The current development of the Aydar-Arnasay lakes system (AALS), which is one of the remarkable examples of the human-induced ecosystems, depends on numerous political and environmental factors. On the one hand, the political tensions and disagreements between Central Asian republics alter the implementation of the coordinated water policy in terms of agreed water discharges to the Aydar-Arnasay lakes. On the other hand, forecasting change of the regional climate has an uncertain influence on these lakes. The overarching goal of the project is to identify which of the elaborated water management scenarios is the most probable in terms of the future development of the Aydar-Arnasay lakes system. The future development of the lakes system implies such important aspects as features of hydrological regime, including level of mineralization; maintenance of fisheries situated in these lakes, conservation of biodiversity, i.e. wetlands of international importance designated as a Ramsar site and various birds and fish species inhabiting these lakes.