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A Description of The San Juan Watershed

Arising on the western slope of the Continental Divide in southwestern Colorado, the San Juan River flows from the San Juan Mountains north of Pagosa Springs, Colorado, and enters the extreme northwestern section of New Mexico via Navajo Reservoir in Rio Arriba County to the west of the Jicarilla Apache Reservation and the Carson National Forest. The course of the San Juan River in New Mexico turns westward for some 140 miles before the river turns back north and re-enters Colorado just a few miles to the east of the cartographic landmark known as "Four Corners". The San Juan River then resumes its westerly direction across Southern Utah towards its confluence with the Colorado River.

The San Juan River is a major tributary of the Colorado River. The watershed in New Mexico is located in the upper northwest corner.

San Juan Basin Map


The San Juan River Basin in New Mexico includes lands from four counties. It encompasses all of San Juan County, most of the northern half of McKinley and western half of Rio Arriba counties, while taking up a relatively small corner of Sandoval County. Parts of the Navajo, Ute Mountain and Jicarilla Apache Reservations are in the basin. The San Juan River portion of the Upper Colorado Basin in New Mexico covers approximately 9,725 square miles, or 25% percent, of the total Upper Colorado drainage and consists of two sub-basins, those of the San Juan River and Navajo River. Water used in the basin largely comes from surface water sources. Ground water is used for domestic purposes and livestock watering. Irrigated agriculture predominately uses surface water withdrawals. Losses from power production and reservoir evaporation also affect the surface water supply.

A number of tributaries arise in southern Colorado to flow south toward their confluences with the San Juan River in New Mexico. These major tributaries are the Los Piņos, Animas, La Plata, and Mancos Rivers. The Navajo River also begins in southern Colorado, enters New Mexico and drains an area of 245 square miles, then turns north near Dulce where it is joined by the Amargo River, and reenters Colorado, discharging into the San Juan River near Juanita. The length of the Navajo River in New Mexico is less than fifteen miles, all within the Jicarilla Apache Reservation. Several tributaries of the San Juan River originate in New Mexico including La Jara Creek, Gobernador Canyon, Canyon Largo, and Chaco Wash, each of which are ephemeral watercourses.


The Colorado Plateau physiographic region extends into the northwestern section of the State of New Mexico, and this plateau region comprises the major portion of the San Juan River Basin of New Mexico. The area is generally one of horizontal sedimentary rocks carved into a gentle relief of broad mesas and valleys, buttes, plateaus, and canyons. The area is termed the Navajo and Canyon Lands section of the Colorado Plateau province.

The New Mexico portion of the San Juan River Basin is delineated on the north by the New Mexico/Colorado State Line and on the west as the New Mexico/Arizona State Line. The southwestern edge of the basin is delineated by the peaks of the Chuska Mountains, which gradually rise to the Continental Divide at the southernmost tip of the basin. The Divide also gives the basin its eastern limits as it extends northward into Colorado.

The basin gradient extends generally westward from the point where the San Juan River flows from Colorado into New Mexico at an elevation of about 6,600 feet. The elevation of the river at Farmington is about 5,500 feet and at the point near Four Corners where the river leaves New Mexico and returns to Colorado the elevation is about 4,800 feet. The botanical species within the basin correspond to changes in elevation. The floor of the San Juan River Valley was originally populated by grasses, but these have mostly been replaced with irrigated croplands. The intermediate broad mesas are now predominately vegetated by grasses, sagebrush, pygmy piņon and junipers. Ultimately, the higher elevations are populated by stands of pine, fir and spruce.

The major portion of the San Juan River Basin consists of broad expanses of grassland and piņon-juniper stands, with an average mild continental climate which lacks extremes in hot or cold conditions. With precipitation under ten inches per year, this zone is principally arid, although rainfall is sufficient for some grasses, but not for dryland farming. The zone can be subdivided into an upper region of piņon/juniper forest where rainfall generally increases with increasing elevation. The lower, more open and arid valley bottoms constitute an area marked by a paucity of trees except along streams and by the scattered grasses, cacti, yuccas, and low desert shrubs.

The lower zone includes an extensive area drained by the San Juan River and its tributaries. This area is characteristically a great open plain with narrow bordering patches of piņon/juniper and scrub oak along the margins of surrounding foothills. This extensive valley bottom is also a region of deep erosion, comprised of many canyons, dry washes, picturesque badlands, rich coal fields, and plentiful fossil beds.

The Chuska Mountains rise along the southwest corner of the basin to between 8,000 and 9,000 feet, and are actually a long mesa or plateau. Most of this table land is of sandstone, with abrupt rim rock margins and ridges of lava and basalt in the northernmost sections.

The summits of the Chuska Mountains are surrounded by forests and shallow lakes, usually without outlets. Many springs and short creeks rise in the canyons below the rim, flowing for short distances down steep slopes or in a few instances out into the nearby valleys. Water is abundant for stock but little is available for irrigation purposes. The vegetation ranges from open forests of ponderosa pine with grasses and shrubs to the colder, upper slopes covered with aspens, firs and spruces. Precipitation in this area progresses from 12 to 16 inches annually with increases in elevation. The eastern reaches of the basin beyond the vast expanses of grasslands, which constitutes the majority of the basin, consists of large stands of piņon/juniper forest gradually changing with increasing elevation into pine forests. Precipitation along the eastern reaches of the basin increases with altitude, from 10 to 18 inches on the average, annually.

The major portion of the San Juan River Basin of New Mexico receives 10 inches or less of average precipitation annually, and is therefore classified as arid. The areas of the basin where rainfall ranges from 10 to 16 inches is classified as semi-arid, although this classification should not be rigidly fixed where stands of piņon/juniper dominate. As the elevation increases towards the periphery of the basin, precipitation increases concomitantly so that above 5,900 and up to 7,200 feet the semi-arid zone is usually prevalent, beyond which the climate becomes more humid and cooler. Below 6,900 feet precipitation is generally too sparse for the maturing of crops, while in the moist zone of the higher elevations the growing season is too short.

The San Juan River Basin is geologically a structural as well as a topographic and hydrologic basin. Deposition of sediments of marine and continental origins, which commenced in early Paleozoic time, has continued in the basin with just a few intermittent interruptions. Sedimentary rocks in the central basin are at least 15,000 feet deep.

The San Juan structural basin extends into southwestern Colorado some 25 miles and slightly into Arizona. The structural basin boundaries on the east are delineated by the Nacimiento and southern San Juan Mountains, on the south by the Zuni Mountains, on the west by the Defiance uplift and the Chuska and Carrizo Mountains, and on the north by the Ute, La Playa, and northern San Juan Mountains.

Alluvium of recent age is found in and along channels of the principal streams and their tributaries and consist primarily of stream deposits and terrace gravel, both largely floodwash residuals. The San Juan River and other major streams of the basin are actively downcutting their channels, which are kept relatively free of thick accumulations of sediment through the action of flood flow and normal streamflow.

Three soil types predominate in the New Mexico portion of the San Juan Basin. Most of the area south of the San Juan River consists of a medium textured, moderately deep to shallow soil that mantles gently rolling topography. Along the San Juan River and its northern tributaries, a medium- to heavily-textured deep soil is found which is suitable for agriculture. In the mountainous terrain of the northeastern part of the basin, shallow to moderately deep soils with light- to medium-textures dominate.

The San Juan River Basin has been associated with energy production and its concomitant environmental pollution problems for the better part of this century. The first oil-and-gas well was drilled near Farmington in 1900. The coal mining industry was started in 1911. Commercial petroleum fuel production was first organized in the 1920's. It was not until the 1950's that the fuel industry boom became a major force in the growth and development of the basin's economy, however, it remains a major economic factor in the Four Corners region today.

Surface Water Quality Concerns in the San Juan River Basin

The New Mexico Oil Conservation Division (OCD) and the United States Bureau of Land Management (BLM) are involved with energy development and associated environmental issues within the San Juan Basin (18). One emerging water quality concern affecting threatened and endangered fish in the region is their vulnerability to Polycyclic Aromatic Hydrocarbons (PAH). BLM, in consultation the State's OCD and NMED as well as other United States Department of the Interior agencies including the Fish and Wildlife Service, Bureau of Reclamation, Bureau of Indian Affairs and USGS, has developed a monitoring plan for the basin aimed at verifying alleged PAH contamination from the oil and gas industry. The monitoring project attempts to identify any possible PAH contamination sources. The plan is part of the BLM's Riparian Program, and was implemented in 1994. Another aspect of the Riparian Program is weed control. The use of herbicides in the oil fields is closely monitored using criteria developed through the use of DRASTIC indexing. DRASTIC is a risk assessment modeling program for evaluating potential ground water pollution which features a numerical rating system developed by EPA. The acronym stands for Depth to water; (net aquifer) Recharge; Aquifer media; Soil media; Topography; Impact on the vadose zone media; and Conductivity. Applicators are limited to sixteen herbicides, and are limited to their area of use by DRASTIC's parameters.

BLM's Riparian Program has also created a demonstration project of its implementation efforts in the Pump Canyon watershed. This relatively large block of public land is drained by an ephemeral tributary to the San Juan River. Their confluence is located approximately eight miles downstream from Navajo Reservoir Dam. The watershed is part of the Fruitland Coal Seam Development area which has sustained heavy industrialized changes in the recent past including considerable road, pipeline, and facility construction.

 One goal of the project includes improving water quality and vegetative diversity through development and implementation of best management practices on existing uses. Accomplishments in the watershed have included initiation of surface water monitoring, several dozen acres of salt cedar treatment, riparian plantings, creating riparian fencing, implementing a moratorium on livestock grazing, developing 150-acre upland vegetative treatment project, and overseeing gas development mitigation efforts. In the San Juan River Basin there are 129.4 assessed river miles that are listed as non- or partially-supporting their designated uses. 

 The specific pollutant or threat in this lack of support are metals, turbidity, nutrients, pathogens, dissolved oxygen and total ammonia, dissolved solids, salinity, temperature, total phosphorus, habitat alteration, grazing and flow alteration. Among the probable sources for these causes are resource extraction, hydromodification, agriculture and overall watershed condition. There are no toxins listed at acute levels in the San Juan River Basin. Chronic levels of toxins have been listed for aluminum, mercury and selenium. A potentially viable salinity control project at the Hammond Diversion near Bloomfield has been identified by the U.S. Bureau of Reclamation (19). The San Juan River downstream of the Hammond Diversion is the only stream in New Mexico currently listed in the State's Fish Consumption Guidelines due to elevated mercury levels in fish. The San Juan River Basin has 15,198 assessed lake acres that are listed as only partially supporting their designated uses. The specific pollutant or threat in this lack of support are attributed to fish tissue mercury and metals. The probable source of these causes is currently unknown. However, aluminum and selenium occur naturally in the sediment in this area. Mercury levels in fish tissue are thought to be due to atmospheric deposition.

Ground Water Quality Concerns in the San Juan River Basin

The majority of ground water concerns in the San Juan River Basin are releases from leaking underground and above ground storage tanks, and from oil and gas production, pipelines, storage, distribution and refining sites. There are two reported cases of ground water contamination from landfills in the San Juan River Basin near Farmington.

Leaking Underground/Above-Ground Storage Tanks and Refined Petroleum Products

As of October 1998, the San Juan River Basin had approximately 165 incidences where leaking underground storage tank sites and one above-ground storage tank site were reported. The majority of these reported ground water contamination cases were due to gas, oil, diesel, gasoline additives, petroleum constituents such as benzene, toluene, ethyl benzene, and xylene and solvents such as chlorinated methane, ethanes, propanes and ethylenes. The bulk of these sites are concentrated around the major industrialized areas such as Farmington, Aztec and Bloomfield in San Juan County and Dulce in Rio Arriba County. These areas typically associated with service stations, liquid petroleum storage and distribution centers, pipelines and oil extraction operations.

Total Dissolved Solids

Point source ground water contamination due to TDS is found near many of the uranium mining and milling in the San Juan River Basin near Crownpoint. TDS also results from natural limestone deposits in this area.


Many landfills in New Mexico have received large amounts of liquid and/or industrial wastes. Ground water contamination has been detected in two landfills in the San Juan River Basin. These landfills are located near Farmington in San Juan County. Contaminants include chlorinated solvents and basic-, neutral- and acidextractable compounds and crude oil.


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This page last updated November 08, 2007

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