Both the lower pH and higher aluminium concentrations in surface water that occur as a result of acid rain can cause damage to fish and other aquatic animals. At pH lower than 5 most fish eggs will not hatch and lower pH can kill adult fish. As lakes and rivers become more acidic biodiversity is reduced. Acid rain has eliminated insect life and some fish species, including the brook trout in some lakes, streams, and creeks in geographically sensitive areas, such as the Adirondack Mountains of the United States. 
However, the extent to which acid rain contributes directly or indirectly via runoff from the catchment to lake and river acidity (i.e., depending on characteristics of the surrounding watershed) is variable. The United States Environmental Protection Agency's (EPA) website states: "Of the lakes and streams surveyed, acid rain caused acidity in 75% of the acidic lakes and about 50% of the acidic streams". Lakes hosted by silicate basement rocks are more acidic than lakes within limestone or other basement rocks with a carbonate composition (i.e. marble) due to buffering effects by carbonate minerals, even with the same amount of acid rain.
Sulfur dioxide and nitrous oxide concentration has many implication on aquatic ecosystems, including acidity change, increased nitrogen and aluminum content, and altering biogeochemical processes. Typically, sulfur dioxide and nitrous oxide do not have direct physiological effects upon exposure; most effects are developed by accumulation and prolonged exposure of these gases in the environment, modifying soil and water chemistry.