Sediment-water fluxes of NH₄⁺, NO₃ ^-, dissolved inorganic carbon, and O₂ were measured in cores collected from the upper Rowley River estuary, Massachusetts, and used to calculate rates of organic nitrogen (N) mineralization, nitrification, and coupled and direct denitrification (DNF). The cores contained ¹⁵N label in benthic microalgae (BMA) and in NO₃^- in the overlying water as a result of an ongoing whole-estuary ¹⁵NO ₃^- enrichment study (NISOTREX II). The tracer allowed for estimation of gross NO₃^- regeneration in sediments and the contribution of BMA derived N to total mineralization. The mean mineralization rate between sites was 16.0 ± 2.0 mmol N m^-2 d^-1. Approximately 13 to 56% of the mineralized N was nitrified at rates ranging from 1.8 to 10.1 mmol N m^-2 d^-1. Total denitrification was dominated by direct DNF (3.6 mmol N m^-2 d ^-1) furthest upstream, where NO₃^- concentrations were highest. Coupled DNF was most important (8.0 mmol N m ^-2 d^-1) in the sediments with high nitrification and low water column NO₃^-. A gross NO₃^- flux from sediments to water of 0.9 to 2.1 mmol N m^-2 d^-1 was estimated from the isotope dilution of δ¹⁵NO ₃^- in the overlying water of the cores. The isotope dilution seen in the cores was also detected as a deviation from conservative δ¹⁵NO₃^- mixing along estuarine transects. Incorporation of this NO₃^- regeneration into the DNF calculations effectively increased the estimate of direct DNF by up to 50% and decreased the coupled DNF estimate by up to 220%. Increasing δ ¹⁵NH₄⁺ in the water of the cores indicated that the ¹⁵N-labelled BMA were preferentially mineralized over bulk sediment organic N. Additional ¹⁵N enrichments in the sediment bacterial biomarker diaminopimelic acid showed a link among ¹⁵N-labeled BMA, active bacteria, and ¹⁵NH ₄⁺released to the overlying water. Based on δ ¹⁵NH₄⁺ enrichments in the cores, BMA accounted for approximately 50 to 100% of the N mineralized. An isotopic enrichment of δ¹⁵NH₄⁺ above background in the estuary was observed at a magnitude consistent with the core-based rates of BMA mineralization. These results provide further evidence that BMA are not unidirectional sinks for water column-dissolved organic nitrogen, but instead act to turn over N between sediments and estuarine water on the scale of days.