The Southwestern freshwater shallow lakes of the Aquitaine coast in France harbour a unique aquatic plant diversity, playing a crucial role in maintaining vital ecosystem functions. However, anthropogenic activities and global changes pose significant threats, leading to local extinctions. This project combines two research questions to enhance our understanding of these ecosystems and guide conservation efforts. First, we will investigate the genetic diversity of nine macrophytes species comprised in isoetid communities across five lakes. Using sequence-based nuclear microsatellites genotyping, we analysed the genetic variation in ca. 4,000 sampled individuals. Assessing the distribution of genetic diversity within and between lakes, we aim to (i) uncover population-level processes, (ii) identify historical and contemporary factors shaping populations structure, and (iii) understand community assemblages. These findings will shed light on adaptation capacity, demographic history, dispersal abilities, and population structure of macrophytes communities. In addition, we aim to explore ecological processes at a larger biological scale by examining the correlation between genetic and taxonomic diversity using the species-gene diversity correlation (SGDC) framework. This approach determine whether similar ecological processes operate across different biological scales and whether taxonomic diversity can serve as a reliable proxy for genetic diversity. By integrating these two research questions, this project should provide valuable information for conservation management plans in the Aquitaine region. Genetic insights will help to assess the adaptive potential of macrophytes populations and to inform conservation strategies to mitigate threats. Furthermore, the examination of ecological processes will strengthen our understanding of community structure and responses to anthropogenic impacts. This knowledge is crucial for developing effective conservation strategies, with the essential collaboration of managers, to protect biodiversity and ecosystem services in the face of ongoing environmental challenges.