Klamath River Basin Hydrologic Conditions 

Prior to the September 2002 Die-Off of 

Salmon and Steelhead

Water-Resources Investigations Report 03–4099

U.S. Department of the Interior

U.S. Geological Survey

U.S. Department of the Interior

U.S. Geological Survey

Klamath River Basin Hydrologic Conditions 

Prior to the September 2002 Die-Off of Salmon 

and Steelhead

By DENNIS D. LYNCH and JOHN C. RISLEY

Water-Resources Investigations Report 03–4099

Portland, Oregon: 2003
ii

U. S. DEPARTMENT OF THE INTERIOR

GALE A. NORTON, Secretary 

U.S. GEOLOGICAL SURVEY

CHARLES G. GROAT, Director

The use of trade, product, or firm names in this publication is for 

descriptive purposes only and does not imply endorsement by 

the U.S. Government. 

____________________________________________________________________________

For additional information: Copies of this report may be

purchased from:

District Chief

U.S. Geological Survey USGS Information Services

10615 S.E. Cherry Blossom Dr. Box 25286, Federal Center

Portland, OR 97216-3159 Denver, CO 80225-0286

E-mail: info-or@usgs.gov Telephone: 1-888-ASK-USGS

Internet: http://oregon.usgs.gov

Suggested citation:

Lynch, D.D. and Risley, J.C., 2003, Klamath River Basin hydrologic conditions prior to the September 2002 

die-off of salmon and steelhead: U.S. Geological Survey Water-Resources Investigations Report 03–4099, 10 p. 
iii

CONTENTS

Abstract ........................................................................................................................................................................ 1

Introduction................................................................................................................................................................. 1

Upper Klamath Lake Inflows and Lake Water Levels ................................................................................................. 3

Upper Klamath Lake Outflows .................................................................................................................................... 3

Diversions from the Trinity River Basin ...................................................................................................................... 5

Flows in Middle and Lower Klamath Basin ................................................................................................................ 5

Ground-Water Conditions in the Upper Klamath Basin .............................................................................................. 6

Water Temperature ....................................................................................................................................................... 8

Summary ...................................................................................................................................................................... 9 

References Cited ........................................................................................................................................................ 10

FIGURES

1. Map showing the location of selected streamflow and temperature monitoring sites in the 

Klamath and Rogue River Basins ....................................................................................................................... 2

2. Graph showing showing relation between average flows for September 1–24, 2002, and for the 1960 to

2002 September period of record at locations along the Klamath River ............................................................ 6

3. Water-level hydrograph from a USGS observation well in the Upper Klamath Lake Basin, Oregon ................ 7

4. Graph showing August and September 2002 daily water temperatures in the Klamath River at Orleans, 

California (USGS station number 11523000)..................................................................................................... 9

TABLES

1. September flow conditions in the Klamath and Trinity River Basins..................................................................4

2. Recent and long-term precipitation at Crater Lake, Oregon ................................................................................5

3. Estimated October mean ground-water discharge above and below the John C. Boyle Reservoir 

on the Klamath River and from the Spring Creek area near Chiloquin, Oregon, 1999–2002.............................7

4. Recent and long-term daily maximum water temperature conditions on the Rogue River near Agness,

Oregon .................................................................................................................................................................8

5. Recent and long-term daily maximum air temperature conditions in Orleans and Yreka, California.................8

6. Average water temperatures for September 1–24, 2002 ......................................................................................9
iv

CONVERSION FACTORS AND VERTICAL DATUM

1

Temperature °C = (temperature °F-32)/1.8

Vertical coordinates in this report are referenced to the National Geodetic Vertical Datum of 1929 (NGVD 

of 1929).

Multiply By To obtain

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km) 

acre 0.004047 square kilometers (km2)

square miles (mi2) 1.590 square kilometers (km2)

degrees Farenheit (°F) (

1

) degrees Celsius (οC)

cubic feet per second (ft3/s) 0.02832 cubic meters per second (m3/s)
1

Klamath River Basin Hydrologic Conditions 

Prior to the September 2002 Die-Off of Salmon

and Steelhead

By Dennis D. Lynch and John C. Risley

Abstract

More than 33,000 salmon and steelhead died 

in the lower Klamath River in late September 2002 

on their way to spawning areas upstream. 

According to the California Department of Fish 

and Game, the cause of death was infection by 

protozoan and bacterial pathogens. Two factors 

that may have contributed to the disease incidence 

are low streamflow and high water temperature.

September streamflows throughout the 

Klamath Basin were low, among the four lowest 

September flows recorded on the main stem since 

1960. The low streamflows were caused by 

below-average snowpack and long-term drought, 

with resulting reduced ground-water discharge to 

streams. 

On the basis of historical climate data from 

the Klamath Basin and historical water temperature data from an adjacent basin, September 2002 

water temperatures were above the long-term 

average. Temperatures in the Klamath River above 

the fish die-off reach exceeded 65 degrees Fahrenheit for nearly all of September; multiple days of 

exposure by fish to temperatures at or above that 

level can greatly increase disease incidence.

This report characterizes streamflow and 

water temperature conditions during the period 

leading up to the die-off and compares them to 

historical conditions in the Klamath River. This 

report is not an exploration of the causative 

mechanism of the die-off; rather, it is intended to 

provide detailed documentation of these 

conditions to be used by those examining the 

cause(s) of the die-off and to provide information 

that can contribute to decisions about future water 

management in the Klamath Basin.

INTRODUCTION

During the last week of September 2002, a 

minimum of 33,000 adult salmon, steelhead trout, 

and other fish species died in the lower 36 miles of 

the Klamath River (fig. 1). A survey of dead fish 

conducted by the California Department of Fish and 

Game found that, of the salmonid species, 95.2 percent 

were Chinook salmon, 0.5 percent were coho salmon, 

and 4.3 percent were steelhead trout. The cause of 

death was infection by the ciliated protozoan Ichthyopthirius multifilis (Ich) and the bacterial pathogen 

Flavobacter columnare (Columnaris). Although both 

pathogens commonly occur naturally worldwide and 

are always present in the Klamath River and other 

aquatic systems, high water temperature, low flow, 

and crowding provided conditions favorable to their 

rapid proliferation and transmission (California 

Department of Fish and Game, 2003).

Soon after the September 2002 die-off, numerous 

reports and media releases attempted to describe the 

hydrologic conditions leading up to the event. Some 

of the descriptions were based on data that were incomplete, unreviewed, or not sufficiently accurate for 

the analyses being done. The purpose of this report is to 

provide a detailed documentation of these conditions, 

using finalized data of known and appropriate quality, 

to be used by those exploring the causes of the die-off 

and to provide information that can contribute to future 

decisions about water management in the Klamath 

Basin.
2

Figure 1. Selected streamflow and temperature monitoring sites in the Klamath and Rogue River Basins.

Clear 

Lake

Reservoir

Tule 

Lake

Meiss

Lake

PACIFIC OCEAN

Sacramento

River

Shasta

Lake

Trinity Mad River

Lake Trinity

Salmon

Redwood Creek

Scott

Shasta

River

River

River

River

River

River

River

Crater 

Lake

Spring

Creek

Summer

Lake

Rogue

Sprague

Upper

Klamath

Lake

Illinois

KLAMATH

RIVER

Williamson

River Wood

River

ACanal

OREGON

CALIFORNIA

0 50 100 KILOMETERS

0 50 100 MILES

Chiloquin

Yreka

Fort

Jones

Seiad

Valley

Agness

Prospect

Somes

Bar

Orleans

Hoopa

Klamath

Keno

Link

River 

Dam

Lewiston 

Dam

John Boyle

power plant

Iron Gate

Dam

X

Lewiston

Lake

Whiskeytown Lake

11502500

11509500

11510700

11516530

11519500

11520500

11522500

11523000

11530500

11525430

11530000

11517500

14330000

14372300

121 ̊

43 ̊

41 ̊

42 ̊

124 ̊ 123 ̊ 122 ̊

EXPLANATION

Flow station and number

 14330000 Rogue River below Prospect 

 11502500 Williamson River near Chiloquin 

 (inflow to Upper Klamath Lake)

 11509500 Klamath River at Keno 

 (below Upper Klamath Lake)

 11510700 Klamath River below John C. Boyle Powerplant

 11516530 Klamath River below Iron Gate Dam 

 11517500 Shasta River near Yreka

 11519500 Scott River near Fort Jones

 11520500 Klamath River near Seiad Valley

 11522500 Salmon River at Somes Bar

 11523000 Klamath River at Orleans

 11525430 Judge Francis Carr Powerplant 

 near French Gulch

 11530500 Klamath River near Klamath

 11530000 Trinity River at Hoopa

Water temperature station and number

 14372300 Rogue River near Agness

 11516530 Klamath River below Iron Gate Dam

 11517500 Shasta River near Yreka

 11520500 Klamath River at Seiad Valley

 11523000 Klamath River at Orleans

 11530000 Trinity River at Hoopa

Precipitation site

OREGON

CALIFORNIA

14330000 11517500

Well

30S/10E

24aab1

(figure 3)
3

This report presents data on streamflows, Upper 

Klamath Lake levels, ground-water conditions, and air 

and water temperatures in the Klamath River Basin 

during September 1–24, 2002, the period preceding the 

peak of the fish die-off, and provides a historical 

perspective on the data. Data in the report are from the 

U.S. Geological Survey (USGS), Western Regional 

Climate Center, and Bureau of Reclamation. 

USGS streamflow records are published annually 

in data reports for each State. The accuracy of USGS 

streamflow records can vary from one site to another 

and from year to year, depending on factors involved 

with data collection and analysis. The accuracy of the 

records partly depends on the accuracy of the 

instantaneous measurements of streamflow made at 

each streamflow gaging station every 4–8 weeks by a 

hydrologic technician. Accuracy decreases under 

difficult conditions, such as an uneven channel bottom, 

shallow water, dense aquatic vegetation, and slow 

water velocity. In addition, the accuracy of records 

partly depends on the stability of the “rating curve,” 

which is the mathematical relation between measured 

instantaneous streamflow and water level. This relation 

is used to convert water-level data collected 

continuously at each gage to computed streamflow. 

Where the channel is unstable the rating curve will be 

constantly changing, and the computed streamflows 

can be unreliable. Channels with bottom sediments that 

are eroding, shifting or infilling, produce unstable 

rating curves. An unstable, sandy channel bed and large 

tidal fluctuations at the USGS streamflow gaging 

station Klamath River near Klamath, California (station 

number 11530500), near the river’s mouth sometimes 

result in unreliable (greater than 15 percent error) 

computed streamflow records. Consequently, data from 

that gage are not included in this analysis.

UPPER KLAMATH LAKE INFLOWS AND LAKE 

WATER LEVELS

Upper Klamath Lake is the primary source of 

water in the Bureau of Reclamation’s Klamath Project. 

Its surface area is large (about 130 mi2

), but it is a very 

shallow lake, averaging about 8 ft (U.S. Army Corps of 

Engineers, 1979). Inflows to Upper Klamath Lake are 

mainly from the Williamson and Wood Rivers (which 

are primarily ground-water fed streams for most of the 

year), and from several hundred cubic feet per second 

(cfs) of ground water that directly enters the lake via 

springs and seeps. Average annual evaporation from 

the lake is about 40 inches (Hubbard, 1970). Because 

the lake’s surface area is so large, evaporation from the 

lake represents a significant loss of water. Outflows 

from Upper Klamath Lake are primarily over the Link 

River Dam into the Klamath River and through the 

A-Canal, which is the primary conveyance of irrigation 

water for the Klamath Project. Many management 

decisions in the basin revolve around balancing the 

amount of water (1) passed over the Link River Dam 

for endangered salmon in the lower Klamath River, (2) 

delivered through the A-Canal to irrigate about 

185,000 acres, (3) retained in Upper Klamath Lake to 

protect habitat for two endangered sucker fish species, 

(4) used for hydroelectric power production, (5) 

released for flood control, and (6) needed for the wildlife refuges (Jim Bryant, Bureau of Reclamation, Klamath Falls, Oregon, written commun., 2002).

September 1–24, 2002, streamflows into Upper 

Klamath Lake via the Williamson River (table 1, fig. 1) 

averaged 414 cfs, which was only 76 percent of the 

long-term (1960–2002) September mean monthly flow 

of 543 cfs. Since 1960, there have been only two 

Septembers with lower flows, and these occurred in 

1992 and 1994 (405 and 382 cfs, respectively). Annual 

precipitation for water years 2001 and 2002 at Crater 

Lake National Park Headquarters, Oregon, was 60 and 

81 percent the long–term average (table 2). Most of the 

streamflow in the upper basin is supported by regional 

ground-water discharge; consequently, streamflow in 

the upper basin responds to multiyear trends in 

precipitation. Several dry years in a row tend to 

produce progressively lower summer streamflows. On 

the basis of historical observation-well and 

precipitation data, ground-water levels and spring-fed 

streamflows in the upper Klamath River Basin 

typically do not increase until precipitation has 

returned to average or above average conditions (U.S. 

Geological Survey, 2001; Western Regional Climate 

Center, no date).

Streams in basins adjacent to the upper part of the 

Klamath River Basin showed similar below-average 

flow conditions as the Williamson River in 2002. For 

example, at the streamflow gage on the Rogue River 

near Prospect, Oregon, which is in the adjoining basin 

to the west, the mean daily flow for September 2002 

was 698 cfs, which was 75 percent of average for the 

period 1969 to the present. Only three Septembers 

since 1969 (1992, 1994, and 2001) had flows lower 

than those recorded in 2002 at that gage. Regionally, 

below-average streamflow conditions occurred at 

many USGS gages in southwestern Oregon and northwestern California in the summer of 2002.
4

1Flow record accuracy, as defined here, means that 95 percent of the daily flows for the 2002 water year were within the reported estimates of error. The 

accuracy of the 2002 flow record from the USGS gage at the Klamath River near Klamath, California (station number 11530500) was greater than 15 

percent error. Hence, that station was not included in the analysis.

2

“September 2002” is the period from September 1–24, 2002.

3

“September 2001” is the entire month of September 2001.

4

“Average September flows” are for entire months of September in the record.

Table 1. September Flow Conditions in the Klamath and Trinity River Basins

[Period of record for all stations is1960–2002 unless otherwise indicated; cfs, cubic feet per second; POR, period of record; see fig. 1 for site location; 

source: USGS NWIS database, http://waterdata.usgs.gov/nwis/sw]

Drainage 

area, in 

square 

miles

September 1–24, 

2002 average 

flow, in cfs

September 

2002 flows,

percent of 

average2

September 

2001 average 

flow, in cfs3

Number of 

Septembers 

with lower 

flows than 

September 

20022

Average 

September 

flows for 

period of 

record, in 

cfs4 Number

Station

location

Flow record 

accuracy1

11502500 Williamson River near 

Chiloquin (inflow to Upper 

Klamath Lake)

Within 10 

percent

3,000 414 76 446 2 543

11509500 Klamath River at Keno 

(below Upper Klamath Lake)

Within 10 

percent

3,920 439 47 683 1 935

11510700 Klamath River below John C. 

Boyle Power plant

Within 10 

percent

4,080 688 58 925 2 1,190

11516530 Klamath River below Iron Gate 

Dam (POR: 1961–2002)

Within 5 

percent

4,630 759 59 1,030 3 1,280

11517500 Shasta River nr Yreka Within 10 

percent

793 30 42 47 2 71

11519500 Scott River nr Fort Jones Within 10 

percent

653 11 23 4.4 4 48

11520500 Klamath River near Seiad 

Valley

Within 5 

percent

6,940 860 57 1,070 2 1,500

11522500 Salmon River at Somes Bar Within 10 

percent

751 127 60 80 4 212

11523000 Klamath River at Orleans Within 10 

percent

8,475 1,290 64 1,220 3 2,000

11530000 Trinity River at Hoopa

 (POR: 1964-2002)

Within 5 

percent

2,853 639 96 633 20 664

The September 2002 minimum water level in 

Upper Klamath Lake was 4,138.6 feet above sea level 

(USGS station number 11507001). This is the seventh 

lowest September lake level recorded since 1960; 

meaning that September lake-levels as low as recorded 

in 2002 occur every 5 to 7 years under the current BOR 

operation of the Klamath Project. Three of the September lake levels lower than those recorded in 2002 

occurred in 1991, 1992, and 1994 (4,138.2, 4,137.4, 

and 4,136.8 feet, respectively), which correspond to the 

low precipitation years of the early 1990s (Western 

Regional Climate Center, no date).
5

1Crater Lake National Park Service Headquarters.

UPPER KLAMATH LAKE OUTFLOWS

Most surface water outflow from Upper Klamath 

Lake occurs at two locations. Flows continuing downstream pass through the Link River Dam. Water needed 

for irrigation in the Klamath Project is diverted through 

the A-Canal. Diversions through the A-Canal in 2002 

were similar to those in many previous years when full 

deliveries have been sent to the Klamath Project. Typically the diversions begin in late March or early April, 

are at maximum in July around 940 cfs, and end in mid 

October. The A-Canal diversions have varied only 

slightly among recent years, except during 2001, when 

deliveries to the Klamath Project were curtailed for 

much of the year in order to keep water levels high 

enough to avoid jeopardy for the two protected sucker 

species. For the period September 1–24, 2002, flows in 

the A-Canal averaged 646 cfs (Jim Bryant, Bureau of 

Reclamation, Klamath Falls, Oregon, written commun., 2002).

September 2002 outflow from Upper Klamath 

Lake, as measured downstream at Keno (table 1), was 

considerably below the long-term average. The Keno 

gage measures outflow from Upper Klamath Lake plus 

the combined effect of several irrigation withdrawals 

and agricultural return flows. It is a good approximation of the overall amount of water leaving Upper Klamath Lake and the Klamath Project area. Flows at the 

Keno gage during September 1–24, 2002, averaged 

439 cfs, or 47 percent of average. This was the second 

lowest September flow since 1960; the lowest September flow averaged 246 cfs in 1992. 

DIVERSIONS FROM THE TRINITY RIVER BASIN

The Trinity River is a major tributary of the Klamath River; their confluence is 43 miles from the 

mouth and upstream of the river reach where the fish 

die-off occurred. Flows on the Trinity River have been 

regulated through storage at Trinity Lake and Lewiston 

Reservoir since 1960 and 1963, respectively. Since 

1963, flows have been diverted from the Lewiston Reservoir out of the Trinity River Basin to the Sacramento 

River Basin. Diversions are sent through a tunnel to the 

Judge Francis Carr Powerplant at Whiskeytown Lake. 

For the period 1963 to 2002, the average September 

flow through the power plant was 1,960 cfs (measured 

at USGS station number 11525430). Average flow 

for the month of September 2001 and the period of 

September 1–24, 2002, was 1,630 and 1,330 cfs, 

respectively. 

FLOWS IN THE MIDDLE AND LOWER KLAMATH 

BASIN

September 1–24, 2002, streamflows in the 

main-stem Klamath River, below Upper Klamath 

Lake, were well below the long-term average for Septembers over the last 40 years (table 1). From upstream 

to downstream along the Klamath River, September 1–

24, 2002, flows were 58, 59, 57, and 64 percent of 

average at USGS streamflow gaging stations below 

John C. Boyle Powerplant, below Iron Gate Dam, near 

Seiad Valley, and at Orleans, respectively (fig. 2). 

Although these September flows did not set new 

records on the main-stem Klamath, there were only a 

few Septembers since 1960 when flows were lower 

(table 1).

The gage at Orleans is about 30 miles upstream 

of where the die-off occurred. Streamflow for September 1-24, 2002, averaged 1,290 cfs, which was the 

fourth lowest September flow recorded since 1960 

(table 1). Lower September flows occurred at the 

Orleans gage in 1991, 1992, and 2001, averaging 

1,200, 790, and 1,220 cfs, respectively. 

September flows at the gaging stations upstream 

of the Orleans gaging station (below John C. Boyle 

Powerplant, below Iron Gate Dam, and near Seiad Valley) were all significantly higher in 2001 than in 2002 

as a result of the larger releases from Upper Klamath 

Lake. However, the reported September flows measured at Orleans were slightly less in 2001 (1,220 cfs)

Table 2. Recent and long-term annual precipitation at Crater Lake, 

Oregon1

[Source: Western Regional Climate Center, no date; a water year is the 

period from October 1 through September 30]

Crater Lake Precipitation

Total, 

in inches

Percent of 

period of record 

average

Water Year 2001 40.2 60

Water Year 2002 54.4 81

Period of record, 1948–2002 67.5
6

Figure 2. Relation between average flows for September 1–24, 2002, and for the 1960 to 2002 September period of record at locations along the 

Klamath River.

250 200 150 100 50 0

MILES FROM THE MOUTH OF THE KLAMATH RIVER

0

500

1,000

1,500

2,000

2,500

3,000

3,500

4,000

DISCHARGE, IN CUBIC FEET PER SECOND

Keno

Boyle

Powerhouse

Shasta

River

Scott

River

Seiad

Valley

Trinity River

confluence1

Orleans

Salmon

River

Irongate

Reservoir

Average for September 1-24, 2002

Average September for 1960 to 2002

1

Sum of flows at Trinity River at 

 Hoopa and Klamath River at Orleans

than in 2002 (1,290 cfs). Flow records at the Orleans 

gaging station in 2001 and 2002 were rated as having a 

level of accuracy within 10 percent (Friebel and others, 

2002). The magnitude of error could account for the 

minimal measured difference between 2001 and 2002. 

With a plus or minus 10 percent margin of error, a value 

reported as 1,290 cfs is known to be between 1,160 and 

1,420 cfs with a 95 percent confidence.

Flows in most Klamath River tributaries were also 

low for September 1–24, 2002 (table 1). The Shasta, 

Scott, and Salmon Rivers flowed 43, 24, and 60 percent 

of average, respectively. These flows were, respectively, 

the 3rd, 5th, and 5th lowest recorded September flows in 

these rivers since 1960. In contrast to these three tributaries, flow in the regulated Trinity River recorded near 

Hoopa, California, was only slightly less than average 

(96 percent) for September 1–24, 2002. 

To estimate the September 1–24, 2002 period 

low-flow conditions in the reach of the Klamath River 

where the fish die-off occurred, average flow measured 

during this period at the Trinity River at Hoopa and the 

Klamath River at Orleans gages were summed and compared with their historical average summed September 

flows. September 2002 flows in the reach where the 

die-off occurred were the sixth lowest since 1964, indicating that flows this low occur (on average) about once 

every 5 to 7 years. On the basis of this analysis, lower 

September flows occurred in 1981, 1991, 1992, 1994, 

and 2001.

GROUND-WATER CONDITIONS IN THE UPPER 

KLAMATH BASIN

Ground-water levels in the principal recharge

areas of the Upper Klamath Basin declined during the 

drought year of 2001 and continue to decline through 

water year 2002. Figure 3 shows the decline in the 

water-table elevation in a well located in the Upper 

Klamath Lake Basin approximately 30 miles east of 

Crater Lake over the past 2 years. The water-level 

hydrograph had the same trend as those from most other 

observation wells located throughout the region, indicating there was little ground-water recharge in the basin 

during both 2001 and 2002 (U.S. Geological Survey, 

2001). Annual precipitation for water years 2001 and 

2002 at Crater Lake National Park, Oregon, was 60 and 

81 percent of the long-term average (table 2). Although 

precipitation during the 2002 water year was closer to 

average than in 2001, much of the precipitation in 2002 

went toward making up a soil-moisture deficit in the 

Klamath Basin from the previous drought year, and thus 

was unavailable to recharge the principle aquifers. 
7

Figure 3.Water-level hydrograph from a USGS observation well in the Upper Klamath Lake Basin, Oregon. The steady decline of the water 

level in this well, which is unaffected by pumping of other wells, was caused by decreased ground-water recharge in the basin during the 

drought of 2001–02. Well location is shown on figure 1.

78

79

80

81

82

83

84

85

DEPTH TO WATER, IN FEET

Well 30S/10E-24aab1

2001 2002 2003

WATER YEAR

OND J FMAMJ J A S OND OND J FMAMJ J A S September September

As ground-water levels continued to decline in 

2002, ground-water discharge to springs and streams 

declined as well, and the effects of the previous year’s 

drought can be seen in the lower-than-average 2002 

streamflows. Data indicate that ground-water discharge 

to streams (baseflow) during summer and fall of 2002 

was similar to or less than for the same period of 2001 

in the upper basin. Estimated October mean groundwater inflows to the Klamath River and tributaries 

between the USGS stream-gaging stations at Keno 

(11509500) and below the John C. Boyle Powerplant 

(11510700) from 1999 to 2002 are shown in table 3. 

The month of October is shown in this analysis because 

it is a period of the year when most flow diversions for 

irrigation have ended and precipitation is still minimal. 

Storage changes in the John C. Boyle reservoir were 

considered in inflow estimates. Although the difference 

in inflow from one year to another is near or within the 

measurement error of these two streamflow-gaging stations, the data show a systematic decline over the 

4 years. 

Table 3 also shows estimated October mean 

inflows from Spring Creek and the region upstream 

and downstream of its confluence with the Williamson 

River near Chiloquin, Oregon. These estimates were 

based on data from nearby USGS gaging stations 

located on the Williamson River near Klamath Agency 

(11493500), Williamson River below Sprague River, 

near Chiloquin (11502500), and Sprague River near 

Chiloquin (11501000). Approximately 90 percent 

of the inflow is from Spring Creek itself, which is 

almost entirely ground-water discharge. A basinwide 

decrease in ground-water discharge in 2002 probably 

explains why inflow to Upper Klamath Lake was less 

than predicted by the BOR based on snowpack estimates alone. 

On the basis of experience in geologically similar 

basins, such as the Deschutes River Basin to the north 

(Gannett and others, 2000), multiple years of normal or 

above-normal precipitation may be required before 

streamflows and spring discharges recover to predrought levels.

Table 3. Estimated October mean ground-water discharge above 

and below the John C. Boyle Reservoir on the Klamath River and 

from the Spring Creek area near Chiloquin, Oregon, 1999–2002

Estimated October mean ground-water inflows, 

in cubic feet per second

Year

Area above and below the 

John C. Boyle Reservoir Spring Creek area

1999 297 334

2000 290 309

2001 257 298

2002 241 294
8

WATER TEMPERATURE 

The USGS has collected water temperature data 

at some of the flow stations in the lower Klamath River 

Basin. Along the Klamath River, these stations include 

Irongate Reservoir, Seiad Valley, Orleans, and Klamath. Water temperature data have also been collected 

on the Shasta River near Yreka and the Trinity River at 

Hoopa Valley. The period of record for these stations 

ranges from 17 to 21 years. All the records start in the 

1960s and end in the 1970s or 1980s. Within the last 

few years these stations have been reactivated. However, the lack of continuity in the records makes it difficult to put the 2002 water temperature conditions into 

historical context to determine whether they were 

unusually warm. 

A longer-term water temperature record exists for 

a station on the Rogue River near Agness, Oregon 

(USGS station number 14372300). The Rogue River 

Basin, which is the adjoining coastal basin to the north 

of Klamath River, is large (3,939 mi2

), and it shares 

similar climatic, geologic, and hydrologic features with 

the Klamath River Basin. Water temperatures were 

measured for 35 years on the Rogue River during the 

periods 1961–1987 and 1995–2002 (table 4). The mean 

daily maximum September water temperature for the 

35-year period of record at this station was 65.7 o

F 

(degrees Fahrenheit). In contrast, the mean daily 

maximum water temperature for September 2002 was 

67.3 o

F. For the period of record, 67.3 oF has a 

percentile rank of 80, which means that it would likely 

be equaled or exceeded once every 5 years. While these 

temperature differences between the period of record 

and 2002 may seem small, small differences in 

temperature can affect the health of migrating 

salmonids when water temperatures approach chronic 

and acute thresholds like they periodically do in the 

Klamath and Rogue River Basins (Poole and others, 

2001; Poole and Berman, 2001).

Stream temperatures typically fluctuate in 

response to changes in the weather, and they closely 

follow patterns of air temperature (Lewis and others, 

2000; Mohseni and Stefan, 1999). Months with 

warmer-than-average air temperatures typically 

have warmer-than-average water temperatures. Consequently, long-term air temperature data in the Klamath 

River Basin below Upper Klamath Lake may be a surrogate for long-term water temperatures in the same 

region (table 5). Two climate stations are located 

upstream of the die-off reach in Orleans and Yreka. For 

the month of September 2002, average daily maximum 

air temperatures for these two stations had percentile 

ranks of 73.8 and 82.5 for the 1960 to 2002 period of 

record. September air temperatures in 2002 were about 

2 oF higher than the long-term average (Jim Ashby, 

Western Regional Climate Center, Reno, Nevada, written commun., 2002).

In 2002 the USGS collected continuous water 

temperature data at several locations in the Klamath 

River Basin (table 6). The daily minimum temperature 

of the Klamath at Orleans, upstream from the die-off, 

remained above 65 o

F for the entire period of September 1–24, 2002 (fig 4). In salmonids, 65 oF is a level at 

which disease rates can be severe (Poole and others, 

2001).

Table 4. Recent and long-term daily maximum water temperature 

conditions on the Rogue River near Agnes, Oregon

[POR, period of record from 1961 to 2002; missing years were 1967, 1974, 

1978, 1988–1994, 1996]

Daily maximum water temperatures, in degrees Fahrenheit

September 2001 mean 67.1

September 2002 mean 67.3

September POR mean 65.7

Percentile rank of the September 2002 mean for the POR 80

Table 5. Recent and long-term daily maximum air temperature 

conditions in Orleans and Yreka, California

[POR, the period of record from 1960 to 2002, 1987 and 1993 were missing 

from the Yreka record; Reference: Jim Ashby, Western Regional Climate 

Center, 2002, Western Regional Climate Center, no date]

Daily maximum air temperatures, in degrees Fahrenheit

Orleans, California Yreka, California

September 2001 mean 87.1 September 2001 mean 85.7

September 2002 mean 89.6 September 2002 mean 86.3

September POR mean 87.4 September POR mean 82.3

Percentile rank of the 

September 2002 mean 

for the POR

73.8 Percentile rank of the 

September 2002 mean 

for the POR

82.5
9

Figure 4. August and September 2002 daily water temperatures in 

the Klamath River at Orleans, California (USGS station number 

11523000).

During the time of the fish die-off, there was 

concern that release of additional water from Upper 

Klamath Lake in September 2002 might worsen the 

water-temperature problem in the lower Klamath 

River. The 2002 water-temperature data from Upper 

Klamath Lake and the Klamath River at Orleans 

suggest that these concerns were unwarranted: Water 

temperatures in the lake were considerably cooler than 

in the river at Orleans. Daily maximum and minimum 

water temperatures in Upper Klamath Lake averaged 

65.3 and 61.9 oF, respectively, for the period 

September 1–24, 2002, as compared to 68.6 and 

67.4 oF in the Klamath River at Orleans. A similar 

temperature differential existed throughout the summer 

be- tween Upper Klamath Lake and the lower Klamath 

River, largely owing to the fact that Upper Klamath 

Lake has a surface elevation of about 4,140 feet, where 

the nights are much cooler.

It should be noted, however, that water released 

from the Upper Klamath Lake during the summer 

months typically warms along its 255-mile course to 

the ocean as it comes into thermal equilibrium with the 

warmer air temperatures at lower elevations in the 

basin. Consequently, any cooling benefit of water 

released from Upper Klamath Lake, by the time it 

reaches the mouth, would probably be minimal.

SUMMARY

• September 2002 streamflows throughout the Klamath Basin were low, averaging about 57 to 64 percent of long-term averages at streamflow gaging 

stations on the main-stem river. In most cases, the 

September 2002 flows were among the four lowest 

September flows recorded since 1960. Similar 

low-flow conditions existed in Klamath River tributaries, including the Williamson (the largest tributary to Upper Klamath Lake), Shasta, Scott, and 

Salmon Rivers. Only the Trinity River, regulated 

by storage reservoirs, had near-average streamflows. 

• September 2002 flows 30 miles upstream of fish 

die-off reach were the fourth lowest since 1960, 

indicating that flows this low occur (on average) 

about once every 10 years; lower September flows 

occurred in 1991, 1992, and 2001. 

Table 6. Average water temperatures for September 1–24, 2002

[

oF, degrees Fahrenheit; na, not available. Temperatures for the Upper 

Klamath Lake averaged from 11 monitors. Temperatures for the Trinity 

River confluence are calculated from a mass balance of average flows and 

temperatures at the Orleans and Hoopa stations]

Station 

number Station name

Average of daily 

maximum

temperatures,

in o

F 

Average of 

daily 

minimum 

temperatures,

 in oF

na Upper Klamath 

Lake

 65.3 61.9

11516530 Klamath River 

below Iron Gate 

Dam

66.1 64.6

11517500 Shasta River near 

Yreka

70.0 59.8

11520500 Klamath River at 

Seiad Valley

na na

11523000 Klamath River at 

Orleans

 68.6 67.4

11530000 Trinity River at 

Hoopa

68.9 65.5

na Trinity River 

confluence

68.7 66.8

60

65

70

75

80

TEMPERATURE,

IN DEGREES FAHRENHEIT

Maximum

Minimum

2002

2 7 12 17 22 27 1 6 11 16 21 26 1

AUGUST SEPTEMBER OCT
10

• The Klamath River Basin was not the only basin 

experiencing low flows in southern Oregon and 

northern California in September of 2002. Similar 

conditions existed in surrounding basins, such as 

the Rogue River Basin in Oregon.

• Ground-water levels in the principal recharge areas 

of the Klamath River Basin declined during the 

drought year of 2001 and continued to decline 

through water year 2002. Although precipitation 

during water year 2002 was closer to average than 

in 2001, much of the precipitation went toward 

making up a soil-moisture deficit from the previous 

drought year. Because streams in the Klamath 

River Basin are fed primarily by ground water, 

2002 streamflows were lower than the Bureau of 

Reclamation expected based on snowpack data 

alone. It may take multiple years of average to 

above average precipitation before ground-water 

levels, and thus streamflows, recover to predrought 

levels.

• Based on long-term water temperatures in the 

nearby Rogue River Basin and air temperatures 

within the Klamath River Basin, September 2002 

water temperatures in the lower Klamath River 

were probably above average.

• Daily minimum temperatures at Klamath River at 

Orleans (upstream from the fish die-off reach) 

remained above 65 oF during the period September 

1–24, 2002, a level at which disease rates in salmonids can be severe.

• The USGS streamflow data used in this analysis 

came from gages for which records are estimated 

to be correct to within a 10 percent margin of error. 

The USGS gage closest to the mouth of the Klamath River was not used in the analysis because its 

2001 and 2002 record had estimated erors greater 

than 15 percent.

REFERENCES CITED

California Department of Fish and Game, 2003, September 

2002 Klamath River fishkill—Preliminary analysis of 

contributing factors: Redding, State of California, The 

Resources Agency, Department of Fish and Game,

63 p. [Also available at http://www.dfg.ca.gov/, 

accessed April 21, 2003]

Friebel, M.F., Freeman, L.A., Smithson, J.R., Webster, 

M.D., Anderson, S.W., and Pope, G.L., 2002, Water 

resources data, California, water year 2001, volume 2: 

U.S. Geological Survey Water-Data Report CA–01–2, 

450 p.

Gannett, M.W., Lite, K.E., Morgan, D.S., and Collins, C.A., 

2000, Ground-water hydrology of the upper Deschutes 

Basin, Oregon: U.S. Geological Survey 

Water-Resources Investigations Report 00–4162, 78 p.

Herrett, T.A., Hess, G.W., House, J.G., Ruppert, G.P., and 

Courts, M.L., 2002, Water resources data, Oregon, 

water year 2001: U.S. Geological Survey Water-Data 

Report OR–01–1, 430 p.

Hubbard, L.L., 1970, Water budget of Upper Klamath Lake, 

Southwestern Oregon: U.S. Geological Survey 

Hydrologic Investigations Atlas HA–351, scale 

1:250,000.

Lewis, T.E., Lamphear, D.W., McCanne, D.R., Webb, A.S., 

Krieter, J.P., and Conroy, W.D., 2000, Regional 

assessment of stream temperatures across Northern 

California and their relationship to various 

landscape-level and site-specific attributes: Arcata, 

California, Forest Science Project, Humboldt State 

University Foundation, [variously paged]. 

Mosheni, O., and Stefan, H.G., 1999, Stream temperature/air 

temperature relationship—A physical interpretation: 

Journal of Hydrology, v. 218, p. 128–141.

Poole, G.C., Dunham, J., Hicks, M., Keenan, D., Lockwood, 

J., Materna, E., McCullough, D., Mebane, C., Risley, J., 

Sauter, S., Spalding, S., and Sturdevant, D., 2001, 

Technical synthesis scientific issues relating to 

temperature criteria for salmon, trout, and char native to 

the Pacific Northwest: U.S. Environmental Protection 

Agency, EPA 910–R–01–007, August, 2001, 21 p.

Poole, G.C., and Berman, C.H., 2001, An ecological 

perspective on in-stream temperature—Natural heat 

dynamics and mechanisms of human-caused thermal 

degradation: Ecological Management, no. 27, p. 787–

802.

U.S. Army Corps of Engineers, 1979, Klamath River 

Basin—Oregon—Reconnaissance report: San 

Francisco, U.S. Army Corps of Engineers, 175 p.

U.S. Geological Survey, 2001, Water-level measurement 

data for selected wells in Upper Klamath Basin, Oregon 

and California: http://oregon.usgs.gov/projs_dir/or180/

waterlevels/index.html, accessed on February 10, 2003.

Western Regional Climate Center, no date, Historical 

climate information: http://www.wrcc.dri.edu/

climsum.html, accessed on November 6, 2002.
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Lynch and Risley — Klamath River Basin Hydrologic Conditions Prior to the September 2002 Die-Off of Salmon and Steelhead — WRIR 03–4099