The development of fish farming in Benin is facing enormous constraints. For sustainability of fish farming systems, these constraints must be removed. The objective of this research is to identify the determinants of the ecological sustainability of fish farming systems in the Ouémé valley in southern Benin. For this, 300 fish farmers randomly selected were surveyed in four communes of the Ouémé Valley. These are the communes of Ouinhi, Bonou, Adjohoun and Dangbo. The Ecological Sustainability Score (EDS) was calculated using the IDAqua Approach that uses the sustainability indicators in aquaculture. Then a multiple linear regression was used to identify the factors determining the level of ecological sustainability of fish farming systems. The results indicate globally, fish farmers have an ecological sustainability score of 39.25 out of 100. The regression carried out showed that the level of ecological sustainability of fish farming systems in the Ouémé valley in southern Benin are economic efficiency, the level of primary schooling, the level of higher education and fish farming as the main activity. The results suggest that the authorities are putting in place policies where fish farmers are themselves trained to produce the foods they use while minimizing production costs. Under these conditions, one could expect an improvement in the ecological sustainability of fish farming systems.