Water is an indispensable natural resource that is often prodigiously threatened by anthropomorphic activities. This study evaluated the physicochemical properties of water and selected heavy metals in edible muscles of a piscivorous fish (Protopterus annectens) from Nyabarongo and Nyabugogo rivers of Rwanda. Edibility health risk was evaluated using the target hazard quotient method. Water samples were taken in triplicate from Ruliba station and Kirinda bridge on Nyabarongo river and Giticyinyoni on Nyabugogo river. Fish samples were obtained from the sampling stations on Nyabarongo river. All samples were analyzed following standard methods and analytical results indicated that the average temperature, pH, total dissolved solids and electrolytic conductivity of water from the rivers were within WHO acceptable limits. The statistical mean concentrations of the ionic components of the water samples were 1.61 ± 0.03, 0.53 ± 0.002, 0.24 ± 0.02 and 0.051 ± 0.01 mg/L for Fe, Mn, Cu and Pb respectively at Ruliba station and 0.63 ± 0.02, 0.02 ± 0.002, 0.09 ± 0.01, 0.06 ± 0.002 and 0.75 ± 0.02 mg/L for Fe, Mn, Zn, Cr and Pb respectively at Kirinda bridge. Water from Giticyinyoni had 1.57 ± 0.02, 0.49 ± 0.03, 0.29 ± 0.058, 0.43 ± 0.058, 0.15 ± 0.00 and 0.59 ± 0.058 mg/L of Fe, Mn, Cu, Zn, Cr and Pb respectively. Zinc, Cu, Cr and Cd were below detection limits in samples from Ruliba station and Kirinda bridge (Nyabarongo river). Edible muscles of P. annectens from Nyabarongo river contained 272.8 ± 0.36, 292.2 ± 0.25, 8.8 ± 0.36, 135.2 ± 0.15, 148.0 ± 0.21 and 432. 0 ± 0.50 mgkg-1 for Fe, Mn, Cu, Zn, Cr and Pb at Ruliba station and 336.0 ± 0.70, 302.6 ± 1.22, 6.4 ± 0.26, 44.7 ± 0.20, 138.2 ± 0.17 and 302.4 ± 1.50 mgkg-1 for Fe, Mn, Cu, Zn, Cr and Pb respectively at Kirinda bridge. Health risk assessment indicated that consumption of the edible muscles of P. annectens may lead to deleterious health effects as reflected by values of target hazard quotients being greater than one. Therefore, the Rwandese government should lay strategies to reduce pollution of the rivers. Further research should evaluate the heavy metal content of metabolically active organs of P. annectens from Nyabarongo river as well as the microbiological profile of water from the rivers.