Air pollutants can harm ecological resources, including water quality, soils, plants and animals. Ozone, for example, causes foliar injury and reduced growth in some sensitive plant species.

Atmospheric deposition of sulfur and nitrogen compounds can cause significant ecosystem effects such as acidification, eutrophication, and changes in soil and water chemistry. Acidification of soils, lakes and streams can result in changes in community structure, biodiversity, reproduction, and decomposition. Documented impacts in some parks include stressed trees, acidified streams, and reduction in species of fish and other aquatic life in affected waters.

Although nitrogen is an essential plant nutrient, increased levels of atmospheric nitrogen deposition can stress ecosystems. Excess nitrogen acts as fertilizer, favoring some types of plants and leaving others at a competitive disadvantage. This creates an imbalance in natural ecosystems, and long–term effects of these changes may include shifts in types of plant and animal species, increase in insect and disease outbreaks, and disruption of ecosystem processes such as nutrient cycling, and changes in fire frequency.

Metals, such as mercury, and persistent organic compounds deposited from the atmosphere can bioaccumulate in the food chain, causing behavioral, neurological and reproductive effects in fish, birds, and wildlife.