The existence of strong potential synergies between the Water Framework Directive (WFD) and the Habitats Directive (HD) is widely acknowledged. Indeed, ensuring favourable conservation conditions for aquatic habitats and species of conservation concern is closely related to the achievement of a good ecological status in water bodies. However, since these two sets of European laws are generally applied without any coordination, an inefficient use of resources may adversely affect their goals. The main negative outcome is an increase in the cost of monitoring programs for collecting data in nature (i.e., physical and chemical parameters, species and habitats, plant communities). The use of macrophytes as a bioindicator, as imposed by the WFD, may instead help to integrate data on aquatic EU habitats and enhance knowledge of such habitats outside the Natura 2000 network. The aim of present study was to evaluate the usefulness of data collected in WFD monitoring surveys as a means of inferring the occurrence and the distribution of lacustrine aquatic habitats in countries belonging to the European Union (EU). The main aim of the analysis was to identify the depth gradient distribution of diagnostic macrophyte taxa in two EU habitats (3140, i.e., Chara-dominated benthic communities, and 3150, i.e., natural eutrophic lakes) using data collected in lakes in Lombardy (northern Italy), some of which are included in the Natura 2000 network (10 out 16). While recognizing the limitations of the data collected within the two frameworks, the results confirmed the marked usefulness of WFD data as a means of enhancing the knowledge available on lacustrine aquatic habitats in the EU. WFD data can actively help to improve the basic information on aquatic habitats, thereby more effectively supporting regional strategies for biodiversity conservation as well as recovery programs.