Despite the increasing concern regarding the ecological risks posed by per- and polyfluoroalkyl substances (PFAS), a lack of comprehensive understanding of their actual ecotoxicity remains. Through a meticulous examination of 91 peer-reviewed studies investigating effects at a population level and constructing probabilistic species sensitivity distributions (PSSDs), we present a state-of-the-science hazard assessment of PFAS in freshwater species. Using data subsets containing suboptimal data led to an overestimation of the predicted no-effect concentrations (PNECs) of PFAS. We report PNECs of perfluoroalkyl carboxylic acids (PFCAs) and perfluoroalkyl sulfonates (PFSAs) in freshwater to be 4.8–2000 μg/L and 0.4–8.9 μg/L, respectively, derived from high-quality data. Statistical analyses revealed that both functional groups and carbon chain length significantly influenced (p < 0.05) the variations in toxicity observed among different PFAS. This study underscores the importance of obtaining high-quality PFAS ecotoxicity data to comprehend associated hazards. The PNECs of PFAS derived in this study are higher compared to those of micro/nanoplastics and persistent organic pollutants. Our research offers valuable insights into prioritizing the regulation of more toxic PFAS.