UNEP and UNDP are implementing this project, with UNEP being the lead implementing agency. UNEP is cooperating with the UNOPS East African Hub (EAH) for the execution of regional activities, and UNDP is executing activities through UNOPS International Water Cluster (IWC).

The project is managed by the regional Project Coordination Unit (PCU), which is based in the UNEP Headquarters in Nairobi, Kenya.

The Regional Steering Committee (RSC) provides strategic guidance to the regional PCU. Members of the RSC are representatives from each participating country, one representative from both implementing agencies and the executing agency team. The RSC acts based upon project progress assessments and related recommendations from the PCU.

In each country a National Steering Committee has been formed which will provide strategic guidance to the national demonstration project and national project execution. The membership of the National Steering Committee will vary between countries according to the specific country circumstances, but in most cases the National Project Focal Point will be the Chair and the IWRM Policy Support Analyst will be the secretary, supported by the Demonstration Project Manager.

The IWRM Policy Support Analyst will support the management, coordination and facilitation of the regional components of the project at the national level. The Demonstration Project Manager is responsible for the day-to-day management of the national demonstration project.