Most lakes and streams have a pH between 6 and 8. However, some lakes are naturally acidic even without the effects of acid rain. Lakes and streams become acidic (pH value goes down) when the water itself and its surrounding soil cannot buffer the acid rain enough to neutralize it. In areas like the Northeastern United States where soil buffering is poor, some lakes now have a pH value of less than 5. One of the most acidic lakes reported is Little Echo Pond in Franklin, New York. Little Echo Pond has a pH of 4.2. Lakes and streams in the western United States are usually not acidic. Because of differences in emissions and wind patterns, levels of acid deposition are generally lower in the western United States than in the eastern United States.

Generally, the young of most species are more sensitive than adults. Frogs may tolerate relatively high levels of acidity, but if they eat insects like the mayfly, they may be affected because part of their food supply may disappear. As lakes and streams become more acidic, the numbers and types of fish and other aquatic plants and animals that live in these waters decrease. Some types of plants and animals are able to tolerate acidic waters. Others, however, are acid-sensitive and will be lost as the pH declines. Some acid lakes have no fish. At pH 5, most fish eggs cannot hatch. At lower pH levels, some adult fish die. Toxic substances like aluminum that wash into the water from the soil may also kill fish.

Together, biological organisms and the environment in which they live are called an ecosystem. The plants and animals living within an ecosystem are highly interdependent. For example, fish eat other fish and also other plants and animals that live in the lake or stream. If acid rain causes the loss of acid-sensitive plants and animals, then fish that rely on these organisms for food may also be affected.