We investigated multiple lines of evidence to determine if observed and paleo-reconstructed changes in acid neutralizing capacity (ANC) in Sierra Nevada lakes were the result of changes in 20th century atmospheric deposition. Spheroidal carbonaceous particles (SCPs) (indicator of anthropogenic atmospheric deposition) and biogenic silica and δ(13)C (productivity proxies) in lake sediments, nitrogen and sulfur emission inventories, climate variables, and long-term hydrochemistry records were compared to reconstructed ANC trends in Moat Lake. The initial decline in ANC at Moat Lake occurred between 1920 and 1930, when hydrogen ion deposition was approximately 74 eq ha(-1) yr(-1), and ANC recovered between 1970 and 2005. Reconstructed ANC in Moat Lake was negatively correlated with SCPs and sulfur dioxide emissions (p = 0.031 and p = 0.009). Reconstructed ANC patterns were not correlated with climate, productivity, or nitrogen oxide emissions. Late 20th century recovery of ANC at Moat Lake is supported by increasing ANC and decreasing sulfate in Emerald Lake between 1983 and 2011 (p < 0.0001). We conclude that ANC depletion at Moat and Emerald lakes was principally caused by acid deposition, and recovery in ANC after 1970 can be attributed to the United States Clean Air Act.