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1 Supplementary Material Table S1. Temporal and spatial resolution of the application of the GREEN, RiverStrahler and SWAT models in this study. Model application for the present study Time step Spatial discretisation of the Seine river basin GREEN RiverStrahler SWAT The GREEN model was applied to all The RiverStrahler model was applied to the The SWAT model was applied to the Seine of Europe by Grizzetti et al. (2012). Seine, Somme and Scheldt basins by Passy river basin at the Poses* gauging station in The results relative to the Seine river et al. (2013). The results relative to the this study. basin at the Poses* gauging station Seine river basin at the Poses* gauging were extracted and used for this station were extracted and used for this study. study. The model produces annual values of nitrogen loads. Sub-basins: 351 sub-basins Stream segments: 351 stream segments corresponding to the 351 sub-basins *The Poses gauging station is the limit (a weir) with the Seine estuary. The model simulates the in-stream processes in the main river axes at a 1-h time step. N concentration in different forms (NO 3, NO 2, NH 4, organic N) are produced at the 10-day time step. Sub-basins: 21 sub-basins Stream segments: 5 main river axes and about 3000 stream segments. The processes in the stream are simulated in each sub-basin, lumping together the stream segments with the same Strahler order, and in the main river axes at 1-km resolution. The model runs on a daily time step. Water flow and N concentration in different forms (NO 3, NO 2, NH 4, organic N) are produced daily and then can be aggregated at monthly and annual time steps. Sub-basins: 45 sub-basins. The sub-basins were divided into 373 Hydrologic Response Units (HRU), which are a unique combination of soil, land cover type and slope. Stream segments: 45 stream segments corresponding to the 45 sub-basins 1

2 Table S2 Representation of the main processes relevant for the nitrogen fluxes and retention in the GREEN, RiverStrahler and SWAT models. The processes are grouped by compartments according to the scheme in Figure 5, to facilitate the comparison of the three models. The processes represented in the models mainly by physically based equations are highlighted with a grey background. The other processes, mainly represented through coefficients of reduction, have a white background. Plant and soils Aquifer Wetland and riparian areas River GREEN RiverStrahler SWAT Nitrogen removal due to crop uptake, volatilisation, denitrification in soils and aquifers is estimated in a lumped manner (basin retention) as a function of the precipitation in each sub-basin. Nitrogen retention in wetland and riparian areas is not separately represented by the model. This removal is accounted for partly in the basin retention and partly in the river retention. Nitrogen removal in rivers is estimated as a function of the river length in each sub-basin. The base flow filter method proposed by Eckhardt (2008) is used to estimate the surface flow and base flow proportion in the measured water flow at the outlet of each sub-basin. The two components of the flow are multiplied by the average nitrogen concentration of surface flow and base flow. The first is computed based on soil nitrogen balance specific to the land use types in each sub-basin. The flow of nitrogen from the aquifer to the river is computed multiplying the average nitrogen concentration in the aquifers and the river base flow estimated with Eckhardt s (2008) filter method. The nitrogen retention in the aquifer is estimated as the difference between the nitrogen concentration in the leaching and the nitrogen concentration in the aquifer, based on measurements available in the Seine basin. Nitrogen fluxes from surface runoff are reduced by the riparian retention, which is simulated by a temperaturedependent reduction factor specific to each sub-basin. Biogeochemical processes involving phytoplankton (diatoms and non-siliceous algae), zooplankton and bacteria are simulated by the model (RIVE model, Garnier et al., 2002). Nitrogen retention is the result of denitrification, sedimentation and uptake by algae. The model simulates the entire nitrogen cycle in soil, including crop growth and the effects of agricultural practices. Nitrogen applied by fertilisers (mineral and manure) is removed by crop harvesting and ammonia volatilisation. In addition, denitrification and mineralisation processes in soils are simulated based on the climate conditions, water saturation and organic carbon content. Nitrogen leaching and transport in surface runoff and lateral flow are also simulated by the model (which describes the entire hydrological components of the water cycle in the river basin). Nitrogen percolated in the (shallow) aquifer is transported to the river with the return flow. A nitrogen degradation factor in the aquifer can also be set. (This was not applied in the present study). Wetland retention is simulated by the model in each sub-basin by a reducing factor, considering the fraction occupied by the wetlands. In addition, filter strips and grassed waterways can be established as management practices at the HRU level. (This option was not used in the present study). Biogeochemical processes involving algae growth are simulated by the model according to the QUAL2E model (Brown and Barnwell, 1987). Nitrogen retention is the result of sedimentation and uptake by algae. Denitrification is not simulated. 2

3 Table S3. Data sources and model representation of the nitrogen sources considered by the GREEN, RiverStrahler and SWAT models in this study. Diffuse sources Mineral fertilisers and manure application Atmospheric deposition GREEN (Grizzetti et al. 2012). RiverStrahler (Passy et al., 2013) SWAT (this study) A European map of mineral and manure nitrogen application was developed for 1985, 1990, 1995, 2000 and 2005, combining (i) the spatial information on areas occupied by agriculture and pasture from the HYDE 3 database (Klein Goldewijk & Van Drecht, 2006), (ii) the geographical location of urban and water cover types from GLC2000 (Bartholome & Belward, 2005) and (iii) the information on crop shares, crop types and fertiliser application rates from the CAPRI database (Britz, 2004) for EU27, Norway and the Balkan region, and from the FAO database (FAO, 2009) for the rest of Europe Total mineral and manure fertilisation are computed for each sub-basin. Nitrogen input from atmospheric deposition was taken from the Cooperative Programme for the Monitoring and Evaluation of the Long- Range Transmission of Air Pollutants in Europe (EMEP, 2001). Total nitrogen from atmospheric deposition (total N) is computed for each sub-basin. Diffuse nitrogen emissions from soils and aquifers are reconstructed using the measured water flow and the nitrogen concentrations calculated from N soil balance based on agricultural statistics. Water flow is divided into base flow and surface runoff on the basis of the Eckhardt (2008) filter and multiplied by the concentration of nitrogen in leaching and aquifers (based on spatially distributed measurements available in the Seine basin). Diffuse nitrogen emissions from soils and aquifers are computed for each subbasin. A land-use map was produced combining the Corine Land Cover map and the information on agricultural practices by PRA (Petites Régions Agricoles) agricultural regions available from INRA (Mignolet et al., 2007; Billen et al., 2013). Major crop rotations per PRA region were established and the associated mineral and organic fertilisation, based on data from Billen et al. (2013). Total nitrogen from fertilisers and manure is computed per day per each HRU, according to the land cover and the management practices established. The average nitrogen concentration in rainfall was calculated based on EMEP data (EMEP, 2001). Nitrogen from the atmospheric deposition is computed per day per sub-basin according to the rainfall (simulated by the model) and the average nitrogen concentration in rainfall. 3

4 Nitrogen biological fixation Scattered dwellings and runoff from urban areas Point sources Wastewaters from sewage systems and industries The nitrogen input from biological fixation was calculated for fodder and leguminous crops based on the nitrogen fixation rate reported by OECD (2008a,b) and the land-use map. Total nitrogen from biological fixation (total N) is computed for each sub-basin. The emissions of households not connected to the sewage system were computed based on the European map of population density, per capita emissions and countries connection rate to the sewage system. Total nitrogen from scattered dwellings (total N) is computed for each sub-basin. Nutrient inputs produced by human settlements were estimated taking into account the European map of population density, the emission rates per person, the percentage of the population connected to the wastewater collection system and the level of treatment (per country). A data set on connection rates and treatment levels of European countries for 1985, 1990, 1995, 2000 and 2005 was built based mainly on the information available from EUROSTAT. Total point sources are computed for each sub-basin and added to the river stretch of the sub-basin. Detailed information on the location and loads per year of wastewater treatment plants in the Seine river basin produced by the Agence de L Eau Seine-Normandie was used. The data set includes the emissions from industry. Total point sources (per N types: NO 3, NH 4, organic N) are computed for each stream segment. SWAT crops database The model simulates plant growth. The capacity to fix nitrogen depends on the crop-specific fixation rate (therefore the amount of nitrogen fixed varies per HRU, according to the climate, plant type and growth). Diffuse nitrogen emissions from paved areas are considered in HRUs occupied by urban areas Total nitrogen from paved areas is computed per day in the HRUs occupied by urban areas (based on emission coefficients of the SWAT database for urban areas). Detailed information on the location and loads per year of wastewater treatment plants in the Seine river basin produced by the Agence de L Eau Seine-Normandie was used. The data set includes the emissions from industry. Total point sources (per N type: NO 3, NH 3, organic N) are computed for each sub-basin and added to the river stretch of the subbasin. 4

5 Table S4. Performance of the simulation of the GREEN, RiverStrahler and SWAT models. E=Nash-Sutcliffe Efficiency (Nash and Sutcliffe, 1970); R=Bravais-Pearson coefficient; R2=Coefficient of determination; MARE=Mean Absolute Relative Error (Bennett et al., 2013). Performance of calibration/validation on the original data set Mean absolute relative error (MARE) of annual nitrogen load/concentration Performance of simulation of annual nitrogen load* Mean absolute relative error (MARE) of average seasonal NO3 concentration** GREEN RiverStrahler SWAT E=0.87 (annual total N load) R=0.11 (10-day NO 3 concentration) Performance of the calibration in the North Sea and Atlantic Sea region, referring to (Grizzetti et al. 2012). MARE=0.43 (annual total N load) The value is computed considering the results of the calibration in the North Sea and Atlantic Sea region ( ). E=0.03 (annual total N compared to measured annual NO 3 load at the Poses gauging station, ) R2=0.79 Performance of the validation at the Poses station on the Seine River, referring to reported by Passy et al. (2013). MARE=0.12 (annual NO 3 concentration) The value is computed considering the results of the calibration at the Poses gauging station ( ). MARE=0.05 (average seasonal NO 3 concentration) The value is computed considering the average seasonal NO 3 concentration at the Poses gauging station ( ). E=0.63 (daily water flow) E<0 (daily NO 3 concentration) E=0.76 (monthly NO 3 load) Performance of the calibration at the Poses station on the Seine River, referring to MARE=0.11 (annual NO 3 concentration) MARE=0.09 (annual NO 3 load) The value is computed considering the results of the calibration at the Poses gauging station ( ). E=0.86 (annual NO 3 load at the Poses gauging station, ) R2=0.89 MARE=0.13 (average seasonal NO 3 concentration) The value is computed considering the average seasonal NO 3 concentration at the Poses gauging station ( ). * For the GREEN model, total nitrogen load (the only nitrogen form predicted by the GREEN model) is compared to NO3 load (the only nitrogen form for which observations were available for this study); the total N predictions are correlated with NO3 observations (R2=0.79), but total N predictions differ systematically (always larger) from the NO3 observation (E=0.03), which can be expected when comparing total N with NO3 loads. The RiverStrahler model simulates NO3 concentration but does not simulate the water flow. For this reason it was not possible to compute the performance in representing the NO3 load. ** The mean absolute relative error (MARE) of average seasonal NO3 concentration was computed considering the average NO 3 concentration in 4 seasons (winter: January, February, March; spring: April, May, June; summer: July, August, September; autumn: October, November, December) at the Poses gauging station for the period The GREEN model produces only annual values. 5

6 References Bartholomé E, Belward AS (2005) GLC2000: a new approach to global land cover mapping from earth observation data. International Journal of Remote Sensing, 26, Bennett, N.D., Croke, B.F.W., Guariso, G., Guillaume, J.H.A., Hamilton, S.H., Jakeman, A.J., Marsili-Libelli, S., Newham, L.T.H., Norton, J.P., Perrin, C., Pierce, S.A., Robson, B., Seppelt, R., Voinov, A.A., Fath, B.D., Andreassian, V., Characterising performance of environmental models. Environmental Modelling and Software 40, Billen, G., Callens, J., Beaudoin, N., Viennot, P., Schott, C., Anglade, J., Benoit, M., Curie, F., Garnier, J., Caractérisation des pressions agricoles et modélisation de leurs effets en matière de contamination azotée de l hydrosystème à l échelle du territoire Seine Normandie. Programme PIREN-Seine Rapport d activité 2012: agriculture, février pp (in French). Britz W (2004) CAPRI Modelling System Documentation, Final report of the FP5 shared cost project CAP-STRAT Common Agricultural Policy Strategy for Regions, Agriculture and Trade, QLTR Universita t Bonn, Bonn. Brown L.C. and Barnwell T.O., The enhanced water quality models QUAL2E and QUAL2E-UNCAS documentation and user manual. EPA document EPA/600/3-87/007. USEPA, Athens, GA. Eckhardt, K., A comparison of baseflow indices, which were calculated with seven different baseflow separation methods. J. Hydrol. 352, EMEP (The Co-operative Programme for the Monitoring and Evaluation of the Long-Range Transmission of Air Pollutants in Europe), (2001) EMEP measurement database. Available at: (accessed 28 October 2011). FAO (2009). Available at: (accessed 28 October 2011). Garnier J., Billen G., Hannon E., Fonbonne S., Videnina Y., Soulie M. (2002)-Modeling transfer and retention of nutrients in the drainage network of the Danube River. Estuar. Coast. Shelf Sci., 54: Grizzetti, B., Bouraoui, F., Aloe, A., Changes of nitrogen and phosphorus loads to European seas, Global Change Biology, 18, Klein Goldewijk K, Van Drecht G (2006) HYDE 3: Current and historical population and land cover. In: Integrated Modelling of Global Environmental Change. An Overview of IMAGE 2.4 (eds Bouwman AF, Kram T, Klein Goldewijk K), pp Netherlands Environmental Assessment Agency (MNP), Bilthoven, the Netherlands. 6

7 Mignolet, C., Schott, C., Benoit, M., Spatial dynamics of farming practices in the Seine basin: methods for agronomic approaches on a regional scale. Sci. Total Environ. 375, Nash, J.E., Sutcliffe, J.V., River flow forecasting through conceptual models. Journal of Hydrology, 10, OECD (2008a) Environmental Indicators for Agriculture Volume 4 (Restricted access). OECD, Paris. OECD (2008b) Environmental Performance of Agriculture in OECD Countries since Paris, France. Available at: (accessed 28 October 2011). Passy, P., Gypens, N., Billen. G., Garnier, J., Lancelot, C., Thieu, V., Rousseau V., Callens, J., A Model reconstruction of riverine nutrient fluxes and eutrophication in the Belgian Coastal Zone since J. Mar. System. 128:

8 Figure S1. Results of daily nitrate (NO 3, right) and phosphate (PO 4, left) concentrations observed (in blue) and simulated by the model SWAT (in pink) at the Poses gauging station. 8

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