According to various embodiments, a biofuel production system includes a plurality of parallel-operated fermenters, a cooling tower water system configured to supply cooling water to the plurality of parallel-operated fermenters, a chiller water system configured to supply chiller water to the plurality of parallel-operated fermenters, and a cooling system coupled to the plurality of parallel-operated fermenters, the cooling tower water system, and the chiller water system. The cooling system controls the flow rates of the cooling water and the chiller water to the plurality of parallel-operated fermenters based upon temperatures of fermentation products of the fermenters.