Effects of inputs of organic matter were studied on bioavailability and cycling of hydrophobic organic contaminants (HOCs) in benthic ecosystems of the Baltic and Kattegat Seas. In laboratory experiments, effects of microalgae additions were studied on the bioaccumulation of HOCs (PCBs and PAHs) by the blue mussel Mytilus edulis, the brittle star Amphiura filiformis, and the polychaete Nereis diversicolor. Contrary to the equilibrium partitioning theory, bioaccumulation was proportional to the concentrations of algae and organic carbon. This was attributed to the high nutritional quality of the algal organic carbon and suggests that feeding rather than equilibrium partitioning governed bioaccumulation in these species. In the field, annual mass fluxes of PCBs in blue mussels and in brittle stars were estimated, as well as contaminant transfer to higher trophic levels. Our results suggest that: i) Eutrophication processes may contribute to increase HOC accumulation in benthic species. ii) Temporal variation in the quantity and quality of organic carbon needs to be considered when assessing contamination of benthic systems. iii) Macrofaunal feeding activities are important for the benthic-pelagic coupling of HOCs. iv) Bioturbation enhances the release of HOCs from sediment to overlying water.