The variability of the dissolved methane content in coastal zones is an important component of the biogeochemical cycle in the marine ecosystem. The objective of this study is to investigate the seasonal variability of dissolved methane distribution in the aerobic shallow coastal zone through the example of the small bay in the northeastern Black Sea. This study is based on the direct observations carried out during a long-term monitoring program conducted in the bay from 1999 to 2016. The seasonal and inter-annual variability of the dissolved methane pattern is considered under the climatic conditions as well as under the influence of extreme flood. The seasonal range of the dissolved methane content variability in the shallow part of the northeastern Black Sea is 1–2 orders of magnitude higher compared with the areas remote from the coast. The dissolved methane content in Golubaya Bay in summer is an order of magnitude higher than the winter values. In particular, local methane maxima located near the river and stream mouths and in the central bottom part of the bay have a well-shown seasonal cycle. The extreme flood conditions observed in July 2012 resulted in high methane concentrations 2 months after the flood event, when the surface concentrations of the dissolved CH4 exceeded the equilibrium with the atmospheric values by a factor of 400. The obtained results provide a unique opportunity to estimate the scale of the biogeochemical processes in marine coastal environments under the influence of climatic and extreme conditions.