H.R. 5466 (109^th): Captain John Smith Chesapeake National Historic Trail Designation Act

12/19/2006. Amends the National Trails System Act to designate the Captain John Smith Chesapeake National Historic Trail (a series of water routes extending approximately 3,000 miles along the Chesapeake Bay and its tributaries in Virginia, Maryland, Pennsylvania, Delaware, and in the District of Columbia that traces the 1607 and 1608 voyages of Captain John Smith to chart the land and waterways of the Chesapeake Bay). Requires the Trail to be administered by the Secretary of the Interior in coordination with: (1) the Chesapeake Bay Gateways and Watertrails Network authorized under the Chesapeake Bay Initiative Act of 1998; and (2) the Chesapeake Bay Program authorized under the Federal Water Pollution Control Act. Prohibits the United States from acquiring for the Trail any land or interest in land outside the exterior boundary of any federally-managed area without the consent of the owner of such land or interest. Amends federal law to decrease the maximum limit on the amount that may be made available with respect to all expenses incident to the examination and establishment of the Park and for the acquisition of lands and/or lands and improvements needed for the completion of the Park, including the securing of options and other incidental expenses.