Mountains regions like Gilgit-Baltistan (GB) province of Pakistan are solely dependent on seasonal snow and glacier melt. In Indus basin which forms in GB, there is a need to manage water in a sustainable way for the livelihood and economic activities of the downstream population. It is important to monitor water resources that include glaciers, snow-covered area, lakes, etc., besides traditional hydrological (point-based measurements by using the gauging station) and remote sensing-based studies (traditional satellite-based observations provide terrestrial water storage (TWS) change within few centimeters from the earth’s surface); the TWS anomalies (TWSA) for the GB region are not investigated. In this study, the TWSA in GB region is considered for the period of 13 years (from January 2003 to December 2016). Gravity Recovery and Climate Experiment (GRACE) level 2 monthly data from three processing centers, namely Centre for Space Research (CSR), German Research Center for Geosciences (GFZ), and Jet Propulsion Laboratory (JPL), System Global Land Data Assimilation System (GLDAS)-driven Noah model, and in situ precipitation data from weather stations, were used for the study investigation. GRACE can help to forecast the possible trends of increasing or decreasing TWS with high accuracy as compared to the past studies, which do not use satellite gravity data. Our results indicate that TWS shows a decreasing trend estimated by GRACE (CSR, GFZ, and JPL) and GLDAS-Noah model, but the trend is not significant statistically. The annual amplitude of GLDAS-Noah is greater than GRACE signal. Mean monthly analysis of TWSA indicates that TWS reaches its maximum in April, while it reaches its minimum in October. Furthermore, Spearman’s rank correlation is determined between GRACE estimated TWS with precipitation, soil moisture (SM) and snow water equivalent (SWE). We also assess the factors, SM and SWE which are the most efficient parameters producing GRACE TWS signal in the study area. In future, our results with the support of more in situ data can be helpful for conservation of natural resources and to manage flood hazards, droughts, and water distribution for the mountain regions.