For thousands of years, Native Americans called the Ohlone managed and harvested the natural bounty of what is now the Presidio. In 1776, Spanish soldiers and missionaries arrived, forever disrupting Ohlone culture and beginning 218 years of military use of the area just south of the Golden Gate. The Presidio served as a military post under the flags of Spain (1776-1822), Mexico (1822-48), and the United States (1848-1994). Today, visitors enjoy the history and beauty of the Presidio. Within its boundaries are more than 500 historic buildings, a collection of coastal defense fortifications, a national cemetery, an historic airfield, a saltwater marsh, forests, beaches, native plant habitats, coastal bluffs, miles of hiking and biking, and some of the most spectacular vistas in the world.

Santa Fe emerged as the hub of the overland continental trade network linking Mexico and United States markets—a network that included not only the Old Spanish Trail, but also the Santa Fe Trail and El Camino Real de Tierra Adentro. After the United States took control of the Southwest in 1848 other routes to California emerged, and use of the Old Spanish Trail sharply declined. Because of its rich history and national significance, the Old Spanish Trail has been designated as a national historic trail.

The California Trail carried over 250,000 gold-seekers and farmers to the gold fields and rich farmlands of California during the 1840's and 1850's, the greatest mass migration in American history. Today, more than 1,000 miles of trail ruts and traces can still be seen in the vast undeveloped lands between Casper Wyoming and the West Coast, reminders of the sacrifices, struggles, and triumphs of early American travelers and settlers. More than 240 historic sites along the trail will eventually be available for public use and interpretation. The trail passes through the states of Missouri, Kansas, Nebraska, Colorado, Wyoming, Idaho, Utah, Nevada, Oregon, and California.

The Pony Express National Historic Trail was used by young men on fast paced horses to carry the nation's mail across the country, from St. Joseph, Missouri to Sacramento, California, in the unprecedented time of only ten days. Organized by private entrepreneurs, the horse-and-rider relay system became the nation's most direct and practical means of east-west communications before the telegraph. Though only in operation for 18 months, between April 1860 and October 1861, the trail proved the feasibility of a central overland transportation route, and played a vital role in aligning California with the Union in the years just before the Civil War. Most of the original trail has been obliterated either by time or human activities. Along many segments, the trail's actual route and exact length are matters of conjecture. However, approximately 120 historic sites may eventually be available to the public, including 50 existing Pony Express stations or station ruins.

The Whiskeytown Unit, with its mountainous back country and large, man-made reservoir, offers many summer activities such as hiking and boating, as well as historical remains of the California Gold Rush of 1849. Whiskeytown Lake, provides 36 miles of shoreline and 3200 surface acres of water, and is excellent for most water-related activities, including swimming, scuba diving, water skiing, boating and fishing. The lake was created by diverting water through tunnels and penstocks, from the Trinity River Basin to the Sacramento River Basin. The most prominent landmark within the Recreation Area is Shasta Bally (elevation 6,209 feet). The summit may be reached on foot and by 4-wheel drive vehicle, but is closed in the winter.