Pradhan Mantri Krishi Sinchai Yojna (Watershed Component) is implemented by the Rural Development Department in Mizoram under which the Mizoram Watershed Development Agency (MzWDA) is the State Level Nodal Agency (SLNA). The MzWDA is chaired by the Chief Secretary of Mizoram while the Secretary, Rural Development Department is the Member Secretary. At the state level, the Director, Rural Development Department is the Chief Executive Officer while the Joint Director, Rural Development Department is the Joint CEO. Along with the Junior Project Officer, they are backed by a supporting staff of 11 members.

       At the district level, the District Watershed Cell cum Data Centre (DWCDC) is headed by the Project Manager who is also the Project Director, DRDA. He is backed by a supporting staff of three-five members depending upon the area covered by the projects in the district.

       The Project Implementing Agency (PIA) reports to the Project Manager, DWCDC. The PIA may be an officer of the Rural Development Department, or of other line departments or a Voluntary Organisation (VO).

      At the village level, the Watershed Development Team works under the PIA, with the Watershed Committee members, who are elected by the Gram Sabha under the supervision of the Village Council. The members consist of representatives of the Village Council, Self Help Groups, User Groups and NGOs present in the village.