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Fish survival in lakes is strongly influenced by water temperature and dissolved oxygen (DO) concentration. A one-dimensional (vertical) lake water quality model MINLAKE 2012 was calibrated in 23 Minnesota lakes and used to simulate daily water temperature and DO concentrations in 36 representative lake types under past (1992–2008) climate conditions and a future climate scenario (MIROC 3.2). The 36 representative Minnesota lake types were developed based on three maximum depths (Hmax = 4, 13, and 24 m), three surface areas (As = 0.2, 1.7, 10 km2), and four Secchi depths (SD = 1.2, 2.5, 4.5, and 7 m, from eutrophic to oligotrophic lake). A fish habitat model using the lethal-niche-boundary curve of adult cisco (Coregnous artedi, a cold-water fish species) was then developed to evaluate cisco oxythermal habitat and survival in Minnesota lakes.The fish habitat model was validated in the 23 Minnesota lakes of which 18 had cisco mortality while 5 had no cisco mortality in the unusually warm summer of 2006. Cisco lethal and habitable conditions in the 23 lakes simulated by the model had anoverall good agreement with observations in 2006. After model validation, cisco lethal days in the 36 lake types were modeled using simulated daily temperature and DO profiles from MINLAKE2012. Polymictic shallow lakes with lake geometry ratio As0.25/Hmax> 5.2 m-0.5 were simulated to typically not support cisco oxythermal habitat under past climate conditions and the future climate scenario. Medium-depth lakes are projected to be most vulnerable to climate warming with most increase in the number of years with cisco kill (average increase 13 years out of 17 simulation years). Strongly stratified mesotrophic and oligotrophic deep lakes are possible to support cisco habitat under both past and future climate conditions, and these deep lakes are good candidates for cisco refuge lakes that should be protected against water quality deteriorations.