The San Pedro River is the central corridor of the Madrean Archipelago of "Sky Islands", high mountains with unique ecosystems different from the ecology of the Sonoran desert "seas" that surround it.

More than 300 species of birds nest in by the river or use this corridor as they migrate between South, Central and North America.
This includes the yellow-billed cuckoo (Coccyzus americanus).
The area provides for more than 80 species of mammals, including jaguar (Panthera onca), coatimundi (Nasua narica), beaver (Castor canadensis frontador), 20 species of bats and several types of rodents.
There are also over 65 species of reptiles and amphibians, among them Sonoran tiger salamander (Ambystoma mavortium stebbinsi) and western barking frog (Eleutherodactylus augusti).
Some notable fish species native to the river are the endangered Gila chub (Gila intermedia), both the longfin and speckled dace, Sonora sucker and desert sucker, and the roundtail chub.
The flora includes Fremont cottonwood (Populus fremontii), Goodding willow (Salix gooddingii), velvet mesquite trees, and the Huachuca water umbel (Lilaeopsis schaffneriana spp.
recurva), Federally listed as endangered.

In recent decades, rapid growth and population increases in southern Arizona has caused concern with this river.
 Several non-profit organizations have risen in recent years to raise awareness of this problem.
The San Pedro Riparian National Conservation Area (SPRNCA) was established in 1988 to protect some forty miles of the upper San Pedro valley.
The Nature Conservancy also owns several preserves in the watershed, including the San Pedro River Preserve,  Aravaipa Canyon Preserve, Muleshoe Ranch Preserve, Ramsey Canyon Preserve, and most recently, Rancho Los Fresnos.
 Rancho Los Fresnos, near the river's source, is the largest ciénega, an isolated desert spring or marsh, remaining in the San Pedro River watershed.
Its protection is important as 99% of the ciénegas in the Southwest have been drained and destroyed.

With large portions of the river dry much of the year, Bureau of Land Management (BLM) wildlife biologist Mark Fredlake proposed restoring beaver to the watershed to retain water flows into the dry season and to support re-growth of the historic riparian vegetation.
Riparian habitat covers only 1% of the Southwest but supports 50% of breeding bird species and is vital as a food source for migrating avifauna.
Fredlake reasoned that beaver dams would raise the water table, allowing groundwater to recharge the river's flow in the dry season.
From 1999 to 2002, 19 beavers were released into the SPRNCA, a 40-mile (64 km) stretch of the river, in Cochise County.
By 2006 there were more than 30 dams.
The beavers also dispersed widely and rapidly.
One beaver migrated to Aravaipa Canyon, more than 100 rivermiles away; another to the river's terminus at the Gila River, earning itself the moniker “the surfing beaver”; and others up into Mexico, building several dams along the river’s upper tributaries.
The program was successful with measurable increases in bird diversity and formation of deep pools and lasting flows.
In 2008, flooding destroyed all the beaver dams and this was followed by a long drought.
However, as in historic times the beaver seems well adapted to the San Pedro River, and the 2009 dam count is back above 30 with a current population between 30 and 120 beavers.
A short video reviews the use of re-introduced beaver to restore the river.
In the upper river, re-introduced beavers have created willow and pool habitat which has extended the range of the endangered Southwestern willow flycatcher (Empidonax trailii extimus) with the southernmost verifiable nest recorded there in 2005.
The San Pedro River is the central corridor of the Madrean Archipelago of "Sky Islands", high mountains with unique ecosystems different from the ecology of the Sonoran desert "seas" that surround it.
More than 300 species of birds nest in by the river or use this corridor as they migrate between South, Central and North America. This includes the yellow-billed cuckoo (Coccyzus americanus). The area provides for more than 80 species of mammals, including jaguar (Panthera onca), coatimundi (Nasua narica), beaver (Castor canadensis frontador), 20 species of bats and several types of rodents. There are also over 65 species of reptiles and amphibians, among them Sonoran tiger salamander (Ambystoma mavortium stebbinsi) and western barking frog (Eleutherodactylus augusti). Some notable fish species native to the river are the endangered Gila chub (Gila intermedia), both the longfin and speckled dace, Sonora sucker and desert sucker, and the roundtail chub. The flora includes Fremont cottonwood (Populus fremontii), Goodding willow (Salix gooddingii), velvet mesquite trees, and the Huachuca water umbel (Lilaeopsis schaffneriana spp. recurva), Federally listed as endangered.
In recent decades, rapid growth and population increases in southern Arizona has caused concern with this river.  Several non-profit organizations have risen in recent years to raise awareness of this problem. The San Pedro Riparian National Conservation Area (SPRNCA) was established in 1988 to protect some forty miles of the upper San Pedro valley. The Nature Conservancy also owns several preserves in the watershed, including the San Pedro River Preserve,  Aravaipa Canyon Preserve, Muleshoe Ranch Preserve, Ramsey Canyon Preserve, and most recently, Rancho Los Fresnos.  Rancho Los Fresnos, near the river's source, is the largest ciénega, an isolated desert spring or marsh, remaining in the San Pedro River watershed. Its protection is important as 99% of the ciénegas in the Southwest have been drained and destroyed.
With large portions of the river dry much of the year, Bureau of Land Management (BLM) wildlife biologist Mark Fredlake proposed restoring beaver to the watershed to retain water flows into the dry season and to support re-growth of the historic riparian vegetation. Riparian habitat covers only 1% of the Southwest but supports 50% of breeding bird species and is vital as a food source for migrating avifauna. Fredlake reasoned that beaver dams would raise the water table, allowing groundwater to recharge the river's flow in the dry season. From 1999 to 2002, 19 beavers were released into the SPRNCA, a 40-mile (64 km) stretch of the river, in Cochise County. By 2006 there were more than 30 dams. The beavers also dispersed widely and rapidly. One beaver migrated to Aravaipa Canyon, more than 100 rivermiles away; another to the river's terminus at the Gila River, earning itself the moniker “the surfing beaver”; and others up into Mexico, building several dams along the river’s upper tributaries. The program was successful with measurable increases in bird diversity and formation of deep pools and lasting flows. In 2008, flooding destroyed all the beaver dams and this was followed by a long drought. However, as in historic times the beaver seems well adapted to the San Pedro River, and the 2009 dam count is back above 30 with a current population between 30 and 120 beavers. A short video reviews the use of re-introduced beaver to restore the river. In the upper river, re-introduced beavers have created willow and pool habitat which has extended the range of the endangered Southwestern willow flycatcher (Empidonax trailii extimus) with the southernmost verifiable nest recorded there in 2005.
San Pedro River (Arizona)