European Biota Quality Standards (EQSbiota), for compounds with low water solubility and high biomagnification, were created to sustain water quality and protect top predators and humans from secondary poisoning. In reality, for multiple compounds, an exceedance of these standards is often reported in literature without a decrease in ecological water quality determined by biotic indices. In the present study, threshold concentrations were defined in biota (from 44 sampling locations throughout Flanders (Belgium)), above which a good ecological water quality, assessed by the Multimetric Macroinvertebrate Index Flanders (MMIF), was never reached. Threshold values were compared to current EQSbiota. Accumulated perfluoroctane sulfonate (PFOS), mercury (Hg), hexabromocyclododecane (HBCD), polybrominated diphenyl ethers (PBDEs), dioxins and polychlorinated biphenyls (PCBs) concentrations were measured in muscle tissue of European yellow eel (Anguilla anguilla) and perch (Perca fluviatilis). Fluoranthene and benzo(a)pyrene were also analyzed in translocated mussels (Dreissena bugensis, D. polymorpha and Corbicula fluminea). Threshold values could only be calculated using a 90th quantile regression model for PFOS (in perch; 12 µg/kg ww), PCBs (in eel; 328 µg/kg ww) and benzo(a)pyrene (in mussels: 4.35 µg/kg ww). The lack of a significant regression model for the other compounds indicated an effective threshold value higher than the concentrations measured in the present study. Alternatively, the 95th percentile of concentrations measured in locations with a good ecological quality (MMIF≥0.7), was calculated for all compounds as an additional threshold value. Finally, fish concentrations were standardized for 5% lipid content (or 26% dry weight content for PFOS and Hg). Threshold values for PFOS and benzo(a)pyrene and the 95th percentiles for dioxins and fluoranthene were comparable to the existing standards. For all other compounds, the 95th percentile was higher than the current EQSbiota, while for HBCD, it was lower. ...