For understanding the functioning of marine systems, and gaining insight into their potential responses to changes such as the riverine or atmospheric nutrient inputs, or hydro-meteorological conditions, we use complex ecosystem models, often coupled to a hydrodynamical host. These so called coupled physical-biogeochemical models are aimed to provide a plausible representation of the system under consideration, as can be inferred from the ability of the models to reproduce the field observations. The Generalized Plankton Model (GPM), the European Regional Seas Ecosystem Model (ERSEM) and the Ecological Tidal Model (EcoTiM) have been among the model systems used in our group so far.