New Jersey/New York Clean Ocean Zone Act of 2006 - Designates the New York/New Jersey Bight as the New Jersey/New York Clean Ocean Zone. Prohibits the Administrator of the Environmental Protection Agency, the Secretary of the Army, and all states from issuing a permit for ocean dumping, or establishing any new disposal site in the Zone, including under specified provisions of existing law. Terminates all existing disposal site designations, subject to exception.
States that the discharge of a pollutant into the Zone from a point source constructed or put into use after enactment of this Act is prohibited under specified provisions of the Federal Water Pollution Control Act. Prohibits permit issuance for such discharge.
Prohibits a state or federal permit issued for the discharge of a pollutant into the Zone from being renewed, reissued, or modified to allow any increase of discharge capacity of any point source or to contain any effluent limitation less stringent than comparable effluent limitations in the permit.
Prohibits the permanent extraction of any nonrenewable natural resource from the Zone for commercial or industrial use, except for the primary purpose of maintaining or establishing navigation channels.
Prohibits the creation, licensing, leasing, easement granting, or right-of-way granting of certain facilities involving nonrenewable energy, including deepwater ports and pipelines.
Prohibits categorically excluding leases, easements, or rights-of-way for renewable energy facilities from specified provisions of the National Environmental Policy Act of 1969.
Prohibits underwater research or exploration in the Zone unless it meets certain requirements.