Sodium-bearing waste (SBW) containing high concentration of 90Sr was accidentally released to the vadose zone at the Idaho Nuclear Technology and Engineering Center, Idaho National Laboratory, Idaho Falls, ID, in 1972. To investigate the transport and fate of the 90Sr through this 137-m-thick, heterogeneous, variably saturated subsurface, we conducted a two-dimensional numerical modeling using TOUGHREACT under different assumed scenarios (low permeability of an entire interbed or just its surface) for the formation of perched water whose presence reflects the unique characteristics of the geologic materials and stratification at the study site. The results showed that different mechanisms could lead to different flow geometries. The assumption of low permeability for the entire interbed led to the largest saturated zone area and the longest water travel time (55 vs. 43 or 44 yr in other scenarios) from the SBW leakage to the groundwater table. Simulated water travel time from different locations on the land surface to the groundwater aquifer varied from <30 to >80 yr. The results also indicated that different mechanisms may lead to differences in the peak and travel time of a small mobile fraction of Sr. The effective distribution coefficient and retardation factor for Sr2+ would change more than an order of magnitude for the same material during the 200-yr simulation period because of large changes in the concentrations of Sr2+ and competing ions. Understanding the migration rate of the mobile Sr2+ is necessary for designing long-term monitoring programs to detect it.