Riverine physical and chemical characteristics are influencing ecosystem integrity while shaping and impacting species richness and diversity. Changes in these factors could potentially influence community structuring through competition, predation and localised species extinctions. In this study, eight sampling sites over multiple seasons were assessed along the streams draining the City of Nelspruit, South Africa, to examine river health based on water and sediment quality, while using macroinvertebrates as bioindicators for pollution. All water variables with the exception for salinity were found to be significantly different among seasons, with sites having significant differences among all water variables. All sediment chemistry variables were also found to be significantly different among sites and seasons, with the exception of K for sites and Zn and Ca for seasons. The PCA factor loadings and two-cluster analysis identified two groupings, i.e. group 1 that consisted of all metals apart from K and Na and group 2 with K and Na metals. A total of 4470 macroinvertebrate taxa were identified, with Crustacea Caridina nilotica and Diptera Chironominae being dominant across seasons, with macroinvertebrate communities being found to be significantly different among sites and seasons. The most common functional feeding groups across sites were the collector-gatherers (52.2%), followed by collector-filters (26.8%), predators (16.4%), scrapers (4.4%) and shredders (0.1%). Boosted regression trees indicated that high variation in species richness occurred with change in resistivity, P, water pH, ORP, conductivity and S concentrations. These results evidence a strong linkage among the sediment, water quality, substratum embeddedness and habitat structure and community structure. It is important to protect the integrity of aquatic ecosystems through effective monitoring due to the increasing water and sediment quality pressures that arise from various anthropogenic activities.