Understanding the long-term controls on cladoceran size structure has important implications for aquatic ecosystems. Although there has been considerable interest in zooplankton size trends for Canadian Shield lakes, data are not available for zooplankton size structure prior to the period of anthropogenic disturbances. Here, we present pre- and post-impact size data for the common pelagic cladocerans Bosmina and Daphnia for 44 well-studied Shield lakes in south-central Ontario (Canada). We show that Daphnia were larger and that the length of Bosmina body appendages (mucrones and antennules) was longer in pre-industrial times than they are today. The reduction in Bosmina appendage length we observed may suggest a reduction in copepod predation pressure since pre-industrial times. Reduced maximum body size in Daphnia is a predicted response to a warming climate in north temperate lakes; however, we suggest that alternate explanations, specifically acidification and subsequent recovery following emission reductions, should also be explored as the primary drivers of Daphnia size changes in this lake set. Overall, our results highlight the importance of pre-impact data for understanding the long-term controls on cladoceran body size from pre-1850 to present.