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For prolonged manned spaceflight, recycling of wastewater is critical to minimize payload costs. We have constructed a pilot-scale, closed-loop water recycling system (CLWRS). Due to slow process dynamics, evaluation of multiple experimental scenarios is very time-consuming. To accelerate evaluation, we have developed mathematical models of the individual reactors, as well as a process model of the pilot plant, which combines nitrification, denitrification, recycle, and degassing steps. The simulation accurately reproduces the 35% total nitrogen (TN) reduction observed experimentally at a 20/1 recycle ratio. Both experiments and simulations indicate that biological CLWRS have significant potential for long-duration manned space flight.