The VES method was used to determine the geoelectric parameters of Cenozoic rocks in the Chuya intermontane basin. It was shown that the polyfacies and polychromous sediments filling the basin are well differentiated by their electrical parameters. A combination of methods used in data acquisition and processing, due to their high resolution capacity at shallow depths, provided information on the structure and physical properties of the Chuya rocks from surface to depths of 250–300 m. Despite a reasonable consistence among these methods to the above depths, the VES method is a more effective tool for detecting shallower layers. Interpretation of the VES data proved the existence of a large outburst channel as new geological evidence for an ice-dammed origin of the Middle Neopleistocene lake. A more detailed layering of the topmost part of the geoelectrical section across the Irbistu–Kokozek interfluve using the VES data revealed a number of fine-grained lenticular structures of the ancient lakes in the Chuya depression, which are hidden beneath a cover of fluvioglacial and lacustrine bouldery pebbles and moraine diamictons.