The study assessed the impact of water and sediment quality on benthic macroinvertebrate assemblages in the Dwars River, a tributary of the Olifants River, Limpopo province, South Africa. Physico-chemical variables, heavy metals and macroinvertebrates were collected using standard methods. A multivariate analysis, Canonical Correspondence Analysis (CCA), was used to examine the macroinvertebrate community structure. Based on the selected physico-chemical variables and metal concentrations assessed, the water quality and sediment quality are deteriorating mainly in the downstream areas. The number of taxa and the Average Score per Taxon (ASPT) were significantly different between sites and seasons, with more taxa recorded in the upstream section of the river and in winter. A higher proportion of sensitive and high-scoring taxa (Ephemeroptera, Plecoptera and Trichoptera) were recorded in upstream and midstream sites and in winter. The CCA analysis showed an association of heavy metal concentration in the sediment with the distribution of macroinvertebrate taxa tolerant to poor water quality in the downstream section of the river. Because of the potential impacts of rapid economic development in the catchment, regular monitoring of the river is recommended, to detect potential river health problems early.