Cockburn Sound is one of the most intensively used marine areas in Western Australia and has a history of major industrial development and nutrient pollution. This has contributed to significant losses of seagrass meadows between the 1950s and early 2000s. However, the Sound retains high ecological values and is regarded as an important area for recreational and commercial activities such as fishing, diving, aquaculture, tourism and shipping. The WA government is examining the potential impact of developing a major port facility in the Sound. This study investigates its potential impacts on food webs and species of interest to conservation (Little Penguin Eudyptula minor), commercial (Pink Snapper, Scaly Mackeral Sardinella lemuru), and recreational groups (Blue Swimmer Crabs and Pink Snapper). Conceptual and qualitative models were developed through workshops and consultation for each of these species to summarise their life-cycles and use of the Sound, and evaluate the impact of different cumulative factors on the species such as climate change, habitat loss, changes associated with port development, and management. The qualitative model for Little Penguins showed that their populations are positively influenced by management actions on land, where breeding colonies are negatively impacted by nest site degradation through increasing temperatures in a warming climate. Other factors influencing Little Penguins include changes in populations of forage fish such as White Bait (Hyperlophus vittatus) and Scaly Mackeral and increased mortality from vessel-strike. They highlight the complexity of cumulative impact assessment. The Pink Snapper qualitative model predicted positive effects of seagrass on Pink Snapper juveniles, flowing through to adults, due to an association with seagrass by the early juveniles. The conceptual and qualitative models have helped to summarise information on the species, communicate on the ecological understanding of the Sound and identify knowledge gaps. They have also informed the development of a quantitative ecosystem model.