The issues discussed in the paper concern the assessment of changes in quantitative and qualitative indicators of water resources in the climatic conditions of the southern part of Kazakhstan. For this purpose, many years of systematic field observations and other continuous data obtained from the functioning measurement and observation stations operating within the Aral-Syrdarya Basin Inspection were used. On the basis of the obtained data, indicators were determined that characterize the quantity and quality of water supplied to the soil in the irrigation process, as well as the quantity and quality of water flowing out of the drainage systems, together with an evaluation of the effectiveness of irrigation and drainage systems. Soil salinity was assessed in five irrigated massifs with a total area of 332.55 thous. ha. For the same irrigated massifs, the annual amounts of water taken for irrigation, the amount of outflowing water and the assessment of the mineralization level were determined. Based on the developed results of field observations characterizing the hydrological and environmental situation of the lower section of the Syr Darya River in 1960-2015, the negative reaction coefficients were calculated for the local population, soil and vegetation for five of the irrigated massifs of the Kyzylorda region. The ecological situation of the habitat of soil and plants in the lower reaches of the Syr Darya River in all irrigation areas deteriorates on a time scale, since as a result of the reclamation of agricultural lands, intensive secondary soil salinization occurs and the formation of infiltration runoff with high mineralization, contributing to the violation of the harmonization of the relationship between nature and man.