The project is supervised at basin level by a Regional Project Steering Committee (RPSC), assisted by a Regional Technical Advisory Committee. It is managed in each country by the Ministries/agencies of agriculture and environmental sectors, by National Project Steering Committees (NPSCs- composed of various sectors and key players and playing both political and technical roles). Joint management is to be facilitated by the rotation of the chair of the regional and national committees between agriculture and environment.

The Regional Project Coordinator is based in Kigali, and a National Project Manager based in the basin in each country: Kabale in Uganda, Bukoba in Tanzania, Bujumbura in Burundi, and Kigali in Rwanda. These five experts are recruited by FAO. The regional coordinator will act as secretary of the RPSC and implement the decisions of the committee. Also the national project managers will assume the role of secretary of the NPSC. Finally, in each of 22 target districts, Facilitators will be identified to support the implementation of project activities with the communities and partners. See project organizational chart below.