Seagrass meadows can play a key role in mitigating the effects of nutrient pollution through their function as a nutrient filter. In addition to assimilating nutrients in biomass, seagrass meadows stimulate biogeochemical activity through the release of oxygen and labile carbon from roots and rhizomes. Nitrate reduction processes in seagrass meadow sediment may therefore be substantial, and the balance between competing processes, including denitrification, anammox, and dissimilatory nitrate reduction to ammonium (DNRA) can determine whether reactive nitrogen is retained in the sediment or is lost as inert nitrogen gas. We used a novel push-pull incubation method and the isotope pairing technique to study nitrate reduction in situ in subsurface sediments of a restored seagrass meadow in the Virginia coastal bays. Denitrification was the dominant nitrate reduction process; however, DNRA was a substantial alternative, accounting for 40% of the total nitrate reduction on average. Anammox rates were minimal. Seasonal measurements of in situ nitrate reduction showed a pattern correlated with seagrass growth; however, rates were highly variable and did not vary significantly with season, likely due to the heterogeneity of the sediment. Rates of denitrification in the seagrass meadow were comparable to rates measured in natural systems, and were greater than rates in adjacent bare sediment. Furthermore, potential rates were an order of magnitude greater than ambient rates, suggesting that an increased nutrient load to the seagrass meadow could enhance denitrification rates and increase the removal of nitrate from the ecosystem. We conducted our study at a large-scale restoration site (>17 km2), and our results suggest that restoration of seagrass meadows is an effective means of creating a natural nutrient filter.