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AbstractFreshwater ecosystems with recurring harmful algal blooms can also be polluted with plastics. Thus the two environmental problems may interact. To test whether microplastics influence the partitioning of microcystins in freshwater lakes, we examined the sorption of four microcystin congeners to different polymers of commercially available plastics (low‐density polyethylene, polyethylene terephthalate, polyvinyl chloride, and polypropylene). We conducted three experiments: a batch sorption experiment in the laboratory with pristine microplastics of four different polymers, a second batch sorption experiment in the laboratory to compare pristine and naturally weathered microplastics of a single polymer, and a 2‐month sorption experiment in the field with three different polymers experiencing natural weathering in a eutrophic lake. This series of experiments led to a surprising result: microcystins sorbed poorly to all polymers tested under laboratory conditions (<0.01% of the initial amount added), irrespective of weathering, yet in the field experiment, all polymers accumulated microcystins under ambient conditions in a eutrophic lake (range: 0–84.1 ng/g). Furthermore, we found that the sorption capacity for microcystins differed among polymers in the laboratory experiment yet were largely the same in the field. We also found that the affinity for plastic varied among microcystin congeners, namely, more polar congeners demonstrated a greater affinity for plastic than less polar congeners. Our study improves our understanding of the role of polymer and congener type in microplastic–microcystin sorption and provides novel evidence from the field, showing that naturally weathered microplastics in freshwater lakes can accumulate microcystins. Consequently, we caution that microplastics may alter the persistence, transport, and bioavailability of microcystins in freshwaters, which could have implications for human and wildlife health. Environ Toxicol Chem 2022;41:3017–3028. © 2022 SETAC