The Agreement on the Organizational Structure of OKACOM entered into in May 2007, by the OKACOM Member States elaborates and outlines the organizational structure of OKACOM. The Agreement effectively defines three organs within OKACOM, mainly the Commission, the Okavango Basin Steering Committee (OBSC) and the Secretariat.

The Commission is made up of three representatives from each riparian country. Technical support and advice is provided by the Okavango Basin Steering Committee which is made up of three representatives from each country, and by issue-based task forces. The Institutional Task Force looks at policies and practices for ensuring effective governance of river basin resources. The Hydrological Task force looks at policies and practices related to collection, management and interpretation of water data for the basin. The Biodiversity Task Force looks at at policies and practices related to conservation of plant and animal life in the basin.

The Okavango River Basin Steering Committee was appointed by OKACOM on 6 June 1995 and it is a technical advisory body to the Commission and consists of permanent and non-permanent members. It is chaired by a Commissioner from the member state holding the Chair of the Commission at the time. The Chairperson of the OBSC is appointed by the member state holding the chair of the Commission. This committee has proven instrumental in implementing the decisions of the OKACOM at national level.

The Secretariat is an internal organ of OKACOM, with the legal capacity and mandate to assist OKACOM in implementing its decisions. It also provides administrative support and assumes an instrumental role in information sharing and communication. The Secretariat is headed by an Executive Secretary who works under the guidance of the Commission.

The Basin Wide Forum was established by OKACOM through the Every River Has Its People Project. It is a transboudary committee comprised of 10 local community representatives from each of the riparian states. At a country level, the members are called Country Forum Members, and they meet twice a year at national level and at least once a year at basin level. The primary aim of the meetings is to share experiences and generate a 'bird's eye view' of the socio-economic and hydro-environmental landscape of the basin in order to help formulate knowledge-based community livelihoods and environmental action plans.