Abstract Understanding of rainfall variability and its changing pattern play a significant role in water resource management. This study examined the seasonal and annual rainfall extent and its linkage with water availability over the Indus, Ganga, and Brahmaputra river basins (IGB) using Tropical Rainfall Measuring Mission (TRMM) from 1998 to 2017. The monsoonal and annual rainfall indicates a significant decreasing trend in the eastern while increasing in the western part of the IGB. Therefore, the Indus basin observed a positive rainfall trend as compared to the Ganga and Brahmaputra basins. However, the precipitation concentration index (PCI) shows irregular distribution with an insignificant trend. Therefore, we have analyzed the changing pattern of climatic variables (air temperature and rainfall) and their influence on terrestrial water storage (TWS) over the study area during 2003–2015. Results indicate a significant increase in mean annual temperature (0.02 ° C yr − 1 ) while a decrease in TWS (−12.6 mm yr − 1 ) over the region. The rainfall shows a positive and negative correlation with TWS (r = 15.8) and air temperature (r = −38.8), respectively. Therefore, the changing pattern of rainfall and air temperature can be attributed to the reduction of TWS in the IGB.