Eutrophication in the Lobo watershed remains a major problem. The work carried out has focused on chemical and biological analyses in the lake or in its immediate environment: they did not sufficiently take into account the diffuse transfer of nutrients over the entire watershed. This study aims to assess the nutrient (N and P) loads in the Lobo watershed, an agricultural area, to understand the spatio-temporal impacts of land management practices on eutrophication. The methodology uses two steps: streamflow calibration and nutrient (N and P) estimation using the Soil and Water Assessment Tool (SWAT) watershed model. Thus, the nutrient inputs were estimated based on the levels of N and P in every kilogram of Nitrogen-phosphorus-Potassium (NPK) type fertilizers applied by farmers. The average quantities of N and P applied to the crops were 47.24 kg ha1 and 21.25 kg ha1. Results show a good performance on flow calibration as evidenced using evaluation criteria R2, NashSutcliffe Efficiency (NSE), and Percent Bias (PBIAS) of 0.63, 0.62, and 8.1, respectively. The yields of inorganic N and soluble P varied from 0 to 0.049 kg ha1 and from 0 to 0.31 kg ha1. These results show that the crops inorganic nitrogen requirements were higher than the demands for soluble phosphorus. Simulations relating to the organic N transfer revealed values ranging from 0.2 to 5 kg ha1, while the transport of organic phosphorus was estimated to vary from 0.3 to 1.3 kg ha1.