Coastal shelf seas are zones of intense nutrient cycling, where a strong coupling between the sediment and the water column enhances primary productivity. To identify factors that control the strength of this benthic-pelagic coupling we measured sediment characteristics, solute fluxes, and porewater nutrient profiles in spring along a south - north transect in the North Sea crossing distinct regions: the shallow Oyster Grounds closest to the Dutch shore, the shallow Dogger Bank, the 80-m deep central North Sea, and the 150-m deep Fladen Grounds between the north of Scotland and Norway. The data were used to constrain rates of different mineralization processes with the 1-D diagenetic model (OMEXDIA). Surprisingly, we found no major differences in the biogeochemical signature along the 670 km long North Sea transect, despite sediments ranging in median grainsize from 25 to 217 μm, and a permeability range >3 orders of magnitude. Total carbon mineralization ranged between 4 and 13.5 mmol C m−2 d−1, and decreased significantly northward. Oxic mineralization was the dominant mineralization process in all studied sites. Finest, least permeable sediments were found in the Fladen Grounds where highest denitrification rates were recorded, linked to high nitrate concentrations in the overlying water. The coarsest, most permeable sediments of the shallow Dogger Bank represented a transition area between the Oyster Grounds, where oxic mineralization was highest (75–90%), and the central North Sea samples, where anoxic mineralization increased relative to oxic mineralization due to higher bioturbation rates (oxic: 59–72%, anoxic: 27–39%). Overall, denitrification rates increased, while phosphorus removal tended to decrease northward. This contrasting behaviour in nitrogen and phosphorus removal was identified as a possible cause for decreasing DIN:DIP ratios in the water column towards the north.