U.S. Department of the Interior

U.S. Geological Survey

Prepared in cooperation with the Upper Loup and Lower Loup Natural Resources Districts and 

the Nebraska Environmental Trust

Groundwater Discharge Characteristics for Selected 

Streams Within the Loup River Basin, Nebraska, 2014–16

Scientific Investigations Report 2018–5093
Cover. Photograph of groundwater discharging from Pliocene gravel deposits near the South Loup 

River, Custer County, Nebraska. Photograph by Chris Hobza, U.S. Geological Survey.
Groundwater Discharge Characteristics 

for Selected Streams Within the Loup River 

Basin, Nebraska, 2014–16

By Christopher M. Hobza and Aaron R. Schepers

Prepared in cooperation with the Upper Loup and Lower Loup Natural Resources 

Districts and the Nebraska Environmental Trust

Scientific Investigations Report 2018–5093

U.S. Department of the Interior

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

RYAN K. ZINKE, Secretary

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2018

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Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials 

as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested citation:

Hobza, C.M., and Schepers, A.R., 2018, Groundwater discharge characteristics for selected streams within the Loup 

River Basin, Nebraska, 2014–16: U.S. Geological Survey Scientific Investigations Report 2018–5093, 50 p., https://

doi.org/10.3133/sir20185093.

ISSN 2328-0328 (online)
iii

Contents

Acknowledgments........................................................................................................................................vi

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

Introduction.....................................................................................................................................................2

Purpose and Scope ..............................................................................................................................2

Study Area Description........................................................................................................................3

Basin and Flow Characteristics of Loup River Basin Streams......................................................4

Geologic Setting....................................................................................................................................6

Approach and Methods................................................................................................................................7

Methods Used to Describe Spatial Characteristics of Groundwater Discharge.......................7

Stream Reconnaissance Methods ...........................................................................................7

Aerial Thermal Infrared Imagery Methods............................................................................12

Aerial Thermal Infrared Imagery Collection.................................................................13

Image Calibration..............................................................................................................14

Orthorectification..............................................................................................................16

Thermal Infrared Imagery Analysis ...............................................................................16

Methods Used to Describe Temporal Characteristics of Groundwater Discharge.................17

Groundwater Discharge Characteristics for Streams in the Loup River Basin ................................17

South Loup River and North Fork South Loup River......................................................................18

Upper South Loup River and North Fork South Loup River.................................................18

Middle South Loup River ..........................................................................................................19

Lower South Loup River............................................................................................................27

Dismal River.........................................................................................................................................28

Upper Dismal River....................................................................................................................28

Lower Dismal River....................................................................................................................32

North Loup River.................................................................................................................................37

Middle Loup River...............................................................................................................................40

Primary Controls on Groundwater Discharge Characteristics Within the Loup River Basin .........44

Summary........................................................................................................................................................45

References Cited..........................................................................................................................................46

Figures

1. Map showing study area, selected stream reaches, and streamflow-gaging

stations, Loup River Basin, Nebraska .......................................................................................3

2. Graph showing flow duration curves for selected streamflow-gaging stations,

Loup River Basin, Nebraska........................................................................................................5

3. Map showing stream reconnaissance locations, self-logging temperature

sensor locations, and reaches where aerial thermal infrared imagery was

collected along the South Loup River and the North Fork South Loup River, 

Nebraska........................................................................................................................................8

4. Map showing stream reconnaissance locations, self-logging temperature

sensor locations, and reaches where aerial thermal infrared imagery was

collected along the Dismal River, Nebraska ............................................................................9
iv

5. Map showing stream reconnaissance locations, self-logging temperature

sensor locations, and reaches where aerial thermal infrared imagery was

collected along the North Loup River, Nebraska ..................................................................10

6. Field photographs of a hydraulic potentiomanometer.........................................................13

7. Graph showing measured streamflow and the estimated density of focused

groundwater discharge points along the upper and middle South Loup River

reaches and North Fork South Loup River .............................................................................19

8. Map showing example aerial thermal infrared imagery collected in 

November 2015............................................................................................................................21

9. Graph showing downstream temperature profiles of the upper South Loup River

and the North Fork South Loup River, above the South Loup River at Arnold,

Nebraska, streamflow-gaging station.....................................................................................23

10. Graphs showing South Loup River at Arnold, Nebraska, streamflow-gaging

station and nearby observation well .......................................................................................24

11. Graph showing downstream temperature profile for the middle South Loup River

created from aerial thermal infrared imagery collected December 2–3, 2015.................25

12. Graph showing downstream temperature profile for the middle and lower South

Loup River created from aerial thermal infrared imagery collected November

23–24, 2015 ...................................................................................................................................25

13. Map showing example aerial thermal infrared imagery from the middle South

Loup River, December 2015.......................................................................................................26

14. Photographs showing two focused groundwater discharge points along the

middle South Loup River............................................................................................................27

15. Graph showing groundwater-level elevation in the South Loup River at the

Pressey Park recorder well and nearby streamflow-gaging station.................................28

16. Graph showing measured streamflow and the estimated density of focused

groundwater discharge points along the lower South Loup River.....................................29

17. Graphs showing South Loup River at Saint Michael, Nebraska,

streamflow-gaging station and nearby observation well ....................................................30

18. Graph showing measured streamflow and the estimated density of focused

groundwater discharge points along the Dismal River........................................................31

19. Photographs of example focused groundwater discharge points along the upper

Dismal River.................................................................................................................................32

20. Map showing example aerial thermal infrared image of Dismal River, December

2015. Photograph of the focused vertical flow conduit identified can be seen in

figure 19A.....................................................................................................................................33

21. Graph showing downstream temperature profile of the upper Dismal River

created from aerial thermal infrared imagery collected December 3–4, 2015.................34

22. Graph showing downstream temperature profile of the lower Dismal River

created from aerial thermal infrared imagery collected November 19–20, 2016.............35

23. Graphs showing Dismal River near Thedford, Nebraska, streamflow-gaging

station and nearby observation well .......................................................................................36

24. Graph showing measured streamflow and the estimated density of focused

groundwater discharge points along the North Loup River................................................37

25. Graph showing downstream temperature profile of the North Loup River created 

from aerial thermal infrared imagery collected November 19–20, 2016............................38

26. Map showing example aerial thermal infrared image of the North Loup River,

November 2016............................................................................................................................39
v

27. Graphs showing North Loup River at Brewster, Nebraska, streamflow-gaging

station and nearby observation well from May 2015 to April 2018.....................................41

28. Graphs showing North Loup River at Taylor, Nebraska, streamflow-gaging

station and nearby observation well from August 2015 to January 2018..........................42

29. Graphs showing Middle Loup River at Dunning, Nebraska, streamflow-gaging

station and nearby observation well from August 2015 to January 2018..........................43

Tables

1. Flow and basin characteristics above six streamflow-gaging stations within the

Loup River Basin, Nebraska........................................................................................................5

2. Streamflow measurement, stream reconnaissance, and self-logging

temperature sensor locations ..................................................................................................11

3. Site number, geographic location, and selected well construction data for

observation wells drilled near streamflow-gaging stations................................................15

4. Summary statistics for stream temperature, streambed temperature, and

hydraulic gradient collected along the North Fork South Loup, South Loup,

Dismal, and North Loup Rivers, Nebraska, August 2014, August or September

2015, and August 2016................................................................................................................20

Conversion Factors

U.S. customary units to International System of Units

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 4,047 square meter (m2)

acre 0.4047 hectare (ha)

acre 0.4047 square hectometer (hm2) 

acre 0.004047 square kilometer (km2)

Flow rate

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

gallon per minute (gal/min) 0.06309 liter per second (L/s)

Hydraulic gradient

foot per foot (ft/ft) 1 meter per meter (m/m)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

 °F = (1.8 × °C) + 32.
vi

Datum

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Elevation, as used in this report, refers to distance above the vertical datum.

Abbreviations

ELM Elkhorn-Loup groundwater-flow Model

GIS geographic information system

GNSS Global Navigation Satellite Systems

GPS Global Positioning System

GSD ground sample distance

IMP integrated management plan

NRD Natural Resources District

NWIS National Water Information System

OPUS Online Positioning User Service

RMSE root mean square error

TIR thermal infrared

USGS U.S. Geological Survey

Acknowledgments

We thank Anna Baum, general manager at the Upper Loup Natural Resources District, and Tylr 

Naprstek, assistant manger at the Lower Loup Natural Resources District, for their assistance 

in grant writing, administration, and landowner coordination. We also thank Kyle Charron, Kyle 

Yrkoski, and Taylor Spencer for their assistance with landowner coordination and data collection 

during the stream reconnaissance. We thank landowners for graciously allowing access to their 

property during data collection.
Groundwater Discharge Characteristics for Selected 

Streams Within the Loup River Basin, Nebraska, 2014–16

By Christopher M. Hobza1 and Aaron R. Schepers2

1

U.S. Geological Survey.

2

Cornerstone Mapping, Inc.

Abstract

Streams in the Loup River Basin are sensitive to groundwater withdrawals because of the close hydrologic connection between groundwater and surface water. Groundwater 

discharge is the primary component of streamflow in the 

Loup River Basin and constitutes more than 90 percent of 

streamflow in the central part of the Sand Hills. To improve 

the understanding of geologic controls and various climatic 

and land-use changes on groundwater discharge, the U.S. Geological Survey (USGS), in cooperation with the Upper Loup 

Natural Resources District (NRD), the Lower Loup NRD, 

and the Nebraska Environmental Trust, studied the spatial 

and temporal characteristics of groundwater discharge within 

the Loup River Basin. This report documents the methods of 

data collection and analysis, which include the collection of 

approximately 350 river miles of aerial thermal infrared imagery and continuous groundwater-level and temperature data 

from six streamflow-gaging stations within the Loup River 

Basin.

The results from the stream reconnaissance and examination of aerial thermal infrared imagery demonstrated the 

influence of the surficial and subsurface geology on the spatial 

characteristics of groundwater discharge to streams in the 

Loup River Basin. At the headwaters of the South Loup River, 

streamflow is sustained and increased from focused groundwater discharge emanating from Quaternary deposits at many 

small (less than 0.1 cubic foot per second) focused points. The 

volume of water produced from this dense network of focused 

groundwater discharge points along the North Fork South 

Loup River is sufficient to provide approximately 40 percent 

of the flow measured at the South Loup River at Arnold, 

Nebraska streamflow-gaging station (USGS station 06781600) 

during the irrigation season. Approximately 5 miles downstream from the South Loup River at Arnold, Nebr., streamflow-gaging station, the river incises into Pliocene-age sand 

and gravel deposits, which provide additional groundwater 

discharge to the stream. The streamflow of the South Loup 

River increases by a factor of 5 across a 62-mile reach of the 

middle South Loup River.

Increases in streamflow along the upper Dismal River 

result from a dense network of focused groundwater discharge 

points within semiconsolidated Pliocene-age deposits. Below 

the Dismal River near Thedford, Nebr., streamflow-gaging station (USGS station 06775900), the Dismal River incises into 

the Ogallala Formation over a short reach before flowing over 

coarser, more permeable Quaternary-age alluvial deposits. Diffuse groundwater discharge sustains and increases the streamflow of the lower Dismal River in this reach.

Groundwater sapping was evident on some stream 

reaches and has increased the size and flow of focused groundwater discharge points. Previous researchers have documented 

streambed incision and groundwater sapping on the upper 

Dismal River that have created and enlarged focused groundwater discharge points capturing additional groundwater. 

Similar processes appear to have played a role in the formation 

of larger focused groundwater discharge points, which sustain 

the flow of the middle South Loup River. The constant flow of 

groundwater into the South Loup River has removed finergrained Quaternary sediments and further exposed Plioceneage gravel deposits. Headward erosion is evident where some 

of the large focused groundwater discharge points have incised 

their own draws and terminate in bowl-like depressions away 

from the stream.

Within the Loup River NRDs, the percentage of groundwater-irrigated land in a stream basin is one factor that affects 

groundwater discharge to streams. A striking example was at 

the South Loup River at Saint Michael, Nebr., groundwater 

and streamflow-gaging station (USGS station 06784000) 

where the shallow groundwater levels declined below the level 

of the stream during the middle to late part of the growing 

season (July to September) when consumptive groundwater 

use was at its peak. The South Loup River Basin above the 

South Loup River at Saint Michael, Nebr., streamflow-gaging 
2 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

station has the highest percentage of groundwater-irrigated 

row crops of all the basins examined in this study. Continuous 

groundwater and surface-water levels measured at the North 

Loup River at the Taylor, Nebr., streamflow-gaging station 

(USGS station 06786000) indicate that the stream is receiving 

groundwater throughout the year; however, when consumptive groundwater use peaks during the middle to late part of 

the growing season (July to September), the difference in 

elevation between the groundwater level and the stream elevation decreases, which indicates a reduction in the amount of 

groundwater discharge received.

Introduction

The State of Nebraska (fig. 1) requires a sustainable 

balance between long-term water supplies and uses of groundwater and surface water (Ostdiek, 2009) and requires Natural 

Resources Districts (NRDs) to include the impact of groundwater withdrawals on surface-water systems as part of their 

integrated management plan (IMP). Recent droughts across 

the State of Nebraska (2000–6; 2012–13) have amplified 

concerns about (1) the long-term sustainability of groundwater 

and surface-water resources and (2) the effect of groundwater 

withdrawals on streamflow in Nebraska. The Upper Loup 

NRD and Lower Loup NRD (fig. 1; collectively referred to 

as the “Loup River NRDs,” in conjunction with the Nebraska 

Department of Natural Resources, have developed voluntary 

IMPs for groundwater and surface water (Lower Loup Natural 

Resources District, 2016; Upper Loup Natural Resources District, 2016). In an effort to support the IMPs, the Loup River 

NRDs are using scientifically based management practices and 

groundwater and surface-water monitoring to guide current 

and future management decisions. Towards those ends, the 

development of water-resource management tools, such as the 

Elkhorn-Loup Model (ELM; Peterson and others, 2008; Stanton and others, 2010), and long-term data collection are key 

components of their water management programs. Large parts 

of the Loup River NRDs are in the Sand Hills (fig. 1), which 

overlies the thickest parts of the High Plains aquifer and is 

drained by the Loup River system, the largest tributary of the 

lower Platte River, which supplies water to large municipalities in the eastern part of Nebraska (Hobza and others, 2011, 

2012).

Streams in the Loup River Basin are sensitive to groundwater withdrawals because of the close hydrologic connection 

between groundwater and surface water (Stanton and others, 

2010). Pumping from aquifers that are hydrologically connected to surface-water bodies can have a substantial effect by 

reducing the groundwater discharge to surface water (Winter 

and others, 1998). An evaluation of any groundwater management strategy needs to involve consideration of potential 

impacts on surface-water resources. Changes in streamflow 

can affect riparian habitat and water available for recreational, 

agricultural, commercial, and domestic uses (Peterson and 

others, 2008). In addition, streamflow affects the sustainability 

of wet meadows to support livestock, migratory and resident 

birds, and other biota. Currently (2018), the complexity of this 

system and the interaction between surface-water and groundwater resources are not fully understood.

Groundwater discharge is the primary component of 

streamflow in the Loup River Basin and constitutes more than 

90 percent of streamflow in the central part of the Sand Hills 

(Szilagyi and others, 2003). Groundwater discharge has been 

estimated using base flow separation methods (Stanton and 

others, 2010) and seepage run data (Peterson and Strauch, 

2007). The base flow separation technique estimates the 

amount of groundwater discharge as a percentage of total 

streamflow for the stream reach above a streamflow-gaging 

station. Groundwater discharge also is estimated by measuring surface-water flow at two places, as much as 15 miles 

(mi) apart, in a stream reach, a practice commonly known as 

a seepage run (Harvey and Wagner, 2000; Rosenberry and 

LaBaugh, 2008). Differences in measured streamflow are 

attributed to groundwater discharge (positive difference or 

increase in flow is a gaining stream) or groundwater recharge 

(negative difference or decrease in flow is a losing stream). 

A groundwater flow model simulates on a cell-by-cell basis, 

but is calibrated to streamflow observation points that can 

be miles apart. As a result, large reaches are often integrated 

together.

Streams in the Loup River Basin are known to receive a 

combination of focused discharge (groundwater discharge as 

springs) and diffuse discharge (relatively uniform discharge 

from an underlying aquifer). These areas of focused groundwater discharge have not been mapped extensively; furthermore, the effect of various climatic and land-use changes 

on groundwater discharge patterns is currently (as of 2018) 

unknown. To improve the understanding of geologic controls, 

such as formation permeability, and various climatic and landuse changes on groundwater discharge, the U.S. Geological 

Survey (USGS), in cooperation with the Upper Loup NRD, 

the Lower Loup NRD, and the Nebraska Environmental Trust, 

collected aerial thermal infrared (TIR) imagery covering about 

350 mi of streams and recorded water level and temperature 

at six streamflow-gaging stations within the Loup River Basin 

(fig. 1). The data collected for this study will improve the 

understanding of geologic controls on groundwater discharge 

and the effects of land use on streamflow.

Purpose and Scope

The purpose of this report is to describe and identify 

potential drivers of the spatial and temporal characteristics of 

groundwater discharge within the South Loup River, Dismal River, and North Loup River Basins (fig. 1). This report 

documents the methods of data collection and analysis, which 

include the collection of approximately 350 river miles of 

aerial TIR imagery during 2015–16 and continuous groundwater-level and temperature data from six streamflow-gaging 
Introduction 3

stations within the Loup River Basin during 2014–16. These 

datasets were collected to improve the understanding of geologic controls and spatial patterns of groundwater discharge. 

The potential land-use and groundwater irrigation effects on 

the temporal variability of groundwater discharge also were 

evaluated. The aerial TIR imagery and water-level and temperature data collected are intended to enhance the understanding 

of groundwater discharge characteristics and to complement 

a seepage run (Peterson and Strauch, 2007) completed during 

the ELM phase 1 study (Peterson and others, 2008).

Study Area Description

The study area for this report is the Loup River NRDs; 

however, data collection was focused on the highlighted 

reaches of the North Fork South Loup, South Loup, North 

Loup, and Dismal Rivers (fig. 1). Physiography and land 

use differ across the study area. The Sand Hills covers about 

56 percent of the 9.4 million-acre study area (fig. 1; Conservation and Survey Division, University of Nebraska-Lincoln, 

2017b). The Sand Hills is an area with grass-covered eolian 

fig 01

Lower Loup Natural Resources District

Upper Loup Natural Resources District

Middle Loup River

Goose Creek

Arnold

Taylor

Dunning

Thedford

Brewster

Mullen

Ravenna

Platte River

Elkhorn River

South Loup River

Loup River

North Platte River

South Platte River

Dismal River

102° 101° 100° 99° 98°

42°

41°

40°

EXPLANATION

Sand Hills

Aerial thermal infrared imagery collected

U.S. Geological Survey streamflow-gaging station

NEBRASKA

Base from U.S. Census Bureau, digital data, 2005, 1:100,000

Lambert Conformal Conic projection

Standard parallels 40° N. and 43° N., central meridian 100° W.

Horizontal coordinate information is referenced to the 

North American Datum of 1983 (NAD 83)

Sand Hills outline from Conservation and Survey Division, 

University of Nebraska-Lincoln, 2017b

Elkhorn-Loup model area

0 60 MILES

0 30 60 KILOMETERS

North Fork 

South Loup River

Saint Michael

06781600

06784000

06785500

06786000

06775900

06775500

Figure 1. Study area, selected stream reaches, and streamflow-gaging stations, Loup River Basin, Nebraska.
4 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

dunes that is dominated by undeveloped rangeland primarily 

used for cattle grazing (Bleed and Flowerday, 1989). The dissected loess plains, to the east of the Sand Hills, cover 34 percent of the study area (Conservation and Survey Division, 

University of Nebraska-Lincoln, 2017b). The dissected loess 

plains are characterized by nearly rolling to steep topography 

with flat upland tables that support a mix of row crops and 

rangeland. About 10 percent of the study area is classified as 

valleys, which are flat areas generally along rivers and larger 

tributaries (Conservation and Survey Division, University of 

Nebraska-Lincoln, 2017b). Valleys are generally well suited 

for irrigated row-crop agriculture, and corn and soybeans are 

the principal crop types (Strauch and Linard, 2009).

Groundwater use differs across the study area, and the 

number of irrigated acres increases from west to east. In 

2013, the Upper Loup NRD reported having 71,500 irrigated 

acres within its 4.3 million-acre district (Nebraska Association of Resource Districts, 2013b), whereas the Lower Loup 

NRD reported having 1.2 million irrigated acres within its 

5.1 million-acre district (Nebraska Association of Resource 

Districts, 2013a). Based on 2000 countywide estimates, the 

highest concentration of groundwater pumpage within the 

study area was in Custer and Buffalo Counties (not shown), 

near the lower reaches of the South Loup River (Hutson and 

others, 2004).

The climate in the study area is typical of continental 

midlatitude locations (Strauch and Linard, 2009), characterized by cold winters and warm summers. Precipitation within 

the study area increases from west to east. The average annual 

precipitation from 1981 to 2010 in Mullen, Nebraska (fig. 1), 

was 21 inches per year (in/yr). During that same period, 

precipitation near Ravenna, Nebr. (fig. 1), averaged 26.5 in/yr 

(National Climatic Data Center, 2017). Potential evaporation, 

similar to precipitation, is greatest during the crop-growing 

season of April through September. Potential evaporation 

peaks in July and often exceeds precipitation (Chen and others, 2003). Most of the annual groundwater recharge is in 

the winter and early spring when precipitation is greater than 

evapotranspiration. Mean annual evapotranspiration in the 

study area ranges from 19 in/yr in the east to 16 in/yr in the 

west (Dugan and Zelt, 2000).

Unique physical characteristics of the Sand Hills 

resulted in a substantial amount of meteoric water being 

stored in the groundwater system (McGuire and others, 2012; 

Stanton and others, 2011). Highly permeable soils allow 

water to infiltrate even during heavy precipitation, resulting in higher recharge rates when compared to the dissected 

loess plains to the east and fewer runoff-induced high-flow 

events. Based on a soil-water balance model approach, Stanton and others (2011) estimated annual recharge rates for the 

Sand Hills at 2.3 in/yr. Recharge in the area to the east of the 

Sand Hills is variable; in areas where the dissected loess plains 

dominate, recharge generally decreases to 0.5 in/yr or less 

because of the low permeability of loess deposits (Stanton 

and others, 2011).

Basin and Flow Characteristics of Loup River 

Basin Streams

Streams within the Loup River Basin have several unique 

characteristics that set them apart from other streams within 

Nebraska. The headwaters for most major streams within 

the Loup River Basin are within the Sand Hills where runoff 

to streams is limited by the dune landscape and permeable 

topsoil (Bentall and Shaffer, 1979), which results in remarkably constant streamflow dominated by groundwater discharge 

(base flow). Basin and flow characteristics for six streamflowgaging stations are presented in table 1, and flow duration 

curves are presented in figure 2. Only 15 percent of the basin 

above the South Loup at Saint Michael, Nebr., streamflowgaging station (USGS station 06784000; hereinafter referred 

to as “Saint Michael streamflow-gaging station”) (table 1) 

is covered by the Sand Hills (fig. 1). Consequently, this 

streamflow-gaging station also had the highest ratio of 95th 

and 5th percentile of ranked daily mean flow (6.44), which 

indicates that the Saint Michael streamflow-gaging station 

can experience higher flows during runoff events and lower 

flows in August and September when evapotranspiration rates 

and groundwater irrigation demands are largest. In contrast, 

the Dismal River near Thedford, Nebr., streamflow-gaging 

station (USGS station 06775900; hereinafter referred to as the 

“Dismal River streamflow-gaging station”) is 100 percent contained within the Sand Hills (fig. 1) and recorded the lowest 

ratio of the 95th and 5th percentile of ranked daily mean flow 

(1.21), which indicates that seasonal climatic variations have 

little effect on streamflow.

Two streamflow-gaging stations on the North Loup 

River had higher ratios of 95th and 5th percentile of ranked 

daily mean flow when compared to the Middle Loup River at 

Dunning, Nebr. (USGS station 06775500; hereinafter referred 

to as the “Middle Loup River at Dunning streamflow-gaging 

station”), and Dismal River streamflow-gaging stations to the 

west (table 1; fig. 1). This comparison is consistent with the 

findings of Chen and others (2003), who compared discharge 

records of streams within the western and eastern parts of 

the Sand Hills. Streams in the eastern part of the Sand Hills 

were more sensitive to periods of drought than streams in the 

western part. Chen and others (2003) attributed this difference 

to the thicker unsaturated zones, which are able to dampen 

varying seasonal and annual climatic effects on streamflow, in 

the Middle Loup and Dismal River Basins.

As streams flow out of the Sand Hills, groundwater discharge, which Stanton and others (2010) define as base flow, 

ranges from about 80 to 95 percent of total streamflow. When 

these streams cross the dissected and loess-covered plains to 

the south and east, they receive less groundwater discharge 

and more surface runoff. The groundwater discharge fraction 

of streamflow drops to between about 60 and 80 percent. As 

streams flow eastward, and the percentage of area covered by 

the Sand Hills decreases, the percentage of irrigated cropland increases because soils developed in the dissected loess 
Introduction 5

Table 1. Flow and basin characteristics above six streamflow-gaging stations within the Loup River Basin, Nebraska.

[Q95, 95th percentile of ranked daily mean flows over the period of record; Q5, 5th percentile of ranked daily mean flows over the period of record; Q95/Q5, 

the ratio between the 95th percentile of ranked daily mean flows and the 5th percentile of ranked daily mean flows over the period of record; Sand Hills area, 

percentage of associated river basin covered by the Sand Hills; Land-use area, percentage of associated river basin; I, irrigated cropland; DL, dryland crops; 

R/U, rangeland, undeveloped; WW, wetlands or water; D, developed; Nebr., Nebraska]

Station name Station 

number

Period of 

record 

Q951

(cubic foot 

per second)

Q51

(cubic foot 

per second)

Q95/Q5 

Sand Hills 

area2

(percent)

Land-use area3 (percent)

I DL R/U WW D 

Middle Loup River at Dunning, Nebr. 06775500 2006–15 577 408 1.41 98.4 0.05 0.03 95.18 4.34 0.39

Dismal River near Thedford, Nebr. 06775900 2006–15 250 207 1.21 100 0.14 0.08 97.29 2.38 0.11

South Loup River at Arnold, Nebr. 06781600 2011–15 63.6 13.3 4.78 57.9 10.54 2.91 83.63 1.02 1.89

South Loup River at Saint Michael, Nebr. 06784000 2006–15 399 62 6.44 14.6 21.22 2.47 70.82 1.52 3.96

North Loup River at Brewster, Nebr. 06785500 2010–15 789 319 2.47 92.7 0.27 0.06 94.31 4.98 0.38

North Loup River at Taylor, Nebr.4 06786000 2006–15 942 240 3.93 91.6 0.56 0.15 94.03 4.64 0.62

1

 U.S. Geological Survey, 2017.

2

From Conservation and Survey Division, University of Nebraska, 2017b.

3

Land-use data from 2009 in Peterson and others, 2016.

4

Flows affected by diversion into Taylor-Ord Canal.

1

10

100

1,000

10,000

0 20 40 60 80 100

Discharge, in cubic feet per second

Percentage of time discharge is equaled or exceeded

06775500 Middle Loup River at Dunning

06775900 Dismal River near Thedford

06781600 South Loup River at Arnold

06784000 South Loup River at Saint Michael

06785500 North Loup River at Brewster

06786000 North Loup River at Taylor

EXPLANATION

Figure 2. Flow duration curves for selected streamflow-gaging stations, Loup River Basin, Nebraska.
6 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

plains and valleys are more conducive to row-crop production. 

Increased groundwater pumping during the growing season 

reduces the amount of groundwater discharge received by 

streams (Peterson and others, 2008; Stanton and others, 2010), 

which affects the flow characteristics shown in figure 2 and 

table 1.

Compared to other streams within Nebraska, streams 

in the Sand Hills are relatively young, and their drainage 

networks still may be developing (Maher and others, 2003). 

Using radiocarbon age dates (Ahlbrandt and others, 1983), 

researchers have estimated that the modern Dismal River 

valley is 3,000 years old or less (Swinehart and Diffendal, 

1989), and the channel of the Dismal River has incised at a 

rate of 3.3 feet (ft) per 100 years over the past 1,500 years 

(Maher and others, 2003). Groundwater sapping, which is the 

process where headward migration of the stream or tributary 

channels happens in response to erosion caused by constant 

discharge of groundwater, is still evident today. Guhman and 

Pederson (1992) studied a reach of the Dismal River above the 

Dismal River near Thedford, Nebr., streamflow-gaging station 

and noted focused groundwater discharge and “boiling” sand 

springs that were actively eroding sediments. Groundwater 

sapping has resulted in the formation of amphitheater like 

cavities and headward erosion of tributaries. These active processes indicate that the Dismal River drainage network is still 

developing and potentially capturing additional groundwater, 

which increases streamflow.

Geologic Setting

The study area overlies the High Plains aquifer system, 

where saturated thicknesses can exceed 1,000 ft (McGuire and 

others, 2012). The High Plains aquifer system is considered 

to be inclusive of all hydrologically connected Tertiary- and 

Quaternary-age units. According to Gutentag and others 

(1984), the Tertiary-age units include the fractured part of the 

Oligocene-age Brule Formation of the White River Group 

(hereinafter referred to as “the Brule”), the Miocene-age 

Arikaree Group (hereinafter referred to as “the Arikaree”), and 

the Miocene-age Ogallala Formation (hereinafter referred to 

as “the Ogallala”). The Quaternary-age units include alluvial 

and eolian deposits. The unfractured Brule or, where the Brule 

is not present, the Cretaceous Pierre Shale generally form the 

base of aquifer. The base of aquifer surface generally dips 

8 feet per mile (ft/mi) east and contains paleovalleys that also 

drain eastward (Peterson and others, 2008).

The geologic history relevant to this study begins about 

70 million years ago with the deposition of Cretaceous-age 

sediments. During the Cretaceous period, much of the study 

area was covered by a shallow inland sea, where marine sediments were deposited to form the Dakota Sandstone, Carlile 

Shale of the Colorado Group, the Niobrara Formation of the 

Colorado Group (hereinafter referred to as “the Niobrara”), 

and Pierre Shale. After regression of the Cretaceous sea, uplift 

resulted in the formation of the Chadron and Cambridge 

arches trending from northwest to southeast across the study 

area (Swinehart and others, 1985). Subsequent fluvial erosion 

removed as much as 1,800 ft of the Cretaceous section and 

created a structural low over the previously uplifted region.

In the western part of the study area, the unfractured 

Brule forms the base of aquifer. The Brule is a massive siltstone consisting of primarily eolian silt but also containing 

some alluvium. Deposits of volcaniclastic sediments and some 

ash derived from volcanic complexes from the western United 

States make up most of its volume in some localities (Souders, 

2000). When unfractured, the Brule is impermeable relative to 

the overlying units.

Overlying the Brule is the Arikaree, which is largely 

limited to the western part of the study area but may exist in 

paleovalleys to the east (Swinehart and Diffendal, 1989). The 

Arikaree is a massive, very fine- to fine-grained sandstone 

with localized beds of volcanic ash, silty sand, and sandy 

clay (Darton, 1903; Condra and Reed, 1943). The Arikaree is 

considered part of the High Plains aquifer system; however, it 

does not yield large quantities of water to wells (Gutentag and 

others, 1984). Within the study area, the Arikaree typically is 

not used as a water source.

The Ogallala is the principal geologic unit in the High 

Plains aquifer system and reaches a thickness of 800 ft beneath 

the study area (Diffendal, 1991). The Ogallala consists of a 

poorly sorted mixture of sand, silt, clay, and gravel (Condra 

and Reed, 1943). The Ogallala is generally unconsolidated 

or weakly consolidated but can contain layers of sandstone 

cemented by calcium carbonate or limestone. When covered 

by younger deposits, the Ogallala has not been subdivided into 

stratigraphic units recognized in other areas because of the 

difficulty correlating these units in the subsurface (Swinehart 

and others, 1985). The Ogallala was deposited by aggrading streams that filled paleovalleys that were eroded into 

pre-Ogallala rocks (Swinehart and others, 1985). The base 

of the Ogallala is a complex surface formed from multiple 

episodes of erosion. The locations of Ogallala paleovalleys 

have been suggested by previous researchers (Swinehart and 

Diffendal, 1989; Swinehart and others, 1985), but these may 

represent only a fraction of the drainage network that existed 

during Miocene time. Much of the deposition was restricted 

to valleys along drainage systems originating from mountains 

in Wyoming and Colorado (Swinehart and others, 1985), but 

deposition may have been on broad low-relief plains as well 

(Swinehart and Diffendal, 1989).

An unconformity of at least 1.5 million years separates 

the Ogallala from the Pliocene-age Broadwater Formation and 

the Pleistocene-age Long Pine Formations (Swinehart and 

Diffendal, 1989); the Pleistocene Long Pine Formation unit 

name is used by the University of Nebraska-Lincoln, Conservation and Survey Division but is not formally recognized 

by the USGS. These fluvial sediments, eroded from central 

Wyoming and northern Colorado (Stanley and Wayne, 1972), 

are unevenly deposited and preserved, contain coarse sand and 

gravel separated by finer-grained deposits, and cover the Ogallala through much of the study area. Swinehart and Diffendal 
Approach and Methods 7

(1989) have identified an area within Thomas, Hooker, and 

McPherson Counties (not shown in fig. 1) where Pliocene-age 

gravels are absent. In the study area, Pliocene- and Pleistocene-age fluvial deposits average 50 ft in thickness, but can 

be as thick as 300 ft (Swinehart and Diffendal, 1989), and 

are hydrologically connected with the underlying Ogallala. 

The Broadwater and Long Pine Formations, as parts of the 

High Plains aquifer system, are used as a water source, where 

present. Distinguishing the age of some of these deposits is 

difficult, if not impossible (Condon, 2005).

Quaternary deposits, which consist of eolian sand, 

wind-deposited silt, clay, and fine-grained sand (together 

called loess), and alluvial deposits of sand and gravel cover 

much of the study area. Researchers (Ahlbrandt and others, 

1983; Loope and Swinehart, 2000) have documented the 

radiocarbon ages of organic material within eolian deposits 

to reconstruct dune activity during the Holocene. Results 

indicated a complex history of deposition within streams and 

valleys and documented major periods of dune mobilization 

and activity 6,000 and 3,000 years before present. Quaternary-age alluvial sand and gravel are in modern stream valleys and often are used as a water source. Where thicknesses 

are sufficient, these coarse deposits can sustain well withdrawals of more than 1,000 gallons per minute (63 liters per 

second) (Peterson and others, 2008). Quaternary deposits can 

be as thick as 700 ft but typically are 150 to 300 ft thick and 

are absent from uplands near the Niobrara River (not shown) 

at the northern border of the ELM area (fig. 1; Conservation and Survey Division, University of Nebraska-Lincoln, 

2017a).

Approach and Methods

This section of the report describes the methods of data 

collection and analysis used to improve upon the understanding of the spatial and temporal characteristics of groundwater 

discharge for streams in the Loup River Basin. The methods 

used to describe the spatial characteristics of groundwater 

discharge are divided into two sections. The first section 

describes the stream reconnaissance methods, which provided additional field data, including discharge, stream and 

streambed temperature, and hydraulic potentiomanometer 

(referred to hereinafter as “potentiomanometer”) measurements to support interpretations of the aerial TIR imagery. The 

next subsection describes the aerial TIR imagery methods, 

which provide information on data collection, processing, and 

interpretation of approximately 350 river miles of aerial TIR 

imagery, which were used to describe the spatial patterns of 

groundwater discharge. The methods used to describe temporal characteristics of groundwater discharge for data collection and analysis, which include the collection and analysis 

of water-level and temperature data at six streamflow-gaging 

stations, are described in a separate subsection.

Methods Used to Describe Spatial 

Characteristics of Groundwater Discharge

Stream reaches where additional information on groundwater discharge was needed were selected by the Loup River 

NRDs to support their voluntary IMPs. These reaches included 

parts of the South Loup, Dismal, and North Loup Rivers 

(fig. 1). Within these reaches, the stream reconnaissance 

focused on specific locations where aerial TIR imagery was 

collected. The collection of discharge, point-scale stream and 

streambed temperature, and potentiomanometer measurements 

would provide useful data in combination with the aerial TIR 

imagery to assess spatial patterns in groundwater discharge.

Stream Reconnaissance Methods

The objective of the stream reconnaissance during 2014–

16 was to collect additional field data at selected locations 

along the South Loup (fig. 3), Dismal (fig. 4), and North Loup 

Rivers (fig. 5) to support interpretations of aerial TIR imagery. 

Location selection involved examining several data sources 

including geologic maps, which could indicate changes in 

subsurface geology adjacent to the stream; aerial photography 

for features such as active gravel mines and tributaries; and 

historical streamflow data. The stream reconnaissance was 

completed during the summer months when the difference 

between stream temperatures and streambed temperatures 

would be largest. During this time of year, cooler streambed 

temperatures would indicate areas of focused groundwater 

discharge.

Streamflow was measured at selected locations (figs. 3, 

4, and 5) using a handheld acoustic Doppler velocimeter in 

accordance with the guidelines and recommendations stated in 

Turnipseed and Sauer (2010) and the USGS Office of Surface 

Water (U.S. Geological Survey, 2004). Streamflow measurements are given in table 2 and stored in the USGS National 

Water Information System (NWIS; U.S. Geological Survey, 

2017). Streamflow measurements collected in 2006 as part of 

a seepage run used in the ELM phase 2 groundwater model 

(Peterson and Strauch, 2007), are included in table 2 for comparison with streamflow measurements collected from 2014 

to 2016. One important difference between these two sets 

of streamflow measurements is the fact that the seepage run 

measurements (Peterson and Strauch, 2007) were collected 

in November, which likely represents base flow conditions 

because there was little precipitation over the study area before 

and during the time the measurements were made; therefore, 

there was little surface runoff to streams. Generally speaking, 

groundwater irrigation for row crops has ceased in September, 

giving impacted stream reaches time to recover. Furthermore, 

riparian vegetation in the study area was dormant this time of 

year, so transpiration of shallow groundwater by plants was 

minimal and did not affect groundwater discharge (Peterson 

and Strauch, 2007).
8 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

fig 03

Sand Hills

0.98-foot thermal infrared imagery

1.64-foot thermal infrared imagery

3.28-foot thermal infrared imagery

U.S. Geological Survey streamflow-gaging station and identifier

Stream reconnaissance and self-logging temperature 

sensor and identifier

Stream reconnaissance and identifier

Self-logging temperature sensor and identifier

"

North Loup River

Platte River

South Loup River

Middle Loup River

Ravenna

100°30' 100° 99°30' 99° 98°30'

41°30'

41°

40°30'

Lower Loup Natural Resources District

Upper Loup 

Natural Resources District

EXPLANATION

NEBRASKA

Pressey Park recorder well

0 12.5 25 MILES

0 12.5 25 KILOMETERS

SL1

SL2

SL4

SL3

M279

M276

L264

L246

L237

L229

Arnold

Saint Michael

Platte River

06781600

SL1

SL3

L246

Base from U.S. Census Bureau, digital data, 2005, 1:100,000

Lambert Conformal Conic projection

Standard parallels 40° N. and 43° N., central meridian 100° W.

Horizontal coordinate information is referenced to the 

North American Datum of 1983 (NAD 83)

Sand Hills outline from Conservation and Survey Division, 

University of Nebraska-Lincoln, 2017b

North Fork 

South Loup River

06781900 (installed July 2017)

06784000

06784000

Figure 3. Stream reconnaissance locations, self-logging temperature sensor locations, and reaches where aerial thermal infrared 

imagery was collected along the South Loup River and the North Fork South Loup River, Nebraska.
Approach and Methods 9

fig 04

"

"

"

Dismal River

North Loup River

Middle Loup River

North Fork 

Dismal River

Dunning

Thedford

Mullen

101° 100°30'

42°

41°30'

Lower Loup 

Natural Resources District

Upper Loup Natural Resources District

NEBRASKA

Base from U.S. Census Bureau, digital data, 2005, 1:100,000

Lambert Conformal Conic projection

Standard parallels 40° N. and 43° N., central meridian 100° W.

Horizontal coordinate information is referenced to the 

North American Datum of 1983 (NAD 83)

Sand Hills outline from Conservation and Survey Division, 

University of Nebraska-Lincoln, 2017b

South Fork

Dismal River

D1 T133

T134

D4 D5

T138

D7 06775500

06775900

06775900

D8

0 5 10 MILES

0 5 10 KILOMETERS

Sand Hills

1.64-foot thermal infrared imagery

3.28-foot thermal infrared imagery

U.S. Geological Survey streamflow-gaging station and identifier

Stream reconnaissance and self-logging temperature 

sensor and identifier

Self-logging temperature sensor and identifier

EXPLANATION

D1

D4

! !

!

!

!

!

!

Figure 4. Stream reconnaissance locations, self-logging temperature sensor locations, and reaches where aerial thermal infrared 

imagery was collected along the Dismal River, Nebraska.
10 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

fig 05

06786000

06785500

06786000

"

"

North Loup River

Middle Loup River

Calf Creek

Goose Creek

Calamus River

Taylor

Brewster

100°30' 100° 99°30'

42°

41°45'

Lower Loup 

Upper Loup Natural Resources District Natural Resources District

NEBRASKA

Base from U.S. Census Bureau, digital data, 2005, 1:100,000

Lambert Conformal Conic projection

Standard parallels 40° N. and 43° N., central meridian 100° W.

Horizontal coordinate information is referenced to the 

North American Datum of 1983 (NAD 83)

Sand Hills outline from Conservation and Survey Division, 

University of Nebraska-Lincoln, 2017b

0 5 10 MILES

0 5 10 KILOMETERS

TAYLOR-ORD CANAL DIVERSION DAM

NL1

T435

NL3 NL4

L428

L427

Sand Hills

3.28-foot thermal infrared imagery

Taylor-Ord Canal

U.S. Geological Survey streamflow-gaging station and identifier

Stream reconnaissance and temperature logger and identifier

Stream reconnaissance and identifier

Self-logging temperature sensor and identifier

EXPLANATION

T435

NL1

NL4

Figure 5. Stream reconnaissance locations, self-logging temperature sensor locations, and reaches where aerial thermal infrared 

imagery was collected along the North Loup River, Nebraska.
Approach and Methods 11

Table 2. Streamflow measurement, stream reconnaissance, and self-logging temperature sensor locations.[Streamflow measurement quality rating, good (2–5 percent error), fair (5–8 percent error), and poor (greater than 8 percent error); discharge measured in November 2006 and reported in Peterson and Strauch, 2007; Self-logging temperature sensor, x indicates a Hobo tidbit V2 temperature logger was deployed in this location during the collection of aerial thermal infrared imagery; Aerial thermal infrared resolution, spatial resolution of aerial thermal infrared imagery at site location; TIR, thermal infrared; R, river; ab, above; N, north; S, south; Nebr., Nebraska; o, degrees of latitude or longitude; ʹ, minutes of latitude or longitude; ʺ, seconds of latitude or longitude; --, indicates that no streamflow was measured or no temperature logger was deployed; cm, centimeter; bl, below; mi, mile; NW, northwest; m, meter; nr, near; W, west; NE, Nebraska; SE, southeast ]

Field 

identifier

Site 

number Station name Latitude Longitude Streamflow date

Streamflow 

(cubic 

foot per 

second)

Streamflow 

measurement 

quality 

rating

November

2006 

streamflow 

measurement 

(cubic foot 

per second)

Stream 

reconnaissance 

year

Self -

logging 

temperature 

sensor

Aerial 

TIR

Aerial TIR 

collection 

date

Upper South Loup River

SL1 413053100221401 South Loup R ab N Fork S Loup R at Hoagland, Nebr. 41o 30ʹ 53ʺ 100o 22ʹ 14ʺ 8/27/2015 3.3 Fair -- 2015 x 30 cm Dec. 2–3, 2015SL2 413055100220901 South Loup R bl N Fork S Loup R at Hoagland, Nebr. 41o 30ʹ 55ʺ 100o 22ʹ 09ʺ 8/27/2015 10.4 Good -- 2015 x 30 cm Dec. 2–3, 2015SL3 413027100183601 South Loup River 8 mi NW of Arnold, Nebr. 41o 30ʹ 27ʺ 100o 18ʹ 36ʺ 8/20/2014 11.2 Poor -- 2014 -- 30 cm Dec. 2–3, 2015SL4 412713100150801 South Loup River 3.5 mi NW of Arnold, Nebr. 41o 27ʹ 13ʺ 100o 15ʹ 08ʺ 8/19/2014 17.1 Good -- 2014 -- 30 cm Dec. 2–3, 2015

Middle South Loup River

M279 412202100050001 South Loup River M279 41o 22ʹ 02ʺ 100o 05ʹ 00ʺ 8/22/2014 45.1 Good 51 2014 x 50 cm Dec. 2–3, 2015M276 412101099595301 South Loup River M276 41o 21ʹ 01ʺ 99o 59ʹ 53ʺ 8/21/2014 57.5 Good 55.8 2014 x 50 cm Dec. 2–3, 2015L264 411134099422901 South Loup River L264 41o 11ʹ 34ʺ 99o 42ʹ 29ʺ 8/26/2015 92.8 Good 93 2015 x 1 m Nov. 23–24, 2015

Lower South Loup River

L246 410235099224501 South Loup River L246 41o 02ʹ 35ʺ 99o 22ʹ 45ʺ -- -- -- 115 -- x 1 m Nov. 23–24, 2015L237 405724099093301 South Loup River L237 40o 57ʹ 24ʺ 99o 09ʹ 33ʺ 8/28/2015 93.5 Fair 137 2015 -- 1 m Nov. 23–24, 2015L229 410131098534601 South Loup River L229 41o 01ʹ 31ʺ 98o 53ʹ 46ʺ 8/25/2015 89.9 Fair 156 2015 x 1 m Nov. 23–24, 201506784000 06784000 South Loup River at Saint Michael, Nebr. 41°01’57” 98°44’26” 8/24/2015 77.1 Fair 1161 2015 -- 1 m Nov. 23–24, 2015

Upper Dismal River

D1 415107101021401 Dismal River at HWY 97 nr Mullen, Nebr. 41o 51ʹ 07ʺ 101o 02ʹ 14ʺ 9/11/2015 95.2 Good -- 2015 x 50 cm Dec. 3–4, 2015T133 415041100492701 Dismal River T133 41o 50ʹ 41ʺ 100o 49ʹ 27ʺ 9/11/2015 139 Good 121 2015 x 50 cm Dec. 3–4, 2015T134 414802100384201 Dismal River T134 41o 48ʹ 02ʺ 100o 38ʹ 42ʺ 9/8/2015 162 Good 163 2015 x 50 cm Dec. 3–4, 2015D4 414644100315101 Dismal River 13 mi S of Thedford, Nebr. 41°46’43” 100°31’31” -- -- -- -- -- x 50 cm Dec. 3–4, 2015

Lower Dismal River

D5 414625100204601 Dismal River 4 mi W of Gem, Nebr. 41o 46ʹ 25ʺ 100o 20ʹ 46ʺ 8/4/2016 342 Good -- 2016 x 1 m Nov. 19–20, 2016T138 414744100154601 Dismal River T138 41o 47ʹ 44ʺ 100o 15ʹ 46ʺ 8/3/2016 365 Fair 323 2016 x 1 m Nov. 19–20, 2016D7 414913100105301 Dismal River 4 mi W of Dunning, Nebr. 41o 49ʹ 13ʺ 100o 10ʹ 53ʺ 8/1/2016 408 Good -- 2016 x 1 m Nov. 19–20, 2016D8 06776500 Dismal River at Dunning, NE 41°49’21” 100°06’01” -- -- -- -- -- x 1 m Nov. 19–20, 2016

North Loup River

NL1 420419100145501 North Loup River near Purdum, Nebr. 42o 04ʹ 19ʺ 100o 14ʹ 55ʺ -- -- -- -- -- x 1 m Nov. 19–20, 2016T435 420043100005401 North Loup River T435 42o 00ʹ 43ʺ 100o 00ʹ 54ʺ 8/16/2016 344 Good 377 2016 x 1 m Nov. 19–20, 2016NL3 415446099465001 North Loup River 4.5 mi SE of Brewster, Nebr. 41o 54ʹ 46ʺ 99o 46ʹ 50ʺ 8/15/2016 394 Good -- 2016 x 1 m Nov. 19–20, 2016NL4 415454099391701 North Loup River 9 mi NW of Almeria, Nebr. 41o 54ʹ 54ʺ 99o 39ʹ 17ʺ 8/18/2016 433 Fair -- 2016 -- 1 m Nov. 19–20, 2016L428 415215099352601 North Loup River L428 41o 52ʹ 15ʺ 99o 35ʹ 26ʺ 8/17/2016 521 Good 478 2016 x 1 m Nov. 19–20, 2016L427 414741099271201 North Loup River L427 41o 47ʹ 42ʺ 99o 27ʹ 12ʺ -- -- -- 528 -- x 1 m Nov. 19–20, 2016

1Streamflow from site identifier 06781530 approximately 200 feet downstream from 06784000.
12 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

Stream temperature, streambed temperature, and potentiomanometer measurements were collocated, typically at 

five points along a stream transect. At the headwaters of the 

South Loup River, collocated measurements were collected at 

only three points because the stream width generally was less 

than 20 ft. The first transect was completed in the location of 

the streamflow measurement cross section, and succeeding 

transects moved upstream or downstream from that initial set 

of measurements. Stream reconnaissance locations are given 

in table 2. Point-measurement locations were recorded with 

a handheld Magellan MobileMapper CX (Magellan, 2007) 

Global Positioning System (GPS) unit. The horizontal precision is generally submeter, which was considered adequate 

for comparison of measurements across stream transects and 

stream reaches. Stream temperature, streambed temperature, 

and potentiomanometer measurements are stored in the NWIS 

(U.S. Geological Survey, 2017) and are available as a USGS 

data release (Hobza and Densmore, 2018).

Stream temperature and streambed temperature were 

collected with an Omega DP8891 waterproof thermometer 

(Omega, 2017). An advantage to using this thermometer was 

that it is equipped with an 18-inch (in.) precision thermistor 

that could be inserted into the streambed. The manufacturer’s 

rated accuracy was plus or minus (±) 1 degree Celsius (oC) 

with a precision of ±0.1 oC. Before data collection in the 

field, the thermometer was tested against a National Institute 

of Standards and Technology (NIST)-certified thermometer, 

which indicated that the Omega thermometer was within 0.2 oC 

at five different points, bracketing the expected environmental 

temperature range. Stream temperature was measured by 

holding the probe near the middle of the water column, allowing adequate time for the temperature to equilibrate within the 

probe. Stream temperature, which is strongly dependent on 

air temperature, typically displays diurnal temperature variation; with minimum temperature occurring around sunrise and 

maximum temperature before sunset. Stream temperatures 

collected during a typical field day often missed the daily 

minimum but captured the daily maximum stream temperature. 

Streambed temperature was collected by pushing the probe into 

the streambed until refusal was reached, generally less than 

12 in. below the streambed surface, allowing adequate time for 

the temperature to equilibrate within the probe. The streambed 

temperature within the hyporheic zone is moderated by groundwater discharged from the underlying aquifer.

A potentiomanometer measures the difference in 

hydraulic head between groundwater and surface water in 

a lake or streambed (Winter and others, 1988; Rosenberry 

and LaBaugh, 2008). The vertical hydraulic gradient can be 

determined by dividing the difference in hydraulic head by the 

depth of a mini-piezometer screen, which is inserted into the 

underlying sediments. The direction of the vertical hydraulic 

gradient is important because it indicates whether a surfacewater body is gaining or losing flow to the groundwater system. The construction of a potentiomanometer and potential 

applications are further described in Winter and others (1988) 

and Rosenberry and LaBaugh (2008).

The potentiomanometer used in the study consists of 

a mini-piezometer connected with a clear piece of flexible 

tubing to an inverted wishbone-shaped tube called a manometer (fig. 6A). The other side of the manometer is connected 

to a tube that is submerged below the surface of the stream. 

A measurement was made by inserting the mini-piezometer 

(fig. 6A) into the streambed to a target depth of 2 ft. This depth 

sometimes was shallower because semiconsolidated deposits 

were within the streambed. The tubing on the stream side of 

the manometer is clamped off while water is pumped through 

the screen of the mini-piezometer from the top of the manometer. Once the water reaches the top of the manometer, the 

tubing connected to the mini-piezometer is clamped off; then, 

the clamp on the stream tubing is opened. Water is pumped 

from the top of the manometer through the stream tubing 

until the water reaches the top of the manometer. When all 

the tubing is filled with water and free of bubbles, air is bled 

into the manometer until the water levels appear on both sides 

of a ruler installed on a board next to the manometer. After 

leveling the manometer board with a hand level and allowing 

time for the water levels to equilibrate (typically 10 minutes 

for coarse-grained sediments), the water levels were measured. 

The difference in water levels is a measure of the pressure or 

hydraulic head difference between the groundwater (streambed) and the surface water (stream; fig. 6B). The difference 

in water levels is divided by the depth of the midpoint of the 

piezometer screen to determine the hydraulic gradient.

Potentiomanometer measurements were collected in 2014 

and 2015 using the design described in Winter and others 

(1988). Two additional potentiomanometers were constructed 

and used in 2016 to increase efficiency. Although the basic 

concept of operation remains the same, the construction was 

modeled after the design described in Kennedy and others 

(2007); however, no oil, which can resolve much smaller head 

differences, was used in the manometer tube. Based on data 

collected in 2014 and 2015, the use of oil in the device was 

considered unnecessary.

Aerial Thermal Infrared Imagery Methods

Civilian use of TIR remote sensing began in 1968 when 

systems first were declassified by the military. Because of the 

relatively coarse resolution of some of the early TIR systems, 

mapping ocean (Anding and Kauth, 1970) and lake temperatures was the primary research focus through the 1980s 

(Atwell and others, 1971; Dugdale, 2016). A local example 

includes a study by Rundquist and others (1985) that used 

TIR in Nebraska to study groundwater discharge patterns in 

the Crescent Lake National Wildlife Refuge area (not shown) 

in the western part of the Sand Hills. As more sophisticated 

TIR technology became available for civilian use, relatively 

inexpensive, high-precision systems were developed enabling 

the use of TIR for mapping temperatures of river and stream 

systems (Dugdale, 2016). Researchers have applied TIR 

remote sensing to assess reach- and watershed-scale streamtemperature patterns (Atwell and others, 1971; Torgersen and 
Approach and Methods 13

others, 2001), identify thermal refugia and habitat suitability 

for fish in streams (Dugdale and others, 2015; Torgersen and 

others, 1999; Vatland and others, 2015), and identify zones 

of groundwater discharge into streams and estuaries (Banks 

and others, 1996; Liu and others, 2016; Loheide and Gorelick, 

2006; Culbertson and others, 2014). Dugdale (2016) published 

a summary of recent TIR-based studies since 2011 and has 

documented an increase in published articles since 1995.

Aerial Thermal Infrared Imagery Collection

Advancements in aerial TIR remote-sensing technology 

have improved its utility for evaluating basin-wide groundwater discharge patterns because of the ability to cover entire 

stream systems with high-resolution imagery using fixed-wing 

aircraft. Groundwater discharge can be detected using thermal imaging technology because of the temperature difference between stable groundwater temperature and seasonally 

variable surface-water temperature. Temperature differences 

between groundwater and surface water are greatest during 

the summer and winter months. It is possible to identify and 

delineate areas of focused groundwater discharge by mapping 

stream surface temperatures (Banks and others, 1996). TIR 

sensors measure radiant energy from an object; therefore, the 

temperature measured from a river is representative of the 

top 0.0001 ft of the stream (Torgersen and others, 2001). As 

a result, groundwater discharge through streambeds within 

deeper parts of the stream channel may go undetected because 

of the extinction of the thermal signal because of stream 

mixing.

For this study, aerial TIR imagery was collected with 

a FLIR midwave TIR camera, model SC8303 (FLIR, 2011) 

mounted to the belly of a Cessna Turbo 206 for all 2015 

flights and a Piper Saratoga for all 2016 flights. The FLIR 

SC8303 has a 0.3 oC sensitivity in the 3- to 5-micron range 

and an absolute temperature accuracy of 2 oC across a range 

from −20 to 500 oC (FLIR, 2011). The FLIR SC8303 camera was controlled by custom software designed for airborne 

data acquisition. The camera was tightly integrated with a 

flight management system, a survey-grade airborne GPS and 

inertial measurement unit. Flight lines were designed before 

each flight to optimize data acquisition over the meandering 

streams. The contractor used the preplanned flight lines and 

the flight management system to ensure proper flying altitude 

and to provide course guidance. The GPS logged actual X, Y, 

and Z location data. The inertial measurement unit logged roll, 

pitch, and yaw orientation data for the camera.

Stream width, which is an important consideration in 

flight planning, differs depending on location. Stream widths 

of the planned study reaches ranged from less than 10 ft to 

approximately 300 ft. A minimum number of 10 image pixels 

was desired to detect and map groundwater discharge. Based 

on that criterion, stream reaches were flight planned for either 

a 0.98-, 1.64-, or 3.28-ft ground sample distance (GSD) based 

on a representative stream width. Image spatial resolution is 

a function of lens focal length and the aircraft altitude during 

image collection. A higher altitude reduces spatial resolution 

because of the increased effective “footprint” or field of view 

of the thermal camera. An increased field of view requires less 

maneuvering and effort for the aircraft to adequately cover a 

Manometer

Groundwater

hydraulic head Surface-water

hydraulic head

Mini-piezometer

Tubing

Tubing

A B

fig 06

Figure 6. Field photographs of a hydraulic potentiomanometer. A, The major components of a hydraulic potentiomanometer. B, A 

typical measurement that indicated a higher hydraulic head in the groundwater (left side of board) compared to the surface water (right 

side of board).
14 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

meandering stream and adjacent low-lying areas, reducing the 

cost of data collection. The dates of data collection and spatial 

resolution of TIR imagery for each dataset are given in table 2.

The thermal imagery was collected when the temperature 

difference of groundwater compared to surface water would 

be at its maximum to optimize the detection of groundwater 

discharge. Aerial TIR was collected in late fall 2015 and 2016, 

before the onset of ice, when the stream temperature is near 

freezing (near 0 oC) and groundwater temperature is typically 

around 13 oC (U.S. Geological Survey, 2017). This time of 

year has the advantage of minimal leaf and vegetative cover 

obstructing an overhead view of the stream surface. Aerial 

TIR imagery was collected at nighttime to reduce the potential 

effects of solar reflection on the stream surface and eliminate 

thermal loading of the land and stream surface. As nighttime 

low temperatures pushed stream temperatures towards freezing, project personnel monitored the water temperature data 

collected at specific streamflow-gaging stations and weather 

forecasts. Caution was used to ensure that stream temperatures 

remained above freezing so that edges were not obscured by 

shore ice, which potentially could mask some focused groundwater discharge points.

In late fall 2015 (table 3), aerial TIR imagery was collected along the South Loup River and the upper Dismal 

River. Aerial TIR imagery was collected with a fixed-wing 

aircraft over approximately 193 mi of the South Loup River, 

starting near its headwaters above the confluence of the North 

Fork South Loup River to the Saint Michael streamflowgaging station (fig. 3). Aerial TIR imagery also was collected along 4 mi of the North Fork South Loup River from 

its headwaters to its confluence with the South Loup River. 

Stream surface temperatures also were mapped along the 

upper Dismal River, which begins at the confluence with 

the North Fork and the South Fork of the Dismal River and 

continues east 34 mi to the Dismal River streamflow-gaging 

station (fig. 4). In late fall 2016 (table 3), aerial TIR imagery 

was collected along the lower Dismal River (fig. 4) and the 

North Loup River (fig. 5). The lower Dismal River begins at 

the Dismal River streamflow-gaging station and continues east 

37 mi to its confluence with the Middle Loup River (fig. 4). 

Aerial TIR imagery was collected along 82 mi of the North 

Loup River, starting 2 mi above the confluence of Calf Creek 

to the North Loup River at Taylor, Nebr., streamflow-gaging 

station (USGS station 06786000; hereinafter referred to as the 

“Taylor streamflow-gaging station”) (fig. 5).

Image Calibration

Before aerial TIR imagery was collected, self-logging 

temperature sensors (Onset, 2017) were deployed at various locations within the stream (table 2; figs. 3, 4, and 5) 

to complement the network of thermistors at streamflowgaging stations (table 1). The recorded water temperature 

data were used to ground truth and correct the aerial TIR data 

as described in the next paragraph. Before deployment, the 

accuracy of all self-logging temperature sensors was verified 

by completing five-point temperature checks bracketing the 

expected range of environmental temperatures (Wagner and 

others, 2006). The temperature checks indicated that all selflogging temperature sensors were within ±0.2 oC of the NISTmeasured temperature over a range from 0 to 30 oC. Selflogging temperature sensors were placed inside a small section 

of polyvinyl chloride (PVC) pipe with holes drilled in it to 

allow water to flow past the logger. The pipe was attached to a 

t-post driven into the streambed. Cross-sectional temperature 

measurements collected at the time of deployment indicated 

that streams were well mixed at all logger locations. Side-byside temperature check measurements, as described in Wagner 

and others (2006), verified that the self-logging temperature 

sensors experienced minimal sensor drift through the duration 

of the deployment. Self-logging temperature sensor locations 

were recorded with a handheld Magellan MobileMapper CX 

(Magellan, 2007) GPS unit. Recorded water temperature data 

are stored in the NWIS (U.S. Geological Survey, 2017).

A TIR camera does not measure the surface temperature 

directly; rather, the camera images the emitted infrared radiation from an object. Images of the emitted infrared radiation 

can be corrected to produce an accurate image of surface 

temperatures by estimating the emissivity of the object, atmospheric temperature, relative humidity, the distance between 

the object and the camera (altitude), and the reflected apparent temperature. The FLIR ResearchIR v4.0 (FLIR, 2014b) 

software package was used to compensate for these effects 

and produce images that represent the true temperature of the 

stream and adjacent areas. Reference temperatures (recorded 

stream temperatures) from the self-logging temperature 

sensors and thermistors at streamflow-gaging stations collected at the time of the aerial TIR data collection were used as 

validation points. The emissivity, which is the effectiveness of 

the target (water) surface to emit energy as thermal radiation, 

was estimated from published literature (FLIR, 2014a). Other 

variables such as atmospheric temperature, relative humidity, 

and atmospheric transmissivity were adjusted iteratively such 

that the best fit was achieved across all reference temperatures 

with corresponding points on the TIR imagery.

The root mean square error (RMSE) was calculated for 

each stream to assess the accuracy of the stream temperatures 

derived from corrected TIR imagery (Mikhail and others, 

2001). The RMSE was quantified as the difference between 

the measured stream temperature and the corrected aerial TIR 

temperature using the following equation:

RMSE

Tmeas Tcorr

n = ∑ − ( )2

(1)

where

RMSE is the root mean square error in degrees 

Celsius,

Tmeas is the temperature measured by the selflogging temperature sensors or thermistors 

at the streamflow-gaging stations,
Approach and Methods 15

Table 3. Site number, geographic location, and selected well construction data for observation wells drilled near streamflow-gaging stations.[NAVD 88, North American Vertical Datum of 1988; T, township; N, north; R, range; W, west; S, section; ABCD, codes for the quarter section, quarter-quarter section, quarter-quarter-quarter section, and quarter-quarter-quarter-quarter sections A, B, C, and D, respectively, where A is northeast, B is northwest, C is southwest, and D is southeast quarter of the next larger unit; o, degrees of latitude or longitude; ʹ, minutes of latitude or longitude; ʺ, seconds of latitude or longitude]

Site number Legal description Station number Station name Latitude Longitude Surveyed elevation, in feet above NAVD 88 Screened interval, in feet below land surface Date drilled Distance from stream (foot)

414952100060301 T22N R24W S33DBCB1 06775500 Middle Loup River at Dunning, Nebr. 41o 49ʹ 51.97ʺ 100o 06ʹ 03.12ʺ 2,612.73 12.3–14.7 9/16/2015 22414643100313101 T21N R28W S23ADAD1 06775900 Dismal River near Thedford, Nebr. 41o 46ʹ 42.91ʺ 100o 31ʹ 30.58ʺ 2,817.55 30–35 10/15/2015 70412522100121201 T17N R25W S21CDDD1 06781600 South Loup River at Arnold, Nebr. 41o 25ʹ 22.00ʺ 100o 12ʹ 12.17ʺ 2,694.38 8.6–11.6 9/22/2014 30410156098442601 T12N R13W S12BBBB1 06784000 South Loup River at Saint Michael, Nebr. 41o 01ʹ 56.38ʺ 98o 44ʹ 25.64ʺ 1,930.56 20–23 9/29/2014 94415630099513601 T23N R22W S27BBBC1 06785500 North Loup River at Brewster, Nebr. 41o 56ʹ 30.26ʺ 99o 51ʹ 36.37ʺ 2,478.11 15.6–18 9/15/2015 33414637099224701 T21N R18W 22DABB1 06786000 North Loup River at Taylor, Nebr. 41o 46ʹ 36.96ʺ 99o 22ʹ 46.93ʺ 2,260.15 16.9–19.3 9/14/2015 33
16 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

Tcorr is the temperature extracted from the 

corrected TIR imagery, and

n is the number of locations where temperature 

comparisons were made.

The RMSE was 0.5 oC for the South Loup River and 

0.4 oC for the Dismal River, indicating that corrected aerial 

TIR imagery adequately characterized stream surface temperatures for these streams. The RMSE for the North Loup River 

was 1.6 oC, the highest for any stream reach as part of this 

study. The difference in temperature between the self-logging 

temperature sensor downstream from the diversion dam to 

the Taylor-Ord Canal (fig. 5) and corrected aerial TIR imagery temperature was approximately 4.2 oC; however, if this 

one data point is omitted, the calculated RMSE is 0.3 oC. The 

cause of the large difference in temperature below the diversion dam currently (2018) is unknown. The cause, however, 

may be from a change in emissivity because of a reduction 

in the suspended sediment in the North Loup River. Approximately 5 mi downstream from the diversion dam at the Taylor 

streamflow-gaging station, the temperature difference was 

0.4 oC, indicating that this affected only a small area.

Orthorectification

For this study, the contractor provided the aerial TIR 

imagery as georeferenced grids (rasters) for interpretation 

within a geographic information system (GIS) environment. 

The TIR images were georeferenced (orthorectified) using 

SimActive 3D Correlator software (SimActive Inc., 2016). 

SimActive 3D Correlator is a photogrammetric software package designed to orthorectify and mosaic aerial imagery. The 

temperature-corrected TIR images, USGS 10-meter digital 

elevation model (Nebraska Department of Natural Resources 

and U.S. Geological Survey, 1998), and exterior camera 

orientation data logged by the GPS/inertial measurement unit 

system were used as data inputs.

Reference imagery was used to provide photograph-identifiable ground control points to help enhance the aerial triangulation solution. For the middle and lower South Loup River 

(downstream from the Pressey Park recorder well, fig. 3), 

four-band orthoimages previously collected by the contractor 

(Cornerstone Mapping, unpub. data, 2015) for other mapping 

purposes were used as reference images. This set of reference 

images was collected with a 2-ft GSD. In 2016, the contractor 

flew 0.98-ft GSD, four-band imagery over the Lower Dismal 

River and North Loup River several weeks before the TIR 

imagery acquisition for this study. The horizontal accuracy 

of the contactor-collected reference imagery was designed to 

meet the American Society for Photogrammetry and Remote 

Sensing Class II accuracy standard.

For some stream reaches within the Upper Loup NRD 

(upper South Loup River and upper Dismal River), the best 

available reference imagery was U.S. Department of Agriculture, Farm Service Agency (2017). The Farm Service Agency 

imagery is collected with a 3.28-ft GSD and a horizontal 

accuracy of 20 ft.

The contractor-supplied imagery was valuable to add 

temporally valid context with high spatial resolution, which 

aided thermal image interpretation. Generally speaking, the 

horizontal accuracy of the orthorectified TIR imagery was 

within 3 ft of the reference imagery. Measured horizontal 

accuracies of each individual stream reach are stated in Hobza 

and Densmore (2018).

Thermal Infrared Imagery Analysis

Georeferenced TIR imagery was interpreted within a GIS 

environment using two different analysis methods. The first 

method involved creating downstream temperature profiles 

where stream surface temperatures are extracted every 6.6 ft 

along a digitized stream centerline. The extracted point temperatures were plotted against distance upstream or downstream from a streamflow-gaging station. Because aerial TIR 

imagery was collected before the onset of ice, warmer stream 

temperatures would be the result of an increase in the proportion of groundwater discharge, relative to total streamflow. 

The downstream temperature profiles included parts of the 

stream that were totally or partially obstructed by bridges and 

overhanging vegetation, which were generally much cooler 

than the stream surface. Tree limbs from deciduous trees, 

which only partially obscure a part of a raster cell, effectively 

decreased the average apparent temperature, creating a negative bias. First, negative spikes of extracted point temperature 

data were removed to retain the overall trend of the downstream temperature profile. A seven-point moving average was 

computed to effectively smooth the downstream temperature 

profile, minimizing the effect of tree cover for the upper and 

middle South Loup River and the upper Dismal River.

The second analysis method estimated the density of 

focused groundwater discharge points along individual stream 

reaches. The density of focused groundwater discharge points 

was assessed by creating an Esri shapefile (Esri, 1998) and 

picking individual focused groundwater discharge points 

through visual inspection of the TIR and reference imagery. Areas of slightly warmer water along stream margins 

and within stream channels were marked with points. For 

each focused groundwater discharge point, the downstream 

distance along the stream centerline was calculated within a 

GIS environment. Interpreted focused groundwater discharge 

points were totaled for each subdivided stream-reach segment. 

Focused groundwater discharge point density was estimated in 

number of points per 1,000 or 5,000 ft.

This approach, although straightforward and simple 

to apply, does have limitations. The approach relies solely 

on visual inspection of aerial TIR imagery and should be 

regarded as semiquantitative because of the difficulty in 

determining the precise number of points where groundwater 

is discharging to the stream. Verification of the interpreted 

groundwater discharge points would be nearly impossible 

because of the number of focused groundwater discharge 

points, length of the reaches studied, landowner permission 

and coordination needed, and site accessibility. Furthermore, 
Groundwater Discharge Characteristics for Streams in the Loup River Basin 17

the tree and vegetative cover that obscured parts of the stream 

channel for some streams undoubtedly prevented the detection of some focused groundwater discharge points with aerial 

TIR imagery. Nevertheless, estimating the density of focused 

groundwater discharge points and interpreting spatial patterns 

have provided meaningful interpretations that are discussed in 

subsequent sections of this report.

Methods Used to Describe Temporal 

Characteristics of Groundwater Discharge

Additional water-level and temperature data were 

collected at six streamflow-gaging stations in 2014, 2015, 

and 2016 (table 1; fig. 1) to assess the temporal variability 

of groundwater discharge. The data collection approach, 

described in Eddy-Miller and others (2012), consists of a 

streamflow-gaging station coupled with an observation well 

completed below the elevation of the streambed and instrumented with a water-level recorder. The comparison of continuous groundwater-level elevation and stream-stage elevation can indicate whether a stream is gaining or losing near the 

streamflow-gaging station. Continuous water temperature was 

collected in the stream and the shallow observation well to 

provide further support to groundwater/surface-water interaction trends. The information provided by a network of instrumented streamflow-gaging stations with differing basin and 

land-use characteristics allows for an analysis of groundwater 

discharge patterns, temporally and spatially (Eddy-Miller and 

others, 2012).

Observation well construction and location information 

is presented in table 3. Observation wells and instrumentation 

were installed at both South Loup streamflow-gaging stations 

in September 2014, and the remaining four listed in table 3 

were installed in September and October 2015. Five of the 

observation wells were installed using a tractor-mounted soil 

coring rig (Model 54TR, Geoprobe Systems, Salina, Kansas). 

A contractor was hired to install the observation well near the 

Dismal River streamflow-gaging station because the semiconsolidated sandstone and siltstone would have prevented the 

tractor-mounted soil coring rig from reaching the target depth. 

Core sections were collected in 4-ft intervals to depths that 

extend below the level of the streambed. Observation wells 

were screened below the bottom of the streambed and were 

within 100 ft of the streambank (table 3).

The observation wells were instrumented with a KPSI 355 

vented pressure transducer (TE Connectivity, 2017) placed near 

the bottom of the well. Groundwater temperature and stream 

temperature data were collected with a pair of H–377 Design 

Analysis water temperature sensors (Design Analysis Associates, Inc., 2017). The groundwater temperature sensor was 

attached to the cable just above the transducer at the bottom of 

the well. The stream temperature sensor was installed within 

a well-mixed part of the stream. All water-level and temperature data were collected following the protocols and guidance 

stated in Cunningham and Schalk (2011), Turnipseed and Sauer 

(2010), and Wagner and others (2006) and are stored in the 

NWIS database (U.S. Geological Survey, 2017).

In order to compare measured groundwater and surfacewater levels at the same datum, elevations were surveyed 

using the Global Navigation Satellite Systems (GNSS) followed by a series of station levels (Kenney, 2010) to tie the 

GNSS-recorded elevation to the streamflow-gaging station 

datum. Static GNSS surveys involved collecting positioning 

data by setting up a GNSS receiver antenna over a benchmark 

cap set into the concrete well pad. A Trimble R8 (Trimble 

Navigation Limited, 2009) GNSS receiver antennae collected 

measurements from positioning satellites for at least 4 hours 

at each observation well (Rydlund and Densmore, 2012). The 

GNSS data collected during static surveys were postprocessed 

later with data collected from nearby control stations to correct 

atmospheric interference errors and to produce survey-grade 

solutions. After each static-survey session, the logged data 

file was sent to the Online Positioning User Service (OPUS; 

https://www.ngs.noaa.gov/OPUS/) to determine the exact 

position of the surveyed test hole. OPUS is a quality-assured 

service provided by the National Geodetic Survey where users 

can process single-base GNSS data through an online-user 

interface. OPUS processes logged data using continuously 

operating reference stations. The accuracy of the solutions was 

reported as peak-to-peak errors, which represent the difference 

between maximum and minimum values of the coordinates 

obtained from the three baseline solutions (Rydlund and Densmore, 2012). Generally speaking, the vertical peak-to-peak 

errors were less than 1 in., indicating that coordinates for all 

surveyed points met the criteria for USGS Level II single-base 

Online Positioning User Service-Static (OPUS–S) survey 

accuracy (Rydlund and Densmore, 2012).

Station levels were completed to tie the established 

streamflow-gaging station datum to the surveyed benchmark 

elevation at the concrete well pad. Station levels were completed using a Sokkia SDL30 (Sokkia Topcon Co., Ltd., 2000) 

electronic digital level system in accordance with the guidelines and procedures stated in Kenney (2010).

Groundwater Discharge 

Characteristics for Streams in the Loup 

River Basin

This section describes the groundwater discharge characteristics of selected reaches of the South Loup, Dismal, and 

North Loup Rivers. The spatial characteristics were studied 

using a combination of stream reconnaissance at selected locations followed by an analysis of aerial TIR imagery. Temporal characteristics were described by examining continuous 

water-level and stream temperature data at six streamflowgaging stations within the Loup River Basin. Interpretations 

and descriptions of the spatial and temporal characteristics are 

presented together for each stream studied.
18 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

South Loup River and North Fork South Loup 

River

Stream reconnaissance data were collected at selected 

locations along the South Loup River during August 2014 

and 2015 (fig. 3). Based on stream reconnaissance data and 

field observations, the South Loup River is divided into three 

reaches. The upper South Loup River, which includes the 4-mi 

reach of the North Fork South Loup River, extends 36 mi to 

the South Loup River at Arnold, Nebr., streamflow-gaging 

station (USGS station 06781600; hereinafter referred to as the 

“Arnold streamflow-gaging station;” fig. 3). The middle South 

Loup River is a 62-mi reach, which extends from the Arnold 

streamflow-gaging station to immediately downstream from 

the Pressey Park recorder well (fig. 3), and the lower South 

Loup River is a 94-mi reach, which extends from the Pressey 

Park recorder well to the Saint Michael streamflow-gaging 

station (fig. 3; table 3). Spatial and temporal characteristics of 

groundwater discharge for each stream reach are described in 

the following subsections.

Upper South Loup River and North Fork South 

Loup River

Streamflow measurements collected in August 2014 and 

2015 along the upper South Loup River indicate a gradual 

increase in streamflow throughout the 36-mi reach (table 2; 

fig. 7). Because of backwater conditions at the mouth, the 

streamflow of the North Fork South Loup River was estimated 

by calculating the difference in streamflows immediately 

above and below the confluence. The estimated flow of the 

North Fork South Loup River was 7.2 cubic feet per second 

(ft3/s), which was more than twice the flow of the South Loup 

River above the confluence. At the time the streamflow measurements were collected (August 2015), the North Fork South 

Loup River provided approximately 40 percent of the flow 

measured at Arnold streamflow-gaging station. Because the 

confluence is away from county roads, the North Fork South 

Loup was not measured in the 2006 seepage run (Peterson 

and Strauch, 2007). Though each set of measurements was 

collected 1 year apart, they likely are comparable between 

years because the median daily flows measured at the Arnold 

streamflow-gaging station during the stream reconnaissance 

were within 2 ft3/s (19.2 ft3/s in 2014 and 17.8 ft3/s in 2015).

Potentiomanometer measurements indicate locally variable vertical hydraulic gradients that ranged from −0.06 to 

0.26 foot per foot (ft/ft; table 4). The median vertical hydraulic 

gradient was 0.01 ft/ft, which was consistent with measured 

streamflow (table 4), indicated gaining conditions. In general, 

streambed temperatures were slightly cooler than the mean 

stream temperature (table 4). Although streambed temperatures were cooler than the stream temperature, which indicates 

groundwater discharge through the streambed, the streambed 

temperature still was much warmer than the ambient shallow groundwater temperature (11 to 14 oC; U.S. Geological 

Survey, 2017). This difference in temperature indicates that 

discharged groundwater mixes with stream water within the 

hyporheic zone.

Aerial TIR imagery indicated numerous small, focused 

groundwater discharge points along the margins of the upper 

South Loup River (fig. 8A) and North Fork South Loup River 

(fig. 8B). In some locations, the South Loup River appears to 

flow through wet meadows where shallow groundwater is discharging into the stream emanating from many focused points. 

The downstream temperature profiles, derived from aerial TIR 

imagery for the South Loup River and North Fork South Loup 

River above the Arnold streamflow-gaging station are shown 

in figure 9. The North Fork South Loup River is warmer than 

the South Loup River, indicating flow is sustained by recently 

discharged groundwater. Generally speaking, the temperature of headwater streams is closer to the local groundwater 

temperatures compared to larger order streams (Caissie, 2006). 

Increases in stream temperature on the South Loup River, 

measured along a 10-mi reach centered on the confluence with 

the North Fork South Loup River (fig. 9), indicate the stream 

is receiving additional groundwater discharge along this reach.

The concentration of focused groundwater discharge 

points along the South Loup River is shown as blue symbols 

in figure 7. Focused groundwater discharge on the upper South 

Loup River tended to be clustered. The density of focused 

groundwater discharge points of the North Fork South Loup 

River generally was higher and appeared to decrease moving downstream to the mouth of the South Loup River. The 

volume of water produced from this dense network of focused 

groundwater discharge points along the North Fork South 

Loup River is sufficient to provide approximately 40 percent 

of the flow measured at the Arnold streamflow-gaging station 

during the irrigation season.

Geologic maps (Souders, 2000) and test holes (Conservation and Survey Division, University of Nebraska-Lincoln, 

2017a) indicate the upper South Loup River has incised into 

a mix of Quaternary eolian silt and fine-grained sand. The 

streambed of the upper South Loup River contains some 

interbedded silt that can restrict the vertical movement of 

groundwater to the stream, which can result in large hydraulic gradients. Groundwater discharge within the upper South 

Loup River and North Fork South Loup River is dominated by 

focused groundwater discharge emanating at many points near 

the stream margin.

The groundwater levels measured near the Arnold 

streamflow-gaging station (fig. 3; table 3) were higher 

than stream-level elevations, indicating gaining conditions 

(fig. 10A). Changes in groundwater elevation track closely to 

the stream elevation, indicating a high degree of connectivity between the stream and shallow groundwater. Groundwater temperature measured in the shallow well displays an 

annual temperature cycle that varies between 7.5 and 14.5 oC 

(fig. 10B). The annual maximum was measured in early fall, 

and its annual minimum was in early spring. The annual 

minimum and maximum groundwater temperatures lag behind 

the annual minimum and maximum stream and, by inference, 
Groundwater Discharge Characteristics for Streams in the Loup River Basin 19

air temperatures. Because the stream is gaining consistently in 

this location, and the direction of groundwater movement is 

towards the stream, the changes in groundwater temperature 

are in response to heat transfer through thermal conduction 

from surface heating and cooling.

Middle South Loup River

Streamflow measurements along the 62-mi reach of the 

middle South Loup River indicated substantial increases in 

groundwater discharge (fig. 7; table 2). Based on discharge 

measurements from August 26, 2015, streamflow increased 

from 17.8 ft3/s at the Arnold streamflow-gaging station 

(U.S. Geological Survey, 2017) to 92.8 ft3/s near the Pressey 

Park recorder well (table 2; fig. 3). In general, streambed 

temperatures were cooler along the middle South Loup River 

compared to the upper South Loup River (table 4). Some 

measured streambed temperatures were cool enough that they 

approached ambient groundwater temperatures (U.S. Geological Survey, 2017), indicating vertical movement of groundwater through the streambed with little to no mixing of surface 

water within the hyporheic zone. The streambed texture 

changes below the Arnold streamflow-gaging station from a 

silty very fine sand to medium to coarse sand. An active sand 

and gravel mining operation is at the margin of the South 

Loup River approximately 3 mi downstream from the Arnold 

streamflow-gaging station.

The aerial TIR imagery acquired along the middle South 

Loup was collected over two flights on November 23–24 and 

December 2–3, 2015. TIR imagery was collected with a 1.64-

ft resolution for the upper 44 mi and with a 3.28-ft resolution 

for the lower 18 mi (table 2; fig. 3). The downstream temperature profile for the middle South Loup River is shown 

in figures 11 and 12. The downstream temperature profile 

indicates a substantial increase in stream temperature starting approximately 5 mi below the Arnold streamflow-gaging 

station (fig. 11), which is the result of increased groundwater 

discharge. Stream temperatures peaked approximately 7 mi 

downstream from the Arnold streamflow-gaging station 

before colder air temperatures decreased stream temperatures. 

Streamflow measurements indicate increases in streamflow 

through the 62-mi middle South Loup reach from groundwater 

discharge (table 2); however, decreases in stream temperature 

result from the fact that the additional warmer groundwater 

discharge constitutes a smaller proportion of total streamflow.

fig 07

0

200

400

600

800

1,000

1,200

1,400

1,600

1,800

2,000

Focused groundwater discharge points per 5,000 feet

Distance, in miles from South Loup at Arnold streamflow-gaging station

Streamflow, in cubic feet per second

0

10

20

30

40

50

60

70

80

90

100

40 20 0 20 40 60

Upstream Downstream

SL1

SL2 SL3

SL4

M279

M276

L264

Upper South Loup River Middle South Loup River

South Loup River at Arnold 06781600

EXPLANATION

Focused groundwater discharge point density,

South Loup River 

Focused groundwater discharge point density,

North Fork of the South Loup River

Streamflow, in cubic feet per second 

(August 2014 and August 2015)

Figure 7. Measured streamflow and the estimated density of focused groundwater discharge points along the upper and 

middle South Loup River reaches and North Fork South Loup River.
20 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16 Table 4. Summary statistics for stream temperature, streambed temperature, and hydraulic gradient collected along the North Fork South Loup, South Loup, Dismal, and North Loup Rivers, Nebraska, August 2014, August or September 2015, and August 2016. [>, greater than] Stream reach Stream temperature (degree Celsius) Streambed temperature (degree Celsius) Vertical hydraulic gradient1 Count Minimum Median Maximum Count Minimum Median Maximum Count Minimum Median Maximum Upper South Loup and North Fork South Loup River2 81 19.6 22.2 25.6 81 18.0 20.7 23.2 35 −0.06 0.01 0.26 Middle South Loup River3 75 18.1 21.3 27.1 75 14.7 18.9 22.0 49 −0.04 0.02 0.10 Lower South Loup River4 45 19.4 24.4 28.6 45 20.3 22.1 23.4 45 −0.01 0.02 0.09 Upper Dismal River5 35 14.3 18.3 21.0 35 13.8 17.4 18.9 33 0.00 0.03 >0.50 Lower Dismal River6 49 20.6 23.8 29.6 50 15.4 20.4 22.8 50 0.00 0.03 0.13 North Loup River 110 20.7 27.3 30.1 110 14.0 23.2 25.6 109 0.00 0.04 0.41

1Positive hydraulic gradient indicates higher water levels in the streambed compared to the stream water level, or gaining conditions.2Reach is from headwaters of the South Loup and North Fork South Loup River to the South Loup River at Arnold, Nebraska, streamflow-gaging station.3Reach is from South Loup River at Arnold, Nebr., streamflow-gaging station to Pressey Park recorder well.4Reach is from downstream from Pressey Park recorder well to the South Loup River at Saint Michael, Nebr., streamflow-gaging station.5Reach is from the confluence of the North Fork and South Fork of the Dismal River to the Dismal River near Thedford, Nebr., streamflow-gaging station.6Reach is from the Dismal River near Thedford, Nebr., streamflow-gaging station to the confluence with the Middle Loup River.
Groundwater Discharge Characteristics for Streams in the Loup River Basin 21 fig 08a

100°13'30" 100°13'45" 100°14'

41°25'50"41°25'40"41°25'30"

Middle Loup River South Loup River

Dismal River

Area pictured

Lower Loup 

Natural Resources District

Upper Loup 

Natural Resources District

Focused groundwater 

discharge points

EXPLANATION

Temperature, in degrees Celsius

5-18

0 0.15 0.3 MILE

0 0.15 0.3 KILOMETER

A

North Fork 

South Loup River

 Image by Aaron Schepers, Cornerstone Mapping Inc.

Figure 8. Example aerial thermal infrared imagery collected in November 2015. A, The upper South Loup River. B, The North Fork South Loup River.
22 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

fig 08b

100°22'30" 100°22'45" 100°23'00"

41°31'30"41°31'20"41°31'10"

Middle Loup River

North Loup River

South Loup River

Dismal River

Platte River

Focused groundwater discharge point

Focused groundwater 

discharge point

EXPLANATION

Temperature, in degrees Celsius

5-18

B

0 0.15 0.3 MILE0 0.15 0.3 KILOMETER

Lower Loup 

Natural Resources District

Upper Loup 

Natural Resources District

Area pictured

North Fork 

South Loup River

 Image by Aaron Schepers, Cornerstone Mapping Inc.

Figure 8. Example aerial thermal infrared imagery collected in November 2015. 

A, The upper South Loup River. 

B, The North Fork South Loup River.—Continued
Groundwater Discharge Characteristics for Streams in the Loup River Basin 23

The middle South Loup River, 5 mi below the Arnold 

streamflow-gaging station, incises into a Pliocene-age gravel 

(Conservation and Survey Division, University of NebraskaLincoln, 2017a; Souders, 2000), which increases the groundwater discharge to the stream. The upper South Loup River, 

which was dominated by focused groundwater discharge, 

transitions to a reach dominated by diffuse groundwater discharge through the streambed as the texture grades from silt 

and fine-grained sand to a more permeable medium to coarse 

sand and fine gravel.

Several large focused groundwater discharge points were 

observed in the aerial TIR imagery along the stream margin 

between the Arnold streamflow-gaging station and the Pressey 

Park recorder well (fig. 3). Some of these focused groundwater discharge points appeared to be up to 75 ft across. Other 

focused groundwater discharge points appeared to be in sandpits from former sand and gravel mining operations where the 

overlying finer-grained Quaternary sediments were removed 

(fig. 13). The aerial TIR-based temperature of the focused 

groundwater discharge points exceeded 4.5 oC. Because of 

their size and location, these focused groundwater discharge 

points appear to be prominent hydrologic features.

In September 2017, several of these groundwater 

discharge points were selected for ground verification and 

visual inspection. Some focused groundwater discharge 

points appeared to have merged from draws that lead to the 

South Loup River (fig. 13). The temperature of the discharged groundwater measured was as low as 13.0 oC, which 

is close to the ambient regional groundwater temperature. 

Groundwater appears to flow from coarse sand to coarse 

gravel at many points within open bowl-shaped depressions 

(figs. 14A and 14B). Discharge from individual groundwater 

discharge points was variable but was estimated to be as 

much as 1.5 ft3/s. The formation of these focused groundwater discharge points appears to be the product of groundwater sapping. With time, the constant flow from focused 

groundwater discharge has removed finer-grained sediments, 

leaving coarser-grained sediments behind. Headward erosion 

seems to have increased the size and discharge of the focused 

groundwater discharge points, which created the bowl-like 

depressions that abruptly end at hillsides (figs. 14A and 14B).

Diffuse groundwater discharge appears to dominate 

the lower end of the middle South Loup River. A recorder 

well was instrumented in spring 2014 to record groundwater 

levels from the Ogallala (USGS station 411126099422501; 

U.S. Geological Survey, 2017). In July 2017, as this report 

was being prepared, a streamflow-gaging station was installed 

on the South Loup River, near the Pressey Park recorder fig 09

-2

-1

0

1

2

3

4

5

Water temperature, in degrees Celsius

Distance, in miles upstreamfrom South Loup River at Arnold streamflow-gaging station

40 35 30 25 20 15 10 5 0 -5

SL1

SL2

South Loup River at Arnold 06781600 

Upper South Loup River

North Fork South Loup River

Self-logging temperature sensor

Thermistor at streamflow-gaging station

EXPLANATION

Figure 9. Downstream temperature profiles of the upper South Loup River and the North Fork South Loup River, 

above the South Loup River at Arnold, Nebraska, streamflow-gaging station. Downstream temperature profiles 

were created from aerial thermal infrared imagery collected December 2–3, 2015.
24 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

fig 10

2,690

2,691

2,692

2,693

2,694

2,695

2,696

Water-level elevation, in feet above North American Vertical Datum of 1988 

June 2014 December 2014 July 2015 January 2016 August 2016 March 2017 September 2017 April 2018

Date

Stage affected by ice

South Loup River stage elevation

Groundwater elevation

EXPLANATION A

-5

0

5

10

15

20

25

30

35

Water temperature, in degrees Celsius

June 2014 December 2014 July 2015 January 2016 August 2016 March 2017 September 2017 April 2018

Date

Stream stage affected by ice

South Loup River temperature

Groundwater temperature

EXPLANATION B

Figure 10. South Loup River at Arnold, Nebraska, streamflow-gaging station (U.S. Geological Survey station 06781600) and nearby 

observation well. A, Stream and groundwater-level elevation. B, South Loup River and groundwater temperature.
Groundwater Discharge Characteristics for Streams in the Loup River Basin 25

fig 11

0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

0 5 10 15 20 25 30 35 40 45 50

Water temperature, in degrees Celsius

Distance, in miles downstream from South Loup River at Arnold streamflow-gaging station

M279

M276

South Loup River at Arnold 06781600 

EXPLANATION

Middle South Loup River

Self-logging temperature sensor

Thermistor at streamflow-gaging station

Figure 11. Downstream temperature profile for the middle South Loup River created from aerial thermal infrared imagery 

collected December 2–3, 2015.

Middle and lower South Loup River

Self-logging temperature sensor

Thermistor at streamflow-gaging station

EXPLANATION

Middle South Loup River Lower South Loup River

0

1

2

3

4

5

6

120 100 80 60 40 20 0

Water temperature, in degrees Celsius

Distance, in miles upstream from South Loup River at Saint Michael streamflow-gaging station

L264

L246

L229

South Loup River at Saint Michael 06784000 

Pressey Park recorder well

Figure 12. Downstream temperature profile for the middle and lower South Loup River created from aerial thermal infrared imagery 

collected November 23–24, 2015.
26 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

fig 13

100°08' 100°08'15"

41°24'10"41°24'00"

Middle Loup River

North Loup River

South Loup River

Dismal River

Platte River

Sandpit

0 0.1 0.2 MILE 0.050 0.1 0.15

0.15

0.2 KILOMETER 0.05

EXPLANATION

Temperature, in degrees Celsius

5-18

Focused groundwater 

discharge points

Area pictured

Lower Loup 

Natural Resources District

Upper Loup 

Natural Resources District

 Image by Aaron Schepers, Cornerstone Mapping Inc.

Figure 13. Example aerial thermal infrared imagery from the middle South Loup River, December 2015. Photograph of one of the focused groundwater discharge points can be seen in figure 14

B.
Groundwater Discharge Characteristics for Streams in the Loup River Basin 27

well (fig. 3; USGS station 06781900; U.S. Geological Survey, 2017). Comparison of groundwater levels indicates that 

groundwater from the Ogallala is discharging through the 

overlying Quaternary alluvial aquifer into the South Loup 

River. Steep drops in water levels associated with pumping 

were recorded from late May through September. Other times 

of the year, during ambient or nonpumping conditions, the 

hydraulic gradient is approximately 0.05 ft/ft, which indicates groundwater discharges from the Ogallala to the stream 

(fig. 15). Streambed temperatures as low as 14.7 oC were 

recorded during the stream reconnaissance along the streambank nearest to the recorder wells. The interpretation that this 

is an area of increased groundwater discharge is consistent 

with the aerial TIR imagery, which indicated a slight increase 

in downstream temperature at the Pressey Park recorder well 

(fig. 12).

Lower South Loup River

The lower South Loup River begins immediately below 

Pressey Park and extends 94 mi downstream to the Saint 

Michael streamflow-gaging station (fig. 3). Stream reconnaissance data indicate that the lower South Loup River receives 

less groundwater discharge compared to upstream reaches. 

Streamflow measurements collected in August 2015 indicate that the stream was either neutral or losing throughout 

its reach (fig. 16). Stream and streambed temperatures were 

warmer compared to upstream reaches. The minimum streambed temperature was 20.3 oC (table 4), which indicates the 

mixing of groundwater with surface water within the hyporheic zone.

Aerial TIR imagery was collected November 23–24, 

2015, at a 3.28-ft spatial resolution (table 2; fig. 3). The 

downstream temperature profile (fig. 12) displayed little 

temperature variation along the reach. Focused groundwater 

discharge points are within the reach but at lower densities 

compared to the upper and middle South Loup River reaches 

(fig. 16).

The temporal variability of groundwater discharge along 

the South Loup River varied with location and season. Streamflow measurements collected during the stream reconnaissance 

indicate an increase in streamflow within the upper and middle 

South Loup River reaches. The measured streamflow for much 

of the lower South Loup River remains relatively constant to 

the Saint Michael streamflow-gaging station. Peterson and 

Strauch (2007) reported streamflow measurements collected in 

late fall 2006 that indicated increasing streamflows along the 

length of the South Loup River. At the Saint Michael streamflow-gaging station, flows in late summer (table 2; fig. 16) 

were much lower compared to flows measured in late fall 

(Peterson and Strauch, 2007). This difference in flow is largely 

attributed to increases in groundwater pumping and evapotranspiration reducing the groundwater discharge received by 

the lower South Loup River.

The groundwater levels measured near the Saint 

Michael streamflow-gaging station indicate seasonally variable groundwater discharge conditions (figs. 17A and 17B). 

During the spring and early summer (March through June), 

the groundwater-level elevation is higher than the stream 

elevation, indicating gaining conditions. Later in the summer 

(July through August), stream elevations are higher than the 

groundwater elevation because of increased evapotranspiration and groundwater pumping. This condition continues into 

the fall until groundwater levels are able to recover. Gaining 

conditions are assumed to continue into the early spring; however, it is difficult to make this determination with continuous 

water levels alone because the gage-height record is affected 

by ice conditions. Ice cover can increase the backpressure 

A B

fig 14

Figure 14. Two focused groundwater discharge points along the middle South Loup River. A, The location is approximately 7 miles 

southeast of the South Loup River at Arnold, Nebraska, streamflow-gaging station (U.S. Geological Survey station 06781600). B, Aerial 

thermal infrared image displaying focused groundwater discharge point can be seen in figure 13 and is approximately 4 miles southeast 

of the South Loup River at Arnold, Nebr., streamflow-gaging station.
28 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

measured by the streamflow-gaging station, which can give 

the impression that the stream is losing flow to the shallow aquifer. An example of this was during December 2016 

through January 2017, when stream-stage elevation remained 

above the groundwater-level elevation, although groundwater 

demands are minimal during the winter. As stream temperatures warmed and ice cover was eliminated, stream stage 

dropped below the groundwater-level elevation, indicating 

gaining conditions.

The groundwater temperature measured in the shallow 

well displays a cyclical pattern that varies between 11 and 

13.5 oC, where its annual maximum is measured in early fall 

and its annual minimum is in early spring (fig. 17B). Similar to what was measured in the observation well near the 

Arnold streamflow-gaging station, the annual minimum and 

maximum groundwater temperatures lag behind the annual 

minimum and maximum stream temperatures. The annual 

temperature variation is much less than the observation well 

near the Arnold streamflow-gaging station, likely because the 

depth of the well is greater and, therefore, affected less by 

surface temperatures.

Dismal River

The 75-mi study reach of the Dismal River extends from 

the confluence of the North and South Forks of the Dismal 

River to its mouth on the Middle Loup River (fig. 4). The 

study reach of the Dismal River was divided into two reaches 

at the streamflow-gaging station near Thedford, Nebr. (fig. 4). 

The Dismal River streamflow-gaging station was chosen as a 

dividing point between the upper and lower reaches because 

the groundwater discharge characteristics of each reach are 

considerably different. These characteristics are described in 

the following subsections.

Upper Dismal River

Streamflow measurements collected during the stream 

reconnaissance indicate increasing streamflow throughout 

the study reach (fig. 18; table 2), which is consistent with 

streamflow measurements reported in Peterson and Strauch 

(2007). Focused groundwater flow emanating from springs and 

vertical conduits (Guhman and Pederson, 1992) helps maintain 

fig 15

July 1, 2017 July 31, 2017 August 30, 2017 September 29, 2017 October 29, 2017

2,376

2,378

2,380

2,382

2,384

2,386

2,388

2,390

2,392

2,394

2,396

Water-level elevation, in feet above North A

merican Vertical Datum of 1988

Date

EXPLANATION

South Loup River stage elevation

Groundwater elevation

Figure 15. Groundwater-level elevation in the South Loup River at the Pressey Park recorder well and nearby streamflowgaging station (installed July 2017).
Groundwater Discharge Characteristics for Streams in the Loup River Basin 29

a relatively constant temperature compared to other stream 

reaches studied. The median stream temperature measured during the stream reconnaissance was 18.3 oC, which is less than 

1 °C greater than the median streambed temperature (table 4). 

The minimum streambed temperature was 13.8 oC (table 4), 

which is within the expected range of the ambient groundwater temperature, indicating that there is vertical movement of 

groundwater through the streambed in some locations, and little 

to no mixing of surface water within the hyporheic zone.

Potentiomanometer measurements collected within the 

streambed indicated substantial variability in vertical head 

gradients across short distances. The active stream channel of 

the Dismal River is incising into the Pliocene deposits, which 

are locally characterized as fine-grained sand and sandstone 

interbedded with siltstone. Some points of focused discharge 

along the upper Dismal River are the result of local confining 

beds of siltstone, which create strong vertical gradients near 

the stream margin and can concentrate groundwater discharge 

to other parts of the stream. Potentiomanometer measurements 

indicated the lateral persistence of the confining beds is variable, even within short distances. The largest head gradients 

measured in this study were approximately 50 ft downstream 

from the Dismal River streamflow-gaging station (fig. 4), 

near the left bank where the vertical head gradient exceeded 

0.5 ft/ft (table 4), which is similar to vertical head gradients 

measured by Guhman and Pederson (1992). At this location, 

the measured streambed temperature was 18.7 oC, which is 

close to the median stream temperature (table 4), indicating that 

there is little groundwater discharge through the streambed at 

this location. The restriction in vertical flow results in the high 

vertical head gradient measured with the potentiomanometer. 

On the right bank, the measured streambed temperature was 

14.1 oC, which indicates the vertical movement of groundwater 

through a more permeable streambed. The measured vertical 

head gradient was an order of magnitude lower (0.07 ft/ft), 

which provides further support to this interpretation.

As part of the stream reconnaissance, a spring inventory 

was completed on the upper Dismal River in early September 

of 2015. The inventory involved floating the stream reach 

through private land in a kayak and taking photographs of each 

visible groundwater discharge point with a GPS-enabled digital 

camera. Examples can be seen in figures 19A–C. Data collection was limited during the spring inventory because landowner access was denied through much of the reach; however, 

locations were recorded and visual estimates of discharge were 

made. Most points of focused groundwater discharge typically were small (less than 0.1 ft3

/s); however, a few focused 

discharge points into the Dismal River exceeded 2 ft3/s.

fig 16

Groundwater discharge points per 5,000 feet

0

20

40

60

80

100

120

0

20

40

60

80

100

120

L264 L237

L229

South Loup River at 

 Saint Michael 0678400

100 90 80 70 60 50 40 30 20 10 0

Distance from South Loup River at Saint Michael streamflow-gaging station, in miles

Streamflow, in cubic feet per second

Focused groundwater discharge point density

Streamflow, in cubic feet per second (August 2015)

EXPLANATION

Figure 16. Measured streamflow and the estimated density of focused groundwater discharge points along the lower 

South Loup River.
30 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

fig 17

1,923

1,924

1,925

1,926

1,927

1,928

June 2014 December 2014 July 2015 January 2016 August 2016 March 2017 September 2017 April 2018

Water-level elevation, in feet above North American Vertical Datum of 1988

A

Date

Stream stage affected by ice

South Loup River stage elevation

Groundwater elevation

EXPLANATION

-5

0

5

10

15

20

25

30

35

40

May 2014 December 2014 July 2015 January 2016 August 2016 March 2017 September 2017 April 2018

Water temperature, in degrees Celsius

B

Date

Stream stage affected by ice

South Loup River temperature

Groundwater temperature

EXPLANATION

Figure 17. South Loup River at Saint Michael, Nebraska, streamflow-gaging station (U.S. Geological Survey station 06784000) and 

nearby observation well. A, Stream and groundwater-level elevation. B, South Loup River and groundwater temperature.
Groundwater Discharge Characteristics for Streams in the Loup River Basin 31

The focused groundwater discharge points, in part, are 

the result of the formation of vertical flow conduits described 

in Guhman and Pederson (1992). One vertical flow conduit, 

locally known as “Blue Pool,” is about 35 ft in diameter and 

145 ft deep. Based on the stratigraphic interpretation of a 

nearby test hole (Ahlbrandt and others, 1983; Conservation 

and Survey Division, University of Nebraska-Lincoln, 2017a), 

some of these vertical conduits are discharging groundwater from the underlying Ogallala. The “Blue Pool” is on a 

hillslope approximately 15 ft above and 100 ft back from the 

active river channel. Guhman and Pederson (1992) pointed 

out that vertical flow conduits generally have firm, semiconsolidated sides, most likely from mineral precipitation, and are 

more resistant to erosion compared to surrounding unconsolidated sediments. Because vertical flow conduits are more 

erosionally resistant, they can persist above the actively incising channel of the Dismal River. Other vertical flow conduits, 

including one approximately 5 mi downstream from the “Blue 

Pool” that is approximately 30 ft across (figs. 19A and 20), 

were observed. Active geomorphic processes such as groundwater sapping processes and active headward migration of 

tributaries, described by Guhman and Pederson (1992), were 

observed during the spring inventory.

Aerial TIR imagery indicated many focused groundwater 

discharge points throughout the upper Dismal reach (above 

the Dismal River streamflow-gaging station; fig. 18). These 

focused groundwater discharge points likely are the result of 

strong upward regional groundwater flow gradients near the 

stream margin and the permeability contrasts of the underlying 

Pliocene-age sediments. Low permeability sediments, such 

as siltstone, can restrict the vertical movement of groundwater and concentrate groundwater discharge at focused points. 

Unfortunately, the “Blue Pool” was not imaged during the 

December 2015 aerial TIR flight because it is within the upper 

5-mi reach where no imagery was acquired; however, other 

focused groundwater discharge points characterized as vertical 

flow conduits was mapped. One such vertical conduit is shown 

in figure 19A. This vertical flow conduit is similar to the “Blue 

Pool” in that it has firm sides indicating that the sediments are 

at least partially consolidated, leaving them resistant to erosion 

compared to the surrounding sediments. The discharge of this 

focused groundwater discharge point, which was the largest 

observed, was estimated to be 2 ft3/s.

The downstream temperature profile of the upper Dismal 

River indicates little change in the rate of input of groundwater discharge (fig. 21), consistent with streamflow measured 

fig 18

0

20

40

60

80

100

120

140

160

180

200

Focused groundwater discharge points per 5,000 feet

40 30 20 10 0 10 20 30 40

0

50

100

150

200

250

300

350

400

450

500

Streamflow, in cubic feet per second

Distance, in miles from Dismal River near Thedford streamflow-gaging station

D1

T133

T134

Dismal River near Thedford 06775900

D5

T138

D7

Upper Dismal River Lower Dismal River

Upstream Downstream

EXPLANATION

Focused groundwater discharge point density

Streamflow, in cubic feet per second (2015)

Streamflow, in cubic feet per second (2016)

Figure 18. Measured streamflow and the estimated density of focused groundwater discharge points along the Dismal 

River.
32 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

in the stream reconnaissance and streamflow reported in 

Peterson and Strauch (2007; table 2). One upward spike in 

the downstream temperature profile was approximately 27 mi 

above the Dismal River streamflow-gaging station (fig. 21). 

This upward spike indicates focused groundwater discharge 

through the streambed near the center of the stream. The 

downward spikes in the downstream temperature profile were 

the result of dense tree cover that obscured parts or nearly the 

entire stream channel. Though only separated by 20 mi, the 

downstream temperature profile of the upper Dismal River 

(fig. 21) was much warmer (7 oC) than the upper South Loup 

River and North Fork South Loup River (fig. 9) at the time of 

the December 2015 flight. The effect of groundwater discharge 

on the stream temperature of the Dismal River during the late 

fall is consistent with the stream temperatures measured in the 

late summer in that stream temperatures were much closer to 

ambient groundwater temperatures.

Lower Dismal River

The lower Dismal River begins just downstream from 

the Dismal River streamflow-gaging station and continues 

downstream to the east to the confluence with the Middle 

Loup River at Dunning, Nebr. (fig. 4). A stream reconnaissance of the reach was completed in August 2016 before the 

collection of aerial TIR imagery. The upper part of this reach, 

just downstream from the Dismal River streamflow-gaging 

station, has no public bridge crossings, which made access to 

this site difficult. The most upstream accessible location was 

approximately halfway between the Dismal River streamflowgaging station and the confluence with the Middle Loup River 

(fig. 4). The lower Dismal River transitions from a meandering stream entrenched within a narrow well-defined valley 

between two barchanoid-ridge dunes to a much wider stream 

with fewer tight meanders. Along some reaches, the stream 

is braided with wide shallow channels and exposed sandbars. 

The streambed texture also transitions from fine sand and 

sandstone interbedded with siltstone to a fine to medium sand 

with some areas of coarse sand to fine gravel. Siliceous plant 

roots, also known rhizoliths or “rootlets,” within the streambed material also were noted at all stream reconnaissance 

locations. Rootlets are a characteristic of the Ogallala (Conservation and Survey Division, University of Nebraska-Lincoln, 

2017a; Divine and others, 2015; Hobza and Sibray, 2014) that 

indicates the stream had incised into the Ogallala at some location upstream.

A

B

C

Vertical flow conduit

fig 19

Figure 19. Photographs of example focused groundwater 

discharge points along the upper Dismal River. A, A large pool 

overlying a vertical flow conduit approximately 5 miles east of the 

confluence of the North and South Fork Dismal River. B, Focused 

groundwater discharge point approximately 1.5 miles east of the 

confluence of the North and South Fork Dismal River. C, Focused 

groundwater discharge point approximately 9 miles east of the 

confluence of the North and South Forks Dismal River.
Groundwater Discharge Characteristics for Streams in the Loup River Basin 33 fig20

100°56'15" 100°56'30"

41°50'50"41°50'40"

Middle Loup River

North Loup River

South Loup River

Dismal River

Platte River

Area pictured

Vertical flow conduit

0 0.1 0.2 MILE 0.050 0.1 0.15

0.15

0.2 KILOMETER 0.05

EXPLANATION

Temperature, in degrees Celsius

5-18

Lower Loup 

Natural Resources District

Upper Loup 

Natural Resources District

 Image by Aaron Schepers, Cornerstone Mapping Inc.

Figure 20. Example aerial thermal infrared image of Dismal River, December 2015. Photograph of the focused vertical flow conduit identified can be seen in figure 19A.
34 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

Streamflow measurements collected during the stream 

reconnaissance generally agree with streamflows measured 

in 2006 (Peterson and Strauch, 2007) and demonstrate that 

flows increase throughout the reach (table 2; fig. 18). Although 

streamflow measurements collected as part of stream reconnaissance for the upper and lower Dismal River reaches were 

collected 1 year apart, some useful observations still can 

be made. The median streambed temperature for the lower 

Dismal River was 3 oC warmer than the upper Dismal River, 

indicating that groundwater discharge through the streambed 

mixes with surface water in the hyporheic zone (table 4). 

The maximum stream temperature measured along the lower 

Dismal River was nearly 9 oC warmer than the maximum 

temperature measured along the upper Dismal River (table 4). 

Warmer streambed and stream temperatures measured along 

the lower Dismal River were expected for a couple of reasons. 

First, the lower Dismal River is more exposed to atmospheric 

conditions because channels are much wider and shallower 

compared to the upper Dismal River. Second, no restrictive 

layers appear to be within the streambed, which would concentrate the vertical movement of groundwater into the stream, 

as were with the upper Dismal River. Based on these observations, groundwater discharge through the streambed is more 

diffuse and mixes with surface water within the hyporheic 

zone. Potentiomanometer measurements indicate positive vertical head gradients between the groundwater system and the 

stream. The largest vertical hydraulic gradient measured was 

much smaller than some vertical hydraulic gradients measured 

along the upper Dismal River (table 4).

The downstream temperature profile for the lower Dismal 

River (fig. 22) indicates a slow decrease in stream temperature 

starting approximately 10 mi downstream from the Dismal 

River streamflow-gaging station. The decrease in temperature 

indicates that a smaller proportion of groundwater discharge 

is entering the stream compared to the total streamflow and 

that the stream generally is wider and more affected by 

atmospheric conditions. Upward spikes in the temperature 

profile are in several locations and are the result of focused 

groundwater discharge through the streambed. These focused 

groundwater discharge points are detectable from aerial TIR 

imagery because of shallow stream depths.

The density of focused groundwater discharge points for 

the upper and lower Dismal River is shown in figure 18. A 

sharp decline in the density of focused groundwater discharge 

points downstream from the Dismal River streamflow-gaging 

station is shown in figure 18. Most likely, this decrease in the 

density of focused groundwater discharge points is related 

to the changes in streambed lithology and underlying geology. Based on mapping by Diffendal (1991), the sediments 

underlying the lower Dismal River transition from the older 

Pliocene-Quaternary-age deposits to modern Holocene-age 

alluvium. This transition is approximately 2 mi downstream 

fig 21

35 30 25 20 15 10 5 0 5

Distance, in miles from the Dismal River near Thedford streamflow-gaging station

0

2

4

6

8

10

12

Water temperature, in degrees Celsius

Upper Dismal River Lower Dismal 

 River

T133

T134

D4

Dismal River near Thedford 06775900

EXPLANATION

Dismal River

Self-logging temperature sensor

Thermistor at streamflow-gaging station

Figure 21. Downstream temperature profile of the upper Dismal River created from aerial thermal infrared imagery 

collected December 3–4, 2015.
Groundwater Discharge Characteristics for Streams in the Loup River Basin 35

from the Dismal River streamflow-gaging station. Based 

on the aerial TIR imagery and stream reconnaissance data, 

the upper Dismal River is dominated by focused groundwater discharge, which increases streamflow across the reach. 

Groundwater discharge most likely originates from focused 

points within Pliocene-age deposits along stream margins, but 

some larger vertical flow conduits originate within the deeper 

Ogallala (Guhman and Pederson, 1992). Downstream from 

the Dismal River streamflow-gaging station, diffuse groundwater discharge through the streambed sustains and increases 

streamflow of the lower Dismal River.

Rootlets in the lower Dismal River indicate that the 

river has incised into the Ogallala at some point upstream. 

As part of the phase 3 ELM, Stanton (2013) subdivided the 

aquifer into two units. Along the Dismal River, those two 

units include the less permeable Tertiary-age Ogallala and 

younger, unconsolidated sand and gravel deposits. Elevations were extracted along the river centerline from a digital 

elevation model (Nebraska Department of Natural Resources 

and U.S. Geological Survey, 1998) and the elevations from 

the base of layer 1 (top of the Ogallala) from Stanton (2013) 

to determine where the Dismal River incised into the Ogallala. Based on these elevations, the Dismal River has incised 

into the Ogallala immediately downstream from the Dismal 

River streamflow-gaging station. Ahlbrandt and others (1983) 

determined the Dismal River most likely has incised into 

Pliocene-age deposits near the confluence of the North Fork 

and South Fork of the Dismal Rivers (fig. 4). Farther to the 

east, closer to the Dismal River streamflow-gaging station, 

the depth of the contact between the Pliocene deposits and the 

Ogallala is much less certain. Though not mapped by Diffendal (1991), the river appears to have incised into the Ogallala a 

short distance downstream from the Dismal River streamflowgaging station.

Water-level and water temperature data collected at the 

Dismal River streamflow-gaging station were examined to 

understand the temporal patterns of groundwater discharge to 

the Dismal River. The groundwater levels measured near the 

Dismal River streamflow-gaging station (fig. 23A) were higher 

than stream-level elevations, indicating that the stream was 

gaining. Changes in groundwater elevation track closely to the 

river stage elevation, indicating a high degree of connectivity 

between the stream and shallow groundwater. Even during 

sharp increases in river stage elevation, which are in response 

to precipitation events, the difference in elevation between the 

stream and the groundwater remains consistent, demonstrating that groundwater discharge and gaining conditions are 

consistent seasonally. The groundwater temperature measured 

in the nearby observation well displays a cyclical pattern that 

varies between 12.5 and 13.5 oC, where its annual maximum 

fig 22

Water temperature, in degrees Celsius

Distance, in miles from the Lower Dismal River near Thedford streamflow-gaging station

5 0 5 10 15 20 25 30 35 40

0

1

2

3

4

5

6

7

Dismal River near Thedford 06775900

D5

T138

D7

D8

Lower Dismal River

Self-logging temperature sensor

Thermistor at streamflow-gaging station

EXPLANATION

Figure 22. Downstream temperature profile of the lower Dismal River created from aerial thermal infrared imagery collected 

November 19–20, 2016.
36 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

fig 23

2,800.0

2,800.5

2,801.0

2,801.5

2,802.0

2,802.5

2,803.0

2,803.5

2,804.0

Water-level elevation, in feet above North American Vertical Datum of 1988

A

August 2015 December 2015 April 2016 August 2016 December 2016 April 2017 August 2017 December 2017

Date

Dismal River stage elevation

Groundwater elevation

EXPLANATION

-5

0

5

10

15

20

25

30

Water temperature, in degrees Celsius

B

August 2015 December 2015 April 2016 August 2016 December 2016 April 2017 August 2017 December 2017

Date

Dismal River temperature

Groundwater temperature

EXPLANATION

Figure 23. Dismal River near Thedford, Nebraska, streamflow-gaging station (U.S. Geological Survey 

station 06775900) and nearby observation well. A, River stage and groundwater elevation. B, Dismal River 

and groundwater temperature.
Groundwater Discharge Characteristics for Streams in the Loup River Basin 37

is measured in early winter and its annual minimum is in 

early summer (fig. 23B). The annual minimum and maximum 

groundwater temperatures lag behind the annual minimum and 

maximum stream temperatures. Because the stream is gaining consistently in this location, the changes in groundwater 

temperature are in response to heat transfer through thermal 

conduction from surface heating and cooling.

North Loup River

Streamflow measurements collected during the stream 

reconnaissance generally agree with streamflows measured 

in 2006 (Peterson and Strauch, 2007) and demonstrate that 

flows were increasing throughout the reach up to the TaylorOrd Canal diversion (table 2; fig. 24). During the stream 

reconnaissance, the Taylor-Ord Canal was diverting water 

from the North Loup River to satisfy downstream irrigation 

demands. At that time, the median streamflow for the Taylor 

streamflow-gaging station was 217 ft3/s, which indicates that 

more than one-half the flow of the North Loup River (521 ft3/s 

at site L428) was diverted. The Nebraska Department of 

Natural Resources operates a streamflow-gaging station on 

the Taylor-Ord Canal (station 107000; Nebraska Department 

of Natural Resources, 2017) approximately 3 mi downstream 

from the diversion from the North Loup River (fig. 5). Adding 

the measured discharge of the Taylor-Ord Canal (213 ft3/s) to 

the discharge measured at the Taylor streamflow-gaging station during the reconnaissance, the North Loup River seemed 

to lose flow just above the Taylor streamflow-gaging station 

(fig. 24).

Median and maximum stream and streambed temperature data collected along the North Loup River were warmer 

than other reaches studied (table 4). The warmer stream and 

streambed temperatures result from the fact that the North 

Loup River is affected heavily by atmospheric conditions 

because the stream is wide and shallow and has little shading 

from vegetation. The stream reconnaissance locations on the 

North Loup River were a greater distance from the headwaters compared to the other streams studied (fig. 1). In some 

locations, the measured streambed temperature approached the 

regional groundwater temperature, indicating focused groundwater discharge through the streambed and little or no mixing with surface water within the hyporheic zone. Potentiomanometer measurements indicated that the North Loup River 

is gaining throughout the study reach and indicated substantial 

variability in vertical hydraulic gradients over short distances 

(table 4).

Taylor-Ord Canal diversion

T435

NL3

NL4

L428

North Loup River at Brewster 06785500

North Loup River at Taylor 

 06786000

L427

L429

L431

T434

T436

T437

T440

0

120

240

360

480

600

0

20

40

60

80

100

90 80 70 60 50 40 30 20 10 0 10

Streamflow, in cubic feet per second

Focused groundwater discharge points per 5,000 feet

Distance, in miles from the North Loup River at Taylor streamflow-gaging station

Focused groundwater discharge point density

Streamflow, in cubic feet per second (August 2016)

Streamflow, in cubic feet per second (November 2006)

EXPLANATION

Figure 24. Measured streamflow (November 2006 and August 2016) and the estimated density of focused groundwater 

discharge points along the North Loup River.
38 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

The downstream temperature profile of the North Loup 

River indicates fairly constant water temperature across the 

study reach (fig. 25). Some of the increases in water temperature were associated with increased groundwater discharge. 

Positive spikes in the downstream temperature profiles that 

indicate points of focused groundwater discharge through 

the streambed were seen approximately 25 mi upstream from 

the North Loup River at Brewster, Nebr., streamflow-gaging 

station (USGS station 06785500; hereinafter referred to as 

the “Brewster streamflow-gaging station”). These points are 

detectable using aerial TIR because they are within shallow 

parts of the stream. A positive spike approximately 48 mi 

above the Taylor streamflow-gaging station (about 15 mi 

upstream from the Brewster streamflow-gaging station) is 

associated with the confluence of Goose Creek (fig. 5), which 

is the largest tributary to the North Loup River within the 

study reach and flows approximately 40 mi before its confluence with the North Loup River. The aerial TIR imagery 

showed the water temperature of Goose Creek was approximately 1.5 oC warmer than the North Loup River, which 

indicated that more of its flow was from recently discharged 

groundwater.

The density of focused groundwater discharge points 

is variable across the study reach. Focused groundwater 

discharge point density varied from nearly 0 to more than 

60 points per 5,000 feet. Focused groundwater discharge 

points were clustered along certain reaches of the North Loup 

River with higher concentrations mapped upstream from site 

NL3 (fig. 24). An area with a large concentration of focused 

groundwater discharge points is near an active gravel mining 

operation, which is at site NL3, approximately 5 mi downstream from the Brewster streamflow-gaging station (fig. 24). 

Sand and gravel outcrops can be seen along the south side of 

Highway 91, 5 miles east of Brewster, Nebr. well above the 

elevation of the current stream channel. The age of the gravel 

currently is not known, but, because a nearly 100-ft elevation difference is between the sand and gravel outcrop along 

Highway 91 and the North Loup River (Nebraska Department 

of Natural Resources and U.S. Geological Survey, 1998), the 

gravel is most likely Pleistocene or Pliocene age. The focused 

groundwater discharge points are along the edges of the modern stream valley and along former channel margins (fig. 26). 

The focused groundwater discharge points are in areas where 

finer-grained sediments that restrict the vertical movement of 

groundwater seem to have been eroded away by a combination 

of headward erosion and groundwater sapping processes.

The North Loup River has incised into Quaternary 

alluvial and eolian deposits (Souders, 2000); however, rootlets 

within the streambed material were noted at every stream 

reconnaissance location, likely because the river incises into 

the Ogallala at multiple points upstream. River elevations 

were extracted along the river centerline from a digital elevation model (Nebraska Department of Natural Resources and 

U.S. Geological Survey, 1998) and the elevations from the 

base of layer 1 (top of the Ogallala) from Stanton (2013) to 

determine where the river is incising into the Ogallala. Based 

L427

0

1

2

3

4

5

6

Water temperature, in degrees Celsius

Distance, in miles from the North Loup at Taylor streamflow-gaging station 

90 80 70 60 50 40 30 20 10 0 10

NL1

T435

North Loup River at Brewster 06785500

NL3 L428

North Loup River at Taylor 

 06786000

North Loup River

Thermistor at streamflow-gaging station

Self-logging temperature sensor

EXPLANATION

Figure 25. Downstream temperature profile of the North Loup River created from aerial thermal infrared imagery 

collected November 19–20, 2016.
Groundwater Discharge Characteristics for Streams in the Loup River Basin 39 fig 26

99°48'00" 99°48'30" 99°49'00" 99°49'30"

41°55'30"41°55'00"41°54'30"

North Loup River

Middle Loup River

Dismal River

South Loup River

Area pictured

Lower Loup 

Natural Resources District

Upper Loup 

Natural Resources District

Focused groundwater 

discharge points

HIGHWAY 91

0 0.4 0.6 0.8 MILE 0.20 0.4 0.6 0.8 KILOMETER 0.2

EXPLANATION

Temperature, in degrees Celsius

5.4-6.2

 Image by Aaron Schepers, Cornerstone Mapping Inc.

Figure 26. Example aerial thermal infrared image of the North Loup River, November 2016.
40 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

on these elevations, it appears that the North Loup River is 

incising into the Ogallala in three different locations; approximately 73, 22, and 8 mi upstream from the Taylor streamflowgaging station (fig. 5). At these locations, the density of 

focused groundwater discharge points approaches 0 (fig. 24), 

which indicates that the vertical movement of groundwater is 

somewhat restricted and that the Ogallala is relatively impermeable compared to the overlying sediments. One hypothesis 

is that the formation of focused groundwater discharge points 

through groundwater sapping processes may be inhibited 

because the Ogallala is a semiconsolidated sandstone that is 

relatively resistant to erosion compared to overlying unconsolidated Quaternary- and Pliocene-age deposits (Gutentag 

and others, 1984).

Results from the stream reconnaissance and examination of aerial TIR imagery indicate that increases in streamflow along the studied reach of the North Loup River are the 

result of a combination of focused and diffuse groundwater 

discharge. Subsurface geologic information indicates that 

the North Loup River most likely flows over an alternating 

sequence of Quaternary-age alluvial sediments, Pliocene- or 

Pleistocene-age sand and gravels, and the Tertiary-age Ogallala. Unfortunately, the precise locations of all these contacts 

remain unclear at this time. The higher concentration of 

focused groundwater discharge points possibly was in areas 

where the North Loup River is flowing over Pliocene-age 

deposits, creating similar patterns in focused groundwater discharge observed along the upper Dismal River (fig. 18), 25 mi 

to the southwest.

Water-level and water temperature data collected at two 

streamflow-gaging stations were examined to understand the 

temporal patterns of groundwater discharge to the North Loup 

River. The groundwater levels measured near the Brewster 

streamflow-gaging station and the Taylor streamflow-gaging 

station (figs. 27A and 28A) were higher than stream-level 

elevations, indicating gaining conditions. Changes in groundwater elevation track closely to the stream elevation, indicating a high degree of connectivity between the stream and 

shallow groundwater. Even during sharp increases in stream 

elevation, which are in response to precipitation events and ice 

formation, the difference in elevation between the stream and 

the groundwater remains consistent, which demonstrates that 

groundwater discharge and gaining conditions are consistent 

seasonally. The groundwater-level elevation at the Taylor 

streamflow-gaging station (fig. 28A) remained above the 

stream elevation throughout the period of record; however, 

this difference in elevation decreased through the summer months. The decreased difference most likely is due to 

increased groundwater pumping and evapotranspiration rates 

that have lowered groundwater levels locally.

The groundwater temperature measured in the shallow 

well near the Brewster streamflow-gaging station displays a 

cyclical pattern that varies between 11.0 and 13.5 oC, where 

its annual maximum is measured in early winter and its annual 

minimum is in early summer (fig. 27B). The annual minimum and maximum groundwater temperatures lag behind the 

annual minimum and maximum stream temperatures. Because 

the stream is consistently gaining in this location, the changes 

in groundwater temperature are in response to heat transfer 

through thermal conduction. The shallow well near the Taylor 

streamflow-gaging station displayed similar seasonal trends; 

however, the temperature varied between 10.0 oC in the fall 

and 13.9 oC in the spring (fig. 28B).

Middle Loup River

Water-level and water temperature data collected at the 

Middle Loup River at Dunning streamflow-gaging station 

were examined to understand the temporal patterns of groundwater discharge to the Middle Loup River, which is immediately above the confluence with the Dismal River (figs. 1 and 

4). The groundwater levels measured near the Middle Loup 

River at Dunning streamflow-gaging station were higher than 

river stage elevations, indicating that the stream was gaining 

additional groundwater (fig. 29A). Changes in groundwater 

elevation track closely to the stream elevation, indicating a 

high degree of connectivity between the stream and shallow 

groundwater. Even during sharp increases in stream elevation, which are in response to precipitation events and ice 

formation, the difference in elevation between the stream and 

the groundwater remains consistent, which demonstrates that 

groundwater discharge and gaining conditions are consistent 

seasonally.

The groundwater temperature measured in the shallow well displays a cyclical pattern that varies between 11.5 

and 14.5 oC, where its annual maximum is measured in early 

winter and its annual minimum is in early summer (fig. 29B). 

The annual minimum and maximum groundwater temperatures lag behind the annual minimum and maximum stream 

temperatures. Because the stream is gaining consistently at 

this location, and the direction of groundwater movement is 

towards the stream, the changes in groundwater temperature 

are in response to heat transfer through thermal conduction 

from surface heating and cooling.

Ice formation within the stream channel appears to have 

an effect on groundwater levels at the stream margin. In 

December 2016 and early January 2017, two periods of ice 

formation on the Middle Loup River caused a sharp increase 

in stream stage that was not associated with an increase in 

stream discharge. The increase in stream stage is the result of 

the backpressure created by ice cover on the stream. Groundwater levels rose in response to this backpressure. Ice conditions temporarily caused the stream elevation to increase and 

surpass the groundwater-level elevation, indicating losing 

conditions. A decrease in groundwater temperature during this 

same time indicated movement of water through the streambed 

back in the shallow aquifer (fig. 28B).
Groundwater Discharge Characteristics for Streams in the Loup River Basin 41

fig 27

2,471.0

2,471.5

2,472.0

2,472.5

2,473.0

2,473.5

2,474.0

2,474.5

2,475.0

2,475.5

2,476.0

May 2015 October 2015 March 2016 August 2016 January 2017 June 2017 November 2017 April 2018

Water-level elevation, in feet above North A

merican Vertical Datum of 1988 

Date

Stream stage affected by ice

Groundwater elevation

North Loup River stage elevation

A EXPLANATION

-5

0

5

10

15

20

25

30

35

Temperature, in degrees Celsius

B

May 2015 October 2015 March 2016 August 2016 January 2017 June 2017 November 2017 April 2018

Date

Stream stage affected by ice

North Loup River temperature

Groundwater temperature

EXPLANATION

Figure 27. North Loup River at Brewster, Nebraska, streamflow-gaging station (U.S. Geological Survey station 06785500) and nearby 

observation well from May 2015 to April 2018. A, Stream and groundwater-level elevation. B, North Loup River and groundwater 

temperature.
42 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

fig 28

2,251.5

2,252.0

2,252.5

2,253

2,253.5

2,254.0

2,254.5

August 2015 January 2016 June 2016 November 2016 March 2017 August 2017 January 2018

Water-level elevation, in feet above North A

merican Vertical Datum of 1988 

Date

Stream stage affected by ice

North Loup River stage elevation

Groundwater elevation

EXPLANATION

-5

0

5

10

15

20

25

30

35

August 2015 January 2016 June 2016 November 2016 March 2017 August 2017 January 2018

Water temperature, in degrees Celsius

Date

Stream stage affected by ice

North Loup River temperature

Groundwater temperature

EXPLANATION

A

B

Figure 28. North Loup River at Taylor, Nebraska, streamflow-gaging station (U.S. Geological Survey station 06786000) and nearby 

observation well from August 2015 to January 2018. A, Stream and groundwater-level elevation. B, North Loup River and groundwater 

water temperature.
Groundwater Discharge Characteristics for Streams in the Loup River Basin 43

fig 29

-5

0

5

10

15

20

25

30

35

Temperature, in degrees Celsius

August 2015 January 2016 June 2016 November 2016 March 2017 August 2017 January 2018

Date

Stream stage affected by ice

Middle Loup River temperature

Groundwater temperature

EXPLANATION B

2,608.0

2,608.5

2,609.0

2,609.5

2,610.0

2,610.5

2,611.0

2,611.5

2,612.0

August 2015 January 2016 June 2016 November 2016 March 2017 August 2017 January 2018

Date

Water-level elevation, in feet above North A

merican Vertical Datum of 1988 

Stream stage affected by ice

Middle Loup River stage elevation

Groundwater elevation

EXPLANATION A

Figure 29. Middle Loup River at Dunning, Nebraska, streamflow-gaging station (U.S. Geological Survey station 06775500) and nearby 

observation well from August 2015 to January 2018. A, Stream and groundwater-level elevation. B, Middle Loup River and groundwater 

water temperature.
44 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

Primary Controls on Groundwater 

Discharge Characteristics Within the 

Loup River Basin

The results from the stream reconnaissance and examination of aerial TIR imagery have demonstrated the effect of the 

surficial and subsurface geology on the spatial characteristics 

of groundwater discharge to streams in the Loup River Basin 

(fig. 1). The patterns and distribution of focused and diffuse 

groundwater discharge from each stream are the result of 

the unique geologic framework and lithologic characteristics 

of Quaternary-, Pleistocene-, and Pliocene-age deposits and 

of the Tertiary-age Ogallala deposits. Diffuse and focused 

groundwater discharge from Quaternary-age deposits of silt, 

sand, and gravel sustain flow for most stream reaches within 

the Loup River Basin. At the headwaters of the South Loup 

River, groundwater discharge is dominated by groundwater 

discharging from Quaternary-age deposits at many small (less 

than 0.1 ft3/s) focused points. The volume of water produced 

from this dense network of focused groundwater discharge 

points along the North Fork South Loup River is sufficient to 

provide approximately 40 percent of the flow measured at the 

Arnold streamflow-gaging station during the irrigation season.

Pliocene-age sand and gravel deposits also have had a 

major influence on the spatial patterns of groundwater discharge to the South Loup River. Approximately 5 mi downstream from the Arnold streamflow-gaging station, the river 

incises into Pliocene-age sand and gravel deposits, providing 

additional groundwater discharge to the stream. The streamflow of the South Loup River increases by a factor of 5 across 

a 62-mi reach of the middle South Loup River. The additional 

streamflow is from a combination of diffuse groundwater discharge through the streambed and large (as much as 1.5 ft3

/s) 

focused groundwater discharge points.

On the Dismal River, the lithologic character of Pliocene- and Quaternary-age deposits has a major influence in the 

distribution and patterns of focused and diffuse groundwater 

discharge. The upper Dismal River is actively incising into 

Pliocene deposits that are described locally as interbedded fine 

sand and weakly consolidated sandstone and siltstone (Conservation and Survey Division, University of Nebraska-Lincoln, 

2017a). The river meanders within a narrow, deep valley 

bound by barchanoid-ridge dunes where high pressure gradients along the stream margin have created conditions favorable for the formation of large focused groundwater discharge 

points and “boiling” sand springs. Increases in streamflow 

along the upper Dismal River result from a dense network of 

focused groundwater discharge points. Just downstream from 

the Dismal River streamflow-gaging station, the Dismal River 

incises into the Tertiary-age Ogallala over a short reach before 

flowing over the top of Quaternary-age alluvial deposits. The 

lithologic character of the Quaternary-age deposits along the 

lower Dismal River generally is coarser and more permeable 

compared to the Pliocene-age deposits along the upper Dismal 

River. Geomorphically, the Dismal River transitions from 

a tightly meandering entrenched stream at its upper reach 

to a wider, shallower, and at times braided stream before its 

confluence with the Middle Loup River. Focused groundwater 

discharge points are relatively rare, and diffuse groundwater 

discharge sustains and increases the streamflow of the lower 

Dismal River.

Groundwater sapping was evident on some stream 

reaches and has increased the size and flow of focused groundwater discharge points. Previous researchers have documented 

streambed incision and groundwater sapping on the upper 

Dismal River that have created and enlarged focused groundwater discharge points capturing additional groundwater 

and increasing discharge in the Dismal River (Guhman and 

Pederson, 1992). This trend can be seen in long-term streamflow records at the Dismal River streamflow-gaging station 

(fig. 4; U.S. Geological Survey, 2017). Groundwater sapping 

also appears to have played a role in the formation of larger 

focused groundwater discharge points, which sustain the flow 

of the middle South Loup River. The constant flow of groundwater removed finer-grained Quaternary-age sediments and 

further exposed Pliocene-age gravel deposits. Headward erosion is evident because some of the large focused groundwater 

discharge points have incised their own draws and terminate 

in bowl-like depressions away from the stream (figs. 14A and 

14B).

The percentage of groundwater-irrigated land within a 

stream basin is one factor that affects groundwater discharge 

to streams within the Loup River NRDs. A striking example 

of this is at the Saint Michael streamflow-gaging station 

(fig. 17A) where the shallow groundwater levels declined 

below the level of the stream during the middle to late part of 

the growing season when consumptive groundwater use was 

at its peak (July to September). Groundwater levels rebounded 

in the fall, indicating a return to gaining conditions. The South 

Loup River Basin above the Saint Michael streamflow-gaging 

station has the highest percentage of groundwater-irrigated 

row crops of all the basins examined. Farther upstream, on 

the middle South Loup River, a groundwater-level recorder 

(USGS station 411126099422501; U.S. Geological Survey, 

2017) indicates that water was discharging from Tertiary-age 

Ogallala into the South Loup River; however, local pumping 

reduced the amount of groundwater that is discharged to the 

stream temporarily. After pumping ceases, groundwater levels 

rebounded to ambient conditions. Continuous groundwater and 

surface-water levels measured at the Taylor streamflow-gaging 

station indicated that the stream was receiving groundwater 

throughout the year; however, when consumptive groundwater 

use peaks during the middle to late part of the growing season 

(July to September), the difference in elevation between the 

groundwater level and the stream elevation decreases, which 

indicates a reduction in the amount of groundwater discharge 

received.
Primary Controls on Groundwater Discharge Characteristics Within the Loup River Basin 45

Summary

Streams in the Loup River Basin are sensitive to groundwater withdrawals because of the close hydrologic connection 

between groundwater and surface water. Pumping from aquifers that are hydrologically connected to surface-water bodies 

can have a substantial effect by reducing the groundwater discharge to surface water. Groundwater discharge is the primary 

component of streamflow in the Loup River Basin and constitutes more than 90 percent of streamflow in the central Sand 

Hills. Streams in the Loup River Basin receive a combination 

of focused discharge (groundwater discharge as springs) and 

diffuse discharge (relatively uniform discharge). These areas 

of focused groundwater discharge have not been extensively 

mapped; furthermore, the effect of various climatic and landuse changes on groundwater discharge patterns currently (as of 

2018) is unknown. To improve the understanding of geologic 

controls, such as formation permeability, and various climatic 

and land-use changes on groundwater discharge, the U.S. Geological Survey (USGS), in cooperation with the Upper Loup 

Natural Resources District (NRD), the Lower Loup NRD, 

and the Nebraska Environmental Trust, studied the spatial and 

temporal characteristics of groundwater discharge within the 

Loup River Basin.

This report documents the methods of data collection 

and analysis, which include the collection of approximately 

350 river miles of aerial thermal infrared (TIR) imagery during 2015–16 and continuous groundwater-level and temperature data from six streamflow-gaging stations during 2014–16 

within the Loup River Basin. These datasets were collected 

to improve the understanding of geologic controls and spatial 

patterns of groundwater discharge.

Georeferenced TIR imagery was interpreted within a geographic information system environment using two different 

analysis methods. The first method involved creating downstream temperature profiles where stream surface temperatures 

are extracted every 6.6 feet along a digitized stream centerline. 

The extracted point temperatures were plotted against distance 

upstream or downstream from a streamflow-gaging station. 

Because aerial TIR imagery was collected before the onset 

of ice, warmer stream temperatures would be the result of an 

increase in the proportion of groundwater discharge, relative 

to total streamflow. The second analysis method estimated 

the density of focused groundwater discharge points along 

individual stream reaches. The density of focused groundwater 

discharge points was assessed by creating an Esri shapefile 

and picking individual focused groundwater discharge points 

through visual inspection of the TIR and reference imagery. 

Focused groundwater discharge point density was estimated in 

number of points per 1,000 or 5,000 feet.

The potential land-use and associated groundwater 

irrigation effects on the temporal variability of groundwater 

discharge also were evaluated. Additional water-level and temperature data were collected at six streamflow-gaging stations 

to assess the temporal variability of groundwater discharge. 

The data collection design consists of a streamflow-gaging 

station coupled with a nearby observation well completed 

below the elevation of the streambed and instrumented with a 

water-level recorder. The comparison of continuous groundwater-level elevation and stream-stage elevation can indicate 

whether a stream is gaining or losing near the streamflowgaging station. Continuous water temperature was collected in 

the stream and the shallow observation well to provide further 

support to groundwater/surface-water interaction trends.

The results from the stream reconnaissance and examination of aerial TIR imagery have demonstrated the influence of 

the surficial and subsurface geology on the spatial characteristics of groundwater discharge to streams in the Loup River 

Basin. The patterns and distribution of focused and diffuse 

groundwater discharge from each stream are the result of 

the unique geologic framework and lithologic characteristics 

of Quaternary, Pleistocene, Pliocene, and Tertiary Ogallala 

deposits. Diffuse and focused groundwater discharge from 

Quaternary deposits of silt, sand, and gravel sustain flow for 

most stream reaches within the Loup River Basin.

At the headwaters of the South Loup River, groundwater discharge is dominated by groundwater discharging from 

Quaternary deposits at many small (less than 0.1 cubic foot 

per second) focused points. The volume of water produced 

from this dense network of focused groundwater discharge 

points along the North Fork South Loup River was sufficient 

to provide approximately 40 percent of the flow measured at 

the South Loup River at Arnold, Nebraska, streamflow-gaging 

station (USGS station 06781600) during the irrigation season. 

Approximately 5 miles downstream from the South Loup 

River at Arnold, Nebr., streamflow-gaging station, the river 

incises into Pliocene-age sand and gravel deposits, providing 

additional groundwater discharge to the stream. The streamflow of the South Loup River increases by a factor of 5 across 

a 62-mile reach of the middle South Loup River. The additional streamflow is from a combination of diffuse groundwater discharge through the streambed and large (as much 

as 1.5 cubic feet per second) focused groundwater discharge 

points.

On the Dismal River, the lithologic character of Pliocene and Quaternary deposits has a major influence in the 

distribution and patterns of focused and diffuse groundwater 

discharge. The upper Dismal River is actively incising into 

Pliocene deposits that are described locally as interbedded 

fine sand and weakly consolidated sandstone and siltstone. 

The river meanders within a narrow, deep valley bound by 

barchanoid-ridge dunes where high pressure gradients along 

the stream margin have created conditions favorable for the 

formation of large focused groundwater discharge points and 

“boiling” sand springs. Increases in streamflow along upper 

Dismal River result from a dense network of focused groundwater discharge points. Just downstream from the Dismal 

River near Thedford, Nebr., streamflow-gaging station (USGS 

station 06775900), the Dismal River incises into the Ogallala Formation over a short reach before flowing over the top 
46 Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16

of Quaternary-age alluvial deposits. The lithologic character 

of the Quaternary deposits along the lower Dismal River 

is generally coarser and more permeable compared to the 

Pliocene-age deposits along the upper Dismal River. Geomorphically, the Dismal River transitions from a tightly meandering entrenched stream at its upper reach to a wider, shallower, 

and at times braided stream before its confluence with the 

Middle Loup River. Focused groundwater discharge points are 

relatively rare, and diffuse groundwater discharge sustains and 

increases the streamflow of the lower Dismal River.

Groundwater sapping was evident on some stream 

reaches and has increased the size and flow of focused groundwater discharge points. Previous researchers have documented 

streambed incision and groundwater sapping on the upper 

Dismal River that have created and enlarged focused groundwater discharge points, capturing additional groundwater and 

increasing discharge in the Dismal River. This trend can be 

seen in long-term streamflow records at the Dismal River near 

Thedford, Nebr., streamflow-gaging station. Groundwater 

sapping also appears to have played a role in the formation of 

larger focused groundwater discharge points, which sustain 

flow of the middle South Loup River. The constant flow of 

groundwater removed finer-grained Quaternary sediments and 

further exposed Pliocene-age gravel deposits. Headward erosion is evident because some of the large focused groundwater 

discharge points have incised their own draws and terminate in 

bowl-like depressions away from the stream.

The percentage of groundwater-irrigated land within a 

stream basin is one factor that affects groundwater discharge 

to streams within the Loup River NRDs. The most striking 

example is at the South Loup River at Saint Michael, Nebr., 

streamflow-gaging station (USGS station 06784000) where 

the shallow groundwater levels declined below the level of the 

stream during the growing season when consumptive groundwater use was at its peak (July to September). Groundwater 

levels rebounded in the fall, indicating a return to gaining 

conditions. The South Loup River Basin above the South Loup 

River at Saint Michael, Nebr., streamflow-gaging station has 

the highest percentage of groundwater-irrigated row crops 

of all the basins examined. Farther upstream, on the middle 

South Loup River, a groundwater-level recorder indicates that 

water is discharging from the Ogallala Formation into the 

South Loup River; however, local pumping can reduce the 

amount of groundwater that is discharged to the stream temporarily. After pumping ceases, groundwater levels rebound 

to ambient conditions. Continuous groundwater and surfacewater levels measured at the North Loup River at Taylor, 

Nebr., streamflow-gaging station (USGS station 06786000) 

indicate that the stream is receiving groundwater throughout 

the year; however, when consumptive groundwater use peaks 

during the growing season (July to September), the difference 

in elevation between the groundwater level and the stream 

elevation decreases, which indicates a reduction in the amount 

of groundwater discharge received.

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For more information about this publication, contact

Director, USGS Nebraska Water Science Center 

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Hobza and Schepers—Groundwater Discharge Characteristics for Selected Streams Within the Loup River Basin, Nebraska, 2014–16—SIR 2018–5093

ISSN 2328-0328 (online)

https://doi.org/10.3133/sir20185093