This study is conducted to characterize the heavy metal contamination of CHU-MEL effluents discharged into the Cotonou lagoon in order to assess the potential risk of these discharges for this ecosystem. To achieve this objective, the effluents collected at the end of the pipes acting as weirs in the lagoon were analyzed. The results from physico-chemical and heavy metals analyzes have made it possible to assess the quality of the effluents. The values of pH, temperature, conductivity, TDS and dissolved oxygen measured in situ are, on average, 7.95; 29.60°C; 639.60 µS/cm; 457.48 mg/l and 0.22 mg/L. The determination of heavy metals in the effluents showed low levels of contamination. The average levels of lead, cadmium, mercury and total iron are 0.1727 mg/L, 0.0261 mg/L, 0.0010 mg/L and 0.25 mg/L, respectively. This study shows that most of the parameters studied in the CHU-MEL effluent are in compliance with the standards. These effluents therefore pose a low risk for the aquatic organisms of the receiving environment, this added to the dilution effect of the effluents in the waters of the lagoon. However, the continual discharge of these effluents into the lagoon with their share of heavy metals.