Large-area environmental management presents several challenges, particularly when the pace of development projects and the scope and pace of scientific studies are not harmonised. Shifting baseline is a pervasive issue, rendering timeseries from sporadic surveys difficult to interpret. The Victorian Department of Energy, Environment, and Climate Action embarked on an Environmental Management Plan process in Port Phillip Bay (Victoria, Australia) to several objectives, including the quantification of the stated bay values and uses and achieving the Biodiversity Plan 2037 objectives of achieving ‘net gain’, expressed as an improvement in the overall extent and condition of native habitats. This required foundational work to define condition and a methodology to quantify its current status, identify suitable benchmarks and trends where possible, and identify key monitoring indicators and sites. Seafloor Integrity is one aspect of Good Environmental Status adopted by DEECA and a 3-year multi-disciplinary Seafloor Integrity study was initiated. The study informed chemical, biological, ecotoxicological and physical components of seafloor integrity. The approach leveraged available historical information, but required a whole-of-area snapshot assessment that focussed on the spatial distribution of pressures existing in the bay and models of the potential ecosystem responses and with direct relevance to environmental management decision-making processes.