Long-term (1860–2010) catchment mass balance calculations rely on models and assumptions which are sources of uncertainty in acidification assessments. In this article, we report on an application of MAGIC to model acidification at the four Swedish IM forested catchments that have been subject to differing degrees of acidification stress. Uncertainties in the modeled mass balances were mainly associated with the deposition scenario and assumptions about sulfate adsorption and soil mass. Estimated base cation (BC) release rates (weathering) varied in a relatively narrow range of 47–62 or 42–47 meq m-2 year-1, depending on assumptions made about soil cation exchange capacity and base saturation. By varying aluminum solubility or introducing a dynamic weathering feedback that allowed BC release to increase at more acidic pHs, a systematic effect on predicted changes in acid neutralizing capacity (ΔANC ca. 10–41 µeq l-1) and pH (ca. ΔpH = 0.1–0.6) at all sites was observed. More robust projections of future changes in pH and ANC are dependent on reducing uncertainties in BC release rates, the timing, and extent of natural acidification through BC uptake by plants, temporal changes in soil element pools, and fluxes of Al between compartments.