Increased surface-water temperatures are predicted to drive dramatic changes to planktonic communities, with consequences for freshwater biodiversity and ecosystem functioning. A large number of short-term mesocosm studies reported temperature-driven changes in plankton, but comparatively few studies captured long-term changes. We used water eDNA metabarcoding to examine communities of phytoplankton, zooplankton, and planktonic protists and fungi in 10 natural lakes in central Poland, five of which have received hot-water discharge from power stations for the past 60 years. eDNA samples were collected in the winter, spring, summer, and autumn of 2020. Heated lakes were 2˚C warmer (annual mean) and had higher concentrations of total phosphorus (TP) and soluble reactive phosphorus (SRP). Based on relative abundance of amplicon sequence variants (ASVs), green algae (Chlorophyta) abundance was up to 15% higher in heated lakes, while that of golden algae (Chrysophyceae) was up to 7% higher in control lakes. ASV richness varied seasonally but was on average two-fold greater in heated lakes, and was consistently higher for phytoplankton, protists, and fungi. Considering the total community, heated and control lakes had distinct plankton assemblages, and there was less temporal variation in heated lakes. Warming was positively related to plankton relative abundance and richness. Our results suggest that increased temperature in heated lakes caused considerable shifts in plankton composition, where groups with preference for cooler temperatures were replaced by those with a preference for warmer conditions.