Abstract Lakes and reservoirs contribute substantially to atmospheric concentrations of the potent greenhouse gas methane. Lacustrine sediments produce large amounts of methane, which accumulate in oxygen-depleted hypolimnia of stratified lakes. Due to climate change and progressing eutrophication, the number of lakes with hypolimnetic methane storage may increase in the future. However, whether stored methane eventually reaches the atmosphere during lake overturn is a matter of controversy and depends critically on the response of the methanotroph assemblage. We show that the methanotroph assemblage in a mixing lake undergoes a substantial bloom and ecological succession. As a result, the methane oxidation capacity of the mixed layer kept pace with the methane supplied from the hypolimnion and most of the stored methane was oxidized. Our work demonstrates a previously unknown component of freshwater methanotroph ecology illuminating the mechanisms limiting methane transfer from lakes to the atmosphere.