Oyster aquaculture is a growing industry in New Hampshire (NH) where the introduction of Vibrio parahaemolyticus, especially the hypervirulent strain ST36, via movement of oyster seed from affected harvest areas is a serious concern. The continued absence of documented illnesses associated with NH product informed policies that restrict seed importation from areas with a history of illnesses. However, this policy remains controversial due to limited knowledge of whether seed is at risk for V. parahaemolyticus contamination, and longstanding presumptions that pathogens will eventually arrive from areas near NH, regardless of human efforts. The policy also limits options for growers in attaining seed of greater diversity. If oyster seed treatment prior to transplantation in NH growing areas could purge pathogens this could safely expand seed access. Therefore, we undertook these studies to 1) document the extent that oyster seed is, or is not, at risk for contamination, 2) examine how the oyster microbiome and V. parahaemolyticus composition develop upon transplantation in local aquaculture areas to document whether existing Vibrio populations persist, and 3) define whether on-shore simulated relay can reduce pathogen load and/or influence susceptibility to contamination as a potential safety measure. These studies revealed that low levels of V. parahaemolyticus were rarely detected in hatchery seed, hatchery water treated to reduce microbial contamination, and algal feed, reinforcing that hatchery seed poses little risk when their source water has low resident pathogen populations. When this seed was acclimated to the Great Bay Estuary (GBE) in NH, the patterns of V. parahaemolyticus mirrored that of local GBE oysters suggesting they readily reflect local conditions rather than maintain the composition at the time of transplantation. Analysis of Vibrio composition following simulated relay in a full factorial design of water source, water temperature, and water salinity indicated that temperature, water source, and their interaction are the primary drivers of abundance, acquisition, and retention of V. parahaemolyticus. The combination of natural offshore, low temperature and relatively higher salinity sea water was the best relay method for reducing V. parahaemolyticus levels, as well as preventing V. parahaemolyticus acquisition and retention in hatchery juveniles once challenged with inoculum after treatment. Combined, these data suggest that if levels of V. parahaemolyticus are low, such as is expected from hatchery seed that has not resided in nurseries and untreated water, and with the potential aid of simulated onshore relay to higher salinity, cooler water, with low abundance of V. parahaemolyticus as a pre-treatment before transplantation, the risk of contamination, and re-acquisition are low. If our ongoing studies with larger oysters’ seed from nurseries and untreated water indicate that onshore relay can assist with purging populations and restricting re-acquisition, this could expand options for seed importation while limiting the risk of introduction of hypervirulent ST36 or other emerging pathogen lineages.