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Najas flexilis (Willd.) Rostk. & Schmidt is a submerged annual macrophyte, rare in Europe, which is protected under the EC Habitats Directive. N. flexilis appears to be decreasing in the British Isles, its main stronghold in Europe. We outline the environmental conditions required for N. flexilis growth, comparing between present and recently extinct sites for the plant. Plant traits (leaf area/shoot length; and reproductive number/shoot length) can be used to assess N. flexilis population success, and models are produced that can predict this. Both the comparison between present and extinct sites, and the models, suggest that eutrophication and acidification of lakes are the main threats to N. flexilis. Acidification appears to reduce the ability of N. flexilis to produce seeds (potentially fatal for an annual). On the other hand, eutrophication leads to conditions where N. flexilis, an obligate carbon dioxide utiliser, cannot photosynthesise due to the predominance of bicarbonate rather than dissolved carbon dioxide in lake water. 2b1af7f3a8