In this study, we propose a model for the simulation of the pH-dependent separation of dicarboxylic acids from aqueous solutions using strongly hydrophobic adsorbents. Building upon results of our previous study, where we experimentally investigated the pH-dependent adsorption behavior of the individual acid species of itaconic acid (IA) on a strongly hydrophobic adsorbent using in-line Raman spectroscopy, we utilize a transport-dispersive model as the basis for our simulation model. Instead of considering IA as a single component in our model, we simulated each acid species of IA individually. For this purpose, we expanded the transport-dispersive model with reaction terms in all aqueous phases. The reaction terms include all dissociation reactions of all involved components for each time step and spatial discretization. This model enables the time and spatial dependent simulation of the pH value in the chromatographic column and thus the time and spatial dependent knowledge of each acid species concentration. The consideration of activity coefficients due to high local ionic strength is achieved using the Truesdell–Jones (TdJ) model. The simulation model is successfully validated using experimental data from our previous study and used in a simulation study that demonstrates the potential of the model approach for analyzing associated separation tasks.