Nutrient fluxes in stream basins need to be controlled to achieve good water quality status. In stream basins with intensive agricultural activities, nutrients predominantly come from diffuse sources. Therefore, best management practices (BMPs) are increasingly implemented to reduce nutrient input to streams. The objective of this study is to evaluate the impact of vegetated filter strip (VFS) application as an agricultural BMP. For this purpose, SWAT is chosen, a semi-distributed water quality assessment model that works at the watershed scale, and applied on the Nif stream basin, a small-sized basin in Western Turkey. The model is calibrated with an automated procedure against measured monthly discharge data. Nutrient loads for each sub-basin are estimated considering basin-wide data on chemical fertilizer and manure usage, population data for septic tank effluents and information about the land cover. Nutrient loads for 19 sub-basins are predicted on an annual basis. Average total nitrogen and total phosphorus loads are estimated as 47.85 t/yr and 13.36 t/yr for the entire basin. Results show that VFS application in one sub-basin offers limited retention of nutrients and that a selection of 20-m filter width is most effective from a cost–benefit perspective.