Understanding of characteristics and transport of perfluoroalkyl acids (PFAAs) in heterogeneous estuarine environments is limited. Furthermore, the role of suspended particles (SPS) in different layers remains unclear. This study explores the multiphase distribution process and mechanism of PFAAs controlled by SPS across surface and bottom layers in five small estuaries. Peaks in PFAA concentrations are consistently observed at strongly stratified sites. Concentrations of the PFAAs in both surface and bottom SPS decreased as the degree of mixing increased from strongly stratified levels to well-mixed levels. The water-SPS partitioning of some short-chain PFAAs (PFBS, PFHxA, and PFHpA) is influenced by environmental factors (pH, depth, temperature, and salinity) due to electrostatic interactions, while the sorption of some long-chain PFAAs (PFOA, PFOS, and PFNA) is controlled by SPS and dissolved organic carbon (OC), driven by hydrophobic interactions. Additionally, SPS dominates OC transport in estuarine systems, except in sandy sediment environments. SPS plays a dominant role in PFAA partitioning in both surface and bottom water-SPS systems (p < 0.05), and salinity only significantly affects PFBS in bottom layer (p < 0.01). These findings are critical for understanding the drivers of PFAA partitioning and the roles of SPS in different layers, underscoring the necessity of considering particle-associated PFAA fractions in future coastal environmental management.