After the collapse of the Soviet Union, the five newly independent Central Asian states saw the need to cooperate on their shared water resources. In September 1991, their ministers of water resources issued a statement in which they declared that joint management of water was necessary to solve the region's water problems and should be carried out based on the principles of equality and mutual benefit.

On 18 February 1992, the five ministers signed the «Agreement on cooperation in joint management, use and protection of interstate sources of water resources». It declared that the quota system established by the Soviet Union (see page 22) should remain in place until a new strategy was developed, and it founded a joint body, the Interstate Commission for Water Coordination (ICWC). This agreement was followed by numerous other ones, such as the 1993 presidential «Agreement on joint actions on resolving the problems related to the Aral Sea and its coastal zone on environmental ­sanitation and socioeconomic development in the Aral Sea region», the Nukus ­Declaration of 1995, the 1999 agreement «On the status of IFAS and its organizations», and others.

The ICWC (Interstate Commission for Water Coordination) was the first regional institution set up after independence. Its main tasks are to control the regulation, efficient use and protection of the waters, to develop a regional common water management policy and to determine annual limits of water use for each state. Its members are the heads of the respective national water ministries or departments, who meet every quarter to determine the exact water distribution-i.e. the translation of the general quotas into exact amounts based on water flow measurements and weather forecasts. Meetings of the ICWC are chaired by the member countries on a rotational basis. All decisions are made unanimously. Operative bodies of the ICWC are the secretariat in Kujand (Tajikistan), a scientific information centre in Tashkent (SIC ICWC) with branches in all member countries and the two river basin organizations (BVOs), which had already been established by the Soviet government. The headquarters of the BVO Syr Darya is in Tashkent (Uzbekistan); the one of the BVO Amu Darya is in Urgench (Uzbekistan).

In 1993, ICAS (Interstate Council for the Aral Sea Basin) was founded with the EC (Executive Committee) as its executive agency. It consisted of five members per republic who met every half year and decided about the plans developed by the EC, which formulated principles, projects and measures. The ICWC was integrated into ICAS. Also in 1993, the International Fund for Saving the Aral Sea (IFAS) was set up in Almaty. All member states were expected to pay 1% of their state expenses to this fund per year. Its Executive Committee (EC IFAS) consists of two representatives for each of the five states. Initially, the role of IFAS was primarily to generate funds from member state fees and donor assistance, while EC ICAS was in charge of the Aral Sea Basin Program (ASBP, see below).

In 1994, a new ecological commission was affiliated, the ICSDSTEC (Interstate Commission for Socioeconomic Development and Scientific and Ecological Cooperation), later renamed the Interstate Commission on Sustainable Development (ICSD). Its main objective is the coordination and supervision of cooperation in the field of environmental protection and sustainable development in Central Asia. The ICSD meets twice a year with the chair rotating among its member states. A Scientific Information Centre (SIC ICSD) is based in Ashgabat.

In 1997, the regional institutions were restructured following an evaluation of the first phase of the ASBP that advised a strengthening of the regional institutions. Because of overlapping responsibilities, ICAS and IFAS were combined under the name IFAS. The chairmanship of IFAS has since then rotated among the presidents of the five member states. The EC IFAS is accordingly located in the respective country. Thus, the Executive Committee has been located in Almaty (1993–1997), Tashkent (1997–1999), Ashgabat (1999–2002), and Dushanbe (2003–2009; the planned move to Bishkek did not take place due to political turmoil in 2005). Since 2009, it has been based in Almaty. Another decision concerned the fees of the member states. As it became obvious that none of the states had fulfilled its financial commitments, contributions were lowered to 0.3% of the state expenses for the rich countries downstream and to 0.1% of state expenses for the poor countries upstream.

In 2002, the IFAS Board decided to establish a Regional Centre of Hydrology (RCH) and attach it to EC IFAS. Its main purpose is to improve the system of hydro-meteorological forecasting, environmental monitoring and data exchange among the national hydro-meteorological agencies in the region. RCH is currently located in Almaty, Kazakhstan. Since then, the structure of the IFAS has read as follows:

Organizational Structure of IFAS