Benthic macroinvertebrates community composition, abundance and distribution was studied in three Lagoons of Côte d’Ivoire (Aby, Tendo and Ehy). Sampling was conducted monthly between February 2012 through March 2013 on 6 sampling stations. The macrofauna surveyed consisted of 21.015 macroinvertebrates individuals belonging to 86 taxa (genera and species), 44 families, 15 orders and 6 classes. The most predominant group was Gasteropoda which make up 64.7% of the taxonomic richness observed. Insecta were the second most predominant. The diversity of macroinvertebrates varied between lagoons (29-33 taxa Aby Lagoon), (56-70 taxa Tendo Lagoon) and (58-68 taxa Ehy Lagoon). Multivariate analyses (RDAs) revealed that benthic macroinvertebrates community composition and abundance variations were mainly controlled by the environmental parameters of the three lagoons, in particular the salinity and conductivity of the water. Thus, two ecological zones were noted: an area influenced by marine waters and another area under influence by waters of Tanoé river and Tanoé-Ehy swamp forest.