The partitioning behavior of per- and polyfluoroalkyl compounds (PFCs) between pore water and sediment in two sediment cores collected from Tokyo Bay, Japan, was investigated. In addition, the fluxes and temporal trends in one dated sediment core were studied. Short-chain perfluoroalkyl carboxylic acids (PFCAs) (C ≤ 7) were found exclusively in pore water, while long-chain PFCAs (C ≥ 11) were found only in sediment. The perfluoroalkyl sulfonates (PFSAs), n-ethylperfluoro-1-octanesulfonamidoacetic acid (N-EtFOSAA), and perfluorooctane sulfonamide (PFOSA) seemed to bind more strongly to sediment than PFCAs. The enrichment of PFCs on sediment increased with increasing organic matter and decreasing pH. The perfluorocarbon chain length and functional group were identified as the dominating parameters that had an influence on the partitioning behavior of the PFCs in sediment. The maximum ΣPFC contamination in sediment was observed in 2001-2002 to be a flux of 197 pg cm ^-2 yr ^-1. Statistically significant increased concentrations in Tokyo Bay were found for perfluorooctanesulfonate (PFOS) (1956-2008), perfluorononanoic acid (PFNA) (1990-2008), and perfluoroundecanoic acid (PFUnDA) (1990-2008). Concentrations of PFOSA and N-EtFOSAA increased between 1985 and 2001, but after 2001, the concentration decreased significantly, which corresponded with the phase out of perfluorooctyl sulfonyl fluoride-based compounds by the 3M Company in 2000.