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 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 of 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.

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