Primary production in the eutrophic Baltic Sea is limited by nitrogen availability; hence denitrification (natural transformation of nitrate to gaseous N(2)) in the sediments is crucial in mitigating the effects of eutrophication. This study shows that dissimilatory nitrate reduction to ammonium (DNRA) process, where nitrogen is not removed but instead recycled in the system, dominates nitrate reduction in low oxygen conditions (O(2) <110 μM), which have been persistent in the central Gulf of Finland during the past decade. The nitrogen removal rates measured in this study show that nitrogen removal has decreased in the Gulf of Finland compared to rates measured in mid-1990s and the decrease is most likely caused by the increased bottom water hypoxia.