Nitrogen transformations and their response to salinization were studied in bottom sediment of a coastal freshwater lake (Haringvliet Lake, The Netherlands). The lake was formed as the result of a river impoundment along the south-western coast of the Netherlands, and is currently targeted for restoration of estuarine conditions. Nitrate porewater profiles indicate complete removal of NO-3 within the upper few millimeters of sediment. Rapid NO-3 consumption is consistent with the high potential rates of nitrate reduction (up to 200 nmolNcm-3h-1) measured with flow-through reactors (FTRs) on intact sediment slices. Acetylene-block FTR experiments indicate that complete denitrification accounts for approximately half of the nitrate reducing activity. The remaining NO-3 reduction is due to incomplete denitrification and alternative reaction pathways, most likely dissimilatory nitrate reduction to NH+4 (DNRA). Results of FTR experiments further indicate that increasing bottom water salinity may lead to a transient release of NH+4 and dissolved organic carbon from the sediment, and enhance the rates of nitrate reduction and nitrite production. Increased salinity may thus, at least temporarily, increase the efflux of NH4+ from the sediment to the surface water. This work shows that salinity affects the relative importance of denitrification compared to alternative nitrate reduction pathways, limiting the ability of denitrification to remove bioavailable nitrogen from aquatic ecosystems.