The cisco (Coregonus artedi) requires cold, well-oxygenated water and is threatened by climate warming and lake eutrophication, especially at the southern edge of its range in the Laurentian Great Lakes region. In this paper, a method is described to assess the quality, quantity, and variability of suitable cisco habitat. Two metrics are proposed to characterize existing cisco oxythermal habitat in this region: water temperature in the water column at a dissolved oxygen of 6 mg/L (TDO6) and “cisco layer thickness” (CLT), the vertical extent of the water column within which water temperature is ≤22.8 °C and dissolved oxygen is ≥6 mg/L. It is proposed that values of TDO6 = 22.8 °C and CLT = 1 m be used as benchmarks to identify cisco lakes with potentially stressful oxythermal habitat. Long-term summer data from 14 Wisconsin cisco lakes with a wide range of limnological characteristics indicated that TDO6 varied from 4.2 to 27.5 °C and CLT from −6.2 to 66.7 m. Cisco abundance across lakes was greater at lower values of TDO6 and higher values of CLT, and non-attainments of the proposed benchmarks were most likely in lakes with remnant or extirpated cisco populations. Non-attainment of benchmarks could occur from late June through September, and three or more samples across the entire summer would be required to have a reasonable probability of detecting a non-attainment in TDO6 or CLT within any given year. Across years, to detect a single year of non-attainment with an 80% level of confidence, two years of sampling would be sufficient for CLT and three years for TD06; to detect more than one non-attaining year, three years of sampling for CLT and six years of sampling for TD06 would be required. Despite relatively high temporal variation in some lakes, the proposed metrics and benchmarks appear to have value for assessing cisco oxythermal habitat in the Great Lakes region.