The paper describes the ecohydrodynamic predictive model - the ecosystem module - for assessing the state of the Baltic marine environment and the Baltic ecosystem. The Baltic Sea model 3D CEMBS (the Coupled Ecosystem Model of the Baltic Sea) is based on the Community Earth System Model, which was adopted for the Baltic Sea as a coupled sea-ice-ecosystem model. The 3D CEMBS model uses: (i) hydrodynamic equations describing water movement, (ii) thermodynamic equations, (iii) equations describing the concentration distribution of chemical variables in the sea, and (iv) equations describing the exchange of matter between individual groups of organisms and their environment that make allowance for the kinetics of biochemical processes. The ecosystem model consists of 11 main components: three classes of phytoplankton (small phytoplankton, large phytoplankton represented mainly by diatoms and summer species, mostly cyanobacteria) expressed in units of carbon and chlorophyll a as separate variables, zooplankton, pelagic detritus, dissolved oxygen and nutrients (nitrate, ammonium, phosphate and silicate). In operational mode, 48-hour atmospheric forecasts provided by the UM model from the Interdisciplinary Centre for Mathematical and Computational Modelling of Warsaw University (ICM) are used. All model forecasts are available on the website http://deep.iopan.gda.pl/CEMBaltic/new_lay/index.php. The results presented in this paper show that the 3D CEMBS model is operating correctly.