The results of the GPR observations carried out in three lakes of Karelia: Lake Verkhneye (the White Sea Biological Research Station of the Moscow State University), Nizhneye Nilmozero and Vendyurskoye, were summarized. A screened 300MHz antenna was used for the survey. The GPR potential, including parameters such as propagation distance in water and in soil, was analyzed. Water resistivity measurements were carried out for each lake. Characteristics of the Quaternary profile (being the main factor that influence the propagation depth of electromagnetic waves) were studied. It was demonstrated that high water resistivity and, possibly, the lack of clay in the profile suggest GPR can perform well for the depth range of 10-15 m below the bottom and at water depths up to 12-15 m. The GPR method, which is far more cost efficient compared to seismoacoustics, can be applied to deals with many production as well as scientific problems.