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 scallop Argopecten 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.