This project has been designed to provide the Western Australian Government and its agencies with improved understanding of the coastal marine environment so that its decision making with regard to development in this zone is environmentally credible and sustainable. The project will deliver this result by the following sequence of research. First, existing data will be appraised in light of a simple system model for inshore coastal waters. This rudimentary understanding will be used to design environmental surveys for three representative coastal systems (chosen in consultation with WA departments and agencies). Whereupon, baseline data will be obtained on biodiversity, biogeochemical processes and environmental quality in these waterways. With this information, the research will then move on to consider the affects of selected stressors (localised sources and diffuse inputs) on the above ecological characteristics, and the potential for irreversible alteration. Where necessary, focussed investigations in the field or laboratory will be used to resolve key mechanisms and also the scale of response. Important outcomes for the project will be the development of validated environmental indicators for the use of coastal managers, and also other resources for them to better understand the complex interactions and inter-relations in coastal marine ecosystems (e.g. via conceptual models). This project will also work with other SRFME projects to improve capacity for prediction and scenario testing in environmental decision making via models and other tools.