Solute transport in unsaturated porous materials is a complex process, which exhibits some distinct features differentiating it from transport under saturated conditions. These features emerge mostly due to the different transport time scales at different regions of the flow network, which can be classified into flowing and stagnant regions, predominantly controlled by advection and diffusion, respectively. Under unsaturated conditions, the solute breakthrough curves show early arrivals and very long tails, and this type of transport is usually referred to as non-Fickian. This study directly characterizes transport through an unsaturated porous medium in three spatial dimensions at the resolution of 3.25 μ m and the time resolution of 6 s. Using advanced high-speed, high-spatial resolution, synchrotron-based X-ray computed microtomography (sCT) we obtained detailed information on solute transport through a glass bead packing at different saturations. A large experimental dataset (>50 TB) was produced, while imaging the evolution of the solute concentration with time at any given point within the field of view. We show that the fluids’ topology has a critical signature on the non-Fickian transport, which yet needs to be included in the Darcy-scale solute transport models. The three-dimensional (3D) results show that the fully mixing assumption at the pore scale is not valid, and even after injection of several pore volumes the concentration field at the pore scale is not uniform. Additionally, results demonstrate that dispersivity is changing with saturation, being twofold larger at the saturation of 0.52 compared to that at the fully saturated domain.