Elevated Arsenic (As) and Manganese (Mn) concentrations in shallow groundwater severely impact human consumption in the transboundary Ganga basin of South Asia. The obscurity in the distribution of these contaminants poses a significant challenge to clean water access initiatives. This study examines how geological and geochemical variations influence regional-scale As and Mn safe groundwater dynamics in shallow aquifers. Hydrostratigraphic models developed using boreholes (n = 75) from the 3 study areas, spanning from the central to lower Ganga basin showed heterogeneity in sedimentation patterns. Groundwater (n = 166) and sediment (n ~1300) samples revealed that sediment color, a geochemical proxy for As-safe groundwater, is limited by geologically-induced diverse sedimentation across the basin. Multivariate statistics on groundwater showed that Fe, As, and Mn mobilization processes are mutually inclusive, with As concentration more correlated with redox variables than Mn. We herein develop a conceptual model that states that overlapping Mn and Fe-reducing redox states induce a “lag-phase” that creates windows where consequent mobilization-immobilization mechanisms lead to Mn and As safe groundwater. The findings suggest that subsurface heterogeneity, resulting from the geodynamic evolution of the basin, causes variability in the redox zones that dictates the concentration of Fe, Mn and As in the groundwater. This study provides a comprehensive regional-scale understanding of the mobility of these geogenic pollutants, thereby enhancing decision-making for sustainable groundwater management.