Although the United Nations General Assembly recognized in 2010, the right to safe and clean drinking water and sanitation as a human right that is essential to the full enjoyment of life and all other human rights, the contamination of water supplies with faecal pathogens is still a major and unsolved problem in many parts of the world. In the present study, faecal indicator bacteria (FIB) including Escherichia coli (E. coli) and Enterococcus (ENT) were quantified over the period of June/July 2014 and June/July 2015 to assess the quality of hospital effluents (n=3: H1, H2 and H3) and of rivers receiving wastewaters from the city of Kinshasa, Democratic Republic of Congo. The water and sediment samples from the river receiving systems were collected in, up and downstream of the hospital outlet pipes (HOPs) discharge. The analysis of E. coli and ENT in water and sediment suspension was performed using cultural membrane filter method. The FIB characterization was performed for general E. coli, Enterococcus faecalis (E. faecalis) and human-specific bacteroides by PCR using specific primers. The results revealed very high FIB concentration in the hospital effluent waters, with E. coli reaching the values of 4.2x105, 16.1x105 and 5.9x105 CFU 100 mL-1, for the hospital effluents from H1, H2, H3 respectively; and Enterococcus reaching the values of 2.3x104, 10.9x104 and 4.1x104 CFU 100 mL-1. Interestingly, the FIB levels in the water and sediment samples from river receiving systems are spatially and temporally highly variables and present in some samples higher values than the hospital effluents. The PCR assays for human-specific bacteroides HF183/HF134 furthermore indicate that more than 98% of bacteria were from human origin. The results of this research therefore confirm the hypothesis of our previous studies indicating that in developing countries (e.g. Democratic Republic of Congo- DR Congo- and South India), the hospital effluent waters can be a significant source of the deterioration of the bacteriological quality for urban rivers. The approach used in this investigation can be furthermore used to decipher the pollution of water resources by human faecal contamination. The results of this research will help to better understand the microbiological pollution problematic in river receiving system and will guide municipality decisions on improving the urban water quality