AquaModel is a sophisticated, PC-based simulation program that provides data needed to evaluate the performance and ecological effects of proposed fish aquaculture farms. It is the first truly comprehensive model for net-pen aquaculture that simultaneously accounts for both water column and benthic effects. Interlinked submodels of fish physiology, hydrodynamics, water quality, solids dispersion, and assimilation were designed and preliminarily validated using field and laboratory data.