In 2015, geoacoustic and gas-geochemical studies of bottom sediments of the Vistula Lagoon of the Baltic Sea and the Sevastopol Bay of the Black Sea were carried out. A comparative analysis showed differences in the particle size distribution and methane content in the sediments of the studied basins. Maximum methane concentrations were observed in the sediments of the central part of the Sevastopol Bay (1856 µmol dm 3), characterized by the highest content of aleuropelite fraction. The diffusion flux of methane at the water-bottom interface was directed from the sediment to water and varied from 0.004 to 0.132 mmol/(m 2 day) in the Sevastopol Bay, and from 0.005 to 0.030 mmol/(m 2 day) in the Vistula Lagoon. The value of methane solubility in pore waters for the Vistula Lagoon, calculated for the average depth of the basin, is significantly lower compared to the same value for the Sevastopol Bay. Despite this, bubble outgassing was not recorded in the Vistula Lagoon, unlike the Sevastopol Bay.