Contamination levels of aquatic ecosystems and ecological effects must be assessed, as stated by the WFD. However, linking both issues remains difficult, yet necessary to implement restoration. Recently an active biomonitoring approach has been developed using caged Gammarus fossarum to assess trends of bioavailable contamination levels in freshwater systems. This new tool overcomes most drawbacks associated to other currently used methods, allowing an accurate comparison of contamination levels between stations, seasons or years. Our study aimed at calibrating this active biomonitoring tool in order to interpret bioavailable contamination levels in term of risk for ecological disturbance. For this, a national scale investigation has been performed to obtain the bioavailable contamination levels and ecological indices (diversity and abundance) for 117 sites representative of French watercourses. Concentrations of 11 metals quantified in G. fossarum have been analysed against ecological indicators. No link was revealed between bioavailable contamination levels and global ecological indicators used for WFD implementation; in contrast, clear relationships were established with sensitive macroinvertebrate abundances. This allowed determining thresholds for five elements above which populations are endangered. These ecological impairment thresholds are discussed accordingly to the bioavailable background accumulated contamination values previously determined in G. fossarum at the French national scale.