The WAMSI Westport Marine Science Program is the largest and most comprehensive marine research initiative undertaken in Cockburn Sound. The program was made possible through a five year partnership with the WA state government’s Westport program for a future container port in Kwinana. The WWMSP was designed to ensure the environmental impact assessment for the container port is informed by rigorous, independent science, in addition to assisting and improving the management of Cockburn Sound now and into the future. Over 150 scientists from 15 organisations contributed to 32 projects across nine themes, including: ecosystem modelling and integration, benthic habitats, fisheries and aquatic resources, apex predators, sediment and water quality, coastal processes, hydrodynamics, underwater noise, and social values. Many applied outcomes were generated under the WWMSP to aid decision making. We highlight the science behind 1) light and burial thresholds for seagrass, 2) beneficial re-use of dredged sediments, 3) a benefit-cost analysis on environmental enhancements and 4) the Cockburn Sound Integrated Ecosystem Model (CSIEM). The science from the WWMSP is currently being used to inform the environmental impact assessment and review stage, largely though operationalisation of CSIEM.