We here report how hydromorphological features determine the macrophyte distribution and species assemblages at different scales in softwater lakes. The coastal dunes of the Aquitaine region (SW France, Bay of Biscay) shelter large and shallow lakes characterized by sandy substrate, low alkalinity and asymmetric bathymetry. Here, macrophyte communities are mainly constituted by Isoetids, Charids and exotic Elodeids, forming remarkable ecosystems in such southern part of Europe. The species composition and abundance of aquatic plants in two lakes (Lacanau and Hourtin-Carcans lakes) were studied on about 1000 shore stretches and 234 quadrats between 2011 and 2014. Concomitantly, we surveyed different physical factors such as slope, depth, sedimentary organic matter and anthropic modifications of the shore. We also calculated the potential effect of waves on the littoral zone and the resulting resuspension of substratum. Charids (Chara fragifera, Nitella confervacea) often occured with Isoetids (Lobelia dortmanna, Littorella uniflora) and preferentially colonized poor-organic sediments and wind-exposed shores. Exotic Elodeids (Egeria densa and Lagarosiphon major) were mostly amassing within mono-specific beds nearby altered areas by human activities (boating, urban environment). This approach allow to infer conditions thresholds for the preservation or the disappearance of macrophyte species.