Improved understanding of flow and radionuclide transport in vadose zone sediments is fundamental to future planning involving radioactive materials. To that end, long-term experiments were conducted at the Savannah River Site in South Carolina, where a series of lysimeters containing sources of plutonium (Pu) in different oxidation states was placed in the shallow subsurface and exposed to the environment for 2 to 11 yr. Then, sediment Pu activity concentrations were measured along vertical cores taken from the lysimeters. Results showed anomalous activity distributions below the source, with significant migration of Pu above the source. A previously developed reactive transport model with surface-mediated redox reactions successfully simulated the lysimeter results below the source, assuming a steady, net downward flow. To simulate more realistic field conditions, a transient variably saturated flow model with root water uptake is developed and coupled to the reactive transport model. Overall, the fully transient analysis shows results nearly identical to the much simpler steady flow analysis. Thus, the surface-mediated redox hypothesis remains consistent with the below-source experimental data, the most important variable affecting transport being the oxidation state of the source material. However, none of the models studied could produce the upward Pu transport observed in the data. The hydraulic and chemical mechanisms tested as potential causes for upward migration—a modified root distribution, hysteresis, and air-content dependent oxidation—yielded little or no enhancement of the upward Pu movement. This suggests another transport mechanism such as root Pu uptake and translocation in the transpiration stream.