In this paper, we review the current understanding on ecosystem and human health impacts from the atmospheric deposition of acidifying pollutants, eutrophying nitrogen (N), polycyclic aromatic hydrocarbons (PAHs), mercury (Hg), trace metals, and ozone (O3), as well as the biological indicators that have been used to assess the health of ecosystems following exposure to these pollutants. We provide overviews of the impacts of deposition for these pollutants and discuss the currently known biomonitors for each pollutant. The deposition of acidifying pollutants impacts terrestrial ecosystems by altering plant physiology and growth and by increasing plant susceptibility to stresses that can be indirectly damaging to the health of fish and birds. Indicators of the deposition of acidifying pollutants include soil base cation content and acid neutralizing capacity, among others. Eutrophying N deposition has been studied extensively; N enrichment directly impacts vegetative plant species cover, richness, growth rates, and susceptibility to other stressors. It indirectly impacts wildlife through changes in their habitats and food sources. Indicators for N deposition include changes in plant species and in tissue and litter N content. The deposition of PAHs has been found to cause significant damage to plant organisms and to be carcinogenic and mutagenic to humans and animals. Useful biomonitors of PAH deposition include lichens, mosses, and pine needles. Deposited Hg can undergo methylation (in the presence of sulphur reducing bacteria); bioaccumulation of methylmercury is highly toxic to animals. Effective biomonitors of Hg contamination of aquatic ecosystems are fish and marine birds. The impacts of O3 are well understood, with well-established “flux” models being vast improvements on the previous AOT40 approaches. This review highlights the impacts that the above-mentioned pollutants have on terrestrial and aquatic organisms and the biomonitors that are currently being used to assess the deposition levels and effects of these pollutants.