Rice irrigation systems in Kazakhstan are located on river terraces and levees of the Syr Darya, Ile, and Karatal rivers’ basins. The geological structure and lithological composition of soils in the aeration zone is characterized by a wide variety, differing in soil fertility, mechanical composition, water and physical properties, water availability and salinity. Alluvial-meadow and takyr soils consist of light and heavy loam, sandy loam, and clay [1,2,3]. Melioration errors of the rice irrigation systems, built in the period from 60s to 80s of the last century, can be described by the fact that the Kubanskaya rice sowing map was built on all soils of river terraces and river banks, with the same parameters of irrigation and drainage, with the share of rice 57.5% and 63% [4]. At the rice irrigation systems, where the geological structure and lithological composition of the aeration zone soils correspond to the irrigation and drainage parameters of the Kubanskaya rice sowing map, the soil fertility and ameliorative status of irrigated land has remained high for many decades. The salt content in the 100 cm soil layer is 0.3-0.4%; in the autumn-winter period ground water is at a depth of 2.0-2.5 m, its mineralization is 5-7 g/l. During the rice irrigation period, ground water does not connect with the water of rice paddies, and the filtration of water from rice paddies is permitted and comprises 12 – 17 mm/day. Rice is grown without flow and discharge of water from rice paddies, the irrigation rate is 21,400 m3/ha, and the yield is 5.2 t/ha. At the rice irrigation systems, where the geological structure and lithological composition of the soil in the aeration zone does not correspond to the irrigation and drainage parameters of the Kubanskaya rice sowing map, the land is saline. During the rice irrigation period, the ground water connects with the water on the rice paddies. On these paddies, due to the convective diffusion of salts from the soil and from ground water, water salinity increases and reaches the critical threshold of toxicity of 2.5 g/l [5]. It is necessary to discharge water to reduce the salinity of water on the rice paddies, which is followed by flooding of water from the irrigation channel. The irrigation rate is 23,500 m3/ha, and the yield is 4.7 t/ha.