Vadose zone hydrologic and biogeochemical processes play a significant role in the capture, storage and distribution of contaminants between the land surface and groundwater. One major issue facing geoscientists in dealing with investigations of the unsaturated zone flow and transport processes is the evaluation of heterogeneity of subsurface media. This chapter presents a summary of approaches for monitoring and modeling of vadose zone dynamics in the presence of heterogeneities and complex features, as well as incorporating transient conditions. Modeling results can then be used to provide early warning of soil and groundwater contamination before problems arise, provide scientific and regulatory credibility to environmental management decision-making process to enhance protection of human health and the environment. We recommend that future studies target the use of RTMs to identify and quantify critical interfaces that control large-scale biogeochemical reaction rates and ecosystem functioning. Improvements also need to be made in devising scaling approaches to reduce the disconnect between measured data and the scale at which processes occur.