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Lake ecosystems are increasingly impacted by eutrophication and climate change. Whole-lake experiments have provided ecosystem-scale insights into the effects of freshwater stressors, yet these are constrained to the duration of monitoring programmes. Here, we leveraged multidecadal monitoring records and century-scale paleogenetic reconstructions for experimentally fertilised and unmanipulated lakes in the IISD Experimental Lakes Area of northwestern Ontario, Canada, to evaluate the responses of algal communities to nutrient and air temperature variation. We first validated the paleogenetic analysis of sediment DNA by demonstrating the synchrony of algal community changes with monitoring records. Algal communities underwent significant compositional shifts across experimental nutrient loading regimes and climate periods, with baseline assemblages informed by paleogenetics. Nonlinear regression modelling of algal community change in monitoring and paleogenetic time series showed the expected response that nutrients were strong drivers in fertilised lakes. Paleogenetic records reflected the century-scale impacts of climate warming and its combined effects with eutrophication, previously underestimated by monitoring. The synergy between eutrophication and warming points to eutrophic priming of the food web to respond to rising temperatures. Overall, the paleogenetic integration of algal diversity across habitats and seasons enables the detection of slow-acting climate change on lake ecosystems increasingly altered by nutrient pollution.