The metabolic inhibitor cycloheximide was used to estimate the influence of primarily unicellular eukaryotes (heterotrophic protozoa) on nutrient recycling in different types of sediments in the North Sea. Fluxes of dissolved inorganic nitrogen across the sediment–water interface were measured in undisturbed sediment cores (controls) and compared to fluxes in sediment cores with cycloheximide added. If eukaryotes play an important role in nutrient recycling, one would expect to find lower nitrogen sediment–water effluxes in cores with cycloheximide due to the inactivation of eukaryotes. This important role hypothesised for eukaryotes was not generally observed: Only at four of the nineteen stations were ammonium effluxes significantly higher in controls than in cores with cycloheximide, and at five stations nitrate effluxes were significantly higher in the controls than in the cores with cycloheximide. Eukaryotic activity apparently contributed to the sediment–water exchange of ammonium through mineralisation of organic matter, nitrification and the subsequent release of ammonium and nitrate at these stations. At most other stations no differences were obtained between controls and cores with cycloheximide. This suggests that bacteria were the most important nutrient mineralisers at these stations at the time of the cruises.