Nitrate in drinking water may cause serious health problems for consumers. Agricultural activities are known to be the main source of groundwater nitrate contaminating rural domestic and urban public water supply wells in farming regions. Management practices have been proposed to reduce the amount of nitrate in groundwater, including improved nutrient management practices and "pump and fertilize" with nitrate-affected irrigation wells. Here, we evaluate the feasibility and long-term impacts of agricultural managed aquifer recharge (Ag-MAR) in the source area of public water supply wells. A numerical model of nitrate fate and transport was developed for the Modesto basin, part of California's Central Valley aquifer system. The basin is representative of semi-arid agricultural regions around the world with a diversity of crop types, overlying an unconsolidated sedimentary aquifer system. A local public supply well in an economically disadvantaged community surrounded by farmland was the focus of this study. Model scenarios implemented include business as usual, alternative low-impact crops, and Ag-MAR in the source area of the public supply well. Alternative nutrient management and recharge practices act as remediation tools in the area between farmland and the public supply well. Improved agricultural source area management practices are shown to be an effective tool to maintain or even enhance groundwater quality in the targeted supply well while remediating ambient groundwater. Best results are obtained when lowering nitrate load while also increasing recharge in the source area simultaneously. This scenario reduced nitrate in the supply well's drinking water by 80% relative to the business as usual scenario. It also remediated ambient groundwater used by domestic wells between the source area farmlands and the supply well and showed 60% more reduction of nitrate after 60 years of application. Increasing recharge led to shorter initial response time (five years) and showed the most sustainable impact. Our analysis further suggests that Ag-MAR in a highly discontinuous, wide-spread pattern leads to slow water quality response and may not yield sufficient water quality improvements.