The features of uranium mining on Kazakhstan’s enterprises have been examined, and uranium deposits located in the Syrdarya and Shu-Sarysu depressions have been described. Actual and projected data on the development of technological blocks in areas with complex geological structures have been analyzed and compared. Core samples were collected and, using X-ray diffraction analysis, quantitative and qualitative characteristics as well as mineral compositions of ores from various productive horizons of uranium deposits in the Syrdarya and Shu-Sarysu depressions were comparatively analyzed. It was determined that the ores in the Syrdarya depression are relatively homogeneous compared to those in the Shu-Sarysu depression, although in some places, clay minerals and gypsum are present, which hinder the uranium leaching processes. In the ores of the Shu-Sarysu depression, clay minerals that impede the uranium leaching processes are present in certain areas. Microscopic analysis of core material samples using a LEICA DM 2500 P microscope revealed particle sizes and shapes, as well as their distribution within the structure of host rocks in the productive horizon. Using X-ray diffraction analysis, mineral compositions of sediment-forming components during uranium well mining in the considered productive horizons were determined and comparatively analyzed. It was established that in the geotechnological wells of the Syrdarya depression, sediments of predominantly chemical origin, such as gypsum, are formed. However, in the geotechnological wells of the Shu-Sarysu depression, sediments of mechanical origin, consisting predominantly of quartz particles and clay minerals, are formed. Based on the obtained data, a method for intensifying underground uranium leaching in complex geological conditions has been developed, which involves dissolving sediment formations and increasing the oxidative–reductive potential of the leaching solution. The proposed and experimentally substantiated universal methodology for enhancing uranium well production involves the dissolution and prevention of precipitation using hydrofluoric acid solutions, as well as the oxidation of uranium dioxide with hydrogen peroxide.