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Managed aquifer recharge (MAR) can provide long‐term storage of excess surface water for later use. While decades of research have focused on the physical processes of MAR and identifying suitable MAR locations, very little research has been done on how to consider competing factors and tradeoffs in siting MAR facilities. This study proposes the use of a simulation‐optimization (SO) framework to map out a cost‐effectiveness frontier for MAR by combining an evolutionary algorithm with two objective functions that seek to maximize groundwater storage gains while minimizing MAR cost. We present the theoretical framework along with a real‐world application to California's Central Valley. The result of the SO framework is a Pareto front that allows identifying suitable MAR locations for different levels of groundwater storage gain and associated MAR project costs, so stakeholders can evaluate different choices based on cost, benefits, and tradeoffs of MAR sites. Application of the SO framework to the Central Valley shows groundwater can be recharged from high‐magnitude (95th percentile) flows at a marginal cost of $57 to $110 million per km³. If the 10 percent largest flows are recharged the total groundwater storage gain would double and the marginal costs would drop to between $30 and $50 million per km³. If recharge water is sourced from outside local basins (e.g., the Sacramento‐San Joaquin Delta), groundwater storage gain is approximately 25%–80% greater than can be achieved by recharging local flows, but the total cost is about 10%–15% higher because of additional lift cost.