The Vhembe Biosphere Reserve, South Africa, contains many wetlands that serve as wildlife habitats and provide vital ecosystem services. Some of the wetlands are continuously being degraded or destroyed by anthropogenic activities causing them to disappear at an alarming rate. Benthic macroinvertebrates are known as good water quality bioindicators and are used to assess aquatic ecosystem health. The current study investigated habitat quality using macroinvertebrate community structure and other biotic variables (i.e. phytoplankton, macrophytes) in relation to environmental variables in the Sambandou wetlands using canonical correspondence analysis (CCA). A total of fifteen macroinvertebrate families were identified over two seasons. The CCA highlighted seven variables, i.e. pH, phosphate concentration, temperature, ammonium, macrophyte cover, conductivity and water depth, which were significant in structuring macroinvertebrate community. Picophytoplankton and microphytoplankton concentrations decreased from winter to summer, whereas nanophytoplankton concentration increased from winter to summer. Thus, the dominance of small-sized phytoplankton indicated nutrient limitation and decreased productivity, whereas winter sites 2 and 3 were dominated by large-celled phytoplankton, highlighting increased productivity. Winter sites were mostly negatively associated with CCA axis 1 and were characterised by high temperature, phosphate and ammonium concentrations, macrophyte cover, pH and conductivity. Summer sites were positively associated with axis 1, being characterised by high water depth and pH levels. The results obtained highlighted that agricultural activities such as cattle grazing and crop farming and sand mining/poaching had a negative effect on macroinvertebrate community structure.