©2019. The Authors. Groundwater aquifers provide an important “insurance” against climate variability. Due to prolonged droughts and/or irrigation demands, groundwater exploitation results in significant groundwater storage depletion. Managed aquifer recharge (MAR) is a promising management practice that intentionally places or retains more water in groundwater aquifers than would otherwise naturally occur. In this study, we examine the possibility of using large irrigated agricultural areas as potential MAR locations (Ag-MAR). Using the California Central Valley Groundwater-Surface Water Simulation Model we tested four different agricultural recharge land distributions, two streamflow diversion locations, eight recharge target amounts, and five recharge timings. These scenarios allowed a systematic evaluation of Ag-MAR on changes in regional, long-term groundwater storage, streamflow, and groundwater levels. The results show that overall availability of stream water for recharge is critical for Ag-MAR systems. If stream water availability is limited, longer recharge periods at lower diversion rates allow diverting larger volumes and more efficient recharge compared to shorter diversion periods with higher rates. The recharged stream water increases both groundwater storage and net groundwater contributions to streamflow. During the first decades of Ag-MAR operation, the diverted water contributed mainly to groundwater storage. After 80 years of Ag-MAR operation about 34% of the overall diverted water remained in groundwater storage while 66% discharged back to streams, enhancing base flow during months with no recharge diversions. Groundwater level rise is shown to vary with the spatial and temporal distribution of Ag-MAR. Overall, Ag-MAR is shown to provide long-term benefits for water availability, in groundwater and in streams.