Lagoons provide critical habitats for many fishes, including coregonine whitefishes, which are a mainstay in many subsistence fisheries of rural communities in Arctic Alaska. Despite their importance, little is known about the overwintering habits of whitefishes in Arctic Alaska due to the challenges associated with sampling during winter. We developed a habitat suitability (HS) model to understand the potential range of physical conditions that whitefishes experience during the Arctic winter, using three indicator lagoons that represent a range of environmental characteristics. The HS model was built using a three-step approach. First, remote sensing that uses interferometric synthetic aperture radar (InSAR) identified areas of floating and bottomfast ice. Second, through in-field ground-truthing, we confirmed the presence and quality of liquid water (water depth, temperature, and dissolved oxygen) beneath the ice cover. Third, we assessed the suitability of that liquid water as habitat for whitefishes based on published literature and expert interpretation of water quality parameters. InSAR determined that 0, 65.4, and 88.2% of the three lagoons were composed of floating ice corresponding with areas of liquid water beneath a layer of ice. The HS model indicated that all three lagoons had reduced suitability as whitefish habitat in winter than in summer due to the loss of habitat because of the presence of bottomfast ice and a reduction in the quality of liquid water due to cold temperatures, high salinities, and low dissolved oxygen levels. However, only the shallowest lagoon had lethal conditions and zero suitability as whitefish habitat. The methods outlined here provide a simple, cost-effective method to identify habitats that consistently provide critical winter habitat and integrate remote sensing in a HS model framework.