The current stage in the development of scientific and technological progress makes it possible to switch to ecological-organic farming. However, the economic difficulties of the workers of the agro-industrial complex in the production of agricultural products, as a result of the reduction in average annual precipitation, agricultural areas, volumes of fresh water suitable for irrigation, pose the task of obtaining guaranteed high yields is practically impossible. In this regard, it is necessary to solve such a problem in stages, ranking the stages of the transition and determining the turn of their implementation. Since the most labor-intensive and resource-intensive production is rice cultivation, the first stage is to develop a new methodology for rice cultivation, which could reduce the cost of rice production, anthropogenic load on the soils of the rice irrigation system and reduce the pollution of water sources with drainage and waste waters. ... In our research, we propose to use an organic method of purifying drainage runoff by halophytes planted in phyto-sections located in the discharge canals of the rice irrigation system. It was found in the work that the use of phyto-sections of various lengths, depending on the chemical composition of drainage and waste waters, allows to clean the drainage runoff from mechanical impurities, organic and biogenic elements, to reduce suffusion and removal of nutrients from rice paddies, to reduce the irrigation rate. by 10 %, to increase the ameliorative condition of soils, and also to reduce the cost of rice production by 7 %.