Dissolution and leaching of soil salts by irrigation water is a primary source of Se to shallow groundwater in the western San Joaquin Valley, California. In this study, the mobility and distribution of selenite and selenate in soils with different irrigation and drainage histories was evaluated using sorption experiments and an advection-dispersion model. The sorption studies showed that selenate (15–12400 µg Se L−1) is not adsorbed to soil, whereas selenite (10–5000 µg Se L−1) is rapidly adsorbed. The time lag between adsorption and desorption of selenite is considerable, indicating a dependence of reaction rate on reaction direction (hysteresis). Selenite adsorption and desorption isotherms were different, and both were described with the Freundlich equation. Model results and chemical analyses of extracts from the soil samples showed that selenite is resistant to leaching and therefore can represent a potential long-term source of Se to groundwater. In contrast, selenate behaves as a conservative constituent under alkaline and oxidized conditions and is easily leached from soil.