In lakes, large amounts of methane are produced in anoxic sediments. Methane-oxidizing bacteria effectively convert this potent greenhouse gas into biomass and carbon dioxide. These bacteria are present throughout the water column, where methane concentrations can range from nanomolar to millimolar. In this study, we tested the hypothesis that methanotroph assemblages in a seasonally stratified freshwater lake are adapted to the contrasting methane concentrations in the epi- and hypolimnion. We further hypothesized that lake overturn would change the apparent methane oxidation kinetics as more methane becomes available in the epilimnion. In addition to the change in the methane oxidation kinetics, we investigated changes in the transcription of genes encoding methane monooxygenase, the enzyme responsible for the first step of methane oxidation, with metatranscriptomics. Using laboratory incubations of the natural microbial communities, we show that the half-saturation constant (K_m) for methane - the methane concentration at which half the maximum methane oxidation rate is reached - was 20 times higher in the hypolimnion than in the epilimnion during stable stratification. During lake overturn, however, the kinetic constants in the epi- and hypolimnion converged along with a change in the transcriptionally active methanotroph assemblage. Conventional particulate methane monooxygenase appeared to be responsible for methane oxidation under different methane concentrations. Our results suggest that methane availability is one important factor for creating niches for methanotroph assemblages with well-adapted methane oxidation kinetics. This rapid selection and succession of adapted lacustrine methanotroph assemblages allowed the previously reported high removal efficiency of methane transported to the epilimnion to be maintained – even under rapidly changing conditions during lake overturn. Consequently, only a small fraction of methane stored in the anoxic hypolimnion is emitted to the atmosphere.