Currently, intensive fish farming using closed water circulation technology is becoming one of the breakthrough technologies in the aquaculture production. Digital transformation for such production is necessary for the effective management of ultra-high-density aquaculture farms. This transformation is based on the digital twin of aqua-biotechnological farms. The authors performed digital modeling & simulation of the biotechnological component of intensive aqua farm. The main equations of the model are presented in the article. Models of lungfish and trout ecosystems are considered. The models were tested as part of the digital twin for the real aqua farm. The qualitative coincidence of the results of modeling & simulation with the behavior of the ecosystem is obtained. The model has not yet achieved sufficient accuracy for commercial use. The reasons for the insufficient accuracy of the simulation are discussed. Some variants of the simulation model’s development for simple closed aquatic ecosystems with a large biological load are considered. It is concluded that it is necessary to integrate a digital twin based on a simulation model of a biosystem with the technology of the Industrial Internet of Things to achieve the necessary accuracy of describing a complex engineering and biotechnological system.