The environmental behavior of per- and polyfluoroalkyl substances (PFAS) in the estuarine and coastal zone remains poorly understood, especially under extreme hydrological conditions. Here, we investigate the seasonal distribution, source apportionment, ecological risk, and transport flux of PFAS along the Pearl River Estuary (PRE) - northern South China Sea (NSCS) continuum during the exceptionally wet year of 2024, which included 13 officially documented flood events. Two field campaigns were conducted following a major spring flood and during the subsequent post-flood period, with 32 targeted legacy and emerging PFAS analyzed in water and suspended particulate matter. Results revealed that short-chain perfluorocarboxylic acids (PFCAs) were the dominant compounds in both seasons. Flooding increased overall PFAS concentrations and compositional diversity across phases. Source apportionment identified six main sources, with industrial emissions dominating the flood period and wastewater treatment plant (WWTP) sources becoming more prominent in the post-flood period. Flood events likely accelerate the transport of industry-related PFAS, including legacy perfluorooctanoate (PFOA) and perfluorooctane sulfonate (PFOS), emerging 6:2 chlorinated polyfluoroalkyl ether sulfonate (6:2 Cl-PFESA), and hexafluoropropylene oxide dimer acid (HFPO-DA), away from source regions and amplify their ecological risks. The PFAS mass loading during the flood period was 18 times higher than that in the post-flood period. These findings highlight the critical role of flood events in modulating the transport and ecological risks of both legacy and emerging PFAS, offering key insights for risk assessment and source management in subtropical estuaries under climate change.