Microplastics (MPs) contaminations of freshwater and marine environments has become a global issue. Lakes in southern Siberia provide a wide range of ecosystem services and are essential elements in the annual and interannual runoff distribution of the Great Siberian Rivers. However, the extent of their MPs pollution remains unknown. In this paper, for the first time, we analyze the concentrations, composition, and spatial distribution of MPs in six lakes in southern Siberia. The studied lakes are located both in the Altai mountains and the West Siberian plain. Some of them are significantly impacted by human activities, while others are located in protected areas with no permanent population. Nevertheless, MPs were detected in all of the studied lakes. MPs concentrations ranged from 4 to 26 MPs L−1. Comparing with other inland lakes, South Siberian lakes presented moderate MPs concentrations. Among the registered MPs forms, fragments and films were dominant, with a size range between 31 and 60 nm. The MPs’ sources depend on local human activities (fishing, transport, landfilling). Therefore, sufficiently high concentrations were observed even in remote lakes. The present study set a baseline that emphasizes the need for increased attention to waste management and sustainable water use in Siberian freshwater environments.