Keep the Colorado River Clean Act

Keep the Colorado River Clean Act - Amends the Strom Thurmond National Defense Authorization Act for Fiscal Year 1999 to direct the United States to convey to the Ute Indian Tribe of the Uintah and Ouray Indian Reservation all Federal lands within the exterior boundaries of NOSR-2 (Oil Shale Reserve Numbered 2), both surface and mineral rights, without retaining any management authority over the conveyed lands or tribal activities thereon, but reserving to the United States: (1) a nine percent royalty interest in the value of any oil, gas, other hydrocarbons, and all other minerals produced, saved, and sold from such lands, the payments to be made by the Tribe to the Secretary of Energy (Secretary) when produced, saved, or sold during the period minerals are being extracted; (2) that portion of the bed of Green River contained entirely within NOSR-2; (3) the lands, including surface and mineral rights, to the west of the river within NOSR-2; and (4) a 1/4 mile scenic easement on the east side of the river within NOSR-2.

Provides that such lands conveyed to the Tribe shall not revert to the United States for management in trust status.

Revokes all existing withdrawals on NOSR-2.

Directs the Secretary of the Interior to administer the lands and interests in lands reserved from such conveyance and to prepare and submit to Congress a land use plan for the management of these lands and interests in lands within three years after the enactment of this Act. Authorizes appropriations.

Provides for the Tribe to pay the royalty interest reserved from conveyance free of all development, production, marketing, and operating expenses. Requires the United States to bear and pay gross production taxes, pipeline taxes, and allocation taxes assessed against the gross production.

Requires the Tribe to: (1) report annually to the Secretary and Congress on its resource development and other activities concerning the property transferred; and (2) submit every five years to a financial audit of such activities, with the first audit taking place five years after the date of transfer and the results of each audit being included in the next annual report after completion.

Requires the Tribe to: (1) manage its lands adjacent to and within a 1/4 mile of the Green River in a protected status and in a manner consistent with the provisions contained in a government-to-government agreement and a specified memorandum of understanding as agreed to by the Tribe and the Secretary of the Interior; (2) protect any plant species listed as endangered or threatened that is located on the NOSR-2 lands conveyed to the Tribe in a manner consistent with the then current levels of legal protection, and this protection to be performed fully under tribal jurisdiction and in accordance with a government-to-government agreement between the Tribe and the Secretary of the Interior; and (3) manage the horses not owned by the Tribe or tribal members that are located or found on such lands in a manner consistent with then current Federal protections granted such animals, provided that the management, control, and protection of such horses will be performed fully under tribal jurisdiction and in accordance with a government-to-government agreement between the Tribe and the Secretary of the Interior.

Requires the Secretary to: (1) prepare a plan to commence, within one year following preparation of such plan, remedial action, including groundwater restoration, at the uranium milling site near Moab, Utah; and (2) retain the amounts received as royalties under this Act (and such amounts shall be available to carry out such remedial action). Requires upon completion of such remedial action all such royalty amounts to be deposited in the general fund of the Treasury. Authorizes appropriations.

Amends the Uranium Mill Tailings Radiation Control Act of 1978 to designate the Moab uranium milling site as a processing site, with specified exceptions.