In many urban and peri-urban areas of developing countries, shallow wells and untreated water from urban rivers are used for domestic purposes, including drinking water supply, population bathing and irrigation for urban agriculture. The evaluation and monitoring of water quality are therefore necessary for preventing potential human risk associated with the exposure to contaminated water. In this study, physicochemical and bacteriological parameters were assessed in an urban river (named Kokolo Canal/Jerusalem River) draining the municipality of Lingwala (City of Kinshasa, Democratic Republic of the Congo) and in two shallow wells used as drinking water supplies, during the wet and dry seasons in order to estimate the seasonal variation of contamination. The faecal indicator bacteria (FIB) isolated strains (Escherichia coli (E. coli) and Enterococcus (ENT)) from water and surface sediment, were characterized for human-specific bacteroides by molecular approach. The results revealed very high faecal contamination of water from the shallow wells, and of water and sediments from the river, during both wet and dry seasons. During the wet season, E. coli reached the values of 18.6x105 and 4.9x105 CFU 100 mL-1 in Kokolo Canal and shallow wells, respectively; and Enterococcus reached the values of 7.4x104 and 2.7x104 CFU 100 mL-1. Strong mutually positive correlation was observed between E. coli and ENT, with the range of R-value being 0.93 < r < 0.97 (p-value < 0.001, n=15). The PCR assays for human-specific Bacteroides indicated that more than 98% of 500 isolated FIB strains were of human origin, pointing out the effect of poor household sanitation practices on surface water but also on groundwater contamination. The water samples from the shallow wells and Kokolo Canal were highly polluted with faecal matter in both seasons. However, the pollution level was significantly higher during the wet season compared to the dry season. Physicochemical analysis revealed also very high water electrical conductivity, with values much higher than the recommended limits of the World Health Organization guideline for drinking water. These results highlight the potential human health risk associated with the exposure to water contamination from shallow wells and Kokolo Canal, due to the very high level of human FIB. Rapid, unplanned and uncontrolled population growth in the city of Kinshasa is increasing considerably the water demand, whereas there is a dramatic lack of appropriate sanitation and wastewater facilities, as well as of faecal sludge (and solid waste) management and treatment. The lack of hygiene and the practice of open defecation is leading to the degradation of water quality, consequently the persistence of waterborne diseases in the neighbourhoods of sub-rural municipalities, and there is a growing threat to the sustainability to water resources and water quality. The results of this study should encourage municipality policy and strategy on increasing the access to safely managed sanitation services; in order to better protect surface water and groundwater sources, and limit the proliferation of epidemics touching regularly the city.