Fish farming activities are a relevant economic resource in coastal waters, which have grown in a significant way in recent decades, often with deleterious environmental effects. The sustainability of the activity requires proper management and especially an appropriate site selection, which avoids use conflicts and considers adequately the potential effects before they occur. For this purpose numerical modeling is a key tool for a sustainable aquaculture. Aquaculture is a complex activity that has environmental effects at different scales and influences and it is also influenced by the surrounding environment. Therefore the correct modeling of the activity must consider the different scales at which the aquaculture could influence, as well as the effect of environment on the activity and the interference of cultured fish over themselves. This work describes the application of a modeling protocol to assessing the carrying capacity of fish culture in marine waters. It is a sequential process which consider the critical condition for environmental factors and culture characteristics.