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Gravity Recovery and Climate Experiment (GRACE) and satellite altimetry are suitable for the precise measurement of terrestrial water storage (TWS) and lake water level variations from space. In this study, two GRACE solutions, namely, spherical harmonics (SH) and mascon (MSC), are utilized with the Global Land Data Assimilation System (GLDAS) model to estimate the spatial and temporal variations of TWS in the Upper Indus Basin (UIB) for the study period of January 2003 to December 2016. The TWS estimated by SH, MSC, and the GLDAS model are consistent and generally show negative trends of -4.47 ± 0.38 mm/year, -4.81 ± 0.49 mm/year, and -3.77 ± 0.46 mm/year, respectively. Moreover, we use the GLDAS model data to understand the roles of variations in land surface state variables (snow water equivalent (SWE), soil moisture, and canopy water storage) in enhancing or dissipating the TWS in the region. Results indicate that SWE, which has a significant contribution to GRACE TWS variability, is an important parameter. Spearman's rank correlations are calculated to demonstrate the relationship of the GLDAS land surface state variables and the GRACE signals. A highly positive correlation between SWE with TWS is estimated by SH and MSC as 0.691 and 0.649, respectively, indicating that the TWS signal is mainly reliant on snow water in the study region. The ground water storages estimated by SH and MSC solutions are nearly stable with slight increasing trends of 0.63 ± 0.48 mm/year and 0.29 ± 0.51 mm/year, respectively. We also take advantage of the potential of satellite altimetry in measuring lake water level variations, and our result indicates that Cryosat-2 SARin mode altimetry data can be used in estimating small water bodies accurately in the high mountainous region of the UIB. Moreover, the climate indices data of El-Niño Southern Oscillation and Pacific Decadal Oscillation are analyzed to determine the influence of pacific climatic variability on TWS.