Selenium (Se) is an essential micro-nutrient for humans, but can be toxic at high levels of intake. Se deficiency and Se toxicity are linked with serious diseases, with some regions worldwide experiencing Se deficiency due to Se-poor rocks and soils and other areas dealing with Se toxicity due to the presence of Se-enriched geologic materials. In addition, Se is consumed primarily through plants that take up Se from soil and through animal products that consume these plants. Hence, the soil and groundwater system play important roles in determining the effect of Se on human health. This paper reviews current understanding of Se fate and transport in soil and groundwater systems and its relation to human health, with a focus on alluvial systems, soil systems, and the interface between alluvial systems and Cretaceous shale that release Se via oxidation processes. The review focuses first on the relation between Se and human health, followed by a summary of Se distribution in soil-aquifer systems, with an emphasis on the quantitative relationship between Se content in soil and Se concentration in underlying groundwater. The physical, chemical, and microbial processes that govern Se fate and transport in subsurface systems then are presented, followed by numerical modeling techniques used to simulate these processes in study regions and available remediation strategies for either Se-deficient or Se-toxic regions. This paper can serve as a guide to any field, laboratory or modeling study aimed at assessing Se fate and transport in groundwater systems and its relation to human health.