Integrated systems, including components for control of contaminants, sound, and humidity, are provided for a fuel cell system. The integrated system combines contamination control, sound control, and water management. The contamination control system provides filtration for the intake air that provides oxygen to the fuel cell cathode, materials removed can include sub-micrometer particulate matter, salts oils, and chemicals. The sound control system reduces the level of noise emitted from the system by attenuating, resonating, or muffling the sound emitting from the air compressor used to move the air. The contamination control system can also provide security downstream of the compressor, by filtering the air to reduce the opportunity of lubricant from reaching the fuel cell. The water management system removes liquid water when excess is present. These systems are integrated in a variety of configurations to provide compact and thorough protection for the fuel cell.