AbstractShallow coastal waters are dynamic environments that dominate global marine methane emissions. Particularly high methane concentrations are found in seasonally anoxic waters, which are spreading in eutrophic coastal systems, potentially leading to increased methane emissions to the atmosphere. Here we explore how the seasonal development of anoxia influenced methane concentrations, rates of methane oxidation, and the community composition of methanotrophs in the shallow eutrophic water column of Mariager Fjord, Denmark. Our results show the development of steep concentration gradients toward the oxic–anoxic interface as methane accumulated to 1.4 μM in anoxic bottom waters. Yet, the fjord possessed an efficient microbial methane filter near the oxic–anoxic interface that responded to the increasing methane flux. In experimental incubations, methane oxidation near the oxic–anoxic interface proceeded both aerobically and anaerobically with nearly equal efficiency reaching turnover rates as high as 0.6 and 0.8 d−1, respectively, and was seemingly mediated by members of the Methylococcales belonging to the Deep Sea‐1 clade. Throughout the period, both aerobic and anaerobic methane oxidation rates were high enough to consume the estimated methane flux. Thus, our results indicate that seasonal anoxia did not increase methane emissions.