Acid rain is caused by increased amounts of nitrogen oxides and sulfur dioxides from automobile and coal-fired power plant emissions. nitrogen oxides and sulfur dioxides are changed to nitric acid and sulfuric acid when they interact with water in the atmosphere. These acids combine with moisture in the air and fall to earth as acid rain or acid snow. Acid rain is responsible for thousands of lakes in eastern Canada, northeastern United States, Sweden, and Finland becoming acidic.

The type of rocks and minerals present in the soil may have a strong influence on the acid levels of the local water. If limestone is present, the alkaline (basic) limestone neutralizes the effect acids might have on lakes and streams. Regions hardest hit by acid rain are usually found downwind of urban/industrial areas and they have little limestone in the soil to reduce the acidity of the water.

Changes in the pH value of water affect the organisms that live there. Most aquatic organisms have adapted to a specific pH and may die if even slight pH changes occur. Serious problems occur in lakes with a pH below 5 or above 9.5.

Immature stages of aquatic insects and young fish are extremely sensitive to low pH values. When acid waters come into contact with certain chemicals and metals that occur in soils and bedrock, they often release them into the waters making them more toxic (poisonous) than normal. Very acidic waters can also cause heavy metals, such as copper and aluminum, to be released into the water. Heavy metals can collect on fish gills or cause deformities in young fish, making it harder for them to survive.