The ability to safely store radioactive materials for long periods of time depends on our understanding of the conditions that mobilize the nuclei, which requires an understanding of the mechanisms of dissolution and transport in aquifers. The objective of this research was to gain an understanding of the dissolution and transport of naturally occurring uranium, thorium, and their radioactive daughter products in groundwater systems without using injected tracers or accidental contaminants. The study involved analyses of groundwater in and around the Brookhaven National Laboratory site and the water supply system. A theoretical model of continuous flow was developed considering chemical, physical, and geologic properties. This is the first model of water transport in the vadose zone and the groundwater table with water-rock interactions supplying insight into the problems of mobilization and precipitation. We derived clear theoretical predictions on U and Th behavior in groundwater. The combination of sound theory and good data was successful. Most of the variation in uranium isotopes was due to the original imprint of near-surface weathering and not to water-rock reactions at depth. It was shown that high radon content was not due to micropores in the minerals but a reflection of thorium precipitation on surfaces during early stages of weathering. A comparison of adjacent but separate aquifers shows that changes in the oxygen content of the water, due most likely to bacterial reactions, can cause the rapid release of large amounts of Th into solution while in oxidized conditions the retention times are 3,000 years. Thus, subtle changes not easily controlled may alter the long-term stability of such storage systems.