We examined fossil Cladocera (Crustacea) communities and their functional assemblages in a~60-year sediment record from Lake Maggiore, northern Italy. Our main objective was to document the response of aquatic community functioning to environmental stress during eutrophication (1960-1985) and recovery (post-1985), and to identify environmental controls on cladoceran functionality. Of the functional groups, large filter feeders and oval epibenthos thrived prior to eutrophication (reference conditions pre-1960) and globular epibenthos and small filter feeders increased during eutrophication and as the lake recovered. Multivariate analyses suggested that bottom-up controls (i.e., total phosphorus) were important for shaping functional assemblages but taxonomic community changes were likely related to top-down control by predators, particularly the predaceous cladoceran Bythotrephes longimanus. Functional diversity (FD) was higher and Daphnia ephippia length (DEL) larger during the reference and early eutrophication periods and decreased during eutrophication and recovery. Both FD (high) and DEL (large) were distinct during reference period, but were similar (FD low, DEL small) between the eutrophication and recovery periods. The functional attributes and the assemblages did not recover post-eutrophication, suggesting that the system exhibited a clear shift to low FD and dominance of small filterers. Cladoceran functionality appears to be related to fundamental ecosystem functions, such as productivity, and may thus provide insights for long-term changes in ecological resilience.