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The use of automation, Internet-of-Things (IoT), and smart technologies is being rapidly introduced into the development of agriculture. Technologies such as sensing, remote monitoring, and predictive tools have been used with the purpose of enhancing agriculture processes, aquaponics among them, and improving the quality of the products. Digital twinning enables the testing and implementing of improvements in the physical component through the implementation of computational tools in a ‘twin’ virtual environment. This paper presents a framework for the development of a digital twin for an aquaponic system. This framework is validated by developing a digital twin for the grow beds of an aquaponics system for real-time monitoring parameters, namely pH, electroconductivity, water temperature, relative humidity, air temperature, and light intensity, and supports the use of artificial intelligent techniques to, for example, predict the growth rate and fresh weight of the growing crops. The digital twin presented is based on IoT technology, databases, a centralized control of the system, and a virtual interface that allows users to have feedback control of the system while visualizing the state of the aquaponic system in real time.