The increasing contamination of fresh water resource by toxic metals and Persistence Organic Pollutants (POPs) is a major environmental concern globally. In the present investigation, surface sediments collected from three main rivers named, Makelele, Kalamu and Nsanga, draining through the city of Kinshasa, Democratic Republic of the Congo, were characterized for grain size, organic matter, toxic metals, POPs (including organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs)), and polycyclic aromatic hydrocarbons (PAHs). Furthermore, enrichment factor (EF) and geoaccumulation index (Igeo) were performed to determine metal source and pollution status. The results highlighted high concentration of toxic metals in all sediment samples, reaching the values (mg kg-1) of 325 (Cu), 549 (Zn), 165 (Pb) and 1.5 (Cd). High values of PCBs and OCPs were detected in sediment samples, e.g. in Makele rivers, PCB values ranged from 0.9-10.9 with total PCBs (∑7 PCBs x 4.3): 169.3 µg kg-1; OCPs from 21.6-146.8 with ∑OCPs: 270.6 µg kg-1. The PBDEs concentrations were higher in investigated rivers comparatively with values detected in many rivers from Sub-Saharan Africa. The PAHs value ranged from 22.6 to 1011.9 µg kg-1. River contamination may be explained by local intense domestic activities, urban and agricultural runoff, industrial and hospital wastewaters discharge into the rivers without prior treatment. This research provides not only a first baseline information on the extent of contamination in this tropical ecosystem but also represents useful tools incorporated to evaluate sediment quality in the river receiving systems which can be applied to similar aquatic environments.