Water diversion is increasingly utilized for water supply, flood control, irrigation, and water quality improvement in many water bodies globally. Our findings indicate that micropollutants such as perfluoroalkyl acids (PFAAs) can be transported via dual-source water diversion projects during water diversion and flood discharge, which may negatively impact both receiving water bodies. However, the sources, spatiotemporal variations, and fluxes of PFAAs under water diversion projects remain unclear. Here we report patterns of 18 PFAA compounds in the surface water at 14 sites of a dual-source water diversion project (Wangyu River) connecting the Yangtze River and Taihu Lake in China. We found multiple contamination hotspots with PFHxA and PFOA dominantly originating from industrial and domestic sources during water diversion from the Yangtze River to Taihu Lake. During the severe flooding in summer 2020, PFAA concentrations ranged from 82.0 to 114.0 ng L⁻¹, while the concentrations and relative contributions of individual perfluoroalkane sulfonic acids (PFSAs) increased along the mainstream due to the tributaries’ contribution and high contamination level in the lake. Based on the spatiotemporal patterns of PFAA pollution, the flux of total PFAAs including both dissolved-phase and SS-phase into Taihu Lake was estimated as 26.6 kg in January 2020 as a reference value for water diversion. To our knowledge, this is the first report to describe the sources, occurrences, and transport of PFAAs in a dual-source water diversion project during water diversion and flooding. The results provide a novel perspective regarding the ecological safety of dual-source water diversion projects.