Under ideal conditions, lakes and streams are protected from the slight acidity found in regular rain because the surrounding soil acts like a filter -- it has a buffering capacity that resists fluctuations towards both acidity and alkalinity. But just like the oil filter in your car engine, overuse can clog it up. When that happens, not only are there increased aluminum levels and ample acidification in the soil, but neighboring bodies of water share the same fate.
This leads to a whole host of problems. While some species can tolerate low pH levels, many are dramatically affected. For example, acid-loaded lakes can kill adult fish populations and keep their eggs from hatching. Nitrogen depletes aquatic oxygen levels and can lead to things like harmful algal blooms and the loss of coral reefs.
Researchers have found trees become stunted and unhealthy, while climate change seems to be confounding chances for recovery. An overall decrease in terrestrial, marine and plant diversity follows prolonged exposure to acid rain, and don't forget, any time a link in the chain goes missing, anything higher up will have trouble putting food on the table.