Aquaculture is the world's fastest-growing food-production sector and a crucial contributor to the United Nations' Sustainable Development Goals. As a group of scientists, ocean-policy experts, aquaculture professionals and technical consultants from international organizations, we argue that, despite recent legislation, fish farms may still be at risk from pathogens in ballast water discharged from ships.

The International Convention for the Control and Management of Ships' Ballast Water and Sediments (go.nature.com/2evuskh) will come into force in September 2017. This will reduce the risks of transfer of organisms larger than 10 micrometres and of bacteria that are harmful to humans, including Vibrio cholerae, Escherichia coli and Enterococcus species. However, the convention does not mention any other aquatic bacteria or viruses that could cause epidemics in the US$160-billion aquaculture industry and threaten food security.

We suggest using a combination of molecular tools, experimental investigation, monitoring data and operational models to evaluate the risks and possible impacts on local aquaculture farms of how, when and where ships discharge ballast water. The findings should be presented to UN-OCEANS (www.unoceans.org) and the Joint Group of Experts on the Scientific Aspects of Marine Environmental Protection (www.gesamp.org) to support existing regulatory frameworks.