Modeling studies project that in the future surface waters in the northeast US will continue to recover from acidification over decades following reductions in atmospheric sulfur dioxide and nitrogen oxides emissions. However, these studies generally assume stationary climatic conditions over the simulation period and ignore the linkages between soil and surface water recovery from acid deposition and changing climate, despite fundamental impacts to watershed processes and comparable time scales for both phenomena. In this study, the integrated biogeochemical model PnET-BGC was applied to two montane forest watersheds in the Adirondack region of New York, USA to evaluate the recovery of surface waters from historical acidification in response to possible future changes in climate and atmospheric sulfur and nitrogen deposition. Statistically downscaled climate scenarios on average project warmer temperatures and greater precipitation for the Adirondack by the end of the century. Model simulations suggest under constant climate, acid-sensitive Buck Creek would gain 12.8 μeq L−1 of acid neutralizing capacity (ANC) by 2100 from large reductions in deposition, whereas acid insensitive Archer Creek is projected to gain 7.9 μeq L−1 of ANC. However, climate change could limit those improvements in acid-base status. Under climate change, a negative offset relative to the ANC increases with no climate change are projected for both streams by 2100. In acid-insensitive Archer Creek the negative offset (−8.5 μeq L−1) was large enough that ANC is projected to decrease by −0.6 μeq L−1, whereas in acid-sensitive Buck Creek, the negative offset (−0.4 μeq L−1) resulted in a slight decline of the projected future ANC increase to 12.4 μeq L−1. Calculated target loads for 2150 for both sites decreased when future climate change was considered in model simulations, which suggests further reductions in acid deposition may be necessary to restore ecosystem structure and function under a changing climate.