The growing demand for aquaculture products can only be maintained by increasing the production of lower trophic species such as bivalves and tunicates. Low trophic species avoid the energy losses during trophic transfers to build animal protein, making them ideal candidates to exploit available resources in coastal waters. In the particular case of fjords, forced upwelling of deep nutrient-rich waters can promote phytoplankton growth, or in other words, the growth of bivalve and tunicate food. However, the density at which bivalves and tunicates are cultured can compromise phytoplankton populations and consequently, marine food chains. A highly configurable environmental model was constructed to study the ecosystem effects and potential biomass production of hypothetical bivalve and tunicate aquaculture scenarios in a Norwegian fjord under forced upwelling conditions. The simulations objectively determined the level of aquaculture development that maximizes the sustainable utilization of resources towards bivalves and tunicates biomass production. The model also highlighted the positive effect of the forced upwelling on both cultured production and phytoplankton abundance under aquaculture scenarios. Finally, the model predicted that tunicates would be more efficient than mussels at extracting resources due to their lower metabolic cost and higher filtration capacity. Although a full economic analysis would be required to decide on the preferred species to be cultured, these results encourage current pilot studies in which tunicates are explored as a sustainable way to efficiently exploit marine resources for aquafeed production.