A fluid heating system including a burner unit is operated based on feedback control loops. The fluid heating system comprises a burner unit configured to heat a fluid, a sensor configured to sense a characteristic of the appliance, and a controller coupled to the burner unit and the sensor. The controller includes an electronic processor and a memory. The controller is configured to receive a first signal corresponding to the characteristic from the sensor, determine, based on the first signal, a first feedback loop control, control combustion of the burner unit based on the first feedback loop control, determine, based on the first feedback loop control, a second feedback loop control, and control combustion of the burner unit based on the second feedback loop control.