As an integral part of our continued development of water quality assessment approaches, we combined integrative sampling, instrumental analysis of widely occurring anthropogenic contaminants, and the application of a suite of bioindicator tests as a specific part of a broader survey of ecological conditions, species diversity, and habitat quality in the Santa Cruz River in Arizona, USA. Lipid-containing semipermeable membrane devices (SPMDs) were employed to sequester waterborne hydrophobic chemicals. Instrumental analysis and a suite of bioindicator tests were used to determine the presence and potential toxicological relevance of mixtures of bioavailable chemicals in two major water sources of the Santa Cruz River. The SPMDs were deployed at two sites; the effluent weir of the International Wastewater Treatment Plant (IWWTP) and the Nogales Wash. Both of these systems empty into the Santa Cruz River and the IWWTP effluent is a potential source of water for a constructed wetland complex. Analysis of the SPMD sample extracts revealed the presence of organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs). The bioindicator tests demonstrated increased liver enzyme activity, perturbation of neurotransmitter systems and potential endocrine disrupting effects (vitellogenin induction) in fish exposed to the extracts. With increasing global demands on limited water resources, the approach described herein provides an assessment paradigm applicable to determining the quality of water in a broad range of aquatic systems.