Owyhee Initiative Implementation Act of 2006 - Requires the Secretary of the Interior to coordinate with the Board of Directors of the Owyhee Initiative Project: (1) in conducting the science review process as described in the Owyhee Initiative Agreement, as amended on May 10, 2006; and (2) with respect to the conservation and research center program.
Designates specified land in Idaho as wilderness components of the National Wilderness Preservation System.
Designates specified creek and river segments within Owyhee County, Idaho, as components of the national and wild and scenic rivers system.
Authorizes the Secretary to acquire any land or property interest identified as eligible for exchange in a specified document, if offered by the owner, and subject to conditions described in this Act.
Directs the Bureau of Land Management (BLM) to: (1) implement transportation plans for land it manages outside wilderness areas in the county; and (2) offer to enter into cooperative agreements with the county to establish a cooperative search and rescue program, and to implement and enforce such plans.
Directs the Shoshone-Paiute Tribes of the Duck Valley Indian Reservation to implement the Shoshone-Paiute Tribal Cultural Resource Protection Plan approved by such Tribes.