The structural organization of the council consists of: The General Assembly, The Board of Governors (BOG), The Executive Committee and The Permanent Secretariat.
- The General Assembly is the source of all powers of the council, responsible for drawing its policies, following up and monitoring its activities.
- The Board of Governors is the supreme body of the council that sets the detailed policies and makes organizational and executive decisions to facilitate the work of the council.
- The Executive Committee is in charge of managing the business of the council.
- Permanent Secretariat is responsible for follow-up of the technical, administrative and financial activities.
AWC was keen to establish affiliate technical institutional bodies for performing strategic studies, promoting capacity building and providing training to all the interested personnel with the aim of outlining water policies, properly managing the water resources and enhancing the water services. For this purpose, AWC has established a series of networks, committees and bodies in several Arab countries in the fields of desalination, wastewater reuse, water ethics, Arab Youth networks, in addition to the Arab Water Academy in Abu Dhabi, and the Mohammed VI International Center for Strategic Water Studies and Research in the Arab World in Rabat.