A pore‐scale simulation technique based on level set interface tracking has been developed for modeling coupled reactive flow and structure evolution in porous media and fracture apertures. Advection, diffusion, and mineral precipitation resulting in changes in pore geometries are treated simultaneously by solving fully coupled fluid flow and reactive solute transport equations. The reaction‐induced evolution of solid grain surfaces is captured using a level set method, and a subgrid representation of the interface based on the level set approach is used instead of a pixel representation of the interface often used in cellular automata and lattice‐Boltzmann simulations. Precipitation processes within a 2‐D porous medium represented by nonoverlapping discs were simulated under various flow conditions and reaction rates, and the resulting changes of pore geometry are discussed. The simulation results indicate that under reaction‐limited conditions, precipitation is nearly uniform over the grain surfaces. However, this is no longer true when reaction is relatively fast and diffusion is the dominant transport process. In such cases, precipitation occurs mostly near the throat inlet and results in rapid permeability reduction with only a small reduction of porosity. In the case of fast reaction with transport dominated by advection (which is mostly likely in engineered remediation applications), solute can be delivered deep into fracture apertures and precipitation occurs mostly along preferential flow paths. Quantitative relationships between permeability and porosity under various flow conditions and reaction rates are also reported.