Cockburn Sound is one of the most intensively used marine areas in Western Australia and has had a history of major industrial development and nutrient pollution which contributed to significant losses of seagrass meadows (~80%) between the 1950s and early 2000s. However, Cockburn Sound remains highly valued by the community as an important area for recreation and commercial activities such as fishing, aquaculture. It continues to support major marine infrastructure through the operations of trade, defence and heavy industry such as shipbuilding. In this study, we developed a quantitative ecosystem model using Ecopath with Ecosim (www.Ecopath.org) to elucidate how the Sound functions, including (1) biomass flow in the food web; (2) identify keystone species; (3) the ecological role of benthic producers (e.g., seagrass and macroalgae); and (4) the ecological role of high trophic level species. The model represents the food web of commercial and recreational fishing species (e.g., Pink Snapper, Blue Swimmer Crab, Southern Garfish, Sandy Sprat), charismatic species (Little Penguin, Bottle-nose dolphin, Australian Sea Lion, Cormorants, migratory Waders), demersal and pelagic fish assemblages, invertebrates and primary producers. We defined 70 functional groups (representing ~110 species) based on biological surveys and expert consultation. This model is a tool for testing hypotheses with respect to trophic interactions of different species and fishing pressures. The analyses undertaken in this study have shown the great complexity of this system and they have improved our understanding of potential ecological flow-on effects from impacts associated with industrialisation of Cockburn Sound.