The St. Johns River watershed located in Florida, USA is the focus of planning efforts to improve the resiliency and management of water resources infrastructure from current and future flood threats. These threats are driven by intense urbanization of the basin combined with increased frequency and intensity of coastal storms made worse by sea level rise. Research efforts have begun to develop a comprehensive system of coupled numerical simulation models of the entire watershed in order to assess the current and long-term risks from flood inundation. This study provides a discussion of the system-wide model design and preliminary development. The study first outlines the project area and various numerical models to be coupled together. Then, the study discusses preliminary model development efforts and challenges. This initial study revealed the overall complexity and size of the undertaking. Overall, the study’s primary conclusion is that while an integrated system of coupled models is feasible and potentially very useful for long-term planning, the computational challenges for such an undertaking are extensive.