Uncertainty assessment of flow and contaminant transport in the vadose zone entails probability density functions (PDFs) of soil hydraulic parameters. An unconventional maximum likelihood (ML) approach was used in this study to estimate the PDFs of water retention parameters (e.g., van Genuchten α and m) for a situation common in field-scale modeling where core samples are sparse and prior PDFs of the parameters are unknown. In this situation, the unconventional ML approach approximates the PDFs as multivariate Gaussian. This study developed a method of estimating the mean and covariance of the multivariate Gaussian PDF based on the results of least square methods that can be easily obtained in practice. The developed method was applied to and evaluated through numerical simulation of unsaturated flow and tracer transport at the proposed Yucca Mountain geologic repository. Another focus of this study was to investigate the effect of uncertainty in the water retention parameters on predictive uncertainty. By comparing the predictive uncertainty before and after incorporating random water retention parameters, it was found that the random water retention parameters had limited effects on the mean predictions of the state variables including percolation flux and tracer travel time from the potential repository to the water table. Incorporating the uncertainty in the water retention parameters, however, significantly increased the magnitude and spatial extent of predictive uncertainty of the state variables. In particular, incorporating the random water retention parameters significantly changed the 5th and 95th percentiles of the tracer travel time by tens of thousands of years.