Carrying capacity models for aquaculture have increased in complexity over the last decades, partly because aquaculture growth, sustainability, and licensing are themselves extremely complex. Moreover, there is an asymmetric pattern to all these components, when considered from an international perspective, because of very different regulation and governance of the aquaculture sector in Asia, Europe, and America. Two case studies were used, from Long Island Sound in the United States, and Belfast Lough, in Europe, to examine the interactions between cultivated shellfish and other autochthonous benthic filter-feeders. The objective is to illustrate how such interactions can be incorporated in system-scale ecological models and analyzed from the perspective of ecological carrying capacity. Two different models are described, one based on equations that relate the filtration rate of the hard clam Mercenaria mercenaria to physiological and population factors and one based on a habitat-specific analysis of multiple species of benthic filter-feeders. Both types of models have relative advantages and challenges, and both were integrated in ecosystem modeling frameworks with substantial numbers of state variables representing physical and biogeochemical processes. These models were applied to (1) examine the relative role of the two components (cultivated and wild) in the filtration of particulate organic matter (both phytoplankton and organic detritus), (2) quantify the effect of wild species on harvest of cultivated organisms (eastern oyster and blue mussel), and (3) assess the role of organically extractive aquaculture and other filter-feeders on top–down control of eutrophication.