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.