Regarded as a biological quality element by the WFD, macrophytes are currently used for the assessment and the classification of the ecological status of 172 lakes in France. Over the past decades, aquatic vegetation from French waterbodies has been studied in order to characterize the community structure and improve the management of invasive alien species. Various sampling protocols have been used, and the comparability between the data obtained at the national scale was quite difficult. In the context of the implementation of the WFD, we developed a standardized sampling method optimising the macrophyte communities assessment. Compliant with European standards, this protocol was tested on 8 lakes corresponding to 8 different national types distributed on the whole French territory and has been used to assess the ecological status of 46 others French lakes since then. After a critical analysis of this protocol compared to previous French protocols and other sampling methods used in other European countries, we propose a first analysis of results of the implementation of this protocol on several French lakes.