Abstract Freshwater biodiversity is experiencing dramatic declines. Despite improvements, the trend remains negative, underlining that effective and coordinated initiatives are needed. Protected areas are considered a global cornerstone of biodiversity conservation, and in Europe, the Natura 2000 network plays a central role in safeguarding biodiversity. In the present study, we examine if designated Annex I listed freshwater habitats of the Habitats Directive are sufficiently represented to enable conservation and restoration efforts, as outlined in Article 4 of the European Nature Restoration Law (NRR), to meaningfully contribute to reversing the ongoing decline in freshwater biodiversity. Additionally, we examine whether freshwater habitats are represented across their full natural geographical range, addressing a key spatial component of long‐term persistence, as reflected in the concept of “favorable reference area” as defined in Article 3 of the NRR. We found that freshwater habitats cover 6.2% of the total area of Natura 2000 sites with running waters covering only 0.4%. In addition to a low spatial coverage, the analyses also indicated that several freshwater Annex I habitats are not represented across their full natural geographical range. Based on the obtained results, we therefore argue that a systematic strengthening of the Natura 2000 network is required, with particular emphasis on: (1) expanding the extent of designated freshwater habitat types in‐ and also outside the existing network if necessary to adequately cover freshwater habitats, and (2) identifying and addressing representation gaps across all relevant biogeographic regions. To support this process, we have developed a webtool based on the datasets underlying the analyses, which enables relevant stakeholders including EU institutions, national agencies, and local managers to examine the distribution of freshwater habitats and species protected within the current Natura 2000 network. The webtool can be accessed at https://www.waterwebtools.com/merlin .