A one-dimensional mathematical model was developed to analyze the influence of different physical and chemical parameters on the performance of an encapsulated phosphate buffer for controlling pH and enhancing a pH-dependent process in a soil column. Three scenarios were investigated where base equivalents are produced through the degradation of the target compound (scenario I), through reactions in the matrix (scenario II), and a combination of both mechanisms (scenario III). In all three scenarios, the production of base equivalents is countered by the release of the acidic core of the encapsulated phosphate, resulting in an enhanced removal of the target compound. A sensitivity analysis on the model shows that under the conditions investigated, the removal of the target compound is dependent on the flowrate, porosity, dispersion coefficient, reaction rate constants, mass of added capsules, and the point of addition of the capsules. The approach can be used to analyze scenarios where encapsulated buffers can control pH and optimize pH-dependent processes in a soil column.