A system and method for determining a loss of cooling fluid from a thermal sub-system in a fuel cell system. The method includes monitoring current feedback from a high temperature pump that pumps the cooling fluid through a coolant loop. A measured current from the pump is compared to an expected current for the system operating conditions, and if that current is significantly less than what is expected, then it may be as a result of low cooling fluid. If the measured current is less than the expected current for a predetermined period of time, then the system can take mitigating action as a result of a low cooling fluid. Further, if the pump speed is too low to provide an accurate current measurement, then it can be increased if an overflow tank level sensor indicates a low cooling fluid level.