This study investigated the levels of Pb, Hg, Cr, Cd, and As in water and sediments from the tributaries of the Mara River, Tanzania. Pollution risk of water and sediments was investigated using seven indices and five metals. During the dry period, the highest concentration of Pb, Hg, Cr, Cd, and As in sediments was 17.45 ± 1.22, 0.01, 1.56 ± 0.5, 1.3 ± 0.09, and 30.81 ± 0.02 mg/kg, respectively. During the wet period, the highest concentration of Pb, Hg, Cr, Cd, and As in sediments was 4.37 ± 0.28, 0.012, 2.58 ± 0.57, 2.25 ± 0.35, and 53 ± 0.02 mg/kg, respectively. For surface water, the respective highest concentrations of Pb, Hg, Cr, Cd, and As were 0.76 ± 0.09, 0.04, 0.68 ± 0.09, 0.74 ± 0.1, and 0.47 ± 0.06 mg/L for the dry period. The wet period max concentrations for Pb, Hg, Cr, Cd, and As in surface water were 0.56, 0.03, 0.55 ± 0.03, 0.48 ± 0.03, and 0.4 ± 0.03 mg/L, respectively. Principal component analysis results indicated dominant loadings for Pb and As in sediments during the dry period. Comparison of sediment concentrations with sediment quality guidelines revealed that As and Cd were enriched. Correlation coefficient results indicated that As had a strong negative correlation with the rest of the elements in sediments during the dry period. In the wet period, As had a significant correlation with Cd (r = 0.92, p < 0.01) in sediments. The analysis of environmental risks indicated significant enrichment of sediments with As and Cd. It is important to put in place relevant control mechanisms targeting metals in the studied tributaries, with a focus on As and Cd.