Atmospheric sulfur (S) emissions peaked in North America in the early 1970s followed by declines in S deposition and sulfate (SO42−) concentrations in surface waters. Changes in S biogeochemistry affect the mobilization of toxic (Al+3, H+) and nutrient (Ca2+, Mg2+, K+) cations, and the acid–base status of ecosystems. We focused on lake/watersheds in the Adirondack Mountains of New York, USA, one of the most acid-sensitive and acid-impacted regions in North America. We used 16 of the 17 original Adirondack Long-Term Monitoring Lakes from 1984 through 2010 and found significant declines (−2.14 µmolc l−1 year−1) in SO42− concentrations. There were significant declines (−0.28 kg S ha−1 year−1) in total S deposition for all lake/watersheds. We constructed S mass balances for 14 lakes/watersheds from wet and dry S deposition and SO42− loss from drainage and found a comparable decline (−0.26 kg S ha−1 year−1) in lake SO42− export. There was a discrepancy (mean 2.34 kg S ha−1 year−1) between atmospheric S deposition and watershed S loss due to internal S sources. Using major solute chemistry including dissolved silica and watershed characteristics, it was evident that the watershed S budget discrepancy increased with thickness of surficial deposits. The annual discrepancies in S mass balances were strongly linked with annual watershed discharge. These results suggest that internal S sources are becoming increasingly important as atmospheric S inputs have declined. The internal SO42− supply of watersheds decreased concomitantly with lake acid neutralizing capacity (ANC). These findings suggest that the limited contributions from internal sources of SO42− will facilitate the recovery of ANC from those lake/watersheds with the lowest ANC. With long-term decreases in atmospheric S deposition, the effects of climate, especially increases in precipitation, will play an increasingly important role in regulating S budgets and the amount of SO42− mobilized from internal watershed sources. Copyright © 2012 John Wiley & Sons, Ltd.