In order to examine the factors contributing to the decline in Manila (Asari) clam stocks, the shell morphology and condition factor (CF) of clams were investigated in Mikawa Bay, and their relationship with water quality was clarified. Samples were collected in gravel fishing grounds protected from physical disturbance in Mikawa Bay from 2020 to 2023. Shell length, shell height, shell width, total and soft-body weight were measured, and round index, vertical index, and CF were calculated. The level of CF varied seasonally, with an increase in spring but a decrease in autumn. Multiple regression analysis of the effect of each water quality on CF using water temperature as a covariate revealed a positive effect of chlorophyll-a concentration on CF. Size dependence was observed in changes in CF, with larger individuals having lower CF than smaller individuals, and particularly lower minimum CF in winter for larger individuals, suggesting that this may be related to reduced fisheries resources due to fall–winter depletion.