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Benthic macrofauna is an important component linking pelagic and benthic ecosystems, especially in productive coastal areas. Through their metabolism and behaviour, benthic animals affect biogeochemical fluxes between the sediment and water column. Mechanistic models that quantify these benthic-pelagic links are imperative to understand the functioning of coastal ecosystems. In this study, we develop a dynamic model of benthic macrofauna to quantify the relationship between organic matter input and benthic macrofaunal biomass in the coastal zone. The model simulates the carbon dynamics of three functional groups of benthic macrofauna and their sediment food sources and is forced by a hydrodynamic-biogeochemical model simulating pelagic physical and biological dynamics. The model reproduces measured time-series of macrofaunal biomass from two coastal sites with contrasting sedimentation in the Baltic Sea in 1993-2005 with comparatively high accuracy, including a major increase at one of the sites dominated by the bivalve Limecola (Macoma) balthica. This shift in community composition suggests altered pathways of organic matter degradation: 39% of simulated sedimentation was mineralised by macrofauna in 2005 compared to 10% in 1995. From the early 2000s onward macrofaunal biomass seems to be food-limited, as ca 80% of organic carbon sedimentation was processed by the deposit-feeding macrofauna at both sites. This model is a first step to help quantify the role of macrofauna in marine coastal ecosystem functioning and biogeochemical cycles and build predictive capacity of the effects of anthropogenic stressors, such as eutrophication and climate change, on coastal ecosystems.