thumb|307x307px|Goosenecks State Park, view of San Juan river from overlook, Utah

The San Juan River is a major tributary of the Colorado River in the Southwestern United States, providing the chief drainage for the Four Corners region of Colorado, New Mexico, Utah, and Arizona. Originating as snowmelt in the San Juan Mountains (part of the Rocky Mountains) of Colorado, it flows through the deserts of northern New Mexico and southeastern Utah to join the Colorado River at Glen Canyon.

The river drains a high, arid region of the Colorado Plateau. Along its length, it is often the only significant source of fresh water for many miles. The San Juan is also one of the muddiest rivers in North America, carrying an average of 25 million US tons (22.6 million t) of silt and sediment each year.

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 of the Four Corners quadripoint) before entering southeastern Utah. West of Bluff, Utah the river slices through the Comb Ridge and enters a series of rugged winding canyons, often over in depth. The lower of the San Juan River, in a remote portion of the Glen Canyon National Recreation Area, are flooded by Lake Powell, which is formed by Glen Canyon Dam on the Colorado River. The San Juan joins the Colorado in San Juan County, Utah at a point about to the north of Navajo Mountain and northeast of Page, Arizona. Southern tributaries such as the Chaco River are mostly ephemeral but can carry large volumes of water during flash floods.

Discharge

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 , per year.

{|class="wikitable sortable collapsible collapsed" border="1" style="float: right; clear: right; margin-left: 0.5em"

!colspan=7|USGS real-time stations on the San Juan River

|-

!Gage location<br>(ID number)

!Start<br>year

!Average<br>discharge

!Maximum<br>discharge

!Minimum<br>discharge

!Drainage<br>area

!Percent of<br>total<br>watershed

|-style="font-size:9pt; text-align:center;"

|Pagosa Springs, CO<br>09342500

|1935

| ft<sup>3</sup>/s<br>(10 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(708 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(0.2 m<sup>3</sup>/s)

| mi<sup>2</sup><br>(728&nbsp;km<sup>2</sup>)

|1.1%

|-style="font-size:9pt; text-align:center;"

|Carracas, CO<br>09346400

|1961

| ft<sup>3</sup>/s<br>(17 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(243 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(0.02 m<sup>3</sup>/s)

| mi<sup>2</sup><br>(3,240&nbsp;km<sup>2</sup>)

|5.1%

|-style="font-size:9pt; text-align:center;"

|Archuleta, NM<br>09355500

|1954

| ft<sup>3</sup>/s<br>(30 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(535 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(0.2 m<sup>3</sup>/s)

| mi<sup>2</sup><br>(8,443&nbsp;km<sup>2</sup>)

|13.3%

|-style="font-size:9pt; text-align:center;"

|Farmington, NM<br>09365000

|1931

| ft<sup>3</sup>/s<br>(56 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(849 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(0.8 m<sup>3</sup>/s)

| mi<sup>2</sup><br>(18,750&nbsp;km<sup>2</sup>)

|29.4%

|-style="font-size:9pt; text-align:center;"

|Shiprock, NM<br>09368000

|1935

| ft<sup>3</sup>/s<br>(56 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(2,265 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(0.2 m<sup>3</sup>/s)

| mi<sup>2</sup><br>(33,400&nbsp;km<sup>2</sup>)

|52.4%

|-style="font-size:9pt; text-align:center;"

|Four Corners, CO<br>09371010

|1977

| ft<sup>3</sup>/s<br>(55 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(479 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(3 m<sup>3</sup>/s)

| mi<sup>2</sup><br>(37,800&nbsp;km<sup>2</sup>)

|59.3%

|-style="font-size:9pt; text-align:center;"

|Bluff, UT<br>09379500

|1914

| ft<sup>3</sup>/s<br>(61 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(1,982 m<sup>3</sup>/s)

| ft<sup>3</sup>/s<br>(0 m<sup>3</sup>/s)

| mi<sup>2</sup><br>(59,700&nbsp;km<sup>2</sup>)

|93.5%

|-

|colspan=7|<small>Stations are listed from furthest upstream to furthest downstream. Although river discharge is generally expected to increase from upstream to downstream, note that discrepancies in the data may be due to differences in the period of record, as well as human modifications, diversions, and dams.</small>

|-

|}

The San Juan River annual hydrograph exhibits large seasonal variations with the highest monthly flow of in June, and the lowest of in December. to less than for the 1964–2016 period, although a minimum release from the dam prevents the river from drying up in the summer. Persistent drought conditions in the 21st century have further reduced the flow of the San Juan River, with an average annual discharge of or between water years 2000 and 2016.

Geology

The oldest geologic feature of the San Juan River basin is the San Juan Mountains, which consist largely of Precambrian and Paleozoic crystalline rock and outcrops of Tertiary volcanic rock. During the Paleocene and Eocene (about 66–34 million years ago), streams draining off the southern flank of the San Juan Mountains terminated in the San Juan Basin around present-day Farmington, slowly filling it with thick layers of sediment. 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.

Fluvial deposits indicate that a stream flowed west across the Colorado Plateau to join the Colorado River at least by the late Miocene (about 5 million years ago). This may have been the ancestral Dolores River, before the uplift of the Ute Mountains diverted it to its present northerly course. When the San Juan Basin filled and overflowed, it formed an outflow channel west into the old Dolores River bed, establishing the San Juan River's modern course.

thumb|left|San Juan River entrenched meanders in the Monument Upwarp, [[Goosenecks State Park, Utah]]

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. The Monument Upwarp consists of a series of parallel anticlines and synclines running generally north to south in an area roughly long and wide. Where the river passes through these formations, it has sliced deep canyons through the reddish rock. In places, the San Juan has entrenched its ancient meanders thousands of feet into the bedrock, as can be observed in Goosenecks State Park, where it winds through a set of horseshoe bends while traveling a straight-line distance of only . The canyon cutting was accelerated during the Pleistocene Ice Ages when the climate of the area was much wetter. The wetter climate resulted in floods of up to –ten times larger than any flooding of the San Juan in recorded human history.

The San Juan River flows through highly erodible sedimentary rock–such as sandstone, siltstone, and shale–that make up rock formations such as the slide-prone Chinle Formation. As a result, the San Juan is an extremely muddy river, contributing more than half of the sediment that occurs in the upper Colorado River above Lees Ferry