River Rwizi originates from the Buhweju hills. It is a major source of water for the inhabitants of Mbarara Municipality and surrounding environment. In this study, spatial variation of water quality in River Rwizi section within Mbarara Municipality was determined using cluster analysis. Laboratory analysis was conducted on water samples from five sites along the river section using standard methods for: pH, EC, TSS, TDS, turbidity, temperature, total hardness, alkalinity, salinity, colour, NH 3-N, 2 4 SO − , BOD, COD, DO, Ca, Mg, Fe, and Mn. Cluster analysis grouped the study sites into slight pollution (Spencon, GBK), moderate pollution (Katete) and high pollution (BSU, Kakoba) for dry season. For rain season, order was: slight pollution (BSU, Spencon), moderate pollution (GBK) and high pollution (Kakoba, Katete), basing on similarity of water quality variables. These results show that water pollution resulted primarily from domestic waste water, agricultural runoff and industrial effluents. Thus, water from River Rwizi is not suitable for drinking in both dry and wet seasons.