Acid rain affects vegetation in a variety of ways. The lowered pH of rainwater destroys the waxy cuticle on the leaves of a plant, interfering with the plant's ability to control its water loss via transpiration. Destruction of the leaf structure compromises the plant's control of oxygen and carbon dioxide levels inside the plant. This interferes with the plant's ability to undergo photosynthesis and respiration.

Acid rain also impacts plants by affecting the pH of the soil. The addition of extra hydrogen ions causes many important nutrients, including potassium, nitrogen, and phosphorus, to leach from the soil before the plants have a chance to utilize them, leading to nutrient deficiencies. The acid rain also increases the amount of toxic metals released from the soil. The most common of these metals, mercury and aluminum, are harmful to the plants as well as animals. Some plants depend on an important mutualistic relationship with a fungus that grows on their roots. The fungus-plant associations known as mycorrhizae dramatically increase the surface area of the plant root and enable it to absorb more nutrients. When the pH of the soil decreases, the fungi die, decreasing the plant's ability to take up water and nutrients.

Though acid rain affects all animals, aquatic animals feel the effects most directly. As the pH decreases, many aquatic organisms cannot survive. Most fish die at a pH lower than 4.6 as a result of interference with their gill function. In freshwater ecosystems, the microorganisms responsible for decomposing organic material in the water cannot survive in acidic conditions, and without them, the decaying material builds up on the lake bottom.

As in the soil, the levels of metals like mercury and aluminum rise in the more acidic water, allowing toxic substances to build up more quickly than normal. The buildup harms humans and other animals that eat fish from these lakes and streams. By consuming plants and other aquatic animals from an acidic environment, they also suffer the effects of the acid rain. Aluminum exposure has been linked to Alzheimer’s disease, and mercury shows a cumulative effect on the nervous system. . .