An autonomous underwater vehicle (AUV) may include a fuel cell charging system including a power generation subsystem having an air breathing subsystem taking intake air from the external atmosphere, a supply of compressed hydrogen in onboard storage tanks, an air-breathing PEMFC receiving the intake air and hydrogen, the PEMFC operable to produce electric energy and generating waste water, a water removal system for discharging the waste water offboard, and the fuel cell charging system having a power storage subsystem including a chargeable battery subsystem to receive electric energy to charge the chargeable battery subsystem. A system manager of an onboard data processing system may be configured to control the fuel cell charging system.