Experimental exposure of early life stage bivalves has documented negative effects of elevated pCO2 on survival and growth, but the population consequences of these effects are unknown. Following standard practices from population viability analysis and wildlife risk assessment, we substituted laboratory-derived stress-response relationships into baseline population models of Mercenaria mercenaria and Argopecten irradians. The models were constructed using inverse demographic analyses with time series of size-structured field data in NY, USA, whereas the stress-response relationships were developed using data from a series of previously published laboratory studies. We used stochastic projection methods and diffusion approximations of extinction probability to estimate cumulative risk of 50% population decline during ten-year population projections at 1, 1.5 and 2 times ambient pCO2 levels. Although the A. irradians population exhibited higher growth in the field data (12% per year) than the declining M. mercenaria population (-8% per year), cumulative risk was high for A. irradians in the first ten years due to high variance in the stochastic growth rate estimate (log λs = -0.02, σ2 = 0.24). This ten-year cumulative risk increased from 69% to 94% and >99% at 1.5 and 2 times ambient scenarios. For M. mercenaria (log λs = -0.09, σ2 = 0.01), ten-year risk was 81%, 96% and >99% at 1, 1.5 and 2 times ambient pCO2, respectively. These estimates of risk could be improved with detailed consideration of harvest effects, disease, restocking, compensatory responses, other ecological complexities, and the nature of interactions between these and other effects that are beyond the scope of available data. However, results clearly indicate that early life stage responses to plausible levels of pCO2 enrichment have the potential to cause significant increases in risk to these marine bivalve populations.