Aquaculture is one of the fastest growing industries in global food production, which raises the need for adopting holistic planning in the allocation of fish farm locations dedicated to aquaculture in the context of an ecosystem approach. The future development and expansion of aquaculture will strongly depend on the availability of space to develop the industry in a sustainable manner, or in finding ways to reduce the environmental impact at existing locations. This study assesses the possibility of reducing the impact of aquaculture farming by optimizing on the spatial stocking design of three generations of caged fish. Three spatial stocking scenarios were analyzed using simulated numerical experiments. The analysis was performed using emission estimates and by modelling the dispersion and deposition of organic matter on the seabed with concomitant effects on oxygen concentration. Emissions were estimated according to fish growth predictions, energy requirements, body chemical composition, daily meal requirements (industrial feed), and proximate chemical composition of the feed in a sea bream fish farm. The simulation results show that an optimized spatial stocking design of fish cages can significantly reduce the environmental footprint while simultaneously allowing for an increase in annual fish production and optimal utilization of the farming site. Additionally, our findings suggest that carrying capacity of the farming site based only on the annual maximum biomass of harvested fish does not give optimal production estimates and may contribute to underestimating the productive capacity of cage fish farms. •Impacts of spatial stocking design of a cage fish farm on the benthic environment.•Numerical modeling simulations performed.•Emission estimates and dispersion and deposition of organic matter on the seabed.•Optimized spatial stocking design can reduce environmental impacts.•Increased production with contributes to sustainable use of fish farms.