{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T12:47:57Z","timestamp":1792068477619,"version":"4.4.0"},"reference-count":42,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T00:00:00Z","timestamp":1776816000000},"content-version":"vor","delay-in-days":21,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T00:00:00Z","timestamp":1775001600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["esajournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Ecological Applications"],"published-print":{"date-parts":[[2026,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    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\u2010term persistence, as reflected in the concept of \u201cfavorable reference area\u201d 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\u2010 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\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/www.waterwebtools.com\/merlin\">https:\/\/www.waterwebtools.com\/merlin<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1002\/eap.70241","type":"journal-article","created":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T11:01:51Z","timestamp":1776855711000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Freshwater habitats within the Natura 2000 network"],"prefix":"10.1002","volume":"36","author":[{"given":"Annette","family":"Baattrup\u2010Pedersen","sequence":"first","affiliation":[{"name":"Department of Biology Aarhus University  Aarhus C Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Baumane","sequence":"additional","affiliation":[{"name":"Department of Biology Aarhus University  Aarhus C Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anders","family":"Nielsen","sequence":"additional","affiliation":[{"name":"WateriTech  Skanderborg Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dennis","family":"Trolle","sequence":"additional","affiliation":[{"name":"WateriTech  Skanderborg Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paulo","family":"Branco","sequence":"additional","affiliation":[{"name":"Forest Research Centre, Associate Laboratory TERRA School of Agriculture, University of Lisbon  Lisbon Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Borgwardt","sequence":"additional","affiliation":[{"name":"University of Natural Resources and Life Sciences, Vienna  Vienna Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Hering","sequence":"additional","affiliation":[{"name":"Faculty of Biology, Aquatic Ecology University of Duisburg\u2010Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Birk","sequence":"additional","affiliation":[{"name":"Faculty of Biology, Aquatic Ecology University of Duisburg\u2010Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,4,22]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/conl.12684"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.14758\/SET-REVUE.2011.3BIS.16"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1139\/er-2022-0126"},{"key":"e_1_2_9_5_1","doi-asserted-by":"crossref","unstructured":"Baattrup\u2010Pedersen A. M.Baumane M. K.Jensen D.Trolle andA.Nielsen.2025.\u201cMaps of Protected Habitats and Species in the Natura 2000 Network \u2010 With Emphasis on Freshwater Habitats Their Restoration Potential and Terrestrial Groundwater\u2010Dependent Ecosystems.\u201d[Data Set]. Zenodo.https:\/\/doi.org\/10.5281\/zenodo.17601833","DOI":"10.1002\/eap.70241"},{"key":"e_1_2_9_6_1","first-page":"162","article-title":"\u00d8kologiske indeks og biodiversitet i vandl\u00f8b","volume":"4","author":"Baattrup\u2010Pedersen A.","year":"2023","journal-title":"Vand & Jord"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1080\/11263504.2013.860055"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00267-002-2737-0"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/avsc.12798"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2019.08.002"},{"key":"e_1_2_9_11_1","unstructured":"EC.2022.\u201cNatura 2000 (vector) \u2013 Version 2021.\u201dhttps:\/\/sdi.eea.europa.eu\/catalogue\/srv\/api\/records\/8c89654c-636a-485f-90b4-3778ea4b7fa3"},{"key":"e_1_2_9_12_1","unstructured":"EC.2025.\u201cThe Habitats Directive.\u201dEU Measures to Conserve Europe's Wild Flora and Fauna.https:\/\/environment.ec.europa.eu\/topics\/nature-and-biodiversity\/habitats-directive_en"},{"key":"e_1_2_9_13_1","unstructured":"EEA.2020.\u201cState of Nature in the EU.\u201dResults from Reporting under the Nature Directives 2013\u20132018: Publications Office of the European Union."},{"key":"e_1_2_9_14_1","unstructured":"EEA.2024a.\u201cEUNIS the European Nature Information System.\u201dhttps:\/\/eunis.eea.europa.eu\/index.jsp"},{"key":"e_1_2_9_15_1","unstructured":"EEA.2024b.\u201cEuropean Red List of Habitats \u2013 Enhanced by EEA.\u201dhttps:\/\/www.eea.europa.eu\/en\/datahub\/datahubitem\u2010view\/de2276d8\u2010e295\u20104cd7\u201089c9\u201088812065db87?activeAccordion="},{"key":"e_1_2_9_16_1","unstructured":"Eionet.2024.\u201cReports on European Red List of Habitats.\u201dhttps:\/\/forum.eionet.europa.eu\/european-red-list-habitats\/"},{"key":"e_1_2_9_17_1","unstructured":"European Environment Agency.2018.\u201cCORINE Land Cover (CLC) 2018 Version 20b2.\u201dhttps:\/\/land.copernicus.eu\/pan-european\/corine-land-cover"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2024.173825"},{"key":"e_1_2_9_19_1","unstructured":"Fredshavn J. R. B.Nygaard R.Ejrn\u00e6s C.Damgaard O. R.Therkildsen P.Wind et al.2019.\u201cBevaringsstatus for naturtyper og arter\u20132019.\u201dHabitatdirektivets Artikel 17\u2010rapportering. Aarhus Universitet DCE\u2010Nationalt Center for Milj\u00f8 og Energi."},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.3389\/fenvs.2023.1122464"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1111\/conl.12249"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.wasec.2019.100049"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06400-1"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/s44358-024-00012-x"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/23876"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.adk1658"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jenvman.2015.07.023"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1752-4598.2011.00175.x"},{"key":"e_1_2_9_29_1","volume-title":"Red List of European Habitats. 2. Terrestrial and Freshwater Habitats","author":"Janssen J. A. 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