Atmospheric deposition of sulfur (S) and nitrogen (N) has decreased steadily in the northeastern U.S. since the federal 1970 Clean Air Act was passed, yet deposition remains elevated above natural background levels throughout the region. Epiphytic macrolichens are highly sensitive to air pollution and their status is a good indicator of ecological health. We used deposition modeling for 2000–2013 and multiple metrics of lichen status (i.e., species composition, species richness, thallus condition, lichen sensitivity indices, lichen elemental analysis) to assess air pollution effects at 24 plots in four federally-mandated Class I areas. The areas (Lye Brook Wilderness, VT; Great Gulf and the Presidential Range-Dry River Wildernesses, NH; and Acadia National Park, ME) encompass a range of high to low deposition sites. We developed thallus condition scores and sensitivity groups and indices for S and N based on species patterns using deposition estimates gleaned from a larger, independent data base. Non-metric multidimensional scaling ordinations differentiated forest structure effects on lichen community composition from more complex deposition and elevation effects. Annual mean and cumulative deposition of N correlated strongly with decreases in lichen species richness and N-sensitive species, and poorer thallus condition. Cumulative dry deposition of S yielded the best fit to decreases in thallus condition, poorer community-based S Index values, and absence of many S-sensitive species. Multiple metrics provided consistent evidence that higher depositional loading was associated with greater adverse effects. In general, stronger correlations between present day lichen metrics and cumulative deposition (post-2000), compared to current deposition, emphasize the long-term nature of emissions impacts and continued need to control S and N emissions to restore the ecological health of lichen communities and linked biota.