—We present the results of gas-geochemical surveys in the sea surface water layer, water column, and bottom sediments of the Tatar Strait (north of the Sea of Japan) in 2012, 2014, 2015, 2017, and 2018. The distribution of methane fluxes at the water–atmosphere interface is examined, and its relationship with the geologic structure of the Tatar Strait area is discussed. Methane emission has been revealed throughout most of the Tatar Strait area. The most intense methane fluxes at the water–atmosphere interface, up to 482 mol/(km2×day), are observed on the gas-bearing southwestern shelf and on the gas hydrate slope of Sakhalin Island. The high concentrations of methane in seawater and the high contents of methane, hydrogen, and helium in the shelf and slope bottom sediments are probably due to the seismotectonic activity in the region, the presence of gas hydrates, gas concentration zones, gas migration channels, and the regional deep structure. Application of the model for calculation of the flux and impurity transfer fields to the studied water area has shown high methane emission from the sea surface in areas of vertical gas migration from lithospheric sources. The contribution of hydrodynamic factors to the formation of such zones of high methane emission is less than that of geologic factors. The obtained data on methane flux at the water–atmosphere interface for a shallow sea gave a detailed insight into the main gas discharge zones in the southern Tatar Strait.