A three-dimensional ecological model (EMT-3D) was applied to Nonylphenol in Tokyo Bay. EMT-3D was calibrated with data obtained in the study area. The simulated results of dissolved Nonylphenol were in good agreement with the observed values, with a correlation coefficient(R) of 0.7707 and a coefficient of determination (R2) of 0.5940. The results of sensitivity analysis showed that biodegradation rate and bioconcentration factor are most important factors for dissolved Nonylphenol and Nonylphenol in phytoplankton, respectively. In the case of Nonylphenol in particulate organic carbon, biodegradation rate and partition coefficient were important factors. Therefore, the parameters must be carefully considered in the modeling. The mass balance results showed that standing stocks of Nonylphenol in water, in particulate organic carbon and in phytoplankton are 8.60×105 g, 2.19×102 g and 3.78×100 g, respectively. With respect to the flux of dissolved Nonylphenol, biodegradation in the water column, effluent to the open sea and partition to particulate organic carbon were 6.02×103 g/day, 6.02×102 g/day and 1.02×101 g/ day, respectively.