Mytilid mussels form abundant, species-rich reefs on rocky substrates, but the role of this key habitat in carbon (C) cycling remains poorly understood. We performed a seasonal study on a 5 m deep photic Mytilus trossulus reef in the Central Baltic Sea to investigate pathways and rates of organic C flow. Reef gross primary production (GPP) and respiration (R) were estimated seasonally using underwater O2 eddy covariance on hourly and daily timescales. Photogrammetry and biotic sampling were used to quantify reef rugosity and mussel coverage, and to derive mussel filtration and biodeposition. Mussels were highly abundant, reaching ~50000 ind. m-2, and the reef structure increased the seabed surface area by 44%. GPPhourly was up to 20 mmol O2 m-2 h-1 and GPPdaily was up to 107 mmol O2 m-2 d-1, comparable to a nearby seagrass canopy. Hourly eddy fluxes responded linearly to light intensity and flow velocity, with higher velocities enhancing reef O2 uptake at night. Reef Rdaily exceeded GPPdaily on 12 of 13 measurement days, and Rannual (29 mol O2 m-2 yr-1) was 3-fold larger than GPPannual. The reef sustained a productive community of microbes and fauna whose activities accounted for ~50% of Rannual. Horizontal water advection promoted food supply to the reef and likely facilitated substantial lateral C export of mussel biodeposits. Our analyses suggest that a reduction in mussel reef extent due to ongoing environmental change will have major implications for the transport and transformation of C and nutrients within the coastal Baltic Sea.