Solving the challenges faced during the measurement of the cross-interface transfer of perfluoroalkyl acids (PFAAs) in lakes is crucial for clarifying environmental behaviours of these chemicals and their efficient governance. This study developed a multimedia fugacity model based on the quantitative water-air-sediment interaction (QWASI) covering abiotic/biotic matrices to investigate the cross-interface transfer and fate of PFAAs in Luoma Lake, a typical PFAA-contaminated shallow lake in eastern China. The accuracy and reliability of the established model were confirmed using Percent bias and Monte Carlo simulation, respectively. Using the QWASI model, the multimedia transfer of the PFAAs and their accumulation and persistence in different sub-compartments were described and measured, and the differences among individual PFAAs were explored. The simulation results showed that the sedimentation and resuspension of PFAAs were the most intense cross-interfacial transfers, and the sediments served as a chemical sink in the long term. A significant negative correlation of NC-F (the number of CF bonds) with the relative outflow flux (TW·out-ct) but a positive correlation with the relative net transfer across the interface between water and aquatic plants (Tp-ct) was detected, indicating that the PFAA migration capacity decreased but the bioaccumulation potential increased with the CF bond number. The persistence in water (Pw) of individual PFAAs ranged from 19.65d (PFOA) to 32.22d (PFOS), with an average of 26.15d; their persistence in sediment (Ps) ranged from 432d (PFBA) to 3216d (PFOS), with an average of 1524d, increasing linearly with an increase in NC-F. The water advection flows into and out of the lake (QW·in and QW·out), the PFAA concentration of water inflow (CW·in), and bioconcentration factor of aquatic plants (BCFp) were the primary parameters sensitive to PFAAs in all sub-compartments, which are essential indexes for exploring promising remediation pathways for lacustrine PFAA contamination based on the fugacity model simulation.