Acidic deposition has impaired the structure and function of acid-sensitive Northern Forest watersheds in the northeastern U.S. In particular many surface waters in the Adirondack region of New York have experienced decreases in pH and acid neutralizing capacity (ANC) due to acidic deposition. In spite of air quality programs over past decades, 128 lakes in the Adirondacks are classified as “impaired” under Section 303(d) of the Clean Water Act in 2010 due to elevated acidity. The biogeochemical model PnET-BGC was developed to improve understanding of the response of forested watershed to effects of air pollution, changing climate and land disturbance. Of particular interest a new algorithm was developed to depict the compensatory response of soil organic acids to decreases in acidic deposition. PnET-BGC was used to relate decreases in atmospheric sulfur and nitrogen deposition to changes in Adirondack lake water chemistry. The model was calibrated and confirmed using observed soil and lake water chemistry data and then applied to calculate maximum atmospheric deposition that the impaired lakes can receive to achieve ANC endpoints. Of the 128 acid-impaired lakes, the analysis suggests that 40 will recover to below an endpoint ANC value of 20 µeq L^-1 without any additional emission controls and another 36 could recover with some additional decrease in atmospheric sulfur deposition by 2050. In contrast by 2200, 80 of the impaired lakes are simulated to recover to ANC values above 20 µeq L^-1 with no additional emission controls and 9 more would recover with additional decreases in acid deposition. This analysis indicates that under current air quality management programs most impaired Adirondack lakes will recover over the very long term (i.e., centuries), but recovery could be accelerated by additional emission controls. Also it appears that about 30% of the impaired Adirondack lakes (39 out of 128) will not recover regardless of the level of reduction in acid deposition.  These lake-watersheds are either naturally acidic or have been acidified by acidic deposition beyond the point of recovery, but could be recovered by other mitigation options such as liming. Our analysis indicated that the enhanced release of naturally occurring organic acids limits the recovery of ANC following decreases in acidic deposition.  We also show the use of empirical spatial relationships of biological acidification indicators in critical load calculations.