The results of the surveys of two small lakes located in the western and southern parts of the Republic of Karelia (Sukkozero and Kedrozero) are reported. Hydrological and hydrochemical indices were analyzed. The water bodies are of glacial genesis, and belong to the catchment of Lake Onego. Human population in the catchments of the lakes is scarce, there are no large industrial enterprises, fish farms, etc. The lakes are classified as β-oligotrophic on the trophicity scale. Some bays and sites of Lake Kedrozero have acquired mesotrophic traits. Hydrobiological data, including the fish population of the lakes, are presented in detail for the first time. The fish species composition, length-weight growth and diet of the prevalent species were studied. The fish population of Lake Sukkozero is represented by 10 species, of Lake Kedrozero – by 14 species. Smelt, perch, roach and bream are the most abundant in both lakes. Atlantic salmon, brown trout, whitefish and vendace are valuable fish. Salmon and trout are included in the Red Data Book of Karelia. A higher growth rate is observed in fish from Kedrozero, obviously due to the richer food resources. A comparative analysis of the data shows that the investigated water bodies have remained practically unchanged over a long time. This situation is now very rare, not only in the region, but also in Russia at large. Water bodies can serve as benchmarks for assessing the state of aquatic ecosystems under a significantly increased human impact. Small lakes, due to the lack of industrial-scope fishing, are promising for amateur, sport fishing and tourism development.