The depletion and variations of groundwater storage~(GWS) are of critical importance for sustainable groundwater management. In this work, we use Gravity Recovery and Climate Experiment (GRACE) to estimate variations in the terrestrial water storage~(TWS) and use it in conjunction with the Global Land Data Assimilation System~(GLDAS) data to extract GWS variations over time for Indus river basin~(IRB). We present a data processing framework that processes and combines these data-sets to provide an estimate of GWS changes. We also present the design of a band-limited optimally concentrated window function for spatial localization of the data in the region of interest. We construct the so-called optimal window for the IRB region and use it in our processing framework to analyze the GWS variations from 2005 to 2015. Our analysis reveals the expected seasonal variations in GWS and signifies groundwater depletion on average over the time period. Our proposed processing framework can be used to analyze spatio-temporal variations in TWS and GWS for any region of interest.