Microbial and toxic metals contamination of freshwater resources is still a major problem in many parts of the world. In this study, water and sediment samples (n=9) were subjected to the microbiological and some physicochemical analysis to assess the water quality of the N'Djili River (Kinshasa, Democratic Republic of Congo). Microbiological analysis was performed for faecal indicator bacteria (FIB) including Escherichia coli (E. coli) and Enterococcus (ENT). The FIB characterization was performed for general E. coli, Enterococcus faecalis (E. faecalis) and human-specific bacteroides by PCR, using specific primers. The physicochemical parameters including pH and electrical conductivity were measured in water samples, and grain size distribution, organic matter and total mercury (Hg) were measured in sediments samples. The results revealed high concentration of FIB, with the maximum values of 1.6x103 and 2.7x103 CFU 100 mL-1 for E. coli and ENT, respectively. The FIB in sediment samples present higher concentration than in water, with maximum values of 9.4x105 and 1.2x105 for E. coli and ENT, respectively. The PCR assays for human-specific bacteroides HF183/HF134 indicated that more than 90% of bacteria were from human origin. The Hg concentration in sediment samples reaches the values of 0.5 mg kg-1. Thus, our results indicate that the uncontrolled landfills and mixing of untreated urban and industrial effluents lead to the deterioration of the water quality of the rivers traversing the economically important cities. This study represents useful tools incorporated to evaluate water and sediment quality in river systems which can be applied to similar aquatic environments.