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) heads the Water Wing of WAPDA for execution of projects in the entire country. For execution of water sector and hydropower development projects General Managers, Chief Engineers and Project Directors are responsible for their implementation and execution. The projects located in Gilgit Baltistan and northern side of Pakistan are being executed by General Manager (Northern Areas), Projects located in Khyber Pakhtunkhwa and Mangla Dam Raising Projects by General Manager (Projects) North, Neelum Jhelum Hydropower Project located in Azad Jammu Kashmir by MD/CEO NJHPC, Projects located in Punjab by General Manager (Central) Water, Projects located in Sindh and Balochistan by General Manager (Projects) South. In addition, the Water Wing has a General Manager (Coordination and Monitoring) Water for coordination between various WAPDA formations with Ministry and other national and international formations, monitoring of WAPDA ongoing, completed and proposed projects, career management and general administration of water wing (Grade-1 to Grade-19). The Planning Division of Water Wing, headed by a General Manager, looks after all planning activities on the water side. The activities of hydropower development are handled by General Manager (Hydro) Planning. Central Design Office is headed by General Manager (CDO) and the matters of land acquisition and resettlement are looked after by General Manager (Land Acquisition and Resettlement). The Environment cell and dam safety organization and other technical services are being headed by General Manager (Technical Services). General Manager (Tarbela) controls the operation and maintenance of Tarbela Dam while General Manager (Ghazi Barotha Hydropower Project) looks after Ghazi Barotha Hydropower Project.