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Central Asia witnessed progressive aridification during the Miocene, commonly related to mountain uplift, the Paratethys retreat and global climate cooling. However, the formation of Miocene lakes in Central Asia seems to oppose drier conditions, suggesting that the precise timing, extent and forcing of the aridification is still not well constrained. This study presents a facies model for the alluvial–lacustrine part of the Middle to Late Miocene of the Ili Basin, obtained from two successions. The model enables the semi‐quantitative assessment of regional water level and salinity, and characterizes the control of water level on evaporite formation and diagenesis. Both the proximal Kendyrlisai and the distal Aktau successions show an overall increase in water availability from dry mudflat deposits to lacustrine sedimentation with a transitional playa phase. Increasing evaporation rates outpaced the water supply and caused groundwater salinization. Subsequent lake expansion coincided with a basin‐wide desalinization and required a shift to a positive water budget. A climatic control of the hydrological evolution is inferred due to abrupt salinization and a minor tectonic influence. The long‐term water accumulation is probably related to the hydrological closure of the basin in the early Middle Miocene (15·3 Ma). Starting at 14·3 Ma, the step‐wise salinization occurred simultaneously with the global cooling of the Miocene Climate Transition. The Miocene Climate Transition led to extreme aridity in the Ili Basin, highlighted by the early diagenetic formation of displacive anhydrite in the basin centre. The expansion of the freshwater lake (12·7 to 11·5 Ma) was possibly promoted by lower evaporation rates due to decreasing air temperatures in the Ili Basin after the Miocene Climate Transition. The extreme aridity in the Ili Basin is interpreted as a continental counterpart to the Badenian Salinity Crisis in the Central Paratethys. This emphasizes the role of atmospheric forcing on evaporite sedimentation across Eurasia during the Middle Miocene. [ABSTRACT FROM AUTHOR]