Intermontane basin aquifers worldwide, particularly in the Himalayan region, are recharged largely by the adjoining mountains. Recharge in these basins can occur either by water infiltrating from streams near mountain fronts (MFs) as mountain front recharge (MFR) or by sub-surface mountain block infiltration as mountain block recharge (MBR). MFR and MBR recharge are challenging to distinguish and are least quantified, considering the lack of extensive understanding of the hydrological processes in the mountains. This study used oxygen and hydrogen isotopes (δ18 O and δ2 H), electrical conductivity (EC) data, hydraulic head, and groundwater level data to differentiate MFR and MBR. Groundwater level data provide information about the groundwater-surface water interactions and groundwater flow directions, whereas isotopes and EC data are used to distinguish and quantify different recharge sources. The present methodology is tested in an intermontane basin of the Himalayan region. The results suggest that karst springs (KS) and deep groundwater (DGW) recharge are dominated by snowmelt (47% ± 10% and 46% ± 9%) as MBR from adjacent mountains, insignificantly affected by evaporation. The hydraulic head data and isotopes indicate Quaternary shallow groundwater (SGW) aquifer system recharge as MFR of local meteoric water with significant evaporation. The results indicate several flow paths in the aquifer system, a local flow for KS, intermediate flow for SGW, and regional flow for DGW. The findings will significantly impact water resource management in the area and provide vital baseline knowledge for sustainable groundwater management in other Himalayan intermontane basins.