Highlights • Ecological risk assessment of metal-contaminated boreal lakes and sediments. • Sediment Quality Triad complemented with bioavailability and body residue studies. • Toxicity studies for natural sediments with several organisms and endpoints • Adverse effects observed. High variation on results between different methods. • Standard toxicity tests not suitable for testing, too low pH hampers the results. There are several methods for studying metal-contaminated freshwater sediments, but more information is needed on which methods to include in ecological risk assessment. In this study, we compliment the traditional Sediment Quality Triad (SQT) approach – including information on chemistry, toxicity and ecological status – with studies on metal bioavailability and metal body residues in local organisms. We studied four mining-affected boreal lakes in Finland by conducting chemical analyses of sediment and water, toxicity tests (L. variegatus, V. fischeri, C. riparius, L. stagnalis), and analysis of benthic organism community structure. In addition, we studied the relationships between metal loading, toxicity, metal bioavailability, and metal body residues in the field-collected biota. Chemistry and benthic organism community structures show adverse effects in those lakes, where the metal concentrations are the highest. However, toxicity was connected to low sediment pH during the experiment, rather than to high metal concentrations. Toxicity was observed in 4 out of 6 toxicity tests including growth test with L. variegatus, bulk sediment test with V. fischeri, and the L. stagnalis toxicity test. The C. riparius test did not show toxicity. Metal body residues in biota were not high enough to induce adverse effects (0.1–4.1 mg Cu/kg fw, 0.01–0.3 mg Ni/kg fw, 2.9–26.7 mg Zn/kg fw and 0.01–0.7 mg As/kg fw). Chemical analyses, metal bioavailability assessment and benthic community structures survey revealed adverse effects in the sediments, where metal concentrations are highest (Lake SJ and Lake KS). Standard toxicity tests were not suitable for studying acid, sulfide-rich sediments and, therefore, benthic structure study and chemical analyses are believed to give more reliable results of the ecological status of these sediments.