
fluence of Inn, Sava and Tisa tributaries were well captured (Fig. 7a).
The SWAT predicted that N-NO3 concentrations decreased stepwise
following the streamflow increase, while the observations are quite
constant from the confluence with the Inn and Tisa Rivers with long
term mean value of about 2 mg/L. Between the confluence of Inn and
the Morava Rivers, the SWAT N-NO3 concentrations were generally
below the observations, while they were above after the confluence
with the Tisa (Fig. 7b). These results confirmed that SWAT could not
capture soil denitrification across the Basin. The inadequacy of the
SWAT model to simulate the spatial distribution of soil denitrification
was also recently pointed out in Epelde et al. (2016).
TN and TP concentrations were close to the observations albeit TP
observations were at times inconsistent along the profile (Fig. 7c and
d). TN concentrations slightly decreased stepwise following the
streamflow increase from the confluence with the Inn River (3 mg/L)
up to the Delta (2.3 mg/L). Before the Inn confluence the simulated TN
concentrations reached the highest values, but the lack of data
prevented the comparison with the observations. The simulated TP con-
centrations slightly increased after the confluence with the Inn River up
to the Drava tributary and then remained constant at 0.12 mg/L. TP con-
centrations usually agreed well with the observations, although obser-
vations appeared to be more variable than SWAT simulations along
the profile. However, we must point out that the simulated TP concen-
trations appeared not to be impacted by the Iron Gates reservoirs as re-
ported in other studies (ICPDR, 2004; Van Gils and Bendow, 2000).
3.4. The water and nutrient balances of the Danube River basin
Fig. 8 shows the long term mean annual water balance for the entire
Danube River Basin as simulated with SWAT for the period 1995–2009.
For the Danube River Basin, it was estimated that 60% of the precipita-
tion (P) was lost through evapotranspiration (ET) and 3% as percolation
in the deep aquifer (DARCHRG), and 37% was discharged in the stream
(water yield, WYLD). Surface runoff (SR) and baseflow (BF) were re-
spectively the main pathways of pollutants losses. The SWAT evapo-
transpiration and water yield results were very close to that reported
in Petrovič et al. (2006) and EnviroGRIDS (2015), confirming the reli-
ability of the model predictions.
Fig. 9a and b show the nitrogen and phosphorus fluxes and reten-
tions in term of specific loads (kg/ha/year) in the Danube River Basin ac-
cording to the SWAT model results. Regarding TN, the diffuse inputs
were estimated at about 86 kg/ha, in which fertilizers application con-
tributed 41.2 kg/ha, nitrogen from atmospheric deposition 13 kg/ha
and the nitrogen fixed by plant 31.8 kg/ha. Point sources instead
amounted to 2.6 kg/ha. The nitrogen removed by crop yield and lost
in soils had the most significant impact on diffuse sources reduction
with a reduction of 60% (48.2 kg/ha) and 37% (30 kg/ha), respectively.
In particular, soil denitrification (constrained in the calibration
210 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218

Fig. 6. Left: distribution of observed values of nutrients loads in each water management region. Right: SWAT simulations of residuals (observed –simulation). The grey continuous lines
indicate the median value of the whole dataset, the grey dotted lines indicate the interquartile range. The numbers of data entries are reported above each box plot.

procedure) was estimated to be around 19 kg/ha (24% of diffuse
sources). Similar results were found in Pérez-Martin et al. (2016) who
estimated a loss of annual average nitrogen surplus from soil of 26% in
the Jùcar River Bain, Spain (43,000 km2) using PATRICAL model, where-
as Hu et al. (2007) simulated a denitrification rate of 22 kgN/ha/year
using SWAT in the upper Embarras River watershed, United States
(482 km2). However, measurements indicate that the denitrification
rates are highly variable in space and time, and are related to soil mois-
ture, nitrate and carbon availability, and generally don't exceed 50 kg/ha
(David et al., 2009). In addition, it was demonstrated that models, in
which the denitrification process was not calibrated, predict long term
average denitrification ranging from 3.8 to 21 kg/ha/year, with a larger
intra-annual variability (David et al., 2009).
The nitrogen loss in the aquifer was estimated at 2.3 kg/ha (3% of dif-
fuse sources reached the aquifers) and spatially decreases across the
Danube Basin from the sources to the Delta (see the Supplementary ma-
terial for the graphical detail). The total N emission, i.e. sum of nitrates
loading to reach in tile drainage system, NTILE, nitrogen in lateral
flow, LFN, in surface runoff, SRN, in baseflow, BF, and the organic nitro-
gen transported with the water yield, ORGN (see Fig. 9), was estimated
 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218 211

Fig. 7. Long term average of monthly streamflow (a) and nutrient concentrations (b, c, d) along the Danube River with SWAT for the period 1995–2009 together with the available
observations recorded at the gauging stations. The observations are represented with bubbles with size proportional to the number of total observations in the simulated period
(1995–2009). The confluences of main tributaries, as well as the main barriers are indicated.

of 6.14 kg/ha (corresponding to 492·103 ton/year during the period
1995–2009, sum of NTILE, LFN, ORGN SRN and BFN in Fig. 9). SWAT
emission estimates were comparable to MONERIS results (ICPDR,
2004) of about 7.8 kg/ha (corresponding to 623 · 103 ton/year during
the period 1998–2000) albeit loss pathways differed quite significantly.
According to MONERIS, the main loss pathway was the groundwater
(53%), whereas SWAT predicted most losses to occur via surface runoff
(44%). Also the tile drain emission was different: for SWAT the tile drain
contributed with 9% of total 492 · 103 emissions in period 1995–2009
(44 · 102 ton/year), while for MONERIS with 11% of total 623·103 ton/
year in the period 1998–2000 (about 68 · 102 ton/year). The riparian fil-
ter strips reduced the diffuse emissions to 4.8 kg/ha, trapping about 20%
of emissions from land. Furthermore, even though the point sources in-
creased the loads in the river to 7.4 kg/ha, the in-stream retention
amounted to about 30%, producing a final load of 5.5 kg/ha (correspond-
ing to 459 · 103 ton/year in the period 1995–2009).
The spatial distribution of nitrogen surplus (the difference between
nitrogen input through inorganic and organic fertilizer application, at-
mospheric deposition, fixation, and nitrogen uptake by crops), is
shown in Fig. 10. Nitrogen surplus summarizes N potential losses from
the subbasins during the period 2000–2010. The mean values at country
level were compared to EUROSTAT gross nutrient surplus (EUROSTAT,
2012) and are shown in the same figure. It is noteworthy that nitrogen
surplus was on average around 27 kg/ha in the whole Danube, with
highest local values in the Upper Danube, Morava, Pannonian Danube
and Sava Basin, where fertilizers application was significantly higher
(see Supplementary material for details of amount of nutrients inputs
by ICPDR regions). The SWAT nitrogen surplus at country level fit well
the EUROSTAT estimations in particular in Romania, Austria, Slovenia
and Germany. Some differences were noticeable in Slovakia where
SWAT underestimated the nitrogen surplus; this may be due to simpli-
fications in the manure fertilization set-up. In terms of TP, fertilizers
212 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218

application was estimated to be around 6 kg/ha, with plant uptake cap-

turing 90% of TP. TP diffuse emissions were estimated at 0.38 kg/ha (i.e.
44 · 103 ton/year for the period 1995–2009), lower than MONERIS
estimate of 0.56 kg/ha (45 · 103 ton/year during the period 1998–
2000; ICPDR, 2004). The main emission pathways were related to the
transport of organic phosphorus via surface runoff and lateral flow in ac-
cordance with other studies (Chardon et al., 1997; Turner and Haygarth,
2000) and to hillslope erosion, which is strongly linked to the catchment
morphology, vegetation and land use (Steegen et al., 2001). The erosion
was the main P pathway also for MONERIS (ICPDR, 2004). Dissolved
phosphate transported via tile drains contributed only about
0.06 kg/ha. The SWAT TP diffuse emission (0.39 kg/ha) were further re-
duced by riparian filter strips to 0.3 kg/ha (about 13% of retention). With
the addition of point sources load (0.26 kg/ha), TP loads reaching the
stream network amounted to 0.55 kg/ha. However, in-stream retention
was 50%, resulting in 0.3 kg/ha of TP loads in the river, corresponding to
25,173 ton/year in the period 1995–2009.

Fig. 8. Long term water annual balance in the Danube River Basin according to SWAT
model results in the period 1995–2009. P, precipitation; ET, evapotranspiration; BF,
3.5. Usefulness of model predictions and future applications
baseflow from shallow aquifer; INF, infiltration in the soil; LF, Lateral flow; SR, Surface
Runoff; QTILE, tile drainage; DARCHRG, the deep aquifer recharge; GWRCHRG, the shallow The analysis of model predictions and limitations related to data
aquifer recharge; WYLD: water yield. availability and model structure, provides valuable insights on water

Fig. 9. Long term mean annual nitrogen (a) and phosphorus (b) fluxes (kg/ha/year) in the Danube River Basin according to SWAT model results in the period 1995–2009. In (a): the diffuse
sources are represented by the sum of nitrogen input via fixation (NFIX), nitrogen transported to the soil with the precipitation (NRAIN) and the nitrogen applied as fertilizer (NAPP); NPS is the
nitrogen loading to the reach from point sources; the diffuse emissions are the nitrates loading to reach in tile drainage system (NTILE), in lateral flow (LFN), in surface runoff (SRN), in
baseflow (BFN) and the organic nitrogen transported with the water yield (ORGN); ORGNRF and SRRF are respectively the organic nitrogen and nitrates reduced by riparian filtering; NLEACH is
the nitrogen leached to aquifer; NPYR, NsoilR, Naq, NRF and NriverR are respectively the reduction of nitrogen applied by plant, soil, aquifer, riparian filter strip and river; NLoad is the total nitrogen
load at the outlet of the Basin. In (b): the diffuse sources are represented by phosphorus applied as fertilizer (PAPP); PPS is the phosphorus loading to the reach from point sources; the diffuse
emissions are the soluble phosphorus (phosphate) transported in tile drainage system (PTILE) and water yield (SOLP), the organic phosphorus loading to the reach (ORGP) and the mineral
phosphorus adsorbed to sediment and transported into the reach (SEDPRF); SOLPRF, ORGNRF and SEDPRF are respectively the soluble, organic and mineral phosphorus reduced by riparian
filtering; PPYR, PsoilR, PRF and PriverR are respectively the reduction of phosphorus applied by plant, soil, riparian filter strip and river; PLoad is the total nitrogen loads at the outlet of the Basin.
 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218 213

Fig. 10. Map of nitrogen surplus in the period 2000–2010 calculated as difference between input (fertilization, nitrogen in rain and nitrogen fixation) and the uptake of plants and
comparison of values by country between European statistics (EUROSTAT) and SWAT. The Countries shares following in the Danube Basin as follows: Germany, DE, 16%; Czech
Republic, CZ, 28%; Slovenia, SI, 80%; Slovakia, SK, 97%; Austria, AT, 97%; Italy, IT, 19%; Bulgaria, BG, 56%; Romania, RO, 100%; Hungary, HU, 100%.

and nutrient processes at different spatial (subbasin, river, basin) and
temporal scales (monthly and annual). This “state-of-the-art” model-
ling of water quantity and quality of the Danube Basin identified critical
spots where additional in-depth investigations may be necessary. For
instance, to better support catchment management the monitoring net-
work of streamflow should be strengthened in the Velika Morava, Mid-
dle Danube, Romanian and Bulgarian Danube, whereas harmonized
monitoring of nutrient concentrations should increase in the Upper
Danube, Sava River Basin and in all regions from Middle Danube to
Delta (Chapman et al., 2016).
Predicting nutrient concentrations rather than loads, as shown in
this study, offers several advantages. First, it avoids the uncertainty
issues related to loads estimation. Second, it supports the implemen-
tation of the EU environmental Directives that set targets in terms of
nitrogen concentration. For example, it can help to control the max-
imum allowable NO3 concentration of 50 mg/L according to the
Drinking Water Directive (98/83/EC) and identify sites where mean
annual NO3 concentrations exceed 50 mg/L as required by the Ni-
trates Directive (91/676/EEC). Third, predicting concentrations pro-
vides information that can be directly used in the definition of the
risk assessment, establishing concentration-effect relationships for
the aquatic ecosystems.
For a direct comparison with the maximum contaminant concen-
tration of nitrate (50 mg/L NO3) for potable water according to the
World Health Organization (WHO), Fig. 11 shows the spatial distri-
bution of long term mean monthly nitrate concentration calculated
from the simulated N-NO3 (conversion factor of 4.427). The figure
shows in detail the variation of nitrate concentration in rivers in
the four seasons, from autumn to summer, for the period 1995–
2009. The highest nitrate concentrations occur during autumn and
winter with median values of 7.3 and 6.5 mg/L respectively (IQR
ranges of [2.8; 14.5] mg/L and [3; 11.8] mg/L respectively), while
they are lower during summer (median of 5 mg/L; IQR range [2;
10] mg/L) and spring (median 4.5 mg/L; IQR range [2.3; 8.6] mg/L).
These values are correlated to the nitrogen surplus in soils and the
dilution effect of stream flow, more pronounced during the spring
season. Nitrate seasonal concentrations are also correlated to the
magnitude of the denitrification process that occurred when soils
are saturated and in an anaerobic environment. This process is heavi-
ly influenced by temperature as well. During autumn and winter the
rate of denitrification is greatly reduced due to the lower tempera-
ture, while during spring and summer the environmental conditions
are more favourable to microbial activity. However, even during
summer, some rivers in the Upper Danube, Pannonian Sava and Mid-
dle Danube exceed the 50 mg/L of nitrate.
Spatially NO3 concentrations exceed 50 mg/L in the Pannonian Dan-
ube, Sava at the outlet and at the entrance into the Middle Danube dur-
ing all seasons with some peaks of concentrations also in the Upper
Danube during autumn and summer (Fig. 10). This distribution can be
explained by the highest percentage of cropland and thus nitrogen in-
puts in the Pannonian Danube.
Besides understanding the processes and pathways responsible
for water nutrient pollution, and identifying problematic areas
where actions should be targeted, the modelling approach presented
in this study can support the analysis of scenario, as internal feed-
backs between water and nutrient cycles are considered, as well as
the effects of crop growth and land and water management. Having
predicted the water, nutrients and sediments (Vigiak et al., 2017)
fluxes in current conditions, the next steps are to assess the impact
of management scenarios on ecosystem services, evaluate best man-
agement practices on the ecological status of the river (Grizzetti et
al., 2016; Vigiak et al., 2016), search for economically effective solu-
tions, and identify trade-offs between economics and pollution sta-
tus (Udias et al., 2016). Finally, the Danube Basin SWAT model
results could support the development of indicators of water, energy
and food securities in a “Nexus Thinking” approach with reference to
214 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218
Fig. 11. Maps and Box and whisker plot of long term mean seasonal nitrate concentration (NO3 mg/L) according to SWAT model results in the period 1995–2009. The nitrate concentration
was calculated from the simulated SWAT N-NO3 using a conversion factor of 4.427.
the Sustainable Development Goals of the United Nations (Giupponi
and Gain, 2016).
3.6. Consideration about the nutrient pollution in the Danube River Basin
and the end up in the Black Sea
The Danube River and its catchment provide many services includ-
ing drinking, industrial and agricultural water supply, hydroelectric
power generation, navigation, tourism, recreational opportunities and
fisheries. These intensive uses have created severe pressures on water
quality and quantity affecting biodiversity in the Basin, and polluting
large areas of the Black Sea (Popovici, 2014).
This study of nutrient balances and the seasonal analysis of ni-
trates has allowed identifying the impact of diffuse and point sources
on the Danube River and its tributaries. Elevated loads of nitrogen
enter the river through diffuse sources such as fertilization. In partic-
ular, the use of mineral fertilizers significantly contributes to the pol-
lution of the Danube River (55%), followed by manure (37%) and
ammonia (8%). However, the agricultural impact is substantially re-
duced by around 90% mainly due to crop uptake, soil denitrification
and riparian filter strips (reduction of 60%, 24% and 2%, respectively).
The nitrogen from urban settlements directly contribute to the load
of the Danube River by about 35%, while the diffuse emissions from
agricultural sector (including the contribution from precipitation)
account for 65%.
Similarly, high phosphorus loads enter in the Danube Basin through-
out fertilizer application (95% of total sources). However, this potential
impact is substantially reduced by plant uptake and only 5% of diffuse
sources reach the river system that is heavily stressed by the phospho-
rus pollution from point sources.
The Black Sea, which ultimately receives the waters of the Danube
Basin, is sensitive to eutrophication and the severe eutrophic conditions
of the late 1980s might occur again if agriculture and waste water treat-
ment plants discharges are not managed properly.
Fig. 12 shows the annual variation of nutrient loads and concen-
tration entering into Black sea in the period 1995–2009 as simulated
by the SWAT model. The Danube on average introduces about
25,000 tonnes of P, 460,000 tonnes of N and 432,000 of N-NO3 into
the Black Sea each year. The concentrations of N-NO 3, N and P are
quite constant in the period 1995–2009 with average values of 2.1,
2.2 and 0.12 mg/L, respectively.
The mean annual specific nutrient fluxes exported from the Danube
Basin to the Black Sea were also compared with the observed riverine
fluxes reported in Billen et al. (2011). The SWAT nitrate-nitrogen and
total nitrogen fluxes exported to the Black sea in the period 1995–
2009, estimated around 540 and 570 kg/km2/year respectively, resulted
similar to that predicted by MONERIS model for the 2001–2005 period
(560 kg/km2/year) but lower than the estimation of Cociasu et al.
(1996) of 860 kg/km2/year for the period 1952–1992. This result con-
firms the efforts done to control nutrient enrichment over the past
30 years Popovici (2014). However, the modelled nutrient fluxes
of the Danube resulted lower than other European basins with sim-
ilar percentage of cultivated land. For instance, the Rhine River
Basin, characterized by 50% of arable land, delivery at the outlet
around 2000 kg/km 2 /year (Lancelot et al., 1991), and the Elbe
(57% of arable land) discharges around 1000 kg/km2/year (Radach
and Pätsch, 2007). The mean annual specific N-NO 3 yield is also
comparable with other basins in Northeastern US (Mayer et al.,
2002), in Germany (Langusch and Matzner, 2002) and in Northern
Taiwan (Kao et al., 2004) that are characterized by small or moder-
ately agricultural extent. Concerning the phosphorus, the SWAT
 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218
Fig. 12. Annual loads (a, b, c) and concentrations (d, e, f) of nitrogen-nitrates, total nitrogen and phosphorus discharge into the Black Sea.
total phosphorus fluxes exported to the Black Sea in the period
1995–2009 was comparable to that estimated by Cociasu et al.
(1996) around 30 kg P/km2/year. This value is lower than the deliv-
ery phosphorus fluxes from other European river basins such as
Rhine (242 kg P/km2/year, Lancelot et al., 1991) and Rhone (78 kg
P/km2/year; Rabouille et al., 2008).
4. Summary
A process-based modelling approach, that involves a systematic
calibration/validation strategy of SWAT model, was developed and
applied in the Danube River Basin to predict streamflow, sediments
and nutrients fluxes at different spatial and temporal scale. The
methodology involved the use of both soft data (i.e. literature infor-
mation of denitrification, crop yields from statistics) and hard data
(i.e. long time series of streamflow and concentrations). The calibra-
tion/validation of streamflow was developed in steps in order to sim-
ulate adequately each hydrological component, while sediment and
nutrients were calibrated using directly the concentrations. The use
of concentrations for model calibration enabled direct support for
the implementation of EU environmental Directives.
215
The results show that SWAT is able to adequately represent crop
yield, monthly streamflow, total nitrogen (TN) and total phosphorus
(TP) concentrations in the Danube Basin, albeit the peaks of TP concen-
tration were at times underestimated. Difficulties were encountered in
reproducing the nitrogen-nitrate concentration seasonality across the
Basin due to the simplification of SWAT model in representing soil deni-
trification process.
Model simulations were analysed per water management re-
gions identifying areas with important knowledge gaps where
an in-depth analysis may be necessary. Furthermore, the analysis
of model results along the Danube River provided insightful infor-
mation on the tributaries impact on Danube water quantity and
quality.
The mean annual water balance has allowed identifying the main
components that affect the water balance giving an overview of the
actual water resources status. This “state-of-the-art” modelling of
the water resources and nutrients pollution in the Danube River
Basin offers an important step forward in large scale integrated
modelling. Despite necessary simplifications, accurate results can
be obtained while keeping realism in the representation of the phys-
ical processes and as such the model can be used to support effective
water management.
216 A. Malagó et al. / Science of the Total Environment 603–604 (2017) 196–218
Acknowledgement
We would like to thanks all the Institutes reported in Table 3 for pro-
viding streamflow and nutrients data.
Appendix A. Supplementary data
Supplementary data to this article can be found online at http://dx.
doi.org/10.1016/j.scitotenv.2017.05.242.
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