The ecotoxicity of elutriated sediments of Aruri river affluent of Rimac river and Upamayo bridge, Lake Junin (Peru), monthly was evaluated from April to October 2000 using two bioassays: the inhibition of the enzymatic activity of the β-galactosidase of Escherichia coli and the survival of first larvae (L 1) of Chironomus calligraphus were determined. The sediment were fractioned in five extracts (F 1(aqueous), F 2(methanol), F 3(EDTA), F 4(methanol + EDTA) and F 5(NaNO3)) to evaluate the effects of different chemical groups. Only for the river Aruri the CI 50 of F 1 for E. coli was higher than CL 50 of C. calligraphus. Among the rest of fractions, F 5 employed for detecting heavy metals resulted producing greater inhibitions on E. coli and mortalities on C. calligraphus in both localities, in comparison with the slender effect from F 3 in both species that block up the effect of heavy metals. The F 3 for Junin Lake for C. calligraphus produced higher effects than E. coli. The sediments of Junin Lake showed significant high level in silt-clay, organic matter in percent, Fe, Pb, Cu, Zn and Cd in comparison to Aruri River during all the monitoring.