The deterioration of water quality in Chesapeake Bay during the summer is a suspected cause of mortality events of cultured oyster larvae. Relative contributions of abiotic stressors (e.g. temperature) and biotic stressors (e.g. harmful algae blooms) are currently unknown. Stressors directly impact larval physiology, and larval health can also be influenced by effects on the larval microbiome. We examined the effects of water quality on larval physiology coincident with effects on microbiomes associated with larvae and culture water. To evaluate the relative role of seasonal shifts in abiotic water quality, we replicated culturing experiments in May, June, and July, 2018. To manipulate the microbiomes available to inoculate oyster embryos, we raised larvae under three treatments: sand-filtered water (MECH), sand-filtered and UV-treated water (STD), and STD water ‘seeded’ with adult oyster microbiome (OJ). Larvae in OJ exhibited the lowest survival, but the growth of surviving larvae was similar among treatments. Larval metabolism differed among treatments, whose relative influence depended on the time of season. Analysis of 16S rRNA gene sequences revealed seasonal variation in larval microbiomes, but not in water microbiomes. The relative effects of treatments on larval microbiomes varied across the season. Microbial taxa associated with larval physiology will be presented. The results of this large collaborative project provide important insight not only on interactions between larval physiology and microbiome, but also on a vexing problem facing the shellfish aquaculture community: the difficulty of overcoming limitations, of uncertain cause, to hatchery production.