The aim of the study was to validate biological tools based on the analysis of sediment-dwelling oligochaete assemblages for assessing the biological quality of sediments in watercourses. The study intended to establish and compare heavy metal toxicity thresholds in streams of two different ecoregions (Geneva area in Switzerland and Artois-Picardie basin in France). The metals Cr, Ni, Cu, Zn, Hg, Pb, Cd, As, Co, Fe and Mn were analyzed. The PEC-Q (Probable Effect Concentration-Quotient) and TEC-Q (Threshold Effect Concentration-Quotient)were used as metal contamination indices. The results showed a significant negative correlation between the oligochaete index of sediment bioindication IOBS and metal contamination indices. Moreover a significant positive correlation between the percentage of Tubificinae without hair setae and metal contamination indices was noticed. Toxicity thresholds of PEC-Q = 0.14–0.18 and TEC-Q = 0.4–0.6 were established. The toxicity thresholds established in the two different ecoregions were consistent. At some sites, the sediment biological quality evidenced by the oligochaete analysis was poor, yet moderate PEC-Q were observed. The effects of confounding factors such as the bioavailability of metals and the presence of other pollutants (PCBs, PAHs and organic pollution) are discussed. Other conflicting results seemed to be explained by a reduced bioavailability of metals due to organic matter and Mn/Fe oxides.