Perfluorooctane sulfonate (PFOS) was quantified in seawater and sediment samples collected from Tokyo Bay, Japan, ranging from 2.0 to 7.3ng/L for surface seawater, 2.2 to 5.7ng/L for intermediate seawater, 1.5 to 5.7ng/L for bottom seawater, and 0.3 to 0.9ng/g dry wt. for sediment. In addition, a 3-D chemical fate prediction model (National Institute of Advanced Industrial Science and Technology - Risk Assessment Model: AIST-RAM) has been applied to determine the accuracy of estimating PFOS in Tokyo Bay. A decreasing trend of PFOS from the northwestern part (i.e., the closed-off section of Tokyo Bay) to the mouth of the bay was observed, and the trend obtained from the actual surveys in this study was accurately represented by simulation with appropriate input parameters for AIST-RAM. From the comparison of observed concentrations with estimated concentrations, AIST-RAM showed a high degree of accuracy in estimating the concentrations of PFOS in seawater, whereas the estimations of PFOS concentrations in sediment had a relatively larger margin of error than those in seawater. However, our results indicate that AIST-RAM allows estimation of PFOS concentrations in seawater and sediment in Tokyo Bay with satisfactory accuracy.