To build capacity AIMS maintains effective collaborative networks and partners with other research providers, managers and industry. AIMS has working relationships with more than 90 organisations across all Australian states and territories, and in 20 countries around the globe. These partnerships have advanced marine science and produced knowledge-based solutions for marine managers and industries such as oil and gas, fisheries, tourism, aquaculture and environmental biotechnology.

The Institute also engages in major collaborative initiatives such as the new Marine and Tropical Sciences Research Facility (MTSRF) and the Western Australian Marine Science Institution (WAMSI) . These multi-agency programs combine the research strengths of universities, research organisations and industry partners.

AIMS takes a leading role in many international coral reef research initiatives, including CReefs , a field program within the  Global Census of Marine Life (CoML) , and the Global Coral Reef Monitoring Network. Through partnerships with international marine science organisations such as the US  National Oceanic and Atmospheric Administration (NOAA) , AIMS is improving its ability to address issues of national and international importance.