An energy storage system includes a plurality of battery strings, each battery string including a plurality of batteries coupled electrically together; a plurality of temperature sensors; an enclosure housing the plurality of battery strings and the temperature sensors; a plurality of fans positioned in different locations within the enclosure; and a temperature control system. The temperature control system includes a heating, ventilation, and air conditioning (HVAC) components, and a controller. The controller is programmed to execute the method that includes determining fan speed operating commands based at least in part on sensed temperatures at the different locations, and operating the fan speed in response to the operating commands provided to the respective fans.