This study developed a fate model of pharmaceuticals and personal care products (PPCPs), including acetaminophen, caffeine, and crotamiton, derived from combined sewer overflow (CSO) in the Tokyo coastal area. The target PPCPs were proposed as promising sewage markers having different persistency during treatment processes and in the environmental water. The PPCP model consists of hydrodynamic calculations and environmental kinetics by biodegradation and photodegradation. We considered inputs from pumping stations, sewage treatment plants, and urban rivers as CSO sources. We measured the PPCPs concentrations, Escherichia coli, and salinity in the collected surface water samples from several locations around Tokyo coastal area for consecutive days after rainfall events in October 2017 (113 mm), June 2018 (81 mm), and July 2018 (67 mm). We found high correspondence between simulation and monitoring results on E. coli and three PPCPs in the coastal locations for all events, suggesting that the model has the potential to quantitatively evaluate CSO-derived contaminants in the Odaiba Seaside Park and nearby locations. Simulation showed that acetaminophen concentration rapidly declined due to its susceptibility to sunlight and biodegradation. Caffeine and E. coli showed different attenuation rates, whereas crotamiton concentration did not change because of its comparable concentration level in CSO.