Variability during the tidal cycle of the biochemical composition and phytopigment content of suspended particulate matter (SPM) in the bottom water were investigated in the Banzu Intertidal Sand Flat, Tokyo Bay, Japan in relation to the feeding environment and diet of Manila clam, Ruditapes phillippinarum. Biochemical composition of SPM in the bottom water showed large tidal variations, such as the ratio of phytopigment content to SPM (Phy/SPM ratio) and particulate organic carbon (Phy/POC ratio) were both higher during high tide periods compared to low tide periods. Therefore, it was considered that high tide periods form a suitable food environment for the clam. The results also indicated that phytoplankton which is transported from offshore at high tide is an important food source for the clam. In addition, results of stable isotope analyses indicated that R. phillippinarum selectively intakes SPM during high tide periods and assimilate selected components among the SPM.