The principle acidic components are sulfuric acid (H₂SO₄), nitric acid (HNO₃), and ammonium (NH₄⁺). Sulfuric acid originates primarily from the burning of fossil fuels, nitric acid from high temperature combustion in internal combustion engines, and ammonium from volatilization of NH₃ from animal wastes and fertilized soils.

Maximum sulfur and nitrogen fluxes from atmospheric deposition are approximately 86 kg S/ha/yr in northeastern Germany (Bredemeier, 1988) and 47 kg N/ha/yr in the Netherlands (Duyzer, 1995). Low to moderate inputs of nitrogen and sulfur may have a beneficial fertilization effect on forest ecosystems deficient in these nutrients. However, when nutrient deposition rates exceed biological requirements, the excess anions (SO₄^2- and NO₃^-) are susceptible to leaching from the ecosystem contributing to enhanced leaching of nutrient cations (Ca²⁺, Mg²⁺, and K⁺) that maintain solution charge balance. Increased soil acidity (higher H⁺ concentrations) leads to increased concentrations of soluble Al at pH values less than 5. The increased concentrations of dissolved H⁺ and Al³⁺ further enhance nutrient cation leaching by displacing base cations from exchange sites, thus lowering base saturation(see diagram). Base cation leaching has lead to severe deficiencies of these nutrients in heavily impacted ecosystems.

Increasing concentrations of atmospheric CO₂ may provide a fertilization effect for forest growth. The exact mechanism(s) for increased productivity is not completely understood; however, increased rates of photosynthesis and increased water-use efficiency are often cited as contributing factors. Several countries (e.g., New Zealand) are considering the use of forest ecosystems to sequester atmospheric CO₂ into soil organic matter and biomass, thus attenuating their contribution to global CO₂ emissions. Other greenhouse gases, such as N₂O and CH₄, are produced or retained by forest ecosystems and may appreciably affect global climate change. Production of these gases is linked to anaerobic conditions and microbial processes and are thus strongly affected by processes occurring within the biosphere and hydrosphere.

Tropospheric ozone concentrations are highly elevated in regions surrounding large metropolitan areas where NO₂ and partially oxidized hydrocarbons catalyze the formation of ozone (O₃). Transport of air pollutants often leads to elevated ozone levels at large distances from source areas where the ozone may cause damage to forest ecosystems, especially those species having high stomatal conductance. Ozone is taken up through stomata causing oxidation of internal cell components and a subsequent increase in maintenance respiration related to cellular repair. Ozone is also implicated in inhibiting winter hardening by disrupting carbohydrate metabolism (reviewed by Taylor et al, 1992). In contrast, depletion of stratospheric ozone has lead to increased levels of UV-B exposure to vegetation. Enhanced UV-B radiation contributes to oxidation of cellular tissues and may affect cellular metabolism and genetic integrity. As a result, plants must spend more photosynthate (energy) on defending themselves from the adverse effects of UV-B radiation leaving less photosynthate available for biomass production.

Atmospheric deposition of heavy metals (e.g., Pb, Cu, Hg, Cr) and pesticides are also reported to have appreciable effects on nutrient cycling. These compounds preferentially affect biochemical reactions, especially microbial processes, such as decomposition/mineralization and mycorrhizae activity. As a result, these compounds may have considerable impacts on nutrient cycling processes in forest ecosystems.