Although Europeans explored the Four Corners region as early as the 1700s, it was not settled until the gold and silver booms of the 1860s, when settlers arrived in large numbers from the eastern United States.

The U.S. federal government has built a number of large dams in the San Juan River system to control floods and to provide irrigation and domestic water supply.

The river flows southwest through the foothills of the Rocky Mountains through the town of Pagosa Springs and reaches the Navajo Lake reservoir just north of the New Mexico border, near Arboles, Colorado.

Below the Navajo Dam, the San Juan River flows west through a narrow farming valley in the high desert country of the Colorado Plateau.

[6] From there it flows west through the Navajo Nation, turning northwest near Shiprock and its namesake monolith, crossing very briefly back into southwest Colorado (within half a mile (0.8 km) of the Four Corners quadripoint) before entering southeastern Utah.

[8][10] According to the U.S. Bureau of Reclamation, the average unimpaired runoff or natural flow of the San Juan River basin over the 1906–2014 period was about 2,900 cubic feet per second (82 m3/s), 2,101,000 acre-feet (2.592 km3) per year.

The U.S. Geological Survey (USGS) stream gaging station at Bluff, Utah, recorded an average annual discharge of 2,152 cubic feet per second (60.9 m3/s), or 1,559,000 acre-feet (1.923 km3), for the 1915–2013 period.

[15] Persistent drought conditions in the 21st century have further reduced the flow of the San Juan River, with an average annual discharge of 1,358 cubic feet per second (38.5 m3/s) or 984,000 acre-feet (1.214 km3) between water years 2000 and 2016.

[18] Over millions of years, the burial of organic material under sedimentary layers created the abundant coal, oil, and natural gas deposits found in the area today.

[18] Though Tectonic forces about 2–3 million years ago caused the terrain to rise across the Monument Upwarp in southeast Utah and northeast Arizona, the river maintained its course as an antecedent stream.

[25] The San Juan River drains approximately 24,600 square miles (64,000 km2) in Colorado, New Mexico, Utah, and Arizona; the watershed land area is almost the same size as the state of West Virginia.

[29] Due to the low rainfall and lack of substantial groundwater reserves, agricultural use is scarce, except for river valleys and in higher foothill areas influenced by wetter montane climates.

Other notable features in the watershed include Shiprock, a nearly 1,600-foot (490 m) high monadnock formation sacred to the Navajo people, and Monument Valley, whose rugged scenery has appeared in many Western films and other media.

[52] The San Juan River and its tributaries were an important water source for Native Americans as early as 10,000 BC, when Paleo-Indians inhabited the Four Corners region.

By 500 BC–450 AD, the Basketmaker culture was succeeded by the Ancestral Puebloans or Anasazi, who developed distinctive irrigation methods and masonry architecture (pueblos);[53] many ruins and sites are preserved in the San Juan watershed in places such as Mesa Verde National Park.

About a decade later, in 1776, the Domínguez–Escalante expedition passed through the San Juan River country, attempting to find a route from Santa Fe to the presidio in Monterey, California.

Domínguez and Escalante crossed the San Juan River near where Navajo Lake is today and described the area as having good land suitable for settlement and farming but also "excessively cold even in the months of July and August.

[63] Neither Spain nor Mexico established permanent settlements in the San Juan River country due to the harsh winter weather and presence of the native population.

"[73][74] However, in 1879 more than 200 Mormon pioneers embarked on the Hole-in-the-Rock expedition which established the agricultural settlement of Bluff, Utah on the lower San Juan River in April 1880.

[75][76] The colony suffered greatly in its early years due to a series of floods, but the settlers persisted, as the LDS church strongly wished to maintain its presence in southeast Utah.

[81] Farmington, the largest city on the San Juan River and in the Four Corners region, was established in 1901 and grew significantly in the 1920s as coal, oil, and natural gas were discovered in the area.

The federal government paid for the cost of relocating the line, which began operating in August 1962; however, this section along the San Juan River was abandoned barely five years later due to falling traffic.

)[86][87] In 2015, one of the worst environmental disasters in Colorado and New Mexico's history occurred when the Gold King Mine near Silverton experienced a massive wastewater spill.

More than 3 million gallons (11,400 m3) of highly acidic waste spilled into the Animas and San Juan Rivers, turning the water a bright yellow-orange color.

The spill temporarily threatened irrigation and domestic water supply as far downstream as the Navajo Nation and contaminated sediment with heavy metals, including lead and zinc.

[92] The U.S. Reclamation Service (now the Bureau of Reclamation) conducted surveys of dam sites on the lower San Juan River in 1914, as part of the Boulder Canyon Project (the so-called "Bluff reservoir" was never built, after engineers determined that the high silt load of the lower San Juan would make a storage reservoir here useless within a short time).

With the exception of trout and dace, which inhabit clear, cold mountain streams in the headwaters, the native fishes are mostly adapted to the warm, shallow and silty characteristics of the lower San Juan.

[9] In addition, the impoundment of water at Navajo Dam does not appear to have a significant effect on the amount of sediment transported in the river; thus, the aquatic environment of the lower San Juan, though somewhat degraded, still resembles pre-development conditions.

Applications for private trips are approved by the Bureau of Land Management's Monticello Field Office via lottery; about 900 spots are awarded each year out of more than 4000 requests.

[118] Below Clay Hills, the San Juan flows through very isolated country to Lake Powell, where a long flat-water paddle is required to reach the closest services at Dangling Rope Marina.