Shallow-lakes ecosystems play a major role in European landscapes in providing multiple ecosystem services, such as biodiversity, human amenities and resource supplying. Macrophytes are key elements of these ecosystems and understanding the processes behind their species assemblages is essential for lake management. In this study, we followed macrophytes communities of 14 lakes in South-Western France since 1984 and explored their structure and composition change with time. We used a set of physical, anthropogenic and landscape variables to understand processes driving local species assemblages. Abundance of invasive species was also included as explanatory variables. Species richness, rank-abundance curves and non-metrical multidimensional scaling were used to investigate macrophyte diversity, and coefficients of these metrics were correlated with previous explanatory variables. We did not find a common response of communities with time, each lake experiencing its own path. However, some variables, such as lake renewal, area of the watershed and lake area were found to be important factors in explaining community changes across time and lead to suggest either an important influence of physic-chemistry variation or regional-dispersion processes. Also, the presence of invasive species and their abundance explained some patterns of macrophytes diversity underlying the importance of biotic interactions. These results suggest that both biotic and abiotic processes influence local macrophytes assemblages and provide new insights in terms of lake management for biodiversity conservation.