In many suburban municipalities of developing countries, the household drinking water comes mainly from groundwater including, wells, streams and springs. These sources are vulnerable because poor hygienic conditions and sanitation prevail causing persistence and recurrent waterborne diseases. In this research, a survey study on water resource use and an epidemiological survey of waterborne diseases were conducted among users of water points and medical institutions in suburban communes of Selembao and Kimbanseke (Kinshasa, the Democratic Republic of the Congo). In addition, physicochemical (temperature, pH, O2, electrical conductivity, and soluble ions: Na+, K+, PO43−, SO42−, NO3−, NO2−) and bacteriological (FIB: faecal indicator bacteria) analyses of water from 21 wells and springs were performed according to the seasonal variations. FIB included Escherichia coli (E. coli), Enterococcus and Total Coliforms. The survey results indicate that more than 75% of the patients admitted to local medical institutions between 2016 and 2019 are affected by waterborne diseases, including typhoid fever, amoebic dysentery, diarrhoea, gastroenteritis disorders and cholera. Except for NO3− in some sites, the water physicochemical parameter values are within WHO permissible limits for drinking/domestic water quality. On the contrary, the results revealed high FIB levels in water from unmanaged wells and springs during rainy and dry seasons. The microbiological pollution was significantly higher in the rainy season compared to the dry season. Interestingly, no FIB contamination was observed in water samples from managed/developed wells. The results from this study will guide local government decisions on improving water quality to prevent recurrent waterborne diseases.