The substratum of Tateno fishing ground of the short-necked clam, Ruditapes philippinarum, Hakodate Bay, Hokkaido, Japan is characterized by higher percentage of cobbles and pebbles compared with other regions. The shell growth rate of the adult clam in this region is slower than that of other fishing grounds. In this study, the relationship between the uncommon sediment composition and the depressed growth was examined from the viewpoint of feeding efficiency of the clam. Infaunal bivalves usually stay with vertically directed siphons up to the sediment surface in suspension feeding, but in this region the clams often burrow into the sediment at an angle when they cannot burrow into sediment deeper. In the laboratory experiment the clam could not turn its valves but often extended its siphons up under condition of restricted burrowing. Filtration rate of the clam, which was estimated by changes in the chlorophyll-α concentration of the diatom Chaetoceros gracilis as an algal diet, was the highest in the vertical position of siphons among all setup directions. Therefore, the short-necked clam cannot keep their body the most effective direction by restricted burrowing due to many cobbles and pebbles, which may cause food intake reduction. It seems one of the reasons for depressed growth of the short-necked clam in this region.