This submission consists of 40 eddy covariance datasets collected from six shallow sites in the Baltic Sea over an 18 month period. Hourly fluxes were extracted from the high-density data streams and were used to compute daily rates of benthic metabolism (gross primary production (GPP), respiration (R), and net ecosystem metabolism (NEM); in mmol O2 m-2 d-1). These were converted to C assuming an O2 : C of 1.0 for GPP and R. A description of the flux data processing protocol is given in the manuscript. These datasets were used to compute annual rates of GPP, R, and NEM at each habitat site. The annual rates were then used to investigate (i) phototrophic biomass turnover rates, by comparing the GPP rates with standing phototrophic biomass measurements, and (ii) the regional importance of benthic metabolism, by upscaling the annual rates to habitat distribution maps. This dataset includes all data on standing biomass and habitat extent.