A study was undertaken to evaluate the processes affecting the chemistry of shallow groundwater associated with agricultural drainage systems in the western San Joaquin Valley, California. The study was prompted by a need for an understanding of selenium mobility in areas having high selenium concentrations in shallow groundwater. Groundwater samples were collected along transects in three artificially drained fields where the age of the drainage system varied (15, 6, and 1.5 years). Selenium concentrations in the drain water also varied (430, 58, and 3700 μg/L, respectively). Isotopic enrichment and chemical composition of the groundwater samples indicate that saline- and selenium-enriched water has evolved as a result of evaporation or transpiration of groundwater. This evaporated, isotopically enriched water is being displaced by more recent, less saline irrigation water percolating through the root zone. This displacement seems to be a process whereby sodium chloride and sodium sulfate water is being replaced by more dilute calcium sulfate and calcium bicarbonate water.