Understanding the sediment release and plant bioaccumulation of per- and polyfluoroalkyl substances (PFASs) under submerge-emerge alternation (SE) is crucial to predicting their transport and fate in the riparian zones. In the present study, a simulational device was firstly constructed to explore the effects of SE on the transport of PFASs in riparian sediment-plant systems and the underlying mechanisms. The submerge (CS) and emerge (CE) situations were compared. The results showed that SE significantly enhanced the transport and bioaccumulation of PFASs in sediments. Compared with the initial concentration, PFASs in sediments decreased by 81.84 %, 50.48 %, and 21.68 % in the SE, CS, and CE groups, respectively. The bioaccumulation of PFASs in plant roots in the SE group was 1.26 and 4.16 times higher than that in the CS and CE groups, respectively, and the bioaccumulation of PFASs in leaves in the SE group was 2.05 and 1.71 times higher than that in the other two groups. Dissolved organic matter (DOM) composition and molecular properties under SE were recognized as the dominant factors regulating the release of PFASs from sediments. Root morphology and low-molecular-weight organic acids (LMWOAs) in root exudates were closely associated with the bioaccumulation of PFASs in plants. Among the substitutes, hexafluoropropylene oxide trimer acid (HFPO-TA) demonstrated greater hydrophobicity, hexafluoropropylene oxide dimer acid (Gen-X) had greater mobility, and 6:2 fluorotelomer sulfonate (6:2 FTS) accumulated more in plants. This study has expanded the understanding of the geochemical cycling of PFASs in riparian sediment-plant systems under submerge-emerge alternation.