Permafrost thawing and erosion results in the enrichment of northern lakes by soil organic matter. These allochthonous organic inputs favour bacterial decomposition processes and cause the rapid draw-down of dissolved oxygen, eventually to anoxic conditions that may favor methanogenesis. Our objective in the present study was to examine the seasonal variation in dissolved oxygen and its potential responses to climate change in permafrost peatland lakes. Limnological variables as well as bacterial metabolic rates were measured in shallow lakes along a longitudinal gradient from continuous to sporadic permafrost. A deterministic, one-dimensional lake model was used to simulate the seasonal fluctuations in water temperature and oxygen concentrations in a three-layer permafrost peatland lake and to investigate potential changes from the recent past up to the year 2095 under two climate scenarios (RCP 4.5 and 8.5). The model showed a reduction in number of anoxic days per year under both climate scenarios. Given reduced ice cover, these systems tended towards greater oxygen concentrations over time. Future warming may transform these ecosystems from anaerobic bioreactors to oxic ecosystems through much of the year, ultimately reducing their net methane emission rates.