We present a methodology to characterize a continuum-scale model of transport in porous media on the basis of pore-scale distributions of velocities computed in three-dimensional pore-space images. The methodology is tested against pore-scale simulations of flow and transport for a bead pack and a sandstone sample. We employ a double-continuum approach to describe transport in mobile and immobile regions. Model parameters are characterized through inputs resulting from the micron-scale reconstruction of the pore space geometry and the related velocity field. We employ the outputs of pore-scale analysis to (i) quantify the proportion of mobile and immobile fluid regions and (ii) assign the velocity distribution in an effective representation of the medium internal structure. Our results (1) show that this simple conceptual model reproduces the spatial profiles of solute concentration rendered by pore-scale simulation without resorting to model calibration and (2) highlight the critical role of pore-scale velocities in the characterization of the model parameters.