Here, we present new results from seismic, geological, and geochemical studies conducted in 2015–2019 in the Petrozavodsk Bay of Lake Onego, NW Russia. The aims of these investigations were to (i) to characterize the structure of Quaternary deposits and (ii) provide new evidence of modern geodynamic movements and gas-seepage in Holocene sediments. The structure of the recovered deposits was composed of lacustrine mud, silt and sands from the Holocene, limno-glacial clays (varved clays) from the Late Glacial–Interglacial Transition, and glacial deposits (till) from the Late Pleistocene. The thickness of these deposits varied in different parts of the bay. Many pockmarks created by gases escaping and reaching sediment-water interface were observed in these deposits. Such pockmarks can play a significant role in the geochemical and biological processes in the bottom sediment surface, and gases that escape might modify the physicochemical characteristics of the environment.