Vessel ballast water is an important vector for the global spread of invasive marine species and pathogens, which have had substantial negative effects on marine environments, economies and the communities that rely on them worldwide. The Department of Agriculture, Fisheries and Forestry is responsible for regulating biosecurity risk associated with ballast water. Australia is a signatory to the International Convention for the Control and Management of Ships’ Ballast Water and Sediments, and the Biosecurity Act 2015 provides regulatory authority for ballast water. From 8 September 2024, vessels are required to comply with a performance-based discharge standard, representing a shift from previous management methods. Most vessels have installed a ballast water management system (BWMS) to achieve this standard. Many BWMS do not operate properly under certain conditions, including when operating in ports with high total suspended solids. These challenging water quality conditions cause crews to bypass their BWMS when facing operational pressures, resulting in uptake of untreated or partially treated ballast water. The accumulation of sediments and organisms in ballast water tanks has implications for ongoing compliance. A range of knowledge gaps and initial options for research to resolve them have been identified.