Sets forth specified terms and conditions regarding the issuance of a special use authorization under this Act.

Idaho Wilderness Water Resources Protection Act - Directs the Secretary of Agriculture (USDA) to issue a special use authorization to the owners of a water storage, transport, or diversion facility located on National Forest System land in the Frank Church-River of No Return Wilderness and the Selway-Bitterroot Wilderness in Idaho for continued operation, maintenance, and reconstruction of such facility if it is determined that: (1) the facility was in existence on the date on which it was designated as part of the National Wilderness Preservation System; (2) the facility has been in continuous use to deliver water for beneficial use on the owner's non-federal land since the date designation; (3) the owner holds a valid water right for use of the water on such land under Idaho state law, with a priority date that predates such date; and (4) it is not practicable or feasible to relocate the facility to land outside of the wilderness and continue the beneficial use of water on the non-federal land.

Requires the Secretary, in a special use authorization under this Act, to: (1) allow the use of motorized equipment and mechanized transport for operation, maintenance, or reconstruction of a facility, if it is determined that the use is necessary to continue delivery of water to the non-federal land for beneficial uses and that the use of nonmotorized equipment and nonmechanized transport is impracticable or infeasible; and (2) preclude use of the facility for the storage, diversion, or transport of water in excess of the water right.

Allows the Secretary, in such an authorization, to: (1) require or allow modification or relocation of a facility in the wilderness, as determined necessary, to reduce impacts to wilderness values if the beneficial use of water on the non-federal land is not diminished; and (2) require that the owner provide a reciprocal right of access across the non-federal property, in which case the owner shall receive market value for any right-of-way or other interest in real property conveyed to the United States. Permits the market value to be paid by the Secretary, in whole or in part, by the grant of a reciprocal right-of-way or by reduction of fees or other costs that may accrue to the owner in obtaining an authorization for water facilities.

Idaho Wilderness Water Resources Protection Act - Directs the Secretary of Agriculture (USDA) to issue a special use authorization to the owners of a water storage, transport, or diversion facility located on National Forest System land in the Frank Church-River of No Return Wilderness and the Selway-Bitterroot Wilderness in Idaho for continued operation, maintenance, and reconstruction of such facility if it is determined that: (1) the facility was in existence on the date on which it was designated as part of the National Wilderness Preservation System; (2) the facility has been in continuous use to deliver water for beneficial use on the owner's non-federal land since the date designation; (3) the owner holds a valid water right for use of the water on such land under Idaho state law, with a priority date that predates such date; and (4) it is not practicable or feasible to relocate the facility to land outside of the wilderness and continue the beneficial use of water on the non-federal land.

Requires the Secretary, in a special use authorization under this Act, to: (1) allow the use of motorized equipment and mechanized transport for operation, maintenance, or reconstruction of a facility, if it is determined that the use is necessary to continue delivery of water to the non-federal land for beneficial uses and that the use of nonmotorized equipment and nonmechanized transport is impracticable or infeasible; and (2) preclude use of the facility for the storage, diversion, or transport of water in excess of the water right.

Allows the Secretary, in such an authorization, to: (1) require or allow modification or relocation of a facility in the wilderness, as determined necessary, to reduce impacts to wilderness values if the beneficial use of water on the non-federal land is not diminished; and (2) require that the owner provide a reciprocal right of access across the non-federal property, in which case the owner shall receive market value for any right-of-way or other interest in real property conveyed to the United States. Permits the market value to be paid by the Secretary, in whole or in part, by the grant of a reciprocal right-of-way or by reduction of fees or other costs that may accrue to the owner in obtaining an authorization for water facilities.