The research in this sub-project focuses on modelling of the regional circulation in the geometrically complex Caribbean bays and lagoons, which are dominated by multi-scale flows. In a sense it explicitly aims to link our interdisciplinary research; from large scale climate change to the small scale biogeomorphology of the coastal bays and lagoons under study. To achieve this we use proven technology; but uniquely couple the effect of long term climate change trends including short term extreme events on calcifying macro algae. We go from the global scales of Sub-Project A to the scale of the Caribbean reefs and lagoons of Sub-Project C. The modelling systems applied in this sub-project will simulate tidal, wind and wave driven flows, wind waves from ocean basin to inlets scales using one integrated model domain and mesh, and a local biogeomorphology model. In particular, hydrodynamic features such as eddies, high flow gradients and wave transformation zones that form within and outside the bay and lagoon systems will be dynamically resolved at very high levels of localized mesh resolution. Parallel scalable model design will ensure that very high resolution grids can be efficiently simulated on high performance computers. We will use the coupled, unstructured mesh, parallel,SWAN+ADCIRC wave-current model developed by Delft University of Technology, the University of Notre Dame, the University of Texas at Austin, and the University of North Carolina at Chapel Hill and Delft3D for the biogeomorphology. The IMAU-Delft-NIOZ-RUN teams will downscale from climate models, to regional models, to bays and lagoons.