Nutrient loading of aquatic ecosystems results in more food for benthic macrofaunal communities but also increases the risk of hypoxia, resulting in a reduction or complete loss of benthic biomass. This study investigates the interaction between eutrophication, hypoxia and benthic biomass with emphasis on the balance between gains and loss of benthic biomass due to changes in nutrient loadings. A physiological fauna model with 5 functional groups was linked to a 3D coupled hydrodynamic-ecological Baltic Sea model. Model results revealed that benthic biomass increased between 0 and 700% after re-oxygenating bottom waters. Nutrient reduction scenarios indicated improved oxygen concentrations in bottom waters and decreased sedimentation of organic matter up to 40% after a nutrient load reduction following the Baltic Sea Action Plan. The lower food supply to benthos reduced the macrofaunal biomass up to 35% especially in areas not currently affected by hypoxia, whereas benthic biomass increased up to 200% in areas affected by eutrophication-induced hypoxia. The expected changes in benthic biomass resulting from nutrient load reductions and subsequent reduced hypoxia may not only increase the food supply for benthivorous fish, but also significantly affect the biogeochemical functioning of the ecosystem.