Agricultural managed aquifer recharge (AgMAR) is a proposed management strategy whereby surface water flows are used to intentionally flood croplands with the purpose of recharging underlying aquifers. However, legacy nitrate (NO3-) contamination in agriculturally-intensive regions poses a threat to groundwater resources under AgMAR. To address these concerns, we use a reactive transport modeling framework to better understand the effects of AgMAR management strategies (i.e., by varying the frequency, duration between flooding events, and amount of water) on N leaching to groundwater under different stratigraphic configurations and antecedent moisture conditions. In particular, we examine the potential of denitrification and nitrogen retention in deep vadose zone sediments using variable AgMAR application rates on two-dimensional representations of differently textured soils, soils with discontinuous bands/channels, and soils with preferential flow paths characteristic of typical agricultural field sites. Our results indicate that finer textured sediments, such as silt loams, alone or embedded within high flow regions, are important reducing zones providing conditions needed for denitrification. Simulation results further suggest that applying recharge water all-at-once, rather than in increments, increases denitrification within the vadose zone, but transports higher concentrations of NO3- deeper into the profile. This transport into deeper depths can be aggravated by wetter antecedent soil moisture conditions. We conclude that ideal AgMAR management strategies can be designed to enhance denitrification in the subsurface and reduce N leaching to groundwater, while specifically accounting for lithologic heterogeneity, antecedent soil moisture conditions, and depth to the water table.