Prepared in cooperation with the

Surface-Water/Ground-Water Interaction along Reaches of 

the Snake River and Henrys Fork, Idaho

U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2004 – 5115

Version 1.0

Idaho Department of Water Resources and

Idaho Power Company
Surface-Water/Ground-Water Interaction along 

Reaches of the Snake River and Henrys Fork, 

Idaho

By Jon E. Hortness, U.S. Geological Survey, and Peter Vidmar, Idaho Power 

Company

Scientific Investigations Report 2004 – 5115

Version 1.0

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia: 2005

For sale by U.S. Geological Survey, Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

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Any 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.

Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Hortness, J.E., Vidmar, Peter, 2005, Surface-Water/Ground-Water Interaction along Reaches of the Snake River and 

Henrys Fork, Idaho: U.S. Geological Survey Scientific Investigations Report 2004-5115, 18 p., 3 apps.
Contents v

Contents

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

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

Purpose and scope .................................................................................... 1

Description of study area ............................................................................ 3

Previous investigations ..................................................................................... 3

Methods for estimating gains and losses ............................................................. 3

Data accuracy and limitations............................................................................. 4

Long-term gaging stations ......................................................................... 4

Acoustic doppler measurements ................................................................. 4

Unmeasured areas ............................................................................. 4

Error ............................................................................................. 5

Current-meter measurements ..................................................................... 6

Irrigation-district records ............................................................................ 6

Visual inspections ..................................................................................... 6

Streamflow gains and losses ............................................................................. 6

Lower Reach (Snake River near Minidoka to Snake River at King Hill) .................... 7

Middle Reach (Snake River near Shelley to Snake River near Minidoka)................. 10

Upper Reach (Henrys Fork near Ashton to Henrys Fork at mouth, near 

Lorenzo / Snake River near Heise to Snake River near Shelley) ................. 12

Comparisons of ground-water levels with streamflow gains and losses ........................ 13

Lower Reach (Snake River near Minidoka to Snake River at King Hill) .................... 13

Middle Reach (Snake River near Shelley to Snake River near Minidoka)................. 16

Upper Reach (Henrys Fork near Ashton to Henrys Fork at mouth, near 

Lorenzo / Snake River near Heise to Snake River near Shelley) ................. 16

Summary ..................................................................................................... 17

References cited ............................................................................................. 18

Appendix A. Summary of streamflow data collected during five seepage studies and

 streamflow gain and loss estimates for the lower reach of the Snake River, 

between the near Minidoka and at King Hill gaging stations, Idaho, 

March 2001 through November 2002 ......................................................... A-1

Appendix B. Summary of streamflow data collected during five seepage studies and 

streamflow gain and loss estimates for the middle reach of the Snake River, 

between the near Shelley and near Minidoka gaging stations, Idaho, 

April 2001 through November 2002 ............................................................. B-1

Appendix C. Summary of streamflow data collected during four seepage studies and 

streamflow gain and loss estimates for the upper reach, along the Henrys Fork 

between the near Ashton gaging station and the mouth, near Lorenzo, and 

along the Snake River between the near Heise and near Shelley gaging

stations, Idaho, October 2001 through November 2002 .................................... C-1
vi Surface-Water/Ground-Water Interaction along Reaches of the Snake River and Henrys Fork, Idaho

Tables

1. Results of mean, standard deviation, and coefficient-of-variation calculations 

for a set of eight acoustic Doppler measurements of discharge at a site. ................ 5

2. Results of mean, standard deviation, and coefficient-of-variation calculations 

for a set of four acoustic Doppler measurements of discharge at a site. ................. 6

3. Summary of streamflow gain and loss estimates for the lower reach of the 

Snake River, between the near Minidoka and at King Hill gaging stations, 

Idaho ...... ................................................................................................................................ 7

4. Summary of streamflow gain and loss estimates for the middle reach of the 

Snake River, between the near Shelley and near Minidoka gaging stations, 

Idaho ..................................................................................................................................... 10

5. Summary of streamflow gain and loss estimates for the upper reach of the 

Henrys Fork and Snake River, between the near Ashton gaging station and 

the mouth, near Lorenzo, and the near Heise and near Shelley gaging 

stations, Idaho ...................................................................................................................... 12

Figures

1. Location of study area, eastern Snake River Plain, southeastern Idaho ..................... 2

2. Typical river cross section and areas where water velocities cannot be

measured using acoustic Doppler instruments ............................................................... 5

3. Locations of sites along the lower reach of the Snake River, southeastern 

Idaho, where streamflow was measured ........................................................................ 8

4. Locations of sites along the middle reach of the Snake River, southeastern 

Idaho, where streamflow was measured ........................................................................ 9

5. Locations of sites along the upper reach of the Snake River and along the 

Henrys Fork, southeastern Idaho, where streamflow was measured ........................ 11

6. Locations of wells on and near the eastern Snake River Plain, southeastern 

Idaho, where water levels were measured during water years 2002–03 .................. 14

7. Water levels in selected wells during water years 2000–03 and estimates of 

gains and losses in selected subreaches of the Snake River and Henrys Fork, 

southeastern Idaho, spring 2001 to fall 2002 ................................................................... 15
Contents vii

Conversion Factors, Datums, and Water Year Definition

Multiply By To obtain

acre-foot (acre-ft) 1,233 cubic meter (m3)

cubic foot per second (ft3/s) .02832 cubic meter per second (m3/s)

inch (in.) 2.54 centimeter (cm)

inch per year (in/yr) 2.54 centimeter per year (cm/yr)

mile (mi) 1.609 kilometer (km)

square mile (mi2) 2.590 square kilometer (km2)

Sea level: In this report, “sea level” refers to the North American Vertical Datum of 1988 

(NAVD of 1988) — a vertical control datum established by the minimum-constraint adjustment of 

Canadian-Mexican-United States leveling observations and held fixed at Father Point/Rimouski, 

Quebec, Canada.

Water year: In U.S. Geological Survey reports, a water year is the 12-month period from 

October 1 through September 30. The water year is designated by the calendar year in which 

it ends; thus, the water year ending September 30, 2001, is called the “2001 water year.”
[This page intentionally left blank]
 

ABSTRACT

Declining water levels in the eastern Snake River Plain 

aquifer and decreases in spring discharges from the aquifer to 

the Snake River have spurred studies to improve understanding of the surface-water/ground-water interaction on the plain. 

This study was done to estimate streamflow gains and losses 

along specific reaches of the Snake River and Henrys Fork and 

to compare changes in gain and loss estimates to changes in 

ground-water levels over time. Data collected during this study 

will be used to enhance the conceptual model of the hydrologic system and to refine computer models of ground-water 

flow and surface-water/ground-water interactions.

Estimates of streamflow gains and losses along specific 

subreaches of the Snake River and Henrys Fork, based on the 

results of five seepage studies completed during 2001 – 02, 

varied greatly across the study area, ranging from a loss 

estimate of 606 ft3/s in a subreach of the upper Snake River 

near Heise to a gain estimate of 3,450 ft3/s in a subreach of the 

Snake River that includes Thousand Springs. Some variations 

over time also were apparent in specific subreaches. Surface 

spring flow accounted for much of the inflow to subreaches 

having large gain estimates. Several subreaches alternately 

gained and lost streamflow during the study.

Changes in estimates of streamflow gains and losses 

along some of the subreaches were compared with changes 

in water levels, measured at three different times during 

2001 – 02, in adjacent wells. In some instances, a strong 

relation between changes in estimates of gains or losses and 

changes in ground-water levels was apparent.

INTRODUCTION

Declining water levels in the eastern Snake River Plain 

(ESRP) aquifer and decreases in spring discharges from the 

aquifer to the Snake River have raised concerns about the 

sustainability of water resources in the ESRP. These trends are 

believed to be the result partly of (1) improvements in the efficiency of irrigation practices that began in the early 1970s that 

have decreased recharge to the aquifer from irrigated lands, 

and (2) increases in ground-water withdrawals for irrigation 

and public supply that began about the same time. The effects 

of these changes in water use have resulted in competition 

between surface-water and ground-water users for the water 

supplies on the plain.

In 1999, the Snake River Plain Hydrologic Modeling 

Committee developed a general strategy to refine and enhance 

the conceptual and computer models of the ESRP hydrologic 

system. The strategy includes modeling and data-collection 

programs that will be implemented through a partnership of 

the Idaho Department of Water Resources (IDWR), the Idaho 

Water Resources Research Institute, the Bureau of Reclamation (BOR), the U.S. Geological Survey (USGS), Idaho Power 

Company (IPCo), and the University of Idaho. The first phase 

of the strategy focuses on (1) enhancing existing flow models 

using advanced computer programs, (2) collecting and evaluating data to improve the conceptual model of critical components of the system such as the aquifer/river boundary, and 

(3) evaluating new developments in aquifer/river simulation 

models and their potential application to the ESRP. The results 

of the first phase will help guide more detailed data-collection 

programs in subsequent phases.

Purpose and Scope

This report presents data and results from a study performed during 2001 – 02 to estimate streamflow gains and 

losses along reaches of the Snake River and Henrys Fork and 

to compare changes in seasonal and long-term gains or losses 

with changes in water levels in nearby wells. Information 

gathered during this study will be combined with the results 

from other studies to enhance the conceptual model of the 

hydrologic system and to refine surface-water/ground-water 

computer flow models of the ESRP.

Seepage studies of three separate reaches of the Snake 

River and Henrys Fork (fig. 1) were designed and conducted 

during 2001 – 02. These reaches were (1) the Snake River from 

the gaging station at Minidoka downstream to the gaging station at King Hill (lower reach); (2) the Snake River from the 

gaging station near Shelley downstream to the gaging station 

near Minidoka (middle reach); and (3) the Henrys Fork from 

the gaging station near Ashton downstream to the mouth, near 

Lorenzo, and the Snake River from the gaging station near 

Heise downstream to the gaging station near Shelley (upper 

Surface-Water/Ground-Water Interaction along Reaches 

of the Snake River and Henrys Fork, Idaho

By Jon E. Hortness and Peter Vidmar
Figure 1. Location of study area, eastern Snake River Plain, southeastern Idaho.

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Methods for Estimating Gains and Losses 3

reach). Data collected in each reach included discharges at 

USGS and/or IPCo gaging stations, discharges at several intermediate sites between gaging stations measured using acoustic 

Doppler current profilers (ADCPs), and measured and/or 

estimated discharges at several miscellaneous inflow (mostly 

tributaries) and outflow (irrigation canals) sites. Locations of 

the intermediate sites were determined by (1) availability of a 

good measurement section, (2) accessibility by road or boat, 

and (3) river distance to adjacent measurement sites.

Water levels in 1,350 wells located on or near the ESRP 

were measured at three different times during 2001 – 02. Wells 

selected for water-level measurements consisted of wells that 

were part of the USGS Regional Aquifer-System Analysis 

(RASA) network in 1980, private wells in the Rexburg area, 

current USGS observation wells, Idaho National Engineering 

and Environmental Laboratory (INEEL) project wells, BOR 

network wells, and IDWR network wells. 

Description of Study Area

The study area is made up of the area commonly referred 

to as the eastern Snake River Plain (ESRP). The ESRP covers 

an area approximately 200 mi long and 60 mi wide across 

south-central and southeastern Idaho (fig. 1) and constitutes about 30 percent of the upper Snake River Basin (area 

upstream from King Hill, Idaho). The climate of the plain 

is semiarid; average precipitation ranges from about 8 to 14 

in/yr. The range in summer and winter temperatures is large, 

and most of the precipitation occurs as rainfall during the 

summer months. Snow accumulation, if any, during the winter 

months is typically only a few inches, with the exception of 

the northeastern part of the plain, where accumulations may be 

higher. In general, the precipitation is not adequate to support 

crops without the use of irrigation. Sources of irrigation water 

include streamflow from mountains adjacent to the plain, 

irrigation reservoirs, and the underlying aquifer.

The underlying aquifer consists of a thick sequence 

of basaltic rocks interconnected with occasional unconsolidated sedimentary deposits. Sediments overlie the basalts in 

most areas. The geologic makeup of the aquifer allows for 

extremely high ground-water transmissivity rates and for the 

storage and yield of large volumes of water (Kjelstrom, 1995).

Ground-water generally flows toward the southwest, and 

most aquifer recharge occurs in the northern and eastern parts 

of the plain. Additional recharge occurs in other parts of the 

plain where streams from adjacent mountain ranges flow onto 

the plain and lose all of their flow to the aquifer (Kjelstrom, 

1988).

The Snake River itself originates in the high mountains 

of Wyoming near the southern border of Yellowstone National 

Park. Much of the river within the study area is entrenched 

in canyons as deep as 700 ft. The river is highly regulated by 

numerous dams that were constructed primarily for agricultural and power-generation purposes. Mean annual inflow 

to the ESRP during 1934 – 80 was about 10.2 million acre-ft 

(14,000 ft3/s) (Kjelstrom, 1988).

Gravity-flow and pumped diversions are predominant 

across the study area. In 1980, total gravity-flow and pumped 

diversions from the Snake River and its tributaries were almost 

8.8 million acre-ft (Goodell, 1988). Gravity-flow diversions 

occur mainly in the upper part of the study area and pumped 

diversions occur mainly in the lower part of the study area. 

Streamflow in the Snake River during the months of April 

through August is significantly affected by these irrigation 

diversions and, to a lesser extent, by the return of irrigation 

water that is not consumed. It is possible for return flows to 

make up a majority of the water in parts of the Snake River 

during drought years (Maupin, 1995).

PREVIOUS INVESTIGATIONS

Many early investigations of water resources in the ESRP 

were related to development of the system for irrigation uses. 

Newell (1928, 1929) analyzed the general characteristics of 

water resources in the American Falls area. Stearns and others 

(1938) presented a water budget for the Snake River Basin 

upstream from Weiser. Mundorff and others (1964) estimated 

recharge to the ground-water system from tributary drainage 

basins and irrigated areas. A report by Norvitch and others (1969) includes a discussion on possible changes in the 

hydrologic systems of the Snake River Plain resulting from 

increased use of ground water for irrigation.

More recent studies by the USGS and BOR specifically evaluated the interaction between the ground-water and 

surface-water systems. Thomas (1969) and Kjelstrom (1992, 

1995) analyzed spring discharges to the Snake River between 

Milner Dam and King Hill. Kjelstrom (1988) also studied 

gains and losses in reservoirs on the Snake River between 

Blackfoot and Milner. The RASA report by Kjelstrom (1995), 

which presents information on streamflow gains and losses in 

the Snake River and ground-water budgets, includes the most 

comprehensive collection of gain and loss data for the Snake 

River before that presented in this report.

METHODS FOR ESTIMATING GAINS 

AND LOSSES

All gain and loss calculations performed during this study 

were based on the basic conservation of mass equation,

Qin +/– ∆S = Qout, (1)

where Qin is the discharge into a specific subreach; ∆S is the 

change in storage within the subreach; and Qout is the discharge 

out of the subreach. For the purpose of this report, a subreach 
4 Surface-Water/Ground-Water Interaction along Reaches of the Snake River and Henrys Fork, Idaho

is defined as a section of the river bounded upstream and 

downstream by sites where discharge data were collected.

For any specific subreach of the study area, the basic 

equation can be rearranged as

 Q = – (Qu/s + Qinflow – Qoutflow + ∆S – Qd/s), (2)

where Q is the gain (positive result) or loss (negative result) 

estimate; Qu/s is the measured discharge in the river at the 

upstream end of the subreach; Qinflow is the total estimated 

inflow to the subreach from tributaries and irrigation-return 

drains; Qoutflow is the total estimated outflow from the subreach 

to irrigation canals; ∆S is the estimated change in storage 

within the subreach; and Qd/s is the measured discharge in the 

river at the downstream end of the subreach.

Performing the seepage studies during the nonirrigation 

season allowed for the removal of the Qoutflow term for most 

subreaches. Coordinating steady releases from the dams and 

powerplants located within the study area virtually negated the 

∆S term in most cases. Thus, the form of the equation most 

often used in the final gain and loss calculations was

Q = –(Qu/s + Qinflow – Qd/s). (3)

Values for the Qu/s and Qd/s terms were obtained from 

either gaging-station data or instantaneous acoustic Doppler 

measurements. If gaging-station data were used, the actual 

value typically was an instantaneous value (not a daily mean) 

based on the estimated traveltime downstream to the next 

measurement site. For one specific subreach where unsteady 

releases from a powerplant resulted in unsteady discharges, 

30-day average discharges at adjacent gaging stations were 

used to obtain a gain or loss estimate for that time period. 

Values for the Qinflow term were obtained from a combination of 

daily mean discharges (where gaging-station data were available), current-meter measurements, and estimates made from 

visual observations. Values for the Qoutflow term were obtained 

from a combination of daily mean discharges from irrigationdistrict records and current-meter measurements.

Because water levels in some of the reservoirs located 

within the study area were changing during the seepage studies, ∆S values for specific time periods were estimated by 

analyzing reservoir-storage data. The estimated ∆S then was 

transformed to an average flow rate for the seepage-study time 

period. It is important to note that, although this method for 

estimating the ∆S of a reservoir was based on the best available data, any gain/loss estimates calculated using a ∆S value 

other than zero could be subject to larger errors than other 

gain/loss estimates.

DATA ACCURACY AND LIMITATIONS

As discussed previously, several different sources of discharge data were used in the calculation of gain / loss estimates. 

Data sources included long-term gaging-station records, 

acoustic Doppler measurements, current-meter measurements, 

irrigation-district records, and visual inspections. Because of 

the variety of methods used in obtaining the data, the accuracy 

could be quite variable.

Long-term Gaging Stations

Streamflow data from long-term gaging stations operated by either the USGS or IPCo were used during this study. 

The accuracy of data from long-term gaging stations depends 

primarily on (1) the stability of the stage-discharge relation, 

(2) the frequency of actual discharge measurements, and (3) 

the accuracy of individual stage and discharge measurements 

(Kennedy, 1983). Streamflow data are published with an 

indicator of the accuracy of the data at each specific gaging 

station. An “excellent” rating indicates that about 95 percent 

of the daily mean discharges are within 5 percent of true; a 

“good” rating, within 10 percent; and a “fair” rating, within 15 

percent. Records that do not meet the criteria are rated “poor.” 

Most gaging-station data used to calculate estimates of gains 

and losses during this study were rated “good.” Instances 

where this was not the case are discussed where appropriate. 

Although a “good” rating indicates an accuracy of at least plus 

or minus 10 percent, in many cases the accuracy is believed to 

be much better. Because a stage-discharge relation is essentially an estimate of the true value based on a sample population, the relation for a site with a very stable control section 

(low variability) and a large number of actual discharge 

measurements (large sample size) likely will have a very high 

degree of accuracy.

Acoustic Doppler Measurements

The use of acoustic Doppler instrumentation specifically 

designed to measure river discharges allows discharges to 

be measured at locations previously very difficult or impossible to measure. However, limitations in the application of 

this instrumentation include the inability to measure water 

velocities in all areas of a specific cross section, which could 

contribute to the overall error of a measurement.

Unmeasured Areas

Acoustic Doppler instruments cannot measure water 

velocities in all areas of a river cross section (Morlock, 1996). 

These unmeasured areas (top, bottom, left edge, and right 

edge) are illustrated in figure 2. The depth of the unmeasured 

top section is a function of the transducer depth (distance the 

transducer extends into the water) and the blanking distance 

(time lag between when the sensor sends a signal and when 

it is ready to receive the return echoes of that signal). Part of 

the flow near the bed of the river channel cannot be measured 
Data Accuracy and Limitations 5

because of side-lobe interference (physical characteristic of 

the acoustic beam where the side lobe reflects off of the bottom before the main beam, which ultimately interferes with 

the reception of the remaining velocity data) (Simpson, 2001). 

Discharges in these top and bottom unmeasured sections are 

estimated using either a power-law or a constant method, 

depending on the velocity characteristics at the section.

Part of the flow at each edge of a cross section also 

cannot be measured because of minimum operational depth 

requirements and beam interference along vertical or nearly 

vertical edges. Beam interference can occur along vertical 

walls in much the same manner as described previously with 

regard to the river bottom. Edge discharges are estimated 

using an interpolation method based on the last recorded water 

velocities and depths, the distance to the edge of water, and 

the general shape of the unmeasured section (triangular or 

vertical).

Error

Two types of error occur during acoustic Doppler 

discharge measurements: random error and systematic error 

(or bias) (Simpson, 2001). Random error can be attributed 

to the accuracy of the instrumentation with regard to pulse 

length, transmit frequency, signal-to-noise ratio, and beam 

angle. Channel and flow characteristics can greatly affect the 

magnitude of random error. The effects of random error can be 

minimized by averaging several individual measurements.

Systematic error, or bias, can be separated into two parts: 

instrument-caused and operator-caused. Instrument-caused 

systematic errors relate to the operation of the instrument and 

the physical properties of the acoustic signal. Most of these 

errors are thought by manufacturers to be small and insignificant (Simpson, 2001). The operator-caused systematic errors 

listed below can be monitored easily and rectified; however, 

failure to do so can significantly affect the accuracy of discharge measurements. Possible errors include

• inaccurate measurement of transducer depth,

• consistent overestimation or underestimation of distance-to-edge values,

• inaccurate characterization of edge shapes, and

• failure to recognize a “moving bed” situation.

It can be very difficult to identify or quantify systematic error from a measurement summary; thus, it is critical 

to ensure that these inaccuracies are avoided. More detailed 

information on random and systematic errors resulting from 

the use of acoustic Doppler instruments is presented in a report 

by Simpson (2001).

The final assessment of the discharge measurement is 

based on a qualitative judgment of measuring conditions 

and a quantitative evaluation of the individual measurements 

(Lipscomb, 1995). The coefficient of variation (COV) is a 

useful statistic for making the quantitative assessment of 

the measurement. The coefficient of variation is equal to the 

standard deviation of a set of individual measurements made at 

a site divided by the mean of those measurements. Results of 

these calculations are illustrated in tables 1 and 2 for different 

numbers of individual measurements.

USGS policy requires that, if the COV of the first four 

individual measurements at a site is greater than 0.05, four 

more individual measurements must be made (Lipscomb, 

1995). The final discharge value is then the average of all eight 

measurements. During this study, IPCo followed similar procedures and, in some cases, made more than eight individual 

measurements at a single site. Commonly, when more than 

four individual measurements were made at a site, the COV 

still was greater than 0.05. Large COVs can indicate variability 

Table 1. Results of mean, standard deviation, and coefficient-of-variation calculations for a set of eight acoustic Doppler 

measurements of discharge at a site

Measurements

Discharge,

in cubic feet

per second

Measurement #1

Measurement #2

Measurement #3

Measurement #4

Measurement #5

Measurement #6

Measurement #7

Measurement #8

Mean

Standard deviation

Coefficient of variation

1,325

1,115

1,297

1,182

1,261

1,291

1,086

1,347

1,238

98

0.08

Figure 2. Typical river cross section and areas where water 

velocities cannot be measured using acoustic doppler 

instruments.

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6 Surface-Water/Ground-Water Interaction along Reaches of the Snake River and Henrys Fork, Idaho

of flow at the time of the measurements and/or the presence of 

random error effects discussed earlier. It is important to note, 

however, that the COV is not a direct indicator of the overall 

accuracy of the measurement; qualitative judgment also is 

used to assess the measurement quality.

Current-Meter Measurements

When applicable, inflows to and outflows from the Snake 

River were measured using standard current meters. Possible 

sources of error in a current-meter discharge measurement are 

(Sauer and Meyer, 1992)

• errors in measurement of the cross-sectional area,

• errors in measurement of the mean stream velocity,

• errors in computation procedures, and 

• general systematic errors, such as changes in stage, 

boundary effects, ice, obstructions, wind, incorrect 

equipment, incorrect techniques, poor distribution of 

measurement verticals, carelessness, and other factors.

The final assessment of a current-meter measurement is 

based commonly on a qualitative judgment of measuring conditions and equipment condition at the time of the measurement (Sauer and Meyer, 1992). An “excellent” rating indicates 

that the hydrographer felt that the measurement was within 

2 percent of true; a “good” rating, within 5 percent; a “fair” 

rating, within 8 percent; and a “poor” rating, over 8 percent 

(Rantz and others, 1982). During this study, most inflows and 

outflows measured using current meters were relatively small 

(one to two orders of magnitude) compared with the overall 

discharge in the main channel. Thus, even large errors in the 

current-meter measurements likely had little or no effect on 

the final gain/loss estimates.

Irrigation-District Records

Daily mean discharge data were available for many of 

the irrigation canals used to divert water from the Snake River. 

Methods and equipment used to obtain this data varied greatly 

by site. As a result, the accuracy of these data also could vary 

greatly. However, since most of the irrigation canals were 

not in service during the spring and fall study periods, any 

errors in the irrigation-discharge data would have had little 

or no effect on the final gain/loss estimates for these seasons. 

Most of the canals were in service during the summer 2002 

study period, and large errors in irrigation-discharge records 

could have had some effect on the final estimates for specific 

subreaches. To help reduce the possibility of error, current 

meters were used, when possible, to measure discharge in 

some of the irrigation canals.

Visual Inspections

Because of the large number of inflow sites along the 

study area, it was not feasible to make actual discharge 

measurements at all of the sites. Therefore, many sites were 

visually inspected and an estimate of discharge was recorded. 

Since the discharges at most of these inflow sites were very 

small (one to three orders of magnitude) compared with the 

discharges in the main channel, even large errors in the estimated discharges likely had no significant effect on the final 

gain/loss estimates.

STREAMFLOW GAINS AND LOSSES

The study area was divided into three reaches primarily 

to improve the efficiency of the data-collection efforts and 

data analyses. Gains and losses in the lower (Snake River 

near Minidoka to Snake River at King Hill gaging stations) 

and middle (Snake River near Shelley to Snake River near 

Minidoka gaging stations) reaches were documented five 

times beginning in March 2001 and ending in November 

2002. Gains and losses in the upper reach (Henrys Fork near 

Ashton gaging station to the mouth, near Lorenzo, and Snake 

River near Heise to near Shelley gaging stations) were documented four times beginning in November 2001 and ending in 

November 2002.

Because of the error inherent in each of the data-collection methods used, relatively small estimates of gains or 

losses for many subreaches were statistically insignificant and 

should be treated as “zero change” estimates. In this report, 

a threshold of 5 percent of the average of the upstream and 

downstream discharge values was used to identify statistically 

significant gains or losses. For example, the loss estimate for 

a reach with upstream and downstream discharge values of 

1,200 ft3/s and 1,000 ft3/s, respectively, would be considered 

significant because 200 ft3/s is approximately 18.2 percent 

Measurements

Discharge,

in cubic feet

per second

Measurement #1

Measurement #2

Measurement #3

Measurement #4

Mean

Standard deviation

Coefficient of variation

932

927

911

951

930

16

0.02

Table 2. Results of mean, standard deviation, and 

coefficient-of-variation calculations for a set of four 

acoustic Doppler measurements of discharge at a 

site.
Streamflow Gains and Losses 7

of the average, 1,100 ft3/s, of the upstream and downstream 

discharge values. Conversely, the estimated loss for a reach 

with upstream and downstream discharge values of 500 ft3/s 

and 480 ft3/s, respectively, would not be significant because 

the estimated loss of 20 ft3/s is approximately 4.1 percent of 

490 ft3/s and, thus, believed to be within the range of probable 

measurement error.

It is important to note that gain/loss estimates that 

included change-in-storage calculations, even if the estimates were determined to be statistically significant, could 

still contain larger errors than estimates that did not include 

change-in-storage calculations. Gain and loss estimates for the 

summer of 2002 were calculated on the basis of estimates of 

irrigation returns that had limited accuracy and main-channel 

discharge and irrigation-withdrawal values that were significantly larger than those during the spring and fall studies. As 

a result, the errors associated with these gain/loss estimates 

likely are larger than those associated with estimates for other 

time periods.

Lower Reach (Snake River near Minidoka to 

Snake River at King Hill)

Data collected during each of the seepage studies of the 

lower reach included discharge data from seven long-term 

gaging stations, acoustic Doppler discharge measurements 

from an additional 13 intermediate sites (fig. 3), and discharge 

data, obtained using current meters or by visual inspection, 

from numerous tributaries and irrigation-return drains. A summary of these data is presented in Appendix A.

It was assumed that the inflow values obtained for each 

subreach during each of the spring and fall seepage studies 

represented most, if not all, of the actual inflows occurring at 

the time of the study. Many irrigation-return drains were active 

during the summer of 2002. For this period, it was assumed 

that the inflow values that were obtained represented about 90 

percent of the actual inflows occurring at that time.

Three structures (Milner Dam, Lower Salmon Falls 

Power Plant, and Bliss Dam; fig. 1) are located within this 

reach. Unsteady releases from these structures and unsteady 

storage conditions upstream from these structures complicated 

the analyses in some instances and could have affected the 

final gain/loss estimates.

The gain/loss estimates for the subreach between the 

Snake River near Minidoka and Snake River at Milner gaging stations (L1 and L4) showed that there were slight gains 

during 2001. By the fall of 2002, this subreach had begun 

to lose a significant amount of streamflow (table 3). The 

gain/loss estimate for the spring of 2002 was essentially zero, 

and the estimate for the summer of 2002 was not statistically 

significant, likely because of the larger measurement errors 

associated with higher flows. Kjelstrom (1995) reported 

that, although this subreach lost streamflow during much of 

water years 1979 and 1980, historically it has been a gaining 

subreach.

Estimates of gains for the subreach between the Snake 

River at Milner and Snake River near Kimberly gaging stations (L4 and L6) ranged from 220 ft3

/s in the spring of 2002 

to 330 ft3/s in the summer of 2002; the average gain for this 

subreach during the study period was about 278 ft3/s (table 3). 

This average gain estimate compared well with Kjelstrom’s 

(1995) average gain estimate of approximately 210,000 acre-ft 

(294 ft3/s) during water year 1980.

Estimates of gains for the subreach between the Snake 

River near Kimberly and Snake River near Buhl gaging stations (L6 and L10) ranged from 918 ft3

/s in the spring of 2001 

to 1,150 ft3/s in the fall of 2001; the average gain was about 

1,030 ft3/s (table 3). The average gain estimate was about 16 

percent smaller than the average gain estimate by Kjelstrom 

(1995) of 1,230 ft3/s (880,000 acre-ft) during water year 1980.

Gain estimates for the subreach between the Snake River 

near Buhl and Snake River below Lower Salmon Falls near 

Hagerman (L10 and L16) gaging stations ranged from 2,700 

ft3/s during the summer of 2002 to 3,450 ft3/s during the spring 

of 2001; the average gain was about 3,100 ft3/s (table 3). This 

subreach receives significant inflows from a few large springs 

and several smaller springs located in the area. In general, the 

gain/loss estimates for this subreach were relatively consistent 

for the entire study period. Kjelstrom (1995) determined the 

gain in this subreach during water year 1980 to be approximately 2,650,000 acre-ft (3,710 ft3

/s), about 95 percent from 

the north side of the river. That estimate was about 19.7 percent larger than the estimate from this study.

Unsteady releases from dams and powerplants and resulting changes in reservoir storage likely affected the measurements and resulting gain/loss estimates during some of the 

seepage studies of the subreaches between the Snake River 

below Lower Salmon Falls near Hagerman and the Snake 

River below Bliss Dam near Bliss gaging stations (L16 and 

L18) and between the Snake River below Bliss Dam and the 

Table 3. Summary of streamflow gain and loss estimates for the 

lower reach of the Snake River, between the near Minidoka and at 

King Hill gaging stations, Idaho

[See figure 3 for locations of subreaches; ft3/s, cubic feet per second; values in 

boldface are statistically significant]

Subreach

Estimates of gains or (losses), in ft3/s

Spring 

2001

Fall 

2001

Spring 

2002

Summer 

2002

Fall 

2002

L1 to L4 44 40 (5) (110) (238)

L4 to L6 248 277 220 330 315 

L6 to L10 918 1,150 994 1,100 986

L10 to L16 3,450 3,310 3,050 2,700 2,970

L16 to L18 (104) 62 260 136 377

L18 to L20 200 (65) (10) 437 (195)
Figure 3. Locations of sites along the lower reach of the Snake River, southeastern Idaho, where streamflow was measured.

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10 Surface-Water/Ground-Water Interaction along Reaches of the Snake River and Henrys Fork, Idaho

Snake River at King Hill gaging stations (L18 and L20). Gain/

loss estimates throughout these subreaches were variable, and 

only two estimates were statistically significant (Appendix A). 

Regardless, even the statistically significant estimates (table 3) 

were significantly smaller than Kjelstrom’s (1995) estimated 

gain for the overall subreach (L16 to L20) of 1,020,000 acre-ft 

(1,430 ft3/s) during water year 1980.

Middle Reach (Snake River near Shelley to 

Snake River near Minidoka)

Data collected during each of the seepage studies of the 

middle reach included discharge data from five long-term gaging stations, acoustic Doppler discharge measurements from 

an additional 11 intermediate sites (fig. 4), and discharge data, 

obtained using current meters or by visual inspection, from 

numerous tributaries and irrigation-return drains. A summary 

of these data is presented in Appendix B.

It was assumed that the inflow values obtained for each 

subreach during each of the spring and fall seepage studies 

represented most, if not all, of the actual inflows occurring 

at the time of the study. Many of the irrigation-return drains 

were active during the summer of 2002. For this period, it was 

assumed that the inflow values that were obtained represented 

about 90 percent of the actual inflows occurring at that time.

Unsteady releases from two structures (American Falls 

Dam and Minidoka Dam; fig. 1) and unsteady storage conditions upstream from these structures complicated the analyses 

in some instances and could have affected the final gain/loss 

estimates. Also, unsteady releases from two small hydrogeneration facilities located on the Snake River near Idaho Falls 

affected streamflows during some of the seepage studies.

The subreach between the Snake River near Shelley and 

Snake River at Blackfoot gaging stations (M1 and M6) lost 

streamflow during each of the five seepage studies. Although 

the gain/loss estimates for this subreach were relatively consistent, ranging from a loss of 310 ft3

/s during the spring of 2002 

to a loss of 555 ft3/s during the summer of 2002 (table 4), the 

gain/loss estimates for the intermediate subreaches were quite 

variable and did include one statistically significant gain during the fall of 2002 (Appendix B). Kjelstrom (1995) noted that 

this subreach alternately gains and loses streamflow depending 

on changes in adjacent ground-water levels, which are affected 

by irrigation withdrawals. This could explain some of the variability in the gain/loss estimates. Variability in the summer of 

2002 also could be partially a result of larger magnitude errors 

associated with larger discharge values.

The subreach between the Snake River at Blackfoot and 

Snake River near Blackfoot gaging stations (M6 and M9) 

also lost streamflow during each of the five seepage studies. 

Estimates for this subreach were relatively consistent, ranging from a loss of 219 ft3

/s during the fall of 2001 to a loss of 

398 ft3/s during the summer of 2002 (table 4). All but two of 

the estimates for the intermediate subreaches showed losses; 

however, all of these estimates were still somewhat variable 

(Appendix B). Kjelstrom (1995) noted that spring discharges, 

which are controlled by ground-water levels, often decrease 

the net loss of streamflow in this subreach.

Kjelstrom (1995) noted that the overall subreach between 

the Snake River near Shelley and Snake River near Blackfoot gaging stations (M1 and M9) lost an estimated 200,000 

acre-ft per year (280 ft3/s) from 1915 to 1927. Data from 1932 

through 1980 showed losses that were variable, ranging from 

around 100,000 to 400,000 acre-ft per year (140 ft3/s to 560 

ft3/s), and very responsive to adjacent ground-water levels. The 

average loss for this overall subreach during the five seepage 

studies was approximately 760 ft3/s (table 4).

The subreach between the Snake River near Blackfoot 

and Snake River at Neeley gaging stations (M9 and M12) 

includes several springs in addition to American Falls Reservoir and historically has gained streamflow. The average gain 

for this subreach during the five seepage studies was about 

1,900 ft3/s, but gains varied from 1,130 ft3/s during the summer of 2002 to 2,680 ft3

/s during the fall of 2002 (table 4). 

Again, this large variability could result partly from difficulties 

in accurately estimating changes in storage in the reservoir. 

Because of the size of the reservoir, even small errors in estimating changes in storage could have significant effects on the 

final gain/loss estimates. Gain/loss estimates for the intermediate subreaches, in some cases, were quite variable (Appendix 

B). Annual gains within this subreach from 1912 to 1980 were 

relatively stable and averaged about 1,800,000 acre-ft per 

year (2,540 ft3/s) (Kjelstrom, 1995). That estimate is about 33 

percent larger than the estimate from this study.

The subreach between the Snake River at Neeley and 

Snake River near Minidoka gaging stations (M12 and M16) 

also includes several springs and a reservoir, Lake Walcott. 

Kjelstrom (1995) noted that this subreach alternately gains 

and loses streamflow, but that annual gains almost always 

have exceeded losses. Variability in gain/loss estimates for 

this subreach is reflected in the estimates for the intermediate 

Table 4.Summary of streamflow gain and loss estimates for the 

middle reach of the Snake River, between the near Shelley and 

near Minidoka gaging stations, Idaho

[See figure 4 for locations of subreaches; ft3/s, cubic feet per second; values in 

boldface are statistically significant]

Subreach

Estimates of gains or (losses), in ft3/s

Spring 

2001

Fall 

2001

Spring 

2002

Summer 

2002

Fall 

2002

M1 to M6

M6 to M9

M9 to M12

M12 to M16

(470) 2

(309)

1,940

(121)

(435)

(219)

2,060

3

114

(310)

(330)

1,690

1,080

(555)

(398)

1,130

87 

1

(480)

(269)

2,680

4

125

1

 An estimate of a gain between sites M2 and M3 was significant.

2

 An estimate of a gain between sites M8 and M9 was significant.

3

 An estimate of a loss between sites M14 and M15 was significant.

4

 An estimate of a loss between sites M13 and M14 was significant.
Figure 5. Locations of sites along the upper reach of the Snake River and along the Henrys Fork, southeastern Idaho, where streamflow was mea

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12 Surface-Water/Ground-Water Interaction along Reaches of the Snake River and Henrys Fork, Idaho

subreaches. Some of the variability, especially the estimate for 

the spring of 2002, could have been the result of difficulties 

in accurately estimating changes in storage in Lake Walcott. 

Excluding the spring 2002 value, statistically significant estimates averaged a gain of 120 ft3

/s (table 4). Kjelstrom (1995) 

estimated a gain of approximately 200,000 acre-ft (280 ft3/s) 

in this subreach during water year 1980. He also noted losses 

that averaged about 15,000 acre-ft per month (252 ft3/s) during 

June, July, and August of 1979.

Upper Reach (Henrys Fork near Ashton to 

Henrys Fork at mouth, near Lorenzo / Snake 

River near Heise to Snake River near Shelley)

Data collected during each of the seepage studies of the 

upper reach included discharge data from eight long-term gaging stations, acoustic Doppler discharge measurements from 

an additional 12 intermediate sites (fig. 5), and discharge data, 

obtained using current meters or by visual inspection, from 

numerous tributaries and irrigation-return drains. A summary 

of these data is presented in Appendix C.

It was assumed that the total inflow values determined for 

each subreach during each of the spring and fall seepage studies represented most, if not all, of the actual inflows occurring 

at the time of the study. Many of the irrigation-return drains 

were active during the summer of 2002. For this period, it 

was assumed that the total inflow values represented about 90 

percent of the actual inflows occurring at that time.

Unsteady releases from two small hydrogeneration 

facilities located on the Snake River near Idaho Falls affected 

streamflows during some of the seepage studies. In an effort to 

reduce the effects of the variable releases from these facilities, 30-day average daily mean discharges were used to 

calculate the gain/loss estimates in the subreach between the 

near Idaho Falls and near Shelley gaging stations (U19 and 

U20). Although the use of average values could have reduced 

some of the variability in the gain/loss estimates, this method 

did not account for variability in inflows or outflows within 

the subreach and could have resulted in estimates with larger 

levels of error. In addition, the Snake River channel upstream 

from the confluence with the Henrys Fork is very active, and 

braided channels and bypass flows are common.

The subreach between the Henrys Fork near Ashton and 

Henrys Fork near St. Anthony gaging stations (U1 and U4) 

generally gained streamflow during the four seepage studies. 

Gain/loss estimates ranged from essentially no gain during the spring of 2002 to a gain of about 235 ft3

/s during the 

summer of 2002 (table 5). Most estimates for the intermediate subreaches within this subreach were gains; however, a 

statistically significant loss between sites U1 and U2 occurred 

in the fall of 2002 (Appendix C).

The subreach between the Henrys Fork near St. Anthony 

and Henrys Fork near Rexburg gaging stations (U4 and U7) 

generally lost streamflow during the four seepage studies; 

however, two statistically significant gains between sites U4 

and U5 were calculated during the study (Appendix C). Loss 

estimates ranged from 71 ft3/s during the spring of 2002 to 

188 ft3/s during the fall of 2001 (table 5). The average loss 

estimate for this subreach during the entire study period was 

about 121 ft3/s.

The subreach between the Snake River near Heise and 

Snake River at Lorenzo gaging stations (U9 and U12) lost 

streamflow during three of the four seepage studies. Estimates 

for intermediate subreaches were losses or essentially no gain 

except that for one subreach: a statistically significant gain 

between sites U11 and U12 was calculated during the summer 

of 2002 (Appendix C), resulting in a near zero loss estimate 

for the subreach. Excluding results for the summer of 2002, 

overall subreach estimates ranged from a loss of 393 ft3/s during the fall of 2001 to a loss of 606 ft3

/s during the spring of 

2002. The average loss estimate for this subreach, excluding 

the summer of 2002, was about 474 ft3/s (table 5). Kjelstrom 

(1995) noted that this reach is very responsive to adjacent 

ground-water levels and often alternates between gaining and 

losing streamflow during any given year. During water years 

1979 and 1980, estimates ranged from a loss of about 590 ft3/s 

to a gain of about 750 ft3/s (Kjelstrom, 1995).

Because of the difficult measuring conditions at the 

Snake River site (U13) immediately upstream from the 

confluence with the Henrys Fork, no gain/loss estimates for 

the intermediate subreaches within the subreach between the 

Snake River at Lorenzo and Snake River near Menan gaging 

stations (U12 and U14) were calculated. In addition, because 

discharge was not measured at site U8 during the fall of 

Table 5. Summary of streamflow gain and loss estimates for the 

upper reach of the Henrys Fork and Snake River, between the near 

Ashton gaging station and the mouth, near Lorenzo, and the near 

Heise and near Shelley gaging stations, Idaho

[See figure 5 for locations of subreaches; ft3/s, cubic feet per second; values in 

boldface are statistically significant]

Subreach

Estimates of gains or (losses), in ft3/s

Fall 2001 Spring 2002 Summer 2002 Fall 2002

U1 to U4 76 3 235 1 210

U4 to U7 (188) 2 (71) 2 (101) (122)

U9 to U12 (393) (606) 3 (8) (424)

U12 to U14 4 319 428 4 228 517

U14 to U19 (142) (352) 5 (300) 6 4

U19 to U20 30 (205) (6) (149)

1 An estimate of a loss between sites U1 and U2 was significant.

2 An estimate of a gain between sites U4 and U5 was significant.

3 An estimate of a gain between sites L11 and L12 was significant.

4 Includes any gains or losses within the subreach between the Henrys Fork 

near Rexburg gaging station and Henrys Fork at the mouth, near Lorenzo. 5 An estimate of a loss between sites U14 and U15 was significant.

6 An estimate of a loss between sites U14 and U15 and an estimate of a gain 

between sites U17 and U18 were significant.
Comparisons of Ground-Water Levels with Streamflow Gains and Losses 13

2001 or the summer of 2002, the estimates for this subreach 

included gains or losses within the Henrys Fork subreach from 

the Henrys Fork near Rexburg gaging station downstream to 

the mouth, near Lorenzo (U7 and U8). Estimates for the spring 

and fall of 2002, which can be attributed solely to streamflow 

gains and losses in the Snake River subreach (U12 to U14), 

showed a relatively consistent gain that ranged from 428 ft3/s 

during the spring of 2002 to 517 ft3/s during the fall of 2002. 

The average gain during these two seepage studies was about 

472 ft3/s (table 5).

Estimates for the subreach between the Snake River near 

Menan and Snake River near Idaho Falls gaging stations (U14 

and U19) were somewhat variable during the four seepage 

studies. The estimates ranged from essentially no change during the fall of 2002 to a loss of 352 ft3

/s during the spring of 

2002 (table 5). Most estimates for the intermediate subreaches 

within this subreach were not statistically significant; however, 

significant losses between sites U14 and U15 were calculated 

during three of the four seepage studies (Appendix C). The 

only statistically significant gain occurred between sites U17 

and U18 during the fall of 2002. In contrast, Kjelstrom (1995) 

described this reach as one that gains streamflow during most 

years and in which gains increase during the irrigation season. 

He also noted a direct relationship between monthly gains and 

nearby ground-water levels.

As previously discussed, because of the probability 

of unsteady discharges from two hydrogeneration facilities 

located downstream from Idaho Falls, 30-day average discharge values were used to calculate gain / loss estimates within 

the subreach between the Snake River near Idaho Falls and 

Snake River near Shelley gaging stations (U19 and U20). For 

the same reason, no intermediate acoustic Doppler measurements were obtained within this subreach. For comparison, 

loss estimates calculated for the subreach between sites U4 

and U7 using 30-day average discharges averaged about 110 

ft3/s; loss estimates calculated for the same subreach using the 

acoustic Doppler discharge measurements and gaging-station 

data averaged about 121 ft3/s. Estimates for the Snake River 

near Idaho Falls to the Snake River near Shelley subreach 

based on the 30-day average discharge values ranged from 

essentially no change during the fall of 2001 and the summer 

of 2002 to a loss of 205 ft3/s during the spring of 2002 (table 

5). Kjelstrom (1995) noted somewhat similar results for water 

years 1979 and 1980: his estimates ranged from very small 

gains to losses exceeding 1,000 ft3/s, depending on adjacent 

ground-water levels.

COMPARISONS OF GROUND-WATER 

LEVELS WITH STREAMFLOW GAINS 

AND LOSSES

Water levels in 1,350 wells located on and adjacent to 

the ESRP (fig. 6) were measured during three separate mass 

measurement efforts. Of the 1,350 wells, 825 either were the 

same wells included in the 1980 RASA study (Lindholm, 

1996) or were suitable replacements (i.e. similar location and 

depth). The remaining wells were private wells in the Rexburg 

area, current USGS observation wells operated in cooperation 

with the State of Idaho, INEEL project wells, BOR network 

wells, and IDWR network wells. Water levels were measured 

before the 2001 irrigation season (beginning in mid-March 

2001), following the 2001 irrigation season (beginning in midOctober 2001), and before the 2002 irrigation season (beginning in late March 2002). Water levels in the wells, with the 

exception of some in the Rexburg area, were measured within 

a 3-week time period during each of the three efforts. Those 

in the Rexburg area were measured only during the final two 

measurement efforts. Water-level data obtained during these 

measurement efforts are available in volume 1 of the water 

year 2002 annual data report for Idaho (Brennan and others, 

2003) and in the USGS National Water Information System 

database. Where possible, data from selected wells were 

analyzed and compared to streamflow gain / loss estimates for 

adjacent subreaches.

Lower Reach (Snake River near Minidoka to 

Snake River at King Hill)

The data for well 9S-25E-23DBA1 (well no. 1; fig. 6), 

which is adjacent to the subreach between the Snake River 

near Minidoka and Snake River at Milner gaging stations (L1 

and L4), showed a decrease in water levels of approximately 

10 ft between 1980 and 2002. An apparent relation between 

water levels in this well and estimates of gains and losses 

within this subreach can be seen in the plot in figure 7. The 

statistically significant estimates of gains for this subreach 

during the spring and fall of 2001 were consistent with 

Kjelstrom’s (1995) findings that this subreach historically 

gains streamflow. The estimated loss during the fall of 2002 

was consistent with Kjelstrom’s (1995) observation that this 

subreach may lose streamflow following a general lowering of 

ground-water levels.

Long-term data for well 10S-20E-27BCC1 (fig. 6) 

adjacent to the subreach between the Snake River at Milner 

and Snake River near Kimberly gaging stations (L4 and L6) 

showed a decrease in water levels of about 8 ft during the 

study period. As discussed previously, estimates of gains 

within this subreach were very consistent and also very 

similar to estimates of gains determined by Kjelstrom (1995). 

The consistency of estimated gains and ground-water-level 

decreases indicated that there was no relation between the 

estimated gains and changes in ground-water levels.

As discussed previously, the average gain estimate for the 

subreach from the Snake River near Kimberly to Snake River 

near Buhl gaging stations (L6 and L10) was about 16 percent 

smaller than that calculated for water year 1980. Head in an 

artesian well (9S-16E-20ADD1; fig. 6) on the south side of 

the Snake River near Twin Falls decreased by more than 30 ft 
Figure 6. Locations of wells on and near the eastern Snake River Plain, southeastern Idaho, where water levels were measured during water year

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Comparisons of Ground-Water Levels with Streamflow Gains and Losses 15

Figure 7. Water levels in selected wells during water years 2000 – 03 and estimates of gains and losses in selected 

subreaches of the Snake River and Henrys Fork, southeastern Idaho, spring 2001 to fall 2002.

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16 Surface-Water/Ground-Water Interaction along Reaches of the Snake River and Henrys Fork, Idaho

between 1984 and 2002. The decrease in estimated gains from 

Kjelstrom’s (1995) estimates to the results from this study for 

this subreach could be related to the relatively large decreases 

in water levels between 1980 and 2002.

The average gain estimate for the subreach between the 

Snake River near Buhl and the Snake River below Lower 

Salmon Falls near Hagerman gaging stations (L10 and L16) 

was about 19.7 percent smaller than that calculated for water 

year 1980. A relation between water levels in well 8S14E-16CBB1 (fig. 6), adjacent to this subreach, and spring 

discharges from the north side of the river was noted by 

Kjelstrom (1995). The water-level decrease in this well of 

approximately 2 ft between 1980 and 2002 could be related 

to the decrease in gains during that time period. Water levels 

during water years 2000 – 03 and gain / loss estimates from the 

seepage studies are presented in figure 7. Although short-term 

water-level variations were relatively small, these variations 

could be related to changes in gain estimates within this 

subreach during the five seepage studies.

A comparison of the average estimate of gains for 1980 

(Kjelstrom, 1995) for the subreach between the Snake River 

below Lower Salmon Falls near Hagerman and the Snake 

River at King Hill gaging stations (L16 and L20) and the 

average estimate of gains for this study showed an apparent 

decrease in gains since 1980. Data for well 6S-11E-6BBA1 

(fig. 6), which is adjacent to this subreach, showed a decrease 

in water levels of nearly 10 ft between 1980 and 2002. Data 

for another well (5S-10E-28CAB1; fig. 6), located about 5 mi 

downstream from the King Hill gaging station, also showed 

significant decreases in water levels. Between 1980 and 

2002, this well changed from an artesian well with a head of 

approximately 5 ft to a well with water levels about 5 to 7 ft 

below land surface.

Middle Reach (Snake River near Shelley to 

Snake River near Minidoka)

Water levels in two wells (2S-35E-22DAC1 and

1S-35E-11CAD1; fig. 6) located adjacent to the subreach 

between the Snake River near Shelley and the Snake RiverBlackfoot gaging stations (M1 and M6) decreased about 9 to 

15 ft between the mid-1980s and 2002. The estimates between 

intermediate sites within this subreach were somewhat vari

able; however, there were insufficient data available to determine if there was a relation between these variations and the 

variations in water levels in the selected wells.

Estimates of losses between intermediate sites within the 

subreach between the Snake River at Blackfoot and the Snake 

River near Blackfoot gaging stations (M6 and M9) were somewhat variable, but these variations did not seem to be related 

to the relatively small changes in water levels recorded during 

the study. Water levels in selected wells (2S-34E-33BBA1 

and 3S-33E-14BBA1; fig. 6) located adjacent to this subreach 

decreased about 3 to 5 ft between 1980 and 2002 and varied 

about 1 to 3 ft during the study. The decrease in ground-water 

levels along the overall subreach between the Snake River near 

Shelley and the Snake River near Blackfoot gaging stations 

(M1 and M9), however, could partially explain the increase in 

losses within this subreach from about 560 ft3/s estimated in 

1980 (Kjelstrom, 1995) to about 750 ft3/s estimated during this 

study.

Gains and losses within the subreach between the Snake 

River near Blackfoot and the Snake River at Neeley gaging 

stations (M9 and M12) likely are affected by American Falls 

Reservoir. Mundorff (1967) related water levels in well 5S31E-27ABA1 (fig. 6) with monthly ground-water discharge to 

American Falls Reservoir. He also noted that gains are affected 

by the stage of the reservoir. As the reservoir stage declines, 

water is released from bank storage; as stage rises, water is 

added to storage. Kjelstrom (1995) showed a distinct relation 

between ground-water levels in well 5S-31E-27ABA1 and 

flows in Danielson Creek, a major spring inflow in the area. 

Although no distinct relation between changes in estimates of 

gains within this subreach and changes in ground-water levels 

during 2001 and 2002 was apparent, the long-term decline 

in water levels in well 5S-31E-27ABA1 of over 5 ft between 

1980 and 2002 could explain the apparent decrease in gains 

since 1980. The average gain estimate for this subreach during 

the seepage studies was about 1,900 ft3/s; the estimate determined by Kjelstrom (1995) for water years 1912 through 1980 

was about 2,540 ft3/s.

Long-term data for two wells (8S-30E-23DCC1 and 

9S-28E-18BAD1) located adjacent to the subreach between 

the Snake River at Neeley and the Snake River near Minidoka gaging stations (M12 and M16) were quite variable but 

showed net decreases in ground-water levels of about 3 to 

8 ft between 1980 and 2002. As discussed previously, this 

subreach historically has alternated between gaining and 

losing streamflow. The variable ground-water levels could 

partially explain the historical changes between gaining and 

losing. However, statistically significant gains within this 

subreach during the study were quite variable and did not 

seem to be related to water levels in adjacent wells.

Upper Reach (Henrys Fork near Ashton to 

Henrys Fork at mouth, near Lorenzo / Snake 

River near Heise to Snake River near Shelley)

Water levels in well 8N-41E-25CBB1 (fig. 6), located 

adjacent to the subreach between the Henrys Fork near Ashton 

and the Henrys Fork near St. Anthony gaging stations (U1 and 

U4), were quite variable during water years 2001 and 2002 

and appear to relate to estimated gains during the same time 

period (fig. 7). During this time, the difference between the 

maximum and minimum water levels was more than 30 ft. 

The estimate of essentially no gain during the spring of 2002 

corresponded to lower ground-water levels, and the estimate 

of a gain of 235 ft3/s during the summer of 2002 corresponded 

to the highest recorded ground-water level during water years 
Summary 17

2001 to 2003. Kjelstrom (1995) noted that ground-water levels 

along this subreach seem to be very responsive to surface 

recharge from irrigation, which, in turn, can affect the rate of 

gain or loss.

The subreach between the Henrys Fork near St. Anthony 

and Henrys Fork near Rexburg gaging stations (U4 and U7) 

generally lost streamflow during the seepage studies. The 

losses ranged from 71 ft3/s to 188 ft3/s. Water levels in well 

6N-39E-10BBB3 (fig. 6), located adjacent to this subreach, 

decreased approximately 8 ft during water years 2001 and 

2002; however, no relation between changes in ground-water 

levels and changes in gain/loss estimates was apparent.

Estimates of losses in the subreach between the Snake 

River near Heise and the Snake River at Lorenzo gaging 

stations (U9 and U12) were somewhat variable during the 

seepage studies. Water levels in well 4N-39E-26DAA1 (fig. 

6), located adjacent to this subreach, also were somewhat 

variable. The relation between changes in water levels in this 

well and changes in gain/loss estimates was strong, with the 

exception of that for the summer of 2002 (fig. 7). This well is 

completed in the alluvial deposits along the river, which could 

explain the strong relation. Gain/loss estimates for the summer of 2002 could have been affected by larger errors associated with measuring larger summer discharges and summer 

outflow estimates. Kjelstrom (1995) also noted a relation 

between gains and losses and water levels in wells adjacent 

to this subreach. He attributed the rise in ground-water levels 

and subsequent increase in streamflow gains during 1980 to 

surface recharge from irrigation. Timing of the increased gains 

during 2001 and 2002 (fig. 7) suggests that surface recharge 

from irrigation was likely also the source of increases during 

this period.

No relation between ground-water levels and estimates 

of gains in the subreach from the Snake River at Lorenzo to 

the Snake River near Menan gaging stations (U12 and U14) 

was apparent. Two possible reasons could be that few wells 

are located adjacent to the reach and, as discussed previously, 

the estimates of gains for two of the seepage studies included 

any gains or losses within the Henrys Fork subreach from near 

Rexburg to the mouth.

Few wells were usable for comparisons along the 

subreach from the Snake River near Menan to the Snake River 

near Idaho Falls gaging stations (U14 and U19). Increases 

and decreases in water levels in the only well located near the 

river, 3N-37E-2CBD1 (fig. 6), were consistent with increases 

and decreases in surface recharge from irrigation; however, 

no relation between the ground-water levels and the estimates 

of gains and losses based on the limited water-level data was 

apparent within the subreach.

A relation between water levels in well 2N-38E-16ADD1 

(fig. 6) and gain / loss estimates between the near Lewisville 

site and the Snake River near Shelley gaging station (U18 and 

U20) was noted by Kjelstrom (1995). A similar relation was 

found during 2001 and 2002 between water levels in the same 

well and estimates of gains and losses between the Snake 

River near Idaho Falls and the Snake River near Shelley gaging stations (U19 and U20; fig. 7). The statistically insignificant estimates during the fall of 2001 and the summer of 2002 

corresponded to higher ground-water levels, and the estimates 

of losses for the spring and fall of 2002 corresponded to lower 

ground-water levels.

SUMMARY

Declining water levels in the eastern Snake River Plain 

(ESRP) aquifer and decreases in spring discharges from the 

aquifer to the Snake River have raised concerns about the 

sustainability of water resources in the ESRP. To address this 

question, the Snake River Plain Hydrologic Modeling Committee developed a general strategy to refine and enhance the 

conceptual and computer models of the ESRP hydrologic system. Because of the need for improved and additional information concerning surface-water/ground-water interactions 

along specific reaches of the Snake River and Henrys Fork 

included in these models, the U.S. Geological Survey (USGS), 

in cooperation with the Idaho Department of Water Resources 

(IDWR) and Idaho Power Company (IPCo), designed and conducted seepage studies in three separate reaches of the Snake 

River and Henrys Fork in southeastern Idaho. Data collected 

in each reach included discharges at USGS and(or) IPCo, discharges at several intermediate sites between gaging stations 

measured using acoustic Doppler current profilers (ADCPs), 

and measured and(or) estimated discharges at several miscellaneous inflow (mostly tributaries) and outflow (irrigation 

canals) sites. Estimates of streamflow gains and losses in 

specific subreaches of the Snake River then were calculated.

Gain / loss estimates varied greatly within and between 

the selected study reaches. Surface spring flow was present 

in many of the subreaches for which large estimates of gains 

were calculated, most notably the reach that includes Thousand Springs. Both gain and loss estimates were calculated for 

some subreaches depending on the time of the study. The overall magnitude of the gains was about 5 times larger than that of 

the losses. Unsteady releases from dams and powerplants and 

changes in reservoir and channel storages probably contributed a large component of the error in several of the calculated 

gain/loss estimates.

In addition to estimates of streamflow gains and losses, 

water levels in 1,350 wells across the study area were measured at three different times during the study period. Relations between gain/loss estimates in each subreach and 

ground-water levels in wells located adjacent to each subreach 

were analyzed. In some instances, general relations between 

changes in gain/loss estimates and changes in ground-water 

levels were apparent.

A comparison of streamflow and water-level data from 

the 1980 Regional Aquifer-System Analysis study (Kjelstrom, 

1995) with data from the 2001 to 2002 study period indicated 

that long-term changes in gain/loss estimates likely were 

related to long-term changes in ground-water levels. Gain 
18 Surface-Water/Ground-Water Interaction along Reaches of the Snake River and Henrys Fork, Idaho

estimates for three of the subreaches located within the lower 

study reach (L6 to L10, L10 to L16, and L16 to L20) were 

more than 15 percent smaller than the estimates determined 

by Kjelstrom (1995). The gain estimate for the subreach that 

includes American Falls Reservoir (M9 to M12) was about 33 

percent smaller than that determined by Kjelstrom (1995). The 

gain/loss estimates for the subreach of the Snake River immediately downstream from the confluence with the Henrys Fork 

(U14 to U19) ranged from no change to statistically significant 

losses. In contrast, Kjelstrom (1995) noted that this historically had been a gaining reach.

REFERENCES CITED

Brennan, T.S., Lehmann, A.K., Campbell, A.M., O’Dell, I., 

and Beattie, S.E., 2003, Water resources data – Idaho, water 

year 2002, volume 1: U.S. Geological Survey Water Data 

Report ID – 02 – 1, 419 p.

Goodell, S.A., 1988, Water use on the Snake River Plain, 

Idaho and eastern Oregon: U.S. Geological Survey Professional Paper 1408 – E, 51 p.

Kennedy, E.J., 1983, Computation of continuous records of 

streamflow: U.S. Geological Survey Techniques of WaterResources Investigations, book 3, chap. A13, 53 p.

Kjelstrom, L.C., 1988, Estimates of gains and losses for reservoirs on the Snake River from Blackfoot to Milner, Idaho, 

for selected periods, 1912 to 1983: U.S. Geological Survey 

Water-Resources Investigations Report 87 – 4063, 62 p.

Kjelstrom, L.C., 1992, Assessment of spring discharge to the 

Snake River, Milner Dam to King Hill, Idaho: U.S. Geological Survey Open-File Report 92 – 147 (Water Fact Sheet), 

[2] p.

Kjelstrom, L.C., 1995, Methods to estimate annual mean 

spring discharge to the Snake River between Milner Dam 

and King Hill, Idaho: U.S. Geological Survey WaterResources Investigations Report 95 – 4055, 9 p.

Kjelstrom, L.C., 1995, Streamflow gains and losses in the 

Snake River and ground-water budgets for the Snake River 

Plain, Idaho and eastern Oregon: U.S. Geological Survey 

Professional Paper 1408 – C, 47 p.

Lindholm, G.F., 1996, Summary of the Snake River Plain 

Regional Aquifer-System Analysis in Idaho and eastern 

Oregon: U.S. Geological Survey Professional Paper 

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measurements using broadband acoustic Doppler current profilers: U.S. Geological Survey Open-File Report 

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Maupin, M.A., 1995, Water-quality assessment of the upper 

Snake River Basin, Idaho and western Wyoming— environmental setting, 1980 – 92: U.S. Geological Survey WaterResources Investigations Report 94 – 4221, 35 p.

Morlock, S.E., 1996, Evaluation of acoustic Doppler current 

profiler measurements of river discharge: U.S. Geological 

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37 p.

Mundorff, M.J., 1967, Ground water in the vicinity of American Falls Reservoir, Idaho: U.S. Geological Survey WaterSupply Paper 1846, 58 p.

Mundorff, M.J., Crosthwaite, E.G., and Kilburn, Chabot, 

1964, Ground water for irrigation in the Snake River basin 

in Idaho: U.S. Geological Survey Water-Supply Paper 1654, 

224 p.

Newell, T.R., 1928, Segregation of water resources, American Falls basin and reservoir: Idaho Falls, Report to Water 

District No. 36, 127 p.

Newell, T.R., 1929, Segregation of water resources, American Falls basin and reservoir: Idaho Falls, Report to Water 

District No. 36, 144 p.

Norvitch, R.F., Thomas, C.A., and Madison, R.J., 1969, 

Artificial recharge to the Snake Plain aquifer, an evaluation 

of potential and effect: Idaho Department of Reclamation, 

Water Information Bulletin no. 12, 59 p.

Rantz, S.E., and others, 1982, Measurement and computation 

of streamflow: U.S. Geological Survey Water-Supply Paper 

2175, 2 v., 631 p.

Sauer, V.B., and Meyer, R.W., 1992, Determination of error in 

individual discharge measurements: U.S. Geological Survey 

Open-File Report 92 – 144, 21 p.

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Survey Open-File Report 01 – 1, 123 p.

Stearns, H.T., Crandall, Lynn, and Steward, W.G., 1938, Geology and ground-water resources of the Snake River Plain in 

southeastern Idaho: U.S. Geological Survey Water-Supply 

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Manuscript approved for publication, June 28, 2004.

Manuscript placed on World Wide Web, March 2005 at URL:

http://id.water.usgs.gov/public/reports.html

Prepared by U.S. Geological Survey Publishing staff, Idaho District, 

Boise, Idaho:

Launa H. Allen

Linda Buckmaster

Richard L. Helton

Barbara N. Kemp

For more information concerning the research in this report, contact

Idaho District Chief

U.S. Geological Survey

230 Collins Road

Boise, Idaho 83702-4520

http://id.water.usgs.gov
U.S. Geological Survey Scientific Investigations Report 2004-5115

Hortness, J.E., and Vidmar, Peter--Surface-Water/Ground-Water Interaction along Reaches of the Snake River and Henrys Fork, Idaho

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