This ecological modelling study is focused on the development of scenarios for the management of the industrially exploited shellfish species and the recovery of the black mussel population. A two-dimensional hydrodynamic model has been developed for a selected region of the Bulgarian Black Sea coast - between Cape Kaliakra and Cape Emine, that allows simulation of sea currents based on several input parameters - wind, water temperature and salinity, etc. This hydrodynamic model forms the basis for subsequent ecological modelling and future projections of the development and mortality of the black mussel (Mytilus galloprovincialis) and Rapa whelk (Rapana venosa) in the selected sector. The ecological model is based on the EcoLab software product and includes three different scenarios of shellfish resource development. The ecological model and generated scenarios could be helpful for the elaboration of management measures and reduction of the pressure on the black mussel population.