Nitrate reduction process rates (denitrification, dissimilatory nitrate reduction to ammonium rate - DNRA, anammox) were collected during a research cruise to the Baltic Sea during May-June 2016 as part of the Vici Project “Response of the Iron Biogeochemical Cycle on Continental Shelves to Seawater Deoxygenation” and the BONUS-COCOA project. Sediment sampling and incubation experiments were carried out onboard the RV Pelagia (NIOZ, Netherlands, cruise 64PE411). Whole cores were incubated on board at in situ bottom water temperature and oxygen conditions in the dark. Stable isotopically labelled nitrate (15N-NO3-) was added to overlying water and cores were capped according to Nielsen et al. (1992). Three cores were 'sacrificed' over time (2, 4h, 6h, 8h) after 15-NO3- addition by slurrying the surface and sampling for dissolved gas and solutes. Slurry experiments were also carried out in parallel to core incubations at each site (Risgaard-Petersen et al., 2003; Song et al., 2013). Analysis of 15N compounds was carried out at the University of Southern Denmark (Dalsgaard et al., 2013). Process rates were calculated according to Song et al. (2016). In addition to the calculated process rates, the dataset includes the following in situ parameters: bottom water salinity, temperature and oxygen (obtained from CTD sensors), nitrate (measured spectrophotometrically according to Schnetget and Lehners, 2014) and total organic carbon data (derived from Hermans et al., 2019).