Ecological effects of mining activity are a global concern; with most studies ascribing the effect on freshwater biota to metal toxicity from metal uptake through dietary or dissolved metal exposure. Although the potential for smothering effects from metal flocs has been suggested, studies have not separated metal toxicity effects and smothering effects from metal flocs on stream macroinvertebrates. We analysed traits of stream macroinvertebrates hypothesised to be sensitive to metal flocs (caused by its smothering effects) and metal toxicity (through metal uptake from dietary and dissolved metal exposure). We analysed data from sites receiving (test sites) and not receiving (reference sites) metal pollution from a disused mine to determine the primary mechanism for biotic impairment (e.g. smothering by metal flocs or metal toxicity). We found macroinvertebrates with traits associated with fine-sediment sensitivity (e.g. traits such as exposed gills) were less abundant at the test sites compared with the reference sites. The differences in the macroinvertebrate traits were consistent with smothering from metal flocs being the chief mechanism by which metals were affecting the macroinvertebrate community at the test sites and inconsistent with metal toxicity being the primary cause. Current water quality criteria only consider metal pollution in terms of toxicity to aquatic life. Yet our findings show that smothering effects from metal flocs can cause significant biological impairment.