The wind wake effect of offshore wind farms (OWFs) affects the hydrodynamical conditions in the ocean, which has been hypothesized to impact nutrient availability in surface waters and consequently marine primary production. However, this has not clearly been shown so far and little is known about the ecosystem response to wind wakes under the premisses of large OWF clusters. Here we show that the wind wakes of large OWF clusters in the North Sea provoke large scale changes in annual primary production with local changes of up to 10%, which occur not only in the direct vicinity of the OWF clusters but are distributed over a wider region. In addition, we found an increase in sediment biomass in deeper areas of the southern North Sea due to reduced current velocities. Our results show that the ongoing OWF developments can have a substantial impact on the structuring of coastal marine ecosystems.