SOOS is overseen by the Scientific Committee on Antarctic Research (SCAR) and the Scientific Committee on Oceanic Research (SCOR). In addition to providing guidance and advice, SCAR and SCOR provide important access for SOOS to engage with intergovernmental agencies, such as the Antarctic Treaty, CCAMLR, and the Intergovernmental Oceanographic Commission. Furthermore, they also sponsor the annual SOOS Scientific Steering Committee (SSC) meeting. SOOS provide an annual report of progress to both SCAR and SCOR.

The strategic vision and direction for SOOS is led by the Executive Committee (EXCOM) comprising a Biological Sciences Co-Chair and Vice Chair, and a Physical Sciences Co-Chair and Vice Chair, and the Executive Officer. The Executive Officer is responsible for the day-to-day management of the SOOS International Project Office and is authorised to make general decisions pertaining to networking, communication, expenditure, and other issues integral to the success of SOOS. The main decision-making body of SOOS is the Scientific Steering Committee. The SSC provides the scientific direction and ensure close connection to the broader community and other international stakeholders.