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Like many lakes worldwide, French sub-alpine lakes (lakes Annecy, Bourget and Geneva) have suffered from eutrophication in the mid-20th century. Although restoration measures have been undertaken and resulted in significant reductions in nutrient inputs and concentrations over the last 30 years in all three lakes, the limnological monitoring does not extend back far enough to establish the reference conditions, as defined by the European Water Framework Directive. The over-arching aim of this work was to reconstruct, using a paleolimnological approach, the pre-eutrophication levels and subsequent temporal changes in the lakes trophic status over the last century. The objectives were three-fold: i) to test whether fossil diatoms archived in deep sediment cores adequately reflect past changes in the planktonic diatom communities for these deep sub-alpine lakes based on data from lake Geneva; ii) to investigate changes in the diatom communities over the last 150 years in the three lakes; and iii) to infer the past total phosphorus (TP) concentrations of the lakes from a diatom based transfer function. Annual paleolimnological and limnological diatom countings for lake Geneva were strongly correlated over the last 30 years. Most notable differences essentially resulted from both taphonomic and depositional biases, as evidenced by the underestimation of thin skeleton species such as Asterionella formosa and Diatoma tenuis in the paleolimnological dataset and the presence of many benthic taxa. The fossil diatom records revealed shifts in the communities in the three lakes over time, most of which were changes typically associated with nutrient enrichment. Indeed, in all three lakes, the proportion of Cyclotella spp. was very high before the 1950s, but these species were then replaced by more eutrophic taxa, such as Stephanodiscus spp, by the mid-20th century. From the 1980s, some but not all diatom species typical of re-oligotrophicated conditions (i.e. Cyclotella sp.) re-appeared in all three lakes. Yet, not all changes that occurred in the diatom communities since then may be attributed to decreasing TP. TP concentrations inferred from weighted averaging with classical deshrinking in lake Annecy and lake Geneva and weighted averaging with inverse deshrinking in Lake Bourget were very close to the monitored values. Comparisons of diatom-inferred TP concentrations to other paleo-proxies for trophic status revealed though that the transfer functions were rather insensitive to changes occurring below 10 µg L–1, which limits the study ability to set accurate TP reference conditions below this threshold. However, current diatom community compositions arestill rather different from the pre-eutrophication ones, suggesting that reference conditions are still not achieved.