The possible effects of trace-gas induced climatic changes on Pyramid and Yellowstone Lakes are assessed using a model of lake temperature. The model is driven by 312 years of hourly meteorological data obtained directly from the output of double-CO₂ experiments (2 × CO₂) conducted with a regional climate model nested in a general circulation model. The regional atmospheric model is the climate version of the National Center for Atmospheric Research/Pennsylvania State University mesoscale model, MM4.

Average annual surface temperature of Pyramid Lake for the 2 × CO₂ climate is 15.5 ± 5.4°C (±1 σ), 2.8°C higher than the control. Annual overturn of the lake ceases as a result of these higher temperatures for the 2 × CO₂ climate. Evaporation increases from 1400 mm yr⁻¹ in the control to 1595 mm yr⁻¹ in the 2 × CO₂ simulation, but net water supplied to the Pyramid Lake basin increases from −6 mm yr⁻¹ in the control to +27 mm yr⁻¹ in the 2 × CO₂ simulation due to increased precipitation.

For the open water periods, the average annual surface temperature of Yellowstone Lake is 13.2 ± 5.1°C for the 2 × CO₂ climate, a temperature 1.6°C higher than the control. The annual duration of ice cover on the lake is 152 days in the 2 × CO₂ simulation, a reduction of 44 days relative to the control. Warming of the lake for the 2 × CO₂ climate is mostly confined to the near-surface. Simulated spring overturn for the 2 × CO₂ climate occurs earlier in the year and fall overturn later than in the control. Evaporation increases from 544 mm yr⁻¹ to 600 mm yr⁻¹ in the 2 × CO₂ simulation, but net water supplied to the Yellowstone Lake basin increases from +373 mm yr⁻¹ in the control to +619 mm yr⁻¹ due to increased precipitation. The effects of these climatic changes suggest possible deterioration of water quality and productivity in Pyramid Lake and possible enhancement of productivity in Yellowstone Lake.