The Natural History of Brown Canyon
The Baboquivari Mountains are the western-most of the sky island mountain ranges in southern Arizona. Their elevation and relative isolation from other similar mountainous areas by intervening by lower elevation desert areas give them  ecosystems with distinctive species.
The Baboquivari Mountains. separate the Altar Valley to the east from the great expanse of Sonoran desert to the west. They are composed of three different named ranges: the Quinlan Mountains. with Kitt Peak, the Pazo Verde Mountains. at the Mexican border and the intervening Baboquivari Mountains that culminate at Baboquivari Peak. 
Brown Canyon along with Thomas Canyon drain the eastern flanks of Baboquivari Peak.

A Google Earth image of the Baboquivari Mountains. looking south. Baboquivari Peak is to the right with Brown Canyon in the foreground. Thomas Canyon is the next canyon south.
At left is a view looking down Brown canyon.

Below is Baboquivari Peak from the north. Brown Canyon is lower left.
As you approach Brown Canyon from east, the Baboquavari Range fills your view. Brown Canyon's stream has deeply dissected the widest part of the range and a broad bajada spreads out to the Altar Wash. The eastern escarpment of the range is remarkable for the intersecting systems of igneous dikes that have weathered out of the rocks.
The Brown Canyon Road crosses the mountain front and follows the narrowing canyon. Brown Canyon stream is intermittent, but as with most arid climate monsoon-active streams, extremely powerful when it flows. The large boulders on the canyon floor are sure evidence of this.
As the canyon floor narrows it quickly transitions from desert scrub to sycamore- lined riparian gallery with Madrean oak woodlands on the higher slopes and upper reaches of the canyon.Click for the Baboquivari Mountain Plants
A few noble saguaros can be seen above the canyon floor. 
Click the image to the left to see a complete view of the canyon with some features located that are mentioned on this page.
The canyon is easily accessible although arrangements must be made with a guide before entering both with a vehicle and on foot. The road passes through a locked security gate and ends at the Brown Canyon Education Center lodge. A trail continues up the canyon where one branch goes to the Arch and the other ends in upper Jaguar Canyon. The canyons are quite different from one another and demonstrate the diversity of this world.
The trail above the Education Center lodge branch after a short distance. The popular Arch Trail continues up to the Arch, which is actually a natural bridge. Jaguar Trail is a wilder hike that disappears as the terrain steepens in the wild and rugged country below the crest of the range
The biological diversity of the Brown canyon area is remarkable. Although ranching occurred in the canyon since the 1870's, its ruggedness minimized the impact. Since it was sold to the Refuge in 1996 its wildness has gradually increased. The last turkey disappeared over 50 years ago and their return in 2010 was cause for celebration. The puma has always occupied the rugged highlands and foraged the foothills for prey. Their numbers have been increasing in recent years. Photo by Arizona Game and Fish
The wildlife is always a delight for visitors to see during the daylight hours, but an early morning walk on the dusty road reveals creatures and dramas that fire the imagination.
The refuge contains seven endangered species which includes Kearny's bluestar
Evidence suggests that early humans frequented Brown Canyon. Petroglyphs attributed to the Hohokam people can be found in the canyon and near its mouth. Today this is the land of the Tohono O'odham. Father Kino noted Baboquivari's castle-like tower on a trip in 1699. Ranching began in the canyon in the 1870's and it is named for its earliest known rancher, Rollin C. Brown. A succession of ranchers and land owners ended in 1995 when the U.S. Fish and Wildlife Service purchased most of Brown Canyon from a group of land owners determined to insure its preservation.
The structures that existed at the time of acquisition have become part of the refuge facilities. Especially notable is the Brown Canyon Environmental Education Center lodge. Here the Friends of Buenos Aires NWR host their outdoor education programs. Information about the lodge can be found on the Brown Canyon Facilities page.
Above are ranching structures and to the left is the Brown Canyon Education Center lodge. Both images courtesy 
Ray Goodwin
http://sonoranconnection.blogspot.com
Above the reach of trails is the west wall of the canyon, the crest of the Baboquivari Mts. and Baboquivari Peak which presides over much of southeastrn Arizona. 
See some spectacular photos around Baboquivari peak taken by Michael Willfall. 

The Arch Trail is an easy hike up the main drainage until it reaches a natural bridge at the end of the Trail 1.7 miles from the lodge. Lunch in the shade of the "arch" is a welcome destination.
A trail leads up Jaguar Canyon until it becomes too steep and rugged. Only lions beyond here!
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