The effects of heavy metal pollution on benthic macroinvertebrate communities in tropical streams draining ultramafic systems have not been explored, despite a pressing need for ecological risk assessment to protect and manage aquatic ecosystems in these areas. The objective of this study was to examine benthic macroinvertebrate community composition in relation to metal concentrations in stream sediments and other physico-chemical variables in the Manyame River system, which drains part of the Great Dyke of Zimbabwe. Benthic macroinvertebrate sampling and community composition analysis, sediment collection, processing and metal analysis and assessment of other variables in the water column were done once at 55 sampling sites: 12 urban, 30 communal (i.e. sparsely populated rural areas, with livelihoods centred around subsistence agriculture) and 11 Great Dyke sites. Canonical correspondence analysis and partial canonical correspondence analysis (pCCA) were used to determine the importance of sediment heavy metal concentrations in explaining benthic macroinvertebrate community composition in comparison with other factors. Water quality ranged from very poor for urban locations due to sewage pollution, to good in communal locations. Significantly high concentrations of metals (ANOVA, p<0.05) and high magnesium/calcium (Mg/Ca) ratio were recorded in sediments for the Great Dyke site locations. The Mg/Ca ratio, Ca2+, Cr3+ and K+ were found to be important metals structuring benthic macroinvertebrate communities in the study streams, with metals explaining a larger percentage (58.0%) of the total variation explained compared to other variables (35.9%). However, taxa richness, diversity, evenness, percentage of Ephemeroptera, Plecoptera Trichoptera related metrics were higher at some Great Dyke sites than at communal sites. Thus, measures of taxa richness, diversity and %EPT may provide misleading information when assessing heavy metals in moderately polluted environments as in this study. Assessment of tropical streams draining ultramafic systems that are heavy metal-contaminated should also include benthic invertebrate community structure analysis, as it is possible that common endpoints, such as %EPT, may not identify impacts to aquatic communities.