In this work, a general overview of the recent progress and the existing difficulties in the implementation of physical and biogeochemical models accompanied with advanced Kalman filtering techniques in regional and shelf areas of the Mediterranean Sea is presented. The hydrodynamics of these areas were simulated with realistic implementations of the Princeton Ocean Model (POM) while the biogeochemistry of the ecosystems was tackled with the European Regional Seas Ecosystem Model (ERSEM). On the other hand, the Singular Evolutive Extended Kalman (SEEK) filter and its ensemble-based variant called the SEIK filter was used to assimilate all physical and biogeochemical data into the models. In these filters the error statistics were parameterized by means of a suitable basis of empirical orthogonal functions (EOFs). This contribution falls into the framework of the ‘Mediterranean ocean Forecasting System: Toward Environmental Predictions (MFSTEP)’ project and synthetically presents the modeling efforts in conjunction with data assimilation techniques for the development of operational systems in regional and shelf areas of the Mediterranean Sea.