Seven fish species were collected from 14 sites on rivers in the Colorado River Basin (CDRB) from August to October 2003. Spatial trends in the concentrations of accumulative contaminants were documented and contaminant effects on the fish were assessed. Sites were located on the mainstem of the Colorado River and on the Yampa, Green, Gunnison, San Juan, and Gila Rivers. Common carp (Cyprinus carpio), black bass (Micropterus sp.), and channel catfish (Ictalurus punctatus) were the targeted species. Fish were field-examined for external and internal anomalies, selected organs were weighed to compute somatic indices, and tissue and fluid samples were preserved for fish health and reproductive biomarker analyses. Composite samples of whole fish, grouped by species and gender, from each site were analyzed for organochlorine and elemental contaminants using performance-based and instrumental methods. 2,3,7,8-tetrachlorodibenzo-p-dioxin-like activity (TCDD-EQ) was measured using the H4IIE rat hepatoma cell bioassay. Selenium (Se) and mercury (Hg) concentrations were elevated throughout the CDRB, and pesticides concentrations were greatest in fish from agricultural areas in the Lower Colorado River and Gila River. Selenium concentrations exceeded toxicity thresholds for fish (>1.0 ?g/g ww) at all sites except from the Gila River at Hayden, Arizona. Mercury concentrations were elevated (>0.1 ?g/g ww) in fish from the Yampa River at Lay, Colorado; the Green River at Ouray National Wildlife Refuge (NWR), Utah and San Rafael, Utah; the San Juan River at Hogback Diversion, New Mexico; and the Colorado River at Gold Bar Canyon, Utah, Needles, California, and Imperial Dam, Arizona. Concentrations of p,p'-DDE were relatively high in fish from Arlington, Arizona (>1.0 ?g/g ww) and Phoenix, Arizona (>0.5 ?g/g ww). Concentrations of other banned pesticides including toxaphene, total chlordanes, and dieldrin were also greatest at these two sites but did not exceed toxicity thresholds. Current-use or unlisted pesticides such as dacthal, endosulfan, '-HCH, and methoxychlor were also greatest in fish from Gila River. Total polychlorinated biphenyls (PCBs; >0.11 ?g/g ww) and TCDD-EQs (>5 pg/g ww) exceeded wildlife guidelines in fish from the Gila River at Phoenix, Arizona. Hepatic ethoxyresorufin O-deethylase (EROD) activity was also relatively high in carp from the Gila River at Phoenix, Arizona and in bass from the Green River at Ouray NWR, Utah. Altered biomarkers were noted in fish throughout the CDRB. Fish from some stations responded to chronic contaminant exposure as indicated by fish health and reproductive biomarker results. Multiple fish health indicators including altered body and organ weights and high health assessment index scores may be associated with elevated Se concentrations in fish from the Colorado River at Loma, Colorado and Needles, California. Although grossly visible external or internal lesions were found on most fish from some sites, histopathological analysis determined many of these to be inflammatory responses associated with parasites. Edema, exophthalmos, and cataracts were noted in fish from sites with elevated Se concentrations. Reproductive biomarkers including gonad development and maturation, vitellogenin concentrations, and steroid hormone concentrations were anomalous in fish from the Gila River at Hayden and Phoenix, Arizona. In addition, intersex fish were found at seven of 14 sites. The intersex condition was identified in smallmouth bass (M. dolomieu), largemouth bass (M. salmoides), channel catfish, and carp and may indicate exposure to endocrine disrupting compounds. Seven of ten male smallmouth bass from the Yampa River at Lay, Colorado were intersex. Male carp, bass, and channel catfish with low concentrations of vitellogenin were common in the CDRB. Comparatively high vitellogenin concentrations (>0.2 mg/mL) were measured in male fish from the Green River at Ouray NWR, Utah and the Colorado River at Im