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The formation of long-term low flow periods increasingly leads to damage, comparable to the consequences of catastrophic floods. In Russia, the amount of extreme low flow events according to Roshydromet is growing every year for the past 25 years. One of the most water-deficient areas is the Don River basin, located in the south of the European part of the country. Since 2007, a series of extreme dry years has been observed. The paper analyzes the dynamics of 20 key climatic parameters that determine river runoff. The trends in characteristics of water intakes are analyzed as well. Remote sensing data for key basins have been used to analyze changes in land cover. As the calculations have shown, the main contribution to the formation of runoff deficit is made by changes in the weather conditions during winter. As a result of the work, multiple regression models were obtained for seasonal runoff. Such climate indicators as the sum of positive temperatures during the winter, the precipitation of the cold period were used as well as river discharge during previous low flow season. In the upper and middle reaches of the Don river, the water intake and the land use changes are not significant, while in the lower – play an important role and making natural water shortage only worse