Theory held that a lake's mixing depth could be predicted quite well if one knew the amount of wind and the orientation of the lake with regard to that wind. Winds blowing in the direction of the longest dimension of a lake have more effect than winds blowing across it. By the mid-1980s, researchers had come to understand that, at least in some lakes, water clarity played an important role in setting mixing depth. New measurements showed that greater water clarity meant more solar radiation absorbed by the water and less solar energy lost back to the air. So, given two otherwise identical lakes, the one with the clearer water will be warmer.
Small phytoplankton have the most obvious effect.
These miniscule floating plants reduce water clarity, and that leads to lower water temperatures. The sun's energy just can't penetrate past all those little green cells. Lakes usually aren't pools of cold green soup mostly because waterborne grazers, from microscopic protozoa to mosquito larvae, devour phytoplankton. By reducing the phytoplankton population, these little animals work to clear the water and thus to make it warmer. But the food chain doesn't stop there.