A pore‐scale numerical model for reactive transport processes based on the Lattice Boltzmann method is used to study the dissolution‐induced changes in hydrologic properties of a fractured medium and a porous medium. The solid phase of both media consists of two minerals, and a structure reconstruction method called quartet structure generation set is employed to generate the distributions of both minerals. Emphasis is put on the effects of undissolved minerals on the changes of permeability and porosity under different Peclet and Damkohler numbers. The simulation results show porous layers formed by the undissolved mineral remain behind the dissolution reaction front. Due to the large flow resistance in these porous layers, the permeability increases very slowly or even remains at a small value although the porosity increases by a large amount. Besides, due to the heterogeneous characteristic of the dissolution, the chemical, mechanical and hydraulic apertures are very different from each other. Further, simulations in complex porous structures demonstrate that the existence of the porous layers of the nonreactive mineral suppresses the wormholing phenomena observed in the dissolution of mono‐mineralic rocks.