One hundred one individuals of Protothaca staminea were live-collected from Argyle Lagoon (sand/mud substrate) and Argyle Creek (gravel/sand substrate), San Juan Island, Washington and examined for trace-producing parasite infestation. Eighty-six percent of individuals contained at least one parasite-induced trace. Trematode-induced pits and blisters were identified on 62% of individual clams. Spionid-induced mudblisters and u-shaped borings were identified on 50% and 29% of individuals, respectively. Trematode and spionid parasites were not selective between the left and right valve when infesting the host. Epifaunal clams from Argyle Creek were significantly smaller than their infaunal counterparts from Argyle Lagoon. This size discrepancy between environments may be related to the reduction of growth rates triggered by environmental stress or parasitism, increased susceptibility to durophagous predators, differences in hydrodynamics, or the comparison of different cohorts. Spionid mudblister-infested clams from Argyle Creek are significantly smaller than noninfested clams from the same environment. This suggests that substrate-induced epifaunality and parasite-induced shell weakening reduced the bivalves’ defenses against durophagous predators. These results suggest that parasites may negatively affect the survival of infested bivalves. The frequent occurrence of trematode and spionid trace-producing parasites in modern bivalve populations suggests that these traces are common in the fossil record, making the systems amenable to study in deep time.