Diffuse pollution has a complex nature depending on various land-use activities like agriculture, livestock breeding and forestry. In this study, an alternative methodology is applied for decreasing the spatial uncertainty of diffuse nutrient load estimations. It is applied in the Melen Watershed, Turkey, which is an important watershed from where additional water will be supplied for the megacity Istanbul via interbasin water transfer. Monthly diffuse nutrient loads were estimated for each subwatershed by utilizing remote sensing (RS) and geographical information systems (GIS). Estimated nutrient loads were considerably different in various months due to the temporally irregular fertilizer application and meteorological conditions. Temporal differences were also predicted in the spatial distribution of the nutrient loads. The methodology is applicable in watershed protection studies, especially where necessary etudes should be conducted in the short term and with limited data. Such efforts in identifying and determining the diffuse loads are important for sustainable management of the watershed.