Despite extensive records of chemical recovery, relatively little is known about recovery of aquatic biota in Sudbury (Ontario, Canada). Cladocera (Branchiopoda) are key components of lake food webs and understanding spatial patterns in their assemblages may emphasize ecosystem recovery challenges. Paleolimnological techniques complement and provide long-term context to modern monitoring. Cladoceran remains from the surface sediments of 67 lakes across a gradient of smelter impacts were examined to determine which measured limnological factors mostly influenced assemblage composition. Lakes were divided into four categories by acidification histories and location: Acidified (pH <6) Urban, Acidified Non-urban, Acidified Killarney, and Reference (pH >6) lakes. Specific conductance, nutrients, alkalinity, and lake depth significantly structured assemblages. Most assemblages were dominated by generalist taxa. Relative abundances of Alona taxa varied strongly along alkalinity and pH gradients. Lakes with high metal concentrations were generally less diverse and dominated by generalist taxa, although metals often co-occurred with other stressors. Recovery targets could be affected by these chemical factors. These data provide useful information for future environmental inferences from cladocerans in metal smelting regions.