In tropical regions, the effects of land-cover change on nutrient and pollutant inputs to ecosystems remain poorly documented and may be pronounced, especially in montane areas exposed to elevated atmospheric deposition. We examined atmospheric deposition and canopy interactions of sulfate-sulfur (SO4(2-)-S), chloride (Cl-), and nitrate-nitrogen (NO(3-)-N) in three extensive tropical montane land-cover types: clearings, forest, and coffee agroforest. Bulk and fog deposition to clearings was measured as well as throughfall (water that falls through plant canopies) ion fluxes in seven forest and five coffee sites. Sampling was conducted from 2005 to 2008 across two regions in the Sierra Madre Oriental, Veracruz, Mexico. Annual throughfall fluxes to forest and coffee sites ranged over 6-27 kg SO4(2-)-S/ha, 12-69 kg Cl-/ha, and 2-6 kg NO(3-)-N/ha. Sulfate-S in forest and coffee throughfall was higher or similar to bulk S deposition measured in clearings. Throughfall Cl- inputs, however, were consistently higher than Cl- amounts deposited to cleared areas, with net Cl- fluxes enhanced in evergreen coffee relative to semi-deciduous forest plots. Compared to bulk nitrate-N deposition, forest and coffee canopies retained 1-4 kg NO(3-)-N/ha annually, reducing NO(3-)-N inputs to soils. Overall, throughfall fluxes were similar to values reported for Neotropical sites influenced by anthropogenic emissions, while bulk S and N deposition were nine- and eightfold greater, respectively, than background wet deposition rates for remote tropical areas. Our results demonstrate that land-cover type significantly alters the magnitude and spatial distribution of atmospheric inputs to tropical ecosystems, primarily through canopy-induced changes in fog and dry deposition. However, we found that land cover interacts with topography and climate in significant ways to produce spatially heterogeneous patterns of anion fluxes, and that these factors can converge to create deposition hotspots. For land managers, this finding suggests that there is potential to identify species and ecosystems at risk of excess and increasing deposition in montane watersheds undergoing rapid transformation. Our data further indicate that montane ecosystems are vulnerable to air pollution impacts in this and similar tropical regions downwind of urban, industrial, and agricultural emission sources.