The success of shellfish aquaculture as well as its sustainability relies on adjusting the cultured biomass to local
ecosystem characteristics. Oyster filter-feeding activity can control phytoplankton concentration, reaching severe
depletion in extreme situations, which can threaten ecological sustainability. A better understanding of oyster–
phytoplankton interaction can be achieved by constructing ecosystem models. In this study, a fully-spatial hydro-
dynamic biogeochemical model has been constructed for the Richibucto Estuary in order to explore oyster carry-
ing capacity. The biogeochemical model was based on a classical nutrient–phytoplankton–zooplankton–detritus
(NPZD) approach with the addition of a Dynamic Energy Budget (DEB) model of Crassostrea virginica. Natural
variation of chlorophyll was used as a benchmark to define a sustainability threshold based on a resilience frame-
work. Scenario building was applied to explore carrying capacity of the system. However, the complex geomor-
phology of the Richibucto Estuary and the associated heterogeneity in water residence time, which is integral in
estuarine functioning, indicate that the carrying capacity assessment must be specific for each area of the system.
The model outcomes suggest that water residence time plays a key role in carrying capacity estimations through
its influence on ecological resistance.