This study aims to determine the nutrient (total nitrogen (TN), total phosphorus (TP)) loads from point and diffuse sources of the river basin, and the effects of the nutrient loads on Ergene River, being one of the most polluted rivers in Turkey. To this end, Geographic Information System (GIS), was used to digitize land-use of the basin; the spatial values of land-use patterns were used to estimate the load coming from diffuse sources, Exponential Function Method was used to make population predictions and calculate the load change based on population, and Export Coefficient Model was used to estimate nutrient loads coming from diffuse sources of contamination. In the estimation of TN (24000 tons/year) and TP (2700 tons/year) loads, it was found that diffuse sources have a large share (about 86%). The large portions of nutrient load coming from point sources (74% TN, 93% TP) are associated with domestic wastewater, and chemical and natural (animal) fertilizers generate almost the total load (83% TN, 93% TP) coming from diffuse sources. When the effects of nutrient loads on surface waters in Ergene Basin are considered, both in ecological and socio-economical terms, it was identified that intended use of water sources changed; agricultural and aquatic production was negatively affected by deteriorated ecological balance at surface water. It was concluded that ecological sanctions at the basin should have the precedence over the socio-economic sanctions.