Critical loads (CLs) and target loads (TLs) are tools used to guide air emissions control strategies for recovery of forest and aquatic ecosystems impacted by elevated atmospheric deposition. We use the dynamic hydrochemical model-PnET-BGC (photosynthesis evapotranspiration biogeochemical) to evaluate biophysical factors that affect CLs and TLs of acidity for the Constable Pond watershed, as an example of a chronically acidic drainage lake in the Adirondack region of New York, USA. These factors included a range of future scenarios of decreases in atmospheric nitrate, ammonium and sulfate deposition from present to 2200; historical forest harvesting; supply of naturally occurring organic acids; and variations in lake hydraulic residence time. Simulations show that decreases in sulfate deposition were more effective in increasing lake acid neutralizing capacity (ANC) than equivalent decreases in nitrate deposition, 4.6 times greater in 2040–2050 but decreasing to 2 times greater by 2200. Future lake ANC is anticipated to increase to a greater extent when the watershed experiences past forest cutting compared to a scenario without historical land disturbance. Under higher rates of watershed supply of naturally occurring dissolved organic carbon (DOC ~1000 µmol C/L), ANC is lower than under relatively low DOC supply (~100 µmol C/L) due to strongly acidic functional groups associated with dissolved organic matter. Lakes with longer hydrologic residence time exhibit less historical acidification and can achieve a greater ANC from recovery than lakes with shorter hydrologic residence times due to in-lake production of ANC. This study improves understanding of how biogeochemical processes at the landscape level can influence the rate and extent of recovery of lake–watersheds in response to decreases in atmospheric deposition.