Permafrost regions, and especially thermokarst lakes, play a major role in the global carbon cycle and in the context of global warming. Thermokarst lakes and lagoons are sources of methane to the atmosphere. This process is restricted by an ice cover during the winter. However, the fate of methane below and in the ice of shallow thermokarst lakes, lagoons and coastal waters is poorly understood. This study focuses on winter ice from two different water bodies in a region of thawing permafrost in northeast Siberia. One is a shallow thermokarst lagoon and the other a bay underlain by submarine permafrost. The two water bodies are semi-closed and open water systems, respectively, with different stages of permafrost degradation. Ice cores were used as records of the freezing process and methane pathways. Hydrochemical parameters, as stable water isotope composition, electrical conductivity, dissolved organic carbon and temperature as well as methane concentrations and stable carbon isotopic signature in the ice were analyzed. Measured parameters differed between and within the two water bodies. The hydrochemical parameters indicated freezing in a semi-closed system for the thermokarst lagoon, where ice growth eventually cuts off exchange between the lagoon and the sea. In the bay, hydrochemistry indicated an open system. Ice on both water bodies was mostly methane-supersaturated with respect to the atmospheric equilibrium concentration. Methane concentration in the ice of the Lagoon varied greatly with highest concentrations at the ice-water interface. Stable isotope signatures indicated that methane above the ice-water interface was oxidized to concentrations close to or below the calculated atmospheric equilibrium concentration. In comparison to the Lagoon, the Bay ice had generally lower methane concentrations. Nevertheless, methane oxidation in ice is a potentially effective process in decreasing methane concentrations in shallow thermokarst lagoons during the winter. As further warming of the Arctic shortens the duration of ice cover, methane pathways will probably shift. An understanding of the limits of methane oxidation in lake and sea ice is critical to understand their role in mitigating Arctic feedbacks to global warming.