The objectives of this research are (1) to numerically examine the multiscale effects of physical and chemical mass transfer processes on watershed-scale, variably saturated contaminant transport and (2) to quantify the uncertainties resulting from imperfect information when small scale processes and parameters are upscaled to watershed scales. Concurrent physical and chemical nonequilibrium, caused respectively by interaggregate concentration differences and intraaggregate adsorption and desorption processes, may arise at various scales and flowpaths. To this date, experimental investigations of these complex processes at watershed scale remain a challenge and numerical studies are often needed for guidance of water resources management and decision making. This research integrates the knowledge bases developed during previous experimental and numerical investigations at a proposed waste disposal site at the Oak Ridge National Laboratory to study the concurrent effects of physical and chemical nonequilibrium. Hydraulic and mass transfer parameters of the individual processes obtained from previous laboratory studies are upscaled using a similar media concept. Measurements of hydraulic conductivity at various locations over the site are used to calculate scaling factors that are needed for the calculations of spatial conditional distributions of model parameters. Multiple realizations of model calculations are compared with field scale observation and the uncertainties attributable to each of the individual processes and parameters are quantified. The intensive computational resources required for such uncertainty quantification are discussed in light of contemporary development of parallel supercomputing.