The Subsurface Disposal Area (SDA) at the Idaho National Engineering and Environmental Laboratory (INEEL) contains low-level, hazardous, and transuranic wastes and is the subject of ongoing environmental assessments. The buried waste is in shallow land burial overlying a 180-m-thick vadose zone comprised of fractured basalts and sedimentary interbeds. Applied simulation studies to predict future contaminant concentrations from this buried waste have been conducted as part of ongoing regulatory-driven environmental assessments for the SDA. An overview of the most recent numerical simulation study is presented along with a treatment of conceptual model uncertainty. The main premise of this paper is that conceptual uncertainty likely dominates parametric uncertainty, and this dominance should be considered when designing characterization studies. Given that the current modeling is uncalibrated due to inconsistent monitoring data in the vadose zone, it is only appropriate to consider conceptual model uncertainty. Conceptual model uncertainty was addressed by modeling different scenarios. Scenarios presented in this paper are the assignment of infiltration boundary conditions, a simplistic approximation to represent facilitated transport, and alternative representations of the moisture characteristic curve for fractured basalts. Results of this subsurface transport modeling have been used in part to guide additional field characterization activities. Eventually, predicted concentrations from this applied model will be used to estimate human health risks for a potential future receptor as part of the environmental assessment process.