The aim of this study was to evaluate the physicochemical and microbiological quality of the waters of Franceville lakes, which are real receptacles for several pollutants. The physico-chemical parameters in situ were measured by means of a multiparameter and other chemical elements as phosphate, sulfate and ammonium were highlighted and measured by a colorimetric and spectrophotometric method. The microbiological parameters were determined by the colony-forming unit (CFU) method on selective agar media. Finally, strains of Escherichia coli were identified by biochemical tests. The results of the physico-chemical parameters show that the waters of Lake Lacaisse have the highest temperature, conductivity, salinity and dissolved oxygen values respectively, 26.71 °C, 398.67 μs/cm, 190 mg/l and 376.4 mg/l. On the other hand, these waters have neutral pH. The results of the bacteriological parameters show that the lake Makana contains the strongest rates of coliformes totals (4.84.105 UFC/100 ml) and of presumptive Escherichia coli in 37°C (3.54.105 UFC/100 ml). Eosin methylene blue medium is the best for counting total coliforms. In addition, (6.45%) colonies of Escherichia coli were identified. So, other coliformes thermotolérants (Entérobacter Sakazakii, Entérobacter cloacae, klebsiella ozaenae, klebsiella Pneumoniae. pneumoniae). In sum, this study shows that the water in Lake Makana appears to be more polluted than Lac Lacaisse.