The historical composition of landscapes is recognized as an important factor for explaining plant diversity patterns, because current species assemblages are not only patterned by current ecological conditions, but also represent legacies of the past. Indeed, historical landscapes can represent past anthropogenic impact on the environment whose effects could still be observed nowadays. However, the influence of history on diversity patterns has mostly been investigated for terrestrial ecosystems, but has rarely been considered for aquatic ones. Here, we examined the effect of historical landscapes and land-use changes on the taxonomic richness and composition of aquatic plant communities in French freshwater shallow lakes and ponds. We aimed to test the relative influence of environmental variables and landscapes legacy on macrophyte species assemblages. We surveyed the macrophytes communities in 100m sections of the shoreline of each lake (N=17) up to 1m depth. We used water chemistry and physical features of lakes as environmental variables, and reconstructed historical land-use of lakes' watershed with aerial pictures of 1945, 1965, 1985 and 2000 for examining historical variables. Landscape changes were examined with transition matrices and principal component analysis (PCA) and species composition with non-metrical multidimensional scaling (NMDS). The relative influence of physical, chemical and historical factors on species richness and composition were tested with variation partitioning methods. We found that the landscape of all lakes' watershed exhibit a trend toward an increase of urban and arable areas at the expense of semi-natural ones. Environmental variables and historical factors are strongly correlated with macrophyte diversity but current landscape composition seems to have only a weak influence. Especially, historical landscape factors appeared to be strongly associated with species macrophyte composition. These results underline the importance of historical factors in explaining aquatic plant diversity and suggest delayed responses of plant communities to anthropogenic pressures. Integrating historical factors in future analyses of aquatic ecosystems would thus greatly contribute to understand ecological processes governing their species assemblages, and would be crucial for their conservation and management.