Constructed and restored wetlands are a common practice to filter agricultural runoff, which often contains high levels of pollutants, including nitrate. Seepage waters from wetlands have potential to contaminate groundwater. This study used soil and water monitoring and hydrologic and nitrogen mass balances to document the fate and transport of nitrate in seepage and surface waters from a restored flow-through wetland adjacent to the San Joaquin River, California. A 39\% reduction in NO\textlessinf\textgreater3\textless/inf\textgreater-N concentration was observed between wetland surface water inflows (12.87±6.43mgL\textlesssup\textgreater-1\textless/sup\textgreater; mean±SD) and outflows (7.87±4.69mgL\textlesssup\textgreater-1\textless/sup\textgreater). Redox potentials were consistently below the nitrate reduction threshold (~250mV) at most sites throughout the irrigation season. In the upper 10cm of the main flowpath, denitrification potential (DNP) for soil incubations significantly increased from 151 to 2437mgNO\textlessinf\textgreater3\textless/inf\textgreater-Nm\textlesssup\textgreater-2\textless/sup\textgreaterd\textlesssup\textgreater-1\textless/sup\textgreater when nitrate was added, but showed no response to carbon additions indicating that denitrification was primarily limited by nitrate. Approximately 72\% of the water entering the wetland became deep seepage, water that percolated beyond 1-m depth. The wetland was highly effective at removing nitrate (3866kgNO\textlessinf\textgreater3\textless/inf\textgreater-N) with an estimated 75\% NO\textlessinf\textgreater3\textless/inf\textgreater-N removal efficiency calculated from a combined water and nitrate mass balance. The mass balance results were consistent with estimates of NO\textlessinf\textgreater3\textless/inf\textgreater-N removed (5085kgNO\textlessinf\textgreater3\textless/inf\textgreater-N) via denitrification potential. Results indicate that allowing seepage from wetlands does not necessarily pose an appreciable risk for groundwater nitrate contamination and seepage can facilitate greater nitrate removal via denitrification in soil compared to surface water transport alone.