Arsenic (As), Barium (Ba), Cadmium (Cd), Cobalt (Co), Chromium (Cr), Copper (Cu), Iron (Fe), Manganese (Mn), Lead (Pb) and Zinc (Zn) concentrations were investigated in sediments collected from sixteen sampling sites in the Lubumbashi river basin and five sites in Kafubu, Kimilolo and Kinkalabwamba rivers during February, March and April 2016. Analyses of the samples were carried out using a portable X-RFS (X-Ray Fluorescence Spectrometer). Water pH and OM (Organic Matter) content of the sediments were also determined. Trace metal toxicity risk to aquatic organisms was assessed using SQGs (Sediment Quality Guidelines)TELs (Threshold Effect Levels) and PELs (Probable Effect Levels)for freshwater sediments. Mean values of pH and OM ranged from 4.2 to 7.8 and from 1.27% to 6.22%, respectively. The highest mean levels of trace metals in sediments were 5,438 mgkg -1 dw and 902.5 mgkg -1 dw for Cu and Co, respectively in Lubumbashi river 1.45 kilometer downward the Lubumbashi Slag heap, 1,534.5 mgkg -1 dw and 342 mgkg -1 dw for Zn and Pb, respectively at the confluence of Lubumbashi and Kafubu rivers, 108,900 mgkg -1 dw, 547 mgkg -1 dw and 174.5 mgkg -1 dw for Fe, Ba and Cr, respectively in Kinkalabwamba river, 531 mgkg -1 dw and 22 mgkg -1 dw for Mn and Cd, respectively in Kimilolo river, and 37 mgkg -1 dw for As at the confluence of Tshondo and Lubumbashi rivers. The mean concentrations of As, Cd, Cr, Cu, Pb and Zn in the sediments exceeded the corresponding SQGs' PELvalues and could have adverse effects on aquatic organisms of those rivers. Trace metal contamination of the studied sediments might be partially attributed to natural processes, unplanned urbanization and poor waste management and mostly to abandoned and ongoing mining and ore processing activities in Lubumbashi city.