This study aimed at characterizing the groundwater flow pattern in a semi-arid agricultural area in northern India crossed by an intermittent monsoon-controlled watercourse, the Najafgarh drain. More specifically, it focused on studying the impact of groundwater recharge from the riverbed to the regional aquifer using hydrogeochemical and isotopic data. Significant hydrogeochemical zonation was observed between the northern, central and southern sides of the drain, linked to different mineralization processes and mixings. Northward from the drain, groundwater was mainly brackish (4.1–23.4 mS/cm), due to dissolution of evaporites (halite and anhydrite). Southward from the drain, mostly fresh groundwater was found (from 0.5 to 2.3 mS/cm), revealing notable cation exchange processes. In the vicinity of the drain (central area), mineralization was intermediate (0.7–4 mS/cm) and groundwater showed low geochemical evolution, supposing a distinct origin. Stable isotopes of water (d18O, d2H) confirmed that central groundwater was not a simple mixing between northern and southern groundwater masses, but had a significant component of infiltrated surface water from the drain. Potentiometric data supported these findings and confirmed the contribution of the drain to the recharge of the aquifer, setting up a hydraulic barrier between north and south, despite surface water availability limited to the monsoon season and low hydraulic conductivity of the riverbed. This study demonstrates the value of the geochemical and isotopic analysis of groundwater to characterize groundwater flow pattern in peri-urban agricultural areas, especially surface water–groundwater interactions.