The tendency of irreversible processes to generate entropy is the ultimate driving force for the evolution of nature. In engineering, entropy production is often used as a measure of usable energy losses. In this study we show that the analysis of the entropy production patterns can help understand the vastly diversified experimental observations of water-rock interactions in natural porous media. We first present a numerical scheme for the analysis of entropy production in dissolving porous media. Our scheme uses a greyscale digital model of natural chalk obtained by X-ray nanotomography. Greyscale models preserve structural heterogeneities with very high fidelity, which is essential for simulating a system dominated by infiltration instability. We focus on the coupling between two types of entropy production: the percolative entropy generated by dissipating the kinetic energy of fluid flow and the reactive entropy that originates from the consumption of chemical free energy. Their temporal patterns pinpoint three stages of microstructural evolution. We then show that the regional mixing deteriorates infiltration instability by reducing local variations in reactant distribution. In addition, we show that the microstructural evolution can be particularly sensitive to the initially present transport heterogeneities when the global flowrate is small. This dependence on flowrate indicates that the need to resolve the structural features of a porous system is greater when the residence time of the fluid is long.