Summary Highly calcareous (marl) lakes are infrequent but important freshwater ecosystems, protected under the EU Habitats and Species Directive. Chara lakes have been considered resistant to eutrophication owing to the self‐stabilising properties of charophyte meadows. However, the opposite is suggested by the large‐scale biodiversity declines in marl lake taxa in Europe, and evidence of charophyte sensitivity to eutrophication. We combined contemporary, palaeolimnological and archival methods to investigate the eutrophication of Hawes Water, a shallow marl lake in north‐west England (U.K.). Changes in aquatic macrophyte and invertebrate communities were reconstructed through the analysis of historical macrophyte surveys and sedimentary plant and animal macrofossils in two dated sediment cores from the littoral and deep zones of the lake. In addition, chlorophyll and carotenoid pigments were analysed to track changes in primary production from benthic and pelagic areas. Substantial changes in macrophyte communities were detected over centennial timescales, suggesting high ecosystem sensitivity considering the presently moderate phosphorus concentrations in Hawes Water (mean annual total phosphorus 20 μg L−1). Two apparent periods of threshold‐like change were identified from the sediment record: (i) changes in cyanobacteria (aphanizophyll + myxoxanthophyll to canthaxanthin + zeaxanthin) and potentially in nutrient stoichiometry, reductions in the maximum macrophyte colonisation depth and water clarity, reduced charophyte and Potamogeton diversity, and increases in Nymphaeaceae; and (ii) severe reductions in light availability inferred from subdecadal doubling in phytoplankton abundance, substantial increases in Daphnia abundance and the extinction of charophytes from higher water depths. Further, change in both the littoral and deeper water has confined key marl lake taxa to smaller niches. In the littoral, increasing siltation and reed and Nymphaeaceae densities caused extinction of Littorella uniflora in the early 1900s and have reduced the evenness of Characeae with suspected imminent extinction of two highly localised Chara spp. In the deeper water, upslope creep of maximum colonisation depth has reduced habitat for intermediate‐depth marl lake taxa leading to the loss of four Potamogeton and one Chara species, and replacement of these taxa by Nuphar lutea. The large changes in macrophyte community composition and increased incidences of turbid water have reduced the distinctive and valued marl lake features of Hawes Water, indicating that marl lakes can, as a habitat type, be highly sensitive to eutrophication. The persistence of abundant generalist macrophyte species at considerable water depth may be a feature of high‐alkalinity lakes in clearwater, macrophyte‐dominated states, but is a distinct eutrophication response in marl lakes rather than an indication of resistance to eutrophication.
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