Aquatic ecosystems and waterbodies are under persistent stress of chemical pollutants, mainly of anthropogenic origin. High concentrations can harm entire ecosystems and be potentially toxic to humans. The European Water Framework Directive (WFD) obliges member states to monitor chemical compounds in surface waters and to set quality standards that protect against detrimental effects of toxic compounds. Generally, most of the target chemical compounds are able to be measured in water or sediment samples. However, the low water solubility of highly hydrophobic compounds precludes direct measurement in water. Accordingly, the WFD has formulated biota quality standards (BQS), for 11 priority compounds and their derivatives, which refer to concentrations of compounds that have to be monitored in fish and bivalves (biota). In the present study, bioaccumulation of hexachlorobenzene (HCBz), hexachlorobutadiene (HCBd), mercury (Hg), polybrominated diphenyl ethers (PBDE), hexabromo-cyclododecane (HBCD), perfluoro-octaansulphonate (PFOS) and its derivatives, dicofol, heptachlor and heptachlor epoxide, and dioxins and dioxin-like compounds were measured in muscle tissue of perch (Perca fluviatilis) and European eel (Anguilla anguilla) originating from different Flemish water bodies. Fluoranthene and benzo(a)pyrene were measured in zebra mussel (Dreissena polymorpha) and quagga mussel (Dreissena bugensis), using active biomonitoring. In every sampling point at least one of both selected fish species could be collected. For fluoranthene an exceedance of the standard was observed in some sampling locations in zebra mussel, for benzo(a)pyrene there were some exceedances for both zebra and quagga mussel. Dioxin concentrations exceeded the standard in 4 sampling locations in eel muscle tissue. For PFOS, an exceedance of the standard was detected at almost every location for both fish species. The biota quality standard for Hg and PBDE was exceeded in every sampling location and for both fish species. One sample had PBDE concentrations below the quantification limit, which is more than 10 times higher than the BQS. Concentrations of HCBd and dicofol were below the quantification limit. Furthermore no exceedances of the standard were found for HCBz and HBCD. For heptachlor all measurements where below the quantification limits (40 times higher than the standard), cis-heptachlor epoxide exceeded the quantification limit in all except one location in eel muscle tissue and in 3 locations in perch muscle tissue. An overall trend of higher concentrations per wet weight in eel than in perch was detected. Nonetheless, after correction for lipid content, this trend was no longer present or even reversed with higher concentrations in perch muscle tissue, indicating the lipophilic properties of these compounds. This was true for all compounds – except for PFOS: in fact, this compound showed the exact opposite trend. Concentrations of PAHs were always higher in zebra mussel than in quagga mussel. This is possibly caused by the higher trophic position of the first. For both fish species, however, we could not find clear differences in trophic level. Finally, calculated concentrations using the passive samplers, compared to existing literature, show promising applicability and incites further development of this tool. Based on the results of the present study and – where possible – a comparison to data present in literature, it is evident that the existing biota quality standards for Hg, PBDE and PFOS are exceeded in all fish species from Flemish and European water bodies.