Growing demands on water supply worldwide have resulted in aquifer overdraft in many regions, especially in alluvial basins under intensive irrigation. Overdraft can further lead to serious deterioration of groundwater quality. Managed aquifer recharge (MAR) has been shown to mitigate groundwater overdraft, but whether MAR can actually stabilize or reverse ongoing declines in regional groundwater quality caused by non-point sources has not been demonstrated. This study addresses the question by investigating the impact of different MAR strategies on regional groundwater quality. A geostatistical model was first used to characterize a heterogeneous alluvial aquifer system in a portion of the Tulare Lake Basin. Three-dimensional numerical models were then employed to simulate groundwater flow and mass transport. Next, MAR strategies were applied in locations with different geological conditions and under different irrigation activities, and their effect on groundwater quality was evaluated. Results demonstrate the potential of significant, long-term benefits for regional groundwater quality by applying strategic, high-intensity recharge operations on geologically favorable subregions. Siting MAR above the incised valley fill (IVF) deposit, a near-surface paleochannel containing unusually coarse, high-conductivity hydrofacies, led to more extensive improvement in groundwater quality (i.e., salinity) due to significant vertical flow and lateral outward flow from the IVF. Overall, decades would be required to alleviate groundwater quality concerns in the studied 189 km^2 region. Simulations indicate that deeply situated concentrations remain below the secondary maximum contaminant level as the solute mass migrates downward with prominent contribution from attenuation via dispersion and matrix diffusion.