The article considers the impact of rice farming on the ecosystem of water bodies in Kuban. It has been established that Krasnodar Krai has conditions for rice production and development of rice farming among other regions. Rice farming is an important strategic direction of Krasnodar Krai's agroindustrial complex economy development. Active development of this industry has led to significant environmental problems. Acute is a problem of discharged water, as one of the sources of pollution of water resources of Kuban is discharged from canals of rice systems. It has been revealed that rice farms use cultivation technology based on the introduction of large amounts of chemical materials, so with discharged water pesticides get into water bodies, which negatively affects fish stocks, fauna and the whole ecosystem of Kuban. Indicators of an annual flow of the Kuban river in a site of a dam of the Krasnodar Reservoir for the period 1975-2021 are analysed. It has been established that there is a threat of deficiency of fresh water because of inefficient water consumption. The necessity of developing measures to reduce water use and rational management of water resources has been revealed. It was proposed to develop the technology of organic rice production without using herbicides and mineral fertilizers taking into account organization of special water regime, which is the main means of weed control. It was concluded that high-tech production of organic rice with efficient water consumption creates an opportunity to preserve the entire ecosystem of the region.