Although acidifying deposition in western North America is lower than in many parts of the world, many high-elevation ecosystems there are extremely sensitive to acidification. Previous studies determined that the Mount Zirkel Wilderness Area (MZWA) has the most acidic snowpack and aquatic ecosystems that are among the most sensitive in the region. In this study, spatial and temporal variability of ponds and lakes in and near the MZWA were examined to determine their sensitivity to acidification and the effects of acidic deposition during and after snowmelt. Within the areas identified as sensitive to acidification based on bedrock types, there was substantial variability in acid-neutralizing capacity (ANC), which was related to differences in hydrological flowpaths that control delivery of weathering products to surface waters. Geological and topographic maps were of limited use in predicting acid sensitivity because their spatial resolution was not fine enough to capture the variability of these attributes for lakes and ponds with small catchment areas. Many of the lakes are sensitive to acidification (summer and autumn ANC < 100 µeq L⁻¹), but none of them appeared to be threatened immediately by episodic or chronic acidification. In contrast, 22 ponds had minimum ANC < 30 µeq L⁻¹, indicating that they are extremely sensitive to acidic deposition and could be damaged by episodic acidification, although net acidity (ANC < 0) was not measured in any of the ponds during the study. The lowest measured pH value was 5·4, and pH generally remained less than 6·0 throughout early summer in the most sensitive ponds, indicating that biological effects of acidification are possible at levels of atmospheric deposition that occurred during the study. The aquatic chemistry of lakes was dominated by atmospheric deposition and biogeochemical processes in soils and shallow ground water, whereas the aquatic chemistry of ponds was also affected by organic acids and biogeochemical processes in the water column and at the sediment–water interface. These results indicate that conceptual and mechanistic acidification models that have been developed for lakes and streams may be inadequate for predicting acidification in less-understood systems such as ponds.