An appropriate description of nutrient exchanges at the sediment–water interface is prerequisite to model the eutrophication process in shallow coastal waters and its response to nutrient reduction policy. Most existing eutrophication models lack such a description due to the complexity of diagenetic processes. In this paper we use a two-layer, analytic diagenetic model applied in the North Sea coastal waters to derive simple mathematical relationships linking benthic N and P fluxes at the sediment water interface to organic matter inputs to the sediment. The two-layer, analytic diagenetic model describes organic matter mineralization, the resulting C, O2, N and P diagenetic processes and the sediment–water nutrient exchange fluxes as a function of bottom water nutrient concentration, total sediment organic matter mineralization, temperature and the sediment characteristics (porosity, tortuosity, bioturbation). The model was first verified by comparing nutrient and oxygen depth profiles and mineralization features along an eutrophication gradient with results obtained under the same conditions with a dynamic, vertically resolved model (OMEXDIA). The model was then applied to several stations in the North Sea characterized by different sediments and the results were compared with available data (NO3, NH4, PO4 and O2 sediment profiles and sediment–water fluxes). Finally, we performed numerous Monte-Carlo model simulations with different parameter values to derive simplified mathematical relationships of benthic N and P fluxes at the sediment water interface.