A two-month survey was conducted in order to evaluate the effects of rainfall on the fate of microorganisms in seawater in the Tokyo Bay, Japan. The seawater sample (1,000 mL) was applied to a method to concentrate virus, followed by a quantification of human adenoviruses using the real-time PCR. Total coliforms and E. coli, which were determined by the colony forming method, were detected in all 47 seawater samples, while human adenoviruses were detected in 38 (81%) of the samples. The concentration of tested microorganisms showed 1-2 log units increase after rainfall events, followed by the gradual decrease to the level before the rainfall within a few days.