Ganga river basin (GRB) in the Indian subcontinent is one of the most heavily irrigated land in the world. According to a book published in 2005 by Central Water Commission (CWC), 57% of the net irrigated land in India lies inside GRB only. Further GRB is also one of the most populous river basins in the world supporting almost 400 million people of India. With increasing use of fertilizers in agriculture and untreated sewage waste from the booming industries, there is need to assess the water quality and the contamination in surface water. We will use Soil Water Assessment Tool (SWAT) to model the hydrology of the river basin. For water quality analysis, SWAT is able to simulate the impact on hydrology, sediment and nutrients load, due to physical changes brought in the large ungauged river basins. We hypothesize that numerous small, rain-fed rivers in the Indo-Gangetic floodplain that are flowing predominantly through agricultural land are important non-point source of Nitrogen(N) and Phosphorus (P) and will control the nutrient budget of large river system. SWAT model will be used to simulate flow and nutrient/sediment concentrations of nitrogen/nitrates, phosphorus and sediment in the upper reach at Uttarkashi and Rishikesh, in the middle reach at Kanpur, Lucknow and Varanasi, and Farakka at the lower reach. SWAT model will be calibrated at daily/monthly time step for flow and monthly scale for water quality parameters. We will analyze the water quality in the basin using widely used Water Quality Index (WQI) considering pH, TDS, BOD, COD, hardness, nitrates, carbonates and silicates. We will use gridded climate data from Indian Meteorological Department (IMD) and water quality data from CWC. SRTM 90 m DEM, 300 m Land use/land cover map from Climate Change Initiative (CCI) and 7 km soil map from Food and Agriculture Organization (FAO).