The Northeast US experienced a rise of Vibrio parahaemolyticus infections that contrasts with historical trends. Increasing ocean temperatures and rapid expansion of oyster aquaculture in the region undoubtably played a role in these epidemiological changes. But without the introduction and establishment of a Pacific lineage of V. parahaemolyticus sequence type (ST) 36 and expansion of an Atlantic endemic lineage ST631 in the region, disease incidence would not have risen so dramatically. Both strains resided in the Gulf of Maine for decades without causing an increase in infection suggesting ecological changes perhaps linked with aquaculture practices could have shifted population dynamics in favor of these pathogens. Though the Great Bay Estuary (GBE) of New Hampshire lies just to the north of aquaculture areas associated with both strains of regional concern, no local-source infections by these pathogenic strains have yet occurred. A temporal analysis of strains from archived and ongoing samples from the GBE reveals an alarming shift in the prevalence of non-native strains harboring genetic markers (hemolysins tdh and trh) associated with pathogens. Whereas between 2007-14 hemolysin-harboring strains were rarely detected, they are now routinely detected and cultured from the environment. Though increasing levels of potentially pathogenic strains were first detected in commercial oysters and later increased in wild oysters, disease incidence remains unchanged. The geographic location of the GBE at the margin of pathogen expansion in the Northeast and documentation of these changes highlights that further study of this population could provide valuable insight into the ecology of pathogen invasion.