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This study aims to quantify the interannual variations of groundwater storage changes (GWSCs) over India. GWSCs are derived from the gravity recovery and climate experiment (GRACE) and global land data assimilation system (GLDAS)-Noah life safety model (LSM) for the period 2003-2015. Estimated GWSCs are validated with the satellite altimetry over the six lake stations. The variability of GWSC and altimetry water-level heights are assessed with the cross-correlation and plotting analysis. Annual trends of GWSC and GRACE in terrestrial water storage (TWS) were estimated using the non-parametric Mann-Kendall test and Sen's slope method. Results suggest that GWSC and TWS have declined in northern India at the rate of approximate to 1.6 cm yr-1 and in southern and western central India at the rate of approximate to 0.5 cm yr-1. Impacts of short-term climate perturbations such as El Nino and La Nina for the GWSCs are assessed. During the El Nino period, the decline of GWSC over northern India enhanced, whereas during the La Nina period, the recovery of GWSC is evident. These interannual variations of GWSCs over India are attributed by interannual precipitation changes. Under the global warming scenario, the occurrences of El Nino events are likely to enhance in the future, and our findings help the water resource management policy makers for necessary actions during such short-term climate perturbations.