Fossil cladoceran remains preserved in surface sediment samples from 44 oligotrophic lakes in south-central Ontario were examined to evaluate the relationships between species assemblages and measured environmental variables. Differences in cladoceran assemblages were related to physical and chemical variables using multivariate techniques. Redundancy Analysis (RDA) identified five environmental variables as significantly influencing assemblage composition: sulphate (SO42- ), calcium (Ca2+), pH, maximum lake depth (Zmax) and dissolved organic carbon (DOC). There was a distinct separation of lakes and taxa along the ion gradient based on SO4, Ca and pH. Additionally, cladoceran communities in coloured, shallow lakes had relatively higher abundances of littoral chydorid species and the pelagic taxa Holopedium spp., and the Daphnia pulex complex. Deep, clear lakes had relatively higher abundances of other pelagic taxa. Predation by fish (measured as presence-absence) and Chaoborus (measured as density) were less significant than some of the physico-chemical variables in influencing cladoceran assemblage structure. However, this could be due to the limited resolution of the predation data that was available at the time of this study. The distribution of cladocerans in the surface sediment, and their relation to these important environmental variables, suggests that there is considerable potential for the use of sedimentary cladoceran remains as environmental indicators in south-central Ontario lakes. © 2007 Springer Science+Business Media B.V.