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Diatom-based paleolimnological studies conducted ~25 years ago on five lakes (i.e., Big Rideau, Upper Rideau, Lower Rideau, Indian and Otter lakes) within the Rideau Canal system (Ontario, Canada) tracked extensive catchment disturbances related to canal construction (starting ca. 1828). Over the past three decades, these lakes have experienced additional environmental stressors including invasive zebra mussels and accelerated climate warming, warranting a paleolimnological re-assessment. We examine diatom compositional changes and visible range spectroscopy-inferred chlorophyll-a (VRS-Chla) trends over the past >200 years from sediment cores collected in 2019-2020 from these same lakes, with the aim of assessing environmental changes registered in these records since the original studies were undertaken ~25-30 years ago. Despite large-scale cultural disturbances, including extensive deforestation and flooding for canal construction, the most ecologically notable diatom changes in all sediment records occurred in the past ~25-30 years, and coincided with increases in VRS-Chla. During this recent period, small cyclotelloid and elongate planktonic diatoms increased in relative abundance, while large-celled Aulacoseira taxa declined. Exceptions to this trend include Upper Rideau Lake, where planktonic diatoms were scarce throughout the core and shifts occurred among benthic taxa, and Big Rideau Lake, which has a large littoral zone, where epiphytic diatoms became prominent in the past decade. These recent diatom changes could not be explained by nutrient enrichment, as measured total phosphorus (TP) concentrations have declined significantly since the 1970s. Increases in small planktonic taxa in some of the lakes also pre-date the ca. 1990 arrival of zebra mussels. We conclude that these recent changes were best explained by regional warming and declining wind speed resulting in new lake physical regimes. Such climate-driven changes are also consistent with the recent development of cyanobacterial blooms in these lakes, despite declining nutrient levels.