Several studies have shown that suspended microphytobenthos are important food source for clams. We hypothesized that the degree of the resuspension flux of microphytobenthos must play important roles in growth rate and size of clams, and investigated it through observations over 2 years at two stations (lake mouth and inner lake) in a subarctic lagoon (Akkeshi Lake) and numerical modeling. Large clams (length > 40 mm) were seldom observed at the inner lake. The growth rates of 40 mm clams incubated in cages at two stations were also much greater at the outer station. Resuspension of microphytobenthos occurred frequently at the lake mouth due to the high current speed. These results indicate that differences in food availability due to the current and resuspension were the primary cause of the growth differences between the two stations. The relationships between environmental factors, food availability, and clam growth were also modeled with long-term simulation. Once more, the different clam growth in the two lake zones was ascribed to the resuspension flux of microphytobenthos. The shell growth limited at approximately 40 mm at the inner lake was due to strong growth limitation. Both filed measurements and modeling demonstrated that microphytobenthos resuspension can be a remarkable food source for clams.