The study area (Alegria watershed, Basque Country, Northern Spain) considered here is influenced by an important alluvial aquifer that plays a significant role in nitrate pollution from agricultural land use and management practices. Nitrates are transported primarily from the soil to the river through the alluvial aquifer. The agricultural activity covers 75% of the watershed and is located in a nitrate-vulnerable zone. The main objective of the study was to find land management options for water pollution abatement by using model systems. In a first step, the SWAT model was applied to simulate discharge and nitrate load in stream flow at the outlet of the catchment for the period between October 2009 and June 2011. The LOADEST program was used to estimate the daily nitrate load from measured nitrate concentration. We achieved satisfactory simulation results for discharge and nitrate loads at monthly and daily time steps. The results revealed clear variations in the seasons: higher nitrate loads were achieved for winter (20,000 kg mo⁻¹ NO₃–N), and lower nitrate loads were simulated for the summer (<1000 kg mo^-1 NO₃–N) period. In a second step, the calibrated model was used to evaluate the long-term effects of best management practices (BMPs) for a 50-yr period by maintaining actual agricultural practices, reducing fertilizer application by 20%, splitting applications (same total N but applied over the growing period), and reducing 20% of the applied fertilizer amount and splitting the fertilizer doses. The BMPs were evaluated on the basis of local experience and farmer interaction. Results showed that reducing fertilizer amounts by 20% could lead to a reduction of 50% of the number of days exceeding the nitrate concentration limit value (50 mg L^-1) set by the European Water Framework Directive.