Nitrates fluxes in the Grand Morin basin (1200 km(2)), that is subjected to intense agricultural pressure, are considered using in-stream observations (around 250 sampling days over 5 years) and physically based simulations using the CAWAQS model (CAtchment WAter Quality Simulator). In-stream nitrate concentration averaged 6 mg N L(-1), increasing by approximately 0.2 mg N L(-1) yr(-1) around this value (period 1991-1996). Our results show that, over the period of 1991-1996, the differences between in-stream observed nitrate concentrations and simulated nitrate concentrations result from nitrate losses at the basin scale. These losses are due to denitrification by transfer through wetlands, alluvial plains, the hyporheic zone, and by benthic processes in rivers. A mean annual mass balance at the basin scale indicates that 40% of the infiltration flux (3360 kg N km(-2) yr(-1)) is removed from the system via the river network, 40% is stored in aquifers and 20% is lost by denitrification (period 1991-1996).