The main objective of this study was to collect new data on the occurrence, levels of priority and emerging organic compounds in freshwater fish sampled in the Rhone River. The 34 studied contaminants included alkylphenols, bisphenol A, polybromodiphenylethers (PBDE), perfluorinated compounds, hexabromocyclododecanes (HBCD), hexachlorobenzene and hexachlorobutadiene (HCBD). About 50 fish samples (individual specimens or pooled fish) were collected from three sites located upstream and downstream of the Lyon metropolitan area in the Rhone River (France). Four species were caught at each site, namely: the barbel (Barbus barbus), the common bream (Abramis brama), the white bream (Blicca bjoerkna) and the chub (Squalius cephalus). Some contaminants were quantified in all the 32 fish samples analysed: 4-nonylphenol, alpha-HBCD, the six PBDE congeners (28, 47, 99, 100, 153, 154), perfluorooctanesulfonate (PFOS) and perfluorodecanoic acid. Twenty three of the 32 samples had a concentration of PFOS above the Environmental Quality Standards (EQS) (up to six times higher than the EQS), and all the 32 samples had concentrations of PBDE above the EQS (up to 4,000 times higher, with the sum of six PBDE varying from 4.5 to 182 ng/g dry weight). Clearly, the interest to consider PFOS and HBCD as new priority substances is confirmed. In contrast, the pertinence of a priority status for HCBD, which was never quantified in our study, might have to be reconsidered in the future.