<p>Lakes in Algonquin Provincial Park (Ontario, Canada) face several potential environmental stressors (e.g., impacts from cottages, campgrounds, roads and road-salt applications, climate warming) despite their relatively remote location and the protected status of the park. While previous studies have shown minimal impacts of shoreline development on water chemistry, algae and chironomid assemblages, the long-term effects on zooplankton remain uncertain. Here, we examine differences between modern (surface) and pre-industrial (prior to European settlement) sedimentary cladoceran assemblages from 54 Algonquin Park lakes (22 with cottage-leases and 32 reference lakes). The modern distributions of cladoceran species were best explained by chloride concentrations, Secchi depth, pH, specific conductance, and elevation. Cottage-lease and reference lakes showed similar directions of compositional change since the pre-industrial era, although with a higher magnitude of change in remote reference lakes. The most notable taxonomic shift across lakes was a decline in the relative importance of littoral taxa and a concurrent increase in small, efficient grazers (i.e., bosminids) in the modern assemblages. This shift towards smaller, pelagic-dominated communities is likely driven by regional stressors such as climate change, suggesting potential alterations in primary production, nutrient cycling, and overall lake-ecosystem dynamics within Algonquin Park lakes. Local stressors, such as cottages and road salt from winter-road maintenance, had minimal effects on cladoceran assemblages over time. The use of paleolimnological methods to extend the monitoring record provided valuable historical context that enhances our understanding of zooplankton communities in Algonquin Park and emphasizes the need for continued monitoring of Boreal Shield lakes in the face of environmental change.</p>