Ecological network analysis and ecological indicators for an intensively used temperate marine embayment

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 (∼80 %) between the 1950s and early 2000s and declines in exploited fish species such as pink snapper ( Chrysophrys auratus ) and blue swimmer crab ( Portunus armatus ). However, Cockburn Sound remains highly valued by the community for its ecological, economic, and recreational attributes. In this study, we developed a quantitative ecosystem model using Ecopath with Ecosim software to identify ecological indicators for ecosystem performance and elucidate how the system functions, including: (1) biomass flow in the food web; (2) identifying keystone species; and (3) defining the ecological network. We defined 73 functional groups based on both local biological surveys from a major research program in 2021–22 and expert consultation. The model identified the ecological role of keystone groups defined as structuring species by processes associated with predation (top-down forces) with sharks, bottlenose dolphin ( Tursiops truncates ), Australian sea lion ( Neophoca cinerea ), and cormorants ( Phalocrocorax spp.) as functionally important species in the system. The results from the mixed trophic impact (MTI) analysis indicated that commercial and recreational fisheries did not have a major impact on the biomass of fished species, but some indirect impacts were found between the squid jigging fishery and dolphins through shared food resources (squid). The ecological indicators generated in this study provide baseline information on the trophic structure, energetics, and function of the Cockburn Sound ecosystem, and can be used to inform managers on how the system may respond to stressors and disturbances e.g., infrastructure development and climate change, and be used in evaluating alternative management strategies. The Ecopath model highlighted the complexity of Cockburn Sound's ecology, showing the role of higher and lower trophic groups in this food web. This is particularly important because understanding the processes and interactions within the system can support plans for conservation and management. • Ecosystem understanding developed for a temperate marine embayment. • Ecopath model with 73 groups, including fishery and conservation species developed. • Ecological indicators e.g. biomass flows, keystone species and networks determined. • Biomass concentrated in the lower trophic levels and keystone species identified. • Model can be used to evaluate future scenarios of change.