Knowing the influence of isomorphic substitutions on the acid-base properties of smectite edge surfaces is an important aspect of the detailed understanding of clay minerals' interfacial properties with implications in the modeling of adsorption processes. We investigated the intrinsic acidity constants of Fe(II)/Fe(III) and Al(III) substituted edge surface sites of montmorillonite with a cis-vacant structure, which includes four crystallographic orientations perpendicular to [010], [010], [110], and [110], using the first-principles molecular dynamics (FPMD) based vertical energy gap method. Fe(II) and Fe(III) substitutions resulted, respectively, in a significant increase and decrease in pKa values of amphoteric groups directly associated with Fe octahedra. In addition, Fe(II) substitution increased the pKa values of the neighboring silanol sites, while Fe(III) substitution had a weak influence on these sites. The Al-substituted tetrahedra had amphoteric sites with higher pKa values than the non-substituted Si tetrahedra, and they increased significantly the pKa values of the sites bridging the tetrahedral and octahedral sheets on surfaces perpendicular to [010] and [110]. The acid-base properties of substituted and non-substituted surface sites of cis-vacant montmorillonite were used to build a state-of-the-art surface complexation model, which successfully reproduced the best available experimental acid-base titration data. This model was further used to predict acid-base properties of dioctahedral smectites (montmorillonite, beidellite, and nontronite) according to their cis- or trans-vacant structures and their layer chemistry. According to these predictions, these smectites exhibit very similar overall pH buffering properties despite significant differences in structure and chemistry. A detailed analysis of the acid-base properties as a function of crystallographic directions demonstrated, however, that these differences should have a large influence on the adsorption of ionic species.