We investigate the flow structure and the porosity-permeability relationship of porous media that undergo morphology modifications due to evaporation or microbially induced calcite precipitation, as well as wettability modifications of the solid-fluid interface due to fluid pH, composition, or salt con¬centration changes. We develop simulation methods based on coupled multi-phase and multi-component Lattice-Boltzmann and solute molecular dynamics simulations, capable of reproducing these processes in detail on the pore scale, yielding results to be used to improve existing continuum models.