Shellfish aquaculture is an expanding industry in coastal British Columbia, Canada, and occurs in important wintering areas for surf scoters (Melanitta perspicillata) and white-winged scoters (M. fusca). We quantified habitat use by scoters in relation to natural environmental attributes and habitat modifications associated with shellfish aquaculture. We found that, despite the extensive clam and oyster farming in our study area, densities of wintering surf scoters and white-winged scoters were related primarily to natural environmental attributes, particularly intertidal area, clam density, and sediment type; shellfish aquaculture variables were generally poor predictors of bird densities. We conclude that current levels and forms of shellfish aquaculture in our study site were not an important determinant of scoter distribution and abundance, suggesting that winter scoter populations and the shellfish aquaculture industry may be mutually sustainable. We caution that intensification or further industrialization of shellfish aquaculture in British Columbia could eventually lead to detrimental effects if some threshold level of habitat modification is exceeded.