National Discovery Trails Act of 1999

National Discovery Trails Act of 1999 - Amends the National Trails System Act to provide for the establishment, as components of the National Trails System, of national discovery trails which shall be extended, continuous interstate trails located so as to provide for outdoor recreation and travel and to connect representative examples of America's trails and communities. Permits designation of any such trail on Federal lands and, with the owner's consent, on any non-Federal lands.

Prohibits a trail from being considered feasible and desirable for designation as a national discovery trail unless it: (1) links one or more areas within the boundaries of a metropolitan area and should join with other trails, connecting the National Trails System to significant recreation and resources areas; (2) is supported by a competent trailwide volunteer- based organization and has extensive local and trailwide support by the public, user groups, and affected State and local governments; and (3) extends and passes through more than one State and, at a minimum, is a continuous, walkable route.

Requires the appropriate Secretary for each national discovery trail to administer the trail in cooperation with a competent trailwide volunteer-based organization.

Designates as a national discovery trail the 6,000-mile American Discovery Trail which shall extend from Cape Henlopen State Park in Delaware to Point Reyes National Seashore in California, traveling northern and southern routes from Cincinnati, Ohio, to Denver, Colorado.

Requires the appropriate Secretary, within three complete fiscal years after enactment of legislation designating a national discovery trail, to submit to specified congressional committees a comprehensive plan for the protection, management, development, and use of the Federal portions of the trail.