This paper describes the development and application of an integrated framework for determination of sustainable carrying capacity in shellfish growing areas. This framework combines field data, experimental results and various types of models, ranging from individual shellfish growth models to broad-scale ecosystem models. The process by which we have integrated and coupled the various types of models is designed to capture the essential signal at each simulation scale, whilst allowing multi-year runs which provide results on cultivation of commercial species, nutrient and chlorophyll cycling, and other outputs of interest to decision-makers. The complete modelling framework enables integrated analyses of animal–environment interrelations affecting overall production at system-scales, according to different temporal and spatial scenarios, accounting for conservation aspects such as the presence of autochthonous wild species. This framework was applied to three loughs in Northern Ireland; Carlingford (a transboundary system), Strangford and Belfast, to provide estimates of harvestable biomass over typical cultivation cycles of 2–3 years in both the blue mussel Mytilus edulis and the Pacific oyster Crassostrea gigas. The model accommodates different types of culture, whether subtidally on the bottom, suspended from rafts or intertidally on trestles. Results predicted for Carlingford and Strangford are within ranges of landings reported by fisheries agencies. In Belfast lough, where 10,000 ton live weight are reported annually, our model framework provides stable results of 8700 ton after a 10 year model run. These models are shown to be useful for driving farm-scale simulations, which are of great interest to producers, and also for analyses of the consequences of changed environmental conditions or in the timing, distribution and/or composition of culture practice. Examples are presented that include (i) an analysis of the spatial redistribution of mussel culture, illustrating changes both to production and to the Average Physical Product; (ii) assessment of the differential effects of climate change on mussel and oyster production, indicating that oysters are significantly less impacted; and (iii) investigation of the consequences of including wild suspension-feeding species in the model framework, resulting in an expected reduction in the capacity for production of cultivated shellfish. These scenarios were produced to illustrate the uses of the modelling approach, and enable better-informed discussion between different stakeholders, towards sustainable aquaculture (ecoaquaculture).