This study is carried out to characterize the CHU-MEL effluents discharged into the Cotonou lagoon to assess the potential hazards of these releases for this ecosystem. To achieve this goal, the effluents collected at the end of the spillways have been analyzed. The results obtained from the physicochemical and microbiological analysis made it possible to assess the quality of the effluents. The pH, temperature and conductivity measured in-situ are, on average, 6.65, 30.3 C and 763 μS/Cm. The average contents of dissolved oxygen, nitrite, nitrate, ammonium and Nitrogen Total Kjedhal (NTK) are respectively 1.92 mg/L, 0.06 mg/L, 7.75 mg/L, 18.45 mg/L and 28.78 mg/L. The Biochemical Oxygen Demand (BOD5) ranges from 38 mg/L to 53 mg/L, the Chemical Oxygen Demand (COD) from 97 mg/L to 274 mg/L, suspended solids (SS) belonging between 47 mg/L-398 mg/L and total phosphorus going from 0.37 mg/L to 13.02 mg/L. The microbiological parameters (total coliforms, faecal coliforms, E. coli, fecal streptococci and anaerobic sulphite reducers’ spores) are generally out of the standard values. These effluents present therefor risks for the fauna and the flora of the Cotonou’s lagoon and it is well indicated to assess them through ecotoxicity tests.