Water temperature affects ecosystem health both directly and indirectly. Temperature directly affects the metabolic rates and biological activity of plants and animals. For example, the timing of the early spring hatch of trout is controlled by temperature, while the rate at which plants grow increases with increased water temperature. Extended exposure to temperatures above 24°C (75.2°F) is lethal for brook trout and extended exposure to temperatures above 29°C (84.2°F) is lethal for most fish.

Temperature can also alter the physical and chemical properties of water, affecting, for example, pollutant toxicity, dissolved oxygen and other dissolved gas concentrations, conductivity, pH, and water density.