Abstract:The deterioration of water quality in our freshwater sources is on the increase worldwide and, in South Africa, mostly due to the discharge of municipal sewage effluent. Here we report on the use of principal component analysis, coupled with factor and cluster analysis, to study the similarities and differences between upstream and downstream sampling sites that are downstream of municipal sewage plants. The contribution of climatic variables, air temperature, humidity, and rainfall were also evaluated with respect to variations in water quality at the sampling sites. The physicochemical and microbial values were higher than the Department of Water Affairs and Forestry (DWAF) and World Health Organization (WHO) guidelines. The cluster analysis showed the presence of two clusters for each of the Mvudi, Dzindi, and Luvuvhu Rivers and Nandoni reservoir sampling sites. The principal component analysis (PCA) accounted for 40% of the water quality variation and was associated strongly with pH, electrical conductivity, calcium, magnesium, chloride, bromide, nitrate, and total coliform, and negatively with rainfall, which represented Mvudi downstream and was attributed to the Thohoyandou sewage plant. The PCA accounted for 54% of the variation and was associated strongly with electrical conductivity, sulfate; total dissolved solids, fluoride, turbidity, nitrate, manganese, alkalinity, magnesium, and total coliform represented Dzindi downstream, with inflows from the Vuwani sewage plant and agriculture. The PCA accounted for 30% of the variation and was associated strongly with total dissolved solids, electrical conductivity, magnesium, fluoride, nitrate, sulfate, total coliform average air temperature, and total rainfall, and negatively associated with manganese and bromide represented Luvuvhu upstream and was associated with commercial agriculture. The PCA accounted for 21% of the variation and was associated strongly with turbidity, alkalinity, magnesium, chloride, fluoride, nitrate, and strongly negatively associated with rainfall, which represented Luvuvhu downstream, associated with inflows from Vuwani oxidation ponds, Elim and Waterval sewage plants, and agriculture. The PCA accounted for 14% of the variation and was moderately associated with rainfall and weakly associated with chloride and bromide and negatively associated with nitrate, which represented the natural Nandoni reservoir system. The continued discharge of effluent may render the raw water supply unsuitable for human consumption and lead to eutrophication due to nitrate enrichment and proliferation of harmful algal blooms and schistomiasis infections in the long term.