Aqueous calcium (Ca) concentrations are currently decreasing in many softwater lakes on the Boreal Shield. As the onset of these declines often pre-date direct monitoring programs, indirect techniques are required to examine the impacts of reduced Ca availability on aquatic communities with relatively high Ca demands such as the Cladocera (Class: Branchiopoda). Among the Cladocera, the family Daphniidae has been identified as a taxonomic group potentially useful for inferring past Ca concentrations due to their high Ca demands and preservation in lake sediments. Here, we use a "top/bottom" paleolimnological analysis to compare present-day cladoceran communities preserved in the surface sediments of 36 softwater lakes in south-central Ontario, Canada, which are potentially vulnerable to Ca decline (i. e. small headwater systems with present-day lakewater [Ca] < 3 mg L -1), with the communities present in lake sediments deposited prior to the onset of regional acid deposition. To distinguish the potential impacts of lake acidification from those of Ca availability (as Ca and pH trends are strongly correlated in this region), the study lakes were chosen to be evenly distributed about a present-day lakewater pH of 6 and Ca concentration of 1. 5 mg L -1 (threshold values). Despite the importance of pH as an explanatory variable for the present-day assemblages, a comparison of the sedimentary remains from the two time periods indicate there have been large declines since pre-industrial times in the relative abundances of Ca-rich Daphnia spp. (particularly of the Daphnia longispina species complex), regardless of present-day pH, accompanied by increases in the Ca-poor species Holopedium glacialis. These observations suggest that recent declines in Ca concentration may have already fallen below baseline conditions, with marked implications for ecosystem function due to the differential responses among cladoceran taxa. © 2012 Springer Science+Business Media B.V.