Many studies have examined the effects of climate warming on lake stability, but few have addressed environmental changes concomitant with climate change, such as alterations in water clarity and lake inflow. Although air temperature rise is a predominant factor linked to lake thermal characteristics, climate-driven changes at watershed scales can substantially alter lake clarity and inflow, exacerbating the effects of future air warming on lake thermal conditions. Without accounting for potential changes in clarity and inflow, future thermal predictions could be inaccurate. We employed the General Lake Model to simulate future thermal conditions (relative thermal resistance to mixing; RTRM) of small (< 12 ha) mountain lakes of the western United States by calibrating the model to a set of lakes in the Southern Rocky Mountains, USA. We found that after air temperature, alterations in inflow had the largest effect on lake thermal conditions, changes in wind had the least effect, and larger lakes experienced more than double the increase in lake stability than smaller lakes. Generally, clear, high inflow lakes had the lowest stability now, and in the future, while the largest overall increase in thermal stability occurred in larger lakes with low inflows and high turbidity. Assuming air temperature rise alone, summer stability of mountain lakes of the western United States was predicted to increase by 15–23% at + 2 °C air temperatures, and by 39–62% at + 5 °C air temperatures. When accounting for associated changes in clarity and inflow, lake stability was predicted to increase by 208% with + 2 °C air warming and 318% with at 5 °C air warming. Thus, ignoring the multivariate effects of climate change can substantially underestimate changes to mountain lake thermal and stratification regimes. Dimictic lakes may become more strongly stratified and polymictic lakes will experience more prolonged stratification. While predicted changes to lake temperatures may not be harmful to trout species that currently inhabit mountain lakes, longer and more intense stratification could cause indirect effects, such as hypoxia, that could reduce growth and survival of these organisms.