Simulations of flow and transport in variably saturated fractured rock generally assume equilibrium conditions between the fractures and the porous matrix, leading to predictions that are dominated by a diffusive process. Contrary to these predictions, an increasing body of evidence suggests that fracture-dominated flow, under nonequilibrium conditions between the fractures and porous matrix, occurs frequently in field and laboratory settings. Flow processes, such as fluid cascades and flow path switching, are often observed in laboratory experiments, but are generally not captured by diffusion-based conceptual and numerical models. Many of these processes are assumed to be averaged out at some representative elemental volume scale; however, anecdotal evidence from field experiments conducted at various scales of investigation suggest that this may not be the case. Comparison of experimental observations with numerical simulations illustrates at least two potential problems with standard equivalent continuum and discrete fracture conceptual models of unsaturated fractured and porous media flow. First, such models tend to overestimate the strength of interaction between the fracture and matrix domains. Second, model calibration may allow diffusion-based models to accurately reproduce experimental observations without providing a complete description of the physics governing the system. Failure to incorporate convective transport, reduced fracture–matrix interaction, and other sub-grid-scale processes in models of flow in fractured porous media may result in erroneous descriptions of system behavior.