Flood managed aquifer recharge (Flood-MAR) is an emerging practice to enhance groundwater sustainability through recharge of aquifers. However, in agricultural systems Flood-MAR may harm groundwater quality, given residual soil nitrate (NO3-). This research evaluated Flood-MAR NO3- leaching risk across a precipitation and soil textural gradient in a globally important agricultural region, California's Central Valley, and whether Flood-MAR timing strategies could mitigate the risk. Using multi-decadal root zone water quality model simulations of irrigated and fertilized maize (250 kg N ha(-1) year(-1)) on well-drained soils as a representative case-study, results suggest Flood-MAR can be used with near-negligible additional NO3- leaching in locations with median annual precipitation >400 mm year(-1). In those locations, wet-year precipitation leached most residual NO3- without practicing Flood-MAR. At drier locations, Flood-MAR NO3- leaching risk increased most clearly in loamy soils. Additional NO3- leaching risk increased in drier climates because minimal precipitation-driven deep percolation maintained residual NO3- accumulation across growing seasons. In fine-texture soils, NO3- leaching risk was mitigated by denitrification, preventing residual NO3- accumulation. Flood-MAR practices diminished denitrification, leaching NO3- rapidly when soils were colder and biogeochemically inactive, and thereby decreased growing season denitrification when soils were warmer and denitrification rates higher. Effects of Flood-MAR timing strategies (January Flood-MAR vs. March Flood-MAR), combined with variable pauses among applications (3- vs. 7- vs. 21-day intervals) were negligible. Infrequent Flood-MAR should be practiced with care in arid climates and especially after prolonged droughts coinciding with more limited irrigation water supplies that constrain salt-leaching practices all favoring residual NO3- accumulation.