Larvae of the Pacific Oyster, Crassostrea gigas, at Whiskey Creek Shellfish Hatchery (WCH) in Netarts Bay, Oregon, are negatively impacted by high-CO₂ water and exposure during the initial shell formation period appears to be particularly damaging. To investigate the mechanism of this early susceptibility, several cohorts of larvae at WCH were monitored for stable isotope incorporation and biochemical composition: one in May 2011 and two in August 2011. The observations presented here focus on the isotopic shifts associated with initiation and rate of feeding, and the catabolism of C-rich (lipid) and N-rich (protein) pools. Persistent ontological patterns in bulk composition among the cohorts suggest that the creation of the initial shell is energetically expensive, and that the major energetic source during this period is maternally-derived egg lipids. The May cohort did not isotopically reflect their food source as rapidly as the August cohorts, indicating slower feeding, higher metabolic demand or lower maternal energy investments. All cohorts turned over organic carbon faster than organic nitrogen. Shell carbon isotopes of all cohorts show a decreasing dependence on ambient dissolved inorganic carbon (DIC) carbon with time and subtle differences in this trend between the May and August cohorts are explored. Patterns in shell δ¹³C suggest greater exposure to ambient conditions during initial shell development, which could be an important process linking ambient carbonate chemistry and larval susceptibility. Scanning electron microscopy (SEM) images are used to document the initial shell formation. Kinetic isotope fractionation, dissolved organic matter (DOM) utilization, and the dissolvability of shell microstructures are also briefly considered in the context of larval susceptibility.