Sediment beds play a key role in supporting benthic ecosystems and regulating condition of Port Phillip Bay, Victoria, however, seabed habitats are at risk of exposure to potential impacts caused by anthropogenic activities within the Bay and the coastal environment. The Victorian Department of Energy, Environment, and Climate Action instigated a study to understand condition of sediment habitats and benthic communities to support marine spatial planning and inform decision-making and monitoring. The Port Phillip Bay Seafloor Integrity Project involves the collection of marine data across multiple studies to investigate biological, physical, and chemical properties of sediments and associated biogeochemistry processes, as well as undertaking ecotoxicological studies and underwater imaging surveys of the benthic ecosystem. The collected data are used to develop a Seafloor Integrity Score, a tool to translate data into knowledge to support decision-making. We developed a score that integrates information on the spatial distribution of Port Phillip Bay marine habitats and the spatial distribution and intensity of activities directly generating pressures on the seabed. The score provides valuable insights into the Bay seafloor and benthic ecosystem condition to aid managers in prioritising areas for further development or protection.