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Blooms of the dinoflagellate, Cochlodinium(a.k.a.Margalefidinium) polykrikoides, have had deleterious effects on marine life across the Northern Hemisphere and, since the early 1990s, have become more frequent and widespread. While the toxic effects of C. polykrikoides have been well-described for finfish, the effects on bivalve molluscs are poorly understood, particularly in ecosystem and aquaculture settings. The purpose of this study was to characterize the comparative effects of C. polykrikoides blooms on North Atlantic bivalves and to identify the environmental factors that influence its toxic effects. The growth and survival of two age-classes (first- and second-year) of the northern quahog (Mercenaria mercenaria), the bay scallop (Argopecten irradians), and the eastern oyster (Crassostrea virginica) were quantified in surface deployments and at depth during annual bloom events in multiple locations across eastern Long Island (NY, USA), capturing a natural gradient in C. polykrikoides. In two consecutive years, scallops deployed within surface locations experienced significant mortality (75-100%) during short-term (1-2weeks) but intense (>1.5x10(4) cells mL(-1)) C. polykrikoides blooms. Conversely, scallops deployed at depth and clams and oysters deployed at either the surface or at depth were more resistant to blooms. First-year oysters and scallops that survived blooms displayed significant reductions in growth rates, while clams and older scallops and oysters did not. Results suggest that blooms of C. polykrikoides pose significant age- and species-specific threats to native and cultured bivalve shellfish and that shellfish deployed in surface waters are at greater risk during blooms than those deployed at depth.