We explore the permeability evolution of fractures in carbonate rock that results from the effects of mechanical stress and nonequilibrium chemistry (pH of fluid). Core plugs of Capitan limestone are saw cut to form a smooth axial fracture that is subsequently roughened to simulate a natural fracture with controlled surface topography. Aqueous solutions of ammonium chloride (pH 5∼7) transit these plugs at confining stresses of 3–10 MPa, with flow rates and mineral mass fluxes measured to constrain competing mechanisms of permeability evolution. The effluent calcium concentrations are always much lower than equilibrium calcium solubility, resulting in the dissolution‐dominant permeability evolution in our experiments. Depending on the combination of confining stress and fluid pH, the fracture apertures either gape (permeability increase) or close (permeability reduction). We quantitatively constrain the transition between gaping (pH < 6.1) and closing (pH > 6.5) with this transition independent of confining stress up to 10 MPa. A transitional regime (6.1 < pH < 6.5) of invariant aperture represents a balance between the two mechanisms of free‐face dissolution and pressure solution at the bridging asperities. We employ a lumped‐parameter model to interpret the dissolution‐dominant evolution of permeability. By considering different dissolution rate constants between noncontacting asperities and the stagnant water film at the contacting asperities, this model replicates the principal characteristics of permeability evolution of the fracture. Observed rates of aperture change are ill matched when the influent pH is 5–6, since wormhole formation is not accommodated in the model. These observations offer a promising pathway to index the switch from aperture gaping to aperture closing for reactive flow as reactivity is reduced and stress effects become more important.