The experience of rice cultivation shows that the land fertility developed for rice begins to fall after a certain period of time (10-15 years). The reasons for this phenomenon are not fully disclosed. The main of them is associated with soil degradation during rice sowing. The degradation of rice field soils means the development of a complex of eluviation processes and intra-horizontal segregation of reduced iron and manganese compounds and the removal of fine particles during flooding. Eventually, degraded horizons acquire signs of podzol or rejuvanated soils. Degradation processes in soils of Kuban rice fields are mainly associated with a decrease in the content of humus, deterioration of its qualitative composition, decalcification of the upper soil horizons and its alkalinization. There is an increase in density to 1.5 g / cm3 and the phenomenon of slithering, as well as a decrease in total porosity. It is necessary to prevent irreversible soil degradation and avert negative impacts on environment. Recently, the need to prepare for decision-making has been recognized. It requires the development of appropriate information and methodological support based on a combination of experience with the results of mathematical modeling. The authors note that in order to ensure effective and sustainable operation of the rice irrigation system, it is necessary to create new management systems focused on the use of a probabilistic approach to solving the problems of technological process management, which ensures the environmentally safe operation of the rice irrigation system and prevents irreversible soil degradation. The authors obtained an expression that allows us to quantify the damage taking into account the probabilistic uncertainty of environmental, economic and other factors of the project.