The characteristics of material transport in a semi-enclosed bay may vary by the influence of the rainfall. Spatial variationsof both suspended substances and chlorophyll-a in the surface layer were investigated using the MODIS sensor imagesand filed data. The data obtained for the event of Oct. 2006 rainfall indicates that the high concentration areas ofboth SS and Chl-a appear around the river estuary in the Ise-Mikawa Bay and spread basically in the directions of riverplumes. The numerical simulation based on the combined MM5 and POM, SWAN, and 3-compartment model reproducesfairly well the surface distributions of both SS and Chl-a, and reveals that both the desorption of phosphorus fromsuspended substances and the release of phosphorus from the bottom sediments contribute to the increase of Chl-a.