Variability of water conditions in coastal environments could affect oyster aquaculture production through three main environmental-tolerance mechanisms: phenotypic plasticity, within-generation carryover effects, and selective mortality. Aquaculture production of eastern oyster, Crassostrea virginica, larvae occurs on weekly timescales in Virginia, with variations in salinity experienced by subsequent larval cohorts. The present study examined the relative importance of within-generation carryover effects – phenotypic changes during a previous life stage that impact a later stage – and phenotypic plasticity in shaping the performance of juvenile oysters after an experience of small differences in salinity (< 2 salinity units) during the larval stage. Genetic diversity was also assessed to rule out large shifts in allele frequencies, or loss of diversity, that would suggest observed effects were the result of selective mortality rather than carryover effects or phenotypic plasticity. Larval oysters were reared through settlement and metamorphosis under two salinities (thirteen and fifteen) that represent small differences between consecutive spawns in a hatchery. Juveniles were then raised in situ in two Virginia tributaries of the lower Chesapeake Bay, the York and Rappahannock rivers. Oyster production occurs within these two tributaries under distinct salinity conditions, with the Rappahannock tending to be of lower salinity. Metrics of survival, growth, oxidative stress, and condition index were compared to assess phenotypic plasticity and within-generation carryover effects. Juvenile oyster survival and physiology correlated with in situ environmental conditions rather than previous larval salinity experience. Specifically, juvenile oysters raised in the Rappahannock River had greater survival (13%), shell length (14%), condition index (38%), and dry tissue weight (78%) than those raised in the York River, regardless of larval salinity. Rappahannock River oysters also had 20% lower total antioxidant capacity than York River oysters. Genetic diversity remained high with no large shifts in allelic frequencies that would suggest non-random loss of alleles attributable to selection. Our results suggest that small salinity differences experienced in shellfish hatcheries 48 h after fertilization likely do not impact juvenile oyster performance during grow-out; rather, phenotypic plasticity likely underpins juvenile oyster performance during the transition from hatchery to farms. The importance of phenotypic plasticity presents another reason why farm site selection is critical to the performance and success of aquaculture product. Future studies are needed to further identify whether larval responses to salinity conditions are dependent on additional environmentally relevant conditions like temperature or the timing of exposure post-fertilization to better understand the relative importance of phenotypic plasticity, within-generation carryover effects, and selective mortality within oyster aquaculture.