Oyster aquaculture is a necessity for maintaining a sustainable food supply, however, naturally occurring human pathogens Vibrio parahaemolyticus (Vp) and Vibrio vulnificus (Vv) remain a significant health concern. This study investigated the impacts of aquaculture practices (AP), weather events (WE), and physicochemical parameters (PP) on vibrios (Vp and Vv) dynamics. Oyster and water samples from AP were collected biweekly from April through October in 2022 and 2023 at three different sites (DE, HR and TA) in the Chesapeake and Delaware Inland Bays. PP were recorded adjacent to AP during collection. Samplings were also conducted before and after WE to determine if changes in species abundance occurred. All samples were analyzed for enumeration of total and pathogenic Vp and Vv using the FDA MPN-qPCR method. The seasonality of Vibrio was demonstrated with gene abundances increasing in warmer months and decreasing in cooler months. Relatively high averages of total Vp and Vv from oyster were in October (1.97 and 1.21 log MPN, respectively) suggesting an increased seasonal spread of the species. No significant differences were found in Vibrio abundances between AP, whether sites were pooled or analyzed individually (p > 0.05). Differences in the detection rates of target genes were observed in aquaculture practices between sites (p < 0.05), likely due to site-specific factors. Vp was positively correlated with temperature and conductivity, while Vv showed correlations with temperature and weak associations with total algae phycoerythrin. Levels of Vp and Vv did not reveal a clear trend in response to WE. This study reveals the extended seasonality of Vp and Vv, site-specific variations with pathogenic Vibrio spp., novel correlations with PP, and updated data for risk assessments to assist the seafood industry