The present study investigates the physical, chemical, and biological characteristics of spring water samples in Shoubak area in the southern Jordan. The samples were collected from May 2004 to May 2005. All samples were analyzed for temperature, conductivity, dissolved oxygen, pH, major cations (Ca2+, Mg2+, K+, Na+), major anions (Cl−, NO 3 − , HCO 3 − , SO 4 2− , PO 4 3− , F−), and trace metals (Fe2+, Al3+, Mn2+, Cu2+, Cr3+, Ni2+, Zn2+, Pb2+, Cd2+). Water quality for available springs showed high salinity through long period of contact with rocks. The ion concentrations in the water samples were from dissolution of carbonate rocks and ion exchange processes in clay. The general chemistry of water samples was typically of alkaline earth waters with prevailing bicarbonate chloride. Some springs showed elevated nitrate and sulfate contents which could reflect to percolation from septic tanks, cesspools, and agricultural practices. The infiltration of wastewater from cesspools and septic tanks into groundwater is considered the major source of water pollution. The results showed that there were great variations among the analyzed samples with respect to their physical, chemical and biological parameters, which lie below the maximum permissible levels of the Jordanian and WHO drinking water standards. The results indicate that the trace metals of spring’s water of Shoubak area do not generally pose any health or environmental problems. Factor analysis was used to identify the contributers to water quality. The first factor represents major contribution from anthropogenic activities, while the second one represents major contribution from natural processes.