Contaminants are serious water quality concern in the Giligel Abbay river basin. Increased N and P contaminants on the river are burdens from the watershed joining it through runoff and leaching. This study aimed to identify the source of pollution, quantifying the contaminant loads to the Giligel Abay river, and testing the application of the Soil and Water Assessment Tool (SWAT) to model N and P transport processes under wet and dry seasons from 1992-2012. The sensitivity analysis of the SWAT model was undertaken for different parameters to identify main sensitive parameters for non-point source pollution in this watershed. Themain sensitive parameters for the watershed were CN2.mgt, GWQMN.gw, and SOL_ALB. Among them, the most sensitive parameter for the SWAT model was found to be the curve number (CN2). The performance of SWAT was found reasonably well based on various performance evaluation criteria such as stream flow, sediment, and contaminant loads parameters which are at the boundary of good to excellent. The analysis result from the watershed showed a significant difference in N and P with the introduction of grazing and fertilizer application, an average annual contaminant load from the watershed was4933.33 ton/yr. and 1150.57 ton/yr. respectively. The temporal variation of pollutions was statistically significant (p<0.05) averagely for dry (December to March) and wet (July) seasons. Spatial analysis using GIS resulted significant color difference showing spatial variation of parameters along the Giligel Abay Watershed. Assessment result indicates higher pollutant loading in 8 sub basins among the total 35. With further refining and updating the SWAT model, it can be applied for quantifying the amount of nitrogen and phosphorus through GIS based sustainable management of systems saves time, money and helps for effective watershed protection and so the river water quality. Keywords: stream flow, Sediment, Water Quality, SWAT_ Upper Giligel Abbay catchment