Water–rock interactions can alter rock properties through chemical reactions during subsurface transport processes like geological CO2 sequestration (GCS), matrix acidizing, and waterflooding in carbonate formations. Dynamic changes in rock properties cause a failure of waterflooding and GCS and could also dramatically affect the efficiency of the acidizing. Efficient numerical simulations are thus essential to the optimized design of those subsurface processes. In this paper, we develop a three-dimensional (3D) numerical model for simulating the coupled processes of fluid flow and chemical reactions in fractured carbonate formations. In the proposed model, we employ the Stokes–Brinkman equation for momentum balance, which is a single-domain formulation for modeling fluid flow in fractured porous media. We then couple the Stokes–Brinkman equation with reactive-transport equations. The model can be formulated to describe linear as well as radial flow. We employ a decoupling procedure that sequentially solves the Stokes–Brinkman equation and the reactive transport equations. Numerical experiments show that the proposed method can model the coupled processes of fluid flow, solute transport, chemical reactions, and alterations of rock properties in both linear and radial flow scenarios. The rock heterogeneity and the mineral volume fractions are two important factors that significantly affect the structure of conductive channels.