The ProDeMo (Production and Destruction of Organic Matter Model), a 3D coupled hydrodynamic-ecological model, was formulated and applied to the whole Baltic Sea and the subregion of the Gulf of Gdańsk. It describes nutrient cycles (phosphorus, nitrogen, silicon) through the food web with 15 state variables, oxygen conditions and the parameterisation of water-sediment interactions. The present version of the model takes two groups of phytoplankton – diatoms and non-diatoms – as well as zooplankton into consideration. It covers the flow of matter and energy in the sea, including river discharges and atmospheric deposition. Numerical applications are embedded on a 1 NMgri d for the Gulf of Gdańsk and a 5 NMgri d for the Baltic Sea. Since the model results largely concur with observations, the model can be regarded as a reliable tool for analysing the behaviour of the Baltic ecosystem. Some examples of the spatial-temporal variability of the most important biological and chemical parameters are presented. The model results are compared with those of other modelling research in the Baltic Sea. Both the ProDeMo model algorithm and its computing procedures need to be further developed. The next version should therefore enable more phytoplankton groups to be defined, for example cyanobacteria, which are able to take up molecular nitrogen from the atmosphere (nitrogen fixation). Additionally, the sediment phase should be divided into active and non-active layers.