Bivalve aquaculture has become increasingly important for marine protein production and is an alternative to exploiting natural resources. Its further and sustainable development should follow an ecosystem approach, to maintain both biodiversity and ecosystem functioning. The identification of critical thresholds to development remains difficult. The present work aims at combining the calculation of the system’s ecological carrying capacity (ECC) with the ecosystem view of resilience for a bay system exposed to bivalve (scallop) aquaculture. Using a trophic food-web model, a stepwise further expansion of culture activities was simulated, and the impact on the system was evaluated twofold: First, a recently developed approach to estimating ECC was used, and second, a resilience indicator was calculated, which is based on the distribution of consumption flows within the trophic network (sensu Arreguín-Sanchez in Ecol Model 272: 27–276, 2014). Results suggest that a culture expansion beyond present-day scale would (a) cause a shift in community composition towards a system dominated by secondary consumers, (b) lead to the loss of system compartments, affecting ecosystem functioning, and (c) result in a decrease in resilience, emphasizing the need to regulate aquaculture activities. The applicability and potential of this presented method in the context of an ecosystem-based approach to aquaculture is discussed. This work aims at adding to the ongoing discussion on sustainable bivalve aquaculture and is expected to help guide aquaculture management.