Groundwater plays a major role in the hydrological processes driven by climate change and human activities, particularly in upper mountainous basins. The Jinsha River Basin (JRB) is the uppermost region of the Yangtze River and the largest hydropower production region in China. With the construction of artificial cascade reservoirs increasing in this region, the annual and seasonal flows are changing and affecting the water cycles. Here, we first infer the groundwater storage changes (GWSC), accounting for sediment transport in JRB, by combining the Gravity Recovery and Climate Experiment mission, hydrologic models and in situ data. The results indicate: (1) the average estimation of the GWSC trend, accounting for sediment transport in JRB, is 0.76?±?0.10?cm/year during the period 2003 to 2015, and the contribution of sediment transport accounts for 15%; (2) precipitation (P), evapotranspiration (ET), soil moisture change, GWSC, and land water storage changes (LWSC) show clear seasonal cycles; the interannual trends of LWSC and GWSC increase, but P, runoff (R), surface water storage change and SMC decrease, and ET remains basically unchanged; (3) the main contributor to the increase in LWSC in JRB is GWSC, and the increased GWSC may be dominated by human activities, such as cascade damming and climate variations (such as snow and glacier melt due to increased temperatures). This study can provide valuable information regarding JRB in China for understanding GWSC patterns and exploring their implications for regional water management.