Process-based models are critical to guide restoration and management efforts, particularly in coastal zones where conditions are ever changing. Modeling oyster reefs represents a challenge in that they are constituted in metapopulations, which can be sustainable as a whole, yet extremely dynamic at a local scale. In this project, we are developing a metapopulation model coupling hydrodynamic/water quality modeling (Hydro) with larval transport modeling (Transport) and on-reef individual based modeling (Reef) to support decision making in Louisiana estuaries (Fig. 1). Environmental variables generated by the Hydro model force the Transport model, which simulates oyster larval settlement over space and time. The Reef model also uses environmental variables from the Hydro model to compute individual oyster bioenergetics on the reef and uses larval settlement from the Transport model to determine population dynamics. Finally, the Reef model provides larvae through spawning to the Transport model, which simulates their dispersal. We present an overview of this model and its application to one major Louisiana estuary for natural oyster reefs and oyster aquaculture. Model outputs include reef connectivity matrices, single reef spawning contribution and available settlement area, on-reef oyster density and individual oyster growth among other metrics. This study provides decision makers with a process-based tool to aid in managing wild populations under current and projected future conditions. It should also provide valuable information for site selection in a developing aquaculture industry in Louisiana.