Coastal lagoons maintain exchanges with marine and continental waters. These exchanges disrupt their settlement. Knowledge of the fish fauna of the Ivorian lagoons is of concern to those responsible for the development of the fishing sector.This study aims to characterize the spatio-temporal variation of the fish fauna and to identify the biological indices which determine the distribution of fish species and the state of exploitation of these fish in the Aghien-Potou lagoon complex. The fish were sampled from April 2019 to March 2021 from monthly experimental catches. Each identified specimen is weighed and measured. This study identified 54 species. This population is largely dominated by Coptodon and Chrysichthys. It is more diversified in the Aghien lagoon (RS = 23) than in the Potou lagoon (RS = 13). The Aghien lagoon communicates with the waters of the continental environment resulting in low salinity and a population with a continental or estuarine tendency. Conversely, the Potou lagoon with its communication with the sea, has a higher salinity and a population of fish with a marine or marine-estuarine tendency. The environment of the Aghien lagoon (w = 0.082) is more stressed than that of the Potou lagoon (w = 0.01). The results of this work constitute a basic element for decision-making in the quest for a strategy for the sustainable management of fisheries resources in Côte d'Ivoire.