As a result, of the management of the irrigation system the most part of the runoff headwaters of the river Kuban was transferred to the arid plains of the Stavropol Territory, Rostov Region and Kalmykia Gravity Water via the water tract of the Kuban-Manych. This system was assumed to be supplied by pure mountain water. In fact, 3-4 class contaminated water currently passes to the water intake of the irrigation system (Nevinnomyssky channel). There is a tendency to the further deterioration in the quality of surface waters. It was determined that in the last decades in the catchment area of the upper reaches of the Kuban (Karachaevo-Cherkessia) the population was determined to increase sharply. As a result the discharge of industrial, agricultural, domestic and recreational waste into the river significantly increased. In that in catchment areas there is practically no infrastructure of the acquisition, processing and recycling of waste for the irrigation system. Intensive recreational and transport development of mountainous areas of Karachay-Cherkessia aggravates the situation and may lead to the need for deep water purification for subsequent consumption already in the vast territories of the Central Caucasus. Due to lack of the infrastructure for the water treatment in the upper reaches of the Kuban, it can lead to the serious systemic crisis. It is proposed to start to create in the catchment areas the cost-based system of recycling waste on the base of their processing by pyrolysis.