TABLE OF CONTENTS:

Title I: Designation of Wilderness Areas

Title II: Biological Connecting Corridors

Title III: National Parks, Preserves, and Related Studies

Title IV: Wild and Scenic Rivers Designations

Title V: National Wildland Restoration and Recovery System

Title VI: Implementation and Monitoring

Title VII: Rules of Construction

Northern Rockies Ecosystem Protection Act of 1999 - Title I: Designation of Wilderness Areas - Designates the following lands in Idaho, Montana, Oregon, Washington, and Wyoming as wilderness and components of the National Wilderness Preservation System (System): (1) Greater Glacier-Northern Continental Divide Ecosystem; (2) Greater Yellowstone Ecosystem; (3) Greater Salmon-Selway Ecosystem; (4) Greater Cabinet-Yaak-Selkirk Ecosystem; (5) Islands in the Sky Wilderness; and (6) Blackfeet Wilderness.

(Sec. 109) Reserves, with respect to each wilderness area designated by this Act, a sufficient quantity of water to fulfill the area's designated purpose.

Title II: Biological Connecting Corridors - Designates: (1) specified wild land areas as Biological Connecting Corridors (Corridors) to protect the life flow of the Northern Rockies Bioregion; (2) the inventoried roadless areas identified as part of the Corridors as components of the System; and (3) certain biological connecting corridors as special corridor management areas. Exempts specified roads and highways from provisions of this Act.

Title III: National Parks, Preserves, and Related Studies - Establishes the Hells Canyon-Chief Joseph National Park and Preserve as a unit of the National Park System.

(Sec. 301) Requires the Secretary of the Interior, acting through the National Park Service, to administer the Preserve.

Requires the Secretary to implement a program to close all vacant livestock allotments and to negotiate the purchase of active livestock allotment grazing allocations from the permittees. Closes all vacant and vacated allotments upon purchase.

Sets forth provisions concerning: (1) motorized uses of the Preserve; and (2) participation of the Department of the Interior in the process by which the Federal Energy Regulatory Commission reconsiders the relicensing of the Hells Canyons dams complex.

Requires the Secretary to implement a program of ecosystem restoration in the Preserve.

(Sec. 302) Requires the Secretary of the Interior, acting through the National Park Service, to study the feasibility of creating a Flathead National Park and Preserve in the area generally known as the Glacier View Ranger District of the Flathead National Forest, excepting those lands south of the Big Mountain Road.

Title IV: Wild and Scenic Rivers Designations - Amends the Wild and Scenic Rivers Act to designate segments of specified rivers and creeks in Idaho, Montana, and Wyoming as components of the National Wild and Scenic Rivers System.

Title V: National Wildland Restoration and Recovery System - Establishes the National Wildland Restoration and Recovery System.

(Sec. 502) Specifies component recovery areas. Requires the U.S. Forest Service, after recovery is achieved for a component area, to evaluate its suitability for inclusion in the System or for other consistent uses. Establishes the National Wildland Recovery Corps (as a special unit of the U.S. Forest Service) to carry out land recovery responsibilities. Requires the Corps to develop a wildland recovery plan for each area of the Recovery System, requiring each plan to take into account the specific conditions of the area. Authorizes appropriations.

Title VI: Implementation and Monitoring - Requires the Secretaries of the Interior and Agriculture to: (1) report to the Congress on implementation of this Act; (2) establish an interagency team to monitor, evaluate, and make recommendations to ensure long-term results required by this Act and to develop a geographic information system for monitoring the Northern Rockies Bioregion; and (3) establish a governmental review board to make recommendations to the Congress on legally restating and unifying the natural resource management mandates of Federal agencies.

(Sec. 605) Requires the Secretaries to assure nonexclusive access to Wilderness areas, National Park and Preserve Study areas, Wildland Recovery areas, and Biological Corridors designated by this Act by Native Americans for traditional cultural and religious purposes.

Requires the Forest Service and Bureau of Land Management to enter into cooperative management agreements with the appropriate Indian tribes to assure protection of religious, burial, and gathering sites, and to work cooperatively on the management of all uses in the protected areas that affect Indian lands and people.

(Sec. 606) Requires the Secretaries to give particular emphasis to the preservation and protection of cultural resources located within the areas.

Title VII: Rules of Construction - Provides that nothing in this Act may be construed as: (1) a relinquishment or reduction of any U.S.-secured water rights; (2) establishing a precedent with regard to any future designations, including wilderness designations; or (3) affecting any Indian treaty or right.