Aquaponics is a promising sustainable farming method that combines aquaculture and hydroponics. It allows the growth of crops without soil, pesticides, or fertilizers, and with a minimum amount of water. In aquaponic systems, the design of the growing area is directly linked to the type of crop about to be planted. The type of crop directly determines, for example, the spacing between plants and between channels, which is critical to determine the footprint required and estimate the system productivity. This paper proposes a knowledge modeling approach to support the design of aquaponic systems by automatically determining the required characteristics of the aquaponic system based on crop selection. The knowledge modeling is outlined as an ontology model that formally describes the existent links between the aquaponic grow bed characteristics and its design parameters. This study gives practitioners the capacity to visualize the impact of the desired crop selection on the aquaponic system design, as well as supporting clearer decision-making regarding production facility layout and system design in aquaponic farms.