Fish can bioconcentrate complex mixtures of xenobiotics arising from exposure to wastewater effluents discharged into surface waters. Wastewaters contain a complex mixture of organic compounds and little is known about their uptake into fish and their health effects. In this study, a chemical profiling approach was used to characterize the profile of xenobiotics and their metabolites (the xenometabolome) in biofluids (bile and plasma) of juvenile rainbow trout (Oncorhynchus mykiss) exposed to a wastewater effluent. Metabolite profiles of effluent-exposed fish were compared with that from control fish exposed to uncontaminated river water. Samples were analysed by ultra performance liquid chromatography-time-of-flight mass spectrometry and data analysed by multivariate statistics. Exposure to effluent resulted in accumulation in trout bile of alkylsulfophenyl and alkylpolyethoxy carboxylates, as well as glucuronide conjugates of nonylphenol ethoxylates, alcohol ethoxylates, naphthols, chlorinated xylenols and phenoxyphenols, chlorophenes, resin acids, mefenamic acid and oxybenzone. Nonconjugated or sulphate conjugates of many of these contaminants were also detected in plasma of effluent-exposed trout. In addition, changes in the concentrations of endogenously derived metabolites were also detected in trout plasma, and these included an increase in blood bile acids, methylbutryolcarnitine and a decrease in sphingosine levels. These observations were verified in a further exposure of sexually mature roach (Rutilus rutilus) to concentrations of the same effluent. Exposure to 50% or 100% effluent resulted in dose dependent increases in blood concentrations of xenobiotics, taurocholic acid, syprinol sulphate and lysophospholipids and decreases in sphingosine levels. This work reveals the complex nature of xenobiotics accumulating in effluent-exposed fish together with the identification of changes in concentrations of lipid metabolites associated with hepatotoxicity. These results reveal, for the first time, that metabolite profiling techniques can be used to screen for uptake of complex mixtures of contaminants into fish and also for the detection of natural metabolite pathways in the organism that are disrupted due to exposure to multiple xenobiotics.