There is still a need for catchment hydrological and transport models that properly integrate the effects of preferential flows while accounting for differences in velocities and celerities. A modeling methodology is presented here which uses particle tracking methods to simulate both flow and transport in multiple pathways in a single consistent solution. Water fluxes and storages are determined by the volume and density of particles and transport is attained by labeling the particles with information that may be tracked throughout the lifetime of that particle in the catchment. The methodology allows representation of preferential flows through the use of particle velocity distributions, and mixing between pathways can be achieved with pathway transition probabilities. A transferable 3-D modeling methodology is presented for the first time and applied to a unique step-shift isotope experiment that was carried out at the 0.63 ha G1 catchment in Gardsjon, Sweden. This application highlights the importance of combining flow and transport in hydrological representations, and the importance of pathway velocity distributions and interactions in obtaining a satisfactory representation of the observations.