In order to meet the expectations of the Water Framework Directive (WFD) concerning the assessment of the ecological status of transitional water bodies, of which lagoons are part, UMR MARBEC (Ifremer, IRD, UM,CNRS) has coordinated the INPOLAG project (2019-2023) in collaboration with CEFREM (Centre de Formation et de Recherche sur les Environnements Méditerranéens-UMR 5110 CNRS-UPVD) and Tour du Valat. This project aimed to develop one of the indicators missing from the WFD requirements: the "Fish in Mediterranean lagoons" indicator adapted to the French context (Ouisse et al., 2023). To this aim, three field surveys were carried out in autumn 2019 and 2020 and in spring 2021 (Motte et al. 2020). The present dataset gathers all the biological and environmental observations obtained in the course of these three surveys.