In 1959, WAPDA was created to undertake the task of investigating, planning and executing schemes for irrigation, drainage, prevention of water logging and reclamation of saline land as an autonomous body responsible for integrated development of water and power resources in Pakistan. The organization was also entrusted with the work of implementing Indus Basin Settlement Plan signed between India and Pakistan in 1960 to develop replacement works for management of river water and irrigation system. Since then it has been engaged in building water development projects which include extensive research and investigation to augment country's water resources.

Member (Water) controls the water Sector in the entire country divided into north, central, south zones, generally covering the North Western Frontier Provinces (NWFP) and the provinces of Punjab and Sindh respectively, for execution of SCARPs and surface water development, projects. Chief Engineers and Project Directors implement projects falling under regions within the zone. In addition, the Water Wing has a C.E (Coordination and Monitoring) for construction and operation of dams and all other projects under Water wing services (TS) and two separate General Managers for Ghazi Barotha Hydropower and National Drainage Project. The Planning Division of Water Wing, headed by a General Manager, looks after all planning activities on the water side. The activities of water resources and hydropower development and vision-2025 are handled by three General Managers i.e. Technical, South, North, GM (P&D) and GM Hydro Development.