The spatial distribution, partitioning, and time trends of perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) were investigated in the water column and bottom sediment of Tokyo Bay, Japan, during 2004-2006. A total of 480 water and 60 sediment samples obtained by regular 20-station samplings ascertained the three-dimensional distributions of these compounds and changes in the seawater structure in the whole bay. The median of volume-based average water-borne concentrations of PFOS and PFOA was 3.7 and 12 ng/L, respectively. The median concentrations in sediment were 0.61 (PFOS) and 0.20 (PFOA) ng/g-dry. Vertical mixing of the water column probably affected the vertical distribution of these compounds. The negative correlations between PFOS and PFOA concentrations and water salinity and the horizontal distributions of their concentrations suggested that freshwater inputs into the bay were the source of these compounds. A mixing model estimated the average PFOS concentration in the freshwater inputs to be 29 ng/L. The common logarithm of the partition coefficients between the dissolved and suspended-particle-sorbed phases varied among samples, with the average of 4.2 (PFOS) and 3.5 (PFOA). Our analyses indicated no apparent time trends in the concentrations of these compounds during 2004-2006 in either the freshwater input or the bay.