BackgroundBioaccumulating contaminants in surface waters are preferably monitored in fish for assessing the related risks to and via the aquatic environment. Consequently, the European Water Framework Directive (WFD) requires a monitoring of certain priority substances such as mercury, polybrominated diphenyl ethers (PBDE), perfluorooctane sulfonic acid and its derivatives (PFOS), hexachlorobenzene (HCB), hexabromocyclododecanes (HBCDD) and polychlorinated dioxins/dioxin-like compounds (dioxins) in freshwater and coastal fish. Tissue levels have to comply with biota environmental quality standards (EQSs) given in Directive 2013/39/EU. EQSs are justified either by risks for human health (assessed on the basis of fillet) or secondary poisoning of wildlife (based on whole fish). To support the practical implementation of the WFD biota monitoring in Germany, comparative investigations of target fish species caught at six sites were performed.ResultsAt each site, at least three fish species listed in a national guidance document were sampled (e.g., chub, roach, bream, perch). Beside biometric data, concentrations of seven priority substances were determined in pooled fillet and carcass samples and whole fish data were calculated. The EQSs for PBDE and mercury were exceeded in nearly all fillet and whole fish samples. PFOS was above the EQS at several sites especially in perch, while HCB exceeded the EQS only at one site (Elbe River). All fillet and whole fish samples complied with the EQSs for dioxins and HBCDD. Based on wet weight concentrations of a homogeneous set of 20 composite sample pairs of 3–5 year-old fish, the following fillet-to-whole fish conversion factors were derived: mercury 0.81, PBDE 5.4, HCB 3.6, PFOS 2.7, dioxins 5.3, and HBCDD 1.8.ConclusionsRecommendations on selection of target fish species, age or tissue given by EU and national guidance documents are practical and feasible. However, further adjustments of the samplings such as the determination of site-specific length–age relationships are required from both ecological and risk assessment perspectives. The derived conversion factors allow the translation of fillet-to-whole fish concentrations (and vice versa), and thus the EQS compliance assessment for the appropriate tissue (fillet for human health, whole fish for wildlife risks) if only one tissue is investigated.