The occurrence and behavior of wastewater indicator compounds in the Santa Ana River (SAR) water and the underlying aquifer recharged by the SAR has been studied. The SAR contains a high proportion of tertiary treated wastewater effluents, up to 100% during summer and fall. The following water quality parameters were quantified: four specific wastewater indicator compounds, ethylene diaminetetraacetic acid (EDTA), nitrilotriacetic acid (NTA), a naphthalene dicarboxylate (NDC) isomer, alkylphenol polyethoxy carboxylates (APECs), and selected haloacetic acids (HAAs), nitrate, dissolved oxygen (DO), DOC, total carbohydrate, and phenolic substances. Statistical analysis indicated that normal distribution was adequate to describe the probability distribution of the constituents in most cases. In the river, the concentrations of wastewater indicator compounds decreased as the fraction of storm runoff increased. EDTA and NDC were detected in a monitoring well near the river and in two production wells 1.8 and 2.7 km down gradient with little apparent attenuation. By contrast, NTA, APECs, bromochloro- and dibromoacetic acids appeared to be attenuated significantly during infiltration of river water and groundwater transport.