The wind wake effect of offshore wind farms affects the hydrodynamical conditions in the ocean, which has been hypothesized to impact marine primary production. So far only little is known about the ecosystem response to wind wakes under the premisses of large offshore wind farm clusters. Here we show, via numerical modeling, that the associated wind wakes in the North Sea provoke large-scale changes in annual primary production with local changes of up to ±10% not only at the offshore wind farm clusters, but also distributed over a wider region. The model also projects an increase in sediment carbon in deeper areas of the southern North Sea due to reduced current velocities, and decreased dissolved oxygen inside an area with already low oxygen concentration. Our results provide evidence that the ongoing offshore wind farm developments can have a substantial impact on the structuring of coastal marine ecosystems on basin scales.