Northern Rockies Ecosystem Protection Act - Designates specified National Forest System lands, National Park System lands, and public lands in Idaho, Montana, Oregon, Washington, and Wyoming as wilderness and as components or additions to existing components of the National Wilderness Preservation System.

Sets forth provisions for the management of the lands designated as wilderness by this Act, including regarding water rights, tribal rights, fish and wildlife, and grazing permits and leases.

Authorizes the Secretaries of the Interior and of Agriculture (USDA) to take necessary measures for the control of fire, insects, and disease on such lands.

Establishes a Northern Rockies Fish and Wildlife Habitat and Corridors Information Program. Requires the development of a Northern Rockies Habitat and Corridors Information System.

Sets forth specified additional provisions with regard to Indian tribes. Permits provisions of the Indian Self-Determination and Education Assistance Act to be applied, as appropriate, in the implementation of this Act.

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.