The Azagny Channel is an estuarine ecosystem connecting Ebrié Lagoon to Bandama River estuary and it is adjacent to Azagny National Park. The aim of this study was to provide the first data on diversity and structure of macroinvertebrates in this estuarine area. Physicochemical parameters were measured monthly in three sampling stations S1, S2 and S3, and the benthic Macroinvertebrates was collected using a Van Veen grab. A total of 28 taxa distributed among 20 families and 11 orders belonging to Annelida, Mollusca, Crustacean and Insecta were collected. The taxonomic richness and diversity were higher in S1 compared to S2 and S3, probably due to its proximity to Bandama estuary. The relative abundance revealed that mollusks represented mainly by Pachymelania aurita (16.04%), P. fusca (15.83%), Anodonta anatina (13.02%) dominated the species assemblage; followed by crustaceans with Macrobrachium vollenhovenii (31.87%) and Potamon sp. (5.01%). Canonical correspondence analysis revealed that the main factors that influenced macroinvertebrates distribution in Azagny Channel were conductivity, salinity and Total Dissolved Solids (TDS). There is a strong correlation between these three abiotic factors and their influence on species assemblage would be linked to proximity of study area to Atlantic Ocean. These findings provide valuable information that can be used to establish biotic indices to monitor the water quality of Azagny Channel.