An evaluation of approximately 250 samples of groundwater in the Amman Zarqa Basin for selenium along with other major and trace elements showed that concentrations of Se ranged between 0.09 and 742 microg/L, with an average value of about 24 microg/L. Selenium concentrations exceeded the recommended threshold for drinking water of the World Health Organization (WHO; 10 micro/L of Se) in 114 samples, with greater than 50 microg/L (quantity equivalent to the Jordanian standard of the allowed concentration of the element in water) of Se in nine cases. The average concentrations of Se in the lower, middle, and upper aquifers of the basin were 3.41, 32.99, and 9.19 microg/L, respectively. Based on the correlation with geologic formations and the statistical analysis of major/minor constituents and Piper tri-linear diagrams, we suggest that carbonate/phosphate dissolution, oxidation-reduction processes, and fertilizers/irrigation return flow are, together, the primary factors affecting the chemistry of the groundwater. Factor analysis helped to define the relative role of limestone-dolomitic dissolution in the aquifers (calcium, magnesium, and bicarbonate), agricultural activities (sulfate, nitrates, phosphorus, and potassium), oxidation-reduction factor (Eh, Fe, Mn, Cu, Zn, and Se), and anthropogenic (industrial) factor (EC, Fe, Cr, Co, Zn, and As). The high variability in Se concentrations might be related to the possibility of a multi-source origin of Se in the area.