The lakes from Medoc (Carcans-Hourtin and Lacanau lakes) are located in the Aquitaine region, France, close to the Atlantic coast of the Bay of Biscay. These shallow lakes are characterized by a sandy substratum and a non-symmetrical slope of the bottom from the west side to the east side of the lakes. They are exposed to the prevailing westerly winds and they are mesotrophic. In 2011, the macrophyte communities of the perimeters of these two lakes were inventoried throughout the littoral zones. The aquatic vegetation in the deepest parts of the lakes was detected with the aid of an echosounder along several profiles perpendicular to the shore line. Samples were taken with a rake or a grapnel at regular points along the profiles for the identification of taxa detected by the echosounding. These communities include species common to lake ecosystems: some are protected species, such as the species of Littorella lawns (Lobelia dortmanna, Littorella uniflora, Isoetes boryana, Caropsis verticillatinundata), and some are exotic invasive species (Lagarosiphon major, Egeria densa, Ludwigia peploides). Moreover, some species of Charophytes are abundant and frequent in these lakes. Chara fragifera colonizes two-thirds of the littoral zone from the shore line to a depth of 4.5 m in Carcans-Hourtin. Nitella confervacea is less abundant and frequent, but it appears to colonize the somewhat deeper parts of the lakes. The distribution of these two species is relatively homogeneous from west to east; they seem to colonize in a similar way both the shores exposed to the prevailing winds and those protected from them. Chara fragifera and Nitella confervacea were not found in the wind-protected fluid organic substrate coves on the west sides of the lakes. The distribution maps of these two species on each lake are presented in this paper. Two other species of Charophytes, Chara globularis and Nitella translucens, are also present in these lakes, but with a more localized distribution. The results of this thorough investigation of the shores and the deepest parts of the lakes correspond with the data available in the literature. The presence of Chara fragifera and Nitella confervacea in the associations of the Littorelletalia with phanerogams such as Lobelia dortmanna and Littorella uniflora, are relatively well described for these lakes, but so far, no geographical localization of the macrophyte populations had been performed. The survey raises many questions related to the management of the water level of the lakes and management of the invasive alien species for the protection of the native aquatic habitats of these lakes, as well as for the other lakes situated along the Atlantic coast, from the south of the Bay of Arcachon to the Adour estuary.