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A theoretical model to evaluate total ammonia concentration in recirculating aquaculture system was established by investigating the relationship between impact factors of total ammonia. Subsequently, a system dynamics model for total ammonia in the recirculating aquaculture system was developed based on the theoretical model. The dynamics of total ammonia concentration in a culture pond during the breeding process was simulated by using STELLA simulation software. The simulation results were consistent with the measured values approximately, indicating that this model could simulate the experimental system to a certain extent and could provide suggestions on design and operation of the recirculating aquaculture system.