Acidic atmospheric deposition has adversely affected aquatic ecosystems globally. As emissions and deposition of sulfur (S) and nitrogen (N) have declined in recent decades across North America and Europe, ecosystem recovery has become evident in many surface waters. However, persistent chronic and episodic acidification remain important concerns in the most vulnerable regions. We evaluated stream acidification in 269 headwaters along the Appalachian Trail (AT) across the eastern U.S. The AT is an ideal study region because it transits several ecoregions, is located downwind of high levels of S and N emission sources and includes heterogeneous soils and geology. Chronic acidification at low flow was substantial as 16% of streams had a mean acid-neutralizing capacity (ANC) <0 meq/L. By applying two new approaches to calculate the extent of episodic acidification, we estimated that streams with ANC <0 meq/L doubled to 32% as discharge increased from the 15^th to 85^th flow percentile. The proportion of chronically and episodically acidic streams decreased from north to south along the AT. Dilution of base cation concentrations explained the greatest amount of episodic acidification among AT streams and variation in sulfate (SO₄^2-) concentrations was a secondary explanatory variable. However, episodic SO₄^2- patterns varied geographically with dilution dominant in northern streams underlain by soils developed in glacial sediment, and increased SO₄^2- concentrations dominant further south in streams with older, more highly weathered soils. Episodic acidification as determined by ANC decline with flow increased as low-flow ANC increased, exceeding 90 meq/L in 25% of the streams. At streams with low-flow ANC values <30 meq/L, episodic increases rather than decreases in ANC was the dominant pattern. Chronic and episodic acidification remain an ecological concern among streams along the AT. The approach developed here could be widely applied to provide estimates of the magnitude of acidification in other regions recovering from decreasing levels of atmospheric S and N deposition.