Many fish species in coastal rivers migrate from freshwater to marine environments to complete their life-cycles. This marine phase provides a potential pathway for migration among coastal river basins leading to a potential metapopulation structure in which individual river basins may act as either sources or sinks of new recruits. Understanding these source-sink dynamics may be critical to effective population management, and in particular in terms of understanding the contribution of individual river-basins to population viability. Persistence and species distributions of diadromous species may also be regulated by local factors in the freshwater environment as well as by conditions in adjacent marine and/or estuarine habitats, which may determine the survival and or reproductive outcomes, especially for catadromous species which migrate to the sea to breed. Here we describe a project to bring together both habitat suitability and metapopulation models to assess the vulnerability of coastal fish species to environmental change in both marine and freshwater environments. The project is separately developing habitat suitability models for freshwater fish, but incorporating marine and freshwater influences for diadromous species, and coupling those models of habitat suitability to estimate carrying capacity of individual river basins within a metapopulaiton modelling framework. We outline the conceptual framework and preliminary modelling results.