Northwest part of India is an agriculturally active region experiencing rapid rise in food production and steep decline in groundwater levels. The freshwater requirement is mostly met by regional aquifers which are inherently heterogeneous and undergoing extensive human inducted perturbations. These factors pose great challenge in planning sustainable groundwater management. In this study, environmental isotopes (²H, ¹⁸O, ¹³C, ³H and ¹⁴C) were applied to understand the regional recharge mechanism during the last 30 ka and hydrogeological controls impacting the aquifer dynamics and inter-aquifer connectivity of the Ghaggar River basin. Rayleigh distillation modeling indicates that major groundwater recharge is through monsoonal rains while rainfall during other seasons is lost either through evaporation or surface runoff. The evaporation loss is estimated to be 1.5 to 10% and more pronounced in the southern part of the study area. Regional recharge from Siwalik foothills contributes to groundwater up to a depth of 250 m below ground level (bgl). The lumped parameter modeling (LPM) using 3H data estimated groundwater ages 34.7 ± 12.1 and 95.8 ± 11.3 years for shallow and deep aquifers respectively. Radiocarbon dating indicates presence of paleogroundwater (0.4 to 28.6 ka before present, BP) in the deeper aquifer of central part of the study area. Interpretation of the paleowater and paleoprecipitation isotope data in conjunction with available paleogeomorphologic information suggests two different recharge phases. Phase I extending from~28.6 to 10.1 ka, showed ~48–61% contribution from isotopically depleted perennial river system. Phase II spanning from ~12.5 to 0.4 ka BP showed insignificant contribution from river recharge, which can be attributed to the decreased strength of the perennial river flows. The research methodology proposed in this study will be beneficial in improving the understanding of groundwater storage and its variability with changes in regional climatic conditions.