Apart from the agreements and regulations related to IFAS, the Central Asian states have made a number of additional multilateral and bilateral efforts to jointly regulate water use.

In 1996, Turkmenistan and Uzbekistan signed a separate permanent agreement for an equal distribution of water resources. It states that 50% of the Amu Darya flow at the Kerki gauging station is allocated through the Karakum Canal to Turkmenistan, and the rest to Uzbekistan.

In 1998, the governments of Kazakhstan, the Kyrgyz Republic and Uzbekistan signed an «Agreement on the Use of Water and Energy Resources of the Syr Darya Basin». This agreement provided that Kyrgyzstan would discharge water from its reservoirs in summer for the downstream states of Kazakhstan and Uzbekistan, while these would deliver fuel to Kyrgyzstan in winter, so that it does not need to produce hydropower. In 1999, Tajikistan joined the agreement so that the working regime of the Karakum reservoir could be included. The agreement requires annual protocols to define exact discharge times and amounts, as well as the price of energy to be sold to the downstream countries during the summer period and on the transfer prices of coal, gas and electricity. The agreement worked well for some years, but in others the promised coal and gas were not delivered to Kyrgyzstan, which then released water in winter to make up for the energy shortfall. From 2003 on, the parties failed to agree on annual protocols. Instead, bilateral and ad-hoc regulations were followed. These are more opaque, do not provide for long-term planning and preclude any possibility of sanctions in case of non-compliance.

The consequences were painfully visible in the winter of 2003/04. Since the summer of 2003 witnessed extraordinary high precipitation downstream and less water for irrigation was required, Kazakhstan and Uzbekistan ceased to deliver the agreed amounts of fossil fuels the following winter. In order to compensate for the loss, Kyrgyzstan produced more hydropower, releasing much more water than usual from the Toktogul reservoir that winter. The flow could not be absorbed by the frozen riverbed of the Syr Darya or the downstream reservoirs and it caused severe flooding in Kazakhstan and fears of dam failure at the Shardara reservoir, where 2 000 people were evacuated.

The failure of the agreement affects not only energy security of the upstream countries in winter and irrigation water security downstream in summer, but also the safety of the dams. During the last few years, the downstream states only minimally participated in the cost of maintenance and renovation works of the upstream reservoirs, the cost of which is covered by the relatively poorer Kyrgyzstan and Tajikistan. The Chu-Talas agreement, which includes cost-sharing mechanisms between Kazakhstan and Kyrgyzstan, is an exception to this overall trend and shows that it can work. For the Syr Darya, it is astonishing that even an obvious win-win arrangement like the water-energy trade was not perceived as having mutual benefits, but rather viewed with mistrust and suspicion. This can be explained by the lack of previous positive examples of cooperation in other fields so far, which led to a preference for self-reliance.

In 2005, another effort was undertaken to tackle water-energy issues in a cooperative manner. With support from the World Bank, a draft framework agreement on a «Water-Energy Consortium» was prepared in the framework of the Central Asia Cooperation Organisation (CACO), a short-lived regional organization that later was integrated into EurAsEC.[The EurAsian Economic Community (EurAsEC) is an international economic organization aimed at economic coordination and creating a joint customs union among its members. The member states are: Belarus, Kazakhstan, Kyrgyzstan, Russia, Tajikistan, and Uzbekistan (suspended).] However, due to different national interests and weak commitment on the part of the Central Asian countries involved (Turkmenistan was not a member of CACO), the process stalled and donors ended their support.