Geophysical studies in mapping and geoenvironmental applications for screening purposes are widely applied in Latvia. Ground-penetrating radar (GPR) as the one method from geophysical toolbox is a non-invasive and non-destructive way where pulsed electromagnetic signal is recorded as scattering from subsurface objects. Aim of two described screening studies was to analyse potential advantages of GPR use for mapping bottom sediments and topography in two lakes and pinpoint challenges to overcome during works. Both lakes are relatively deep and of sub-glacial origin that became lakes after the ice retreat from Baltic region. Characterization of bottom sediments as well as full core description of upper limnic layers for comparison with GPR signals were performed. Major results show that GPR, coring and laboratory analysis can be used simultaneously, however, ground penetration radar sometimes fails to recognize full picture needed for geoenvironmental application needs. Proper treatment of data nevertheless diminish the necessity of dense coring in lakes when budgets are strict.