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• Links between nutrients and predators can be investigated using ecosystem models. • Nutrient-driven covariance patterns are documented in a coastal area of the Baltic. • Local declines in productivity affected entire benthic food web, including birds. With successful mitigation of eutrophication and the reductions in nutrient concentrations and productivity of coastal waters, the targets set in nature protection legislation in the EU and the United States may no longer be achievable in regions where key ecological functions are coupled to benthic productivity. Yet, due to both the patchiness of invertebrate distribution and the fragmented and non-integrated nature of monitoring data direct coupling between nutrients, productivity and predators has proven difficult to achieve. As a result, assessments of the status of food webs based solely on monitoring data remains an almost impossible task. The aim of this modelling study was to test the application of fine-scale ecosystem models for assessing cost-benefits or food-web consequences of management decisions in relation to water quality of coastal waters. We applied a fine-scale ecosystem model calibrated against measurements in a coastal area in the Baltic Sea to quantify responses in higher trophic levels to changes in eutrophication over a 18-year period, 1990-2007. The resulting spatio-temporal trends reveal a number of characteristic responses and spatial dimensions in coastal food webs. The coupled hydrodynamic, bio-geochemical and waterbird energetics modules indicated nutrient-related changes and fine-scale covariance patterns across all trophic levels. A 50 % decline in bivalve biomass was predicted in a zone characterised by the overall highest biomass of bivalves and highest densities of bivalve-feeding waterbirds. The nutrient-driven local decline in productivity affected the entire food web with a predicted annual mortality of 72,000 Long-tailed Ducks Clangula hyemalis. This model-based study suggests a strong nutrient control of the available food supply to bivalve-feeding birds in coastal areas. Our results also show that high-resolution ecosystem models are required to resolve the heterogeneous distribution of effects. [ABSTRACT FROM AUTHOR]