Ocean acidification, characterized by elevated partial pressure of CO₂ (pCO₂), generally has negative effects on early life stages of invertebrates. We tested the idea that fertilization is a critical CO₂ exposure stage for the bay scallopArgopecten irradians by determining the effects on bay scallops of exposure to high CO₂ (pCO₂ ~2600 ppm, pH ~7.30) from fertilization to 7 d old. To assess the possibility of persistent effects of exposure during fertilization, further treatments included switches from high CO₂ to ambient CO₂ (pCO₂ ~480 ppm, pH ~7.96) and from ambient CO₂ to high CO₂ at 2 h post-fertilization. Survival of larvae decreased significantly when they were fertilized in high CO₂. A switch in CO₂ conditions 2 h post-fertilization did not change this effect, suggesting that the critical exposure window for this survival effect is within the first 2 h. In contrast, CO₂ conditions during fertilization did not affect larval shell size, but the switch treatments showed that exposure to high CO₂ after 2 h post-fertilization decreased shell size, indicating that the exposure window for a size effect was later in development, possibly during shell calcification. Finally, a shell deformity was seen in scallops with continuous exposure to high CO₂ and those switched from ambient CO₂ to high CO₂ at 2 h post-fertilization. Decreased survival during fertilization and smaller larval shell size due to ocean acidification could ultimately reduce the population size of this commercially important bivalve, which has already seen dramatic population decline due to loss of juvenile habitat.