Abstract A biological one-dimensional water column model for the simulation of the annual cycles of the phytoplankton dynamics and a physical transport model are coupled into a three-dimensional primary production model to estimate the annual primary production of the North Sea and its regional differences. The simulations are driven with actual forcing, taking into account monthly river loads from 14 rivers, daily velocities and diffusivities from a baroclinic North Sea model, and solar radiation calculated every 30 min. The high variability of the forcing generates considerable variability in the physical and biological dynamics. The simulated annual cycles of chlorophyll, phosphate and daily net primary production are validated with available data from different years in the sense that the simulated single year can be compared to the measured variability. Such comparisons show that the simulation reproduces the general features of annual phytoplankton cycles in terms of chlorophyll and the triggering nutrient phosphate. This establishes confidence in the calculated annual primary production of the North Sea area. The simulation of 1986 yields an integrated annual water column net production ranging between 92 and 345 g C m −2 yr −1 for different regions. The simulated annual production agrees quite well with the general quantitative knowledge of the observed yearly production, except for the British coast, where the production is overestimated due to lacking inorganic suspended matter attenuation. The mean net primary production of the North Sea is 145 g C m −2 yr −1.