The 1986 Chornobyl Nuclear Power Plant accident caused radioactive contamination of water bodies within the Pripyat River floodplain, resulting in the accumulation of radionuclides by macrophytes, which are fundamental species in water ecosystems. Yellow water lily Nuphar lutea (L.) Smith., a macrophyte playing a significant role in the formation of vegetation cover in aquatic ecosystems, is commonly considered as a bioindicator of water pollution. In this study, we investigate the potential of N. lutea as an indicator of radionuclide contamination in water bodies, particularly through changes in its reproductive structures, such as pollen viability, morphology of pollen grains, seeds, and fruits. Our findings reveal that pollen viability remains stable at total absorbed dose rates below 14.4 μGy/h, with only 1–4% of sterile grains. However, beyond this threshold the percentage of sterile grains increases nearly fivefold, pointing to high internal plant exposure to 90Sr. A similar trend was observed in the allometry and size of pollen grains, where small and flattened grains are formed in the reservoir with the highest external radiation dose rate (≥14.4 μGy/h). On the other hand, while morphometric parameters of fruits are influenced by radiation, their variation appears to be the result of a combination of physicochemical factors and the trophic status of a water body. Our research highlights the adverse impact of long-term radiation exposure on the male reproductive system of N. lutea and shows the potential of using the pollen grains sterility as an indicators of heavily radionuclide-contaminated water bodies. Additionally, we observed gradual changes in a pollen allometric length-to-width coefficient as the radiation dose level increases.