The eastern oyster, Crassostrea virginica (Gmelin, 1791) has been in decline along the eastern seaboard, and especially in Chesapeake Bay, for decades because of over-harvesting, disease and declines in water quality and suitable habitat. Eutrophication has also been increasing over the past half century, leading to increases in hypoxia and harmful algal blooms (HABs). The effects of two common Chesapeake Bay HAB dinoflagellates, Karlodinium veneficum, and Prorocetnrum minimum were tested on larvae of C. virginica and the Asian oyster being considered for introduction to Chesapeake Bay, C. ariakensis. When embryos from freshly spawned C. virginica and C. ariakensis were exposed immediately to K. veneficum at 104 cells mL−1, virtually all of the developed larvae were deformed within 48 h in one experimental trial, but not in a second trial in which algae were at a different growth stage. No deformities, and mortalities of <45%, were observed in controls to which a standard diet of the haptophyte Isochrysis was added. When 2-wk-old larvae of both species were exposed to the same HAB species, the effect was a severe reduction in motility with K. veneficum, but with P. minimum only C. ariakensis was affected and not C. virginica. Comparisons were made of the frequency of these HABs in Chesapeake Bay from long-term data analysis and the temporal period of spawning. Whereas both blooms are more common during the summer months, the frequency of blooms of K. veneficum and the period of oyster spawning, June to September, coincide more strongly. To compare spatial similarity, results of a larval transport model were compared with observational data for K. veneficum. This comparison demonstrated a significant overlap in July, particularly in the northern reaches of the Bay. These eutrophication-related HABs thus have the potential to reduce survival of early life history stages of oysters and hence to reduce oyster recruitment. Any reduction in recruitment either spatially or temporally, combined with an overall reduction in sheer numbers of larvae that survive, will make restoration or establishment of significant, self-sustaining populations of natural or introduced oyster species much more difficult.