Field experiments were conducted at brackish-water sites (Lake Hinuma, Hinuma River, and Naka River) to investigate oxidative stress responses of a brackish-water clam, Corbicula japonica, to sediment composition and water quality. To ascertain the influence of the sediment composition, clams were subjected to three test sediments with different contents of clay/silt and organic matter from the same site. Sediment with ~33% of clay/silt content and ~10% of ignition loss exhibited decreased oxygen radical absorbance capacity (ORAC) within two weeks (p < 0.05). However, sediment with less than ~20% of clay/silt content and/or ~7% of ignition loss had no influence on ORAC (p > 0.05). To ascertain the influence of the water quality, clams were placed in baskets without sediment at four brackish-water sites. Significant differences in ORAC were observed in response to salinity and chlorophyll a (Chl a) (p < 0.05). Multiple regression analysis indicated that the levels of salinity and water temperature as well as variations in Chl a, dissolved oxygen, and turbidity for 1 d prior to the sampling date affected ORAC. We concluded that natural influencing factors need to be considered in ORAC assays for C. japonica, when anthropogenic impacts are assessed.