A bill to repeal certain sections of the Act of May 26, 1936, pertaining to the Virgin Islands.

Title I: Saramento-San Joaquin Delta - (Sec. 101) Directs the Secretary of the Interior, acting through the Commissioner of Reclamation, to deposit specified funds authorized to be appropriated under this Act for FY2007-FY2012 into the Delta Flood Protection Fund to be used for reimbursement for the Sacramento-San Joaquin Delta project, California.

Prohibits the Bureau of Reclamation from using more than 1% of appropriated funds to cover administrative and overhead costs.

Directs that any amounts expended under this Act be considered nonreimbursable federal expenditures.

Title II: National Historic Preservation Act Amendments - National Historic Preservation Act Amendments of 2006 - (Sec. 202) Amends the National Historic Preservation Act (NHPA) to prohibit a federal agency from requiring an applicant for federal assistance, licenses, or permits to take into account the effects of a federal undertaking that occur outside the area of potential effects as determined by the federal agency.

Declares that, if a State Historic Preservation Officer or a Tribal Historic Preservation Officer fails to concur within 30 days of receipt of an adequately documented finding of either "no historic properties affected" or "no adverse effect," the applicant or agency may proceed with the undertaking.

(Sec. 203) Specifies additional criteria for certification of local governments to implement the NHPA.

(Sec. 204) Extends through FY2015 the period of funding for the Historic Preservation Fund.

(Sec. 205) Expands: (1) from four to seven the number of federal agencies on the Advisory Council on Historic Preservation (Council); and (2) from nine to eleven the number of Council members constituting a quorum.

Grants the Council discretion to reach an agreement with any federal agency other than the Department of the Interior, or with a private entity, to provide the Council with financial and administrative services.

Authorizes appropriations as necessary for the Advisory Council on Historic Preservation. (Currently, such provision authorizes specified appropriations through FY2005.)

(Sec. 206) Authorizes the Council to enter into cooperative agreements with any federal agency that administers a grant or assistance program for the purpose of improving the effectiveness of program administration.

Permits such cooperative agreements to: (1) modify the selection criteria for a grant or assistance program to further NHPA purposes; or (2) allow the Council to participate in the selection of recipients.

Authorizes the Council to review the operation of any federal grant or assistance program to evaluate its effectiveness in meeting NHPA purposes and policies.

Title III: Repeal of Certain Laws Pertaining to the Virgin Islands - (Sec. 301) Repeals specified provisions of the Act of May 26, 1936 pertaining to real property taxation in the U.S. Virgin Islands, effective July 22, 1954.

Title IV: National Park System Special Resources Study, Newtonia Civil War Battlefields, Missouri - (Sec. 401) Directs the Secretary of the Interior to conduct a special resource study and report to the appropriate congressional committees respecting the First and Second Battles of Newtonia (Missouri) during the Civil War, including an evaluation of the feasibility of adding the battlefields and related sites as part of Wilson's Creek National Battlefield or designating such battlefields and sites as a unit of the National Park System.