The physical, chemical and microbiological properties of three freshwater systems contributing inflows to the Bayhead Canal of the Durban Harbour: the Umhlatuzana and Umbilo Rivers, and the Amanzimnyama Canal of KwaZulu-Natal, South Africa are presented. Parameters targeted for analysis collectively included pH, total dissolved solids, dissolved oxygen, biological oxygen demand, chemical oxygen demand, conductivity, ammonium ions, phosphorous, sodium ions, sulphur, copper, calcium, magnesium, chromium, aluminium, nickel, lead, vanadium, mercury, potassium ions, Escherichia coli and total coliforms. These parameters were analyzed seasonally during the wet and dry seasons in relation to land use change for spatial characterization. Comparisons with relevant South African Water Quality Guidelines for freshwater systems showed that pollution associated with catchment activities was the main factor governing water quality, with nutrient concentrations that frequently exceeded prescribed standards and often rendered the system hypertrophic. In addition, the sanitary state of the rivers across all land use types was shown to be contaminated and polluted. This study also attempted to determine spatiotemporal (dis)similarity in the water quality of sample sites through Principal Components Analysis (PCA) with varimax rotation. Results show that although these systems were separated on the basis of water quality (both spatially and temporally), there were generally no apparent trends in water quality based on specific land use patterns which linked sites across different catchments. In the wet season, a few exceptions were noted for residential sites across the Umbilo and Umhlatuzana catchments and industrial sites across the Amanzimnyama catchment which showed spatial similarity. Finally, the study examined the impacts of the three freshwater systems on the water quality of the Bayhead Canal of the Durban Harbour, and identified the Amanzimnyama Canal as the most influential on heavy metal and microbiological contamination near the confluence.