Darcy-scale models of flow and transport in porous media often fail to describe experimentally observed phenomena, while their pore-scale counterparts are accurate but can be computationally prohibitive. Most numerical multiscale models, which seek to combine these two descriptions, require empirical closures and/or assumptions about the behavior of pore-scale quantities at the continuum (Darcy) scale. We present a general formulation of an iterative hybrid numerical method that links the pore and continuum scales without resorting to such approximations. The algorithm treats the fluxes exchanged at internal boundaries between the pore- and continuum-scale domains as unknown, and allows for iteratively determined boundary conditions to be applied at the pore-scale in order to guarantee flux continuity. While the algorithm proposed is general, we use it to model transport in a fracture with chemically reactive walls. Results demonstrate significant improvement upon standard continuum-scale formulations.