In this paper, we present an algorithm for the numerical simulation of reactive transport at the pore scale to facilitate observation of pore space and rock matrix evolution. Moreover, simulation at the pore scale opens up the possibility of estimating changes in the transport properties of rocks, such as permeability and tortuosity. To quantitatively analyze pore space evolution, we developed a numerical algorithm that can be used to construct persistence diagrams of the connectivity components for pore space and the rock matrix, which characterize the topology evolution during rock matrix dissolution. Introducing the “bottle-neck” metric in the space of the persistence diagrams, we cluster the numerical experiments in terms of similarities in topology evolution. We demonstrate that the application of this metric to the persistence diagrams allowed us to distinguish topologically different dissolution scenarios, for instance, the formation of a dissolution front near the inlet, homogeneous dissolution of the matrix inside the core sample, and formation of wormholes. We illustrate that the differences in topology evolution lead to cross-correlations among the transport properties of rocks (porosity-permeability-tortuosity).