We measured fluxes of NH₄⁺ and NO₃⁻ and δ¹⁵N of NH₄⁺, sediment, and porewater NH₄⁺ from incubated sediment cores along a nitrate gradient and in different seasons from Childs River, MA. NH₄⁺ flux was low at the downstream site with the lowest concentration of organic matter (high salinity) but otherwise did not differ along the estuary. The δ¹⁵N of regenerated NH₄⁺ ranged from +6.1‰ to +15.3‰ but did not vary significantly with season or salinity; the mean for the entire estuary was +10.4 ± 0.5‰. Based on differences between the δ¹⁵N of regenerated NH₄⁺ and sediment, and expected isotopic fractionation due to remineralization, we concluded that nitrification occurred after remineralization of NH₄⁺. Differences between the δ¹⁵N of regenerated NH₄⁺ and the δ¹⁵N of porewater NH₄⁺ provided further evidence of nitrification. We estimated that 11% to 48% of remineralized NH₄⁺ underwent coupled nitrification–denitrification before release into the water column. In spite of losses to denitrification, NH₄⁺ flux released 1.4 mol N m⁻² year⁻¹ to the water column and could provide 42% of phytoplankton nitrogen requirements.