Availability of water flow for assessing in transboundary river basin is a crucial issue and is necessary for water sharing and management. As a Transboundary river, Ganga has created water conflict between India and Bangladesh, related to water sharing at Farakka. Under these circumstance, applying hydrological model SWAT, measurement and understanding of water availability is important. This paper examines the spatio-temporal distribution of surface water in the entire Ganga basin to understand the actual causes of water shortage during lean season. Based on DEM, slope, soil, LULC and weather data, the SWAT model has been run at the catchment scale with a good performance under R2 and NSE evaluation methods. The study shows that annually Ganga basin of India is rich in water (average 1216165.5 cumec) and majority of the catchments delivers enough water to the main stream but during lean season only above Ramganga, Ghaghara, Gandak and Yamuna lower are active, which together contributes 60.6% of the lean season water discharge to the main channel of Ganga. Likewise, India, annual discharge in Bangladesh (average 65764 cumec) is satisfactory, but lean season water flow has only 3% of the annual, is very meagre which affects actual water availability of northwestern part of the country. The study also established that actual evapotranspiration of the entire basin is much higher than precipitation during the lean season and indicated a great deviation between supply and demand which concluded water stress condition in the Ganga basin.