For decades, the Ébrié Lagoon in Côte d'Ivoire has been the receptacle of wastewater effluent and household waste transported by runoff water. This work assesses the spatio-temporal variability of the Ébrié lagoon water quality at the city of Abidjan. The methodological approach used in this study is summarized in three stages: the choice and standardization of the parameters for assessing water quality for uses such as aquaculture, irrigation, watering, and sports and recreation; the weighting of these parameters using the Hierarchical Analysis Process (AHP) of Saaty; and finally, the aggregation of the weighted parameters or factors. Physicochemical and microbiological analysis data on the waters of the Ébrié lagoon for June and December of 2014 and 2015 were provided by the Ivorian Center for Anti-Pollution (Centre Ivoirien Anti-Pollution, CIAPOL) and the concentrations of trace elements in sediments (As, Cd, Cr, Pb, Zn) were used. The aggregation of standardized and weighted parameters allowed the determination of the Water Quality Indices (WQI) by usage for each bays of the lagoon. The results show that in both 2014 and 2015, the waters of the Ébrié lagoon were generally of poor quality for the different uses examined in this study (aquaculture, irrigation, watering and sport and recreation) with an accentuation in 2015. However, some bays of the lagoon have waters of dubious to satisfactory quality. This study contributes an improved evaluation of the Ébrié lagoon waters.