Rice is the main crop in the irrigated agriculture zone of the Aral Sea region of Kazakhstan. Rice culture is hygrophytic and requires a large amount of irrigation water and a washing irrigation regime, which contributes to the leaching of salts from rice paddies. In the rice crop rotation, an active process of salt accumulation in the soil occurs after the rice stage. This happens because of secondary soil salinization. The aim of the research was to study salt tolerance and soil desalting properties of the new varieties of melilot during cultivation in the rice crop rotation in the irrigated area of the Aral Sea region of Kazakhstan. The research showed that the cultivation of the “Arkas” variety of white melilot and the “Saraichik” variety of dentated melilot on saline soils in the rice crop rotation leads to soil desalination. According to the results of the research, content of salt solid residue in the arable layer (0-30 cm) was lower under the “Saraichik” variety of dentated melilot than under the “Arkas” variety of white melilot. The level of groundwater rises and the process of salinization intensifies during the cultivation of crops. The transition from subsaline soils to soils with a high degree of salinization occurs. Rates of development and growth are slow during the first year in melilot varieties, however, despite the low indicator values, harvest results in a single mowing were high (229-309 kg/ha of herbage and 57.2-74.3 c/ha of hay). The “Saraichik” variety has large leaves, branching stems and high foliage. “Saraichik” dentated melilot has a beneficial feature. This variety is able to use groundwater with high salt content more efficiently for its growth and development. The melilot yield of the first year was harvested in the region without irrigation, and it grew using the moisture reserve accumulated in the soil during the previous year from the watering of the previous culture – rice. Therefore, results of the study demonstrated that “Arkas” white melilot and “Saraichik” dentated melilot are promising cultures that can be introduced into the rice crop rotation in the areas with saline soils in rice field systems of the Aral Sea region of Kazakhstan