Water Wing Member controls the wing through its divisions including North, Central, South and Northern Areas in addition to project specific zones including Mangla, Neelum Jhelum, Mohmand Dam, Diamer Basha Dam and Dasu Hydropower Projects. In general, these zones cover Khyber Pakhtunkhwa, Punjab, Sindh and Balochistan, Gilgit-Baltistan and AJ&K. The activity of water wing involves execution of water storage Dams conveyance canals development of hydropower projects, Salinity Control & Reclamation Projects (SCARPS) and research in water sector. Chief Engineers and Projects Directors at various levels are responsible for effective and timely implementation of Water Wing Projects. Financial affairs of this wing are looked after by GM Finance (Water). Apart from project offices, there are other offices including Hydro Resources Management (HRM), Technical Services (TS), Hydro Planning, Coordination & Monitoring (C&M) and Central Design Office (CDO) which provide various technical services to different projects.

Hydro Resources Management (HRM) is responsible for the management of water resources throughout the country which includes various tasks like monitoring, collection, evaluation and publishing of hydro-meteorological data, coordination with federal/provincial flood management and reservoir operation authorities and forecasting of water availability for distribution among provinces. This also includes annual, periodic and special inspections of water sector projects, evaluation of proposals submitted by consultants and reviewing PCII & PC-I for various projects.

Technical Services (TS) provides technical advisory services on different water resources and hydropower projects.

Central Design Office (CDO) is responsible for providing one window design services for projects such as dams, power houses, irrigation and drainage networks, flood protection, roads and buildings. It also provides technical support to the field formations of WAPDA (Water Wing), GENCO, NTDC, DISCOs etc. during the implementation/construction of the new projects and remedial measures for already completed projects. Reviewing of detailed designs, tender/construction drawings, technical specifications implied/used by Consultants appointed for study of WAPDA Projects, imparting training to water wing drafting staff required for the departmental promotion and establishing drafting standards, schedule of rates and verification of nonscheduled rates etc.

Hydro Planning Organization (HPO) is responsible for planning and feasibility studies of hydropower & water resources projects in the country and presently has a total capacity of over 20,000 MW across different projects.

The Office of Coordination & Monitoring, Water provides streamlined information of Water Wing to the Government functionaries and Ministries. This office also has the responsibility of Human Resource Management & Administration to all WAPDA Water Wing offices.