Shallow lakes provide multiple ecosystem services, and macrophytes are key elements of these systems. Understanding the processes behind their species assemblages is thus essential for lake management. In this study, we surveyed macrophyte communities of 14 lakes and ponds 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 the coefficients of these metrics were correlated with previous explanatory variables. We did not find a common temporal response of communities. However, some variables, such as residence time, watershed and lake areas were found to be important factors in explaining community changes across time and led to suggest either an important influence of physico-chemistral variation or regional-dispersion processes. Also, the presence of invasive species and their abundance explained some patterns of macrophyte diversity underlying the importance of biotic interactions. These results suggest that both biotic and abiotic processes influence local macrophyte assemblages and provide new insights in terms of lake management for biodiversity conservation.