The aim of this paper is to characterize various lagoon and delta environments through the analysis of ostracod fauna. Various aquatic environments from the Mediterranean coastline of the Gulf of Lions (Languedoc-Roussillon, France) and Ebro delta (Catalonia, Spain) were studied. The sample sites (60) are different in terms of marine and fluvial influence. Environmental parameters (salinity, water depth, sedimentary texture, plant cover) were measured and compiled from available data in order to characterize the biotopes. We interpreted the species distribution as related to the degree of isolation from the sea, the hydrological internal currents and the proximity of river mouths. Moreover, the assemblage composition seems influenced by the lagoon vegetation growth. These data can be used for the palaeoenvironmental reconstructions, particularly in Holocene deltaic context where the mobility of river mouths and the forming and evolution of sand bars and lagoons are recurring issues.