Understanding recharge in the Mekong Delta is critical for the delta's groundwater resources, and requires the investigation of recharge processes at the local scale. In this study of the north eastern area of the Mekong Delta, time-series of environmental tracer data (δ18O, δ2H, major ions and 3H) and markers of rural pollution (NH4 and NO3) were used to highlight localized recharge and impacts on groundwater quality. Results highlighted new hydrological insights into recharge processes, including that the Pleistocene aquifer receives recent recharge (< 60 years), predominantly during high rainfall months (> 100 mm/month). However, due to shallow clay layers there are significant spatial variations in these recharge processes, which were observed in the seasonal fluctuation of groundwater δ18O values in groundwater. Wet season δ18O changes ranged from below analytical uncertainty (≤ 0.10 ‰) to up to 0.56 ‰, and the calculated fraction of rainfall contribution to the aquifer is ≤5 % to 16 %. Rainfall recharge via the acrisol soils results in low groundwater EC (20–55 μS/cm), acidic groundwater (pH 3.6–5.6), and may also have resulted in the low groundwater NO3 concentrations (≤ 5.3 mg NO3/L) at many sites due to adsorption, therefore delaying not reducing NO3 contamination. Site specific variations in nitrogen processes includes increased NO3 (to 29.7 mg/L) from fertiliser transfers or nitrification, and increased NH4 (to 1.4 mg/L) likely due to the recharge of irrigation waters. Unlike other recharge areas across the northern Mekong Delta, this north-eastern region provides a groundwater resource unaffected by arsenic contamination. Therefore, these results should inform on priority areas for protection from further contamination by rural anthropogenic activities.