Eutrophication-induced hypoxia in a coastal estuarine system results in the deterioration of water quality, which is a growing issue worldwide. In early August 2016, an anoxic event caused the mortality of up to 75 percent of cultured oysters in aquaculture leases of northern Tracadie Bay, New Brunswick (TNB). Field observations revealed that, although the occurrence of summer hypoxia in north TNB is linked with anthropogenic stressors, changes in the geomorphology of one of the bay’s inlet are likely to play a significant role in escalating the eutrophic conditions. However, adequate information on the circulation dynamics of TNB estuarine system was lacking. To address this knowledge gap, a high-resolution spatially-explicit hydrodynamic model was developed for TNB to evaluate the possible physical processes involved in generation of hypoxia leading to oyster mortality. The model showed high skill (0.93) in south TNB in simulating water level elevations and slightly lower skill (0.85) in north TNB. Findings from modeling scenarios based on past, present and future inlet geomorphology suggest that it has strong consequences on intricate circulation patterns, renewal of water and transport. Further, the model is coupled with a volume advection-dispersion tracer module to track the dissemination of effluent and identify areas at risk of hypoxia. Residual flow estimates revealed poorly-circulated stagnant areas, consistent with hot spots in sediment organic matter content. Outcomes from this study will be of relevance for the management of water quality and aquaculture practices.