The present work focused on the synergistic utilization of Gravity Recovery and Climate Experiment (GRACE) and GRACE-Follow On (FO) derived Ensemble Terrestrial Water Storage Anomaly (TWSA) from Jet Propulsion Lab (JPL), Centre for Space Research (CSR) and Goddard Space Flight Centre (GSFC), downscaled (GOU) TWSA and a gap filled JPL TWSA data and other hydrological variables to assess variability in groundwater storage (GWS) change in the last two decades (2002-2022) over Indus and Ganga river basins. The Indus basin witnessed a significant decline with a rate of change between -2.11 to -3.0 cm/yr and Ganga basin witnessed a significant decline of -1.27 cm/yr to -1.88 cm/yr after removing soil moisture estimates respectively. GWSA obtained from downscaled TWSA also indicated a significant negative trend. However, the magnitude of trend was considerably lower (0.9 cm/yr) than the ensemble (-1.27 cm/yr) and gap filled (-1.88 cm/yr) datasets. Ground observations also indicated a decline in GWSA in the Ganga basin with a rate of change -0.26 cm/yr. Validation of results with in-situ well data showed highest positive correlation (R = 0.78) and least Root Mean Squared Error (RMSE = 17.5 cm) with in-situ GWSA in the Indus basin during 2002-2022. Downscaling of GRACE TWSA employing self-supervised data assimilation can significantly reduce the general overestimation of trends in GWSA computed from GRACE and GRACE FO observations.