A high activity of decomposition consumes much oxygen especially in the sediment, and the overlying water. Low oxygen gives uncomfortable condition for biota to live in, which will increase the mortality rate. Death biota decomposition will again use oxygen for the process and consequently will generate the septic and eutrophic condition in the overlying water. In this study, an integrated 3-D model, which represents the above phenomenon was developed considering some interactions between the physical, chemical and biological processes. The coastal waters off the Abukuma River Mouth were selected for the research location as it has the records of high flood. The Princeton Ocean Model (Blumberg et.al., 1987) was used as the basic computation of the hydrodynamic simulation. It employs the sigma coordinate system for the vertical gridding. The ecological concept of the nutrient model was adopted from previous research (Yanagi, 1999). The concept was modified to clarify the settling and leaching processes, which were importantly involved in supporting the phenomenon mentioned above. Oxygen consumption by decomposition of organic matter contained in the sediment is also an important mechanism to stimulate the leaching process. Results show that the particulate forms of the nutrients were dominating the bottom layer, which cause the decreasing of oxygen concentration. A 15-25% of the settled nitrogen and 5-11% settled phosphorus were leached into the water column within 15 days in the first stage after the flood event.