We report on methane (CH4) concentration measurements in the northern Black Sea area conducted during 6 cruises with R/V Professor Vodyanitsky from 2017 to 2019. Our work is a multi-season study at a uniform station grid covering an area of 88 × 103 km2 and including three latitudinal transects that comprises both surface and vertical profile water-column measurements. The main goal of the work was to assess the seasonal patterns of vertical CH4 structure in the aerobic water column (upper 100 m) and its emission to the atmosphere.In surface waters, the mean dissolved CH4 concentration ranged from 2.6 nmol L−1 detected in November 2018 to 11.5 nmol L−1 measured in June–July 2018, respectively. Calculated CH4 seawater-air fluxes and saturations were mostly positive (i.e. net flux to atmosphere), and winter fluxes (2.6 μmol m−2 d−1) were higher than summer fluxes (1.6 μmol m−2 d−1) due to the higher wind speed. The integral CH4 flux from the whole study area (88 × 103 km2) ranged from 84 to 235 kM day−1.It was shown that, on average, the methane concentration in the upper layer for deep-water stations where the seabed is located at depths >160 m (σt >16.2) was lower compared to stations at shallow water depths (28–140 m, σt <16.2). The most distinct difference was obtained for the summer season (June–July 2018) and a less significant difference – for spring (April–May 2019) and winter season (November–December 2018). During these seasons the water column was also considerably less saturated in CH4 compared to the entire monitoring period. We observed subsurface maxima, which were generally located at the base of the thermocline and exceeded 100 nmol L−1 at some stations. Exceptions were observed in October 2019 (cruise 110), when vertical CH4 distributions were characterized by two-peaks at ∼20 and ∼50 m depth. The strong influence of the thermohaline structure on the water column CH4 distribution has also been shown in studies of daily dynamics of CH4 vertical profiles in the shallow water region. Despite the high variability of CH4 concentrations, significant similarities in vertical distributions of CH4 and chlorophyll-a for which sub-surface maxima coincided at some stations, are shown. Extremely high concentrations of CH4 (up to 351 nmol L−1) in the near-bottom water layer were revealed during all seasons at the station near the Dnieper paleo-channel at the northwestern edge of the study area. This enrichment is assumed to be caused by methane emissions from gas seeps densely located in this region.