UC Davis

Abstract Agricultural managed aquifer recharge (AgMAR) is a strategy whereby surface water is used to intentionally flood croplands to recharge underlying aquifers. However, nitrate (NO 3 − ) contamination in agriculturally intensive regions poses a threat to groundwater resources under AgMAR. We use a reactive transport model to understand the effects of AgMAR management strategies (i.e., by varying the frequency, duration between flooding events, and amount of water) on NO 3 − leaching to groundwater under different stratigraphic configurations and antecedent moisture conditions. We examine the potential of denitrification and nitrogen retention in deep vadose zone sediments (∼15 m) using variable AgMAR application rates on two‐dimensional representations of differently textured soils, soils with discontinuous bands/channels, and with preferential flow paths characteristic of agricultural fields. Simulations indicate finer textured sediments, alone or embedded within/adjacent to high flow regions, are important reducing zones providing conditions needed for denitrification. Simulation results suggest that applying water all‐at‐once rather than in increments transports higher concentrations of NO 3 − deeper into the profile, which may exacerbate groundwater quality. This transport into deeper depths can be aggravated by wetter antecedent soil moisture conditions. However, applying water all‐at‐once also increases denitrification within the vadose zone by promoting anoxic conditions. We conclude that AgMAR can be designed to enhance denitrification in the subsurface and reduce NO 3 − leaching to groundwater, while specifically accounting for lithologic heterogeneity, antecedent soil moisture conditions, and depth to the water table. Our findings are potentially relevant to other systems that experience flooding inundation such as floodplains and dedicated recharge basins. Key Points A modeling study shows that agricultural managed aquifer recharge (AgMAR) variably impacts the timing and quantity of nitrate loading to groundwater as a function of stratigraphy Under AgMAR, finer textured sediments are important reducing zones acting as permanent sinks of nitrate via denitrification Model results pertaining to different denitrification rates under varied ponding conditions are relevant to other landscape settings