Levels of metals were determined in river sediment, rice and sugarcane juice from Lake Victoria basin where small-scale gold processing activities are carried out to assess levels of contamination. Concentrations of metals in river sediments were generally high in areas that were closest to gold ore processing sites. For instance, mercury was highest (36.3 ±12.8 mg/g dw) in river sediments of Tigiti River in Mugumu District. Other heavy metals (Cd, Pb, Zn and Cu) had highest concentrations (2.20±0.71, 208±19.3, 412±20.1 and 132.7±11.9mg/g dw, respectively) in sediment samples from Kagota. The concentration of arsenic was highest (985.0±67.2 mg/g dw) in Mugusu River sediment. Mercury concentration in rice was highest (378.5±15.1mg/kg dw) in samples from Lwamgasa wetland and lowest (47.9±2.9 mg/kg dw) in samples from Saragurwa wetland. Cadmium concentrations in rice ranged from 2.3-5.5mg/kg dw, Zn and Cu ranged from 16340-27280mg/kg dw and 1150-2240mg/kg respectively. Arsenic was not detected in any rice sample. Lead was only detected in rice from Sengerema (150±12mg/kg dw), in a wetland that is close to the main road. Mercury concentrations in sugarcane juice were below the limit of detection (0.01mg/l) in all samples even those that were harvested closest to the gold ore-washing site at Samina. It is concluded that small-scale gold mining activities contaminate watercourses close to ore washing sites.