Multiple factors may affect the scale-up of laboratory multi-tracer injection into structured porous media to the field. Under transient flow conditions and with multiscale heterogeneities in the field, previous attempts to scale-up laboratory experiments have not answered definitely the questions about the governing mechanisms and the spatial extent of the influence of small-scale mass transfer processes such as matrix diffusion. The objective of this research is to investigate the effects of multiscale heterogeneity, mechanistic and site model conceptualization, and source term density effect on elucidating and interpreting tracer movement in the field. Tracer release and monitoring information previously obtained in a field campaign of multiple, conservative tracer injection under natural hydraulic gradients at a low-level waste disposal site in eastern Tennessee, United States, is used for the research. A suite of two-pore-domain, or fracture-matrix, groundwater flow and transport models are calibrated and used to conduct model parameter and prediction uncertainty analyses. These efforts are facilitated by a novel nested Latin-hypercube sampling technique. Our results verify, at field scale, a multiple-pore-domain, multiscale mechanistic conceptual model that was used previously to interpret only laboratory observations. The results also suggest that, integrated over the entire field site, mass flux rates attributable to small-scale mass transfer are comparable to that of field-scale solute transport. The uncertainty analyses show that fracture spacing is the most important model parameter and model prediction uncertainty is relatively higher at the interface between the preferred flow path and its parent bedrock. The comparisons of site conceptual models indicate that the effect of matrix diffusion may be confined to the immediate neighborhood of the preferential flow path. Finally, because the relatively large amount of tracer needed for field studies, it is likely that source term density effect may exaggerate or obscure the effect of matrix diffusion on the movement of tracers from the preferred flow path into the bedrock.