The chemical and isotope (11B/10B, 87Sr/86Sr, 18O/16O, 2H/H, 13C/12C, 14C, and 3He/3H) compositions of groundwater from the upper aquifer system of the Salinas Valley in coastal central California were investigated in order to delineate the origin and processes of groundwater contamination in this complex system. The Salinas Valley has a relatively deep, confined ‘‘400- foot’’ aquifer, overlain by a ‘‘180-foot’’ aquifer and a shallower perched aquifer, all made up of alluvial sand, gravel and clay deposits. Groundwater from the aquifers have different 14C ages: fossil (14C = 21.3 percent modern carbon (pmc) for the 400-foot aquifer and modern (14C = 72.2–98.2 pmc) for the 180-foot aquifer. Fresh groundwater in all aquifers is recharged naturally and artificially through the Salinas River. The two modes of recharge can be distinguished chemically.We identified several different saline components with distinguishable chemical and isotopic fingerprints. Saltwater intrusion in the northern basin has C1 concentrations up to 1700 mg/L, a Na/Cl ratio less than seawater, a marine Br/Cl ratio, a Ca/Cl ratio greater than seawater, d11B between +17 and +38% and 87Sr/86Sr between 0.7088 and 0.7096. Excess dissolved Ca, relative to the expected concentration for simple dilution of seawater, correlates with 87Sr/86Sr ratios, suggesting base exchange reaction with clay materials. (2) Agriculture return flow is high inNO3 and SO4, with a 87Sr/86Sr = 0.7082,d11B = 19% and d13C between 23 and 17%. The 3H–3He ages (5–17 years) and 14C data suggest vertical infiltration rates of irrigation water of 3–10 m/yr. (3) Nonmarine saline water in the southern part of the valley has high total dissolved solids up to 3800 mg/L, high SO4, Na/Cl ratio >1, d11B between +24 and +30%, and 87Sr/86Sr = 0.70852. This groundwater may have acquired its geochemical signature from leaching of sedimentary rocks associated with the Coast Range marine deposits of Mesozoic to early Cenozoic age. The combination of different geochemical and isotopic fingerprints enables us to delineate the impact of salt sources in different areas of the valley and to reconstruct the origin of the SO4-enriched NO3-depleted saline plume that is located west of the city of Salinas. We suggest that the latter is derived from a mixture of different natural saline waters rather than from anthropogenic contamination.