U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2016–5004

Prepared in cooperation with the National Park Service

Effects of Streamflows on Stream-Channel Morphology 

in the Eastern Niobrara National Scenic River, Nebraska, 

1988–2010
Cover. View of Niobrara River looking downstream from bluff near Mariaville, Nebr. Photograph 

taken by Jason Alexander, U.S. Geological Survey. 

Right side photographs, top to bottom. Aerial photograph of Niobrara River near Meadville, Nebr., 

in 1999. Photograph from U.S. Geological Survey. Aerial photograph of Niobrara River near Meadville, 

Nebr., in 2003. Photograph from U.S. Department of Agriculture.
Effects of Streamflows on StreamChannel Morphology in the Eastern 

Niobrara National Scenic River, 

Nebraska, 1988–2010

By Nathaniel J. Schaepe, Jason S. Alexander, and Kiernan Folz-Donahue

Prepared in cooperation with the National Park Service

Scientific Investigations Report 2016–5004

U.S. Department of the Interior

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

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Director

U.S. Geological Survey, Reston, Virginia: 2016

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Suggested citation:

Schaepe, N.J., Alexander, J.S., and Folz-Donahue, Kiernan, 2016, Effects of streamflows on stream-channel morphology in the eastern Niobrara National Scenic River, Nebraska, 1988–2010: U.S. Geological Survey Scientific Investigations Report 2016–5004, 30 p., http://dx.doi.org/10.3133/sir20165004.

ISSN 2328-0328 (online)
iii

Contents

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

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

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

Description of Study Area ............................................................................................................................2

Physiography and Fluvial Geomorphology .......................................................................................4

Hydrology and Water Development..........................................................................................4

Recent Climatic Variability ..................................................................................................................5

Methods...........................................................................................................................................................5

Streamflow.............................................................................................................................................5

Channel Morphology............................................................................................................................7

Quantification of Uncertainty..............................................................................................................8

Effects of Streamflows on Stream-Channel Morphology .....................................................................10

Streamflow...........................................................................................................................................10

Peak Flows..................................................................................................................................10

Seasonal Distribution of Monthly Flows ................................................................................10

Summer Low Flows of Niobrara River....................................................................................13

Summer Flows of Long Pine Creek .........................................................................................13

Channel Morphology..........................................................................................................................16

Channel Metrics.........................................................................................................................16

Statistical Comparisons...................................................................................................16

Cross-Sectional Width Analysis..............................................................................................19

Effects of Streamflows on Stream-Channel Morphology Changes ...........................................23

Summary........................................................................................................................................................27

References Cited..........................................................................................................................................28
iv

Figures

1. Map showing study segments of eastern Niobrara National Scenic River and 

surrounding area in north-central Nebraska...........................................................................3

2. Graph showing summary of monthly mean streamflow of Niobrara River near

Sparks, Nebraska, and Palmer Drought Severity Index for north-central region of 

Nebraska, water years 1946–2010 .............................................................................................6

3. Map showing digitized features on 2003 aerial photograph of example segment of

eastern Niobrara National Scenic River in north-central Nebraska...................................9

4. Graph showing annual series of peak flows for Niobrara River near Sparks,

Nebraska, 1988–2010..................................................................................................................11

5. Graphs showing median monthly streamflows for selected streamgages near the

study area ....................................................................................................................................12

6. Graphs showing annual measures of streamflow of Niobrara River near Sparks,

Nebraska, 1988–2010..................................................................................................................14

7. Graphs showing annual measures of streamflow for Long Pine Creek near

Riverview, Nebraska, 1988–2010 ..............................................................................................15

8. Graphs showing channel-width metrics and total area of islands plus incipient

flood-plain surfaces of the eastern Niobrara National Scenic River, Nebraska, 

for 1993, 1999, 2003, 2006, and 2010..........................................................................................18

9. Boxplot diagrams of the frequency distribution of cross-section scale changes in

channel-width metrics from aerial photography between consecutive pairs of

study years, study segment 1, eastern Niobrara National Scenic River, Nebraska,

1993–2010 .....................................................................................................................................20

10. Boxplot diagrams of the frequency distribution of cross-section scale changes in

channel-width metrics from aerial photography between consecutive pairs of

study years, study segment 2, eastern Niobrara National Scenic River, Nebraska,

1993–2010 .....................................................................................................................................21

11. Boxplot diagrams of the frequency distribution of cross-section scale changes in

channel-width metrics from aerial photography between consecutive pairs of

study years, study segment 3, eastern Niobrara National Scenic River, Nebraska,

1993–2010 .....................................................................................................................................22

12. Graph showing longitudinal trend in total channel width for reach in study segment

1, 53,000 to 63,000 meters upstream from study area boundary, eastern Niobrara

National Scenic River, Nebraska, 1993–99, highlighting an area of bank erosion ..........23

13. Maps showing channel change delineated on aerial photographs of eastern

Niobrara National Scenic River, Nebraska, highlighting areas that underwent 

substantial bank erosion in a part of segment 1....................................................................24

14. Graph showing longitudinal trend in total channel width for reach in study

segments 1 and 2, 40,000 to 50,000 meters upstream from study area boundary,

eastern Niobrara National Scenic River, Nebraska, 1999–2003, highlighting an area

of island attachment to bank ....................................................................................................25

15. Maps showing channel change delineated on aerial photographs of eastern 

Niobrara National Scenic River, Nebraska, highlighting an area of island 

attachment to a bank in a part of segment 1..........................................................................26
v

Tables

1. Characteristics of aerial photography used for calculating channel metrics,

eastern Niobrara National Scenic River, 1993–2010...............................................................8

2. Average areal uncertainty of digitized features in the eastern Niobrara National

Scenic River, Nebraska, 1993–2010 .........................................................................................11

3. Statistical analysis test results of measured active channel width between 1993

and 2010 for three segments of the eastern Niobrara National Scenic River..................16

4. Measures of channel morphology for three segments of the eastern Niobrara 

National Scenic River, north-central Nebraska, as measured from aerial imagery 

for selected years, 1993–2010...................................................................................................17

Conversion Factors

[International System of Units to Inch/Pound]

Multiply By To obtain

Length

centimeter (cm) 0.393701 inch (in.)

meter (m) 3.281 foot (ft)

kilometer (km) 0.6212 mile (mi)

Area

square meter (m2

) 0.000247 acre

square kilometer (km2

) 247.105 acre

square meter (m2

) 10.76 square foot (ft2)

square kilometer (km2

) 0.3861 square mile (mi2)

Flow rate

cubic foot per second (ft3

/s) 0.0283 cubic meter per second (m3/s)

Volume

cubic kilometer (km3

) 0.2399 cubic mi (mi3)

A water year is the 12-month period from October 1 through September 30 of the following year 

and is designated by the calendar year in which it ends.

Datum

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

(NAVD 88).
vi

Abbreviations

GIS geographic information system

lidar light detection and ranging

NPS National Park Service

NWIS National Water Information System

PDSI Palmer Drought Severity Index

RMSD root-mean-square difference

USFWS U.S. Fish and Wildlife Service

USGS U.S. Geological Survey

WSRA Wild and Scenic Rivers Act
Effects of Streamflows on Stream-Channel Morphology 

in the Eastern Niobrara National Scenic River, Nebraska, 

1988–2010

By Nathaniel J. Schaepe, Jason S. Alexander, and Kiernan Folz-Donahue

Abstract

The Niobrara River is an important and valuable economic and ecological resource in northern Nebraska that 

supports ecotourism, recreational boating, wildlife, fisheries, 

agriculture, and hydroelectric power. Because of its uniquely 

rich resources, a 122-kilometer reach of the Niobrara River 

was designated as a National Scenic River in 1991, which has 

been jointly managed by the U.S. Fish and Wildlife Service 

and National Park Service. To assess how the remarkable 

qualities of the National Scenic River may change if consumptive uses of water are increased above current levels, the U.S. 

Geological Survey, in cooperation with the National Park 

Service, initiated an investigation of how stream-channel morphology might be affected by potential decreases in summer 

streamflows. The study included a 65-kilometer segment in the 

wide, braided eastern stretch of the Niobrara National Scenic 

River that provides important nesting habitat for migratory 

bird species of concern to the Nation.

The study focused on three river segments, separated at 

the confluences with two tributaries, Plum Creek and Long 

Pine Creek. With an overall temporal scope of 1988–2010 that 

includes a short interval preceding and a long interval following the Niobrara National Scenic River Designation Act of 

1991, the study analyzed five separate time periods: 1988–93, 

1994–99, 2000–3, 2004–6, and 2007–10, each of which 

ended with a year in which aerial photography coverage was 

available.

Streamflow duration was analyzed for one streamgage 

upstream from the study area and two streamgages on tributary streams within the study area. Summer streamflows (July, 

August, and September) were targeted for analysis because 

median flows of the Niobrara River are lowest during those 

3 months. In addition, peak flows during the study period were 

used to estimate bankfull discharge, which is one determinant 

of channel dimensions.

Changes in channel morphology were examined using 

aerial photographs from 1993, 1999, 2003, 2006, and 2010 to 

measure channel width, area of islands, and incipient floodplain surfaces, and to compute the braided index. Channel 

metrics were computed for each photography year and summarized by river segment. Additionally, at fixed-location cross 

sections, photography analysis identified localized geomorphic 

change to infer processes. Accuracy of geomorphic feature 

classification was estimated and the root-mean-square difference (RMSD) between aerial photographs was calculated to 

determine associated errors in channel metric calculations. The 

horizontal accuracy of boundaries delineated in the classification was estimated as 5 meters (m) for boundaries based on 

1993 aerial photography and 4 m for all other aerial photography. The RMSD between aerial photography years ranged 

from 3.04 m to 4.16 m.

The largest measurable changes in channel metrics were 

measured between 1993 and 1999 and between 1999 and 

2003. Between 1993 and 1999, average total channel width 

increased by 9 m (3 percent) and 14 m (5 percent) in segments 2 and 3, respectively; average active channel width 

increased by 13 m (5 percent) in segment 3 and decreased by 

6 m (4 percent) in segment 1; and incipient flood-plain-surface 

area increased by 40, 44, and 33 percent in segments 1, 2, and 

3, respectively. Changes in channel metrics between 1999 

and 2003 included a decrease in average total channel width 

of 14 m (5 percent) in segment 2; a decrease in active channel widths of 8 m (3 percent) and 6 m (2 percent) in segments 

2 and 3, respectively; and an increase of 5 m (3 percent) in 

segment 1. Incipient flood-plain areas decreased by 22 and 

33 percent in segments 1 and 2, respectively, and increased by 

42 percent in segment 3. 

Large changes were measured between 1993 and 1999, 

and between 1999 and 2003, at many of the fixed-location 

cross sections. Large changes (that is, greater than 25 percent) 

in total channel width were measured in all three segments 

between 1993 and 1999 and again between 1999 and 2003; 

large increases were dominant between 1993 and 1999 and 

large decreases were dominant between 1999 and 2003. Segment 1 was the most susceptible to localized changes as there 

was only one period (between 2003 and 2006) in which the 

active channel width largely changed in fewer than 10 percent 

of the cross sections.

Changes in channel metrics generally corresponded to 

changes in streamflow conditions, but other than changes in 
2 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

incipient flood-plain area, these changes were small and were 

not measured in all three segments simultaneously. Increases 

in total channel width (except in segment 1) and incipient 

flood-plain area between 1993 and 1999 corresponded to 

increases in streamflow. Channel narrowing (except in segment 1) between 1999 and 2003 corresponded to lower summer streamflows and extended durations of very low summer 

streamflow. Although the pattern of low summer streamflow 

and extended durations of very low summer streamflow continued during the 2004–6 period and at the beginning of the 

2007–10 period, no further narrowing was measured. Consistent tributary summer inflows help to explain the resistance 

of segments 2 and 3 to further narrowing. Because segment 1 

is already much narrower than segments 2 and 3, its average 

current velocity is likely to be swifter and, therefore, competent to offset further effects of the processes that led to its 

narrowness.

Introduction

The Niobrara National Scenic River in north-central 

Nebraska (fig. 1) is an important economic and ecological resource that supports ecotourism, recreational boating, 

wildlife, fisheries, hydroelectric power, and agriculture. It has 

a diverse ecosystem with many plant and animal species and 

is used as a stopover for migratory bird species that include 

several threatened or endangered species (Ducey, 1989). 

The Niobrara National Scenic River was established by the 

Niobrara Scenic River Designation Act of 1991 to protect this 

valuable resource. The Niobrara Scenic River Designation Act 

cited protections of the Niobrara River under the Wild and 

Scenic Rivers Act of 1968 (WSRA), and administration of 

the Niobrara Scenic River Designation Act was delegated to 

the U.S. Fish and Wildlife Service (USFWS) and the National 

Park Service (NPS). Under the specific language of the WSRA 

(Public Law 90-542; 16 U.S.C. 1271 et seq., 1968):

It is hereby declared to be the policy of the United 

States that certain selected rivers of the Nation 

which, with their immediate environments, possess outstandingly remarkable scenic, recreational, 

geologic, fish and wildlife, historic, cultural, or 

other similar values, shall be preserved in freeflowing condition, and that they and their immediate 

environments shall be protected for the benefit and 

enjoyment of present and future generations.

Much of the Niobrara River is west of the 100th meridian, which roughly separates temperate climates to the east 

from the semi-arid or steppe climates to the west (Powell, 

1879). The semi-arid agricultural lands adjacent to and 

upstream from the Niobrara National Scenic River generally require irrigation for dependable crop yields, and future 

expansion of irrigated agriculture may increase consumptive 

use of water supplies such that some tributary inflows that 

presently sustain the Niobrara National Scenic River could be 

placed at risk of becoming seasonally intermittent. 

The juxtaposition of irrigated agriculture and federally 

mandated protections of the Niobrara National Scenic River 

represents a potential long-term conflict over water in the 

Niobrara River. Scientific information is needed to assess how 

potential changes in streamflows from increased consumptive uses may affect the Niobrara National Scenic River. In 

cooperation with the NPS Water Rights Branch, the U.S. 

Geological Survey (USGS) initiated a study to investigate 

how channel morphology in the eastern part of the Niobrara 

National Scenic River might be affected by potential decreases 

in summer streamflows. The eastern region of the Niobrara 

National Scenic River was selected because the river channel 

is wide and braided, provides important nesting and roosting 

habitat for Federal- and State-listed bird species, and a change 

in river stage of as little as 50 centimeters (cm) can inundate 

or expose a large fraction of the river bed.

This study focused on channel morphology changes on 

the Niobrara River associated with changes in streamflow, 

especially low flows, for two reasons. First, the Niobrara 

River is strongly dependent on groundwater seepage, making 

its base flows potentially vulnerable to the effects of pumpage from the shallow alluvial aquifers that recharge the river 

(Soenksen and others, 2010). Second, irrigation withdrawals 

from the river are temporally coincident with the typically 

low-flow months from July through September, making it a 

period of particular vulnerability.

Purpose and Scope

The purpose of this report is to present the results from 

a study of the potential effects of variable streamflows on 

stream-channel morphology along a 65-kilometer (km) segment of the eastern Niobrara National Scenic River. Special 

consideration is given to address how periods of decreased 

low flows may have preceded periods of channel narrowing. 

The study focused on the time period preceding and following the designation of the Niobrara River as a National Scenic 

River in 1991, specifically 1988–2010. This period was split 

into five separate analysis periods based on the availability of 

aerial photography: water years 1988–93, 1994–99, 2000–03, 

2004–6, and 2007–10. A water year is the 12-month period 

from October 1 through September 30 of the following year 

and is designated by the calendar year in which it ends.

Description of Study Area

The study area extends 65 km along the Niobrara River 

from Norden to Mariaville, Nebraska (fig. 1). The studied 

river segments are characterized by a wide, braided channel 

and a wide valley (Alexander and others, 2010). Tributaries 

discharging into the study area include Plum and Long Pine 
Description of Study Area 3

101° 100°30' 100° 99° 99° 98°30'

43°30'

43°

42°30'

0 10 20 30 MILES

0 10 20 30 KILOMETERS Sandhills from U.S. Geological Survey, 1970; 

Niobrara River Basin from U.S. Geological Survey 

and U.S. Department of Agriculture, 2008

#

1

U.S. Geological Survey streamgage 

Niobrara National Scenic River 

(reach managed by the 

National Park Service)

Study river-segment number

Base from U.S. Geological Survey National Atlas 

hydrography and county boundary data, 2014; 1:1,000,000 scale

Universal Transverse Mercator projection, zone 14 

Transportation data from National Highway Planning Network, 2011, 

1:100,000 scale, and Nebraska Department of Roads, 1995, 1:24,000 scale

EXPLANATION

Niobrara

River Basin

Sandhills

SOUTH DAKOTA

NEBRASKA

MINNESOTA IOWA

WYOMING

COLORADO

Map area

CHERRY

BROWN

ROCK

HOLT

BOYD

KEYA PAHA

NEBRASKA

SOUTH DAKOTA

TODD

MELLETTE

TRIPP

GREGORY CHARLES 

MIX

DOUGLAS

BRULE AURORA

1

2 3

06461500

#

#

G 06463500

#

06463500

06462500

# #06463720

06462000

Norden

Meadville

Mariaville

MERRITT DAM

Winner

Mission

Gregory

Valentine

O’ Neill

183

281

137

20

83

281

183

83 18 Missouri River

Niobrara River

Snake River

Long Pine Cr

Keya Paha River

Plum

Cr

Figure 1. Study segments of eastern Niobrara National Scenic River and surrounding area in north-central Nebraska.
4 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

Creeks (fig. 1), each of which contributes roughly 10 percent 

of the annual streamflow at Mariaville (Fischer, 1987).

The study area was divided into three segments based 

on the locations of tributary confluences. Segment 1 begins at 

a county-road bridge south of Norden, Nebr., and ends at the 

confluence with Plum Creek. Segment 2 begins at the confluence with Plum Creek and ends at the confluence with Long 

Pine Creek. Segment 3 begins at the confluence with Long 

Pine Creek and ends at the Nebraska State highway 137 bridge 

north of Mariaville, Nebr. (fig. 1).

Physiography and Fluvial Geomorphology

The Niobrara River flows across 900 km of the Great 

Plains of North America (Fenneman, 1946) and drains 

approximately 35,000 square kilometers (km2

) along its course 

(Alexander and others, 2010). Although the Niobrara River 

basin (fig. 1) includes parts of east-central Wyoming and 

southern South Dakota, most of the drainage basin and main 

stem of the river lie in north-central Nebraska. Approximately 

40 percent of the river basin is within the Nebraska Sand Hills 

region (hereinafter referred to as “the Sandhills”) of the Great 

Plains (Omernik, 1987), a vast region of wind-blown sand, 

stabilized by prairie vegetation, mantling Neogene- to Cretaceous-age bedrock (Bleed and Flowerday, 1990). The bedrock 

units include Brule of the White River Group and Arikaree of 

Paleogene to Neogene age and Pierre Shale of Late Cretaceous 

age. Modern basin physiography is the result of initial relief, 

geologic character, and climatic effects (Schumm, 2005); each 

of these aspects is considered in turn.

Total relief in the Niobrara River basin is approximately 

1,300 meters (m) above the base level altitude at the Missouri 

River confluence of 370 m (North American Vertical Datum of 

1988 [NAVD 88]). Through geologic time, the multiple levels 

of terrace deposits along the middle Niobrara Valley indicate 

there have been periods when the base level fluctuated and 

valleys were filled to a much greater extent with thick alluvial 

sequences. In recent time, the river has evacuated most of its 

alluvium and locally exhibits geologic grade control where 

resistant bedrock underlies the channel. The modern valley gradient along the Niobrara River averages 0.15 percent 

(Alexander and others, 2009) between Dunlap Diversion Dam 

(upstream from and not shown in fig. 1) and the Missouri 

River confluence. 

Along its traverse across northern Nebraska, the physical 

characteristics of the Niobrara River change with additions 

of tributary and groundwater inflows and changes in local 

geologic controls. In eastern Cherry County, the Niobrara 

transitions from a narrower river confined by bedrock canyon 

walls to a much wider channel flowing through a wide alluvial 

valley (Alexander and others, 2010). For the last 200 km of 

its length, the Niobrara River channel is complex, flowing in 

multiple threads separated by islands, broad sand flats, and 

sandbars (Buchanan, 1981). Although the exact geologic 

mechanism for the change in channel planform has not been 

determined, Alexander and others (2010) determined that the 

channel planform transitions where the bedrock at river level 

changes from the Brule of the White River Group and Arikaree of Paleogene to Neogene age to the Pierre Shale of Late 

Cretaceous age.

Buchanan and Schumm (1990) identified streamflow and 

channel ice formation as the principle geomorphic agents of 

channel change in the Niobrara River. Ice formation on sandbars can drastically shift channel location from fall to spring. 

In the fall, the flow becomes shallow and spreads out with 

no discernible thalweg. During winter, ice forms on shallow 

sandbars, stabilizing the bars and constricting the flow, which 

creates a narrow thalweg. As more of the channel freezes, the 

flow becomes further constricted in the thalweg and scours 

the bed below (Buchanan and Schumm, 1990). Alexander 

and others (2010) determined that ice jams caused flooding 

of the modern, active flood plain and low terraces along the 

valley bottom. During ice-free periods, streamflow magnitude 

was identified as the primary agent of geomorphic change. 

Buchanan (1994) also indicated that peak flows removed 

vegetation from bars and eroded banks. During periods of 

low flows, the channel narrowed as islands formed or became 

attached to the flood plain. Buchanan and Schumm (1990) also 

noted some narrowing at tributary confluences where flood 

plains impinge on the main-stem channel.

Hydrology and Water Development

Because of their high infiltration capacity, the Sandhills are a region of groundwater recharge to the High Plains 

Aquifer (Szilagyi and others, 2005). Rivers flowing through 

the Sandhills region are known for small runoff to precipitation ratios and a lagged responsiveness to drought conditions 

(Wang and others, 2009; Istanbulluoglu and others, 2008; 

2012). For example, Istanbulluoglu (2008, p. 30) determined 

that streamflow measured at the Niobrara River at Sparks 

(USGS site 06461500, fig. 1) has a precipitation memory of 

as many as 5 years, which means streamflow could be higher 

than average in a normal precipitation year if the previous 

years were wet, and conversely, if the previous years were dry, 

streamflow could be lower than normal. The strong linkage 

between groundwater storage and surface water makes the 

streams in the Sandhills somewhat resilient to typical 3–4-year 

duration (Istanbulluoglu, 2008) dry periods, but sensitive to 

long-term increased consumptive uses of groundwater (Stanton and others, 2010).

 Irrigation water demand in the Niobrara River basin 

has led to increases in groundwater usage and development 

of streamflow diversions and dams within the Niobrara River 

basin during the last 75 years (Shaffer, 1975). Approximately 

1.082 cubic kilometers (km3

) of water are currently used in 

the Niobrara River basin each year to provide water to an 

estimated 3,215 irrigated km2

. Of that irrigated area, approximately 83 percent is irrigated from groundwater sources and 

17 percent from surface water (Bureau of Reclamation, 2013). 
Methods 5

Box Butte Dam (upstream from the area shown in fig. 1) 

on the Niobrara River and Merritt Dam (fig. 1) on the Snake 

River have had the largest effects on the Niobrara River’s 

hydrology. Box Butte Dam was constructed in 1945 to provide 

water for the Mirage Flats irrigation project. On average, 

0.013 km3

 of water are diverted to irrigate approximately 

47 km2. Merritt Dam was constructed on the Snake River, the 

third largest tributary by drainage area to the Niobrara River, 

to provide water for the Ainsworth Irrigation District (Bureau 

of Reclamation, 2013). The Ainsworth Irrigation District 

provides 0.093 km3

 (Shultz, 2010) annually from reservoir 

storage to irrigate 137 km2

 (Bureau of Reclamation, 2013). 

This is approximately 40 percent of the mean annual runoff 

for the contributing drainage area upstream from Merritt Dam 

(Bureau of Reclamation, 2013). Since the filling of Merritt Reservoir began in 1964, mean annual streamflows on 

the Niobrara River downstream from the Snake River have 

decreased by about 13 percent (Niobrara River near Sparks, 

Nebr., USGS site 06461500; Istanbulluoglu, 2008) to 15 percent (Niobrara River near Norden, Nebr., USGS site 06462000 

[discontinued in 1986]; Buchanan, 1981). Mean monthly 

streamflows measured at the Niobrara River near Sparks, 

Nebr. (USGS site 06461500), have decreased in all months 

except January, with the largest decreases taking place during 

June (9.5 percent), July (24.4 percent), August (25 percent), 

September (24.7 percent), and October (24.7 percent) (Istanbulluoglu, 2008). The 1-day low flow and 14-day low flow 

measured at the Niobrara River at Mariaville, Nebr. (USGS 

site 06463720 [discontinued in 1991, reinstated in 2012]) 

decreased by 162 cubic feet per second (ft3

/s) and 200 ft3/s, 

respectively (Fischer, 1987). These changes in hydrology led 

to channel narrowing processes such as island formation and 

attachment of islands to the flood plain (Buchanan, 1994).

Recent Climatic Variability

The north-central region of Nebraska that encompasses 

the study area had abnormally wet and dry periods before and 

after the Niobrara River’s designation as a National Scenic 

River in 1991. Climatic indices such as the Palmer Drought 

Severity Index (PDSI) provide a quantitative method for 

comparing climate conditions during different time periods. 

The PDSI quantifies climatic conditions by comparing moisture supply and demand to calculate a “moisture anomaly” 

index that expresses the relative departure of weather conditions from historical average moisture conditions (Palmer, 

1965; Alley, 1984). The National Oceanic and Atmospheric 

Administration (NOAA) calculates PDSI as a monthly time 

series using monthly precipitation and temperature data along 

with their historically near-normal conditions (Palmer, 1965). 

The PDSI values for the north-central region of Nebraska 

were obtained from NOAA’s National Climatic Data Center 

(National Oceanic and Atmospheric Administration, 2014). 

In 1988, the region had a wet period (PDSI greater than 1 for 

a majority of the year) followed by a dry period (PDSI less 

than -1 for a majority of the year) during 1989–91 (fig. 2). 

During 1990, the driest year during the study period, average monthly PDSI was -2.84. Immediately after the National 

Scenic River designation in 1991, the north-central Nebraska 

region had an extended wet period (1992–99), followed by a 

dry year in 2000, a wet year in 2001, and a dry 3-year period 

during 2002–4. This 3-year dry period (average monthly PDSI 

value of -2.23) was similar to the dry period during 1989–91 

(average monthly PDSI value of -2.26). Near-normal climatic 

conditions followed until 2007 when a 4-year wet period 

extended through 2010 (fig. 2). During 2010, the wettest year 

during the study period, average monthly PDSI was +6.66.

Methods

The purpose of the study described in this report was to 

develop an understanding of how changes in streamflow affect 

stream-channel morphology in the Niobrara National Scenic 

River. The study focused on a time period prior to designation of the Niobrara National Scenic River through 2010. 

The study used a three-stage approach: (1) analysis of hydrologic variability, (2) quantification of channel morphology 

over time, and (3) development of basic statistical relations 

between measures of channel morphology and hydrology. 

Aerial imagery was available for 1993, 1999, 2003, 2006, 

and 2010; therefore, the analyzed time periods were 1988–93, 

1994–99, 2000–3, 2004–6, and 2007–10. 

Streamflow

Streamflow data were downloaded from the USGS 

National Water Information System (NWIS) (U.S. Geological 

Survey, 2015) web service. Daily mean streamflow and annual 

peak discharge values were downloaded for three streamgages 

located in the vicinity of the study area: Niobrara River near 

Sparks, Nebr. (USGS site 06461500); Long Pine Creek near 

Riverview, Nebr. (USGS site 06463500); and Plum Creek at 

Meadville, Nebr. (USGS site 06462500). These sites will hereinafter be called Niobrara River near Sparks, Long Pine Creek 

near Riverview, and Plum Creek at Meadville, respectively.

Flood-frequency curves provide critical information for 

historical hydrologic analysis and water resources planning 

(Dunne and Leopold, 1978). Although the focus of this report 

is on low flows, a simple statistical analysis of flood-frequency 

curves was used to establish a typical bankfull discharge, 

which is an important benchmark for determining how well 

a river maintains its channel’s average state (Leopold, 1994). 

Peak flows after Merritt Dam began operating in 1964, hereinafter referred to as “post-regulation,” were used to estimate 

the bankfull discharge for the Niobrara River near Sparks. 

Discharge was associated with the 1.5-year (or 0.6667 annual 

occurrence probability) recurrence interval flood, which is 

widely considered a reasonable estimate of bankfull discharge 

(Leopold, 1994; Hortness and Berenbrock, 2004) when only 
6 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

10/1/1945 10/1/1955 10/1/1965 10/1/1975 10/1/1985 10/1/1995 10/1/2005

0

400

800

1,200

-10

-5

0

5

10

10/1/2010

EXPLANATION

Monthly mean streamflow

12-month moving average of monthly mean streamflow

Palmer Drought Severity Index

Extremely wet

Very wet

Moderately wet

Slightly wet

Mild drought

Incipient to near-normal conditions

Moderate drought

Severe drought

Extreme drought

Palmer Drought Severity Index classifications

Streamflow, in cubic feet per second

Palmer Drought Severity Index

Merritt Reservoir

begins operating

Niobrara Scenic River Designation 

Act of 1991 signed into law

Year

Figure 2. Summary of monthly mean streamflow of Niobrara River near Sparks, Nebraska (U.S. Geological Survey site 06461500),

and Palmer Drought Severity Index (National Oceanic and Atmospheric Administration, 2014) for north-central region of Nebraska, 

water years 1946–2010.

limited observations of channel hydraulics are available. 

The 1.5-year flood for the river segment used for this study 

was estimated using the USGS computer program, PeakFQ 

(Veilleux and others, 2014), and the annual instantaneous 

peak-flow values for the Niobrara River near Sparks. Only 

the values after 1964 were used to estimate the 1.5-year flood. 

Analysis was done for a period of regulated streamflow, so the 

station skew option was selected based on recommendations 

in “Guidelines for determining flood frequency” (Interagency 

Advisory Committee on Water Data, 1982). The discharge 

associated with the1.5-year flood for the post-regulation period 

was 1,829 ft3

/s and is consistent with Alexander and others 

(2010), who determined that the flood plain in the canyon section of the river upstream from the study area was inundated 

by a discharge between 1,530 and 2,150 ft3

/s. Peak flows at 

Niobrara River near Sparks were compiled for 1988–2010 

(years shortly preceding and following the Niobrara National 

Scenic River Designation Act of 1991) and compared to the 

1.5-year flood.

The statistical likelihood of daily and monthly streamflows within the study area was characterized using flowduration curves. Flow-duration curves indicate how likely it is 

that a particular streamflow magnitude will take place during 

a particular period (Krstolic and Ramey, 2012) and represent 

cumulative percentiles of streamflow. Flow-duration curves 

were calculated using USGS tools within the TIBCO Spotfire 

S+® software package (S+; TIBCO Software, Inc., 2008).

Flow-duration curves using daily streamflow values were 

developed for three USGS streamgages: Niobrara River near 

Sparks, Plum Creek at Meadville, and Long Pine Creek near 

Riverview. Flow-duration curves were computed by month for 

all streamgages. Monthly flow-duration curves were computed 

using all years within the study period (1988–2010), as well 

as for each of the individual time periods (1988–93, 1994–99, 

2000–3, 2004–6, and 2007–10) for the USGS streamgages 

Niobrara River near Sparks and Long Pine Creek near Riverview. The starting year, 1988, was selected on the basis 

of Istanbulluoglu’s (2008) determination that the Niobrara 

River streamflow may be influenced by precipitation from as 

many as 5 previous years. Only daily streamflow from 1988 

to 1994 was used for analysis of the Plum Creek at Meadville 

streamgage because the streamgage was decommissioned at 

the end of 1994. Median monthly streamflow calculated for 

Niobrara River near Sparks indicated that for the 1988–2010 

study period streamflow was lowest during the 3 months of 

July, August, and September. 
Methods 7

The late summer months of July, August, and September 

(hereinafter referred to as “summer”) were thus identified as 

the low-flow season and targeted for further in-depth analysis. 

The 10th, 25th, 50th, and 75th percentiles were calculated for 

the low-flow season for Niobrara River near Sparks and Long 

Pine Creek near Riverview. Low-flow season percentiles and 

duration curves were not calculated for Plum Creek at Meadville because the streamflow record (1948–94) did not extend 

throughout the overall study period. For duration curves for 

July through September, streamflow percentiles were calculated for each year from 1988 to 2010 independently as well as 

for the entire post-regulation period (1964–2011). The summer 

low-flow percentiles calculated for the post-regulation period 

were then compared to each year’s summer low-flow percentiles to calculate summer median departures and number of 

days with streamflow below the 10th percentile of summer 

low flow, which is a good indicator of the severity of a dry 

season (Krstolic and others, 2006). 

Channel Morphology

Analysis of aerial photographs was used to identify 

changes in channel morphology during the study period. 

Delineations of channel morphologic features were digitized 

into a geographic information system (GIS). Feature layers 

were registered to rectified and georeferenced digital aerial 

photographs. Aerial photographs from 1993, 1999, 2003, 

2006, and 2010 were selected for analysis (table 1). The 1993 

aerial photographs were assumed to best represent the state 

of the Niobrara River at the time of designation as a National 

Scenic River. The photographs were taken during periods 

of varying discharges (table 1). By delineating only identified islands, incipient flood-plain surfaces, and high banks, 

the authors were able to reduce positional uncertainty caused 

by imprecision in the exactly coincident discharge for each 

photograph. To quantify channel alterations spatially and 

temporally, specific channel metrics were selected for analysis. 

Channel width, braided index, percentage of cross sections 

intersected with incipient flood-plain surfaces and islands, and 

area of incipient flood-plain surfaces and islands were calculated. These geomorphic characteristics were selected because 

they can be identified during various flow conditions and 

indicate if the channel is becoming overly vegetated, which 

reduces bird habitat.

Quantification of channel morphology focused on 

identifying areas of the channel that were vegetated and 

non-vegetated, and followed a simplified version of the 

flood-plain development model described by Reinfelds and 

Nanson (1993). Channel morphologic features were digitized 

on-screen into a GIS. Three primary features were digitized 

in each photograph: (1) top-of-bank along the active channel, 

(2) top-of-bank for mature islands (defined as being within 

the channel area bounded by active-channel bank lines and 

covered with mature shrubs or woodland vegetation) within 

the active channel, and (3) boundaries of incipient flood-plain 

surfaces (defined as being within the active channel and covered with small shrubs or herbaceous vegetation, and previously not having vegetation cover) within the active channel. 

Areas outside the active channel and islands were considered 

to be established flood plain or terraces and were identified 

by their generally taller vegetation and visually coarse texture 

(from vegetation), by comparison with previous aerial photos 

and by comparison of land-surface height relative to that of 

adjacent surfaces. The latter comparison was made using a 

digital elevation model. Incipient flood-plain surfaces within 

the channel banks were identified as those that (1) were not 

vegetated in a previous photo, and (2) were lighter in tone and 

finer in texture than nearby areas of established flood plain 

in the same photograph. Incipient flood-plain surfaces were 

considered transitional between active channel and established flood plain. If an incipient flood-plain surface persisted 

(apparently) by appearing also in the subsequent set of aerial 

photographs, the incipient flood-plain surface was identified as established flood plain in the subsequent set of aerial 

photographs.

Morphologic features were identified from each year’s 

aerial photographs using interpretation and analysis by one 

GIS technician and then were checked and edited by a geomorphologist. Features were digitized at a scale of 1:2,000 to 

1:4,000 depending on the resolution and quality of the photograph. Channel and island bank lines were digitized along the 

tops of banks. Incipient flood-plain surfaces were digitized at 

the edges of vegetation patches (fig. 3). If a questionable area 

in one photograph (mainly 1993, which had lesser quality) 

showed up as vegetated in the subsequent year’s photograph, 

then the photograph in question was assumed to also be 

vegetated. A 2-m digital elevation model obtained from light 

detection and ranging (lidar) data from 2012 overflights (Merrick and Co., 2012) was used to help differentiate between 

incipient flood-plain surfaces and established flood plain in 

the 2010 aerial photographs. The established floodplain was 

generally at least 0.2 m higher than the incipient flood-plain 

surfaces. Channel centerlines were created for each year to 

provide a longitudinal stationing system. Centerlines were 

developed using the Channel Planform Statistics Toolbox 

(Lauer, 2006). The tool was used to create centerline vertices 

at 30-m longitudinal intervals, approximately a one-tenth average channel-width spacing. Cross sections were also created at 

each 30-m longitudinal interval (fig. 3) and used to calculate 

the following river-channel metrics: (1) channel width, (2) 

channel braided index, and (3) percent of channel width intersecting established islands and incipient flood-plain surfaces. 

Results of GIS analysis were summarized by study segment. 

The study segments are described in the “Description of Study 

Area” section.

Channel width.—Channel width was analyzed using two 

separate classifications: total channel width, which excludes 

islands, and active channel width, which excludes islands and 

incipient flood-plain surfaces. Cross sections were truncated 

(“clipped”) at the boundaries of the channel (banklines) and 

then the digitized islands were clipped from the subsequent 
8 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

Table 1. Characteristics of aerial photography used for calculating channel metrics, eastern Niobrara National Scenic River, 1993–

2010.

[RMSD, root-mean-square difference; 2003 aerial photographs used as reference for registration error calculations. Streamflows are mean daily streamflows for 

U.S. Geological Survey streamgage Niobrara River near Sparks, Nebraska; uncertainty of positions compared between photography years assumes independent 

registration errors; --, not applicable]

Year Source Image type

Registration 

RMSD,

in meters

Resolution, 

in meters Imagery dates

Streamflow, 

in cubic feet per 

second

1993 U.S. Geological Survey (1993) panchromatic 3.41 2 June 20, 21, July 29, 

Sept. 15 

549–862

1999 U.S. Geological Survey (1999) panchromatic 4.16 1 April 17–19 927–934

2003 U.S. Department of Agriculture 

(2003)

color 0.00 1 July 14–July 24, 2003 499–566

2006 U.S. Department of Agriculture 

(2007)

color 3.04 1 July 12–July 26, 2006 384 –456

2010 U.S. Department of Agriculture 

(2010)

color 3.78 1 June 24–July 16, 2010 650–1,190

RMSD of compared feature position, in meters

Compared with aerial photography 

from year 2

Aerial photography from indicated year 1

1999 2003 2006 2010

1993 5.4 3.4 4.6 5.1

1999 -- 4.2 5.2 5.6

2003 4.2 -- 3.0 3.8

2006 5.2 3.0 -- 4.8

2010 5.6 3.8 4.8 --

line features to provide measures of total channel width. 

Lastly, the digitized incipient flood-plain surfaces were clipped 

from the total width line features to obtain active channel 

width.

Braided index.—Braided index was calculated for each 

study segment by summing the total number of line segments 

that resulted from splitting the cross sections using mature 

island and incipient flood-plain surfaces, and dividing that 

number by the total number of cross sections in the study 

segment. This method of calculating braided index differs 

from that used by some previous investigators (for example, 

Elliott and Jacobson, 2006) who included sandbars as well as 

islands when computing a braided index. The quality of many 

photographs used for this study did not allow analysts to confidently distinguish between wetted and non-wetted sandbars; 

therefore, a braided index summing the number of channels 

between incipient flood-plain surfaces and islands was used 

herein.

Measures of island and incipient flood-plain extent.—The 

percent of cross sections intersecting islands and incipient 

flood-plain surfaces was calculated within each segment as 

well as the area of these surfaces per river kilometer. The 

number of cross sections split by each of incipient flood-plain 

surfaces and islands was summed and then divided by the 

total number of cross sections to determine the percentage of 

cross sections within a study segment that intersected incipient 

flood-plain surfaces or islands. The area of islands and incipient flood-plain surfaces was summed for each segment. Areas 

of incipient flood-plain surfaces and islands were then divided 

by the segment length to obtain the segment-mean area of 

incipient flood-plain surfaces and islands per kilometer.

Additionally, total channel width and active channel 

width were analyzed using the 1993 centerline for all photography years, which allowed comparison of site-specific 

changes between years, analogous to paired samples. The 

paired comparison assisted in identification of specific reaches 

that had large geomorphic changes and the associated geomorphic processes that likely caused the changes.

Quantification of Uncertainty

Uncertainty in the classification process was quantified 

to determine if measured differences were real or within the 

range of error and therefore negligible. Various quantifications of classification accuracy and error were estimated. The 

root-mean-square difference (RMSD) was used to quantify 

differences between identical geolocations shown in different photographs, which is important when comparing colocated cross sections. Precision of the classification process 

also was estimated and the associated areal uncertainty was 

quantified. These two uncertainty metrics are pertinent to 
Methods 9

Aerial photograph from U.S. Department of Agriculture 

National Aerial Imagery Program, 2003 

Incipient flood-plain surface

Island

Channel cross section

N

EXPLANATION

0

0

0.05

0.05

0.1 0.15

0.150.1

0.2 MILE

0.2 KILOMETER

Figure 3. Digitized features on 2003 aerial photograph of example segment of eastern Niobrara National Scenic River, in northcentral Nebraska.

all segment-scale gross calculations (average width, braided 

index, and vegetated area summations). 

RMSD.—Horizontal positional difference between 

photography years was determined for each set of aerial 

photographs by calculating the RMSD of co-located groundreference points (roof corners, building edges, fence corners) 

that were matched to the reference base map. The 2003 

imagery was used to identify original reference points because 

these photographs had a combination of high spatial resolution 

and natural color that improved edge detection and contrast 

(table 1). For each photography year, reference points were 

located at a spacing of 3 river kilometers or less (measured 

longitudinally along the river centerline), which resulted in 

at least 27 points for each photography year. These reference 

points were used to calculate the RMSD where:

RMSD

P x p x P y p y

n

a

n

a a a a

= ∑ ( ) ( ) − + ( ) ( ) − ( ) 2

(1)

where

RMSD is root-mean-square difference in horizontal 

position between the co-located points 

of the target photography year and 2003 

(basemap reference),

P x a ( ) is the location in the x direction of point a in 

the 2003 aerial photographs,

p x a ( ) is the location in the x direction of point a in 

the target year’s aerial photographs,

P y a ( ) is the location in the y direction of point a in 

the 2003 aerial photographs,

p y a ( ) is the location in the y direction of point a in 

the target year’s aerial photographs, and

n is the total number of co-located points.

Spatial errors are inherent in the rectification process 

of aerial photographs, so the RMSD is used to assess and, if 

rectification can be repeated, to subsequently minimize these 

errors. The RMSD quantifies the minimum detectable change 

of co-located channel morphologic features between years. 

For instance, in the case of a 3-m RMSD, the channel cross 

section being analyzed could be mislocated (relative to another 
10 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

photo) on the photograph 3 m upstream or downstream from 

where the cross section appears to be located on another year’s 

photograph. RMSD results for this study ranged from 3.04 to 

4.16 m by year of aerial photography and from 3.0 to 5.6 m for 

year-to-year aerial photography feature comparisons (table 1).

Classification accuracy.—Errors of commission or omission caused by assigning areal units to categories are often tabulated for a sample of “ground truth” points, and the resulting 

contingency table may be analyzed to quantify the classification accuracy. Because historical photographs were analyzed 

for this study, ground truthing generally was not possible, so 

classification accuracy was not estimated.

Classification and areal uncertainty.—Classification 

uncertainty was estimated by summing the resolution of the 

aerial photographs with an estimate of feature boundary identification uncertainty. The horizontal resolution of aerial photographs varied from 1 to 2 m depending on the year (table 1). 

An additional error of as much as 3 m was estimated to correspond to feature-boundary uncertainty experienced during the 

classification process as a result of poor clarity in some of the 

photographs. Based on these factors, the horizontal uncertainty 

of the banklines, island boundaries, and incipient flood-plain 

surface boundaries are estimated at as much as 4 m for sets 

of aerial photographs with 1-m resolution (1999, 2003, 2006, 

and 2010) and as much as 5 m for aerial photographs with 2-m 

resolution (1993). This means that any detectable changes in 

width between 1993 and 1999 of less than 5 m and less than 

4 m between subsequent periods are negligible. Following the 

reasoning and methodology of Dunn and others (1990), the 

average discrepancy in the classification of a particular feature 

by the same technician was estimated based on two assumptions: the range of delineation errors, assumed to be 5 m on 

either side of the actual boundary; and the frequency distribution of errors, assumed to follow a beta distribution with shape 

parameter 9. The median width, w, of the uncertainty band 

along delineations was estimated as the average interquartile 

range of discrepancies from a Monte Carlo simulation (Fishman, 1995) of 1,000 repetitions, or 2.24 m. Consequently, the 

areal uncertainty of delineated map units was then estimated 

as the mean polygon perimeter length multiplied by w along 

the perimeter. The average areal uncertainties of each type of 

in-channel feature are presented in table 2. These areal uncertainties apply to the calculated areas of islands and incipient 

flood-plain surfaces. Expressed as percentages of the feature 

classes’ average area by segment during the study period, 

uncertainties were no more than 18.7 percent for incipient 

flood-plain area, and no more than 47.5 percent for island 

area (table 2). Because the errors are dependent on the size 

of feature, error as a percentage of average feature area was 

higher in segments with features that had higher perimeter to 

area ratios. For example in segments 2 and 3 the islands were 

wider so the percentage of error was no greater than 10.6 percent (table 2). Conversely in segment 1 for 2003 there was 

only one narrow island and so the percentage of error was 47.5 

percent (table 2).

Effects of Streamflows on StreamChannel Morphology 

Streamflow

In this section, results of the hydrologic analysis are presented and compared among the five analyzed time periods—

first for peak flows, then for monthly flows for all seasons, and 

lastly two subsections focus on streamflow during the summer season only. The first summer subsection is focused on 

summer low flows in the Niobrara River, whereas the second 

addresses summer low flows in Long Pine Creek. 

Peak Flows

Maximum instantaneous peak flows at Niobrara River 

near Sparks during the first two study periods were generally higher than those during the latter three periods (fig. 4). 

The largest peak was in 1994 and the smallest peak was in 

2004 (fig. 4). The large peak in 1994 was an estimated value 

(4,800 ft3

/s) and was at a stage higher (2.74 m) than what is 

usually expected for that magnitude of streamflow, because of 

backwater from ice breakup. For comparison, peak-flow stages 

unaffected by backwater ranged from 0.94 to 1.51 m during 

the study period.

Peak flows were expressed as departure from estimated 

bankfull discharge (fig. 4), because bankfull discharge can 

be an important factor in determining how well the river 

maintains the average state of the channel (Leopold, 1994). 

The calculated 1.5 year flood (1,834 ft3

/s) was used as the 

estimated bankfull discharge. There were 2 years during the 

analysis period of 1988–93 (water years 1989 and 1990) with 

peak discharges more than 50 percent greater than the bankfull discharge (fig. 4). For the remainder of the study period, 

there were only 2 years (water years 1994 and 2001) with a 

peak discharge more than 50 percent greater than the bankfull 

discharge (fig. 4). 

The longest duration of time without a peak flow greater 

than the bankfull discharge was 3 years. This happened 

three times during the study period (1991–93, 1997–99, and 

2002–4), illustrating again how typical this duration is of dry 

spells in the basin. Of the five analysis time periods, 2004–6 

had the smallest peak flows with an average peak flow 22.4 

percent below the bankfull discharge. Of the study years in 

which aerial photographs were analyzed, only 2006 and 2010 

had peak flows greater than bankfull discharge either during 

the year of the photography or in the antecedent year.

Seasonal Distribution of Monthly Flows

Monthly flow-duration curves calculated for the study 

period indicated that the three lowest months for streamflow 

at Niobrara River near Sparks were July through September 

(fig 5A). Monthly median streamflows decreased by about 
Effects of Streamflows on Stream-Channel Morphology 11

Table 2. Average areal uncertainty of digitized features in the eastern Niobrara National Scenic River, Nebraska, 1993–2010.

[NA, not applicable]

Year

Average areal uncertainty of indicated feature class

Incipient flood plain, 

in square meters

Island, 

in square meters

Incipient flood plain, 

in percentage of indicated 

feature classes’ average area 

during study period

Island, 

in percentage of indicated 

feature classes’ average area 

during study period

Segment 1

1993 1,046 634 17.2 19.1

1999 1,178 475 13.4 17.7

2003 983 220 18.7 47.5

2006 1,306 0 15.7 NA

2010 1,116 1,064 14.6 11.8

Segment 2

1993 956 1,328 15.2 7.9

1999 1,270 1,230 9.1 8.1

2003 914 844 16.1 10.6

2006 1,295 811 13.3 10.5

2010 934 840 14.3 10.6

Segment 3

1993 986 1,378 15.6 6.2

1999 871 2,092 17.6 5.0

2003 916 1,651 14.2 6.0

2006 1,297 1,900 14.4 5.9

2010 948 2,256 14.7 6.2 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010

Year

1988

-50

0

50

100

150

1988–93 1994–99 2000–3 2004–6 2007–10

Departure from bankfull discharge, in percent

Figure 4. Annual series of peak flows for Niobrara River near 

Sparks, Nebraska, 1988–2010. Peak-flow values are reported as 

a percentage departure from the bankfull discharge, which was 

estimated using the 1.5-year flood discharge.
12 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

1988–2010

1988–93

1994–99

2000–3

2004–6

2006–10

EXPLANATION

Discharge, in cubic feet per second

January

February

March

April

May

June

July

August

September

October

NovemberDecember

C

100

110

120

130

140

Month

400

500

600

700

800

900

1,000 A

140

160

180

200

220 B

Figure 5. Median monthly streamflows for selected 

streamgages near the study area. A, Niobrara River near 

Sparks (USGS site 06461500), 1988–2010; B, Long Pine 

Creek near Riverview (USGS site 06463500), 1988–2010; 

and C, Plum Creek at Meadville, Nebraska (USGS site 

06462500) , 1988–94.
Effects of Streamflows on Stream-Channel Morphology 13

200 ft3/s from June to July in most years. By October, streamflows begin to rebound, coincident with the end of irrigation 

season, but autumn (October through November) streamflows 

remain lower than those in winter (December through February) and spring (March through May). Median monthly 

streamflows were highest during the 1994–99 period for 7 

of the 12 months (fig. 5A). The 2004–6 period was the only 

period with July, August, and September median-monthly 

streamflows all below those for 1988–2010. The 2004–6 

period also had the two lowest median monthly streamflows, 

which were in August and September (479 ft3/s and 486 ft3/s, 

respectively). The 1994–99 period had the highest median 

monthly streamflows for all summer months except July where 

it had the second highest.

By contrast, median monthly streamflow for Long Pine 

Creek indicates a seasonal pattern driven by irrigation return 

flows during May through September. From 1988 to 2010, 

Long Pine Creek median monthly streamflows were consistent, differing by only 20 percent, between driest (January) 

and wettest (June) months (160 ft3/s to 192 ft3/s, respectively) 

(fig. 5B). Similar to Niobrara River near Sparks, the period 

from 1994 to 1999 generally had the highest median monthly 

streamflows. The 2004–6 period had lowest median streamflows in all months except September.

Plum Creek is less consistent than Long Pine Creek and 

lacks the signature of return flows during the irrigation period. 

Only March through June had median streamflows greater 

than 120 ft3/s. The highest monthly flows correspond to snowmelt (typically March) and spring rains on the Great Plains. 

Median flows for the remaining 8 months reflect steady base 

flow and differed by only 7 ft3/s (fig. 5C). The streamgage 

Plum Creek at Meadville was discontinued in 1994; therefore, 

comparison of the three analysis periods was not possible.

Summer Low Flows of Niobrara River

Summer low-flow analysis for Niobrara River near Sparks 

indicated that of the five analysis periods, 2000–3 and 2004–6 

had the most extended periods of low streamflow (fig 6A). In 

both periods, 25 percent of flows were below 500 ft3/s for all 

years but one (fig. 6A). During the 1988–93 period, 3 of the 

6 years had similarly low summer streamflow and the 2007–10 

period began with 2 low-flow years as well. The 1994–99 

period had no years with similarly low streamflow.

The wetter period from 1994 to 1999 ended with 3 wet 

years, each with a 50th (median) percentile of summer streamflow greater than 600 ft3

/s. In contrast, the 1988–93 period had 

only 1 year (1993) with a median summer streamflow greater 

than 600 ft3/s, and no years following 1999 had a median 

summer streamflow greater than 600 ft3/s. The lowest median 

summer streamflow (442 ft3/s) occurred in 2002, whereas the 

largest median summer streamflow (653 ft3/s) occurred during 

1997 (fig. 6A).

Median summer streamflow was more than 10 percent 

less than the post-regulation period median summer streamflow (526 ft3

/s) during 4 years (2002, 2005–7) in the 2000s. 

Median summer streamflow fell more than 10 percent below 

the historical median in only 1 year (1989) during 1988–93, 

and no years during 1994–99 (fig. 6B). The annual series of 

departures from the long-term median also show that departures of greater than 7 percent generally lasted from 2 to 4 

years.

During the study period, several years had extended 

periods of extremely low flow (extremely low flow defined 

hereinafter as daily mean streamflow below the 10th percentile 

of post-regulation summer flows) (fig. 6C). During the 2004–6 

period, 2 years (2005 and 2006) had 10 or more summer days 

of extremely low flow (fig. 6C). Three other periods (1988–93, 

2000–3, and 2007–10) had 1 year with more than 10 days of 

extremely low flow. Two extremely dry years (2002 and 2006) 

had more than 30 summer days with extremely low streamflow (fig. 6C). During 2002, there were three events of at least 

7 consecutive days with streamflow below the 10th percentile. 

Two of these events were only separated by 1 day of respite, 

which prevented the low-flow event from lasting 21 consecutive days; instead, it was a 7-day low-flow event followed by 

a 13-day low-flow event. During 2006, there was a 27-day 

low-flow event, which was the longest low-flow event during 

the study period.

Summer Flows of Long Pine Creek

Summer flows of Long Pine Creek generally were higher 

than flows during the remainder of the year (fig. 5B), a pattern 

that contrasted with that of summer low flows of the Niobrara 

River. The summer flows of Long Pine Creek provided a substantial source of summer streamflow to the Niobrara River. 

Median summer streamflow of Long Pine Creek near Riverview was 170 ft3

/s during the post-regulation period, which 

is about 30 percent of total summer median streamflow of the 

Niobrara River near Sparks.

Similar to the Niobrara River near Sparks summer 

streamflows, the summer streamflows at Long Pine Creek 

were highest during the 1994–99 study time period (fig. 7A–B) 

when the average 50th percentile of summer streamflow was 

200 ft3

/s. The 1988–93, 2000–3, and 2004–6 time periods had 

the lowest summer streamflows, with each period having multiple years with median summer streamflow less than 180 ft3

/s.

Only 3 years (1989, 2002, and 2006) had summer median 

streamflow less than the post-regulation median summer 

flow (fig. 7B). All these years corresponded to years in which 

summer median streamflow at Niobrara River near Sparks 

was below the post-regulation median summer flow. Although 

these years had summer median flows below the post-regulation period median, none of these departures exceeded 8 

percent (fig. 7B).

The annual 10th percentile of summer streamflows and 

overall 10th percentile of summer streamflows were higher 

during the study period (1988–2010) than the long-term 

(1943–2011) 10th percentile of summer streamflows (fig. 7C). 

Even the lowest 10th percentile of summer streamflows during 

the study period was not substantially lower than the median 
14 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

Year

Streamflow, in cubic feet per second 

19881989199019911992199319941995199619971998199920002001200220032004200520062007200820092010

0

10

20

30

Number of days

-20

-10

0

10

20

Departure of summer median streamflow from post-regulation 

summer median streamflow, in percent

25th percentile

50th percentile

75th percentile

EXPLANATION A

B

C

Study time period

198819901992199419961998200020022004200620082010

400

500

600

700

Figure 6. Annual measures of streamflow of 

Niobrara River near Sparks, Nebraska, 1988–2010. 

A, summer (July through September) flow-duration 

statistics; B, departures of summer median 

streamflow from post-regulation (1964–2010) 

summer median streamflow (post-regulation 

period is after storage began at Merritt Dam); and 

C, number of very-low-flow summer days (that is, 

daily mean streamflow below the 10th percentile of 

summer low flow).
Effects of Streamflows on Stream-Channel Morphology 15

-10

0

10

30

Departure of summer median streamflow from post-regulation 

summer median streamflow, in percent

A

B

C

100

120

140

160

180

Streamflow, in cubic feet per second 

Summer 10th-percentile 

flow for 1988–2010 period

Summer 10th-percentile 

flow for long-term record

19881989199019911992199319941995199619971998199920002001200220032004200520062007200820092010

19881989199019911992199319941995199619971998199920002001200220032004200520062007200820092010

140

180

220

260

Streamflow, in cubic feet per second 

Year

25th percentile

50th percentile

75th percentile

EXPLANATION

Study time period

Figure 7. Annual measures of streamflow for Long 

Pine Creek near Riverview, Nebraska, 1988–2010. A, 

summer seasonal (July through September) flowduration statistics; B, departures of summer median 

streamflow from post-regulation median summer 

streamflow; and C, 10th percentile of summer 

streamflow.
16 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

summer streamflow (161 ft3/s ) for the long-term record. The 

10th percentile of summer streamflows was about 140 ft3

/s 

during the lowest years (fig. 7C), which is only 30 ft3

/s less 

than the post-regulation period median summer streamflow. 

This 30-ft3

/s decrease equates to 6 percent of the median summer streamflow of the Niobrara River near Sparks; therefore, 

the difference of a low-flow summer from an average summer 

flow in Long Pine Creek might be barely measureable after its 

confluence with the Niobrara River, given the typical plus or 

minus 5-percent uncertainty in a discharge measurement there.

Channel Morphology

Channel morphologic changes were measured and 

analyzed for the five analysis periods. The results for channel morphology are presented as segment-level measures of 

channel change and multitemporal comparisons of selected 

morphometry at fixed-location cross sections. A discussion 

of these changes as they relate to the hydrologic and climatic 

conditions of the five analysis periods (1988–93, 1994–99, 

2000–3, 2004–6, 2007–10) is included in the “Effects of 

Streamflows on Stream-Channel Morphology Changes” 

section.

Channel Metrics

Measures of channel morphology indicate that channels changed substantially between 1993 and 1999, and then 

reversed much of this change between 1999 and 2003. There 

were generally increases in all measures of channel width 

between 1993 and 1999 and decreases between 1999 and 

2003, but the magnitude of these changes differed by river 

segment. The largest channel changes among these years were 

measured in river segments 2 and 3 (fig. 1).

Statistical Comparisons

The Kruskal-Wallis test was used to determine if there 

were statistical differences in active channel width for each 

segment between photography years. The Kruskal-Wallis rank 

sum test identifies whether or not the distributions of multiple sample sets are identical or different (Helsel and Hirsch, 

2002). The active channel width was tested as an overall 

indication because of its sensitivity to changes in all other 

geomorphic features (channel boundary, islands, and incipient flood-plain surfaces). At the 90-percent confidence level 

(p-value < 0.1), tests for segments 2 and 3 rejected the null 

hypothesis that the multitemporal measurements originated 

from the same frequency distribution (table 3). At the 95-percent confidence level (p-value < 0.05), only segment 2 rejected 

the null hypothesis (table 3). This indicates that average active 

channel width varied the most in segment 2.

Further evaluation was done using Wilcoxon ranksum tests to compare active channel width in sequential 

photography years for segments 2 and 3. Since there were 

no statistically significant differences in the distribution of 

Table 3. Statistical analysis test results of measured active 

channel width between 1993 and 2010 for three segments of the 

eastern Niobrara National Scenic River.

[df, degrees of freedom; p-value, probability value; n1, number of cross sections in first year of period; n2, number of cross sections in last year of period]

Kruskall-Wallis test

Segment Number of df cross sections p-value

1 2,919 4 0.371

2 3,243 4 0.014

3 4,662 4 0.092

Period

Wilcoxon rank sum test

n1 n2 p-value

Segment 2

1993–99 649 649 0.743

1999–2003 649 649 0.031

2003–6 649 648 0.585

2006–10 648 648 0.542

Segment 3

1993–99 934 930 0.01

1999–2003 930 933 0.436

2003–6 933 933 0.723

2006–10 933 932 0.782

active channel measurements in segment 1 at the 90-percent 

confidence level no further analysis was performed for that 

segment. For segment 2, the 1999–2003 period was the only 

period that had a statistically significant difference at the 

95-percent confidence level (table 3). For segment 3, only the 

1993 to 1999 comparison was significantly different at the 

95-percent confidence level (table 3). 

Segment 1.—Segment 1 is much narrower than segments 

2 and 3, with average active channel width approximately 

100 m less than those of segments 2 and 3. Despite this, segment 1 had more incipient flood-plain area per river kilometer 

than both segments 2 and 3 (table 4). Average total channel 

width remained relatively consistent with only one change 

(2003–6) between study years greater than the estimated error, 

whereas small (less than 4 percent) changes in average active 

channel width were measured between 1993 and 1999, 1999 

and 2003, and 2006 and 2010 (table 4, fig. 8A). For comparison, the Platte River (not labeled on fig. 1), a Nebraska river 

that has narrowed due to water development, had channelwidth reductions of about 10–20 percent per decade due to 

island expansion or attachment and flood-plain expansion 

(Johnson, 1994); however, during a 17-year interval from 1993 

to 2010, the Niobrara’s active channel width narrowed by 7 m 

(4 percent) and total channel width widened by 6 m (3 percent). These are considered real changes because they exceed 

the uncertainty bandwidth, because the classification error 
Effects of Streamflows on Stream-Channel Morphology 17

Table 4. Measures of channel morphology for three segments of the eastern Niobrara National Scenic River, north-central Nebraska, 

as measured from aerial imagery for selected years, 1993–2010.

Channel morphology 1993 1999 2003 2006 2010

Segment 1

Segment length, in kilometers 17.5 17.4 17.5 17.5 17.5

Average total channel width, in meters 179 181 180 185 185

Average active channel width, in meters 162 156 161 160 155

Average braided index, in number of channel threads 1.12 1.15 1.11 1.14 1.18

Percent of cross sections that intersected incipient flood plain 51.0 60.0 70.0 73.3 73.5

Percent of cross sections that intersected islands 1.9 1.4 0.3 0.0 1.2

Total non-active channel (incipient surface or island), in square meters 

per river kilometer

18,616 25,966 19,889 27,057 32,274

Incipient flood-plain surface area, in square meters per river kilometer 18,046 25,352 19,863 27,057 31,759

In-channel island area, in square meters per river kilometer 570 614 26 0 515

Segment 2

Segment length, in kilometers 19.5 19.5 19.5 19.4 19.4

Average total channel width, in meters 281 290 276 275 277

Average active channel width, in meters 269 270 262 259 260

Average braided index, in number of channel threads 1.18 1.10 1.18 1.12 1.18

Percent of cross sections that intersected incipient flood plain 33.4 37.0 38.7 41.3 45.4

Percent of cross sections that intersected islands 13.6 11.2 2.6 2.3 2.3

Total non-active channel (incipient surface or island), in square meters 

per river kilometer

23,695 28,706 15,805 19,197 19,736

Incipient flood-plain surface area, in square meters per river kilometer 15,067 21,705 14,584 18,012 18,519

In-channel island area, in square meters per river kilometer 8,627 7,001 1,221 1,185 1,217

Segment 3

Segment length, in kilometers 28 27.9 28 28 28

Average total channel width, in meters 264 278 276 280 280

Average active channel width, in meters 257 270 264 265 263

Average braided index, in number of channel threads 1.18 1.16 1.25 1.18 1.22

Percent of cross sections that intersected incipient flood plain 17.6 26.7 29.6 35.9 41.7

Percent of cross sections that intersected islands 14.0 15.6 11.6 11.5 10.8

Total non-active channel (incipient surface or island), in square meters 

per river kilometer

19,422 25,351 23,681 25,401 27,328

Incipient flood-plain surface area, in square meters per river kilometer 6,771 9,029 12,849 15,100 18,195

In-channel island area, in square meters per river kilometer 12,651 16,322 10,832 10,300 9,134

measurements for 1993 and 2010 photography indicate that 

changes up to 5 m are within the uncertainty band (assuming 

errors were independent). The most noticeable changes in segment 1 were substantial areal increases in incipient flood-plain 

surfaces between 1993 and 1999 (40 percent; table 4) and again 

between 2003 and 2006. The increases in incipient flood-plain 

surface areas correspond to the small decrease in average 

active channel width during the study period. Between 1999 

and 2003, many of the incipient flood-plain surface areas were 

reactivated in the river channel (22 percent decrease; table 4). 

After 2003, incipient flood-plain surface area once again 

increased so that by 2010 its area and average active channel 

width were both similar to their 1999 measures (table 4).

Segment 2.—The most substantial changes to segment 2 

were measured between 1993 and 1999 and 1999 to 2003. 

Changes between subsequent pairs of study years were small. 

Between 1993 and 1999, total channel width increased by 9 m 

(3 percent) but the increase in average active channel width 

was insignificant (table 3), because the increase in the average total channel width was offset by a 44 percent increase 

in incipient flood-plain surface area (table 4). Between 1999 

and 2003, there were decreases of 14 m (5 percent) and 8 m 

(3 percent) in average total channel width and average active 

channel width, respectively (table 4, fig. 8B). During this early 

phase of a dry period, island area decreased by 83 percent. 
18 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

A

B

C

Total area of islands and incipient flood plain, 

in square meters per kilometer

Active channel width (channel width excluding 

islands and incipient flood plain)

Channel width, in meters, excluding islands

EXPLANATION

1993 1999 2003 2006 2010

252

257

262

267

272

277

18,000

20,000

22,000

24,000

26,000

250

260

270

280

290

12,000

17,000

22,000

27,000

150

160

170

180

15,000

20,000

25,000

30,000

Island and incipient flood-plain area, in square meters per kilometer 

Width, in meters

Year

Figure 8. Channel-width metrics and total 

area of islands plus incipient flood-plain 

surfaces of the eastern Niobrara National 

Scenic River, Nebraska, for 1993, 1999, 

2003, 2006, and 2010. A, by segment 1; B, by 

segment 2; and C, by segment 3.
Effects of Streamflows on Stream-Channel Morphology 19

Visual observation of the aerial photographs verified that the 

bank attachment of large islands was the main contributor 

to decreases in channel width (total and active). After 2003, 

average channel width in segment 2 remained constant; that is, 

differences were within the measurement uncertainty (table 4). 

Because the decreases between 1999 and 2003 were greater 

than the increases between 1993 and 1999, the active channel 

of segment 2 experienced net narrowing of 9 m between 1993 

and 2010.

The spatial frequency of incipient flood plain increased 

between 1999 and 2010 in segment 2 although the total area 

of incipient flood-plain surfaces did not. By 2010, 45 percent 

of cross sections intersected an incipient flood-plain surface 

compared to 37 percent in 1999 (table 4). However, incipient 

flood-plain surface area decreased by 15 percent between 1999 

and 2010. Based on visual inspection of the aerial photographs, in 2010 there were more incipient flood-plain surfaces 

which were extensive longitudinally, but these features were 

not as wide laterally as the incipient flood-plain surfaces in 

1999.

Segment 3.—Segment 3 underwent morphologic changes 

similar to those in segment 2. Average total channel width and 

average active channel width increased by 14 m (5 percent) 

and 13 m (5 percent), respectively, between 1993 and 1999 

(table 4). Between 1999 and 2003, average total channel width 

and average active channel width decreased. The decreases 

of 2 m (within measurement uncertainty) and 6 m (2 percent) 

were not as substantial as the increases during the previous 

period and, as mentioned in the “ Statistical Comparisons” 

section, these were not considered statistically significant. 

Decreases in average total channel width coincided with a 

decrease in island area, similar to segment 2, but the decrease 

in island area was not as substantial (34 percent decrease 

compared to 83 percent decrease for segment 2). Channel 

morphologic changes were small after 2003 with no changes 

in average channel width of more than 1.5 percent, which 

allowed channel widths to have small net increases overall 

during 1993–2010 (table 4). The area of incipient flood-plain 

surfaces steadily increased during the study period, and by 

2010, incipient flood-plain surface area was 169 percent larger 

than in 1993 and 42 percent of all cross sections intersected 

incipient flood-plain surfaces compared to 18 percent in 1993 

(table 4). This trend coincided with a net decrease in area of 

islands so active channel width remained steady through 2010 

(fig. 8C).

Cross-Sectional Width Analysis

Analysis of individual channel cross sections constructed 

in the GIS at fixed locations (using the 1993 channel centerline) indicated that morphologic changes in channel width 

(total channel width and active channel width) between study 

years were large at some individual cross sections even though 

the segments (discussed in the “Channel Metrics” section) as a 

whole did not have large changes. Cross-section analysis indicated that the largest changes in channel width were measured 

between 1993 and 1999, and between 1999 and 2003 (figs. 

9–11). This pattern was consistent with the changes noted at 

the segment scale in the previous “Channel Metrics” section.

Although change in average total and active channel 

width between any consecutive pair of study years was never 

greater than 5 percent (table 4), there were many individual 

cross sections in each segment that had large increases or 

decreases in channel width (large change being defined hereinafter as a change of 25 percent or more between consecutive studied years), indicating the Niobrara River’s channelforming and bank-eroding processes are engaged in a dynamic 

struggle. Although average channel width as a whole in 

segment 1 did not change substantially (as noted in the “Channel Metrics” section), the time series of cross-sectional active 

channel-width measurements indicated that many individual 

segment 1 cross sections experienced large changes, both 

decreases and increases between all compared study years 

(fig. 9A–B). In segment 2, at least 3 percent of cross sections 

indicated large decreases in active channel width between 

1993 and 1999, and many more large decreases between 1999 

and 2003, but large changes after 2003 were more evenly 

balanced between increases and decreases (fig. 10B). In segment 3, large changes in active channel width were measured 

in 7 percent of cross sections between 1993 and 1999, but 

its cross sections did not indicate many large changes thereafter (fig. 11B). Fifteen percent of cross sections in segment 

1 had large decreases in active channel width between 1993 

and 1999, whereas 10 percent of its cross sections had large 

increases (fig. 9B), which generally corroborates the discovery 

of balancing gains and losses noted in the “Channel Metrics” 

section. Only one period (between 2003 and 2006) had fewer 

than 10 percent of segment-1 cross sections with large changes 

in active channel width, which indicates a very fluid segment 

of the river that is continually reworking its sediment by constructing and altering its flood plain.

Total channel width changes during 1993–99.—Large 

increases in total channel width were measured at many fixed 

cross sections from 1993 to 1999. The majority of the large 

increases in total channel width were attributed to bank and 

island erosion, and other large increases were related to channel avulsion between 1993 and 1999, which left new incipient 

flood-plain surfaces behind. An example of an area where 

bank erosion was evident is shown for segment 1 in figures 

12–13. Segments 1 and 3 had the greatest number of large 

changes in total channel width with 9 and 12 percent of cross 

sections widening by at least 25 percent, respectively (figs. 

9A and 11A). Only 3 percent of cross sections in segment 2 

had large increases in total channel width. Large increases of 

total channel width in segment 1 were offset by large losses 

at 11 percent of cross sections. Segments 2 and 3 did not have 

similar offsetting losses as only 0.1 percent and 0.3 percent, 

respectively, of cross sections experienced large losses (figs. 

10A and 11A).

Total channel width changes during 1999–2003.—From 

1999 to 2003, many cross sections in all three segments 

experienced narrowing. The largest decreases in total channel 
20 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska Change in width, in percent

1993–99 1999–2003 2003–6 2006–10

-100

-50

0

50

150

200

250

300

350

-100

-50

0

50

150

200

250

300

350

A

B

Value greater than 1.5 times the interquartile range 

above upper quartile

Largest value within 1.5 times the interquartile range 

above upper quartile

75th percentile

50th percentile 

(median)

25th percentile

Smallest value within 1.5 times the interquartile range 

below lower quartile

Value greater than 1.5 times the interquartile range 

below lower quartile 

Interquartile

range

EXPLANATION

Years

Figure 9. Frequency distribution of cross-section scale changes in channel-width metrics from aerial photography between 

consecutive pairs of study years, study segment 1, eastern Niobrara National Scenic River, Nebraska, 1993–2010. A, Total channel 

width and B, active channel width.
Effects of Streamflows on Stream-Channel Morphology 21

Change in width, in percent

Value greater than 1.5 times the interquartile range 

above upper quartile

Largest value within 1.5 times the interquartile range 

above upper quartile

75th percentile

50th percentile 

(median)

25th percentile

Smallest value within 1.5 times the interquartile range 

below lower quartile

Value greater than 1.5 times the interquartile range 

below lower quartile 

Interquartile

range

EXPLANATION

A

B

-80

-40

0

40

80

120

-60

-40

-20

0

20

40

1993–99 1999–2003 2003–6 2006–10

Years

Figure 10. Frequency distribution of cross-section scale changes in channel-width metrics from aerial photography between 

consecutive pairs of study years, study segment 2, eastern Niobrara National Scenic River, Nebraska, 1993–2010. A, Total channel 

width and B, active channel width.
22 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska Change in width, in percent

A

B

-80

-40

0

40

80

120

-50

-25

0

25

50

75

100

1993–99 1999–2003 2003–6 2006–10

Value greater than 1.5 times the interquartile range 

above upper quartile

Largest value within 1.5 times the interquartile range 

above upper quartile

75th percentile

50th percentile 

(median)

25th percentile

Smallest value within 1.5 times the interquartile range 

below lower quartile

Value greater than 1.5 times the interquartile range 

below lower quartile 

Interquartile

range

EXPLANATION

Years

Figure 11. Frequency distribution of cross-section scale changes in channel-width metrics from aerial photography between 

consecutive pairs of study years, study segment 3, eastern Niobrara National Scenic River, Nebraska, 1993–2010. A, Total channel 

width and B, active channel width.
Effects of Streamflows on Stream-Channel Morphology 23

Width, in meters

EXPLANATION

62,000 60,000 58,000 56,000 54,000

0

100

200

300

400

Distance upstream, in meters, 

from downstream boundary of study area 

1999

1993

Area of 

erosion

Figure 12. Longitudinal 

trend in total channel 

width for reach in study 

segment 1, 53,000 to 63,000 

meters upstream from study 

area boundary, eastern 

Niobrara National Scenic 

River, Nebraska, 1993–99, 

highlighting an area of bank 

erosion.

width at individual channel cross sections were measured 

during this period. Large decreases in total channel width 

between 1999 and 2003 were related to channel narrowing as a result of flood-plain encroachment (figs. 14 and 15). 

Eight percent of cross sections in segments 1 and 2 had large 

decreases in width (figs. 9 and 10). Only 3 percent of cross 

sections in segment 3 had large total channel width decreases 

(fig. 11). The narrowing in segment 1 was offset by large 

increases at 9 percent of cross sections. Only 0.3 percent of 

segment 3 had large total channel width increases between 

1999 and 2003 and no large increases in channel width were 

measured in segment 2 (figs. 10 and 11).

Morphologic changes in segment 3 were generally 

restricted to the same cross sections, whereas in segments 1 

and 2 the locations of changes fluctuated. Of the cross sections in segment 3 that had large decreases in total channel 

width between 1999 and 2003, 71 percent had large increases 

between 1993 and 1999 (fig. 11). Comparatively, in segments 

1 and 2, 8 and 29 percent, respectively, of cross sections with 

large decreases in total channel width between 1999 and 

2003 had large increases in channel width between 1993 and 

1999. Based on visual observation of the aerial photographs, 

the areas susceptible to change in segment 3 were located in 

depositional areas of small inflowing tributaries or areas where 

the river widened abruptly. 

Total channel width changes after 2003—Between 2003 

and 2006 and from 2006 to 2010, there were fewer large 

changes than for the previous analysis periods (figs. 9–11). 

No large changes in total channel width were measured in 

segment 3 during these periods (fig. 11). Segment 1 was most 

geomorphically active as 3 percent of cross sections increased 

in total channel width between 2003 and 2006, and 6 percent 

of cross sections increased in total channel width between 

2006 and 2010 (fig. 9). No offsetting decreases in total channel 

width were measured in segment 1 between 2003 and 2006 

but 5 percent of cross sections decreased in total channel width 

between 2006 and 2010 (fig. 9). Two percent of the cross sections in segment 2 had large decreases in total channel width 

between 2003 and 2006 followed by large increases in total 

channel width at 2 percent of cross sections between 2006 and 

2010 (fig. 10).

Effects of Streamflows on Stream-Channel 

Morphology Changes

As discussed in the foregoing “Channel Morphology” 

subsections, there were some changes in channel width and 

incipient flood-plain surface area in each segment, especially 

between 1993 and 1999 and between 1999 and 2003. Overall, 

these percentage changes were small at the segment scale; 

however, large changes were measured at many fixed cross 

sections in all three segments. Moreover, not all three segments 

responded in the same way. Responses in segments 2 and 3 

generally were similar, but the responses in segment 1 seemed 

independent, which could be related to the instability of the 

channel that was identified in the “Cross-Sectional Width Analysis” section. The only consistent changes in all three segments 

were increases in incipient flood-plain surface area between 

1993 and 1999 and between 2003 and 2006, and a decrease in 
24 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

Base from U.S. Geological Survey aerial photographs

1993 2-meter resolution and 1999 1-meter resolution 

57,900

57,900

57,600

57,600

57,300 57,300

N

N

1993 incipient flood-plain surface

1999 incipient flood-plain surface

1999 channel boundary

Upstream stationing, in meters

EXPLANATION

1993 channel boundary

57,900

A. 1993

B. 1999

0

0

0.05

0.05

0.1 0.15

0.150.1

0.2 MILE

0.2 KILOMETER

Figure 13. Channel change delineated on aerial photographs of eastern Niobrara National Scenic River, Nebraska, 

highlighting areas that underwent substantial bank erosion in a part of segment 1. A, 1993 and B, 1999.
Effects of Streamflows on Stream-Channel Morphology 25

1999

2003

EXPLANATION

48,000 46,000 44,000 42,000 40,000

 0

100

200

300

400

Width, in meters

Area of island

attachment

Distance upstream, in meters, 

from downstream boundary of study area 

Figure 14. Longitudinal 

trend in total channel width 

for reach in study segments 

1 and 2, 40,000 to 50,000 

meters upstream from study 

area boundary, eastern 

Niobrara National Scenic 

River, Nebraska, 1999–2003, 

highlighting an area of island 

attachment to bank.

island area between 1999 and 2003 (table 4). Each of these 

consistent changes among the study segments corresponded to 

changes in streamflow conditions, as will be next discussed.

The feature classification accuracy for 1993 and 1999 

photography (table 1) indicate that changes up to 5 m are 

within the uncertainty band, so the widening of the total 

channel at segments 2 and 3 during 1993–99 is considered 

real, but its change at segment 1 (2 m) was less than measurement uncertainty. The increases in channel widths from 1993 

to 1999 could be related to the extended duration of higher 

streamflows throughout the period, the large flood event of 

1994, or effects from the ice breakup related to the large 1994 

flood event. Higher flows correspond to swifter current velocity, which corresponds with generally higher rates of bank erosion and greater bed shear stress that inhibits vegetation from 

stabilizing bars. Large floods usually erode flood plains at cutbanks and construct new depositional surfaces (herein referred 

to as “incipient flood plains”) that generally will aggrade over 

time to the elevation of the modern flood plain (Wohl, 2014). 

These processes, along with localized changes in slope and 

sediment-grain size, could explain the channel widening at 

the segment scale as well as the channel erosion measured at 

the cross-section scale. Alternatively, the channel widening 

could have resulted from a combination of the flood pulse followed by continued wide-channel maintenance facilitated by 

greater duration of high streamflows. The 1994 flood was not 

only a large event, but also was a large ice-jam event. Ice-jam 

floods or ice-dam breakout floods can have higher flood stages 

than ice-free floods, and based on stage records this was the 

case with the 1994 event. These types of floods may leave a 

depositional record at an elevation higher than the modern 

flood plain. Ice jams reportedly have created new channels and 

eroded gulleys in meander-lobe flood plains and braided rivers 

(Smith and Pearce, 2002), which could explain the channel 

widening and increases in incipient flood-plain surface area 

that were measured between 1993 and 1999. If ice jams during 

the 1994 flood created new channels occupied only at higher 

stages than those of flows normally contained within the main 

channel, the appearance of a new incipient flood-plain surface 

is logical in 1999 photography, when streamflow had for several years not reoccupied these chutes. 

Channel width initially narrowed from 1999 to 2003 in 

response to extended duration of summer low flows. This was 

related to at least two processes by which channels narrow: (1) 

encroachment of banks, some of which involves attachment 

(accretion) of islands as indicated by the decrease in island 

area during this time period; and (2) conversion of incipient 

flood-plain surfaces to mature flood plain as they become 

stabilized by the successional trend of riparian vegetation, possibly undergo further aggradation, and become incorporated 

within the existent flood plain. Although extended periods of 

low summer flow continued (especially in 2006), no additional narrowing was measured. Summer streamflow at the 

Niobrara River near Sparks was typically 450 ft3

/s or greater 

after 2003 (fig. 6A). This magnitude of streamflow combined 

with the downstream inflows of Plum Creek and Long Pine 

Creek (typically 160 ft3/s for Long Pine, and 110 ft3/s for Plum 

Creek; figs. 7A and 5C) likely kept the duration of summer 

flows above 700 ft3/s at a high frequency. This amount of flow 

was enough to prevent further narrowing after 2003. Segment 
26 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

Base from U.S. Geological Survey aerial photographs

1999 1-meter resolution and 2003 1-meter resolution 46,500 46,500

46,200

46,200

45,900

45,900

A. 1999

B. 2003

N

N

1999 incipient flood-plain surface

2003 incipient flood-plain surface

2003 channel boundary

Upstream stationing, in meters

EXPLANATION

1999 channel boundary

1999 island

46,500

0

0

0.05

0.05

0.1 0.15

0.150.1

0.2 MILE

0.2 KILOMETER

Figure 15. Channel change delineated on aerial photographs of eastern Niobrara National Scenic River, Nebraska, 

highlighting an area of island attachment to a bank in a part of segment 1. A, 1999 and B, 2003.
Summary 27

1 was about 100 m narrower than segments 2 and 3, and 

thus may have previously undergone the channel-narrowing 

processes outlined above and has approached an equilibrium 

between those processes and the widening processes. 

Summary

The Niobrara River is an important and valuable economic and ecological resource in northern Nebraska. It has 

a diverse ecosystem with many plant and animal species and 

is used as a stopover for migratory bird species that include 

several threatened or endangered species. It provides opportunities for ecotourism and recreational boating, and supports 

hydroelectric power and agriculture. Since its National Scenic 

River designation in 1991, a 122-kilometer (km) reach of the 

river has been managed jointly by the U.S. Fish and Wildlife 

Service and the National Park Service. The U.S. Geological 

Survey (USGS), in cooperation with the National Park Service, investigated the effects of potential changes in summer 

streamflow on channel morphology in the eastern region of the 

Niobrara National Scenic River. The goal was to assess how 

potential decreases in summer streamflow resulting from a 

postulated increase of consumptive water uses may affect the 

channel morphology of the Niobrara National Scenic River 

that provides important nesting habitat for migratory bird 

species.

The study focused on three segments within a 65-km 

eastern segment of the Niobrara National Scenic River. The 

studied main-stem segments were separated at the confluences 

with two tributaries, Plum Creek and Long Pine Creek. With 

an overall temporal scope of 1988–2010 that includes a short 

interval preceding and a long interval following the Niobrara 

National Scenic River Designation Act of 1991, the study analyzed five separate time periods: 1988–93, 1994–99, 2000–3, 

2004–6, and 2007–10, each of which ended with a year in 

which aerial photography coverage was available.

Flow duration was analyzed for a USGS streamgage 

along the Niobrara River upstream from the study area as 

well as for two tributaries (Plum Creek and Long Pine Creek) 

within the study area. Late summer flows (July, August, and 

September) were targeted for analysis based on monthly flow 

statistics indicating that median flows were lowest at Niobrara 

River near Sparks, Nebraska (USGS site 06461500) during 

those 3 months. Flood-frequency analysis was completed to 

compute a bankfull discharge (1.5-year flood), which was used 

to compare with peak flows during the study period.

Flow analysis indicated that the Niobrara River had high 

flows, including a large flood peak (1994) during the 1994–99 

period and lower summer flows during the 2000–3 and 2004–6 

periods. Summer streamflow for Long Pine Creek was also 

highest during the 1994–99 period. Summer streamflow was 

lower for Long Pine Creek during the 1988–93, 2000–3 and 

2004–6 study time periods but only 3 years (1989, 2002 and 

2006) had summer median streamflow below post-regulation 

median summer streamflow and the departures were less than 

8 percent. 

Aerial photographs taken after the Niobrara River was 

designated a National Scenic River were used to determine 

changes in channel characteristics. Photographs from 1993, 

1999, 2003, 2006, and 2010 were analyzed. Channel metrics 

of width (total channel width, active channel width), area of 

islands and incipient flood-plain surfaces, and braided index 

were computed for each photography year and summarized 

by the three individual river segments. Additionally, at 

fixed-location cross sections, photography analysis identified 

localized geomorphic change to infer processes. Accuracy of 

geomorphic feature classification was estimated and the rootmean-square difference (RMSD) between aerial photographs 

was calculated to determine associated errors in channel 

metric calculations. The horizontal accuracy of boundaries 

delineated in the classification was estimated as 5 meters (m) 

for boundaries based on 1993 aerial photography and 4 m 

for all other aerial photography. The RMSD between aerial 

photography years ranged from 3.04 m to 4.16 m. The RMSD 

is only relevant to comparisons of the fixed-location cross section because it compared co-located cross sections, whereas 

the summary of channel metrics was concerned with average 

characteristics throughout an entire river segment.

Statistical analysis using the Kruskal-Wallis test showed 

that segments 2 and 3 had significant differences in the distributions of calculated active channel width. Further analysis 

using the Wilcoxon rank sum test determined that the significant differences were between the 1999 and 2003 active 

channel-width datasets for segment 2, and the 1993 and 1999 

active channel datasets for segment 3.

The largest changes in channel metrics were measured 

between 1993 and 1999 and 1999 and 2003. These included 

measurable increases in channel width in segments 2 and 3 

between 1993 and 1999 and subsequent decreases between 

1999 and 2003. Between 1993 and 1999, total channel width 

increased by 3 percent in segment 2 and 5 percent in segment 

3, and active channel width increased by 5 percent in segment 3. Changes in channel width between 1999 and 2003 

included a decrease in average total channel width of 14 m (5 

percent) in segment 2, and a decrease in active channel widths 

of 8 m (3 percent) and 6 m (2 percent) in segments 2 and 3, 

respectively.

Large changes were measured between 1993 and 1999, 

and between 1999 and 2003, at many of the fixed-location 

cross sections. Large changes (that is, greater than 25 percent) 

in total channel width were measured in all three segments 

between 1993 and 1999 and again between 1999 and 2003; 

large increases were dominant in the earlier period, and large 

decreases were dominant between 1999 and 2003 except 

in segment 1. These patterns reflected the analysis results 

reported in the segment average summaries. Segment 1 was 

the most susceptible to localized changes as there was only 

one period (between 2003 and 2006) in which large changes in 

active channel width were measured in fewer than 10 percent 

of the cross sections.
28 Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska

Changes in channel metrics generally corresponded to 

changes in streamflow conditions, but other than changes in 

incipient flood-plain area, these changes were small and were 

not measured in all three segments simultaneously. Increases 

in total channel width (except in segment 1) between 1993 

and 1999 corresponded to increases in streamflow. A large 

ice-jam flood in 1994 could also have contributed to channel 

widening. The flood along with the increase in streamflows 

also corresponded to an increase in incipient flood-plain area. 

This increase indicated the flood and high streamflows created new depositional surfaces. Channel narrowing (except 

in segment 1) between 1999 and 2003, which was caused by 

encroachment of banks, some of which involved attachment 

(accretion) of islands, corresponded to lower summer streamflows and extended durations of very low summer streamflow. 

Although the pattern of low summer streamflow and extended 

durations of very low summer streamflow continued during 

the 2004–6 period and at the beginning of the 2007–10 period, 

no further narrowing was measured. Consistent tributary summer inflows help to explain the resistance of segments 2 and 

3 to further narrowing. Because segment 1 is already much 

narrower than segments 2 and 3, its average current velocity is 

likely to be swifter and, therefore, competent to offset further 

processes that led to its narrowness.

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For more information concerning this publication, contact:

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Or visit the Nebraska Water Science Center Web site at:

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Schaepe and others—Effects of Streamflows on Stream-Channel Morphology in the Eastern Niobrara National Scenic River, Nebraska—SIR 2016–5004

ISSN 2328-0328 (online)

http://dx.doi.org/10.3133/sir20165004