Abstract: For the first time in Ukraine, a process-based watershed model SWAT was applied for the analysis of a surface water body contamination by nitrogen and phosphorus compounds. The model was applied in a small Holovesnya River Catchment (area 30.4 km2) located in the forest zone of Ukraine on the territory of the Desna water-balance station. The model run was in daily step for years 1985−1988, 2007, 2009, 2010, 2012. The calibration and validation within SWAT-CUP showed good results for streamflow (NS, R2 > 0.6, PBIAS < 4%), acceptable for nitrogen and phosphorus loads (NS > 0.6, RSR < 0.6, PBIAS < 43%).Streamflow and removal of nitrogen and phosphorus mineral compounds were to estimate the dependence of nutrient wash-off on the amount and practice of fertilizing were evaluated to provide recommendations for agricultural management. Increase of the amount of fertilizer results in the reduction of its efficiency. Divided application of fertilizer leads to the nitrate wash-off reduction by 66%.