A mobile emissions control system is provided for diesel engines operated on ocean-going ships at-berth. The emissions control system comprises two essential elements: an emissions capturing system and an emissions control system. The emissions control system may be mounted on a towable chassis or mounted on a barge, allowing it to be placed alongside ocean-going ships at-berth. The emission capturing system captures exhaust from a ship's diesel engine and conducts it into the emissions control system, which cleans the exhaust and then passes clean air into the atmosphere through an exhaust outlet.