Biological Assessment

Navajo Reservoir Operations, Colorado River Storage Project

Colorado-New Mexico-Utah

Bureau of Reclamation

Upper Colorado Region

Western Colorado Area Office

July 24, 2002 

(Revised July 2003)

Contents

Page

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . J-1

Background . . . . . . . . . . . . . . . . . . . . . . . . . . . J-3

San Juan River . . . . . . . . . . . . . . . . . . . . . . . . . J-5

Project Description . . . . . . . . . . . . . . . . . . . . . . . J-7

Flow Recommendations . . . . . . . . . . . . . . . . . . . . J-14

Hydrology and Water Quality . . . . . . . . . . . . . . . . J-17

Hydrology . . . . . . . . . . . . . . . . . . . . . . . . . J-17

Water Quality . . . . . . . . . . . . . . . . . . . . . . . J-19

Species Accounts . . . . . . . . . . . . . . . . . . . . . . . J-22

Endangered Species . . . . . . . . . . . . . . . . . . . . J-22

Colorado Pikeminnow . . . . . . . . . . . . . . . . J-22

Razorback Sucker . . . . . . . . . . . . . . . . . . J-30

Bonytail and Humpback Chub . . . . . . . . . . . J-32

Interior Least Tern . . . . . . . . . . . . . . . . . . J-32

Southwestern Willow Flycatcher . . . . . . . . . . . J-32

California Condor . . . . . . . . . . . . . . . . . . . J-34

Black-Footed Ferret . . . . . . . . . . . . . . . . . J-34

Threatened Species . . . . . . . . . . . . . . . . . . . . J-34

Bald Eagle . . . . . . . . . . . . . . . . . . . . . . . J-34

Navajo Sedge . . . . . . . . . . . . . . . . . . . . . J-35

Mexican Spotted Owl . . . . . . . . . . . . . . . . . J-35

Species of Concern . . . . . . . . . . . . . . . . . . . . J-35

American and Arctic Peregrine Falcons . . . . . . J-35

Black Tern . . . . . . . . . . . . . . . . . . . . . . J-36

White-Faced Ibis . . . . . . . . . . . . . . . . . . . J-36

 Yellow-Billed Cuckoo . . . . . . . . . . . . . . . . J-36

Roundtail Chub . . . . . . . . . . . . . . . . . . . . J-36

New Mexico Silverspot and San Juan Checkerspot

Butterflies . . . . . . . . . . . . . . . . . . J-37

San Juan Tiger Beetle . . . . . . . . . . . . . . . . J-37

Gunnison Sage Grouse . . . . . . . . . . . . . . . . J-37

Other Species of Concern . . . . . . . . . . . . . . . . J-37

Golden Eagle . . . . . . . . . . . . . . . . . . . . . J-38

Bluehead Sucker . . . . . . . . . . . . . . . . . . . J-38

Mottled Sculpin . . . . . . . . . . . . . . . . . . . . J-38

Northern Leopard Frog . . . . . . . . . . . . . . . J-38

Bighorn Sheep . . . . . . . . . . . . . . . . . . . . J-38

Alcove Rock Daisy . . . . . . . . . . . . . . . . . . J-38

Literature Cited . . . . . . . . . . . . . . . . . . . . . . . . J-39
ii

Attachments

Attachment

A River Mile Demarcations, San Juan River

B Depletion Table Utilized in Hydrology Analysis

C Hydrology Analysis Tables and Figures

D Existing Water Contracts from Navajo Reservoir

E Water Quality Data
Biological Assessment –

Navajo Reservoir Operations

Introduction

This biological assessment is prepared pursuant to Section 7

of the Endangered Species Act of 1973 (ESA), as amended, to

address impacts of a proposal to operate Navajo Dam and

Reservoir on threatened or endangered species, species that

are candidates for listing, and other species of concern. 

Included are the impacts of depletions from evaporation from

Navajo Reservoir. A biological assessment was originally

prepared in July, 2002; this 2003 version replaces the July

version and addresses several questions and concerns brought

up by the Fish and Wildlife Service (Service) in a

memorandum dated October 30, 2002 (Service, 2002a) and in

subsequent meetings.

Navajo Dam was constructed between 1958 and 1963 under the

Colorado River Storage Project Act of 1956 (CRSP) to meet

multiple water resource purposes. The dam is located on the

San Juan River approximately 44 miles upstream from

Farmington, New Mexico. The reservoir created holds

approximately 1.7 million acre-feet of water and extends into

both New Mexico and Colorado. The reservoir has a surface

area of 15,610 acres and has

150 miles of shoreline. The normal operating range for the

reservoir is between 5,990 feet and 6,085 feet. Navajo

Reservoir has a maximum content of 1,701,300 acre-feet. 

Below

5,985 feet the inactive pool contains 625,675 acre-feet.

CRSP authorized the Navajo Unit to regulate the flow of the

San Juan River to make it possible for Upper Basin States to

consistently use their Upper Colorado River Basin Compact

(Compact) apportionments. The components of the Compact

apportionment for New Mexico and Colorado supported by the

Navajo Unit include the San Juan-Chama Project, the Navajo

Indian Irrigation Project (NIIP), the Jicarilla Apache Nation

water right settlement, and the Animas-La Plata Project (ALP

Project) as well as numerous smaller water uses, both existing

and proposed. The Unit provides the benefits of river
J-2

regulation, flood control, recreation, fish and wildlife, and

generation of hydroelectric power. Reclamations proposed

reoperation of Navajo Reservoir must be compatible with the

authorizing legislation for the Navajo Unit.

In addition to regulating riverflows, the reservoir stores water

for the Navajo Indian Irrigation Project (NIIP) and various

municipal and industrial uses. At the present time, NIIP

diverts an average of approximately 160,000 acre-feet from

the reservoir for irrigation south of Farmington. In the

future this use is expected to approximately double. Navajo

Dam provides flood control and also recreation and fishery

benefits.

After completion of the Navajo Unit in 1962, criteria governing

releases of water from the dam focused primarily on meeting

irrigation needs, providing flood control, maintaining stable

river flows, and providing a recreation pool in Navajo

Reservoir. Native fish populations and their habitat have been

adversely affected or modified by the Navajo Unit.
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Some of the other factors affecting native fish in the San

Juan are loss of riverine habitat to Lake Powell, introduction

of non-native fish, past control of native fish to enhance

recreational fisheries, migration barriers, and channel

modifications.

Reclamation requested initiation of ESA consultation on the

operation of Navajo Dam in a memorandum to the Service

dated July 30, 1991. The Service (1991) concurred with a

later request from Reclamation that consultation on the

operation of Navajo Dam and Reservoir under Section 7 of the

ESA be extended while research was conducted on flow needs

of endangered fish in the San Juan River. During the

research period, which extended from 1991 to 1997,

Reclamation provided test flows to mimic a natural

hydrograph. Following the research period, a report on Flow

Recommendations for endangered fish was prepared (Holden,

1999). Holden (2000) presents an evaluation of the results of

the research period.

The Service and Reclamation have consulted formally and

informally throughout the 1990s regarding the potential

impacts of operation of Navajo Dam on listed species. 

Previous versions of this biological assessment have previously

been provided the Service and Tribal governments.

Reclamation plans to implement the proposed actionto

operate Navajo Dam to meet Flow Recommendations for

endangered fish- by modifying the operation decision criteria

of the dam to provide sufficient releases of water at times,

quantities, and durations necessary to protect endangered fish

and their designated critical habitat while meeting the

authorized purposes of the Navajo Unit and enabling future

water development to proceed in compliance with Federal and

State laws, interstate compacts, court decrees, and Indian

trust responsibilities. Reclamation plans to complete a final

environmental impact statement (EIS) and Record of Decision

prior to finalizing operation plans and criteria.

The Services Region 2 (2001a) has provided the following list

of endangered, threatened, and species of concern that could
J-4

potentially be affected by the EISs proposed operation

changes.

Bald eagle (Haliaeetus leucocephalus)

Interior least tern (Sterna antillarum athalassos)

Southwestern willow flycatcher (Empidonax trailii

extimus)

Colorado pikeminnow (Ptychocheilus lucius)

Razorback sucker (Xyrauchen texanus)

American peregrine falcon (Falco peregrinus anatum)

Arctic peregrine falcon (Falco peregrinus tundrius)

Black tern (Chlidonias niger)

White-faced ibis (Plegadis chihi)

Yellow-billed cuckoo (Coccyzus americanus)

Roundtail chub (Gila robusta)

New Mexico silverspot butterfly (Speyeria nokomis

nitocris)

San Juan checkerspot butterfly (Euphydryas anicia

chuskae)

San Jaun tiger beetle (Cicindela lengi jordai)

Threatened

Endangered

Endangered

Endangered

Endangered

Species of concern

Species of concern

Species of concern

Species of concern

Species of concern

Species of concern

Species of concern

Species of concern

Species of concern
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Region 6 of the Service (with responsibilities in the Utah

portion of study area) has reviewed the above list and has

added the following additional species for consideration

(Service, 2001b):

Navajo sedge (Carex specuicola)

Bonytail (Gila elegans)

Humpback chub (Gila cypha)

California condor (Gymnogyps

californianus)

Mexican spotted owl (Strix occidentalis

lucida)

Black-footed ferret (Mustela nigripes)

Gunnison sage grouse (Centrocercus

minimus)

Threatened

Endangered

Endangered

Endangered

Threatened

Endangered

Candidate

Indian Tribes and Nations in the area have been requested to

provide lists of species of concern to the Tribes. The Navajo

Nation (2001) provided a list of species of special concern

that could occur within the project impact area. Species

included the golden eagle (Aquila chrysaetos), bluehead sucker

(Catostomus discobolus), mottled sculpin (Cottus bairdi),

southwestern willow flycatcher, peregrine falcon, roundtail

chub, bald eagle, Colorado pikeminnow, northern leopard frog

(Rana pipiens), razorback sucker, yellow-billed cuckoo, bighorn

sheep (Ovis canadensis), and alcove rock daisy (Perityle

specuicola).

This assessment concludes that the operational changes in the

Proposed Plan may affect, but not likely adversely affect the

following listed species: Colorado pikeminnow, razorback

sucker, southwestern willow flycatcher, and bald eagle. It is

predicted that these species will be benefitted by the new flow

regime that improves their habitat conditions. Depletions

from the reservoir evaporation and other Unit depletions are

considered an adverse effect on listed fish; however, the

proposed plan should be beneficial.

Background

On August 6, 1991, the Service issued an updated Recovery

Plan for the Colorado pikeminnow that identified the San Juan
1

 The Animas-LaPlata Project would deplete flows from the Animas River, a major tributary of the

San Juan River upstream from critical fish habitat. See the FSFEIS (Reclamation, 2000) for further information.

J-6

River from Farmington, New Mexico to Lake Powell as a

recovery area. The Service issued a final biological opinion

for the ALP Project1

 in 1991 with a reasonable and prudent

alternative that included: seven years of research to determine

endangered fish habitat needs in the San Juan; operation of

Navajo Dam to provide water for a wide range of flow

conditions for the endangered fish; a guarantee that the

Navajo Reservoir would be operated to mimic a natural

hydrograph and such operation would be based on research;

legal protection for the reservoir releases to and through the

endangered fish habitat to Lake Powell; and a commitment to

develop and implement the San Juan River Basin Recovery

Implementation Program (SJRBRIP). As a result of this

opinion, the SJRBRIP was formulated (Service, 2000).
2

 The SJRBRIP is a major cooperative effort among entities interested in the goals of endangered fish recovery,

maintenance of existing Navajo Dam and Reservoir authorized purposes, and additional water development in the San Juan River

Basin. In addition to Reclamation, participants include the Service, Bureau of Indian Affairs, Bureau of Land Management,

Southern Ute Indian Tribe, Ute Mountain Ute Tribe, Navajo Nation, Jicarilla Apache Nation, water development interests, and

the States of Colorado and New Mexico.

J-7

The SJRBRIP2

 was established in 1992 to protect and recover

the Colorado pikeminnow and razorback sucker in the San

Juan Basin while water development proceeds in compliance

with applicable Federal and State laws, including fulfillment of

Federal trust responsibilities to several Indian tribes. 

Research goals of the program were to determine limiting

factors to the endangered fish and to determine measures to

eliminate or reduce the limiting factors. Holden (2000)

summarizes research findings and provides direction for future

activities under the SJRBRIP.

The SJRBRIP is intended to provide measures for compliance

with the ESA for water development and water management

activities in the San Juan River Basin. The program includes

elements to protect the genetic integrity of the species, to

augment populations through stocking, to protect and restore

habitat, to protect water quality, to address non-native fish

competition, and to monitor endangered fish population status

and trends. Further information can be found at the

programs website: <http://southwest.fws.gov/ sjrip/>. 

Operating Navajo Reservoir to meet Flow Recommendations is

an important component of the overall program.

In 1994 critical habitat was designated for the Colorado

pikeminnow including the San Juan River from Farmington to

Lake Powell and for the razorback sucker, from the Hogback

Diversion to Lake Powell.

In 2000, the Service issued a new biological opinion on the

ALP Project that included a conservation measure in which . .

.Reclamation is committing to operate Navajo Reservoir to

mimic the natural hydrograph of the San Juan River to

benefit endangered fishes and their critical habitat. Mimicry

of the natural hydrograph will be achieved by following the

San Juan Riverflow Recommendations (Holden, 1999) and

subject to completion of the Navajo Operations EIS and

execution of a Record of Decision (Service, 2000).
J-8

In addition to the ALP Project, other projects in the San Juan

Basin, for example completion of the Navajo Indian Irrigation

Project (NIIP), rely on the SJRRIP, including the reoperation of

the Navajo Unit according to the Flow Recommendations, to

comply with the ESA.

The Coordination Committee of the SJRBRIP has adopted

principles for conducting ESA consultations (SJRBRIP, 2001c) on

water development and these should be referred to for

information on ESA consultation for existing and future water

developments. The Service uses these principles to evaluate

water project compliance with the ESA. When consultation is

initiated, the Service determines if progress toward recovery

has been sufficient for the SJRBRIP to serve as a reasonable

and prudent alternative or measure. The Service also

considers whether the probable success of the SJRBRIP is

compromised as a result of new depletions.
J-9

San Juan River

The San Juan River Basin encompasses approximately 25,000

square miles and the river extends 350 miles from its

headwaters in the San Juan and La Plata Mountains of

Colorado to Lake Powell. The river crosses the Southern Ute

and the Ute Mountain Ute Reservations and the Navajo Nation. 

Approximately 225 miles of the San Juan River are between

Navajo Dam and Lake Powell; the lower 180 miles downstream

from Farmington are designated as critical habitat for the

Colorado pikeminnow and the lower 155 miles as critical

habitat for the razorback sucker. Mean annual runoff in the

river at Farmington just downstream from the confluence with

the Animas River is 1.3 million acre-feet; near Bluff, Utah,

this increases to about 1.4 million acre-feet.

Below Navajo Reservoir, the San Juan River is joined by its

largest tributary, the Animas River, at Farmington before

flowing westward to the Navajo Nation boundary west of

Waterflow, New Mexico. The river continues west and

northwest before entering Colorado near the Four Corners

landmark and flowing into Utah and then Lake Powell.

Since the late 1880s over 20 non-native fish have been

introduced to the San Juan River drainage; channel catfish

and common carp are two of the more common introduced

species in the river. In addition to the Colorado pikeminnow

and razorback sucker, six other native species occur. The

Colorado River cutthroat trout is found in isolated tributaries. 

The roundtail chub is found in very low numbers in the San

Juan and Animas but can be locally common in smaller

tributaries. Bluehead and flannelmouth suckers are found in

both the Animas and San Juan as is the speckled dace which

occurs in upstream areas. Mottled sculpin are found

primarily in the Animas River.

The San Juan River supports a high quality trout fishery for 7

miles downstream from Navajo Dam and a good trout fishery

for the next 10 miles to the Hammond Diversion. According

to a draft report by New Mexico Game and Fish Department

(Wethington and Wilkinson, 2003), native fish declined
J-10

significantly in the river around the Hammond Diversion,

possibly due to increased spring flows. Throughout the 28-

mile reach from the Hammond Diversion downstream to

Farmington, native fish populations increase as habitat

becomes more favorable for those species, although

populations may be limited due to reductions in physical

habitat related to existing flow depletions. The Hammond

Diversion to Farmington reach of river has the highest

percentage of native fish; however, non-native fish such as

carp and fathead minnows are still common in this reach.

The reach between Farmington and Lake Powell maintains the

rivers most natural hydrologic conditions, primarily due to

the influence of the Animas River which is largely unregulated. 

This area includes designated critical habitat for the Colorado

pikeminnow and razorback sucker and supports other native

fish such as the bluehead and flannelmouth suckers. Early

fishery studies and anecdotal information indicate that both

the pikeminnow and razorback were common to fairly common

in the San Juan River in the early years of settlement

(Holden, 2000). Non-native fish are now common in this

reach, particularly downstream from the Public Service of New

Mexico (PNM) diversion dam.

The historic San Juan was similar to other rivers in the upper

Colorado River Basin with large flows during spring snowmelt

followed by low (base) flows the rest of the year; however,

summer and fall spike flows occur due to thunderstorm

events to a greater degree than in other rivers. Following

Navajo Dam construction, spring peaks were reduced by nearly

half and base flows increased (Bliesner and Lamarra, 2000). 

In general, upper reaches of the river are cobble-dominated

and lower reaches are sand-dominated; much of the lower

reaches are canyon-bound. Summer water temperatures have

been lowered in the upper reach of the river due to cold

water releases from Navajo Dam. 

Sediment inflow to the river is significant during summer and

fall thunderstormsthere is historical evidence that this was

much greater around the turn of the century, when there was

rapid erosion of the watershed due to overgrazing or other
J-11

factors. In the 20th century there was also a large invasion

of non-native vegetation into the rivers riparian area. 

Overall, the combination of accelerated erosion in the

watershed, invasion of non-native plants, and regulation of

flow by Navajo Dam has probably created a quite different

river environment than occurred 150 years ago.

The first 7 miles of the river downstream from Navajo Dam

supports a significant wetland/ riparian zone; this section of

river is upstream from irrigation diversions so wetland

vegetation receives water primarily from the river and

tributary groundwater. Important wetlands, extending

approximately 2 miles downstream from the dam, have

developed in areas formerly used for construction borrow

along the river. On the 40 mile reach of river between

Archuleta and Farmington, riparian areas have been impacted

by agriculture, grazing, natural gas development, and

commercial developments. Many of the wetlands in this area

receive water from irrigation ditch seepage and return flows.

From Farmington to Lake Powell, riparian areas of varying

sizes and quality exist and are mainly dependent on

riverflows. While spring peaks have been reduced in this

reach, flows are more natural in this area, but riparian areas

are impacted by livestock grazing and invasion by non-native

plants. The San Juan River corridor supports riparian species

such as cottonwood, willow, and non-native tamarisk and

Russian olive. Non-native species dominate, with native

willows and cottonwoods accounting for less than 15 percent

of the riparian vegetation (Bliesner and Lamarra, 2000). 

Sedges, rushes, reed canary grass, cattails, bulrushes, alkali

sacaton, and galleta grass are typical herbaceous species (BLM,

2002b).

The upland region north and south of the San Juan River is

characterized by desert physiography; broad dry washes carry

significant sediment loads during periodic thunder-storm

events. The project area is semi-arid to arid; the major part

of the basin is less than 6,000 feet in elevation and receives

less than 8 inches of precipitation annually. Vegetation

ranges from pinon-juniper areas around Navajo Reservoir to
J-12

desert shrubs and grasses around the lower San Juan River. 

The pinon-juniper areas are characterized by pinon pine, Utah

juniper, Gambels oak, mountain mahogany, big sagebrush, and

bitterbrush. Scattered ponderosa pine and Douglas fir also

occur.

Towns and communities in the study area include Farmington

at the confluence with the Animas; and Bloomfield, Blanco,

and Archuleta upstream and Fruitland, Shiprock, Bluff, and

Mexican Hat downstream from Farmington. Energy

development, agriculture, and tourism and recreation are

important industries in the area. In particular, agriculture

and recreation are closely related to Navajo Reservoir and its

operation and to flow patterns in the San Juan River.

The frontispiece map shows the general project area and

attachment A provides a demarcation of the river with river

mile designations, starting with River Mile 0 above the high

water line of Lake Powell and ending at River Mile 225 at

Navajo Dam (these River Mile locations will be referred to

throughout the text).

Project Description

The Bureau of Reclamation (Reclamation) proposes to operate

Navajo Dam and Reservoir to implement Endangered Species

Act (ESA)-related Flow Recommendations on the San Juan

River. This change in reservoir operation, along with other

elements of the Recovery Program, would assist in conserving

endangered fish in the San Juan River downstream from

Farmington, New Mexico, and in enabling water development to

proceed in the San Juan River Basin in compliance with

applicable laws, compacts, court decrees, and American Indian

trust responsibilities. To accomplish this action, Reclamation

would continue to operate Navajo Dam to meet the authorized

project purposes while modifying reservoir release patterns to

meet Flow Recommendations which are designed to maintain

or improve habitat for the razorback sucker and Colorado

pikeminnow. Additional information can be found in the

environmental impact statement on the project (Reclamation,
3

 The SJRBRIP Biology Committee acknowledged that some flexibility exists in interpreting the meeting of the upper

limit of 1,000 cfs during the irrigation season. The Biology Committee indicated that during the irrigation season (March through

October) “it may not be effective or necessary to lower releases below 500 cfs until water use in the basin increases to the point

that the water is needed to meet runoff period recommendations. This flexibility is extended only to the irrigation season as

defined...and only until water development reaches the level that additional water is needed for Spring releases” (February 21,

2002, memorandum from Biology Committee to Reclamation).

J-13

2002b).

The twofold purpose of the Proposed Alternative (also referred

to as the 250/5000 Alternative or the Preferred Alternative) is

to (1) develop operating criteria for Navajo Dam and Reservoir

in order to assist in creating and maintaining habitat in the

San Juan River to help conserve and recover populations and

designated critical habitat of the Colorado pikeminnow and

razorback sucker, and (2) maintain the authorized purposes of

the Navajo Unit, including enabling future water development.

This Proposed Alternative is designed to mimic a natural

hydrograph downstream from the confluence of the Animas

River. Navajo Dam would be operated so that releases range

from 250 cubic feet per second (cfs) to 5,000 cfs and

flexibility would be retained to adjust release rates within this

range to respond to new information as it becomes available. 

The SJRBRIP uses a process that involves annual monitoring

and continued research, so the Flow Recommendations may be

refined in response to new information. Reclamation expects

the Service will periodically review operations to determine if

the Flow Recommendations are being met. This will be done

by reviewing operations in light of forecasted inflow and by

reviewing river gage data.

The spring peak release will be planned to meet the statistical

requirements of the spring flow recommendations and will

involve 5,000 cfs releases from Navajo Dam. The decision

chart on the following page will be used to determine spring

releases. The spring peaks would occur in approximately 70

percent of the years. The summer, fall and winter base

releases are also intended to meet the flow recommendation

targets in the river downstream of Farmington of 500 to 1,000

cfs for habitat protection and water storage.3

The proposed operation will help meet or exceed endangered
J-14

fish spring peak recom-mendations. The operation criteria

are also designed and intended to consistently meet

endangered fish minimum base flows downstream from

Farmington (500 cfs). Maximum recommended base flows

(1,000 cfs) downstream from Farmington will occasionally be

exceeded because of high inflows from the Animas Riverthis

would occur even with

250 cfs releases from Navajo Dam.

The Flow Recommendations call for using a moving average of

2 of the 4 downstream gages to monitor whether flows are

kept between 500 and 1,000 cfs. There can be significant

variability in these gage readings and the selective use of any

2 gages could give results above or below the intent of the

Flow Recommendations. Because of this, in 2002 the Biology

Committee of the SJRBRIP suggested that flows be monitored

by following: Use the lesser of the average of Bluff, Four

Corners and Shiprock (gages) and the average of Farmington,

Shiprock, and Four Corners (gages). . .extreme conditions (low

or high flows) identified by. . .Reclamation will be handled on

a case-by-case basis with recommendations of the Biology

Committee. The Service has provided written support of this

approach to monitoring.

Reclamations intent, which will be documented in the FEIS,

will be to maintain the recommended base flows in the

critical habitat reaches by using the best available gage

information. In practice, Reclamation and the Service will

discuss flows routinely during the irrigation season and as

needed the remainder of the year to determine the operation

needed to meet the base flows. Reclamation, in consultation

with the Service, will use the lesser of the weekly moving

average of the Bluff, Four Corners, and Shiprock gages and

the average of the Farmington, Shiprock, and Four Corners

gages as the guide in meeting this intent.

In periods of severe drought, Reclamation will work with the

Service to arrive at operating criteria to respond to these

conditions. For example, in 2002, Reclamation and the

Service agreed to reduce target base flows in the critical

habitat reaches to 350 cfs due to the extreme drought
J-15

conditions. This is an example of how extreme conditions can

be handled. If water shortages to Navajo Reservoir water

users, including the endangered fish, occur, all users will

share the shortage as an equal percentage. For example, a

10 percent shortage would reduce water supply to the fish

and to Navajo water users by 10 percent.
J-16

Determine

Available Water

No Release

<114,000 af

>114,000 af

No 

Yes

Yes No 

Spill Probable

Spill >344,000?

Yes

Was there

a release

Yes

No 

No 

Perturbation? >344,000 af?

 >344,000 af?

No 

Available

Water 

Yes

114,000 af

No 

>114,000?

Release

Yes

No 

 >344,000 af?

>166,000 af?

Yes

Release Full

Hydrograph

No Yes

No Release No 

Perturbation?

Yes

Release > of

114,000 af

No 

or Spill

Release > of

166,000 af

or Spill

Yes

 >344,000 af?

>166,000?

or Spill

166,000 af

Release > of Release > of

114,000 af or Spill

Yes

Yes

No 

No Release 

Maximum

Available

Draft:

San Juan Model

Operating Rule Decision Tree

for a 5000 cfs peak release

* *

Taken from: May 1999 SJRIP Biology Committee flow recommendations Report
J-17

If reservoir releases need to be increased in the late summer

or fall due to heavy monsoonal moisture upstream from the

reservoir, the unusually high inflows will be released as a fall

spike.

Reclamation will utilize existing Navajo Reservoir Operations

Meetings, held three times a year, to discuss the upcoming

periods operations. At these meetings, held in January, April,

and August of each year, Reclamation will solicit input

regarding the many and diverse affected resources on the San

Juan River from members of the public, government (local,

state, Federal) agencies, tribes, and others to gain the

required information needed to set water releases from Navajo

Reservoir. For each operation meeting, Reclamation will also

utilize existing water inflow forecasts, reservoir level, and

historic averages to predict the upcoming water supply

available to meet endangered fish Flow Recommendations and

authorized purposes. This information along with the decision

tree for peak flows will be analyzed and considered by

Reclamation to develop an operation plan. The operations will

fall within the sideboards analyzed within the Navajo Reservoir

Operations EIS, with releases between 250 and 5,000 cfs. 

Reclamation will be responsible for implementing the operation

plan following completion of a Record of Decision under the

NEPA process.

Inherent in the operation of Navajo Dam there exist variables

that influence dam operations under all conditions and these

must be considered when evaluating operations. These

influences include changes or errors associated with inflow

forecasts, fluctuations in the Animas River, strong precipitation

events, the waters travel time down the river after an

adjustment at the dam occurs, gage errors and discrepancies,

contractual obligations with the city of Farmington (powerplant

operations), and unexpected maintenance needs at Navajo Dam. 

Reclamation will take these variables into account when

making operating plans to meet the Flow Recommendations.

Two areas of flexibility exist in the reservoirs operations. 

First, water committed for future development (e.g.,

completion of NIIP) but not currently used offers flexibility in
J-18

reservoir releases. This may be a significant amount of water

in many, but not all, years. The release of this water will be

incorporated into operations to augment the 250 cfs minimum

release during the irrigation season; the goal will be to

maintain irrigation season releases between 350 and 500 cfs,

while assuring a spring release as described in the Flow

Recommendations will not be affected and assuring

recommended minimum flows are met. Water forecasted to be

available for this flexibility will be identified and quantified to

the extent possible during the Navajo Reservoir Operations

Meetings and the scheduling of its release will be discussed. 

Based on recommendations from resource experts, options will

be presented for the use of this water and comments will be

solicited from the public. Reclamation will use these

comments to make decisions on the release of water.

The second area of flexibility exists as full water development

occurs. Minimum releases would be no lower than 250 cfs,

but in the long term, flexibility will diminish; in drought

years, flexibility may not exist at all. Existing flexibility

within the endangered fish Flow 

Recommendations could occasionally allow minimum summer

releases to be above 250 cfs. During the Navajo Reservoir

Operations Meetings and in discussions with the Service, an

operation plan to meet endangered fish flows, authorized

project purposes, and water
J-19

development needs will be prepared. Unutilized or

unaccounted for water, resulting from the aforementioned

variables, would be identified and used to increase irrigation

season releases or for other uses.

Part of the SJRBRIP is to implement a process of adaptive

management, whereby the effects of dam operations on

endangered fish and their habitat and downstream resources

would be monitored and the results of that monitoring would

form the basis for possible future tests or modifications of

dam operations and/or the Flow Recommendations.

Uncertainties are recognized in both the EIS alternatives for

Navajo Dam re-operation and in the overall SJRBRIP recovery

plan for the endangered fish. For example, hydrology

modeling assumed that future precipitation and runoff

patterns are reflected in the historic hydrologic record. If

this is not correct, Flow Recommendations may be more or

less difficult to meet. Responses of the endangered fish to

the Flow Recommendations and other recovery elements have

been predicted based on scientific studies of the fish and

their habitat, but only actual monitoring of the fish and

habitat over a period of years will give conclusive evidence of

the responses. Also, it is uncertain to what extent nonnative fish will benefit from the recommended flows and

whether these benefits will offset the positive effects of the

modified hydrology on endangered fish.

Scientific monitoring conducted through the SJRBRIP will

determine the status and

trends of the endangered fish and their habitats following

implementation of the Flow Recommendations and other

recovery activities. Criteria established to determine positive

population responses and overall species recovery are

discussed elsewhere in this biological assessment. The Biology

Committee of the SJRBRIP, which includes Federal, State, Tribal

and water development interests, would be responsible for

conducting monitoring and research, and for communicating

results of this work to stakeholders and the public during

Navajo Reservoir operation meetings. The Biology Committee

can also recommend recovery actions that would address all

of the recovery factors related to the endangered fish. These
J-20

actions may include experimentation to test new hypotheses,

modifications to the Flow Recommendations, or control actions

directed against non-native fish, if warranted by monitoring

and research results. Any adjustments in, or modifications to,

the Flow Recommendations must be approved by the

Coordination Committee, which is the governing committee of

the SJRBRIP. 

Recommendations for dam release modifications can then be

considered by Reclamation, the agency ultimately responsible

for Unit operations. Recommendations for changes not under

Reclamations authority would be considered by the

appropriate agency. Thrice-yearly Navajo Reservoir operation

meetings will provide the forum for all interested parties to

discuss Navajo Unit operations and recovery program progress

and recommendations. The SJRBRIP Biology Committee and

other scientists will be invited to each meeting to discuss the

effects of dam operations and other resource management

actions on the endangered fish. Flexibility in dam releases

will also be discussed at these meetings. Future changes in

the Flow Recommendations, dam operations, and other

management policies could be implemented long-term after

compliance with applicable law.
J-21

The anticipated long-term species response to the proposed

reoperation, in concert with other recovery actions, is

attainment of Recovery Goals. These goals (Service, 2002b and

2002c) are summarized later in the species accounts for the

pikeminnow and razorback and basically present a method to

determine when listed fish species are eligible for removal

from threatened or endangered status. Positive population

response criteria (Reclamation, 2001) have also been developed

for the San Juan River as part of the ALP Project ESA

consultation; the purpose of these criteria is to provide

measurable criteria to determine

if populations in the San Juan are responding to management

actions and showing improvement prior to attainment of the

Recovery Goals. The Service (2001e) has concurred with the

criteria. The positive population response criteria include

criteria not specifically identified in the Recovery Goalsfor

example, the presence of larval or young-of-the-year fishes

and range expansion. Criteria are summarized in the table 1. 

If, based on SJRBRIP monitoring results, flow recommendations

and other recovery elements do not result in positive

population responses in the time frames outlined in the

recovery goals and positive population response criteria,

reinitiation of section 7 consultation on San Juan River water

projects may be required by the Service.

As indicated previously, in addition to meeting flow

recommendations, the Proposed Plan is intended to maintain

the authorized purposes of the Navajo Unit. The Unit, along

with other major storage units, was authorized by the

Colorado River Storage Project (Act of April 11, 1956, ch. 203,

70 Stat. 105). The storage units were authorized to:

‘ Regulate the flow of the Colorado River

‘ Store water for beneficial consumptive use,

making it possible for the States of the Upper

Basin to utilize the apportionments made to

and among them in the Colorado River

compacts

‘ Provide for irrigation
4

 Hydropower was not authorized at Navajo; however, the city of Farmington’s power plant was licensed under the

Federal Power Act

J-22

‘ Provide for flood control

‘ Provide for the generation of hydroelectric

power4

‘ Provide for recreation and facilities to mitigate

or enhance fish and wildlife

Both the Flow Recommendations, described later in this

assessment, and the Units authorized purposes can be met

under the Proposed Plan. The effects of meeting authorized

purposes are discussed in more detail at the beginning of the

Species Accounts section of this biological assessment.
J-23

Table 1.—Summary of criteria that denote a positive population response for endangered fish in the San Juan River1

Species

Criteria for an interim positive

population response (2002-2006)

Criteria for a positive population

response (2007-2011)

Colorado pikeminnow 1A – Collection of 10 or more ($ to

350 mm) during the annual adult fish

community SMP2

or

1B – A population estimate which is

significantly greater than the Ryden

(2000) estimate of fish $ 350 mm

or

1C – A river wide population estimate

of age 5+ subadults that exceeds

500

and

2A – Presence of wild larval or YOY in

SMP collections in at least 2 of 5 years

or

2B – Range expansion above Hogback

Diversion

1 – Collection of 10 or more ($ to

450 mm) in at least 2 of 5 years by the

adult fish community SMP

and

2A – A positive trend of increasing

numbers of adult/subadult fish based

on the SMP

or

2B – A river wide population estimate

of age 7+ adults that exceeds 400

and

3 – Presence of larval or YOY in SMP

collections in 3 of 5 years

and

4A – Density of 0.67 larval

pikeminnow/1,000 cubic meters in

SMP drift collections

or

4B – A density of 0.5/100 square

meters wild YOY pikeminnow in low

velocity habitats as detected during the

SMP

and

5 – Range expansion above Hogback

Diversion

Razorback sucker 1A – Collection of 20 or more

adult/subadults ($ to 300 mm) during

the annual adult community SMP

or

1B – An increase in the catch per unit

effort of adult/subadults ($ to 300 mm)

to 0.15 fish/hour during the adult fish

community SMP

and

2 – Evidence of reproduction

(i.e., presence of wild larvae and/or

YOY) in at least 2 of 5 years

1A – Collection of 80 or more adults

($ to 400 mm) during the adult fish

community SMP

or

1B – An increase in the catch per unit

effort of adults ($ to 400 mm) to 

0.6 fish/hour during the adult fish

community SMP trip

and

2 – A river wide population estimate of

adult fish $ to 2,900 fish

and

3 – Evidence of increased reproduction

(i.e., presence of wild larvae and/or

YOY) in at least 3 of

5 years

 1

 Source: Bureau of Reclamation. 2001. Positive population response criteria for Colorado pikeminnow and razorback

sucker in the San Juan River. Memorandum from Area Manager, Grand Junction, Colorado, to Colorado State Supervisor,

Fish and Wildlife Service, Denver. July 6, 2001.

 2

 Standardized Monitoring Program.
J-24

Flow Recommendations.—Mimicry of a natural hydrograph

downstream from Farmington is the basis of the flow

recommendations for the San Juan River. The

recommendations provide flow variability that is at this time

considered necessary to

create and maintain habitat for the Colorado pikeminnow and

razorback sucker. The recommendations integrate hydrology,

geomorphology, habitat, and biology to define flow magnitude,

duration, and frequency for the spring runoff period and base

flows for the non-runoff periods.

In general the flow recommendations provide for a spring

peak flow and a base flow

at other times of the year. For a complete description of

the recommendations, refer to

Flow Recommendations for the San Juan River prepared by the

SJRBRIP (Holden, 1999).

The . . .flow/duration/frequency recommendations will result

in a naturally varying hydrograph, providing high-flow and

low-flow years. These recommendations also provide for

adequate base flow conditions and peak flow conditions of

sufficient magnitude, duration, and frequency to provide

suitable conditions for the endangered species. They can be

achieved by using the operating criteria for Navajo Dam

outlined (in the Flow Recommendation Report). . .By

recommending operating rules, natural variability in the

hydrograph is maintained and decision making for annual

releases from Navajo Dam is simplified. (Holden, 1999).

The Proposed Plan follows the recommended operating rules

and meets or exceeds flow criteria according to model results. 

This model uses long-term historic flow data which encompass

a great variety of wet and dry conditions; however, there is

always a level of uncertainty in future climatic conditions

which could have a positive or negative effect on water

availability to meet the flow recommendations. For example,

the drought of 2002 was worse than any years in the period

of record used.

The operating criteria are considered recommendations; any
J-25

operating procedure that would allow the flow

recommendations to be met would be acceptable. Flow

Recommendations are targeted for the 180 miles of the San

Juan River between the Animas River confluence and Lake

Powell.

A summary of flow recommendation criteria follows:

A. Category: Flows >10,000 cfs during runoff

Duration: A minimum of 5 days between March 1 and

July 31

Frequency: 20% of years, with maximum number of years

between events 10 yrs.

B. Category: Flow >8,000 cfs during runoff

Duration: A minimum of 10 days between March 1 and

July 31

Frequency: 33% of years, with maximum number of years

between events 6 yrs.

C. Category: Flows >5,000 cfs during runoff

Duration: A minimum of 21 days between March 1 and

July 31

Frequency: 50% of years, with maximum number of years

between events 4 yrs.

D. Category: Flows >2,500 cfs during runoff

Duration: A minimum of 10 days between March 1 and

July 31

Frequency: 80% of years, with maximum number of years

between events 2 yrs.

E. Category: Timing of peak flows

Timing: Within 5 days of historical mean peak date of

May 31

F. Category: Target base flows (mean weekly)

Level: 500 cfs target from Farmington to Lake Powell

with 250 cfs minimum release from Navajo

Dam. Range-500-1,000 cfs.
5

 Reclamation projects in the depletion table will complete ESA consultation. Projects include the Hammond Project,

the Florida Project, the Pine River Project, and the Mancos Project. This biological assessment is not intended to serve as ESA

compliance for these projects. Reclamation’s priority has been to complete consultation on major projects (such as major CRSP

storage units) with the most flexibility to assist in recovery efforts. These future consultations will be scheduled to be completed

in the next 5 years. Reclamation has no authority in the private depletions and cannot lead consultation on them.

J-26

G. Category: Flood control releases

Control: Handle as a high magnitude, short duration

spike and release when flood control rules

require, except that the release shall not occur

earlier than September 1. If an earlier release

is required, extend duration. 

Statistics for criteria A-E are measured at the Four Corners

gage. Statistics for criteria F will be measured as a weekly

moving average of downstream gages as discussed previously. 

Additional details on the recommendations are included in the

Flow Recommendation Report. By applying operating rules

based on the Flow Recommendation Report, the Flow

Recommendations can be met while the depletions shown in

the table entitled Summary of San Juan River Basin

Depletions in attachment B are occurring. The depletions

shown in attachment B are for existing private and public

projects that affect San Juan River flows-some of these

projects have undergone ESA compliance and others have not.5

The table also includes future projects that have been cleared

under the ESA and NEPA; these projects include the ALP

Project, completion of the NIIP Project, and the Jicarilla

Apache Nation water sale to Public Service Company of New

Mexico. Depletions due to evaporation of water from Navajo

Reservoir are also included in the table. The table represents

the baseline used in this analysis for depletions in the basin

and is also representative of cumulative impacts on the

hydrology of the river.

The majority of the depletions shown in attachment B are

independent of the Navajo Unit; however, certain of the

depletions occur in relation to meeting the purposes of the

Unit and are interrelated with the Unit. These depletions

directly related to the Unit are listed below. These

depletions, with the exception of the Navajo Reservoir

evaporation, have been previously consulted on under the ESA.
J-27
6

 Principles for Conducting ESA Section 7 Consultations on Water Development and Water Management Activities

Affecting Endangered Fish Species in the San Juan River Basin.

J-28

‘ Navajo Indian Irrigation Project 280,600

acre-feet

‘ Navajo Reservoir evaporation 27,428 acre-feet

‘ San Juan power plant contract 16,200 acrefeet

‘ Minor depletions (small contracts) <1,000 acrefeet

It is intended for the Proposed Plan to meet the flow

recommendations, thereby complying with the ESA for Navajo

Reservoir operations and its evaporation depletions. This

biological assessment is not intended to provide ESA

compliance for any depletions in the table, other than Navajo

Reservoir evaporation (average annual depletion of 27,428

acre-feet). 

It should be noted that full development of State compact

water and Indian trust water is not included in the depletion

table. Only existing public and private projects along with

future projects with ESA and NEPA compliance are included in

the table of depletions.

Significantly more depletions are shown in the table under the

Proposed Action than under the No Action Alternative. This is

because certain depletions, such as would occur under the

completion of NIIP and the ALP Project, depend on reoperation

of Navajo Reservoir as part of their separate ESA compliance

and are more likely to occur under the proposed action.

The Proposed Plan also does not preclude depletions beyond

those shown in the depletion table; however, additional

evaluation, NEPA compliance, and ESA consultation would be

necessary for any depletions beyond these. The SJRBRIP has

developed principles6

 that explain and outline the process

under which additional water projects and depletions will be

evaluated:

The SJRBRIP will produce a list of actions defined in a

Long Range Plan that can be implemented to assist in
J-29

the recovery of the fish. When ESA consultation is

initiated on a new water depletion, the Service will

determine if progress toward recovery has been

sufficient for the Program to serve as a reasonable

and prudent alternative or measure. The Service will

also consider whether the probable success of the

SJRBRIP is compromised as a result of a specific

depletion or the cumulative effects of depletions. The

Service will assess the sufficiency of Program actions

in proportion to the potential impactsthat is, the

smaller the impact of the action, the lower the level

of actions by the SJRBRIP or others needed to avoid

jeopardy and/or destruction or adverse modification of

critical habitat. The Service will determine whether

progress by the SJRBRIP is sufficient to provide a

reasonable and prudent alterative or measure based on

the following factors: ( 1) Actions that will result in a

measurable positive population response, a measurable

improvement in habitat for the fishes, legal protection

of flows
J-30

needed for recovery, or a reduction in the threat of

immediate extinction.

(2) Status of fish populations. (3) Adequacy of flows. (4)

Magnitude of the impacts

of the activities.

If the Service finds that SJRBRIP and other efforts are

sufficient, the biological opinions will identify that

these are a reasonable and prudent alternative. If the

Service finds that they are not sufficient, the biological

opinion will be written to identify actions that must be

taken to provide a reasonable and prudent alternative.

Hydrology and Water Quality

Hydrology.—This section of the biological assessment

addresses changes to hydrology that would occur with

implementation of the Proposed Plan for reservoir operations. 

In general, the changes will involve a long-term change in

operations to provide for a spring peak and maintenance of a

base flow. Maintenance of the base flow will generally cause

releases to be lower than presently occur, although at certain

times during the summer (particularly during dry years),

releases will be increased over existing conditions to meet

base flow requirements.

Flow recommendations were developed using U.S. Geological

Survey (USGS) flow data records from 1929 to 1993. This

extensive record includes a variety of wet and dry periods;

however, it must be recognized that there is a degree of

uncertainty that this record will accurately represent

conditions that occur in the future.

Prior to Navajo Dam, approximately 73 percent of the total

annual flow occurred during spring runoff (March-July)

(Bliesner and Lamarra, 2000) with mean daily peaks at Bluff,

UT ranging from 3,810 to 33,800 cfs and averaging 10,500 cfs. 

The highest peaks have actually occurred during summer and

fall thunderstorms and reached an estimated 70,000 cfs at

Bluff, UT in September 1927 (USGS data). Prior to Navajo

Dam, annual flow was quite variable, ranging from 618,000
J-31

acre-feet to over 4,000,000 acre-feet at Bluff; median annual

flow was 1,620,000 acre-feet. Summer low flows occasionally

reached zero pre-dam and monthly mean flows were as low

as 65 cfs. While low summer flows are a natural condition,

these very low flows occurred due to a combination of

irrigation diversions and dry periods. Following operation of

Navajo Dam, spring peaks were substantially decreased (postdam peaks averaged 54 percent of pre-dam peaks) and flows

for the remainder of the year increased (August-February

flows averaged 168 percent higher).

Beginning in 1991, test flows to determine effects on

endangered fish were provided from Navajo Dam, including

spring releases of 5,000 cfs to increase downstream peaks. 

This test period showed that operation changes could

successfully better mimic a natural hydrograph (see

attachment C for graph of flows during test period). The test

period also showed that the cooling effect of Navajo Dam on

water flows extended further downstream with the high

releases.
7

 As indicated previously, during the interim period prior to additional water development, there is flexibility to keep

irrigation season releases above 250 cfs; these percentages do not reflect this flexibility.

J-32

Tables and figures in attachment C compare average reservoir

elevations and riverflows between the No Action Alternative

and the Proposed Plan. The No Action Alternative represents

the baseline for reservoir and river conditions:

‘ Table C-1 San Juan Riverflows at Archuleta

‘ Table C-2 San Juan Riverflows at Bluff

‘ Table C-3 Seasonal Frequency Distribution of

Navajo Reservoir Releases

‘ Table C-4 San Juan River at Bluff-Distribution

Frequency of Monthly Flow

‘ Table C-5 Summary of Streamflows Measured

During 2001 Summer Low Flow Test

‘ Figure C-1 San Juan River near Bluff, Average

Daily Flow, Compares pre-Dam, post-Dam, and

Natural Flow

‘ Figure C-2 Average Monthly Navajo Dam

Releases

‘ Figure C-3 Degree to which Flow

Recommendations Met under Proposed Plan

Under the Proposed Plan and following full development of

NIIP and the ALP Project, average monthly releases of 250 cfs

would occur 28 percent of the months in the winter and 29

percent of the months in the March thru November period. 

Overall monthly releases would be below 500 cfs 98 percent of

the time in the winter and 65 percent of the time the

remainder of the year.7

The Archuleta gage is approximately 6 miles downstream from

the dam and approximately 1 mile upstream from the

Citizens Ditch, a major diversion. Thus, flows would be much
J-33

lower downstream from the Citizens Ditch than shown at the

Archuleta gage. Even lower flows would occur just

downstream from the Hammond Diversion Dam, approximately

20 miles downstream from the dam. During the 2001 Low

Flow Test (Dam releases were lowered to around 250 cfs),

flows fell to 133 cfs downstream from the Citizens Ditch and

63 cfs downstream from the Hammond Diversion (Reclamation,

2002a). Under actual low flow releases, flows may be less or

greater than these amounts. Table C-5 in attachment C

summarizes riverflows measured during the Low Flow Test. 

These low flows should not occur in early years of operation

changes because of the flexibility of using undeveloped water

to supplement low summer releases as explained previously. 

In the long term as development occurs, however, these low

flows are expected to occur frequently.

The No Action Alternative does not mimic the natural

hydrograph and it is assumed that projects that rely on such

mimicry for ESA compliance (e.g., ALP Project and completion

of NIIP) would require reinitiation of consultation. Under No

Action, it is assumed that Navajo Dam would be operated as it

was from 1973 to 1991, with a minimum release of

500 cfs. Operational goals would be to store as much water

in the reservoir as possible and to maintain uniform flows

downstream.

Water Quality.—The San Juan River is characterized by

good water quality when flows are released from Navajo Dam,

but water quality progressively degrades downstream due to

natural and induced bank erosion, diversions, agricultural and

municipal return flows, and tributary contributions. The State

of New Mexico has listed reaches of the San Juan River where

water quality does not fully support intended uses. Turbidity,

fecal coliform, and sediments impact the designated uses of

the river most often. Several trace elements (selenium,

aluminum, arsenic, mercury, copper, and zinc) have

occasionally exceeded State standards from Navajo Dam to

Farmington, New Mexico (Reclamation, 2000a).

Water quality standards for the San Juan River are based on
J-34

water uses. For example, some river segments may be

considered of a quality to classify them as cold water

fisheries, while others would be classified as suitable for

irrigation or other uses. The river segment from Navajo Dam

to the Blanco Bridge is classified by the State of New Mexico

as a high quality cold water fishery. From there to the

confluence with the Animas River, it is considered a marginal

cold water fishery, with different physical standards than the

segment upstream.

San Juan River water quality generally declines to Shiprock,

New Mexico, with the stretch of the river between Farmington

and Shiprock having the highest number of water quality

standard exceedences. At the Four Corners gage/sampling

site, water quality improves and the number of exceedences

decreases, but water quality declines again from Four Corners

to Mexican Hat, Utah (Reclamation, 2000a).

Studies used in analyzing water quality impacts in the Navajo

Operations DEIS included extensive water quality studies that

have been conducted on the San Juan River and its

tributaries within the last 10 years. The USGS has conducted

studies under the Department of the Interiors National

Irrigation Water Quality Project (Blanchard et al., 1993; Thomas

et al., 1998). The SJRBRIP, initiated in October 1991, has

been collecting data on water quality on the San Juan River

ever since. In addition, water quality data were collected and

analyzed as part of the NIIP environmental studies on the San

Juan River mainstem as

well as on tributaries, seeps, springs, ponds, and wells on the

project lands. The table in attachment E is a summary of

historical water quality data collected on the San Juan River

at the USGS gaging stations.

The early USGS investigations (Blanchard et al., 1993) were

reconnaissance-level studies to identify whether irrigation

drainage: (1) has caused or had the potential to cause

adverse harmful effects to human health, fish, and wildlife; or

(2) may adversely affect the suitability of water for other

beneficial uses in the San Juan Basin. It concluded that

selenium was the major trace element of concern in all
8

 The Navajo Nation Water Quality Standards are awaiting Environmental Protection Agency approval.

J-35

sampled media (water, bottom sediments, and biota). The

USGS performed a detailed study of selenium and selected

constituents in water, bottom sediments, soil, and biota

associated with irrigation drainage in the San Juan River area

(Thomas et al., 1998). Selenium was much less concentrated

in water samples than in bottom sediment, soil, or biota

samples. Mean selenium concentrations in water samples were

greatest from seeps and tributaries draining irrigated lands;

less concentrated at irrigation-drainage sites and ponds on

irrigated land; and least concentrated at irrigation-supply

sites, backwater, and San Juan River sites. Other elevated

trace elements in water, bottom sediments, soils, or biota

included lead, molybdenum, strontium, zinc, vanadium, barium,

cadmium, chromium, iron, mercury, and aluminum.

The NIIP Biological Assessment (Bureau of Indian Affairs, 1999)

assessed the impacts from full development of NIIP. The

"Water Quality Analysis" section concluded that NIIP will

increase arsenic, copper, selenium, and zinc levels in the San

Juan River. It was concluded that levels of arsenic and zinc

concentrations would be below levels of concern for the two

endangered fish species. Conclusions on copper were less

certain but levels are not expected to impact the two

endangered fish species. Selenium received a low hazard

potential, but uncertainty about actual levels in biota

downstream from the project and chronic toxicity to

razorback sucker leaves the possibility of some impact to the

recovery of the species. The Navajo Nation developed water

quality regulations in 1999.8

 The predicted arsenic, copper,

selenium, and zinc levels in the biological assessment are

below the Navajo Nation water quality standards. The

predicted dissolved selenium level is 1.9 μg/L, while the

standard for total selenium is 2.0 μg/L in the San Juan River. 

The NIIP Biological Assessment assumed that the minimum

release rate from Navajo Reservoir would be 250 cfs in the

future.

The SJRBRIP study on environmental contaminants in aquatic

plants, invertebrates, and fishes of the San Juan River
9

 The "Mixer area" is a suspected Colorado pikeminnow spawning site.

J-36

mainstem was completed in 1999. The trace elements

evaluated included aluminum, arsenic, copper, selenium, and

zinc. Aluminum appeared to be related to sediment

geochemistry, and most life forms associated with sediment

had elevated levels. Arsenic levels showed no consistent

pattern for any river reach or site. Elevated arsenic levels

were found in most plants and some invertebrates and fish. 

Elevated copper levels were found in the trout from upstream

coldwater river reaches. Generally, copper concentrations in

plants, invertebrates, and fish increased downstream from the

coldwater areas. Selenium concentrations were clearly

elevated in all biota above ambient background concentrations. 

Zinc concentrations in plants, invertebrates, and fish below

Farmington to the "Mixer area" (RM 128)9

 were generally

higher than the rest of the river, and it appears the source

may be the Animas River. The study found no consistent

correlation between contaminant concentrations and river

discharges.

Studies under the SJRBRIP have identified contaminants of

concern to be arsenic, copper, selenium, zinc, and polycyclic

aromatic hydrocarbons (PAHs) (Simpson and Lusk, 1999). 

These studies pointed out potential water quality problems

that could affect the endangered fish, and also concluded that

concentrations of contaminants in biota inhabiting the

mainstem of the San Juan River were not consistently

correlated with riverflows. These studies did not include

extensive sampling of backwater habitats which are important

habitats for the endangered fish. The Service (2000) discusses

San Juan River water quality concerns in more detail. 

Information on PAHs in the river can be found in BLM

(2002b).

The ALP Project FSEIS reports: These historic values could be

slightly affected by the operation of Navajo Dam for

endangered fish. The increase in spring runoff flows will

result in improvement of water quality during the runoff

period, but the lower flows during the rest of the year will

provide less dilution and may impact the water quality of the
J-37

San Juan River. Monitoring over the last 7 years of modified

flows (reflects 500/5000 Alternative due to releases above 500

cfs) has not detected a measurable change in water quality.

Under the No Action Alternative, no significant changes in

Navajo Reservoir water quality are expected. Releases from

Navajo Reservoir would be similar to those under historical

1973 - 1991 period operations. Water quality parameters in

the reservoir and in the San Juan River downstream to Lake

Powell would probably be similar to existing conditions. 

Under the No Action Alternative, flow releases from Navajo

Dam would not fall below 500 cfs under normal operations. 

Sources of pollutants along the river include municipal,

industrial, and irrigation returns, and bank destabilization

could occur mostly from Navajo Dam to Shiprock, New

Mexico. Water quality in the San Juan River can also change

rapidly from thunderstorm runoff in streams and washes

entering the river.

Under the Proposed Alternative, the spring releases from

Navajo Reservoir would be designed up to 5,000 cfs, but

releases the rest of the year could be lowered to 250 cfs. 

The increased spring releases under the Proposed Plan would

lower concentrations of pollutants because of dilution, while

the lower releases during other periods would increase

concentrations. This would be most apparent in the reach of

river upstream from the Animas River confluence. A 250 cfs

release from Navajo Reservoir during the irrigation season

would result in low flows (in the range of approximately 60-

150 cfs) from Citizens Ditch (river mile 217) diversion to

Farmington (river mile 181) due to irrigation demands. 

During the Summer Low Flow Test (Reclamation, 2002a),

several water quality parameters (temperature, aluminum, fecal

coliform, total organic carbon, and conductivity) exceeded the

State standards for this reach. Exceedences of water quality

standards would probably increase at these lower flows over

the long term.

Water quality parameter exceedences in the San Juan River

from Farmington to Lake Powell would probably increase

slightly, but significant increases in exceedences would
J-38

probably not occur due to maintenance of the 500 cfs

minimum flows in the critical habitat sections.

A few exceedences occur under the Proposed Plan at

Archuleta, Farmington, Four Corners, and Bluff USGS gages. 

The increase in exceedences at Shiprock occurs in fecal

coliform, temperature, turbidity, and mercury. The

exceedences in mercury probably occur because of the 

habitat standards are lower than the other Navajo Nation

water use standards and other regulatory agencies have the

San Juan River designated as a warm water fishery.

Species Accounts

The following sections address the effects of the proposed

action on threatened and endangered species, candidate

species, and other species of special status. Table 2

summarizes the findings of this assessment. Information is

provided on species distribution and habitat needs, and

impacts of the proposed operation changes are presented. 

For some species there is an abundance of literature on

habitat requirements and other factors; this assessment

summarizes appropriate information and the reader should

refer to technical reports and papers for detailed information.

Research and monitoring on the endangered fishes continues. 

Work includes completion

of a population model, water temperature analysis and

modeling, characterization of spawning areas, study of

hybridization, and monitoring of larval fish, channel

morphology, and water quality (UCRRP/SJRRIP, 2002).

The purposes of the Proposed Plan are twofoldmeeting the

Flow Recommendations and continuing to meet Navajo Unit

authorized purposes. Table 3 summarizes information on the

effects of the authorized purposes on meeting Flow

Recommendations and on endangered species that utilize the

river.

Endangered Species.—

Colorado Pikeminnow.—The Colorado pikeminnow is

endemic to the Colorado River system and occurs in low

numbers in the Green River and the Colorado River upstream

from Lake Powell and in their major tributaries. The species
J-39

does not reproduce in reservoirs and construction of Glen

Canyon Dam has generally isolated the San Juan River

population from other Upper Colorado River populations since

the 1960s.

According to reports reviewed in Holden (1999), there is little

information on historical abundance in the San Juan River

although anecdotal information and early fishery inventories

suggest the pikeminnow was common and extended upstream

into what is now Navajo Reservoir and into tributaries such as

the Animas River. Based on SJRBRIP surveys, there were likely

fewer than 100 adult pikeminnows and maybe fewer than 50

reported in Holden (1999). Wild pikeminnow numbers are

probably now lower.

Critical habitat has been designated for the pikeminnow along

the lower San Juan River as follows:

 New Mexico, San Juan County, and Utah, San Juan County. 

The San Juan River and its 100-year flood plain from the

State Route 371 bridge in T.29N., R.13W., section 17 (New

Mexico Meridian) to Neskahai Canyon in the San Juan arm

of Lake Powell in T.41S., R.11E., section 26 (Salt Lake

Meridian) up to the full pool elevation.

Ryden (2000) reported on the updated status of the fish in

the San Juan. Only 19 wild (not stocked) adult and juvenile

pikeminnows were located during SJRBRIP electrofishing surveys

between 1991 and 1996most were found in the relatively

short reach of river between the Mancos River confluence and

the Cudei Diversion Dam (RM 120-145). In
J-40

Table 2.—Effect of Proposed Plan on species

Species and status Effect

Colorado pikeminnow-endangered May affect, not likely to adversely

affect1

Razorback sucker-endangered May affect, not likely to adversely

affect1

Southwestern willow flycatcherendangeredMay affect, not likely to adversely

affect

Bonytail and humpback chubendangeredNo effect

California condor-endangered No effect

Black-footed ferret-endangered No effect

Bald eagle-threatened May affect, not likely to adversely

affect

Navajo sedge-threatened No effect

Mexican spotted owl-threatened No effect

Gunnison sage grouse-candidate No effect

Black tern-special concern No effect

White-faced ibis-special concern No effect

Yellow-billed cuckoo-special concern May affect, not likely to adversely

affect

Roundtail chub-special concern May affect, not likely to adversely

affect

New Mexico silverspot and San Juan

checkerspot butterflies-special concern

No effect

San Juan tiger beetle-special concern May affect, not likely to adversely

affect

Peregrine falcons–special concern No effect

Golden eagle-special concern No effect

Bluehead sucker-special concern May affect, not likely to adversely

affect

Mottled sculpin-special concern May affect, not likely to adversely

affect

Northern leopard frog-special concern May affect, likely to adversely affect
J-41

Bighorn sheep-special concern No effect

Alcove rock daisy-special concern No effect

 1 The depletion from Navajo Reservoir evaporation and depletions from authorized

purposes are considered an adverse effect on the endangered fish. Overall, however,

the reoperation under the Preferred Alternative is not likely to adversely affect these

species.
J-42

Table 3.—Navajo Unit purposes related to Flow Recommendations

and endangered species

Navajo Unit purpose Effects

Regulate flow of the

Colorado River

In general, the unit operates to store water

during spring runoff for use by NIIP or

downstream releases. This, along with nonrelated water storage, decreases spring peaks

that are important for maintaining endangered

fish habitat and terrestrial riparian habitats. The

Flow Recommendations, which are designed to

help restore habitats, can still be met while this

regulation occurs. The regulation also increases

base flows which offset non-related depletions in

the base flow periods. Hypolimnic releases

reduce summer water temperatures and may

restrict upstream expansion of native fish.

Storing water for beneficial

consumptive use

The unit provides water by contract to several

users. A total of 23,020 acre-feet (of depletion)

has been contracted. This water is primarily

used for municipal or industrial purposes,

although 210 acre-feet are for irrigation. More

information on these contracts, including the

ESA consultation status, is included in

attachment D. The consumptive use is included

in the baseline for this biological assessment and

Flow Recommendations can be met with these

uses occurring. It is possible that future

contracts may be sought; these would be subject

to ESA consultation which would address effects

on Flow Recommendations. See irrigation

discussion below for further information.

Assisting States in

compact water

development

By storing water during high flow months and

wet years, a more dependable water supply is

made available for water users. 

Providing for irrigation Under separate authorization, the Navajo Indian

Irrigation Project diverts water directly from

Navajo Reservoir. Existing and future depletions

reduce water available to maintain habitat in the

San Juan River. Both the existing and future

(ESA consultation complete) depletions of the

irrigation are included in the baseline for this

assessment. Flow Recommendations can be

met with these depletions occurring.
J-43

Flood control Navajo Reservoir is operated to reduce both

spring runoff flooding and flooding from

monsoonal moisture that occurs upstream from

the reservoir. This has the effect of reducing

high spring flows that are important for

maintenance of endangered fish habitat and

riparian areas. The Flow Recommendations can

be met along with flood control under the

Proposed Plan.
J-44

Table 3.—Navajo Unit purposes related to Flow Recommendations

and endangered species (continued)

Hydroelectric power The city of Farmington operates a hydropower

plant at Navajo Dam. It operates as a “run of the

river” plant and thus does not affect riverflows or

the ability to meet Flow Recommendations. 

There is a contractual notification process prior

to making flow changes and this can affect

responding to base flow changes as quickly as

would otherwise occur, but Reclamation does

not consider this a significant problem in

meeting Flow Recommendations.

Recreation Under the Unit, recreation facilities have been

constructed around the reservoir and in the

tailwater area. These do not affect flows,

reservoir levels, or the ability to meet Flow

Recommendations. Standard environmental

safeguards are used to minimize pollution

potential from marine fuel use.

Fish and wildlife mitigation

and enhancement

Fish and wildlife facilities do not affect reservoir

releases or reservoir levels nor the ability to meet

Flow Recommendations.

addition to actual captures, 12 pikeminnow were observed,

mostly between the Four Corners and the Cudei Diversion. 

The furthest upstream a pikeminnow was observed was near

the Hogback Diversion (RM 160). Only one adult wild Colorado

pikeminnow has been captured in the last several years in the

river (SJRBRIP, 2001b). Fish passages opened in 2003 are

expected to increase the upstream range of the fish.

Larval and juvenile pikeminnows have been collected, all

downstream from a presumed spawning area near River Mile

129-133 (referred to as the Mixer); however, the number of

larval fish has been very low. There is concern that larval

fish can be quickly transported downstream and lost to

predation in Lake Powell.

Beginning in1996, Colorado pikeminnow were stocked near

Shiprock and Mexican Hat (River Miles 148 and 53) and at

least some of these are surviving in the river (Ryden, 2000). 

In 2001, 148 adult Colorado pikeminnow were stocked in the

San Juan River and approxi-mately 250,000 fingerlings were

stocked in the fall of 2002 above the Hogback Diversion. The
J-45

Service (Ryden, 2003a) has published an augmentation plan for

the San Juan River which contains more details on stocking

plans and their role in recovery efforts.

Habitat of the fish in the San Juan River includes a complex

mix of low-velocity habitats such as eddies, pools, and

backwaters adjacent to swifter run and riffle habitats. A

natural hydrograph (high spring flows, lower base flows) is

important in maintaining the habitat and one of the main

effects of Navajo Reservoir under historic operations has been

to reduce high spring flows while increasing base flows. Miller

and Ptacek (2000) and Holden (1999 and 2000) discuss habitat

types seasonally used by the pikeminnow and should be

referred to for specific information.
J-46

Habitat types used varies seasonally. During the pre-spawn

period, pikeminnow use mainly slower velocity habitats,

including mouths of tributaries such as the Mancos River. 

During spawning, higher velocity and often complex habitat

areas are used. Riffles, runs, and chutes with adjacent lowvelocity habitats seem preferred for spawning. Following

spawning the fish move into simpler habitat complexes such

as runs and pools; and runs and low-velocity areas provide

fall and winter habitat.

After eggs hatch, larval fish drift downstream into low-velocity

habitats such as backwaters. Juvenile fish prefer shallow, low

velocity habitats including backwaters, shoals, eddies, and

pools. These low velocity habitats comprise less than 15

percent of the rivers habitats (Bliesner and Lamarra, 1996).

Tributaries have been shown to be important to pikeminnow in

the Green River and may have been historically important in

the San Juan; however, migration barriers and extensive

dewatering on San Juan tributaries have greatly reduced their

use.

Loss of habitat, competition from non-native fish, possible

water quality problems, and migration barriers are all thought

to be factors in the fishes decline. Reductions of water

temperatures due to the operation of Navajo Reservoir may

also be a factor in reducing the range of the species, and

habitat in the lower river was lost when Lake Powell was

filled. Larval fish that drift into Lake Powell may all be lost

due to predation.

Non-native fish are common throughout the critical habitat

reach and include channel catfish, carp, fathead minnows, and

other species. During monitoring trips on the river in 2000,

striped bass were also common (SJRBRIP, 2001b). Striped bass

represent a predatory threat to native fish. There is an

active program to remove nonnative fish from the river,

concentrating on channel catfish and common carp

(UCRRP/SJRRIP, 2002).

There were five major diversion structures between RM 142
J-47

and RM 178, which impede

fish movement to varying degrees (Masslich and Holden, 1996);

and these may strongly influence the range of the pikeminnow

which is a migratory species. A fish passage has been

completed at the Hogback Diversion; passages are scheduled

for the Public Service Company of New Mexico (PNM) Diversion

and the Arizona Public Service weir; and the Cudei Diversion

was removed (UCRRP/SJRRIP, 2002).

Recovery Goals for the pikeminnow were approved by the

Service in 2002 (Service, 2002b) and are summarized below.

The Colorado pikeminnow will be eligible for removal from the

list of threatened and endangered species when:

‘ A self-sustaining population exceeding 2,500

adults is maintained over a 7-year period

beyond downlisting in the Green River

‘ A self-sustaining population exceeding 1,000

adults is maintained over a 7-year period

beyond downlisting in the Upper Colorado River
J-48

‘ A self-sustaining population exceeding 700

adults is maintained and a self-sustaining

population exceeding 800 adults is maintained

over a 7-year period beyond downlisting in the

San Juan River

‘ All management actions identified in the

Recovery Goals are implemented and achieved,

including necessary flow regimes provided;

passage of fish assured in the Green, Upper

Colorado, Gunnison and San Juan rivers;

entrainment of subadults minimized; adequate

protection from overutilization; adequate

protection from effects of diseases and

parasites; nonnative fish stocking procedures

implemented; mechanisms determined for legal

protection of habitat; conservation plans

identified for long-term protection; hazardous

materials emergency response plans revised to

ensure protection; shut-off valves installed

in petroleum-product pipelines within the 100-year

floodplain; and effects of selenium identified and

mediated

The Flow Recommendations are specifically designed to create

and protect habitats used

by the fish (Holden, 1999). Higher spring flows (>10,000 cfs)

generate new cobble sources, channel diversity, and provide

nutrient loading. Lower peaks provide and maintain spawning

habitat. The proposed operation should meet or exceed

recommendations for spring flows. Table 4 indicates how the

frequency of spring flows is met under the proposed action

and No Action Alternatives. This material is also presented in

graph form in attachment C. Overall, the No Action

Alternative fails to meet the desired frequency and duration of

the three categories of spring flows (>10,000 cfs, >8,000 cfs,

>5,000 cfs). Under the Proposed Plan, the desired frequency

and duration of the categories are fully met or exceeded. 

Because of this, the spring flows under the proposed action

should meet many of the purposes of the flow

recommendations, including generation of new cobble sources,
J-49

creation of channel diversity, provision of nutrient loading,

maintenance of spawning areas, and creation and maintenance

of backwaters and other low-velocity habitats.

Maintaining low, stable base flows enhances nursery habitat

conditions and flows between 500 and 1,000 cfs optimize

backwater conditionsselecting flows at the low end of the

range increases the availability of water for development and

spring releases. Bliesner and Lamarra (2000) reported that

backwater habitats, which are extremely important for the

endangered fish, demonstrated a high degree of variability at

low flows; but low flows clearly maximized this habitat. 

Juvenile low velocity habitat is likely maximized between 800

and 1,000 cfs (Service, 2001d).

Bliesner and Lamarra (2000) report on studies that relate flow

levels to habitat creation and maintenance and should be

referred to for further information.

The Proposed Plan includes operations to attempt to maintain

the base flows in the 500 to 1,000 cfs range in areas of

critical habitat; however, this cannot always be accomplished. 

Inflows from tributaries, combined with even minimum releases

from Navajo Dam, will cause the 1,000 cfs to be exceeded at

times. This is particularly true during spring runoff when

downstream tributaries are high and during the frequent

summer thunderstorms that
J-50

Table 4.—Summary statistics of meeting Flow Recommendations criteria for alternatives retained for further analysis

No Action Alternative 250/5000 Alternative 500/5000 Alternative

>10,000 >8,000 >5,000 >2,500 >10,000 >8,000 >5,000 >2,500 >10,000 >8,000 >5,000 >2,500

Duration Average frequency (percent) Average frequency (percent) Average frequency (percent)

1 day 26.2 36.9 53.8 100.0 33.8 56.9 73.8 95.4 27.7 43.1 55.4 96.9

5 days 18.5 33.8 43.1 90.8 27.7 47.7 69.2 86.2 21.5 35.4 47.7 86.2

10 days 7.7 30.8 38.5 81.5 15.4 38.5 66.2 81.5 13.8 29.2 44.6 80.0

15 days 4.6 23.1 36.9 72.3 7.7 30.8 56.9 75.4 6.2 27.7 41.5 72.3

20 days 13.8 69.2 24.6 72.3 21.5 66.221 days 36.9 53.8 40.0

30 days 7.7 35.4 61.5 13.8 44.6 64.6 13.8 33.8 60.040 days 30.8 50.8 32.3 55.4 27.7 49.250 days 26.2 46.2 26.2 49.2 23.1 40.060 days 16.9 40.0 18.5 41.5 15.4 33.880 days 7.7 30.8 9.2 30.8 6.2 26.2

Maximum duration between events

Flow criteria - Max duration Allowed Modeled Allowed Modeled Allowed Modeled

9,700 cfs for 5 days - 10 years 10 14 10 10 10 14

7,760 cfs for 10 days - 6 years 6 7 66 6 14

4,850 cfs for 21 days - 4 years 4 7 44 4 7

2,450 cfs for 10 days - 2 years 2 2 2 2 2 2

Note: Shaded cells containing bolded numbers indicate failure to meet Flow Recommendations.

Flow recommendations flow/duration statistics

Discharge

>10,000 >8,000 >5,000 >2,500

Duration Average frequency (percent)

1 day 30.0 40.0 65.0 90.0

5 days 20.0 35.0 60.0 82.0

10 days 10.0 33.0 58.0 80.015 days 5.0 30.0 55.0 70.020 days 20.0 65.021 days 50.030 days 10.0 40.0 60.040 days 30.0 50.050 days 20.0 45.060 days 15.0 40.080 days 5.0 25.0
J-51

can add sudden spike flows to the river. In addition, there

are difficulties with travel time for changed releases to reach

critical habitat and discrepancies with gage readings in the

critical habitat area.

Holden (2000) discussed the effect of flow recommendations on

both the pikeminnow and razorback sucker:

If Navajo Dam is operated as prescribed in the flow

recommendations, key habitats for the endangered fish

species will be maximized in both quantity and quality,

and they will be provided at the proper time of the

year for use by the fish, based on information

gathered during the 7-year research period. New

information may improve the flow recommendations

through adaptive management. However, larval habitat

availability, a major potential habitat limitation for

both endangered fish species, was not explored. In

addition, YOY (young of year) razorback sucker habitat

availability was not researched. These potential habitat

limitations will be studied when the adult populations

of both species increase sufficiently to produce millions

of larvae.

There is potential that water contaminants may also affect the

fish; these include selenium and PAHs. Further studies are

needed to determine if water quality in the main river and in

tributary inflow areas are affecting the species. The proposed

action will affect water quality in the San Juan River. 

Releases from Navajo Reservoir of high quality water generally

dilute pollutants downstream. This dilution effect will be 

increased during certain periods under the Proposed Plan but

will be decreased in the winter months and periodically at

other times of the year as releases are reduced. 

Contaminants of concern include PAHs and trace elements

such as selenium, arsenic, copper, and zinc. Simpson (1999)

concluded . . .that the concentrations of contaminants in

biota inhabiting the mainstem of the San Juan River were not

consistently correlated with instream flow discharges.

Holden (2000) summarized contaminant studies on the San
J-52

Juan:

In summary, investigations by the SJRIP showed that

some contaminant issues occurred in the San Juan

River Basin, but they tended to be limited to irrigation

drainage areas. It is also possible that contaminants

were more prevalent during low-flow periods. It is

doubtful that any of the populations of native fishes

studied during the 7-year research period were limited

by contaminants. However, this does not mean that

contaminants were not a major limiting factor at some

time in the past, when safeguards were not as

prevalent as they are today.

There is some belief that a more natural hydrograph may

result in some natural control of non-native fish that

compete with the endangered fish. This hypothesis was

studied and initial conclusions are that a negative response of

non-natives in the San Juan River to the more natural

hydrograph during the test flow period did not occur (Brooks

et al., 2000).
J-53

It is possible that in the future, the Colorado pikeminnow will

expand its range upstream into the reach of river between

Farmington and the Hammond Diversion as populations

increase and migration barriers are reduced. This area is

expected to have periods of lower base flows than now occur

because of reduced releases from Navajo Reservoir to meet

flow recommendations and because of future diversions to NIIP

and other water users. The Recovery Program includes a

program whereby the effects of dam operations and other

Recovery Program actions would be monitored and the results

of that monitoring would form the basis for possible future

tests or modifications of dam operations and/or flow

recommendations. Reclamation believes it is the Recovery

Programs responsibility to monitor this reach of river and

modify flow recommendations if warranted. If this reach of

river becomes important habitat to the pikeminnow, it would

represent a change of conditions that could trigger

reconsultation on projects such as NIIP or Navajo Reservoir

reoperation that affect this reach.

Overall, the proposed action should beneficially affect the

Colorado pikeminnow and its designated critical habitat;

however, water quality changes associated with low flows may

have adverse impacts under certain conditions when dilution

flows are reduced, and depletions from reservoir evaporation

adversely affect this species. Depletions reduce the water

supply available to maintain various habitat types; however,

the proposed flow regime is designed to offset these losses. 

The proposed action also provides for adjustments that can be

made to reflect new research and findings. Combined with

other elements of the SJRBRIP, the proposed action should

provide the best opportunity for recovery of the species.

Razorback Sucker.—The razorback is endemic to the

Colorado River Basin with a wide historical distribution. 

Historically the razorback occurred in the San Juan and

Animas Rivers but little is known about population abundance

(Holden, 1999). Through-out its range the species is now

very rare with low to nonexistent recruitment. Small

concentrations of razorback suckers have been reported in the
J-54

inflow area in the San Juan arm of Lake Powell. Ryden

(2000) reports that no wild razorback suckers had been

collected in the San Juan River since 1988, when one

individual was collected near Bluff (Holden, 1999). Overall this

species is extremely rare in the San Juan River. 

The lower San Juan River is designated as critical habitat for

the razorback as follows:

New Mexico, San Juan County, and Utah, San Juan

County. The San Juan River and its 100-year flood

plain from the Hogback Diversion in T.29N.,R.16W.,

section 9 (New Mexico Meridian) to the full pool

elevation at the mouth of Neskahai Canyon on the San

Juan arm of Lake Powell in T.41S., R.11E., section 26

(Salt Lake Meridian).

Experimental stocking began in 1994 and these stocked fish

have been observed in spawning condition. Since 1994,

approximately 6,835 adult and subadult razorback suckers

have been stocked in the San Juan River; approximately 2,000

adult fish will be stocked in 2002 (UCRRP/SJRRIP, 2002). Ponds

have been developed to raise fish for stocking in the river; in

2001, 16.5 surface acres of new growout ponds for the

razorbacks were build on the Navajo Indian Irrigation Project

lands. Spawning activity of stocked fish has been recorded at

a specific area near RM 100 (SJRBRIP, 2001b). Larval fish

were collected between Bluff and Montezuma Creek in 1997

(Service, 2000a) and larval fish have been collected every year

since with a positive trend in abundance. This indicates that

stocked fish are successfully reproducing. The razorbacks

current distribution in the San Juan, counting introduced fish,

is from Lake Powell to near the Hogback Diversion (RM 158). 

Twenty-one of the stocked razorbacks were recaptured during

a May 2001 monitoring trip (SJRBRIP, 2001b). An

augmentation plan for the San Juan River has been published

(Ryden, 2003b) and should be referred to for more details.

Razorbacks spawn on the ascending limb of the hydrograph;

thus, they spawn earlier than the pikeminnow. Razorbacks

use backwaters or flooded bottomlands prior to spawning; they
J-55

generally spawn in runs over gravel or cobble. Backwaters

and flooded bottomlands are important to complete the life

cycle of the species; drifting larva enter backwaters where

food sources can be abundant.

The razorback decline has probably occurred for similar

reasons as the pikeminnows decline. Loss of backwaters and

predation by non-natives in remaining backwaters is a major

problem as are migration barriers. In addition, larval fish

may be lost due to predation in Lake Powell.

Recovery Goals for the razorback were approved by the

Service in 2002 (Service, 2002c) and are summarized below.

The razorback will be eligible for removal from the list of

threatened and endangered species when:

‘ A self-sustaining population exceeding 5,800

adults is maintained over a 5-year period in

the Green River

‘ A self-sustaining population exceeding 5,800

adults is maintained over a 5-year period in

either the Upper Colorado River or the San

Juan River

‘ Genetic refugia are maintained in Lake Mohave

over a 5-year period

‘ Two self-sustaining populations each exceeding

5,800 adults are maintained over a 5-year

period in the Lower Colorado River Basin

‘ All management actions identified in the

Recovery Goals are implemented and achieved,

including: necessary flow regimes identified and

implemented; passage of fish established in the

Green, Upper Colorado, Gunnison, and San Juan

rivers; entrainment of subadults identified and

actions taken to minimize; appropriate

bottomland sites identified and acquisition
J-56

assessed; protection from over-utilization

implemented; protection from effects of

diseases and parasites implemented; nonnative

fish stocking procedures implemented; control

of nonnative fish implemented; mechanisms

determined for legal protection of habitat;

conservation plans identified for long-term

protection; levels of hybridization with white

sucker assessed; hazardous materials emergency

response plans revised to ensure protection;

shut-off valves installed in petroleum-product

pipelines within the 100-year floodplain; and

effects of selenium identified and mediated

Overall, the proposed action should benefit this species and its

critical habitat by improving riverine and backwater habitat

conditions; and, in combination with other SJRBRIP recovery

elements should assist in species recovery. As with the

pikeminnow, periodic lower flows may adversely affect water

quality in the razorbacks habitat and depletions from

reservoir evaporation and water uses reduce water available to

maintain habitat. In the future, it is possible that the

razorbacks present range may expand upstream toward the

Hammond Diversion. Effects of new flow regimes in this reach

would be similar to those discussed for the Colorado

pikeminnow previously.

Bonytail and Humpback Chub.—These endangered fish do

not occur in the

San Juan River and would not be affected by the operation

changes of the Proposed Plan. Historical presence or absence

is unclear; however, there is some evidence that the bonytail

occurred in the river prior to the 20th Century (Service,

2001d). If introductions are made in the future to the San

Juan River, new operations under the proposed action may

benefit these species.

Interior Least Tern.—The interior least tern is a small,

migratory, piscivorus tern associated with shallow waters of
J-57

lakes and rivers. These birds are primarily found in the

Mississippi Basin, although a breeding population occurs at

Bitter Lake National Wildlife Refuge in Chaves County New 

Mexico. Nesting occurs in late May. The New Mexico

Department of Game and Fish (NMDGF) reports infrequent

sitings in San Juan County in the project area. The BLM

(2002b) reports that it may be an occasional visitor to rivers

in the area.

The interior least tern is not known to depend on the

habitats along the San Juan River and Navajo Reservoir

potentially affected by the Proposed Plan and thus should not

be affected.

Southwestern Willow Flycatcher.—The southwestern willow

flycatcher is a small, migratory passerine bird that has lost

habitat due to water diversion and floodplain channelization,

introduction of non-native vegetation, livestock grazing, and

brown-headed cowbird nest parasitism. The birds nest in

dense riparian vegetation with a nesting period from May

through July. Willow flycatchers typically nest in native

vegetation; they also use areas dominated by tamarisk or

Russian olive. Surface water or saturated soils are often

present in nesting areas and may be correlated with food

supplies. Only 986 nesting territories have been identified in

the United States, with four of these in the San Juan Basin

(Sogge et al., 2002). A recovery plan was approved for this

species in 2002 (Service, 2002d) and can be referred to for

information on habitat, distribution, and other information. 

Habitat loss, habitat fragmentation, and brood parasitism are

significant problems for the survival of this species.

Potential habitat in the project impact area occurs along the

arms of Navajo Reservoir and downstream along the San Juan

River. Data suggest that the better willow flycatcher habitat

exists downstream from the Animas River confluence (CUP,

2001), although some areas immediately downstream from

Navajo Dam provide excellent potential habitat.

Willow flycatchers were observed along the Piedra Arm of
J-58

Navajo Reservoir in 1999 but were not confirmed to be nesting

(Reclamation, 1999). Additional surveys are being conducted

in 2003 and results will be distributed when available. Lowgradient inflow areas to the reservoir have developed

willow/cottonwood habitat areas that are supported by both

reservoir water levels and tributary inflow in conjunction with

sediment deposition from the tributaries. These areas have

developed under fluctuating reservoir conditions (drawdowns of

over 35 feet have occurred in 5 of the last 16 years). In

2002 the drawdown exceeded 75 feet.

CUP (2001) provides detail on habitat conditions and willow

flycatcher distribution along the river downstream from Navajo

Dam. The public lands immediately downstream from the dam

were rated as marginal to excellent potential habitat. Along

the San Juan, particularly in downstream areas, habitat is now

dominated by tamarisk and Russian olive, although native

willow stands occur.

Studies reported by Johnson and OBrien (1998) indicate that

the lower river in Utah is primarily used by migrating birds

and, as such, serves as an important stopover to replenish

strength for the continued migration to breeding grounds. 

Migrating willow flycatchers have also been observed along the

river in New Mexico. BLM surveys between 1993 and 2002 of

their lands along the San Juan River have not detected

nesting birds but have recorded migrants.

The river area also provides suitable nesting habitat that may

be used in the future (CUP, 2001). In 1997, one nesting pair

was documented along the San Juan River in New Mexico

downstream from Shiprock. Nesting was confirmed in this

area again in 1998 but not in 1999 (BIA, 1999 and CUP, 2001).

The proposed action could affect willow flycatchers by either

affecting habitat or changing the level of human disturbance. 

Under the proposed action, Navajo Reservoir elevations would

change in response to meeting Flow Recommendations. 

Beginning in mid- to late May, reservoir levels would, on

average, be 5 to 10 feet lower than under the No Action
J-59

Alternative because of the release of water for spring peaks in

most years under the Flow Recommendations. (It should be

noted that this has been occurring in recent years as spring

peak releases have been made for research purposes). It is

difficult to predict if this new operation, in the long term,

will affect the willow/cottonwood habitat. Vegetation in the

spring of 2003 does not appear to be stressed despite very

large, drought-related drawdowns, and spring releases have

been ongoing in recent years. Accordingly, although there is

an indication that potential habitat will not be affected by the

proposed action, the actual vegetation response may not be

apparent for many years; thus, the new operations may affect

the quality or extent of potential habitat along the reservoir.

In potential habitat areas in the first few miles downstream

from Navajo Dam, high spring releases should benefit habitat

and reduce human disturbance during the high flow period. 

On the other hand, releases of 250 cfs outside of the spring

peak could increase disturbance to potential habitat by

anglers who can more easily wade the river and travel up and

down the river bank. Low flows could also stress vegetation,

although river elevations and associated groundwater changes

are only about 4.5 inches when flows drop from 500 to 250

cfs. Between Archuleta and Farmington, irrigated fields border

the river and

ground water from irrigation helps maintain riparian

vegetation and should moderate

low-flow effects. In this area, and especially downstream

from Farmington, the high spring releases (and reduced lowflow periods downstream from Farmington) would favor more

natural river characteristics that should benefit riparian

vegetation and potential willow flycatcher habitat.

Overall, the more natural flow regime under the Proposed Plan

may benefit this species.

California Condor.—Relocation efforts involving this large

raptor have resulted in the introduction of this species to

northern Arizona. Previously the species occurred in recent

years only in California, where it was extremely rare. 
J-60

Individuals from the northern Arizona population have traveled

into Utah and Colorado, and certainly could occur on an

irregular basis in the project area. The bird is a carrion

feeder and generally nests in cliff areas. Existing or potential

habitat for the species would not be affected by the Proposed

Plan and there would be no effect on the species.

Black-Footed Ferret.—There are no recent reports of this

species, which is closely associated with prairie dog towns, in

the project area. The species has not been observed in the

wild in New Mexico since 1934 (BLM, 2002b). Potential habitat

of the species would not be affected by the proposed action.

Threatened Species.—

Bald Eagle.—Bald eagles occur around Navajo Reservoir

and along the San Juan River, primarily during the winter.

Peak use at the reservoir occurs in December through

February. Average numbers of birds observed on the New

Mexico portion of the reservoir was 35 in February surveys

between 1993 and 2001 (BLM, 2002b). No bald eagle nesting is

known to occur in the New Mexico portion of the project area

(Reclamation, 1999), but

an active nest occurs in Colorado on private lands north of

Navajo Reservoir. Winter concentration areas occur around

Navajo Reservoir and some of its tributaries. Winter

concentration areas have been designated along the Piedra,

San Juan, and Lost Pinos rivers and reservoir arms in

Colorado and in several areas around the reservoir in New

Mexico. BLM has identified 32 Areas of Critical Environmental

Concern for wintering eagles on the New Mexico portion of the

reservoir. Food sources include fish, waterfowl, and carrion. 

Night roost sites, consisting of undisturbed cottonwood groves

or ponderosa pine groves from which eagles disperse daily for

feeding, are important factors in maintaining wintering

populations.

The bald eagle is not expected to be adversely affected by the

proposed action. A more natural hydrograph along the San

Juan River should maintain and possibly enhance regeneration
J-61

of cottonwood trees along the San Juan River which are

important winter habitat. In addition the periodic high spring

flows may discourage human encroachment into floodplain

areas thus indirectly benefitting the eagles habitat. Increased

riverflows will cause more loss of mature trees to bank

erosion, possibly offsetting this benefit. Although some

changes in fish populations are anticipated, food supplies in

the waterways affected should not be significantly affected. 

Reduced reservoir levels may stress cottonwood trees

developing around Navajo Reservoir, thus reducing roosting

areas. Overall there should be no adverse effect on this

species.

Navajo Sedge.—This member of the sedge family occurs

only in a few localities in Arizona (Apache, Coconino, and

Navajo Counties) and Utah (San Juan County), although surveys

are incomplete. Its specialized habitat consists of seepsprings on vertical cliffs

of Navajo sandstone or other eolian sandstone formations. 

One population is reported

1.5 miles south of the San Juan River (Utah Division of

Wildlife Resources, 1998). Threats may include grazing,

trampling, and disturbance to ground water supplies. The

proposed action would not affect the types of habitat used by

this species.

Mexican Spotted Owl.—The Mexican spotted owl inhabits

canyon and montane forest habitats in a range that includes

southern Utah and Colorado, New Mexico, and Arizona. Critical

habitat has been designated on 4.6 million acres in the 4

states. Critical habitat does not include the project area but

does include portions of the San Juan arm of Lake Powell

(Service, 2001c).

Mixed conifer forests are commonly used; and in the northern

part of its range (which would be the project area), the owls

primarily occur in rocky canyons. Prey species are thought

to primarily be small, nocturnal mammals. Habitat types

used or potentially used by this species would not be affected
J-62

by the proposed action.

Species of Concern.—

American and Arctic Peregrine Falcons.—These two species

occur in Colorado and New Mexico, with nesting of the

American peregrine falcon occurring in both states. There are

no known nests around Navajo Reservoir (Reclamation, 1999). 

Potential nesting habitat occurs on cliffs along the San Juan

River. Riparian areas in the project region provide migration

and foraging habitat. These habitats should not be

significantly affected by the proposed action.

Black Tern.—The black terns would most likely be

encountered in the project area during spring migration. 

Habitat includes lakes and reservoirs and other open fresh

water; nesting occurs in large marshes adjacent to open

water. Nesting populations occur in northern Utah around

waterways and in wetland areas in eastern Colorado and

Colorados San Luis Valley. Populations have been declining

due to losses of habitat and possibly pesticides. Suitable

habitat should not be affected by the Proposed Plan.

White-Faced Ibis.—The white-faced ibis typically nests in

colonies in dense marsh habitats and feeds in shallow water

and flood-irrigated fields. Nesting does not occur in the

project area and the species is considered a casual migrant

(BIA, 1999; BLM, 2002a; and Reclamation, 1999). However

nesting has been confirmed in Montezuma County, Colorado

just north of the project area, indicating that nesting in the

project area

is possible. Suitable habitat should not be affected by the

Proposed Plan.

Yellow-Billed Cuckoo.—The yellow-billed cuckoo would be

considered a rare summer resident in the project area. 

Populations have declined significantly throughout the species

range; a major factor has probably been the loss of mature
J-63

riparian forests. Loss of prey insects to pesticides is also

believed to be a factor. Protection of riparian areas is

critical to this species. Surveys of portions of the San Juan

River in 1997 and 1998 indicated that the birds are present

in small numbers during migration and there is some evidence

of breeding (Johnson and OBrien, 1998). BLM (2002a) report

that they are very rare in the San Juan River valley. Sites

where birds have been observed generally consist of dense

Russian olive, tamarisk, and willow with and associated stand

or an overstory of cottonwoods. No birds were observed in

sites with little vegetative understory. Factors that adversely

affect populations along the river may include grazing, oil/gas

exploration, and agricultural practices (Johnson and OBrien,

1998).

The Proposed Plan is not anticipated to significantly affect

this species. While a more natural hydrograph seen under the

proposed action may scour some of the riverbank riparian

areas, they also may be more conducive to maintenance and

establishment of important cottonwood groves along the river.

Roundtail Chub.—While this species is relatively common

in parts of the Upper Colorado River Basin, it is uncommon in

the project area. The roundtail chub sustains a small

population in the San Juan River downstream from Navajo

Dam and also occurs in tributaries such as the LaPlata and

Mancos Rivers (BIA, 1999 and Propst, 1999). The species also

occurs in the San Juan above the reservoir (Reclamation,

1999). Ryden (2000) collected this species between River Miles

78 and 177, but the species was uncommon.
J-64

The roundtail was one of the most common fishes collected

from Navajo Reservoir within the first few years after the dam

was closed in the mid-1960s. It is now rarely collected,

indicating that much of its reproductive habitat was lost to

the reservoir.

Habitat used most commonly are pools with some type of

cover, and spawning occurs in pool-riffles or in riffles

upstream from pools (Propst, 1999). Loss of habitat through

flow depletion or channel modification, and competition from

non-native fish are probably factors in their low populations

in the San Juan. Olson (1962) attributed low numbers to

changes in water temperatures below Navajo Dam and due to

early efforts to remove nongame fish from the river.

The more natural hydrograph downstream from Farmington

may benefit these species by reducing non-native fish that

compete and by providing more natural habitat conditions.

Upstream from Farmington, adverse effects are possible

because of reduced habitat associated with lower summer

flows and possibly by water quality declines; however, the fish

is very uncommon in this area.

New Mexico Silverspot and San Juan Checkerspot

Butterflies.—These insect species are native species with limited

distribution. Populations are affected by habitat losses and in

some cases collection. Habitat includes moist habitats around

marshes and along streams. The proposed action should not

affect these species, although it would provide a more natural

river and floodplain condition which may benefit them.

San Juan Tiger Beetle.—Tiger beetles are common but

some species have limited distribution. Habitat includes sandy

areas and sandy washes, including riparian areas. As a native

species, the San Juan tiger beetle would be expected to

benefit from a more natural riparian area; the Proposed Plan

should have either a neutral or beneficial effect.
J-65

Gunnison Sage Grouse.—The Gunnison sage grouse

currently occurs in eight isolated populations in western

Colorado and southeastern Utah. The species has been in

decline, presumably due to habitat loss and fragmentation. 

Habitat includes large expanses of sagebrush with a diversity

of grasses and forbs and healthy riparian areas. Existing or

potential habitat of this species would not be affected by the

proposed reoperation of Navajo Reservoir.

Other Species of Concern.—The Navajo Nation provided a

list of species of special concern that included several of the

species discussed above, but contained the following additional

species:
J-66

Golden Eagle.—The golden eagle uses a variety of

habitats in the San Juan basin including the San Juan River

corridor. Nesting occurs on cliffs or large trees. Primary

foods include small mammals and carrion although birds and

fish can be included. Habitat used by these birds should not

be adversely affected by the Proposed Plan.

Bluehead Sucker.—Bluehead suckers tend to occur more

frequently in the upper reaches of the San Juan River and

occur both upstream and downstream of Farmington, including

tributaries that feed Navajo Reservoir. Propst (1999) reported

them as common

in the San Juan River system. Ryden (2000) indicated that

during the period of testing recommended flows, there was an

overall improvement for this species in the San Juan. This

may be related to maintenance of cobble areas which provide

feeding habitat. Based

on results of the test flows, it is anticipated that this species

will benefit from the proposed action. The exception to this

may be in areas between Farmington and Navajo Dam that will

have significant flow reductions in summer and fall months,

reducing water quality and perhaps reducing the quality of

cobble feeding areas.

Mottled Sculpin.—Ryden (2000) reported collections of

mottled sculpin between River Miles 155 and 178 in the San

Juan River. Miller and Rees (2000) reports the species as

common to abundant in the Animas River and tributaries

upstream from Navajo Reservoir. They were also common in

the upper LaPlata River. The species is less common in

New Mexico and Propst (1999) reported the species may

warrant state protection. More natural flows and maintenance

of channel conditions may benefit this species under the

proposed alternative.

Northern Leopard Frog.—This frog is associated with

wetlands and waterways along the San Juan River. Reduced

summer flows between Navajo Dam and Farmington under the
J-67

Proposed Plan may adversely affect its habitat, particularly in

the extensive wetlands just downstream from Navajo Dam. 

Water supply to these wetlands will be reduced when summer

releases from Navajo Dam are reduced from 500 to 250 cfs.

Bighorn Sheep.—Desert bighorn sheep are often

associated with river canyons, including the lower reaches of

the San Juan River. The sheep can utilize rivers for drinking

water and some use of riparian areas can occur. There is no

indication that this species would be affected by riverflow

changes under the Proposed Plan.

Alcove Rock Daisy.—This species occurs in southeastern

Utah and is reported from the canyons of the Colorado River

from its confluence with the Dolores River on the north to

San Juan County on the south. The species grows in alcove

sites in sandstone cliffs that receive little direct sunlight and

in sites with drier conditions (Utah Division of Wildlife

Resources, 1998). Habitat of this species would not be

affected by project alternatives.
J-68

Literature Cited

Blanchard et al. 1993. Reconnaissance investigation of water

quality, bottom sediment, and biota associated with

irrigation drainage in the San Juan River area, San Juan

County, Northwestern New Mexico, 1990-1991. U.S.G.S.

Water Resources Investigations Report 93-4065.

141 pp.

Bliesner, Ron and V. Lamarra. 1996. San Juan River habitat

studies, 1995 Annual Report--

San Juan River Recovery Implementation Program, USFWS,

Albuquerque, NM.

_____. 2000. Hydrology, geomorphology and habitat

studies-San Juan River Recovery Implementation Program,

USFWS, Albuquerque, NM.

Brooks, James E, M. Buntjer, and J. Smith. 2000. Non-native

species interactions: management implications to aid in

recovery of the Colorado pikeminnow and razorback sucker

in the San Juan River-San Juan River Recovery

Implementation Program, USFWS, Albuquerque, NM.

Holden, P.B. 1999. Flow recommendations for the San Juan

River. San Juan River Basin Recovery Implementation

Program, USFWS, Albuquerque, NM.

_____. 2000. Program evaluation report for the 7-year

research period (1991-1997). San Juan River Basin

Recovery Implementation Program, USFWS, Albuquerque, NM.

Johnson, Matthew J. and C. OBrien. 1998. Southwestern willow

flycatcher and western yellow-billed cuckoo surveys along

the San Juan River, Utah, 1998 (Four Corners BridgeMexican Hat). Colorado Plateau Field Station, Flagstaff, AZ.

Masslich, William and P. Holden. 1996. Expanding distribution

of Colorado squawfish in the San Juan River, a discussion

paper. Prepared for Biology Committee of SJRBRIP. 

Logan, UT.
J-69

Miller, William and J.A. Ptacek. 2000. Colorado Pikeminnow

habitat use in the San Juan River, New Mexico and UtahSan Juan River Recovery Implementation Program, USFWS,

Albuquerque, NM.

Miller, William and D. Rees. 2000. Ichthyofaunal surveys of

tributaries of the San Juan River, New Mexico. San Juan

River Recovery Implementation Program, USFWS,

Albuquerque, NM.

The Navajo Nation. 2001. Letter from Navajo Fish and

Wildlife Department, Window Rock, AZ to Area Manager,

Reclamation, Grand Junction, CO. Subject: Proposal to

Modify Operations of Navajo Dam and Reservoir. May 21,

2001.

Propst, David. 1999. Threatened and endangered fishes of

New Mexico. Technical Report No. 1. New Mexico

Department of Game and Fish, Santa Fe, NM.

Ryden, Dale. 2000. Adult fish community monitoring on the

San Juan River, 1991-1997-San Juan River Recovery

Implementation Program, USFWS, Albuquerque, NM.

_____. 2003a. An augmentation plan for Colorado

pikeminnow in the San Juan River. U.S. Fish and Wildlife

Service, Grand Junction, CO.

_____. 2003b. An augmentation plan for razorback sucker

in the San Juan River. U.S. Fish and Wildlife Service,

Grand Junction, CO.

San Juan River Basin Recovery Implementation Program. 

2001a. Draft meeting summary of May 15-16, 2001

Biology Committee.

_____. 2001b. Meeting Summary of February 5-6 Biology

Committee.

_____. 2001c. Principles for conducting Endangered Species
J-70

Act Section 7 consultations on water development and

water management activities affecting endangered fish

species in the San Juan River Basin. Coordination

Committee.

_____. 2002. Memorandum from SJRRIP Biology Committee,

Bill Miler, Chair to Ed Warner, Bureau of Reclamation. 

Subject: San Juan River Base Flow-Guidance for Navajo

Reservoir Operations, July 16, 2002.

Simpson, Zachery R. and J. D. Lusk. 1999. Environmental

contaminants in aquatic plants, invertebrates, and fishes of

the San Juan River Mainstem, 1990-1996. Prepared for

San Juan River Recovery Implementation Program.

Sogge, M.K., S. J. Sferra, T.D. McCarthy, S.O. Williams and B.E.

Kus. 2002. Southwestern willow flycatcher breeding site

and territory survey. U.S. Geological Survey

Thomas et al. 1995. . Detailed study of selenium and

selected constituents in water, bottom sediment, soil, and

biota associated with irrigation drainage in the San Juan

River Area,

New Mexico. U.S.G.S. Water Resources Investigations Report

98-4213.

(UCRRP/SJRBRIP) Upper Colorado River Endangered Fish

Recovery Program and San Juan River Basin Recovery

Implementation Program. 2002. Program Highlights,

2001-2002.

U.S. Bureau of Indian Affairs. 1999. Navajo Indian Irrigation

Project Biological Assessment. Prepared by Keller-Bliesner

Engineering, Logan UT and Ecosystems Research, Logan UT.

U.S. Bureau of Land Management. 2002a. Farmington

Resource Management Plan and Environmental Impact

Statement (draft). Farmington, NM.
J-71

_____. 2002b. Draft biological assessment: impacts to

threatened and endangered species related to the resource

management plan revision, BLM Farmington Field Office.

Prepared by Science Applications International Corp,

Albuquerque, NM..

U.S. Bureau of Reclamation. 1999. Biological Assessment,

Animas-LaPlata Project, Colorado-New Mexico. Prepared by

Miller Ecological Consultants, Fort Collins, CO.

_____. 2000. Animas La Plata Project Colorado-New Mexico. 

Final Supplemental Environmental Impact Statement. Salt

Lake City, UT.

_____. 2001. Positive population response criteria for

Colorado pikeminnow and razorback sucker in

the San Juan River. Memorandum from Area Manager, Grand

Junction CO to Colorado State Supervisor, Fish

and Wildlife Service, Denver. July 6, 2001.

_____. 2002a. Summer low flow test-San Juan River New

Mexico and Utah. Western Colorado Area Office, Grand

Junction and Durango, CO.

_____. 2002b. Draft Environmental Impact Statement:

Navajo Reservoir Operations, Colorado River Storage Project,

Colorado-New Mexico-Utah. Salt Lake City, UT.

U.S. Department of the Interior. 2001. Southwestern willow

flycatcher San Juan River habitat evaluation and

conservation management strategies. Central Utah Project

(CUP) Completion Act report, Provo, UT.

U.S. Fish and Wildlife Service. 1991. Memorandum from

Regional Director, Region 2 to Regional Director, Bureau of

Reclamation, Salt Lake City concerning Navajo Dam

Operations Consultation under Section 7 of the Endangered

Species Act. August 19, 1991.

_____. 2000. Final Biological Opinion for the AnimasLaPlata Project, Colorado and New Mexico. Colorado Field
J-72

Supervisor, Lakewood CO.

_____. 2001a. Letter from Field Supervisor, Albuquerque, NM

to Area Manager, Reclamation, Grand Junction, CO. 

Subject: Species List for the Modified Operations of Navajo

Dam and Reservoir, Colorado and New Mexico. March 8,

2001.

_____. 2001b. Letter from Utah Field Supervisor, Salt Lake

City, UT to Technical Services Manager, Reclamation, Grand

Junction, CO. Subject: Compliance with the Endangered

Species Act, Proposal to Modify Operations of Navajo Dam

and Reservoir. August 24, 2001.

_____. 2001c. Designated critical habitat for the Mexican

spotted owl (website) Ecological Services, Southwest Region.

_____. 2001d. Draft Fish and Wildlife Coordination Act

Report for Navajo Reservoir Operations. New Mexico

Ecological Services Field Office, Albuquerque, NM.
J-73

_____. 2001e. Memorandum from Colorado Field Supervisor,

Lakewood CO to Area

Manager, Reclamation, Grand Junction, CO. Subject:

Positive Population Response Criteria for Colorado

Pikeminnow and Razorback Sucker in the San Juan River

as part of the Animas-La Plata Biological Opinion. August

8, 2001. 

_____. 2002a. Memorandum from New Mexico Field

Supervisor, Albuquerque, NM to Area Manager, Reclamation,

Grand Junction, CO. Subject: Review of Biological

Assessment for Navajo Reservoir Operations, Colorado River

Storage Project, Colorado,

New Mexico, and Utah. October 30, 2002.

_____. 2002b. Colorado pikeminnow (Ptychocheilus lucius)

recovery goals: amendment and supplement to the

Colorado Squawfish Recovery Plan. Region 6, Denver CO.

_____. 2002c. Razorback sucker (Xyrauchen texanus)

recovery goals: amendment and supplement to the

Razorback Sucker Recovery Plan. Region 6, Denver CO.

_____. 2002d. Southwestern willow flycatcher recovery plan. 

Region 2, Albuquerque, NM.

Utah Division of Wildlife Resources. 1998. Inventory of

sensitive species and ecosystems in Utah. Prepared for

Utah Reclamation Mitigation and Conservation Commission

under the Utah Project Completion Act.

Wethington, C. Mark and P. Wilkinson. 2003. Long-range

management plan for the San Juan River special trout water

(Draft). New Mexico Game and Fish Department, Albuquerque

NM.
Attachment A

River Mile Demarcations

San Juan River
J-43

River mile Location

0 Paiute Farms (Lake

Powell)

53 Mexican Hat

68 Chinle Creek

80 Bluff UT

100 McElmo Creek

confluence

105 Aneth UT

120 Four Corners

128 The Mixer

148 Shiprock

158 Hogback Diversion

180 Animas River

confluence

208 Hammond Diversion

217 Hammond Diversion

220 Archuleta Gage

225 Navajo Dam
J-44
Attachment B

Depletion Table Utilized in

Hydrology Analysis
J-45

Table B-1.—Summary of San Juan River Basin depletions for each alternative1, 2, 3

Depletion category

No Action

Alternative

(acre-feet/year)

250/5000

Alternative

(acre-feet/year)

500/5000

Alternative

(acre-feet/year)

New Mexico depletions

Navajo lands irrigation depletions

Navajo Indian Irrigation Project

Hogback

Fruitland

Cudei

Chaco River offstream depletion

Whiskey Creek offstream depletion

4

143,600

26,163

10,233

900 6

2,832

6

523

4

280,600

5

12,100

5

7,898

900 6

2,832

6

523

4

280,235

5

12,065

5

7,898

900 6

2,832

6

523

 Subtotal 184,252 304,853 304,454

Non-Navajo lands irrigation depletions

Above Navajo Dam – private

Above Navajo Dam – Jicarilla

Animas River

La Plata River

Upper San Juan

Hammond Area

Farmers Mutual Ditch

Jewett Valley

Westwater

738

2,190

36,711

9,739

9,137

10,268

9,532

3,088

110

738

2,190

36,711

9,739

9,137

10,268

9,532

3,088

110

738

2,190

36,711

9,739

9,045

10,164

9,532

3,088

110

 Subtotal 81,513 81,513 81,318

 Total New Mexico irrigation depletions 265,765 386,366 385773

Non-irrigation depletions

Navajo Reservoir evaporation

BHP Navajo Coal Company

San Juan power plant

Industrial diversions near Bloomfield

Municipal and industrial uses

Scattered rural domestic uses

Scattered stock ponds and livestock uses

Fish and wildlife

29,209

39,000

7

16,200

2,500

8,454

6

1,400

6

2,200

6

1,400

27,428

39,000

7

16,200

2,500

8,454

6

1,400

6

2,200

6

1,400

26,274

38,981

7

16,200

2,500

8,432

6

1,400

6

2,200

6

1,400

 Total New Mexico non-irrigation depletions

San Juan-Chama Project exportation

Unspecified minor depletions

Animas-La Plata Project

100,363

107,514

8

1,500

0

98,582

107,514

9

4,500

13,600

97,387

107,514

9

4,486

13,600

 Total New Mexico depletions 475,142 610,562 608,760
J-46

Table B-1.—Summary of San Juan River Basin depletions for each alternative1, 2, 3 (continued)

Depletion category

No Action

Alternative

(acre-feet/year)

250/5000

Alternative

(acre-feet/year)

500/5000

Alternative

(acre-feet/year)

Colorado depletions

Upstream of Navajo Reservoir

Upper San Juan

Navajo-Blanco

Piedra

Pine River

10,858

7,865

8,098

71,671

10,858

7,865

8,098

71,671

10,858

7,865

8,098

71,671

 Subtotal 98,492 98,492 98,492

Downstream of Navajo Reservoir

Florida

Animas

La Plata

Mancos

McElmo Basin imports

28,607

25,113

13,049

19,530

(11,769)

28,607

25,113

13,049

19,532

(11,769)

28,607

25,113

13,049

19,532

(11,769)

 Subtotal 74,530 74,532 74,532

Animas-La Plata Project 0 43,533 43523

 Total Colorado depletions 173,021 216,557 216,546

Colorado and New Mexico combined depletions 648,163 827,119 825,306

Utah depletion

Arizona depletion

6, 109,140 6

10,010

6, 109,140 6

10,010

6, 109,140 6

10,010

 Grand total 667,313 846,269 844,456

 1 The State of New Mexico does not necessarily agree with the depletions shown in terms of constituting evidence of

actual water use, water rights, or water availability under the Compact. The SJRBRIP Hydrology Committee uses a

hydrology model disclaimer that reads in part, “The model data methodologies and assumptions do not under any

circumstances constitute evidence of actual water use, water rights, or water availability under Compact apportionments and

should not be construed as binding on any party.” 

 2

 The New Mexico Interstate Stream Commission (NMISC) and the San Juan Water Commission (SJWC) believe there

are inconsistencies in depletion calculations (communications from NMISC and SJWC dated April 3 and March 21, 2002,

respectively).

 3

 It should be noted that full development of State compact water and Indian trust water is not included in this table. Only

existing projects and projects with Endangered Species Act and NEPA compliance are included in the depletion table.

 4

 Includes 10,600 acre-feet per year of annual groundwater storage. At equilibrium, the No Action Alternative drops to

133,000 acre-feet per year and the action alternatives drop to 270,000 acre-feet per year.

 5

 Accounts for 16,420 acre-feet per year transferred from Hogback, including the Hogback Extension, and Fruitland

Projects to NIIP.

 6

 Indicates offstream depletion accounted for in calculated natural gains.

 7

 Water contract with the Jicarilla Apache Nation (Public Service of New Mexico).

 8

 1,500 acre-feet per year of depletion from minor depletions approved by SJRBRIP in 1992. 

 9

 3,000 acre-feet per year of depletion from 1999 Inter-Service consultation, a portion of which may be in Colorado.

 10 1,705 acre-feet per year San Juan River depletion, 7,435 acre-feet per year offstream depletion.
Attachment C

Hydrology Analysis Tables and Figures
J-47

Table C-1.—San Juan River flows at Archuleta monthly summary statistics for the

No Action, 250/5000, and 500/5000 Alternatives (1929 – 93 data)

San Juan at Archuleta

No Action 250/5000 500/5000

Average monthly flows

(cfs)

Average monthly flows

(cfs)

Average monthly flows

(cfs)

Month Mean Maximum Minimum Mean Maximum Minimum Mean Maximum Minimum

October 984 3,791 500 388 1,010 250 501 957 0

November 1,015 3,126 500 321 1,554 250 507 1,189 0

December 978 1,782 500 360 1,617 250 544 1,780 0

January 887 1,290 500 296 433 250 486 500 0

February 500 500 500 287 444 250 488 500 0

March 606 4,929 500 672 5,000 250 715 4,250 500

April 1,144 5,000 500 1,260 5,000 250 1,063 4,750 500

May 1,323 5,000 500 2,195 5,000 250 1,795 5,000 500

June 1,798 5,000 500 2,215 3,937 250 1,660 3,749 500

July 1,022 4,590 500 386 1,476 250 538 1,454 227

August 898 3,465 500 471 1,104 250 531 1,081 0

September 1,004 4,339 500 459 1,027 250 517 1,004 0

Average 1,013 3,568 500 776 2,300 250 779 2,184 186

Maximum 1,798 5,000 500 2,215 5,000 250 1,795 5,000 500

Minimum 500 500 500 287 433 250 486 500 0

Note: Minimum flows of zero are shown under the 500/5000 Alternative because the reservoir is occasionally drawn down

below the NIIP inlet works. In actuality, the reservoir inflows would be bypassed to meet downstream water rights. 
J-48

Table C-2.—San Juan River flows at Bluff, Utah, monthly summary statistics for the

No Action, 250/5000, and 500/5000 Alternatives (1929 – 93 data)

San Juan at Bluff

No Action 250/5000 500/5000

Average monthly flows

(cfs)

Average monthly flows

(cfs)

Average monthly flows

(cfs)

Month Mean Maximum Minimum Mean Maximum Minimum Mean Maximum Minimum

October 1,668 10,189 455 1,012 7,338 525 1,127 7,285 36

November 1,548 4,982 644 824 3,261 525 1,010 2,895 249

December 1,415 2,806 742 777 2,645 525 964 2,808 261

January 1,309 2,717 734 716 1,743 525 907 1,993 367

February 1,154 3,036 729 940 2,792 547 1,141 3,014 503

March 1,303 6,332 451 1,329 6,285 525 1,372 5,535 525

April 2,130 8,079 220 2,151 7,704 525 1,956 7,454 525

May 3,232 12,934 380 4,017 12,863 525 3,621 12,872 525

June 4,317 10,314 509 4,680 9,081 609 4,113 8,944 609

July 2,102 7,836 258 1,465 4,715 525 1,618 4,692 525

August 1,522 8,223 67 1,110 5,175 525 1,171 5,183 435

September 1,538 8,218 182 990 4,288 525 1,050 4,296 42

Average 1,936 7,139 448 1,668 5,657 534 1,671 5,581 384

Maximum 4,317 12,934 742 4,680 12,863 609 4,113 12,872 609

Minimum 1,154 2,717 67 716 1,743 525 907 1,993 36
J-49

Table C-3.—Seasonal frequency distribution of monthly Navajo Reservoir

releases

for the three alternatives (based on 1929 – 93 hydrology)

Release range

(cfs) Number of occurrences Occurrences as percent1

All months

No

Action

250/500

0

500/500

0

No

Action 250/5000

500/500

0

0 249 0 0 15 0 0 2

249 251 0 222 0 0 28 0

251 350 0 191 0 0 24 0

350 499 0 144 0 0 18 0

499 501 345 3 593 44 0 76

501 1,000 185 103 93 24 13 12

1,000 2,500 196 38 24 25 5 3

2,500 5,000 54 79 55 7 10 7

Total number of

months 780 780 780 100 98 100

December through February

No

Action

250/500

0

500/500

0

No

Action 250/5000

500/500

0

0 249 0 0 6 0 0 3

249 251 0 54 0 0 28 0

251 350 0 121 0 0 62 0

350 499 0 16 0 0 8 0

499 501 109 0 185 56 0 95

501 1,000 16 0 0 8 0 0

1,000 2,500 70 4 4 36 2 2

2,500 5,000 0 0 0 0 0 0

Total number of

months 195 195 195 100 100 100

March through November2

No

Action

250/500

0

500/500

0

No

Action 250/5000

500/500

0

0 249 0 0 9 0 0 2

249 251 0 168 0 0 29 0

251 350 0 70 0 0 12 0

350 499 0 128 0 0 22 0

499 501 236 3 408 40 1 70

501 1,000 169 103 93 29 18 16

1,000 2,500 126 34 20 22 6 3

2,500 5,000 54 79 55 9 14 9

Total number of

months 585 585 585 100 102 100
J-50

 1 Total percentages differ slightly from 100 percent due to using rounded monthly percentages.

 2

 As planned, minimum releases would be released during the irrigation season until additional water development occurs. 

This increase is not reflected in the table.
J-51

Table C-4.—San Juan River at Bluff – distribution frequency of monthly flow 1929 – 93

Percent of time mean monthly 

streamflow is less than 500 cfs1

Percent of time mean monthly

streamflow is between 500 and

800 cfs

Percent of time mean monthly

streamflow is greater than 800 cfs

Month

No

Action

250/

5000

500/

5000

No

Action

250/

5000

500/

5000

No

Action

250/

5000

500/

5000

January

February

March

April

May

June

July

August

September

October

November

December

0.0

0.0

3.1

12.3

1.5

0.0

4.6

6.2

12.3

3.1

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.0

3.1

0.0

0.0

0.0

0.0

0.0

0.0

1.5

3.1

3.1

3.1

3.1

6.2

12.3

23.1

21.5

6.2

1.5

10.8

15.4

10.8

15.4

9.2

7.7

78.5

49.2

55.4

44.6

9.2

3.1

18.5

40.0

53.8

66.2

67.7

76.9

26.2

12.3

29.2

40.0

9.2

1.5

13.8

36.9

41.5

43.1

18.5

26.2

93.8

87.7

73.8

66.2

92.3

98.5

84.6

78.5

76.9

81.5

90.8

92.3

21.5

50.8

44.6

55.4

90.8

96.9

81.5

60.0

46.2

33.8

32.3

23.1

70.8

87.7

70.8

60.0

90.8

98.5

86.2

61.5

55.4

53.8

78.5

70.8

 1

 While the goal is to remain above 500 cfs, it is anticipated that flows will occasionally fall below 500 cfs.

Table C-5.—Summary of streamflows measured during 

the 2001 Summer Low Flow Test

Location

River

 Mile

Average

Flow

(cfs)

San Juan River at Soaring Eagle Lodge (below

Citizens Ditch)

216.4 132.7

San Juan River above Turley Inlet Channel 214.4 131.4

San Juan River below Hammond Diversion 209.1 63.0

San Juan River below Blanco Bridge 207.0 87.7

San Juan River above Bloomfield Bridge 195.8 130.0

San Juan River below Bloomfield Sewer discharge 194.8 131.1

San Juan River below Lees Acre Bridge 188.5 185.7

San Juan River 1/4 mile above Animas River

confluence

181.4 218.7
J-52
J-53
J-54

Degree to Which Viable Alternatives Meet Flow Recommendations

0%

20%40%60%80%

100%120%140%160%180%200%

No Action 250/5000 500/5000 No Action 250/5000 500/5000 No Action 250/5000 500/5000 No Action 

1 days 5 days 10 days 15 days 20 days Alternatives by Flow Range 21 days 30 days 40 days 50 days 60 days 80 

>10,000 cfs > 8,000 cfs > 5,000 cfs > 2,500 

Exceeded Criteria Failed Criteria

Durations
Attachment D

Existing Water Contracts from

Navajo Reservoir
J-56

Colorado River Storage Project

Navajo Unit Water Service Contract1

Contractor Effective date Type of water use

Acre-feet

deplation ESA consultation status

Public Service

Company of

New Mexico

1977 Industrial 16,200 Included in baseline; consulted on

as a Jicarilla Nation subcontract

Williams Gas

Processing

1988 Industrial 50 Included in baseline2

San Juan Refining

Company

2001 Industrial 340 Included in baseline; subcontract

with Jicarilla3

San Juan Water

Haulers Assoc.

2001 Industrial 200 Included in baseline; subcontract

with Jicarilla2

Jesus Villalobos 2001 Irrigation 150 Included in baseline; subcontract

with Jicarilla2

Douglas Lee 2001 Irrigation 60 Included in baseline; subcontract

with Jicarilla2

Elks Lodge No. 1747 2001 Municipal 20 Included in baseline; subcontract

with Jicarilla2

 1 Diversions to NIIP are not considered a contract. These diversions are projected to deplete the river by 280,600 acrefeet. Consultation has been completed on this water use.

 2

 ESA consultation status not determined.

 3

 ESA consultation completed under minor contracts.
Attachment E

Water Quality Data
J-58

Table E-1.—Historical (1950-1998) water quality measurements on the San Juan River

Farmington Shiprock Four Corners Bluff

Parameter n Mean n Mean n Mean n Mean

Alkalinity total (mg/L as CaCO3) 607 114 646 119 59 121 2,333 147

Aluminum dissolved (:g/L as Al) 34 34.4 138 58.5 40 63.9 174 64.1

Aluminum total (:g/l as Al) 30 5,283 83 15,636 30 11,373 134 20,500

Arsenic dissolved (:g/L as As) 76 1.9 267 2.3 78 1.8 345 1.9

Arsenic total (:g/L as As) 78 2.8 224 4.4 72 3.8 309 4.3

Boron dissolved (:g/L as B) 315 49.5 678 103.9 45 126.0 1,720 68.7

Cadmium dissolved (:g/L as Cd) 11 0.8 71 0.9 15 1.2 56 1.0

Cadmium total (:g/L as Cd) 12 5.7 29 3.6 7 3.7 15 3.7

Calcium dissolved (mg/L as Ca) 859 61.6 1,178 72.4 135 65.6 2,627 93.8

Calcium total (mg/L as Ca) 5 71.5 12 70.8 6 78.8 23 88.8

Chloride total in water (mg/L) 830 9.8 1,084 16.9 104 13.5 2,568 20.6

Chromium dissolved (:g/L as Cr) 4 11.3 53 3.2 4 2.9 48 2.5

Chromium total (:g/L as Cr) 9 51.8 25 22.5 5 17.0 17 52.1

Cobalt dissolved (:g/L as Co) 9 1.5 67 1.4 10 1.6 53 1.5

Cobalt total (:g/L as Co) 13 44.4 29 22.9 7 10.6 21 41.7

Copper dissolved (:g/L as Cu) 45 3.8 165 4.2 48 5.0 203 4.9

Copper total (:g/L as Cu) 45 29.5 121 35.5 42 20.8 163 35.8

Fecal coliform (counts/100 mL) 93 10,588 162 1,040 23 256 72 185

Hardness calc. (mg/L as CaCO3) 859 189 1,154 237 123 222 2589 326

Hardness total (mg/L as CaCO3) 824 189 969 245 45 224 2423 336

Iron dissolved (:g/L as Fe) 164 47.2 251 31.2 42 22.0 69 30.5

Iron total (:g/L as Fe) 15 25,691 39 30,449 13 13,405 201 4,809

Lead dissolved (:g/L as Pb) 67 0.7 256 1.5 70 0.8 343 1.0

Lead total (:g/L as Pb) 79 30.3 222 27.6 71 23.6 305 26.1

Magnesium dissolved (mg/L as Mg) 859 8.4 1,176 13.4 135 14.4 2,628 25.0

Magnesium total (mg/L as Mg) 5 11.9 12 14.0 6 17.4 23 27.1

Manganese dissolved (:g/L as Mn) 26 22.3 110 45.0 30 6.3 86 6.1

Manganese total (:g/L as Mn) 20 852 56 978 27 449 39 1,109

Mercury dissolved (:g/L as Hg) 70 0.12 254 0.13 75 0.10 338 0.11

Mercury total (:g/L as Hg) 78 0.14 225 0.15 71 0.13 309 0.14
J-59

Table E-1.—Historical (1950-1998) water quality measurements on the San Juan River (continued)

Farmington Shiprock Four Corners Bluff

Parameter n Mean n Mean n Mean n Mean

Nickel dissolved (:g/L as Ni) 28 6.1 146 4.6 36 5.2 184 4.6

Nickel total (:g/L as Ni) 28 6.8 105 12.1 39 9.7 144 15.5

Nitrite + nitrate total (mg/L as N) 47 0.27 98 0.39 27 0.74 55 0.78

Oxygen dissolved (mg/L) 251 9.5 455 9.8 159 9.5 478 9.2

pH lab (standard units) 879 7.81 1,097 7.89 107 8.25 1,357 7.78

pH field (standard units) 60 8.13 190 8.26 60 8.25 285 8.20

Phosphorus total (mg/L as P) 59 0.27 164 0.32 31 0.37 95 0.58

Residue total filtrable (dried at

180o

 C) (mg/L)

374 382 667 498 102 422 1,313 656

Selenium dissolved (:g/L as Se) 81 0.6 277 1.0 78 1.3 349 1.1

Selenium total (:g/L as Se) 76 0.7 227 0.9 71 1.6 309 1.4

Selenium total recoverable (:g/L as

Se) 

10 0.5 29 1.0 10 0.9 47 0.8

Silver dissolved (:g/L as Ag) 2 0.75 51 0.56 n/a n/a 45 0.56

Silver total (:g/L as Ag) 2 0.75 10 1.10 n/a n/a 9 2.06

Sodium dissolved (mg/L as Na) 836 44.7 951 64.6 112 49.3 2,047 79.2

Sodium total (mg/L as Na) 5 37.7 12 38.5 6 43.8 23 58.2

Solids susp.-residue on evap. at 180

o

C (mg/L)

59 242 191 956 60 663 283 934

Specific conductance (:mhos/cm @

25 o

 C)

905 550 1136 716 112 644 2,020 931

Sulfate total (mg/L as SO4) 827 154 1,083 225 104 193 2,568 329

Turbidity (NTU, FTU, JTU) 117 158 142 527 104 406 92 503

Water temperature (o

C) 60 10.6 227 12.2 79 12.4 343 12.6

Zinc dissolved (:g/L as Zn) 80 9.2 268 9.2 77 7.8 346 15.7

Zinc total (:g/L as Zn) 75 92.9 224 114.1 71 204.0 306 109.6

 Source: Final Supplemental Environmental Impact Statement, Animas-La Plata Project, Technical Appendices, Water

Quality Analysis (Reclamation, 2000a).