Temperate snakes occupy overwintering sites for most of their annual life cycle. Microhabitat characteristics of the hibernaculum are largely undescribed, yet are paramount in ensuring snake overwintering survival. We hypothesized that snakes survive hibernation within a vertical subterranean space that we termed a “life zone” (LZ), that is aerobic and flood and frost free throughout winter. We studied an isolated, endangered population of Massasaugas (Sistrurus catenatus) inhabiting an anthropogenically altered peatland and monitored the subterranean habitat during a period of environmental stochasticity. Initial radio telemetry confirmed that snakes moved between altered and natural habitats during the active season and showed hibernation-site fidelity to either habitat. We used a grid of groundwater wells and frost tubes installed in each hibernation area to measure LZ characteristics over 11 consecutive winters. The LZ within the impacted area was periodically reduced to zero during a flood–freeze cycle, but the LZ in the natural area was maintained. Model selection analysis revealed that soil depth and flood status best predicted LZ size. Thermal buffering and groundwater dissolved oxygen increased with LZ size, and annual Massasauga encounters were significantly correlated with LZ size. This analysis suggests a population decline occurred when LZ size was reduced by flooding. Our data give support to the importance and maintenance of an LZ for successful snake hibernation. Our methods apply to subterranean hibernation habitats that are at risk of environmental stochasticity, causing flooding, freezing, or hypoxia.