Conservation organizations have most often focused on land-use change, climate change, and invasive species as prime threats to biodiversity conservation. Although air pollution is an acknowledged widespread problem, it is rarely considered in conservation planning or management. In this synthesis, the state of scientific knowledge on the effects of air pollution on plants and animals in the Northeastern and Mid-Atlantic regions of the United States is summarized. Four air pollutants (sulfur, nitrogen, ozone, and mercury) and eight ecosystem types ranging from estuaries to alpine tundra are considered. Effects of air pollution were identified, with varying levels of certainty, in all the ecosystem types examined. None of these ecosystem types is free of the impacts of air pollution, and most are affected by multiple pollutants. In aquatic ecosystems, effects of acidity, nitrogen, and mercury on organisms and biogeochemical processes are well documented. Air pollution causes or contributes to acidification of lakes, eutrophication of estuaries and coastal waters, and mercury bioaccumulation in aquatic food webs.