Lakewater calcium (Ca) decline affects softwater lakes across the Canadian Shield. Ca decline is one consequence of acid deposition, and has impeded biological recovery in formerly acidified lakes. Reduced Ca availability may advantage taxa better adapted to low Ca waters. Crosson Lake in south-central Ontario (Canada) has an extensive monitoring record and has experienced strong Ca decline since the late 1970s, recently falling below 1.5 mg L−1, a threshold value for some large Daphnia O.F. Müller, 1785 taxa. Paleolimnological analysis of the sedimentary cladoceran assemblages revealed that changes associated with the Ca decline began in the early 1970s. Relative abundances of the jelly-clad Holopedium glacialis Rowe, 2007 and the Daphnia pulex complex increased while Ca-sensitive members of the Daphnia longispina complex decreased. Zooplankton net hauls (1981–2010) corroborate the paleolimnological analysis, revealing that increases in the D. pulex complex were due to Daphnia catawba Coker, 1926 (a taxon tolerant of low Ca). Lakewater Ca, dissolved organic carbon and total phosphorus explain a significant amount of variation within the cladoceran community; however, the relationship between Ca concentration and the daphniid community was most apparent. The Crosson Lake paleolimnological and direct monitoring data may describe ecological changes that are also occurring in many other softwater lakes across the Canadian Shield and elsewhere.