The lawsuit, filed Monday in U.S. District Court in Trenton, seeks to enjoin the Corps from moving ahead without obtaining state permits.
The Corps announced last month that it would begin the dredging in December or January without state permits, citing its duty to maintain navigation.
The $300 million project calls for deepening 102 miles of the main channel from Philadelphia to the mouth of the Delaware Bay.
Supporters say it's need to keep the ports competitive. Opponents say it will stir up toxic sediment and harm water quality.
Delaware officials filed a similar suit on Friday.