Physical, chemical, and biological properties in lakes are all sensitive to changes in climate, but the interaction and response of these properties to climate changes is not yet fully understood. This dissertation has two main objectives: (1) characterize the role of lake depth and lake surface area on the physical response of water temperature and ice cover to air temperature (AT) and wind speed (WS) changes and (2) determine the response fish habitat to climate-caused changes in the physical parameter of temperature chemical parameter of dissolved oxygen. To fulfill these objectives, a one-dimensional lake hydrodynamic, ice, and water quality model is utilized on three lakes near Madison, WI. Chapter 2 investigates the response of lake water temperatures and stratification to AT increases and WS decreases for three Madison area lakes. Results indicate that surface area is more important than depth when determining the response of water temperature, stratification, and stability and increasing AT and decreasing WS have a cumulative effect for all variables except hypolimnion temperature, where they have opposing influences. Chapter 3 investigates the response of ice cover duration and ice thickness to AT increases for the same three lakes, and results show that lake depth is the greater influence on ice cover response, with shallow lakes being more resilient to changes in AT. Chapter 4 investigates the role of meteorological drivers and water quality drivers on oxythermal habitat of cisco. Results show that summer AT, spring phosphorus load, and spring inflow volume drive habitat loss, but effects of AT increases can be offset by decreases in phosphorus loading. Finally, Chapter 5 develops a novel metric, cumulative oxythermal stress dosage (COSD), to quantify oxythermal habitat of yellow perch in Fish Lake, WI. Results show that COSD is a good predictor of fish declines, COSD values are closely tied to the July – September AT, and perturbation scenarios identify 3°C AT increase as a possible threshold for yellow perch extirpation.