An elevated nitrogen concentration in water is one of the main problems affecting water quality in Mediterranean rivers. The objectives of this study were (1) to evaluate the contribution of the Tafna catchment to the nitrate load entering the Mediterranean Sea, (2) to quantify the impact of agriculture on the nitrate concentration in water bodies, (3) to evaluate nitrate loads entering groundwater, and (4) to quantify the role of reservoirs in nitrate retention. A SWAT model was applied during the period 2003 to 2011. The discharge calibration was based on a previous study by Zettam et al. (2017). NSE efficiencies ranged from 0.421 to 0.75, R2 ranged from 0.25 to 0.84, and PBIAS ranged from 3.68 to 39.42. The simulations of monthly nitrate loads were satisfactory in the upstream sampling stations, with NSE between 0.48 and 0.65 and R2 between 0.63 and 0.68. The PBIAS was satisfactory in all the sampling stations (− 36.30 to 10.42). In the downstream sampling stations, the calibration of the monthly nitrate loads was unsatisfactory (NSE ranged from − 0.26 to 0.21 and R2 ranged from 0.02 to 0.25). Fertilisation was the main N input in the catchment, while the main N output was plant uptake. The Tafna River carried an annual average of 37 to 85.5 t N year−1 into the Mediterranean Sea. The simulation also showed that reservoirs in the Tafna basin contain a large quantity of nitrates, i.e. 62% on average of the total amount of nitrates transported annually by the Tafna River.