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We assessed long-term aquatic biodiversity patterns, with a focus on functional diversity (FD), by using sedimentary Chironomidae and Cladocera assemblages in four mountain lakes in the Austrian Alps. The objectives were to detect whether the invertebrate communities exhibited similar recent diversity trends in climate-sensitive alpine lakes, to observe how lake-specific limnological shifts affect biodiversity, and to test the relationship between taxonomic diversity (TD) and FD for paleolimnological biodiversity evaluations. We applied traditional TD indices to the sedimentary assemblages and used an FD index that was based on functional traits of the encountered taxa of both invertebrate groups. There were some similar long-term trends in invertebrate FD and TD among the lakes; e.g. chironomid diversity increased in two lakes and cladoceran diversity in three lakes toward the twentieth and twenty-first century, but in general the diversity patterns were variable between lakes. Overall, FD had a positive relationship with TD suggesting that functionality can be used in paleolimnological studies as a measure of biodiversity. However, cladoceran taxon richness did not correlate with FD in two lakes suggesting that TD is not always a surrogate for FD. Furthermore, TD of chironomids tended to increase more pronouncedly than FD in the top core sections indicating that increasing TD does not necessarily enhance FD and that different taxonomic entities may play similar functional roles in ecosystems. Accordingly, when evaluating biodiversity and ecological redundancy, functionality of the species pool should be carefully considered and highlighted also in paleolimnological research. [ABSTRACT FROM AUTHOR]