Fine-scale models with multiple depth layers describing the ocean circulation and coupled to a biogeochemical model of the ecosystem are of paramount importance management tools. These can efficiently simulate the pathways of dissolved inorganic nutrients, the fate of particulate organic matter, and the variability of the living functional groups (phyto/zooplankton, bacteria, etc). We are developing a 3D coupled physical-biological system to model and study the Red Sea ecosystem. The system is composed of the MITgcm hydrodynamic model which provides the background physical information to the ecological model, based on the European Regional Seas Ecosystem Model (ERSEM). The ecological model is generic and has successfully been applied in a wide range of ecosystems with a significant degree of complexity. This model allows for good representation of all those processes that are significant in the functioning of an ecosystem.