Artificial recharge of groundwater is an increasingly important method for augmenting groundwater supply and can have a positive or negative influence on the quality of water resources. We instrumented a managed aquifer recharge (MAR) pond in central coastal California to assess how patterns of infiltration and recharge affect the load of nitrate delivered to the underlying aquifer. The concentration of nitrate in infiltrating water consistently decreased during passage through the first metre of subsurface soils. Enrichment of 18O and 15 N in the residual nitrate in infiltrating water proceeded in a ratio of 1:2, indicating that denitrification plays a significant role in the quantitative reduction of nutrients exported during infiltration through shallow soils. The extent and rate of nitrate removal was spatially and temporally variable across the bottom of the recharge pond, with 30% to 60% of the nitrate load being removed over the first 6 weeks of managed aquifer recharge operation. During the period of highest N loading to the system, when the average infiltration rate was > 1 m/day, the recharge pond achieved a load reduction efficiency of 7 kg NO3−-N/day/ha, which compares favourably to nitrate load reductions achieved by treatment wetlands. Groundwater mounding and water composition below the recharge pond suggest that recharge and subsequent lateral transport occur heterogeneously in the underlying aquifer. Nitrate concentrations in the aquifer following infiltration were lowered primarily by dilution, with little evidence for additional denitrification occurring in the aquifer in comparison to high rates documented during shallow infiltration. Copyright © 2011 John Wiley & Sons, Ltd.