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We explored patterns of aquatic macrophyte diversity in four waterbody types, rivers, streams, ponds and ditches, across three Central European regions. By analyzing local (\u03b1), among-site (\u03b2) and regional (\u03b3) diversity, we assessed the roles of these ecosystems as biodiversity hotspots, particularly for red-listed species. Sampling 220 sites across Slovakia and Slovenia, we recorded 113 macrophyte taxa (31% of which were red-listed), with ponds and ditches consistently supporting higher \u03b1 and \u03b3 diversity than running waters. \u03b2 diversity was primarily driven by species turnover, with ponds displaying high heterogeneity linked to environmental variability. Our findings highlight the conservation value of artificial habitats like ditches and ponds, harbouring significant macrophyte diversity, including unique and threatened species. These results underscore the need to prioritize small waterbodies in biodiversity conservation strategies within agricultural landscapes.<\/jats:p>","DOI":"10.3389\/fpls.2025.1536731","type":"journal-article","created":{"date-parts":[[2025,3,6]],"date-time":"2025-03-06T06:53:03Z","timestamp":1741243983000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Comparative diversity of aquatic plants in three Central European regions"],"prefix":"10.3389","volume":"16","author":[{"given":"Marek","family":"Svitok","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Igor","family":"Zelnik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kate\u0159ina","family":"Bub\u00edkov\u00e1","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mateja","family":"Germ","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alenka","family":"Gaber\u0161\u010dik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Judita","family":"Kochjarov\u00e1","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helena","family":"O\u0165ahe\u013eov\u00e1","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Pa\u013eove-Balang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Hrivn\u00e1k","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,3,6]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1572","DOI":"10.1111\/jbi.2013.40.issue-8","article-title":"Spatial extent, regional specificity and metacommunity structuring in lake macrophytes","volume":"40","author":"Alahuhta","year":"2013","journal-title":"J. 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