U.S. Department of the Interior

U.S. Geological Survey

Scientific 

Investigations 

Report 2010–5141

Prepared in cooperation with the Nebraska Game and Parks Commission

Hydrogeomorphic Segments and Hydraulic Microhabitats of 

the Niobrara River, Nebraska—With Special Emphasis on 

the Niobrara National Scenic River
Front and back cover. Niobrara River near Norden, Nebraska. Photograph by Jason Alexander, U.S. Geological Survey.
Hydrogeomorphic Segments and Hydraulic 

Microhabitats of the Niobrara River, 

Nebraska—With Special Emphasis on the 

Niobrara National Scenic River

By Jason S. Alexander, Ronald B. Zelt, and Nathan J. Schaepe

Prepared in cooperation with the Nebraska Game and Parks Commission

Scientific Investigations Report 2010–5141

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2010

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Suggested citation:

Alexander, J.S., Zelt, R.B., and Schaepe, N.J., 2010, Hydrogeomorphic and hydraulic habitats of the Niobrara 

River, Nebraska—with special emphasis on the Niobrara National Scenic River: U.S. Geological Survey Scientific 

Investigations Report 2010–5141, 62 p. 
iii

Contents

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

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

Purpose and Scope .............................................................................................................................4

Description of the Niobrara River Basin...........................................................................................4

Physiographic and Geologic Setting ........................................................................................4

Hydrogeomorphic Characteristics of the Niobrara River.....................................................6

Water Development History and Channel Effects..................................................................7

Background............................................................................................................................................8

Hydraulic Geometry of the Niobrara River..............................................................................8

Hydrogeomorphic Segments of the Niobrara River.............................................................13

Approach and Methods..............................................................................................................................13

Basin-Scale Methods.........................................................................................................................13

Statistical Analysis of Fluvial Geomorphic Provinces and 

Hydrogeomorphic Segments of the Niobrara River...............................................13

Geographic Information System Analysis of Niobrara River and 

Valley Morphometry.....................................................................................................17

Calculation of Hydraulic Microhabitats in Fluvial Geomorphic 

Provinces of the Niobrara River ................................................................................20

Study Reaches along the Niobrara National Scenic River..........................................................20

Characterization of Fluvial Landforms and Bed Sediment .................................................20

Fluvial Landforms..............................................................................................................23

Bed Sediment ....................................................................................................................23

Hydraulics, Hydraulic Geometry, and Bed Adjustment ......................................................24

Hydraulic Microhabitats ..........................................................................................................26

Hydrogeomorphic Segments and Hydraulic Microhabitats.................................................................26

Basin-Scale Results ...........................................................................................................................26

Statistical Analysis of Hydrogeomorphic Segments ...........................................................26

Hydrogeomorphic Characteristics of the Niobrara River ..................................................33

Hydraulic Microhabitats of Differing Fluvial Geomorphic Provinces ...............................35

Study Reach Results ..........................................................................................................................40

Fluvial Landforms ......................................................................................................................40

Bed Sediment .............................................................................................................................42

Hydraulic Geometry and Hydraulics ......................................................................................42

Bed Adjustment .........................................................................................................................47

Hydraulic Microhabitats...........................................................................................................52

Summary........................................................................................................................................................53

Acknowledgments.......................................................................................................................................58

References Cited..........................................................................................................................................58
iv

Figures

1. Map showing location of study area, basin boundary, and National River 

reaches of the Niobrara River....................................................................................................3

2. Schematic diagram showing longitudinal profile of the Niobrara River 

from the Missouri River upstream to Dunlap Diversion Dam................................................5

3–4. Graphs showing:

3. At-a-station hydraulic geometry relations for selected 

streamflow-gaging stations on the Niobrara River........................................................9

4. Downstream hydraulic geometry relations for the Niobrara River 

between the streamflow-gaging station near Hay Springs, Nebraska, 

and the streamflow-gaging station near Verdel, Nebraska .......................................11

5–6. Maps showing:

5. Extents of Niobrara River fluvial geomorphic provinces, location of 

main-stem streamflow-gaging stations used in hydraulic microhabitat 

analysis for each province, and locations of streamflow-gaging 

stations used to construct longitudinal hydrology curves..........................................15

6. Example of digital geographic data sets used to sample Niobrara 

River channel and valley morphologic characteristics...............................................17

7. Graph showing longitudinal hydrology curves of the Niobrara River used 

for along-stream calculation of unit stream power..............................................................19

8–9. Maps showing:

8. Location of four reaches within Niobrara National Scenic River where 

fluvial landforms, bed sediment, and channel hydraulic geometry and 

hydraulics were studied ...................................................................................................22

9. Layout of channel cross sections at Niobrara River upstream from 

Crooked Creek near Sparks, Nebraska (425429100235301), 

exemplifying four study reaches.....................................................................................23

10. Graph showing mean daily discharge of the Niobrara River near Sparks, 

Nebraska, for the study period October 1, 2007, to November 30, 2008, 

showing reach-scale discharge measurement time periods .............................................24

11. Map showing location of study area, basin boundary, and upstream 

boundaries of hydrogeomorphic segments by fluvial geomorphic province...................31

12–14. Graphs showing:

12. Longitudinal distribution of hydrogeomorphic characteristics of the 

Niobrara River from Dunlap Diversion Dam to the Missouri River............................36

13. Distribution of available hydraulic microhabitats within four reaches 

at streamflow-gaging stations of the Niobrara River, Nebraska, for a 

range of discharges ..........................................................................................................38

14. Frequency and cumulative-frequency distributions of the elevation 

of fluvial landforms in four study reaches of Niobrara National Scenic 

River, Nebraska..................................................................................................................40

15. Schematic of active fluvial landforms surveyed in study reaches of Niobrara 

National Scenic River, Nebraska .............................................................................................40

16. Graphs showing bed-sediment grain-size cumulative frequency distributions 

for four study reaches within Niobrara National Scenic River, Nebraska .......................44

17–20. Scatter plots showing:

17. At-a-station hydraulic geometry relations for four study reaches in 

Niobrara National Scenic River, Nebraska, water years 2008–09 ............................45
v

18. Variation in selected hydraulic parameters over a range of discharges 

in four study reaches of Niobrara National Scenic River, Nebraska

water years 2008–09..........................................................................................................50

19. Relation of unit stream power to median grain-size diameters sampled 

over the range of discharges measured in three study reaches of the 

Niobrara National Scenic River, Nebraska ...................................................................51

20. Relation of Froude number to dimensionless relative roughness ratio 

over the range of discharges measured in three study reaches of the 

Niobrara National Scenic River, Nebraska ...................................................................51

21–22. Graphs showing:

21. Seasonal changes in bed elevation of river channel at cross sections 

within four study reaches of Niobrara National Scenic River, Nebraska. ..............52

22. Distribution of available hydraulic microhabitats within four study 

reaches of the Niobrara National Scenic River, Nebraska, for a 

range of discharges ..........................................................................................................56

Tables

1. At-a-station hydraulic geometry relations for eight selected Niobrara River 

streamflow-gaging stations ......................................................................................................10

2. Downstream hydraulic geometry relations for the Niobrara River between 

Hay Springs and Verdel, Nebraska..........................................................................................12

3. Segment-scale geomorphic classification system for the Niobrara River, 

Nebraska......................................................................................................................................14

4. Names and abbreviations for hydrogeomorphic variables used in statistical 

analysis of hydrogeomorphic segments.................................................................................16

5. Streamflow-gaging stations used to construct longitudinal hydrology curves 

of the Niobrara River from Dunlap Diversion Dam to the Missouri River .........................19

6. Typical association between fish species and matrix of depth and velocity 

combinations defined as hydraulic habitat niches for microhabitat analysis..................21

7. Stations used to index study reaches within the 76-mile Niobrara National 

Scenic River, Nebraska .............................................................................................................22

8. Hydraulic parameters used to characterize flow and adjustment in 

Niobrara River study reaches...................................................................................................25

9. Number of geomorphic element classes identified by ANOVA multiple 

comparision analysis .................................................................................................................27

10. Cross-validation results from discriminant analyses of sampling points of 

the Niobrara River, Nebraska, by geomorphic element class ............................................28

11. Distribution of classes assigned using discriminant analyses to sampling 

points within each hydrogeomorphic segment defined by Alexander and 

others (2009) for the Niobrara River, Nebraska .....................................................................29

12. Hydrogeomorphic segments of the Niobrara River between Dunlap 

Diversion Dam and the Missouri River, Nebraska ................................................................32

13. Physical characteristics of hydrogeomorphic segments of the Niobrara 

River between Dunlap Diversion Dam and the Missouri River, Nebraska........................34

14. Hydraulic-microhabitat information over a range of flow conditions for 

reaches at selected Niobrara River gaging stations in differing fluvial 

geomorphic provinces ...............................................................................................................39

15. Fluvial landforms at cross sections within four study reaches of the 

Niobrara National Scenic River, Nebraska ............................................................................41
vi

16. Grain-size distributions of selected bed-sediment samples from four 

study reaches in the Niobrara National Scenic River, Nebraska.......................................43

17. At-a-station hydraulic geometry relations for four study reaches within 

Niobrara National Scenic River, Nebraska ............................................................................46

18. Summary of channel discharge, geometry, and hydraulic parameters 

calculated from measurements made in 2008 at four study reaches in 

Niobrara National Scenic River, Nebraska. ...........................................................................48

19. Hydraulic microhabitat distribution over a range of streamflow conditions 

for four study reaches in Niobrara National Scenic River, Nebraska ...............................54

Conversion Factors and Datums

Inch/Pound to SI

Multiply By To obtain

inch (in.) 2.54 centimeter (cm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

square foot (ft2) 0.0929 square meter (m2)

square mile (mi2) 2.590 square kilometer (km2) 

cubic foot (ft3) 28.32 cubic decimeter (dm3) 

cubic foot (ft3) 0.02832 cubic meter (m3) 

foot per second (ft/s) 0.3048 meter per second (m/s)

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

pound-force per square foot (lb/ft2) 47.89 newton per square meter (N/m2)

pound per foot-second (lb/ft-s) 14.59 newton per meter-second (N/m-s)

SI to Inch/Pound

Multiply By To obtain

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6212 mile (mi)

square meter (m2) 10.76 square foot (ft2)

square kilometer (km2) 0.3861 square mile (mi2)

cubic meter (m3) 264.2 gallon (gal)

cubic meter (m3) 0.0002642 million gallons (Mgal) 

meter per second (m/s) 3.281 foot per second (ft/s)

cubic meter per second (m3/s) 35.31 cubic feet per second (ft3/s)

newton per square meter (N/m2) 0.1622 pound-force per square foot (lb/ft2)

newton per meter-second (N/m-s) 0.0685 pound per foot-second (lb/ft-s)

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

(NAVD 88).

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

Water year is defined as the 12-month period October 1 through September 30.

The water year is designated by the calendar year in which it ends.
Hydrogeomorphic Segments and Hydraulic Microhabitats 

of the Niobrara River, Nebraska—With Special Emphasis 

on the Niobrara National Scenic River

By Jason S. Alexander, Ronald B. Zelt, and Nathan J. Schaepe

Abstract

The Niobrara River is an ecologically and economically 

important resource in Nebraska. The Nebraska Department 

of Natural Resources’ recent designation of the hydraulically 

connected surface- and groundwater resources of the Niobrara 

River Basin as “fully appropriated” has emphasized the importance of understanding linkages between the physical and 

ecological dynamics of the Niobrara River so it can be sustainably managed. In cooperation with the Nebraska Game and 

Parks Commission, the U.S. Geological Survey investigated 

the hydrogeomorphic and hydraulic attributes of the Niobrara 

River in northern Nebraska. This report presents the results 

of an analysis of hydrogeomorphic segments and hydraulic 

microhabitats of the Niobrara River and its valley for the 

approximately 330-mile reach from Dunlap Diversion Dam to 

its confluence with the Missouri River. Two spatial scales were 

used to examine and quantify the hydrogeomorphic segments 

and hydraulic microhabitats of the Niobrara River: a basin 

scale and a reach scale.

At the basin scale, digital spatial data and hydrologic data 

were analyzed to (1) test for differences between 36 previously 

determined longitudinal hydrogeomorphic segments; (2) quantitatively describe the hydrogeomorphic characteristics of the 

river and its valley; and (3) evaluate differences in hydraulic 

microhabitat over a range of flow regimes among three fluvial 

geomorphic provinces.

The statistical analysis of hydrogeomorphic segments 

resulted in reclassification rates of 3 to 28 percent of the 

segments for the four descriptive geomorphic elements. The 

reassignment of classes by discriminant analysis resulted in 

a reduction from 36 to 25 total hydrogeomorphic segments 

because several adjoining segments shared the same ultimate 

class assignments. Virtually all of the segment mergers were 

in the Canyons and Restricted Bottoms (CRB) fluvial geomorphic province. The most frequent classes among hydrogeomorphic segments, and the dominant classes per unit length 

of river, are: a width-restricted valley confinement condition, 

sinuous-planview pattern, irregular channel width, and an 

alternate bar configuration. 

The Niobrara River in the study area flows through a 

diversity of fluvial geomorphic settings in its traverse across 

northern Nebraska. In the Meandering Bottoms (MB) fluvial 

geomorphic province, river discharge magnitudes are low, and 

the valley exerts little control on the channel-planview pattern. 

Within the CRB province, the river flows over a diversity 

of geologic formations, and the valley and river narrow and 

expand in approximate synchronicity. In the Braided Bottoms 

(BB) fluvial geomorphic province, the river primarily flows 

over Cretaceous Pierre Shale, the valley and channel are 

persistently wide, and the channel slope is generally uniform. 

The existence of vegetated islands and consequent multithread 

channel environments, indicated by a higher braided index, 

mostly coincided with reaches having gentler slopes and less 

unit stream power. Longitudinal hydrology curves indicate 

that the flow of the Niobrara River likely is dominated by 

groundwater as far downstream as Norden. Unit stream power 

values in the study area vary between 0 and almost 2 pounds 

per foot per second. Within the MB province, unit stream 

power steadily increases as the Niobrara gains discharge from 

groundwater inflow, and the channel slope steepens. The 

combination of steep slopes, a constrained channel width, 

and persistent flow within the CRB province results in unit 

stream power values that are between three and five times 

greater than those in less confined segments with comparable 

or greater discharges. With the exception of hydrogeomorphic 

segment 3, which is affected by Spencer Dam, unit stream 

power values in the BB province are generally uniform. 

Channel sinuosity values in the study area varied generally 

between 1 and 2.5, but with locally higher values measured in 

the MB province and at the entrenched bedrock meanders of 

hydrogeomorphic segment 18 in the CRB province. 

The differences in channel morphology and hydraulic 

geometries between fluvial geomorphic provinces are evident 

in the types, relative abundance, and response of hydraulic 

microhabitats to changing discharges. The four gaging stations 

chosen for hydraulic microhabitat analysis are distributed 

among three different fluvial geomorphic provinces. In the 

MB province, the smaller channel and lower discharges 

resulted in the dominance of shallow and intermediate-depth 

hydraulic environments with the vast majority of hydraulic 
2 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

microhabitat restricted to shallow categories even during 

upper-decile discharges. In the CRB province, intermediatedepth hydraulic conditions, particularly intermediate-swift, 

dominate over all ranges of discharge. Hydraulic microhabitat 

conditions were most diverse in the BB province, with most 

hydraulic microhabitat categories present over the entire 

range of discharges analyzed. The calculated differences in 

hydraulic microhabitat distributions, abundance, and adjustments between streamflow-gaging stations were the result of 

differences in physical structure of the channel and subsequent 

channel hydraulic geometry. 

At the reach scale, field measurements made in water 

years 2008 and 2009 in four study reaches within the Scenic 

Reach were used to (1) characterize the elevation and geomorphic processes associated with fluvial landforms, (2) build 

hydraulic geometry relations, (3) examine flow hydraulics 

over a range of discharges, and (4) examine the types and 

responses of hydraulic microhabitats to a range of flow 

magnitudes. Four landform groups were identified and named 

in order of increasing elevation: low flood plains, intermediate 

flood plains, low terraces, and high terraces. The terraces were 

poorly characterized because the surveys did not extend across 

the full width of the alluvial valley bottom. The two lowest 

fluvial landforms are likely active in the modern hydroclimatic 

regime. Sediment samples obtained in the study reaches indicate that the primary bed material in the active channel ranged 

in size from coarse silt to coarse sand. Grain-size distributions 

from samples also indicate that the bed of the Niobrara River 

among the study reaches coarsens and has increasing grainsize variability in the downstream direction.

Values of at-a-station hydraulic geometry exponents 

indicate that the Niobrara River in the study reaches adjusts its 

geometry to changing discharges primarily through increases 

in flow depth and velocity. Relations at one cross section 

indicated that, at least locally, changes in width were also an 

important channel adjustment mechanism. Hydraulic behavior 

over the range of flows measured was not consistent among 

all study reaches, but two general modes of hydraulic behavior were observed in the reaches with substantial coverage 

of the bed by fine sediment. At the Sunny Brook and Muleshoe study reaches, average boundary-shear stress remained 

approximately constant, and hydraulic resistance decreased, 

for discharges below 900 cubic feet per second (ft3/s). Above 

900 ft3/s, average boundary shear stress and hydraulic resistance both increased. The Rock Barn study reach did not 

exhibit the same two-mode hydraulic behavior observed at the 

Sunny Brook and Muleshoe reaches. The coincident increase 

in boundary shear stress above 900 ft3/s observed at the Sunny 

Brook and Muleshoe study reaches represents a potential 

hydraulic threshold above which bedload transport rates were 

likely to increase markedly. No consistent bed-adjustment 

pattern (scour or fill) was identified in the study reaches over 

the range of flows or over the measurement season.

Analysis of hydraulic microhabitats over the range of 

discharges measured at the study reaches indicates that some 

percentage of most habitat niche categories was available for 

at least one discharge condition, but the majority of hydraulic 

habitat available was within the intermediate-swift and deepswift habitat niche categories. Deep-swift conditions dominated nearly all study reaches under all measured discharge 

conditions. Slight differences in habitat distributions were 

observed between the study reaches with substantial coverage of the bed by fine sediment—Sunny Brook, Muleshoe, 

and Rock Barn—and the bedrock-dominated reach, Crooked 

Creek. Although the four study reaches occupy three different 

hydrogeomorphic segments, the types, relative abundance, 

and response of hydraulic microhabitat niche distributions to 

changing discharge conditions generally were similar among 

all reaches. 

Introduction

The Niobrara River of Nebraska is an ecologically and 

economically important resource, renowned for its biological 

diversity, paleontological richness, and abundant recreational 

opportunities (Johnsgard, 2001, 2007). The steady, dependable 

flow of the Niobrara River makes it an important source of 

irrigation water for local agriculture, which is the foundation 

of the regional economy. The geographic setting and physiography of the Niobrara River Valley facilitate the convergence, 

hybridization, and survival of at least five terrestrial ecosystem community types within a relatively narrow corridor 

(Johnsgard, 2001). This unique quality was recognized by the 

United States Congress in 1991 when a portion of the river 

was granted Federal protection under the Wild and Scenic 

Rivers Act of 1968 (Roeder, 2004). The 76-mile (mi) reach of 

river is now recognized as the Niobrara National Scenic River 

(hereinafter referred to as the “Scenic Reach”) near Valentine, 

Nebr. (fig. 1) and is cooperatively managed by a consortium of private landowners, and State and Federal agencies. 

The 28-mile reach of the Niobrara River upstream from the 

Missouri River (hereinafter named the “Recreational Reach”) 

are protected within the Missouri National Recreational River 

(fig. 1). 

The Nebraska Department of Natural Resources’ 

(NDNR) recent designation of the hydraulically connected 

surface- and groundwater resources of the Niobrara River 

Basin as “fully appropriated” (Nebraska Department of 

Natural Resources, 2007) has emphasized the importance of 

understanding linkages between the physical and ecological dynamics of the Niobrara River so it can be sustainably 

managed. Among the key questions identified for study by an 

interagency working group are:

1. What flow regime is needed to maintain the present quantity and diversity of stream physical habitats that distinguish the Niobrara as a healthy ecosystem?

2. What frequency, duration, and timing of infrequent hydrologic disturbances (floods, droughts, ice jams) are needed 
Figure 1. Location of study area, basin boundary, and National River reaches of the Niobrara River.

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Cornell Dam

Merritt Dam

Spencer Dam

Box Butte Dam

Fort Randall Dam

Niobrara

River

Missouri River

Snake River

Keya

Paha

River

Hay Springs

Gordon Valentine Norden

Long Pine O'Neill

Spencer Cody

Verdigre Creek Dunlap

Diversion Dam

Mariaville

SOUTH DAKOTA

NEBRASKA

WYOMING

Cherry County

Holt County Sioux County Sheridan County

Goshen County

Todd County Niobrara County

Dawes County

Fall River County Tripp County

Brown County Rock County

Shannon County Bennett County

Morrill County Garden County

Box Butte County

Grant County

Charles Mix County

Blaine County Hooker County

Knox County

Loup County Thomas County

Boyd County

Keya Paha County

Scotts Bluff County Garfield County Wheeler County

Custer County

Boone County

Banner County Arthur County

Douglas County

McPherson County Valley County Logan County

Mellette County

Greeley County

Jackson County

Gregg County

Antelope 

County

0 25 50 MILES0 25 50 KILOMETERS

104° 103° 102° 101° 100° 99° 98°

43°

42°

Base from U.S. Geological Survey National Elevation Dataset, 2006;National Hydrography Dataset, 2007; State boundaries, 2005,1:2,000,000Basin boundary modified from U.S. Department of Agriculture,Natural Resources Conservation Service Watershed Boundary Dataset, 2008Universal Transverse Mercator projectionZone 14Horizontal coordinate information is referenced to theNorth American Datum of 1983 (NAD 83) 

EXPLANATION

Sand Hills (Soller and Reheis, 2003)

Niobrara River Basin boundary

Portion of Niobrara River within study areaPortion of Niobrara River outside of study area

National River reach (reach managed by  the U.S. National Park Service)

Large dams

MONT.

WYO.

COLO.

S. DAK.

MINN.

IOWA

NEBR.

KANS.

MO.

Area of larger map

Index map

Scenic reach

Recrational

reach

Introduction 3
4 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

to maintain a dynamic equilibrium of fluvial geomorphic 

processes to sustain the present channel character?

To begin to address either question, an understanding of 

the Niobrara River’s present channel character and associated 

diversity of stream physical attributes is necessary. Additionally, an investigation of Niobrara River channel hydraulics 

may assist in understanding channel adjustment and maintenance processes, as well as flood plain connectivity. Numerous 

scientific studies have investigated the physical and hydraulic 

attributes of the Niobrara River along isolated reaches (Colby 

and others, 1953; Colby and Hembree, 1955; Hearty, 1978; 

Buchanan, 1981; Swinehart and others, 1985; Voorhies, 

1987; Cole, 1996; Skelly, 1998; Etheridge and others, 1999); 

however, none have placed these characteristics within a spectrum of fluvial settings at the basin scale. Such a study may 

provide the physical context for water-management strategies 

and serve as a framework for integrated physical and biological investigations. 

In cooperation with the Nebraska Game and Parks 

Commission (NGPC), the U.S. Geological Survey (USGS) 

investigated the hydrogeomorphic and hydraulic attributes of 

the 330-mi reach of the Niobrara River from Dunlap Diversion 

Dam in western Nebraska (fig. 1) to the confluence with the 

Missouri River in northeastern Nebraska.

Purpose and Scope 

The purpose of this report is to present the results of 

an analysis of hydrogeomorphic segments and hydraulic 

microhabitats of the Niobrara River and its valley for the 

approximately 330-mi reach from Dunlap Diversion Dam to 

its confluence with the Missouri River (hereinafter referred 

to as the “study area”) (fig. 1). Two spatial scales were used 

to examine and quantify the hydrogeomorphic segments and 

hydraulic microhabitats of the Niobrara River: a basin scale 

and a reach scale. At the basin scale, digital spatial data and 

hydrologic data were analyzed to (1) test for differences 

between 36 previously determined longitudinal hydrogeomorphic segments; (2) quantitatively describe the hydrogeomorphic characteristics of the river and its valley; and (3) evaluate 

differences in hydraulic microhabitat over a range of flow 

regimes among three fluvial geomorphic provinces. The 

periods of record examined at each streamflow-gaging station 

were variable, and spanned water years 1950 through 2008. 

At streamflow-gaging stations downstream from the confluence of the Snake River, only the period of record available 

after water year 1963 was used because the operations of a 

large dam began in water year 1964. At the reach scale, field 

measurements made in water years 2008 and 2009 in study 

reaches within the Scenic Reach were used to (1) characterize 

the elevation and geomorphic processes associated with fluvial 

landforms, (2) build hydraulic geometry relations, (3) examine 

flow hydraulics over a range of discharges, and (4) examine 

the types and responses of hydraulic microhabitats to a range 

of flow magnitudes. 

Description of the Niobrara River Basin

Geologic formations described in subsequent sections of 

this report have been compiled from various resources for the 

purposes describing variation in physical characteristics of the 

Niobrara River Basin. Some of the geologic nomenclatures 

described below are from the University of Nebraska-Lincoln. 

Where appropriate, the sources of the geologic information 

have been cited.

Physiographic and Geologic Setting

The Niobrara River originates in the tablelands of 

east-central Wyoming and flows eastward approximately 

560 mi, mainly through northern Nebraska, before reaching its 

confluence with the Missouri River in northeastern Nebraska 

(fig. 1). The Niobrara River Basin drains about 13,480 square 

miles (mi2), including parts of Nebraska, South Dakota, and 

Wyoming. The headwaters of the Niobrara River lie at an 

elevation of approximately 5,500 feet (ft), and the descent of 

the river is approximately 4,280 ft. Average annual rainfall 

increases from approximately 14 inches in the west to 24 

inches in the east (Dugan and Zelt, 2000). A large part of the 

basin lies within the Nebraska Sand Hills (sandhills), a vast 

region of vegetation-stabilized sand dunes (fig.1). The high 

infiltration capacity of the sandhills virtually eliminates direct 

surface runoff from precipitation, and, instead, water is fed to 

adjacent streams through groundwater seepage (Bentall and 

Shaffer, 1979). West of Valentine, Nebr., groundwater is the 

primary source of flow in the Niobrara River. The discharge 

of the river is steady and persistent, and overbank flooding is uncommon, except during winter ice jams (Missouri 

River Basin Inter-Agency Committee, 1967; Shaffer, 1975; 

Voorhies, 1987). The steady nature of the flow regime of the 

Niobrara River is less apparent downstream from Valentine, 

because of increasing volumes of precipitation, increases in 

storm runoff from small tributaries, and changes in soil infiltration rates near the eastern margin of the sandhills (Shaffer, 

1975; Hearty, 1978; Istanbulluoglu, 2009). 

The Niobrara River in the study area flows alternately 

through wide alluvial valleys, valleys bound by escarpments, and narrow sinuous canyons (University of NebraskaLincoln, Conservation and Survey Division, 1986; Alexander 

and others, 2009). For much of its length, the valley of the 

Niobrara River is incised into sedimentary bedrock of late 

Cretaceous and Tertiary ages (fig. 2), most of which is gently 

sloping from east to west (Hearty, 1978; Swinehart and 

others 1985; Burchett, 1986; Voorhies, 1987). Swinehart and 

others (1985) divided the Tertiary-age sediments into two 

major packages: an older, generally homogenous package 

of fine-grained volcaniclastic rocks deposited by wind, and 

a younger, coarser package composed primarily of alluvial 

deposits. The older package is composed primarily of the 

White River Group and Arikaree Group, and the younger 

package is composed primarily of the Ogallala Group. The 
Braided Bottoms

Meandering Bottoms

Canyons and Restricted Bottoms

4,0003,5003,0002,5003,0001,5001,000500

400 350 300 250 200 150 100 50 0

0 *UNL- University of Nebraska-Lincoln, Conservation and Survey Division 

Open RestrictedEntrenched

ValleysEscarpments and bluffs 

EXPLANATION

Ogallala GroupArikaree GroupWhite River GroupPierre ShaleNiobrara Chalk 

Tertiary ageCretaceous age

Knick zoneBed elevation

Straight-line slope between mouth and head of study area

Confluence with at least 5 percent increasein drainage areaConfluence with less than 5 percent increasein drainage area

Niobrara River longitudinal profile

 (Alexander and others, 2009)

Bedrock at river level (Burchett, 1986)

Topographic regions (UNL*, 1986)

Valley confinement condition 

(Alexander and others, 2009)

Fluvial geomorphic province

1

2

3

4

Dunlap Diversion Dam

Rush Creek

Antelope Creek

Bear Creek

Snake River

Cornell Dam

Norden Chute

Keya Paha River

Spencer Dam

Pine Creek

Box Butte Creek

Leander Creek

Medicine Creek

Gordon Creek

Minnechaduza Creek

Fairfield Creek

Plum Creek

Long Pine Creek

Big Sandy Creek

Eagle Creek

Redbird Creek

Verdigre Creek

Schlagel Creek

ELEVATION, IN FEET ABOVE NORTH AMERICAN VERTICAL DATUM OF 1988

DISTANCE ALONG CHANNEL CENTERLINE FROM MISSOURI RIVER, IN MILES

1

2

3 4

Figure 2. Longitudinal profile of the Niobrara River from the Missouri River upstream to Dunlap Diversion Dam, showing (1) bed elevation, and location of major tributaries and manmade structures; (2) bedrock unit at river level; (3) topographic regions; and (4) valley confinement conditions and fluvial geomorphic provinces (adapted from Alexander and others, 2009).

Introduction 5
6 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

dramatic bluffs of the Scenic Reach are composed of the resistant Rosebud Formation of the White River Group overlain 

by the less resistant Valentine unit and highly resistant Cap 

Rock Member of the Ash Hollow Formation of the Ogallala 

Group (Voorhies, 1987). East of Norden, the Niobrara flows 

over Cretaceous-age rocks, including the Pierre Shale and the 

Niobrara Chalk. In a previous study, convexities in the longitudinal profile of the river, along with deeply entrenched and 

restricted reaches, indicated that bedrock exerted a significant 

control on the characteristics of channel form, particularly the 

channel slope (Alexander and others, 2009). The slope of the 

Niobrara River becomes more uniform, and the river channel 

shifts from a narrow sinuous pattern to a wide, braided pattern 

downstream from where it crosses the Tertiary-Cretaceous 

rock contact. Upstream from the contact, changes in river 

slope are located near changes in bedrock type at river level 

as well as bedrock structural features (Swinehart and others, 

1985; Alexander and others, 2009). 

Hydrogeomorphic Characteristics of the 

Niobrara River

As a river traverses a landscape, it gathers both water 

and sediment, and adjusts its geometry (width, depth, and 

slope) to efficiently transport the sediment load with the given 

flow regime and under the physical constraints imposed by 

the landscape itself, such as geology and vegetation (Leopold 

and Maddock, 1953; Wolman and Gerson, 1978; Huang and 

Nanson, 2000). The term “hydrogeomorphic” is used herein to 

encompass the host of form characteristics and processes associated with the interactions of water (hydro) and the landscape 

through which it flows (geomorphic). These characteristics 

and processes include the caliber and quantity of the sediment load, the geometric characteristics of the river channel; 

the composition of the river bed, banks, and fluvial landforms 

(bars, flood plains, and terraces); and river hydrology and 

hydraulics (flow regime).

Measurements of sediment discharge and samples of bed 

material indicate that the sediment load of the Niobrara River 

is well-sorted, almost entirely finer than 1.0 millimeter (mm; 

0.03937 in.), and does not fine dramatically in the downstream 

direction (Colby and others, 1953; Colby and Hembree, 1955; 

Buchanan, 1981). Colby and Hembree (1955) measured 

sediment discharge near Cody, Nebr. (fig. 1). They reported 

a median bed-material size between 0.25 and 0.30 mm and 

estimated that between 40 and 60 percent of the sediment 

discharge of the Niobrara River was carried as bedload. Colby 

and others (1953) reported nearly identical results for bedmaterial grain sizes and ratios of bedload to total sediment 

load at the Niobrara River near Valentine, Nebr. Buchanan 

(1981) sampled bed material along several transects downstream from Norden and reported median grain sizes ranging 

from 0.2 to 0.3 mm. 

The Niobrara River in the study area has several reaches 

where the river banks are alluvial, but the river is flowing 

directly over bedrock, indicating that the relative sediment transporting capacity of the river is, in some places, 

much higher than the supply being delivered from upstream 

(Howard, 1987, 1998). At two of these reaches, one near 

Cody, Nebr., and the other near Norden, the river has incised 

bedrock chutes with pronounced bedrock shelves for banks 

(fig. 1); both sites were previously used by the USGS as 

streamflow-gaging stations because of their cross-sectional 

and hydraulic control stability. Immediately upstream from 

Dunlap Diversion Dam, the Niobrara River has alluvial banks, 

but flows over bedrock, locally derived angular gravels, and 

sparse sand dunes (Randle, 2002). The sand acquired from 

bank erosion downstream from Box Butte Dam accumulates 

at Dunlap Diversion Dam and must occasionally be dredged 

(Randle, 2002), potentially indicating that the bed of the 

Niobrara River downstream from Dunlap Diversion Dam also 

may be sediment starved, and flowing over bedrock for some 

distance. Within the Scenic Reach, the river banks are alluvial, 

but the bed is a mix of bedrock and sand dunes (Colby and 

others, 1953). Immediately downstream from Norden, Bureau 

of Reclamation bore-hole logs indicate that the alluvium is as 

thick as 60 ft (Buchanan, 1981). The steadier channel slope 

and deeper alluvium downstream from Norden suggest the 

transporting capacity of the river is likely in dynamic equilibrium with its upstream sediment supply and geologic controls 

(Alexander and others, 2009). 

Previous geomorphic investigations of the Niobrara River 

bottomlands generally have been focused within the Scenic 

Reach. Hearty (1978) investigated the reach of the Niobrara 

valley between Cornell Dam and Norden and divided the area 

into six geomorphic regions: dune-mantled terraces south of 

the river; rolling hills and depressions of low relief on the 

tablelands north of the river; deeply dissected canyons draining the tablelands north of the river; low terraces adjacent to 

the river; a steep, south cutbank of the river; and the river and 

its modern flood plain. Hearty suggested that mass-wasting, 

mainly seepage-induced landsliding on the south side of the 

river, was the dominant channel-form process within the 

confined sections of the Scenic Reach. The landslides ranged 

in age from 9 months to 30 years, and intermittently delivered between 130 and 900 cubic meters (m3

) of sediment, 

as well as large woody debris, to the river bottom. Hearty 

also noted that the steep dissected canyons north of the river 

had narrow, v-shaped channels, and were prone to severe 

flash flooding, delivering their sediment episodically during 

summer thunderstorms. 

Buchanan (1981) investigated the dynamics of the 

wide, braided section of the Scenic Reach between Norden 

and Mariaville, Nebr. (fig. 1) and presented four geomorphic elements that define the wide, braided reaches of the 

Niobrara River: channels, bars, sand flats, and vegetated 

islands. Buchanan described the seasonal variation in Niobrara 

River channel planform within the wide, braided reaches. 

During high flows, the channel consisted mainly of a thalweg, 

which meandered through extensive, emergent sand flats; as 

the season persisted and flows decreased, the thalweg was 
Introduction 7

aggraded by low-amplitude sand waves. The sand flats were 

flooded, and the river eventually occupied the entire active 

channel within the flood plain. High flows were usually coincident with ice breakup in the late winter or early spring. 

Channel flood plain connectivity of the Niobrara River 

is not well-documented. Flooding on the Niobrara is mainly 

associated with winter ice jams, and has resulted in occasional 

damage to bridges and roadways (Missouri Basin InterAgency Committee, 1967). Hearty (1978) mapped the alluvial 

landforms of the river bottom within the Scenic Reach and 

classified alluvial terraces into three groups: those between 

8.2 and 29.5 ft (2.5 and 9 m), those between 49.2 and 164 ft 

(15 and 50 m), and those between 197 and 312 ft (60 and 

95 m) higher than the modern flood plain. The elevation of 

the modern flood plain above any reference discharge was 

not reported. Hearty also investigated terrace stratigraphy 

and reported that numerous soil horizons buried by crossstratified river alluvium indicated that deposition was rapid 

and episodic, a finding that is consistent with occasional, 

ice-induced flooding. Likewise, Buchanan (1981) reported that 

river stage near Norden was up to 3 ft higher for discharges 

during heavy ice cover than those without ice cover. 

Water Development History and Channel Effects

The Niobrara River and its tributaries have numerous 

dams and diversions (Alexander and others, 2009). Two of 

these dams, Box Butte Dam and Merritt Dam, have altered the 

hydrology of the Niobrara River by diverting water for irrigation (fig. 1). Box Butte Dam, located on the main stem of the 

Niobrara River approximately 10 miles upstream from Dunlap 

Diversion Dam, began storing water in 1945 for the Mirage 

Flats Irrigation Project (Shaffer, 1975). Box Butte Reservoir 

releases water for diversion into a delivery canal at Dunlap 

Diversion Dam. Below Dunlap Diversion Dam, average daily 

flows are reduced by 90 percent relative to inflow to Box Butte 

Reservoir, but the river regains significant flow in the miles 

downstream from the diversion, mainly from groundwater 

seepage (Bentall and Shaffer, 1979). Merritt Dam, located 

along the Snake River, a large tributary to the Niobrara River, 

began storing water for the Ainsworth Irrigation Project in 

1964. Storage in the reservoir behind Merritt Dam reduced 

the base flows (flows exceeded 99 percent of the time) of the 

Snake River below the dam by 95 percent but had less effect 

on the discharge of the peak flows (Shaffer, 1975). Buchanan 

(1981) reported a reduction of 15 percent in mean annual 

flows since 1964 at the Niobrara River streamflow-gaging 

station near Norden (station number 06462000). He also 

reported reductions of nearly 19 and 28 percent in the mean 

annual monthly maximum (March) discharge and mean annual 

monthly minimum (August) discharge, respectively, at the 

Norden gage. 

The main stem of the Niobrara River also has had two 

hydroelectric dams: Cornell Dam, near Valentine, Nebr., 

and Spencer Dam, near Spencer, Nebr.. Cornell Dam was 

constructed in 1915, but has been inactive since 1986. Since 

that time, the holding basin behind the dam has completely 

filled in with sediment, and the river likely passes the entire 

upstream sediment load. Spencer Dam was constructed in 

1927 and remains active as a run-of-river power-generating 

facility. The holding basin behind Spencer Dam filled with 

sediment within a few years after dam construction (Nebraska 

Game and Parks Commission, 1980), and sediment now is 

flushed twice annually to evacuate storage volume. Thus, 

the daily operations of Spencer Dam have little effect on the 

downstream hydrology, but the dam acts as a seasonal barrier 

to the upstream sediment supply (Gutzmer and others, 1996). 

The seasonal disruption of sediment supply has altered the 

channel form of the Niobrara downstream to at least Eagle 

Creek, the first tributary downstream from the dam (Cole, 

1996; Alexander and others, 2009). 

Investigations of channel change associated with natural 

and human-induced alterations to flow and sediment regimes 

of the Niobrara River have been focused in reaches downstream from Norden, Nebr. Buchanan (1981) documented 

changes in channel morphology associated with natural and 

human-forced shifts in hydrology and used aerial photographs 

to identify two episodes of channel narrowing. The first 

narrowing episode occurred during the prolonged drought of 

the 1930s and was followed by a subsequent period of widening; the second narrowing episode occurred after closure of 

Merritt Dam on the Snake River. Changes in channel width 

at 16 transects indicated that the river width decreased by a 

median of 19 percent after closure of Merritt Dam. The magnitude of narrowing was greatest in the widest reaches, and no 

measureable changes in channel width were observed at naturally constricted reaches of the river. The process of narrowing 

involved the formation of vegetated islands, sedimentation of 

side channels, and attachment of vegetated islands and bars to 

the flood plain (Buchanan, 1981). 

The construction of two multipurpose flood control dams 

in the 1950s on the Missouri River upstream and downstream 

from the mouth of the Niobrara River resulted in substantial 

changes to the morphology and channel dynamics of the last 

12 miles of the Niobrara River channel (Etheridge and others, 

1999). The reduction of flood magnitudes on the Missouri 

River upstream from the Niobrara River mouth and creation 

of a reservoir downstream from the Niobrara River mouth 

decreased both the load and sediment-transport capacity of the 

Missouri River, and the sediment load of the Niobrara River 

began building a delta. Between 1950 and 1996, the bed of 

the Niobrara River at the Missouri River confluence rose by 

as much as 7.5 ft (2.3 m) (Bristow and others, 1999). Between 

1950 and 1989, the dominant channel adjustment was bed 

aggradation and channel narrowing by island and flood plain 

deposition. Beginning in 1989, episodes of channel avulsion, initiated primarily by ice or debris jams, have created a 

network of distributary channels, separated by vast, vegetated 

islands (Etheridge and others, 1999). 
8 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

Background

The geometry of an alluvial river channel is affected by 

several physical stressors, including the nature of the flow 

regime, geologic setting, caliber and quantity of the sediment 

supply, and valley pattern and confinement, and by biological stressors such as vegetation growth and beaver activity 

(Leopold and Maddock, 1953; Hey and Thorne, 1986; Parker 

and others, 2007; Shafroth and others, 2010). These stressors interact in time and space to determine the configuration 

and dynamics of the river bed, channel hydraulics, and the 

chemistry of its waters, which subsequently interact to create 

the natural physical habitat attributes of any particular patch 

of river space (Poff and Ward, 1990; Power and others, 1995; 

Doyle and others, 2005). Human or natural alterations to the 

flow regime, surrounding landscape, or channel geometry 

may interact to produce alterations in a river’s physical habitat 

attributes that are detrimental to ecosystem function (Junk 

and others, 1989; Poff and others, 1997). An investigation and 

description of the broad physical attributes of a river system 

and the dynamics of hydraulic adjustment may act as an 

organizing framework for sustainable management of a river 

basin by identifying the range of different fluvial settings and 

their associated (or potential) physical processes (Kondolf and 

Downs, 1996).

Hydraulic Geometry of the Niobrara River

Hydraulic geometry relations use the hydrographer’s 

streamflow measurement notes from individual gaging stations 

(at-a-station geometry) to relate wetted-channel geometry and 

water velocity to river discharge. The relations use a series of 

empirical models in the form of power laws as presented by 

Leopold and Maddock (1953):

w = aQb (1)

d = cQf (2)

v = kQm (3)

The variables w, d, and v are wetted-channel top width, mean 

depth, and mean velocity of the cross section, respectively; a,

c, k, b, f, and m are numerical constants; and Q is a reference 

discharge. The product of w, d, and v are equal to Q, an equation known to hydrologists as “continuity” because, over short 

distances, the discharge of a river must be the same, even if 

the geometry of the river changes. Therefore, by substitution, 

we obtain: 

Q = aQb * cQf * kQm (4)

By continuity, the exponents of equations 1–3 must sum to 

unity, and the products of the coefficients of equations 1–3 

must be unity. 

b + f + m = 1 (5)

a * c * k = 1 (6)

The magnitude of the exponent for each equation describes 

the slope of a best-fit (least-squares regression) line through 

a logarithmically scaled scatter plot of the relation, with 

discharge as the independent variable. The magnitude of the 

slope is a measure of the rate of adjustment of each variable at 

a cross section over a range of discharges. 

Hydraulic geometry relations are commonly developed 

at two scales: a local scale, referred to as “at-a-station,” and 

a basin scale referred to as “downstream” hydraulic geometry. At-a-station hydraulic geometry relations describe how 

a channel at a particular location within a basin adjusts to 

temporally changing discharges, and downstream-hydraulic 

geometry relations describe how the river channel adjusts 

in the downstream direction to increases in basin area and 

discharge. In the United States for rivers of the semi-arid 

Southwest and Great Plains, Leopold and Maddock (1953) 

reported at-a-station averages of 0.26, 0.40, and 0.34 and 

downstream averages of 0.5, 0.4, and 0.1 for exponents b, f,

and m (width, depth, and velocity), respectively; these values, 

however, have been shown to be highly variable depending on regional climate and physiography (Knighton, 1974; 

Park, 1977). 

In the previous study by Alexander and others (2009) the 

nature of channel adjustment in the Niobrara River Basin from 

Dunlap Diversion Dam to the Missouri River was investigated using hydraulic-geometry relations. Only the records 

from water years 1964 through 2008 were used, except those 

stations near Hay Springs and Cody, which are upstream from 

the Snake River confluence, and are therefore not affected by 

operations at Merritt Dam. At-a-station exponents averaged 

0.14, 0.40, and 0.45 for b, f, and m, respectively; however, the 

width exponent b exhibited a range from 0.00 to 0.32 (fig. 3; 

table 1). The variability of the at-a-station width exponent 

at two gaging stations located one-half mile apart along the 

Niobrara accounted for most of the range of exponent variability because one gage was located at a bridge across an unrestricted section and the other was located near a natural river 

constriction. Downstream hydraulic geometry exponents for 

the median-annual discharge of the Niobrara River were 0.53, 

0.26, and 0.21 for b, f, and m, respectively (fig. 4; table 2). 

Although the downstream width exponent, b, generally 

conforms to the widely reported value of 0.5, it was suspected 

that the wide range in the at-a-station width exponent, b, in 

particular the very low values at bedrock constrictions, skewed 

the downstream hydraulic geometry width exponents low. 
Figure 3. At-a-station hydraulic geometry relations for selected streamflow-gaging stations on the Niobrara 

River, showing relations between discharge and (A) wetted channel top-width; (B) average water depth; and 

(C) average current velocity (from Alexander and others, 2009).

Near Hay Springs

Near Gordon

Near Cody

Near Sparks

Near Norden

At Mariaville

Near Spencer

Near Verdel (pre-1985)

Near Verdel (post-1985)

EXPLANATION

Niobrara River

0.1

10

100

10 100 1,000 10,000 100,000

0.1

10

10

100

1,000

A

B

C

AVERAGE CURRENT VELOCITY, 

IN FEET PER SECOND AVERAGE WATER DEPTH, IN FEET WETTED CHANNEL TOP WIDTH, IN FEET

DISCHARGE, IN CUBIC FEET PER SECOND

1

1

Introduction 9
Table 1. At-a-station hydraulic geometry relations for eight selected Niobrara River streamflow-gaging stations. 

[All stations are located in Nebraska; all data from Alexander and others, 2009; period of record for each streamflow-gaging station expressed in water years; 

period of record used for hydraulic geometry analysis may differ from total available period of record for streamflow gage listed; a, width coefficient; b, width 

exponent; c, depth coefficient; f, depth exponent; k, velocity coefficient; m, velocity exponent; Q, water discharge, in cubic feet per second; w, channel top width, 

in feet; d, average channel depth, in feet; v, mean current velocity in feet per second; <, less than; >, greater than; ft3/s, cubic feet per second; --, not applicable; 

COD, coefficient of determination for least-squares estimate of regression equation]

Parameter or 

statistic

Station name, number, and period of record

Niobrara 

River near 

Hay 

Springs1, 

06456500, 

1951–63

Niobrara 

River near 

Gordon, 

06457500, 

1964–90

Niobrara 

River near 

Cody, 

06459000, 

1949–56

Niobrara 

River near 

Sparks, 

06461500, 

1964–2007

Niobrara 

River near 

Norden 

06462000, 

1964–83

Niobrara 

River near 

Mariaville, 

06463720, 

1986–90

Niobrara 

River near 

Spencer, 

06465000, 

1964–2000

Niobrara 

River near 

Verdel2, 

06465500, 

1964–85

Niobrara 

River near 

Verdel2, 

06465500, 

1986–2007

Average 

of 

stations

Number of measurements used in hydraulic geometry analysis

35 589 142 485 196 34 331 238 117 241

Maximum discharge of included measurements, in ft3/s

168 1,380 3,340 3,940 3,990 3,520 12,500 8,680 7,610 5,014

Minimum discharge of included measurements, in ft3/s

10 49 197 203 357 946 540 474 975 417

Width coefficients and exponents (equation 1; w = aQb)

a 27 21 53 81 24 292 34 230 53 91

b .12 .22 .05 .10 .19 .00 .27 .01 .32 .14

p-value3 .05 <.0001 <.0001 <.0001 <.0001 >.5 <.0001 .14 <.0001 --

COD .11 .11 .42 .12 .24 .00 .20 .01 .12 --

Depth coefficients and exponents (equation 2; d = cQf)

c 0.11 0.22 0.17 0.11 0.10 0.06 0.15 0.07 0.08 0.12

f .46 .31 .39 .40 .46 .44 .34 .46 .34 .40

p-value3 <.0001 <.0001 <.0001 <.0001 <.0001 <.0001 <.0001 <.0001 <.0001 --

COD .70 .25 .69 .58 .70 .52 .23 .73 .24 --

Velocity coefficients and exponents (equation 3; v = kQm)

k 0.34 0.31 0.11 0.11 0.41 0.06 0.19 0.07 0.23 0.20

m .42 .39 .57 .51 .35 .55 .39 .53 .34 .45

p-value3 <.0001 <.0001 <.0001 <.0001 <.0001 <.0001 <.0001 <.0001 <.0001 --

COD .78 .47 .73 .79 .48 .60 .41 .80 .34 --

Product of coefficients

1.00 1.48 0.97 1.00 1.00 1.00 0.99 1.03 1.00 1.05

Sum of exponents

1.00 0.92 1.01 1.00 1.00 1.00 1.00 1.00 1.00 0.99

1

Measurement record for gage near Hay Springs was unavailable for water years 1956–1960.

2

Verdel gage was moved in 1985.

3

Probability (p-value) that regression slope is zero (no correlation between discharge and geometric variable); values less than 0.10 indicate model significance at the 90-percent confidence level.

10 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
Figure 4. Downstream hydraulic geometry relations for the Niobrara River between the streamflow-gaging 

station near Hay Springs, Nebraska, and the streamflow-gaging station near Verdel, Nebraska, showing 

downstream relations between discharge and (A) wetted channel top-width; (B) average water depth; and 

(C) average current velocity (from Alexander and others, 2009). AVERAGE CURRENT VELOCITY, IN FEET PER SECOND AVERAGE WATER DEPTH, IN FEET CHANNEL WETTED TOP WIDTH, IN FEET

1

10

0

1

10

10

100

1,000

Vertical dashed 

line identifies 

two Verdel 

gaging-station 

hydraulic 

geometries

Mean

10-percent exceedance

50-percent exceedance

75-percent exceedance

Mean

10-percent exceedance

50-percent exceedance

75-percent exceedance

EXPLANATION

Fitting line Streamflow condition

10 100 1,000 10,000 100,000

A

B

C

DISCHARGE, IN CUBIC FEET PER SECOND

Introduction 11
Table 2. Downstream hydraulic geometry relations for the Niobrara River between Hay Springs and Verdel, Nebraska.

[All data from Alexander and others, 2009; %, percent; a, width coefficient; b, width exponent; c, depth coefficient; f, depth exponent; 

k, velocity coefficient; m, velocity exponent; Q, water discharge, in cubic feet per second; w, channel top width, in feet; d, average channel 

depth, in feet; v, mean current velocity in feet per second; <, less than; >, greater than; ft3/s, cubic feet per second; COD, coefficient of determination for least-squares estimate of regression equation]

Parameter or 

statistic

Mean annual 

discharge

Flow exceedance1

10% 50% 75% 

Maximum discharge used in regression model, in ft3/s 

1,708 2,695 1,540 1,180

Minimum discharge used in regression model, in ft3/s 

29 40 24 18

Width coefficients and exponents (equation 1; w = aQb)

a 4.72 4.08 5.29 5.95

b .54 .54 .53 .52

p-value2 <.001 <.001 <.001 <.001

COD .76 .77 .75 .75

Depth coefficients and exponents (equation 2; d = cQf)

c 0.28 0.29 0.26 0.25

f .25 .25 .26 .26

p-value2 .01 .01 .01 .01

COD .61 .62 .63 .63

Velocity coefficients and exponents (equation 3; v = kQm)

k 0.76 0.81 0.73 0.69

m .21 .21 .21 .21

p-value2 <.001 <.001 <.001 <.001

COD .77 .79 .77 .77

Product of coefficients

0.99 0.97 1.00 1.01

Sum of exponents

1.00 1.00 1.00 1.00

1

Refers to the percentage of days from period of record that flow exceeded a particular magnitude. See table 1 for values associated with a 

particular streamflow-gaging station; exceedance was calculated for each gaging station for its particular period of record and used to develop 

the data values to which hydraulic geometry relations were fitted.

2

Probability (p-value) that regression slope is zero (no correlation between discharge and geometric variable); values less than 0.10 indicate 

model significance at the 90-percent confidence level.

12 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
Approach and Methods 13

Hydrogeomorphic Segments of the 

Niobrara River

The hydrogeomorphic characteristics of the Niobrara 

River change dramatically along its journey across northern 

Nebraska. In the previous study by Alexander and others 

(2009) a process-based classification scheme, composed of 

four primary descriptive geomorphic “elements” (table 3), was 

proposed and used to qualitatively describe the longitudinal 

variation in the physical characteristics of the river: degree 

of valley confinement, channel-planview pattern, channelwidth variation, and bar configuration. The term “geomorphic 

segment” was defined as a length of river that has a relatively 

uniform host of hydrologic and morphologic characteristics. 

For this report the term “hydrogeomorphic segment” is used 

instead of “geomorphic segment” to be more consistent with 

the defined characteristics. Aerial photos and topographic 

maps of the river valley were used to classify the river into 

36 individual hydrogeomorphic segments, each of which 

had a hypothesized difference in one of the elements from its 

upstream and downstream bounding segments, but may have 

been similar to segments elsewhere in the study area. Most 

of the Niobrara River between Dunlap Diversion Dam and 

the Missouri River was dominated by width-restricted valley 

settings, a sinuous channel pattern, highly variable channelwidth, and a braided-bar bed configuration. Although segment 

boundaries were assigned using the physical descriptors from 

the classification scheme, no quantitative procedure was 

applied to test for measurable differences between hydrogeomorphic segments. 

Based on natural breaks in the characteristics of the 

36 hydrogeomorphic segments, the Niobrara River was 

divided into 3 broad fluvial geomorphic provinces: an upper 

province where the channel is narrow and meanders across 

a broad flood plain; a middle province where the river flows 

through mixed-valley settings, including narrow canyons and 

valleys bound by escarpments; and a lower province where 

the valley and channel are wide, and the river is persistently 

braided (fig. 5). These provinces were named the Meandering Bottoms (MB), Canyons and Restricted Bottoms (CRB), 

and the Braided Bottoms (BB), respectively (Alexander and 

others, 2009) (fig. 5). The fluvial geomorphic provinces also 

corresponded closely in space to changes in bedrock lithology 

at the level of the river with the CRB province exhibiting the 

greatest range in channel-form characteristics, channel slope, 

and bedrock lithology among segments (fig. 2). 

Approach and Methods

The study described in this report builds upon previous work by Alexander and others (2009) and is intended 

to compile a hydrogeomorphic framework for future, more 

detailed physical and biological investigations. The study 

approaches the analysis of hydrogeomorphic segments and 

hydraulic microhabitats of the Niobrara River at two spatial 

scales. First, a characterization of the physical attributes along 

the length of the Niobrara River and its valley is presented at a 

basin scale and hydraulic microhabitats are assessed for fluvial 

geomorphic provinces within the basin. Second, at the reach 

scale, field measurements from four study reaches are used to 

examine the variation of elevation and geomorphic processes 

associated with fluvial landforms, and the channel hydraulic 

geometry, hydraulics, and hydraulic microhabitats within the 

Scenic Reach of the Niobrara River. 

Basin-Scale Methods

Existing topographic data, aerial photographic images, 

and stream-hydraulic information were compiled and used 

to investigate the longitudinal variation in the hydrogeomorphic, hydraulic, and aquatic microhabitat attributes of the 

Niobrara River from Dunlap Diversion Dam to the Missouri 

River (fig. 1). The basin-scale investigation included three 

tasks: a GIS analysis and characterization of the longitudinal 

hydrogeomorphic attributes of the river; statistical analysis 

of previously determined longitudinal hydrogeomorphic 

segments (Alexander and others, 2009); and estimation of 

hydraulic microhabitat characteristics in the three fluvial 

geomorphic provinces of the Niobrara River. Although the 

GIS analysis was used as the basis for the statistical analysis, the methods for the statistical analysis are presented first 

because the results of the statistical analysis ultimately had an 

effect on the organization and final descriptions of the physical 

characteristics of the geomorphic segments.

Statistical Analysis of Fluvial Geomorphic 

Provinces and Hydrogeomorphic Segments of 

the Niobrara River

A river can be described in many different ways, and 

numerous classification systems, spanning several scientific 

disciplines, have been proposed and used by water resource 

scientists and managers (Kondolf, 1995). The process-based, 

segment-scale classification scheme for the Niobrara River 

is composed of a framework of four primary geomorphic 

“elements” (table 3): (A) degree of valley confinement; 

(B) channel-planview pattern; (C) channel-width variation; and (D) bar configuration. Each element has three or 

more “classes” that broadly describe the variation in physical “condition” within each element (table 3). Boundaries of 

hydrogeomorphic segments were assigned where an abrupt 

and persistent difference in one or more of the classes was 

identified in the river by examining aerial photographs. The 

classification used the assumption that broad differences in 

channel form characteristics were the result of differences 

in river processes, and these differences likely translate into 

variation in aquatic and riparian macro-habitat characteristics. 

Although this assumption is potentially a drastic simplification of the Niobrara River aquatic and riparian ecosystems, it 
Table 3. Segment-scale geomorphic classification system for the Niobrara River, Nebraska (adapted from Alexander and others, 2009).

Scale Condition Class Definition

Geomorphic element [A]. Degree of valley confinement

Valley Entrenched 1 Valley confinement such that the river pattern is forced by the valley configuration, making the 

river and valley pattern nearly identical; consequently the river persistently flows parallel to 

the valley direction, and adjustment of the broad-scale channel pattern is not possible. Flood 

plains are present but commonly are less than one channel width across. 

Restricted Phase 2 Valley confinement such that the planview river pattern largely is controlled by valley pattern, 

valley width irregularities, or tributary alluvial fans. The valley is generally wide enough for 

a flood plain of several channel widths, but the river is intermittently entrenched. The river 

commonly flows parallel to the valley direction and impinges on the valley wall at most outer 

bends. The term “phase” is used to imply that the overall amplitude and wavelength (phase) of 

the river pattern is largely controlled by the valley phase.

Width 3 Valley confinement such that the valley is wide enough for a flood plain of several channel 

widths and the effect of the valley pattern on river channel pattern generally is limited to 

redirection of the channel towards the opposite valley wall at outer bends. 

Open 4 Valley pattern has little to no effect on the dominant river pattern. Channel interaction with the 

valley wall is infrequent. Channel form adjustments such as large meander-loop cutoffs or 

long anabranching channels are possible. 

Geomorphic element [B]. Channel-planview pattern

Reach Straight 1 Channel pattern such that the channel centerline length between two endpoints divided by the 

straight-line length between the same two endpoints is less than or equal to 1.05.

Sinuous 2 Channel pattern such that the channel centerline length between two endpoints divided by the 

straight-line length between the same two endpoints is between 1.06 and 1.49.

Highly sinuous 3 Channel pattern such that the channel centerline length between two endpoints divided by the 

straight-line length between the same two endpoints is greater than or equal to 1.5.

Geomorphic element [C]. Channel-width variation

Reach Equiwidth 1 Channel width generally does not vary by more than a factor of two for the length of the reach.

Irregular 2 Channel width varies progressively or intermittently along the reach by more than a factor of 

two.

Highly irregular 3 Channel width varies by a factor of two for lengths as short as a single channel width, with the 

appearance as a series of bulges and narrows in planview. 

Geomorphic element [D]. Bar configuration

Bar Alternate 1 Bar configuration such that a single thalweg is dominant and flows alternately between bars that 

migrate freely within the channel banks. Alternating bars may be covered with herbaceous or 

immature vegetation.

Lateral 2 Bar configuration such that a single thalweg flows around stable laterally deposited bars that 

grow oblique or orthogonal to the dominant flow direction. 

Braided 3 Bar configuration such that several thalwegs exist and migrate between complexes of emergent 

and submerged channel sandbars.

Island 4 Bar configuration such that several thalwegs exist and channel flows between sandbars occupied 

by mature vegetation and whose dimensions generally are proportional to the active channel 

width.

Bedrock1 5 River bed consists primarily of bedrock or shallow bedrock with a veneer of sand that may or 

may not be organized into series of bars. The river planform frequently interacts with the 

bedrock valley walls.

1

Added by the authors for this study.

14 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
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EXPLANATION

Hay Springs

Cody Sparks Verdel

06456500

06459000 06461500

06465500 Niobrara River

Missouri Ri ver

06457500 06459500

06462000 06462500

06463500

06463720

06464900

06465000

06465310

06465440

06465700

0 20 40 MILES 100 20 40 KILOMETERS 10

Portion of Niobrara River outside of study area

Niobrara River main stem by fluvial geomorphic province 

Braided Bottoms (BB)Canyons and Restricted Bottoms (CRB)Meandering Bottoms (MB)

Tributary used in longitudinal hydrology curves 

06461000

Base from U.S. Geological Survey National Elevation Dataset, 2006;National Hydrography Dataset, 2007; State boundaries, 2005,1:2,000,000Basin boundary modified from U.S. Department of Agriculture,Natural Resources Conservation Service Watershed Boundary Dataset, 2008Universal Transverse Mercator projectionZone 14 

SOUTH DAKOTA

NEBRASKA

WYOMING

Missouri River Streamflow-gaging station used for construction of longitudinal  hydrology curves and hydraulic microhabitat analysisStreamflow-gaging station used for construction of longitudinal  hydrology curves

104° 103° 102° 101° 100° 99° 98°

43°

42°

Niobrara River Basin boundary

Figure 5. Extents of Niobrara River fluvial geomorphic provinces, location of main-stem streamflow-gaging stations used in hydraulic microhabitat analysis for each province, and locations of streamflow-gaging stations used to construct longitudinal hydrology curves (extent of provinces from Alexander and others, 2009).

Approach and Methods 15
Table 4. Names and abbreviations for hydrogeomorphic variables used in statistical analysis of hydrogeomorphic segments.

Variable name Abbreviation Definition

Channel sinuosity SIN_100 Ratio of the channel centerline length between two points divided by the straight-line 

length between the same two points as calculated over 100 channel widths centered 

on the sampling point.

Valley confinement CHAN_VAL_RAT Ratio of the channel width to the valley width at the sampling point.

Braided index BI Number of channel threads averaged over a 30-channel width window centered on the 

sample point.

Stream power SP_90 Unit stream power of the sampling point at the 90th-percentile (10 percent-exceedance) 

discharge.

Wall proximity WAL_PROX Minimum distance from a channel bank, right or left, to the valley wall.

Channel-width variability CHAN_CV Ratio of the standard deviation to the mean of channel width as measured over a 

distance of 100 channel widths centered on the sampling point.

Valley sinuosity CH_VAL_LEN Ratio of the centerline length of the river channel to the centerline length of the bounding valley as calculated over 100 channel widths centered on the sampling point.

16 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

provides an initial basis to describe and quantify the spatial 

variation of the river within the study area. 

The purpose of the statistical analysis herein is to assign 

physiographic and hydrogeomorphic metrics to the descriptive elements, and use them to determine if the hydrogeomorphic segments, as defined by their various combinations of 

descriptive elements (table 3), are measurably different from 

their upstream and downstream bounding segments. For this 

analysis, each of the 36 hydrogeomorphic segments, although 

assigned manually, were hypothesized to have measureable differences in one or more of the classification elements 

(table 3) from an upstream or downstream bounding segment. 

It also was assumed that the classes from each of the primary 

geomorphic elements (table 3) were assigned to each segment 

in a mostly correct manner. For example, the bar configuration class assigned to each segment was assumed to be the 

dominant bar type, but surely not the only bar type present, 

and, therefore, human error could have assigned the incorrect dominant bar type. Based on field observations, reaches 

classified as “entrenched” with no bars visible in the aerial 

photographs were assumed to be bedrock-dominated on the 

bed or banks. Subsequently, a fifth class, bedrock, was added 

to the bar configuration element proposed by Alexander and 

others (2009) to account for the dominance of bedrock in such 

reaches (table 3). 

Seven hydrogeomorphic variables (table 4) were derived 

from the GIS analysis, hydrology data, and elevation data, and 

for each of the channel centerline sampling points (identified using the GIS centerline addressing system described in 

the next section), the value of each variable was measured or 

estimated. The variables chosen were primarily based on a 

combination of descriptive power, simplicity, and geomorphic 

relevance. Additionally, because the study area spans over 350 

mi of the Niobrara River, and the river grows dramatically 

in width and discharge over this length, the variables chosen 

were either dimensionless, width-normalized, or were not 

directly related to the width or discharge of the channel (table 

4). Variable simplicity was necessary to efficiently derive the 

metrics from the GIS sampling scheme. For example, numerous ways of calculating the sinuosity and braided index of 

a river channel have been used in the geomorphic literature 

(Knighton, 1998); however, for the purposes of this analysis, 

the most basic forms of sinuosity and braided index were used 

because these metrics were suited to rapid, consistent, and 

straightforward calculation from the GIS sampling data set. 

The statistical procedure consisted of two primary steps: 

(1) assignment of variables to each element using an analysis 

of variance (ANOVA) and multiple comparison procedure, 

and (2) discriminant analysis of hydrogeomorphic segments 

using the assigned hydrogeomorphic variables as predictors. 

All statistical procedures were performed using Spotfire S+ 

software (TIBCO Software Incorporated, 2008). Only the 

ordinal ranks of the points for each variable were used, as 

opposed to the variable values themselves, for all steps in 

the statistical procedures, so that no distribution or variance 

assumptions were necessary (non-parametric). Although 

non-parametric techniques reduce the inferential power of 

these procedures for variables with normal distributions of 
Figure 6. Example of digital geographic data sets used to sample 

Niobrara River channel and valley morphologic characteristics.

572000 573000

4727000

4728000

Base from U.S. Department of 

Agriculture Farm Service Agency, 2003

Universal Transverse Mercator projection 

Zone 14

Horizontal coordinate information is 

referenced to the North American 

Datum of 1983 (NAD 83) 

0 1,300 2, 600 FEET

0 300 600 METERS

Channel transect

Valley wall boundary

Channel centerline

Sampling mode

Island boundary (1999)

Channel boundary (1999)

Approach and Methods 17

constant variance, sample sizes were large enough to reduce 

the need for the power of parametric procedures (Helsel and 

Hirsh, 2002). 

Although numerous statistical methods exist for classifying objects based on a given set of variables, assumptions 

were made on the basis of the previous investigation (Alexander and others, 2009) that the number of descriptive elements 

and their associated number of classes were adequate, and that 

the chosen variables were adequate descriptors of at least some 

of those classes (table 4). Using these assumptions, ANOVA 

models (TIBCO Software Inc., 2008) were created for each 

hydrogeomorphic variable to test its ability to distinguish the 

previously assigned classes within each geomorphic element. 

To test if each variable could distinguish between the assigned 

classes, multiple comparison analysis (MCA) procedures 

were performed on each ANOVA model using an alpha value 

of 0.05 (95 percent confidence). The Tukey (1953) multiple 

comparison test was used for all elements with three or more 

classes. The Fisher (1949) least-significant differences test was 

used for the “Channel Planview Pattern” element because only 

two classes were identified for the element within the study 

area by Alexander and others (2009). If either MCA analysis 

indicated that a variable was capable of distinguishing the 

same number of classes as had previously been defined for the 

associated geomorphic element, then it was assumed to be a 

candidate or potential predictor for multivariate discriminant 

analysis. 

Once each variable had been tested for its discriminating ability, an iterative procedure was used to build a final, 

predictive discriminant function for each element. First, a 

primary hydrogeomorphic variable was chosen from the pool 

of predictor variables on the basis of results from the ANOVA 

procedure. The primary hydrogeomorphic variable was 

different for each geomorphic element, and was considered to 

be the most physically relevant to the associated element. For 

example, channel sinuosity was chosen as a primary predictor 

of channel-planform pattern, and braided index was chosen 

as a primary predictor of channel-bar configuration (table 4). 

Discriminant analysis was first applied using this single 

primary variable as a class predictor. The remaining candidate 

variables were added iteratively to the discriminant model, 

and remained in the model only if the maximum class error 

(maximum misclassification rate among individual classes) 

and overall model prediction error (total misclassification 

rate) were both reduced by the inclusion of the variable in the 

discriminant function. The procedure was continued until all 

candidate predictor variables had been tested. The discriminant function with the lowest maximum and total error then 

was used to assign each channel-sampling point to a class 

for each geomorphic element. In addition to error percentage, the Wilks’ lambda test statistic was used to assess the 

proportion of the variance in the multi-variate combination of 

variables that was unaccounted for by grouping (discriminating) using the geomorphic element classes (Everitt and Dunn, 

1991). The Wilks’ lambda test statistic was approximated to an 

F distribution, and assigned a probability value (p-value) at the 

95-percent confidence level. A low probability value for the 

Wilks’ lambda test statistic was interpreted as a signal that the 

means between element classes were statistically distinguishable (unequal). 

The combination of predicted class assignments then 

was compared to the hydrogeomorphic segment combinations proposed by Alexander and others (2009). If a particular 

segment showed any different class assignments, the new 

combination was compared to bounding upstream and downstream segment class combinations to determine if either was 

classified differently. If the combination was different from the 

upstream and downstream segments, the segment remained a 

unique segment. If the segment was classified identically to an 

upstream or downstream bounding segment, it was considered 

statistically indistinguishable and combined with that segment. 

Geographic Information System Analysis of 

Niobrara River and Valley Morphometry

In collaboration with the University of Nebraska Center 

for Advanced Land Information Technologies (CALMIT), four 

primary spatial data sets were constructed and used to quantify 

the longitudinal variation in Niobrara River hydrogeomorphic 

characteristics: Niobrara channel centerline, active channel 

boundaries, island boundaries, and valley-wall boundaries 

(fig. 6). The Niobrara channel centerline was constructed by 

digitizing onscreen in a GIS while superimposed on the 2003 

Farm Service Agency natural-color aerial-ortho photographs 

at 1:5,000 scale (U.S. Department of Agriculture, 2004). 
18 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

The Niobrara active channel boundaries and valley-wall 

boundaries were constructed from the 1999 U.S. Geological Survey aerial-ortho photographs (Nebraska Department 

of Natural Resources, 2004). The non-vegetated area of the 

visible channel was used as a proxy for the “active” channel, 

a method that has been used widely by other investigators of 

alluvial rivers (Williams, 1978; Nadler and Schumm, 1981; 

Johnson, 1994; Van Steeter and Pitlick, 1998; Allred and 

Schmidt, 1999; Grams and Schmidt, 2002). Where visible, 

the boundaries of vegetated islands within the active channel 

also were digitized as individual polygons. The 1999 blackand-white aerial photographs were used to define the active 

channel boundaries because the period of water years 2000 

to 2006 included several years of unusually low flow, and 

the channel may have narrowed temporarily during that short 

period. Finally, the boundaries of the valley wall were digitized based on a combination of the 2003 U.S. Department 

of Agriculture, Farm Service Agency (FSA) natural-color 

aerial-ortho photographs and the digital USGS 7.5-minute 

topographic quadrangles (http://topomaps.usgs.gov/drg/). The 

valley-wall boundary was defined as the across-valley interface between landforms created by hillslope processes and 

landforms deposited by alluvial processes. Tributary alluvial 

fans depositing on the valley flat and terrace deposits were 

considered part of the alluvial valley bottom, and, therefore, 

were not used as valley-wall boundaries. 

To systematically quantify the width of the channel, 

width of the valley bottom, and number of islands within the 

Niobrara River, a longitudinal sampling strategy was devised 

using an addressing system along the channel centerline. The 

active-channel boundaries of the river within the study area 

were converted to a single polygon. The polygon was then 

subdivided into three separate polygons using the boundaries of the three fluvial geomorphic provinces: the Meandering Bottoms, Canyons and Restricted Bottoms, and Braided 

Bottoms (fig. 5). The average channel width of each fluvial 

geomorphic province was estimated by dividing the area of 

each polygon by the centerline length of the Niobrara River 

within it. The channel centerline within each fluvial geomorphic province was converted into a series of sampling nodes, 

spaced one average channel width apart (fig. 6). A centerline 

distance was assigned to each sampling node beginning at 

the former Chicago and Northwestern Railroad Bridge near 

the Missouri River confluence. A transect was centered on 

each sampling node, aligned perpendicular to the channel 

centerline, and spanned at least the width of the channel. The 

location of each transect upstream from the Missouri River 

was assigned using the centerline distance of the sampling 

node it was centered on. The width of the active channel was 

estimated at each node by clipping the transect lines using the 

active-channel boundary data set, then subtracting the width 

of the transect that intersected each island. To calculate the 

number of islands at each sampling node, the transect lines 

were intersected with the island polygons in the GIS, which 

erased the portion of each transect outside of the islands, and 

assigned the identification number of the overlying transect to 

each island. The number of islands at each node was counted 

by summing the number of lines with common identification 

codes. It should be noted that the width of the river in a short 

segment below Dunlap Diversion Dam could not be digitized 

accurately at the 1:5,000 scale, nor any scale, because of a lack 

of photographic resolution of channel boundaries in the 1999 

photographs. For this section of river, the approximate boundaries of the channel were digitized and adjusted based on the 

ratio of the average width of the channel as compared to the 

average width of the river at 60 sampling nodes immediately 

upstream and downstream from the short segment. 

The potential for a river to transport sediment is largely 

based on a combination of its flow regime and channel geometry, the latter of which may be affected by bedrock geology or 

vegetation. Stream power is a metric commonly used by engineers and geomorphologists to assess the energy expenditure 

of the river on its bed and banks and may be used as a measure 

of the potential for a river to transport sediment (Bagnold, 

1977; Bull, 1979). Stream power (Ω) is defined as:

Ω = γQs (7)

The variables γ, Q, and s, are the specific weight of water, 

river discharge, and channel slope, respectively. To compare 

rivers and reaches of river with largely differing discharges, 

stream power often is divided by channel width to determine 

“unit stream power.” Unit stream power can be used as a predictor of sediment transport (Yang, 1973), particularly bedload 

transport (Bagnold, 1977), as well as a predictor of channel 

bedforms (Simons and Richardson, 1966). 

As a measure of the longitudinal variation in sediment 

transport potential, unit stream power was estimated at each 

sampling node. Calculation of longitudinal unit stream power 

required the assignment of discharge and slope values to each 

sampling point. Longitudinal hydrology curves were generated 

using the Niobrara main channel and tributary streamflowgaging station data. The locations of main stem and gaged 

tributaries were assigned distances along the Niobrara River 

channel centerline using the addressing system for sampling 

nodes described above. The daily streamflow data for each 

main stem gage was used to create discharge duration curves 

and derive the mean, median, and 10-percent exceedance 

(90th percentile) discharge for each of the streamflow-gaging 

stations (table 5). To maintain consistency with a previous 

study (Alexander and others, 2009), where possible, only 

the post-1963 period of approved record (through water 

year 2008) was used to create the discharge duration curves. 

The longitudinal hydrology curves were formulated by linear 

interpolation between each successive gage for a particular 

discharge-frequency value while taking into account any 

abrupt increases (of the same discharge-frequency value) from 

gaged tributaries between the two stations (fig. 7). Discharge 

for a particular exceedance frequency at each sampling point 

was estimated by interpolating along the slope between gages 

and tributaries. Finally, the longitudinal profile of the Niobrara 

River (fig. 2) was used to assign elevation values to each 
Table 5. Streamflow-gaging stations used to construct longitudinal hydrology curves of the Niobrara River from Dunlap Diversion Dam 

to the Missouri River.

[Gages listed in order from upstream to downstream; all stations are located in Nebraska; River mile, location along channel centerline in distance upstream 

from the Missouri River confluence with the Niobrara; Qxx, discharge of “xx” percentile frequency from discharge duration curve; ft3/s, cubic feet per second]

Station name Station number Period of record River mile Q50 (ft3/s) Qmean (ft3/s) Q90 (ft3/s)

Niobrara River near Hay Springs1 06456500 1952–1964 317 23 27 40

Niobrara River near Gordon 06457500 1947–1991 281 105 115 162

Niobrara River near Cody1 06459000 1950–1957 204 303 314 400

Snake River near Burge 06459500 1964–1994 173 187 154 272

Minnechaduza Creek at Valentine 06461000 1949–1994 150 30 34 56

Niobrara River near Sparks1 06461500 1964–2007 143 720 736 1,000

Niobrara River near Norden 06462000 1964–1983 119 787 810 1,120

Plum Creek at Meadville 06462500 1964–1994 109 96 104 130

Long Pine Creek near Riverview 06463500 1964–2007 97 159 168 209

Niobrara River at Mariaville 06463720 1986–1991 80 1,260 1,358 1,870

Keya Paha River near Naper 06464900 1958–1994 59 74 139 290

Niobrara River near Spencer 06465000 1964–2001 39 1,400 1,541 2,380

Eagle Creek near Redbird 06465310 1979–1991 34 45 51 77

Redbird Creek at Redbird 06465440 1981–1994 28 34 41 66

Niobrara River near Verdel1 06465500 1964–2007 15 1,530 1,705 2,700

Verdigre Creek near Verdigre 06465700 2003–2007 5 100 117 172

1

Used in hydraulic microhabitat analysis.

0

500

1,000

1,500

2,000

2,500

3,000

Mean daily discharge

Median daily discharge

90th-percentile discharge

EXPLANATION

300 250 200 150 100 50 0

MILES UPSTREAM FROM THE MISSOURI RIVER

Keya Paha 

River

confluence Plum Creek

confluence

Snake River

confluence

Niobrara River 

near Hay 

Springs 

Niobrara River 

near Cody 

Niobrara River 

near Sparks 

Niobrara River 

near Norden 

Niobrara River 

near Spencer 

Niobrara River 

Niobrara River near Verdel 

near Gordon 

DISCHARGE, IN CUBIC FEET PER SECOND

Figure 7. Longitudinal hydrology curves of the Niobrara River used for along-stream calculation of unit 

stream power.

Approach and Methods 19
20 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

sampling point. The average channel slope assigned to each 

sampling point then was calculated across 100 channel widths, 

centered on the sampling point (50 channel widths upstream 

and 50 channel widths downstream). In reaches near main 

channel dams, the slope calculations were truncated at the 

dam. For example, the slope for a point immediately upstream 

from the dam crest would only include the 50 channel widths 

upstream and none downstream; the slope for a point immediately downstream from the dam face only included the 

50 channel widths downstream. 

Calculation of Hydraulic Microhabitats in Fluvial 

Geomorphic Provinces of the Niobrara River

At the scale of a river reach, hydraulic variables such as 

flow depth and velocity exert important effects on the types of 

aquatic habitat available for organisms (Stalnaker and others, 

1996; McKenny, 1997). The distributions of flow depth and 

velocity combinations in a reach of river are a function of 

several factors including channel geometry, bed configuration, 

and flow regime (Maddock, 1999; Bridge, 2003). The automatic hydraulic microhabitat calculator developed by Ginting 

(Ginting and Zelt, 2008) was used to demonstrate the types 

and extents of hydraulic habitats available in different fluvial 

geomorphic provinces over a range of flow regimes. This tool 

characterizes the extent of hydraulic habitat niches along the 

cross section using a matrix of three depth and three velocity 

classes (table 6). Depth classes were defined as shallow, intermediate, and deep, corresponding to class boundaries of less 

than 1 ft, 1 to 2 ft, and deeper than 2 ft, respectively. Velocity 

classes were defined as slow, moderate, and swift, corresponding to class boundaries of less than 1 ft per second (ft/s), 1 to 

2 ft/s, and greater than 2 ft/s, respectively. The hydraulic 

habitat nomenclature uses the respective depth and velocity class names. For example, an area of the channel with 

depth less than 1 ft and velocity between 1 and 2 ft/s would 

be classified as “shallow-moderate.” Although the hydraulic 

habitat niches were originally defined for fish species of the 

Platte River (Peters and Holland, 1992), many of the same fish 

species were found in samples of the main stem and tributaries 

of the Niobrara National Scenic River (Dietsch, 2007). 

To compare differences in habitat types and distributions 

in different geomorphic provinces of the Niobrara study area, 

four gaging stations were chosen to represent the hydraulic 

environments of each province. The Niobrara River near Hay 

Springs (station number 06456500) was chosen to represent 

the Meandering Bottoms (MB) province; the Niobrara River 

near Cody (station number 06459000) and near Sparks (station 

number 06461500) were chosen to represent the Canyons 

and Restricted Bottoms (CRB) province; and the Niobrara 

River near Verdel (station number 06465500) was chosen to 

represent the Braided Bottoms (BB) province (fig. 5). For 

convenience, these stations are hereinafter referred to only 

as Hay Springs, Cody, Sparks, and Verdel, respectively. To 

investigate the range of habitat types and distributions at each 

gage over a range of flow regimes, two measurements were 

chosen from each of three flow exceedance categories: upper 

decile (less than 10-percent exceedance), median quantile 

(25- to 75-percent exceedance), and lower decile (greater than 

90-percent exceedance). 

Study Reaches along the Niobrara National 

Scenic River

Hydrogeomorphic segments are composed of several 

individual river reaches. The term “reach” is used herein to 

describe a length of river space that has one or more repeated 

sequences of hydraulic characteristics (Frissel and others, 

1986). A familiar example of such a sequence would be 

a pool-riffle coupling in a meandering river channel. The 

USGS and NGPC selected four study reaches within the 

Scenic Reach of the Niobrara River to investigate reach-scale 

hydraulics, hydraulic geometry, bed-sediment characteristics, 

fluvial landforms, and hydraulic microhabitats (fig. 8). For the 

purposes of brevity, these reaches are hereinafter referred to 

as Crooked, Sunny Brook, Muleshoe, and Rock Barn, respectively (table 7). 

The locations of each study reach were identified by 

USGS and NGPC personnel prior to the hydrogeomorphic 

segmentation process and were selected primarily on the basis 

of a combination of hydraulic uniformity along the reach, 

presence of alluvial banks and landforms, and access considerations. Hydraulic uniformity was important to minimize 

uncertainty in the discharge and channel resistance measurements, and alluvial banks were important to accommodate 

unrestricted alluvial channel adjustments over a range of 

discharges. Four cross sections were established within each 

study reach, spaced approximately one channel width apart 

(fig. 9). Initial topographic surveys of the cross sections were 

performed by NGPC personnel using real-time kinematic 

(RTK) Global Positioning System (GPS) technology (J. Miller, 

Nebraska Game and Parks Commission, unpublished data, 

2008). The cross sections at each study reach were numbered 

in downstream order from 1 to 4. 

Characterization of Fluvial Landforms and 

Bed Sediment 

Rivers adjust their banks and build flood plains such 

that the channel geometry is capable of efficiently transporting, within an associated hydrologic regime, the caliber and 

mass of sediment received from upstream. For the purposes 

of this report, Nanson and Croke’s (1992) definition of a 

“genetic” flood plain was used: the largely horizontally bedded 

alluvial landform adjacent to a channel, separated from the 

channel by banks, and built of sediment transported by the 

present flow regime. Flood plains are primary depositional 

features of alluvial rivers, and their treads are commonly used 

as indicators of the elevation of the stage of some physically relevant discharge (bankfull, dominant, or effective 
Table 6. Typical association between fish species and matrix of depth and velocity combinations defined as hydraulic 

habitat niches for microhabitat analysis (adapted from Ginting and Zelt, 2008).

[Depth and velocity classes and associated species based on Peters and Holland (1992), except where indicated; ft, foot; ft/s, feet per second]

Water depth Current velocity

Slow (slower than 1 ft/s) Moderate (1–2 ft/s) Swift ( faster than 2 ft/s)

Shallow (shallower than 1 ft) Notropis blennius Hybognathus placitus Aplodinotus grunniens

(River shiner) (Plains minnow) (Freshwater drum)

Cyprinella lutrensis

(Red shiner) Hybognathus argyritus

Notropis stramineus (Silvery minnow)

(Sand shiner) 

Hybognathus placitus Platygobio gracilis

(Plains minnow) (Flathead chub)

Hybognathus argyritus

(Silvery minnow) Ictalurus punctatus

Platygobio gracilis (Channel catfish)

(Flathead chub)

Carpiodes cyprinus

(River carpsucker)

Carpiodes carpio

(Quillback)

Intermediate (1–2 ft) Cyprinella lutrensis Ictalurus punctatus

(Red shiner) (Channel catfish)

Ictalurus punctatus

(Channel catfish) Aplodinotus grunniens

Aplodinotus grunniens (Freshwater drum)

(Freshwater drum)

Deep (deeper than 2 ft) Cyprinella lutrensis lctalurus punctatus Ictalurus punctatus

(Red shiner) (Channel catfish) (Channel catfish)

Ictalurus punctatus Aplodinotus grunniens Aplodinotus grunniens

(Channel catfish) (Freshwater drum) (Freshwater drum)

Scaphirhynchus sp.1

(Sturgeon)

1

Based on studies by Bramblett and White (2001) and Wildhaber and others (2007); the deep-swift niche is the preferred habitat by pallid 

sturgeon (Scaphirhynchus albus) and shovelnose sturgeon (Scaphirhynchus platorynchus) during their adult life.

Approach and Methods 21
Table 7. Stations used to index study reaches within the 76-mile Niobrara National Scenic River, Nebraska. 

Station name Station number Short name 

used in text

Location in miles 

upstream from 

Missouri River1

Reach length, 

in feet2

Upstream of Crooked Creek near Sparks, Nebraska 425429100235301 Crooked 144.8 460

At Sunny Brook Campground near Norden, Nebraska 425013100105801 Sunny Brook 129.9 430

At Muleshoe Creek near Norden, Nebraska 424925100083201 Muleshoe 126.7 530

At Rock Barn Campground near Norden, Nebraska 424809100065001 Rock Barn 123.8 530

1

Refers to location of station point indexed in U.S. Geological Survey National Water Information System (http://waterdata.usgs.gov/nwis).

2

Straight-line distance between the center points of the most upstream and most downstream cross sections within the reach.

WYO.

NEBRASKA

SOUTH DAKOTA Area of larger map Base from U.S. Geological Survey National Hydrography 

Dataset, 2007; County boundaries from U.S. Census 

Bureau, 2007, 1;100,000

Universal Transverse Mercator projection

Zone 14

Horizontal coordinate information is referenced to the

North American Datum of 1983 (NAD 83) 

100°30′

42°55′

42°50′

100°20′ 100°10′

Fort Niobrara

National Wildlife

Refuge

Cornell Dam

Niobrara River

Niobrara River near 

Sparks, Nebraska 

(station number 06461500)

20

20

83

83

12 12

0 2 4 MILES

0 2 4 KILOMETERS

EXPLANATION

Niobrara National Scenic River

Streamflow-gaging station

Study reach

Dam

Keya Paha County

Cherry County

Brown County

Sparks

Valentine

Niobrara River 

upstream of 

Muleshoe Creek

Niobrara River 

at Rock Barn 

Campground

Niobrara River 

at Sunnybrook 

Campground

Niobrara River upstream 

of Crooked Creek

Minnechaduza Creek

Schlager Cr eek

Index map

Figure 8. Location of four reaches within Niobrara National Scenic River where fluvial landforms, bed sediment, and channel hydraulic 

geometry and hydraulics were studied.

22 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
Figure 9. Layout of channel cross sections at Niobrara 

River upstream from Crooked Creek near Sparks, Nebraska 

(425429100235301), exemplifying four study reaches.

A!

0 100 200 FEET

0 20 40 METERS

1

2

3

4

1

2

3

1

2

3

4

1

2

3

4

385800 385900

Base from U.S. Department of Agriculture,

Farm Service Agency

Universal Transverse Mercator projection

Zone 14

Horizontal coordinate information is referenced to 

the North American Datum of 1983 (NAD 83) 

4751600

4751500

Direction of 

streamflow

Cross-section trace

Stage-only gage

Approach and Methods 23

discharge), which may or may not be responsible for the 

maintenance and configuration of the present-day channel 

geometry (Nanson, 1986; Knighton, 1998). Abandoned flood 

plains, also known as terraces, may be indicative of several 

geomorphic processes, which may or may not be ongoing 

during the present-day hydrologic regime including: channelbed incision, changes in flood-discharge magnitudes, channel 

backwater hydraulics from debris or ice jams, or catastrophic 

floods (Kochel and Baker, 1988; Pazzaglia and others, 1998; 

Pederson and others, 2006; Moody and Meade, 2008; Boucher 

and others, 2009). 

Fluvial Landforms

A combination of field observations and survey data from 

each of the four cross sections within the study reaches was 

used to characterize and classify the flat-lying alluvial surfaces 

adjacent to the channel. The ranges of elevations of the fluvial 

landforms were indexed by referencing the elevation of the 

brink (the minimum elevation) of each surface to the local 

elevation of the stage of the long-term median daily discharge 

from the Niobrara River near Sparks (station number 

06451500). The stage of the long-term median discharge was 

determined first by linearly interpolating between the stages of 

the bracketing discharge measurements. The elevation of the 

stage of the median discharge at cross sections where stages 

were not recorded was estimated by linearly interpolating 

using the average water-surface slope and the channel centerline distance between cross sections. 

At the Crooked study reach, the record from a continuous-recording stage sensor (stage-only gage) was used in 

combination with the 15-minute interval gage record from the 

Niobrara River near Sparks to approximate a stage-discharge 

relation; the stage-discharge relation was approximated by 

applying a 1-hour lag time to the stage data from the Niobrara 

River upstream from Crooked and assigning the associated 

15-minute interval discharge data from the Niobrara River 

near Sparks. The 1-hour lag time was used as an estimate of 

the average travel time of water between the two stations. 

This rough stage-discharge relation was applied in the 

Crooked study reach only, and enabled a coarse estimate of 

the discharge associated with inundation of the fluvial landforms. The height assigned to fluvial landforms in all study 

reaches was used as a basis for fluvial landform classification. First, the heights of all landforms from all cross sections 

and study reaches were plotted as a frequency histogram and 

a cumulative frequency curve. Second, boundaries between 

fluvial landform classes were visually assigned at natural data 

gaps in the histogram or slope breaks along the cumulative 

frequency curve. Landform classes then were compared to 

hydrologic and river ice-level data to speculate on the nature 

of their formation. 

Bed Sediment

The bed of the Niobrara River within the study reaches 

was typically observed to be bedrock overlain by a veneer of 

sand. The veneer of sand varied in thickness from tenths of 

an inch to several feet; where there was no sand, undulating 

and rilled bedrock was dominant with sparse pockets of fine 

gravel, which appeared to be bedrock disintegrating in-situ. 

The bed also contained infrequent and isolated boulders, 

which were suspected to have been rafted or transported into 

the reaches by winter ice jams. For the purpose of characterizing the particle sizes on the bed that may be in transport during 

the ice-off season, bed-material sampling was restricted to the 

veneers and patches of fine sediment.

Bed sediment in the study reaches was sampled in 

November and September of water year 2008 using a BMH-53 

piston sampler (Edwards and Glysson, 1999). At all but the 

Crooked study reach, samples of bed material were obtained 

for the alluvial parts of the upstream and downstream cross 

sections by wading across the channel, driving the BMH-53 

into the bed of the river, covering the base of the sampler, 

removing the cylinder, and placing the sample into a plastic 

sample bag. At the Crooked study reach, alluvial bed material generally was limited to isolated, vegetated sand dunes 

surrounded by bedrock; in this case, bed-material sampling 

was limited to subsamples of several of the dunes across the 

length of the reach. All bed-material samples were analyzed 

for grain-size distribution at the USGS Iowa National Sediment Laboratory, Iowa City, using methods described in 

Guy (1969). 
Figure 10. Mean daily discharge of the Niobrara River near Sparks, Nebraska, for the study period October 1, 2007, to November 30, 

2008, showing reach-scale discharge measurement time periods.

300

500

700

900

1,100

1,300

1,500

1,700

10/1/07 11/1/07 12/1/07 1/1/08 2/1/08 3/1/08 4/1/08 5/1/08 6/1/08 7/1/08 8/1/08 9/1/08 10/1/08 11/1/08 12/1/08

MEAN DAILY DISCHARGE, IN CUBIC FEET PER SECOND

DATE

Niobrara River near Sparks, Nebraska, average daily discharge

Discharge measurement interval at the four study reaches

Water year 2008 Water year 2009

24 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

Hydraulics, Hydraulic Geometry, and Bed 

Adjustment 

Discharge measurements were made to investigate 

channel and hydraulic adjustment processes within the study 

reaches. Discharge measurements were made over a range 

of discharge magnitudes during water years 2008 and part of 

2009 (fig. 10) by NGPC personnel (S. Schainost, Nebraska 

Game and Parks Commission, unpublished data, 2008), in 

collaboration with the USGS. Cross sections 1 and 4 (most 

upstream and downstream, respectively) were used as the 

locations for discharge measurements at each study reach, 

except at Crooked, where cross sections 1 and 3 were used. 

Measurements were made at multiple sections along the cross 

section in an attempt to capture no more than 5 to 10 percent 

of the total discharge within any single increment (Rantz 

and others, 1982). Measurements primarily were made by 

wading the channel; nonwadeable sections were measured by 

suspending a velocity meter from a canoe tethered to a cable 

that spanned the channel cross section. Although the alteration 

of the local hydraulic field by the canoe could have affected 

measured velocities, direct comparison of velocity measurements made from the canoe with those made at the same 

location by wading indicated that the canoe had no detectible 

effect on local flow velocities when the instrument was placed 

an arm’s length away from the side of the canoe. Additionally, 

at least one of the cross sections was wadeable, except during 

the highest flows, such that a quality-assurance comparison 

of discharge magnitudes across both methods could be made. 

All discharge measurements made on the same day within 

the same reach were within 10 percent of each other, and the 

majority of measurements were within 5 percent of each other. 

Measurements of water-surface slope also were made during 

the discharge measurements using RTK-GPS, auto-level, or 

total-station survey instruments.

Hydraulic geometry relations were developed for each 

of the study reaches using the field measurements of channel 

discharge. The relations were developed using methods 
Table 8. Hydraulic parameters used to characterize flow and adjustment in Niobrara River study reaches.

[γ, specific weight of water (62 pounds per cubic foot); R, hydraulic radius of wetted channel calculated as the area of channel divided by wetted perimeter 

(feet); S, slope of the water surface (dimensionless); v, mean velocity of water in the channel (feet per second); Q, water discharge in the river channel (cubic 

feet per second); w, top width of the water surface of the wetted channel (feet); g, gravitational constant (32.174 feet per second squared); d, average depth of 

water (feet)]

Parameter name Symbol Equation Explanation

Mean boundary shear stress τ τ = γRS Measure of flow force exerted on the boundary of the river channel, 

expressed in pound-force per square foot.

Mean boundary roughness n n = (1.486*R2/3*S1/2)/v Manning boundary roughness coefficient. Measure of flow 

resistance.

Unit stream power Ω Ω = (γQS)/w Measure of energy expenditure on the bed of the river normalized 

by wetted channel width; expressed in units of pounds per foot 

per second.

Froude number F F = v/(gd)1/2 Ratio of inertial to gravitational forces; dimensionless. Used as a 

measure of flow regime, upper or lower (F above or below 1, 

respectively).

Reference bed elevation Zb Zb = ZQ–Di Elevation of the river bed expressed as the elevation of the stage of 

a reference discharge (ZQ) minus the depth to the river bed at a 

particular measuring poing (Di). 

Approach and Methods 25

outlined by Leopold and Maddock (1953), using the notation of equations 1 through 3 described in the Hydraulic

Geometry of the Niobrara River section of this report. The 

at-a-station relations in the linear form of the power functions 

(equations 1 through 3) were developed using ordinary leastsquares (OLS) regression of data pairs from the hydrologic 

technician’s measurement notes. In all cases, the discharge 

calculated from the measurement was the independent variable 

(Q), and the dependent variable was the channel-top width 

(w), the average channel depth (d, wetted area divided by top 

width), or average channel velocity (v, discharge divided by 

wetted area). The OLS regression-line slope value (exponent), 

regression-line intercept value (coefficient), probability values 

(p-values), and coefficients of determination (COD) for all 

at-a-station hydraulic geometry relations were estimated using 

standard statistical tools in Excel®, Microsoft Corp, Redmond, 

Wash. OLS regression-slope values were tested for statistical 

significance at the 90-percent confidence level; p-values less 

than 0.10 were interpreted to indicate that the slope coefficient 

estimated for the at-a-station hydraulic geometry relation was 

significantly different than zero. The COD, which indicates the 

fraction of the variance in the dependent variable explained 

by the regression model, was used as a secondary indicator of 

model goodness-of-fit. 

At the reach scale, water depth and current velocity 

interact in a complex feedback with the channel bed, bank 

geometry, and erodibility as well as with the deformation and 

configuration of bedforms such as ripples, dunes, and bars 

(Leopold and others, 1964; Knighton, 1998). Field observations in the study reaches indicated that bedrock was very 

shallow or, in the case of the Crooked reach, the dominant bed 

material. However, the bed at the Sunny Brook, Muleshoe, 

and Rock Barn study reaches had substantial coverage by fine 

sediment, indicating bed deformation and scour were feasible. 

To further investigate the nature of channel hydraulic adjustments to changing discharges in the study reaches, the channel 

geometry and discharge measurement data were used to 

calculate additional hydraulic and channel topographic parameters. Mean boundary shear stress, mean boundary roughness 

(Manning’s roughness coefficient, also known as Manning’s 

n), and unit stream power were calculated as measures of flow 

force, resistance, and energy expenditure, respectively (table 

8). Froude number was calculated as a measure of flow state 

(quiescent or rapid). Reference bed elevation was used as a 

measure of channel bed scour and fill behavior over the study 

period (table 8). Reference bed elevation was calculated only 

for those discharge measurements that could be referenced to a 

common vertical datum within each reach. 
26 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

Hydraulic Microhabitats 

Discharge data from each of the study reaches also were 

used to investigate the range of available hydraulic microhabitats within each reach using the hydraulic microhabitat 

calculator of Ginting and Zelt (2008). Because a limited range 

of discharges was measured, hydraulic microhabitat distributions for all of the discharge frequency categories used in the 

basin-scale analysis could not be analyzed. In particular, no 

discharges below the 90-percent exceedance (lower-decile) 

flow were measured. Instead, the lowest available measured 

discharge at each study reach was analyzed for comparison 

with higher discharges. At the Crooked study reach, no high 

flow (upper-decile) discharge measurements were obtained 

during the study period. Because the study reaches are not 

located at bridges, the analysis was used as a measure of 

difference in hydraulic microhabitats in more natural, less 

engineered river reaches.

Hydrogeomorphic Segments and 

Hydraulic Microhabitats

Statistical analysis of hydrogeomorphic segments 

resulted in a reduction in the number of segments from 36 to 

25 by merging adjacent segments which were identified as 

having identical combinations of element classes. The physical 

and hydraulic diversity of the Niobrara River is reflected in the 

presentation of longitudinal hydrogeomorphic characteristics 

and the hydraulic microhabitat distributions among differing 

fluvial geomorphic provinces. Data from study reaches in the 

Niobrara National Scenic River indicate a host of hydrogeomorphic processes are acting on the river including two types 

of flooding processes, downstream coarsening of bed material, 

and a two-mode hydraulic regime. 

Basin-Scale Results

Statistical Analysis of Hydrogeomorphic 

Segments

Table 9 presents the results of the multiple comparison analysis (MCA) for the ANOVA models for each of the 

hydrogeomorphic variables associated with the four descriptive geomorphic elements (table 3). All variables successfully 

distinguished the total number of classes (table 9) for the 

valley confinement and channel-planview pattern descriptive 

elements. However, in the case of channel-planview pattern, 

only the comparison between classes 2 and 3 (sinuous and 

highly sinuous, respectively) was possible, because only two 

of the three possible classes actually were used from the classification proposed by Alexander and others (2009). 

Ninetieth-percentile unit stream power (SP_90), which is 

a function of streamflow and channel slope, was surprisingly 

the least powerful of the variables across classes, only distinguishing between the maximum possible numbers of classes in 

the valley confinement geomorphic element. Although many 

of the variables were able to distinguish between all possible 

classes, not all variables added additional information to the 

discriminant function (table 9). For example, in the case of 

channel-planview pattern, only two of the seven variables 

were used to build the discriminant function ultimately used to 

classify each sampling point. 

Overall classification error rates in the discriminant 

models varied from 23 to 29 percent among descriptive 

geomorphic elements, with error rates among individual 

classes within the elements having a much wider range of 2 

to 60 percent (table 10). Two of the classes, class 2 of valley 

confinement (phase-restricted) and class 3 of bar configuration (braided bars), returned error rates of nearly 60 percent. In 

both cases, the high error rate was associated with a class that 

would have been expected to be difficult to distinguish from 

another class. For valley confinement, most of the classification error of class 2 (phase-restricted) was from points being 

classified as class 3 (width-restricted); both class 2 and class 3 

were presented as “restricted” valley settings previously 

(Alexander and others, 2009). For bar configuration, most 

of the classification error in class 3 (braided bar) was associated with assignment as class 1 (alternate bar), a distinction 

that is difficult because of the co-existence of both bar types 

within many segments. Moreover, the prediction of bar types 

in general is a discharge-dependent exercise (Bridge, 2003). 

Although some of the reclassification rates for individual 

element classes were relatively high, the p-values associated 

with the Wilks’ lambda test statistic for multivariate equality of means indicate that the probability of the means of the 

element classes being equal is extremely low (table 10). 

The statistical analysis of hydrogeomorphic segments 

resulted in reclassification rates of 3 to 28 percent of the 

segments for the four descriptive geomorphic elements 

(table 11). The largest rates of class reassignments were for 

the valley confinement (28 percent) and channel-bar configuration (25 percent) categories. Sinuosity and channel-width 

variation had relatively minor shifts of 3 and 14 percent, 

respectively, among segments. The reassignment of classes 

by the discriminant analysis resulted in a reduction from 36 to 

25 total hydrogeomorphic segments because several adjoining segments shared the same ultimate class assignments 

among individual descriptive geomorphic elements (fig. 11). 

Virtually all of the segment mergers were in the CRB fluvial 

geomorphic province, where reassignment of valley confinement and width variation classes alone resulted in numerous 

segment mergers (table 12). Class reassignments and merger 

of hydrogeomorphic segments did not result in changes to 

the statistical modal class for any descriptive geomorphic 

element relative to those reported previously (Alexander and 

others, 2009) for the study area (table 12). The most frequent 

conditions (modal classes) among hydrogeomorphic segments 

are a width-restricted valley confinement condition, sinuousplanview pattern, irregular channel width, and an alternate 
Table 9. Number of geomorphic element classes identified by ANOVA multiple comparision analysis.

[No., number; sig., significant; bordered cells indicate variable was used in discriminant analysis procedure; shaded cells indicate variable was used as primary variable in discriminant analysis procedure]

Geomorphic element

Classes1 Hydrogeomorphic variable name2

Number of 

classes3

Number of 

classes 

identified4

Number of 

class 

combinations5

SIN_100 CHAN_VAL_ RAT BI SP_90 WAL_PROX CHAN_CV CHAN_VAL_ LEN

Degree of valley confinement 4 4 6

No. of sig. classesNo. of sig. class combinations6

46

46

46

46

46

46

46

Channel-planview pattern7 3 2 1

No. of sig. classesNo. of sig. class combinations7

21

21

21

21

21

21

21

Channel-width variation 3 3 3

No. of sig. classesNo. of sig. class combinations6

33

33

33

22

33

33

33

Channel bar type8 5 5 10

No. of sig. classesNo. of sig. class combinations6

5

10

5

10

5

10

39

28

39

5

10

1Classes associated with geomorphic classification system in table 3.2Variable name from table 4.3Number of classes proposed in classification system of Alexander and others (2009).4Number of proposed classes actually assigned by Alexander and others (2009).5Maximum number of possible class combinations tested.6Number of class comparisions distinguishable by multiple comparision analysis using the Tukey (1953) method at an alpha level of 0.05.7Fisher (1949) least significant difference method was used in multiple comparison analysis instead of Tukey method.8Alexander and others (2009) originally proposed four “bar type” classes; 5th class was added for this study.

Hydrogeomorphic Segments and Hydraulic Microhabitats 27
Table 10. Cross-validation results from discriminant analyses of sampling points of the Niobrara River, Nebraska, by geomorphic 

element class.

[NA, no class available or assigned for geomorphic element; classification error rate is defined as the percentage of sampling points reassigned to a different 

geomorphic element class by the discriminant function; overall, statistics for the classification performance across all classes; <, less than]

Geomorphic 

element class 

(from table 3)

Geomorphic element classes assigned by discriminant analysis Classification 

error rate, 

percent

Wilks’ 

lambda1 p-value2

1 2 3 4 5

Geomorphic element [A]. Degree of valley confinement

1 2,065 101 208 0 NA 13

2 313 850 808 106 NA 59

3 134 406 2,303 40 NA 20

4 13 98 70 2,461 NA 7

Overall 23 0.13 <0.0001

Geomorphic element [B]. Channel-planview pattern

2 NA 8,299 137 NA NA 2

3 NA 232 1,308 NA NA 15

Overall 4 0.62 <0.0001

Geomorphic element [C]. Channel-width variation

1 4,461 299 12 NA NA 7

2 213 2,984 370 NA NA 16

3 104 642 891 NA NA 46

Overall 16 0.26 <0.0001

Geomorphic element [D]. Bar configuration

1 1,496 551 236 22 513 47

2 291 3,123 0 1 77 11

3 480 28 464 76 107 60

4 1 0 2 134 0 2

5 258 71 131 47 1,867 21

Overall 29 0.19 <0.0001

1

Wilks’ lambda value for test of multivariate equality of means between geomorphic element classes.

2

Probability of obtaining indicated test statistic when class mean values are the same.

28 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

bar configuration. The class reassignments and segment 

mergers did, however, result in changes to the dominant 

classes per unit length of river, which are now the same as the 

modal classes. The braided bar class was eliminated from all 

segments within the CRB province, resulting in a switch to 

alternate bars being the dominant bar configuration per unit 

stream length in the study area. The open valley class was 

eliminated from valley-confinement conditions within the 

CRB province but remained the dominant valley-confinement 

condition in the MB. 

The characteristics of those reaches with assignment 

changes in at least one of the geomorphic element categories 

were spot-checked to ensure that the new classification did 

not contradict those that were visible and unambiguous in the 

color aerial photographs. Although much of the class reassignment and segment merging occurred because of physical characteristics that were difficult to objectively assess 

within a broader physical context, some class reassignments 

were obvious errors. Specifically, the discriminant analysis 

reassigned bar configuration classes in segments 7 and 8 

(table 12) that were in deviation from those visible in aerial 

photographs, and from the authors’ observations in the field. 

Segment 8, which includes the reach immediately upstream 

from Cornell Dam, was reassigned from a “braided” bar 

condition to a “bedrock” bar condition by the discriminant 

analysis. Although segment 8 is confined by bedrock laterally, 

the bar configuration is dominated by braided bars at least 

partially because of the backwater effect from Cornell Dam. 

The bed of the river in segment 7, which includes the segment 

immediately downstream from Cornell Dam, was noted during 

field visits by the authors to be dominated by bedrock, though 

alternate bars do occur. 
Table 11. Distribution of classes assigned using discriminant analyses to sampling points within each hydrogeomorphic segment 

defined by Alexander and others (2009) for the Niobrara River, Nebraska.

[Orig., original; %, percent; shaded cells indicate change from original class]

Segment 

number

Sample 

size

Geormorphic element [A]. Degree of valley confinement Geomorphic element [B]. Channel-planview pattern

Orig. 

class

Classes New 

class

Orig. 

class

Classes New 

class 1 2 3 4 2 3

Braided Bottoms fluvial geomorphic province

1 17 3 12 5 0 0 1 2 17 0 2

2 126 3 0 3 123 0 3 2 126 0 2

3 31 3 0 0 31 0 3 2 31 0 2

4 119 3 12 10 97 0 3 2 119 0 2

5 271 3 4 15 252 0 3 2 271 0 2

6 102 2 0 13 89 0 3 2 102 0 2

Canyons and Restricted Bottoms fluvial geomorphic province

7 316 2 112 180 24 0 2 2 283 33 2

8 597 1 563 23 11 0 1 2 597 0 2

9 212 1 161 5 46 0 1 2 212 0 2

10 107 3 14 9 84 0 3 2 107 0 2

11 255 3 0 61 194 0 3 2 255 0 2

12 146 3 0 65 81 0 3 2 146 0 2

13 248 2 0 7 241 0 3 2 248 0 2

14 169 3 1 18 150 0 3 2 169 0 2

15 210 2 76 91 43 0 2 2 210 0 2

16 253 3 2 89 162 0 3 2 253 0 2

17 460 2 97 245 118 0 2 2 460 0 2

18 184 1 143 3 38 0 1 2 154 30 2

19 403 3 4 29 358 12 3 2 403 0 2

20 267 2 16 71 180 0 3 2 267 0 2

21 90 4 12 58 1 19 2 3 90 0 2

22 53 3 50 3 0 0 1 2 37 16 2

23 929 1 917 12 0 0 1 3 73 856 3

24 99 3 37 32 30 0 1 2 99 0 2

25 352 1 259 23 70 0 1 2 350 2 2

26 231 3 2 4 222 3 3 2 231 0 2

27 100 1 11 38 51 0 3 2 100 0 2

28 186 3 0 2 175 9 3 2 186 0 2

29 165 2 13 9 131 12 3 2 165 0 2

30 170 3 0 23 130 17 3 2 170 0 2

31 74 4 0 7 46 21 3 2 74 0 2

32 246 3 0 17 229 0 3 2 246 0 2

33 309 2 0 210 8 91 2 2 309 0 2

Meandering Bottoms fluvial geomorphic province

34 1,689 4 0 36 23 1,630 4 2 1,671 18 2

35 521 4 0 0 0 521 4 3 68 453 3

36 269 4 0 0 0 269 4 2 232 37 2

reclassification rate 28% reclassification rate 3%

Hydrogeomorphic Segments and Hydraulic Microhabitats 29
Table 11. Distribution of classes assigned using discriminant analyses to sampling points within each hydrogeomorphic segment 

defined by Alexander and others (2009) for the Niobrara River, Nebraska.—Continued

[Orig., original; %, percent; shaded cells indicate change from original class]

Segment 

number

Sample 

size

Geomorphic element [C]. Channel-width variation Geomorphic element [D]. Channel-bar configuration

Orig. 

class

Classes New 

class

Orig. 

Class

Classes New 

class 1 2 3 1 2 3 4 5

Braided Bottoms fluvial geomorphic province

1 17 3 0 3 14 3 4 0 0 0 17 0 4

2 126 3 0 15 111 3 3 16 0 84 26 0 3

3 31 2 0 7 24 3 1 16 0 15 0 0 1

4 119 3 0 13 106 3 4 2 0 6 111 0 4

5 271 3 0 43 228 3 3 20 0 240 11 0 3

6 102 3 0 41 61 3 3 46 1 55 0 0 3

Canyons and Restricted Bottoms fluvial geomorphic province

7 316 1 278 38 0 1 2 168 98 0 0 50 1

8 597 1 550 47 0 1 5 353 1 45 0 198 1

9 212 2 0 201 11 2 3 49 0 74 0 89 5

10 107 2 0 76 31 2 3 72 0 35 0 0 1

11 255 2 0 213 42 2 1 129 77 20 14 15 1

12 146 3 0 82 64 2 3 112 0 14 20 0 1

13 248 2 0 234 14 2 1 181 48 19 0 0 1

14 169 2 24 145 0 2 1 60 109 0 0 0 2

15 210 2 4 203 3 2 1 146 13 17 0 34 1

16 253 2 0 210 43 2 1 209 22 22 0 0 1

17 460 2 0 439 21 2 1 351 42 36 0 31 1

18 184 2 49 127 8 2 1 26 0 28 0 130 5

19 403 3 111 226 66 2 3 346 26 29 0 2 1

20 267 2 0 264 3 2 1 124 46 37 0 60 1

21 90 1 80 10 0 1 2 0 88 0 0 2 2

22 53 1 53 0 0 1 2 3 15 0 0 35 5

23 929 1 851 62 16 1 5 23 75 0 7 824 5

24 99 2 34 50 15 2 1 75 5 0 3 16 1

25 352 3 23 186 143 2 1 229 2 46 0 75 1

26 231 2 17 179 35 2 1 182 40 9 0 0 1

27 100 3 0 98 2 2 1 93 3 4 0 0 1

28 186 2 3 165 18 2 1 160 16 10 0 0 1

29 165 2 57 108 0 2 1 90 27 0 0 48 1

30 170 2 40 122 8 2 1 116 53 1 0 0 1

31 74 2 13 61 0 2 1 46 28 0 0 0 1

32 246 2 4 242 0 2 2 111 135 0 0 0 2

33 309 1 273 36 0 1 2 0 309 0 0 0 2

Meandering Bottoms fluvial geomorphic province

34 1,689 1 1,575 114 0 1 2 0 1,689 0 0 0 2

35 521 1 502 19 0 1 2 0 521 0 0 0 2

36 269 1 269 0 0 1 2 0 269 0 0 0 2

reclassification rate 14% reclassification rate 25%

30 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
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Cornell Dam

Merritt Dam

Spencer Dam

Box Butte Dam

Fort Randall Dam

Niobrara

River

Missouri River

Snake River

Keya

Paha

River

Hay Springs

Gordon Valentine Norden

Long Pine O'Neill

Spencer Cody

Verdigre Creek Dunlap

Diversion Dam

Mariaville

SOUTH DAKOTA

NEBRASKA

WYOMING

Cherry County

Holt County Sioux County Sheridan County

Goshen County

Todd County Niobrara County

Dawes County

Fall River County Tripp County

Brown County Rock County

Shannon County Bennett County

Morrill County Garden County

Box Butte County

Grant County

Charles Mix County

Blaine County Hooker County

Knox County

Loup County Thomas County

Boyd County

Keya Paha County

Scotts Bluff County Garfield County Wheeler County

Custer County

Boone County

Banner County Arthur County

Douglas County

McPherson County Valley County Logan County

Mellette County

Greeley County

Jackson County

Gregg County

Antelope 

County

0 25 50 MILES0 25 50 KILOMETERS

104° 103° 102° 101° 100° 99° 98°

43°

42°

Base from U.S. Geological Survey National Elevation Dataset, 2006;National Hydrography Dataset, 2007; State boundaries, 2005,1:2,000,000Basin boundary modified from U.S. Department of Agriculture,Natural Resources Conservation Service Watershed Boundary Dataset, 2008Universal Transverse Mercator projectionZone 14Horizontal coordinate information is referenced to theNorth American Datum of 1983 (NAD 83) 

EXPLANATION

Sand Hills (Soller and Reheis, 2003)

Niobrara River Basin boundary

Portion of Niobrara River within study areaPortion of Niobrara River outside of study area

National River reach (reach managed by  the U.S. National Park Service)

Large dams

Braided BottomsCanyons and Restricted BottomsMeandering Bottoms

Upstream boundary of hydrogeomorphic segments  by fluvial geomorphic province

MONT.

WYO.

COLO.

S. DAK.

MINN.

IOWA

NEBR.

KANS.

MO.

Area of larger map

Index map

Scenic reach

Recrational

reach

Figure 11. Location of study area, basin boundary, and upstream boundaries of hydrogeomorphic segments by fluvial geomorphic province.

Hydrogeomorphic Segments and Hydraulic Microhabitats 31
Table 12. Hydrogeomorphic segments of the Niobrara River between Dunlap Diversion Dam and the Missouri River, Nebraska 

(modified from Alexander and others, 2009).

[River mile, miles upstream from Missouri River; S.A., percent of total length of Niobrara main stem channel in study area; values in () indicate class reassigned 

on basis of field observations; shaded cells indicate segment includes part of Niobrara National Scenic River]

Segment 

number

River 

mile

Percent of 

S.A. length

Descriptive geomorphic elements and assigned condition classes

[A] 

Degree of valley 

confinement

[B] 

Channel-planview 

pattern

[C] 

Channel-width 

variation

[D] 

Bar 

configuration

Braided Bottoms fluvial geomorphic province

1 12 3.6 1 2 3 4

2 34 6.6 3 2 3 3

3 39 1.6 3 2 3 1

1

4 60 6.2 3 2 3 4

5 125 19.6 3 2 3 3

Canyons and Restricted Bottoms fluvial geomorphic province

6 134 2.7 2 2 1 1

7 150 5.0 1 2 1 1 (5)

1

8 156 1.8 1 2 2 5 (3)

9 178 6.4 3 2 2 1

10 182 1.4 3 2 2 2

11 188 1.8 2 2 2 1

12 195 2.1 3 2 2 1

13 208 3.9 2 2 2 1

14 213 1.6 1 2 2 5

15 232 5.6 3 2 2 1

16 234 0.8 2 2 1 2

17 236 0.4 1 2 1 5

18 262 7.8 1 3 1 5

19 275 3.8 1 2 2 1

20 300 7.8 3 2 2 1

21 307 2.1 3 2 2 2

22 316 2.6 2 2 1 2

Meandering Bottoms fluvial geomorphic province

23 326 3.2 4 2 1 2

24 330 1.0 4 3 1 2

25 332 .6 4 2 1 2

Mode2

3 2 2 1

Per unit stream length3

3 2 2 1

1

Reach includes backwater of mainstem dam.

2

Mode refers to the most frequently occuring condition class among segments.

3

Per unit length refers to the condition class that is most frequent when considering total channel length within the study area.

32 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
Hydrogeomorphic Segments and Hydraulic Microhabitats 33

Hydrogeomorphic Characteristics of the 

Niobrara River 

The Niobrara River in the study area flows through a 

diversity of fluvial geomorphic settings in its traverse across 

northern Nebraska. The most distinct differences are among 

the settings found in the three fluvial geomorphic provinces. 

The river channel increases in width within the study area 

from a median of approximately 30 ft in the MB province to a median of over a 1,000 ft near the Missouri River 

(table 13). With the exception of the MB fluvial geomorphic province, valley width and channel width increase and 

decrease in general synchronicity (fig. 12), indicating that 

bedrock geology, in addition to hydrology, acts as an important control in Niobrara channel form. This is especially the 

case in the CRB fluvial geomorphic province, where gains 

in river discharge do not necessarily translate into gains in 

channel width because valley width is limiting (fig. 12). In 

the MB province, river discharge magnitudes are low, the 

median channel width varies from 20 to 30 ft, but the valley 

is over 3,000 ft wide in places, and exerts little control on 

the channel-planview pattern. Within the CRB province, the 

river flows over a diversity of geologic formations, and the 

valley and river narrow and expand in approximate synchronicity, in some cases forming entrenched canyons, with steep 

channel slopes, yet highly sinuous channel patterns. In the BB 

fluvial geomorphic province, the river primarily flows over 

Cretaceous Pierre Shale (fig. 2), the valley and channel are 

persistently wide, and the channel slope is generally uniform 

(fig. 12).

The existence of vegetated islands and consequent multithread channel environments, indicated by a higher braided 

index, mostly coincided with reaches having gentler slopes 

and less unit stream power (figs. 12B and 12D). In general, 

island environments are most sparse or do not exist in reaches 

where the channel slope is greater than 0.15 percent. Within 

the MB province, stream power is relatively low, but channel 

slope is persistently steeper than 0.15 percent, and no islands 

were identified in the GIS. Within the CRB province, channel 

slope is highly variable, braided index rarely exceeds 2, and 

islands are concentrated mainly in the reaches having mild 

slopes and lower unit stream power (figs. 12B and 12D). In 

the BB province, braided index was, on average, higher than 

in the upstream provinces, but islands are mainly concentrated 

in the delta reach near the mouth at the Missouri River and in 

the reach immediately upstream from Spencer Dam (fig. 12B). 

Within these reaches, river slope and unit stream power are 

lower, on average, than much of the study area, and the river is 

persistently anastomosing. The combination of lower channel 

slope and unit stream power are typical characteristics of 

anastomosing rivers (Smith and Putnam, 1980; Knighton and 

Nanson, 1993); however, the higher braided index values for 

these reaches likely are affected primarily by the backwater 

effects from Spencer Dam and sedimentation at the delta at the 

confluence with the Missouri River. The higher braided index 

in the lower slope regions of the river seemingly contradicts 

the statistical models proposed by Leopold and Wolman 

(1957), which indicates that braided rivers typically have 

steeper slopes than straight or meandering rivers. However, 

much of the Niobrara could not be considered “fully” alluvial 

because of the considerable influence of bedrock on channel 

slope and planform characteristics (fig. 2). Therefore, much 

of the CRB province and parts of the BB province do not 

meet the primary assumption of a channel with an adjustable 

or “mobile” boundary to qualify for comparison with such 

models. Furthermore, the segments with the highest braided 

index values are functionally most similar to deltaic environments, where deposition and avulsion, as opposed to sediment 

transfer, are the primary fluvial processes. 

Longitudinal hydrology curves indicate that the flow of 

the Niobrara River likely is dominated by groundwater as far 

downstream as Norden (fig. 12C). Upstream from Norden, 

the mean daily, median, and 90th-percentile discharge curves 

have approximately the same longitudinal slope and have only 

minor differences in overall magnitude. Between the Snake 

River confluence and Norden, all three hydrologic curves 

begin to diverge, indicating the hydrologic regime becomes 

more variable as the river flows out of the CRB and into the 

BB province. Flood-frequency values published by Soenksen and others (1999) share a similar pattern with 2- and 

5-year return-flood values increasing only slightly upstream 

from Norden, but substantially increasing downstream from 

Norden. The effect of groundwater also is visible by comparing longitudinal increases in drainage area with the longitudinal hydrology curves (fig. 12C). Although many of the upper 

study area tributary streams were ungaged or not included in 

the analysis, the graph trace between main-stem streamflowgaging stations indicates that large increases in drainage area, 

such as those at Pine Creek (fig. 12C), do not correspond to 

proportional increases in main-stem discharge. This pattern 

persists until at least the Snake River confluence, where 

increases in drainage area begin to have proportional increases 

in flow (runoff). 

Unit stream power values in the study area vary between 

0 and almost 2 pounds per foot per second (fig. 12D). Within 

the MB province, unit stream power steadily increases as the 

Niobrara gains discharge from groundwater inflow, and the 

channel slope steepens. At the downstream end of the MB 

province, the channel slope decreases, and flow and channel 

width steadily increase, causing a drop in unit stream power 

values as the Niobrara transitions into the CRB province. The 

combination of steep slopes, a constrained channel width, 

and persistent flow within the CRB province results in unit 

stream power values that are between three and five times 

greater than those in less confined segments with comparable 

or greater discharges (table 13). Two reaches with relatively 

high unit stream power values in the study area are within two 

narrow canyon sections, an entrenched meandering-canyon 

reach (segment 18) and the canyon within the Scenic Reach 

(segment 7) (fig. 12D). Both of these segments were classified as having bedrock-dominated bed conditions (table 12). 

The higher unit stream power values and bedrock bed indicate 
Table 13. Physical characteristics of hydrogeomorphic segments of the Niobrara River between Dunlap Diversion Dam and the Missouri River, Nebraska.

[River mile, location of the upstream end of reach in miles upstream from the Missouri River; Q1, value of 25th percentile of cumulative frequency distribution; M, median of cumulative frequency distribution; Q3, value of 75th percentile of cumulative frequency distribution; values shaded in gray indicate segment includes a portion of the Niobrara National Scenic River]

Segment 

number

River 

mile

Channel width, in feet Valley width, in feet Channel sinuosity Braided index (number channels) Unit streampower at 90th-percentile of discharge (pounds/foot-second)

Q1 M

Q3 Q1 M

Q3 Q1 M

Q3 Q1 M

Q3 Q1 M

Q3

Braided Bottoms fluvial geomorphic province

1 12 750 1,030 1,260 3,740 4,740 5,420 1.34 1.46 1.55 2.4 2.5 2.6 0.17 0.23 0.302 34 840 1,070 1,280 3,080 3,670 4,280 1.05 1.06 1.07 1.1 1.2 1.5 .17 .20 .253 39 410 550 880 2,650 2,790 3,030 1.09 1.09 1.10 1.1 1.1 1.3 .21 .34 .45

1

4 60 900 1,210 1,510 2,830 3,080 3,420 1.11 1.13 1.19 1.6 1.7 1.9 .12 .15 .205 125 560 910 1,150 2,100 2,410 2,690 1.06 1.08 1.11 1.1 1.1 1.2 .14 .17 .24

Canyons and Restricted Bottoms fluvial geomorphic province

6 134 120 140 160 1,150 1,480 1,770 1.17 1.23 1.37 1.0 1.0 1.0 0.62 0.73 0.887 150 130 150 170 410 580 770 1.16 1.25 1.30 1.0 1.0 1.0 .51 .61 .75

1

8 156 230 340 470 420 570 760 1.11 1.26 1.45 1.0 1.0 1.0 .15 .20 .279 178 130 210 320 1,200 1,510 1,810 1.10 1.14 1.20 1.0 1.0 1.1 .19 .29 .46

10 182 80 100 120 1,300 1,580 1,830 1.11 1.14 1.16 1.0 1.0 1.0 .43 .58 .77

11 188 90 120 180 470 600 850 1.13 1.16 1.42 1.0 1.0 1.1 .27 .46 .75

12 195 100 130 180 840 1,060 1,380 1.13 1.15 1.22 1.0 1.1 1.2 .17 .27 .3813 208 90 120 160 520 720 890 1.15 1.21 1.36 1.0 1.0 1.0 .22 .34 .4514 213 100 120 160 220 270 340 1.24 1.32 1.48 1.0 1.0 1.0 .19 .30 .3715 232 140 220 280 920 1,390 1,710 1.11 1.17 1.28 1.0 1.0 1.0 .11 .14 .1916 234 60 70 80 1,430 1,960 2,470 1.42 1.45 1.52 1.0 1.0 1.0 .43 .54 .7117 236 60 70 80 580 710 840 1.42 1.47 1.52 1.0 1.1 1.1 .40 .49 .5518 262 60 60 80 260 320 420 1.73 1.99 2.42 1.0 1.0 1.1 .33 .46 .6619 275 100 140 170 350 470 570 1.19 1.26 1.41 1.0 1.0 1.1 .10 .13 .1920 298 90 120 150 790 1,030 1,360 1.15 1.19 1.28 1.0 1.0 1.1 .08 .10 .1421 307 50 70 90 820 910 1,060 1.16 1.17 1.19 1.0 1.0 1.0 .10 .14 .1822 316 20 30 30 1,030 1,210 1,490 1.20 1.22 1.27 1.0 1.0 1.0 .17 .21 .25

Meandering Bottoms fluvial geomorphic province

23 326 20 20 30 1,440 2,080 3,300 1.13 1.19 1.27 1.0 1.0 1.0 0.04 0.11 0.1924 330 20 20 20 3,130 3,330 3,550 1.65 1.79 2.32 1.0 1.0 1.0 .00 .04 .1025 332 20 30 30 3,070 3,250 3,850 1.23 1.27 1.37 1.0 1.0 1.0 .01 .03 .04

1Reach includes backwater of main stem dam.

34 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
Hydrogeomorphic Segments and Hydraulic Microhabitats 35

that these two segments likely transport the entire load of 

sediment delivered from upstream or originating within the 

reach annually. With the exception of segment 3, which is 

affected by Spencer Dam, unit stream power values in the BB 

province generally are uniform. This consistency results from 

downstream increases in discharge that are offset by steady 

decreases in channel slope and steady increases in channel 

width downstream from Norden. Within segment 3, the reach 

immediately below Spencer Dam, the Niobrara River narrows 

abruptly, and the channel steepens, causing a consequent 

spike in unit stream power values (fig. 12D). The segment 

downstream from Spencer Dam is another reach that, although 

not classified as a bedrock-dominated bed, is known to have 

reaches that have shallow and or visible bedrock outcropping 

on the channel bed. The pre-dam morphology of the Niobrara 

River immediately below Spencer Dam was not investigated, 

and, therefore, whether Spencer Dam operations are the 

primary reason for channel steepening or morphologic change 

is inconclusive. However, the seasonal disruption of sediment 

loads in the Niobrara below Spencer Dam undoubtedly has 

some effect on overall channel morphology in this reach.

Channel sinuosity values in the study area (table 13) 

varied generally between 1 and 2.5, but with locally higher 

values measured in the MB province and at the entrenched 

bedrock meanders of segment 18 in the CRB province 

(fig. 12E). Within segment 24 of the MB province, the 

Niobrara River has very little flow, and the channel has a 

two-phase meander pattern (lower amplitude and shorter 

wavelength pattern superimposed on a larger-scale meander 

pattern). Within segment 18, the river has a highly sinuous 

pattern that is entrenched in bedrock, and the presence of 

rincons (abandoned bedrock meander bends) and the bedrock 

bed indicate that the river is cutting down through the bedrock 

at a relatively rapid rate. These two highly sinuous reaches 

likely have very different dominant fluvial processes. In the 

MB province, the highly sinuous planform is the result of 

channel meandering across the valley bottom, resulting in 

active flood plain destruction and deposition, and subsequent 

riparian forest recruitment that is in alignment with the overall 

channel pattern. In segment 18, the highly sinuous pattern is 

entrenched, indicating that the lateral migration rate (meandering) is much slower than the rate of channel downcutting. 

The highly sinuous pattern of segment 18 is in this sense a 

relict form, and the flood plain is limited to production along a 

narrow strip, and likely home to a mature and diverse riparian 

forest, possibly similar to that found in the canyon segment 

of the Scenic Reach (segment 7). Channel sinuosity is lowest 

in the long, generally straight, braided reaches of the BB 

province. Channel sinuosity within the BB province is greatest 

near the delta, where the river makes a large turn toward the 

Missouri River, and the channel threads migrate around the 

abundant vegetated islands. 

Hydraulic Microhabitats of Differing Fluvial 

Geomorphic Provinces

The differences in channel morphology and hydraulic 

geometries between fluvial geomorphic provinces are evident 

in the types, relative abundance, and response of hydraulic 

microhabitats to changing discharges. The four gaging stations 

chosen for hydraulic microhabitat analysis are distributed 

among three different fluvial geomorphic provinces (table 12); 

Hay Springs (Meandering Bottoms), Cody (Canyons and 

Restricted Bottoms), Sparks (Canyons and Restricted 

Bottoms), and Verdel (Braided Bottoms) streamflow-gaging 

stations are located in hydrogeomorphic segments 23, 13, 

7, and 2, respectively. In figure 13, lower-decile, medianquantile, and upper-decile discharges are defined as those 

exceeded 90, 25 to 75, and 10 percent of all days during the 

period of record indicated for each gage by Alexander and 

others (2009). The hydraulic microhabitat availability was 

calculated as the average for two discharges (when available) within each exceedance category (table 14). At Hay 

Springs, the smaller channel and lower discharges result in 

the dominance of shallow and intermediate-depth hydraulic 

environments with the vast majority of hydraulic microhabitat restricted to shallow categories even during upper-decile 

discharges (fig. 13). Hydraulic microhabitat distributions and 

responses over the range of discharge frequencies analyzed 

are similar at the Cody and Sparks gaging stations. Over all 

ranges of discharge, intermediate-depth hydraulic conditions, 

particularly intermediate-swift, dominate at both gages; as 

discharge increases, intermediate-depth hydraulic conditions are mainly exchanged for deeper hydraulic conditions 

(table 14). Hydraulic microhabitat conditions are most diverse 

in the wide, braided reach of Verdel, with most hydraulic 

microhabitat categories present over the entire range of 

discharges analyzed. During lower-decile flows, the channel 

at Verdel is dominated by shallow hydraulic conditions. As 

discharge increases to upper-decile flow conditions, hydraulic 

microhabitats are more evenly distributed, with no hydraulic 

habitat category covering more than 25 percent of the total 

channel width (fig. 13C). 

The calculated differences in hydraulic microhabitat distributions, abundance, and adjustments between 

streamflow-gaging stations are the result of differences in 

physical structure of the channel and consequent channel 

hydraulic geometry. For example, Alexander and others 

(2009) reported that the channel of the Niobrara River at the 

Hay Springs, Cody, and Sparks streamflow-gaging stations 

adjusted to increases in discharge mainly through changes in 

velocity and depth. These adjustment mechanisms are evident 

in this hydraulic microhabitat analysis because shallower and 

slower hydraulic conditions are mainly exchanged for deeper 

and faster conditions with increasing discharge at these sites. 
Figure 12. Longitudinal distribution of hydrogeomorphic characteristics of the Niobrara River from Dunlap 

Diversion Dam to the Missouri River, including (A) channel and valley width, location of major tributaries, and 

location of hydrogeomorphic segments and fluvial geomorphic provinces; (B) channel slope and braided index; 

(C) cumulative drainage area, longitudinal hydrology curves, and flood frequencies; (D) unit stream power; and 

(E) channel sinuosity.

Spencer 

Dam Norden 

Chute

Cornell Dam

U.S Geological Survey 

gage near Cody

Canyons and Restricted Bottoms Braided Bottoms

Meandering Bottoms

Entrenched 

meanders

Niobrara River 

Scenic Canyon

Beginning of Niobrara 

River delta

Pine 

Creek

Keya Paha 

River Plum 

Creek

Snake River

Bear 

Creek

Niobrara River near 

Hay Springs 

Niobrara River 

near Cody 

Niobrara 

River near 

Sparks Niobrara River 

near Norden 

Niobrara River 

near Spencer 

Niobrara River 

near Verdel 

Niobrara River 

near Gordon 

A

C

B

Channel width

Valley width

Tributary confluence

Upstream boundary of hydrogeomorphic segment

0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

EXPLANATION

BRAIDED INDEX, IN NUMBER OF 

CHANNEL THREADS

CHANNEL AND VALLEY WIDTH, IN FEET

CHANNEL SLOPE, IN PERCENT DISCHARGE, IN CUBIC FEET PER SECOND

DRAINAGE AREA, IN SQUARE MILES

1

2

3

4

5

6

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

Slope—10-mile moving average

Number of channel threads—instantaneous sample point

Braided index—100 channel-width moving average

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

8,000

9,000

300 250 200 150 100 50 0

MILES UPSTREAM OF THE MISSOURI RIVER

Mean-daily discharge curve (this study) 

Median-daily discharge curve (this study)

90th percentile discharge (this study)

2-year peak recurrence flood (Soenksen and others, 1999)

5-year peak recurrence flood (Soenksen and others, 1999)

Cumulative drainage area (this study)

Fluvial geomorphic province (Alexander and others, 2009)

36 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
D

CHANNEL SINUOSITY

UNIT STREAM POWER, IN POUNDS 

PER FOOT PER SECOND

E

1

2

3

4

5

6

300 250 200 150 100 50 0

MILES UPSTREAM FROM THE MISSOURI RIVER

100-channel-width window

Channel sinuosity

50-channel-width window

90th percentile

Unit stream power

Mean daily

0.0

1.0

2.0

Entrenched meanders Two-phase

 meandering reach

Niobrara 

delta Bend at 

Keya Paha River

Spencer Dam

Canyons and Restricted Bottoms Braided Bottoms

Meandering Bottoms

Figure 12. Longitudinal distribution of hydrogeomorphic characteristics of the Niobrara River from Dunlap 

Diversion Dam to the Missouri River, including (A) channel and valley width, location of major tributaries, 

and location of hydrogeomorphic segments and fluvial geomorphic provinces; (B) channel slope and 

braided index; (C) cumulative drainage area, longitudinal hydrology curves, and flood frequencies; (D) unit 

stream power; and (E) channel sinuosity.—Continued

Hydrogeomorphic Segments and Hydraulic Microhabitats 37

At the Verdel streamflow-gaging station, it was previously 

shown that the Niobrara River accommodated increasing 

discharge with nearly equal changes in width, depth, and 

velocity (Alexander and others, 2009). The greater role of 

width-based adjustments at Verdel is reflected in the increase 

in abundance of intermediate- and shallow-water hydraulic 

conditions with increasing discharge. This response is the 

result of the Niobrara River progressively occupying more and 

more of its channel width, including active-channel sandbars 

that were not submerged during lower flows, a reflection of 

its wide and braided nature in the BB fluvial geomorphic 

province. 

The analyses of hydraulic microhabitat conditions 

presented here emphasize the importance of flow diversity in 

the creation of a range of hydraulic microhabitat conditions. 

Intermediate-depth microhabitat conditions, for example, 

which are preferred by larger fish species (table 6), are absent 

at the Hay Springs streamflow-gaging station until upperdecile discharge conditions are reached. Similarly, the deeper 

hydraulic microhabitat conditions are relatively scarce at Cody 

and Sparks during median-quantile and lower-decile discharge 

conditions but increase in abundance during the higher 

discharge conditions. At Verdel, hydraulic-habitat diversity is 

apparent during all discharge conditions, but the diverse conditions are most balanced, and include increased extent of intermediate and deeper hydraulic niches during higher-magnitude 

discharges (fig. 13). These deeper, swifter hydraulic niches 

are likely important seasonal habitat conditions for larger fish, 

particularly the endangered pallid sturgeon (Scaphirhynchus

albus), which has been observed in the recreational reach of 

the Niobrara River in segment 1 (Wanner and others, 2009).
Figure 13. Distribution of available hydraulic microhabitats within four reaches at streamflowgaging stations of the Niobrara River, Nebraska, for a range of discharges including (A) lower-decile 

discharges; (B) median-quantile discharges; and (C) upper-decile discharges.

0

10

20

30

40

50

60

70

80

0

10

20

30

40

50

60

70

80

0

10

20

30

40

50

60

70

80

Shallow-slow

Shallow-moderate

Shallow-swift

Intermediate-slow

Intermediate-moderate

Intermediate-swift

Deep-slow

 Deep-moderate

Deep-swift

PERCENTAGE OF WETTED WIDTH PERCENTAGE OF WETTED

WIDTH

Niobrara River near Hay Springs (06456500)

Niobrara River near Cody (06459000)

Niobrara River near Sparks (06461500)

Niobrara River near Verdel (06465500)

EXPLANATION

PERCENTAGE OF WETTED WIDTH

A

B

C

HYDRAULIC MICROHABITAT NICHE CATEGORY

38 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
Table 14. Hydraulic-microhabitat information over a range of flow conditions for reaches at selected Niobrara River gaging stations in 

differing fluvial geomorphic provinces.

[All references to stream discharge frequency are from the periods of record at the gage indicated as reported by Alexander and others (2009); meas., measurment; no., number; ft3

/s, cubic feet per second; values shaded with gray indicate a difference of at least a factor of two in the values used to calculate the average; NA, not available]

Discharge (ft3/s) or 

hydraulic microhabitat niche 

category4 (percentage of 

wetted channel width)

Upper decile1 Median quantile2 Lower decile3

Meas. no.5

Average

Meas. no.5

Average

Meas. no.5

Average 1 2 1 2 1 2

Niobrara River near Hay Springs, Nebraska (06456500)

Discharge (ft3/s) 48 47 47 24 22 23 10 11 11

Shallow-slow .0 5.0 2.5 36.4 58.3 47.3 47.8 75.7 61.8

Shallow-moderate 78.3 65.0 71.6 63.6 41.7 52.7 52.2 24.3 38.2

Shallow-swift 4.3 15.0 9.7 .0 .0 .0 .0 .0 .0

Intermediate-slow 2.2 .0 1.1 .0 .0 .0 .0 .0 .0

Intermediate-moderate 15.2 1.0 12.6 .0 .0 .0 .0 .0 .0

Intermediate-swift .0 5.0 2.5 .0 .0 .0 .0 .0 .0

Deep-slow .0 .0 .0 .0 .0 .0 .0 .0 .0

Deep-moderate .0 .0 .0 .0 .0 .0 .0 .0 .0

Deep-swift .0 .0 .0 .0 .0 .0 .0 .0 .0

Niobrara River near Cody, Nebraska (06459000)

Discharge (ft3/s) 419 427 423 305 289 297 225 221 223

Shallow-slow 6.4 5.0 5.7 4.6 2.1 3.4 5.0 7.9 6.4

Shallow-moderate 2.8 .0 1.4 .0 1.4 .7 .0 .0 .0

Shallow-swift .0 .0 .0 .0 .0 .0 4.3 .0 2.1

Intermediate-slow .0 .0 .0 .0 5.0 2.5 7.9 .0 3.9

Intermediate-moderate 9.2 7.9 8.5 20.4 8.6 14.5 17.9 15.7 16.8

Intermediate-swift 49.6 61.4 55.5 71.4 60.0 65.7 53.6 65.7 59.6

Deep-slow .0 .0 .0 .0 .0 .0 .0 .0 .0

Deep-moderate .0 .0 .0 .0 .0 .0 .0 .0 .0

Deep-swift 31.9 25.7 28.8 3.6 22.9 13.2 11.4 10.7 11.1

Niobrara River near Sparks, Nebraska (06461500)

Discharge (ft3/s) NA 1,027 NA 605 749 677 407 446 427

Shallow-slow NA 7.72 7.72 3.48 1.57 2.53 5.03 1.89 3.46

Shallow-moderate NA .00 .00 .00 .00 .00 .00 .00 .00

Shallow-swift NA .00 .00 .00 .00 .00 .00 .00 .00

Intermediate-slow NA .00 .00 5.70 .00 2.85 6.92 2.52 4.72

Intermediate-moderate NA .00 .00 11.71 14.78 13.24 16.35 22.96 19.65

Intermediate-swift NA 62.65 62.65 79.11 60.38 69.75 71.70 72.64 72.17

Deep-slow NA .00 .00 .00 .00 .00 .00 .00 .00

Deep-moderate NA 4.94 4.94 .00 .00 .00 .00 .00 .00

Deep-swift NA 24.69 24.69 .00 23.27 11.64 .00 .00 .00

Niobrara River near Verdel, Nebraska (06465500)

Discharge (ft3/s) 2,965 3,013 1,606 1,634 1,024 976

Shallow-slow 6.1 13.7 9.9 46.5 8.8 27.7 21.6 28.8 25.2

Shallow-moderate 22.5 5.7 14.1 1.8 5.4 3.6 32.1 50.8 41.4

Shallow-swift 20.3 4.5 12.4 .0 5.4 2.7 12.2 .0 6.1

Intermediate-slow 4.7 4.7 4.7 .0 .0 .0 .0 .0 .0

Intermediate-moderate .5 20.8 10.7 3.9 .0 1.9 3.6 6.1 4.8

Intermediate-swift 19.2 27.7 23.5 22.9 66.8 44.8 5.0 4.9 5.0

Deep-slow 2.3 .0 1.2 .0 .0 .0 .0 1.5 .8

Deep-moderate 2.3 .0 1.2 3.5 .0 1.8 2.1 .0 1.1

Deep-swift 21.9 22.7 22.3 21.4 13.5 17.5 23.4 8.0 15.7

1

Refers to river discharges exceeded 10 percent of the time. 

2

Refers to river discharges within 25 percent of the median discharge.

3

Refers to river discharges exceeded 90 percent of the time. 

4

Refers to the depth velocity combinations in table 6.

5

If available, two measurements were used to calculate an average hydraulic 

microhabitat extent by percentage of wetted channel width.

Hydrogeomorphic Segments and Hydraulic Microhabitats 39
Figure 14. Frequency and cumulative-frequency distributions of the 

elevation of fluvial landforms in four study reaches of Niobrara National 

Scenic River, Nebraska.

0

10

20

30

40

50

60

70

80

90

100

0

1

2

3

4

5

6

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

FREQUENCY

HEIGHT OF FLUVIAL LANDFORM, IN FEET ABOVE STAGE 

OF MEDIAN DISCHARGE

CUMULATIVE PERCENT

Assigned frequency 

break in landforms

Figure 15. Schematic of active fluvial landforms surveyed in 

study reaches of Niobrara National Scenic River, Nebraska.

?

? ?

?

?

?

?

?

? ?

Bedrock

Alluvium Alluvium

Low flood plain—inundated 

by about 2-year return 

interval discharge

Intermediate flood plain— 

inundated only during ice jams 

or extremely rare floods Terraces

Terraces

40 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

Study Reach Results

Fluvial Landforms 

Several topographic levels of flood plains and terraces 

exist within the surveyed parts of the four study reaches 

at Crooked, Sunny Brook, Muleshoe, and Rock Barn. The 

frequency distributions of the heights of fluvial landforms, 

measured as height above the stage of median discharge, 

indicate at least three gaps in the distribution or breaks in 

slope—two breaks separating lower landforms and one break 

separating much higher surfaces, for a total of four landform 

groups (fig. 14). For descriptive purposes these four landform groups were named in order of increasing elevation as 

the low flood plains, intermediate flood plains, low terraces, 

and high terraces. The terraces were poorly characterized 

because the surveys did not extend across the full width of 

the alluvial valley bottom. In the discussion below, all references to discharge frequency statistics are in reference to the 

streamflow record of the Niobrara River near Sparks, Nebr. 

(06461500), streamflow-gaging station. 

The two lowest fluvial landforms are likely active in the 

modern hydroclimatic regime (fig. 15). The low flood plains 

are narrow strips of land varying between 3 and 7 ft in width 

and were only identified on surveyed cross sections in the 

Crooked study reach (table 15). The elevation of the stage 

where inundation of the low flood plain begins varies between 

0.8 and 1.3 ft above the stage of the median discharge, 

and corresponds to a discharge of approximately 1,530 to 

2,150 ft3/s or slightly less than the 2-year recurrence flood of 

2,470 ft3/s (Soenksen and others, 1999). The low flood plain is 

inundated in most years by the annual peak flood and may be 

“genetic,” in the sense that it is constructed of sediments transported by the annual spring flood regime (Nanson and Croke, 

1992). Although the low flood plain was only evident in the 

surveyed cross sections of one of the four study reaches, it was 

observed in several other reaches of segments 6, 7, and 8. The 

discontinuous nature of the low flood plain is likely the result 

of occasional destruction or erosion by the higher stages of 

ice-jam-induced floods. 

The intermediate flood plains were identified in all 

study reaches and vary in width between 4 and 38 ft across 

and between 2.4 and 6.7 ft above the stage of the median 

discharge. The intermediate flood plain heights are, on 

average, approximately 3.4 ft higher than those of the low 

flood plain. A stage change of 3.4 ft at the nearby Niobrara 

River near Sparks streamflow-gaging station corresponds to a 

gain of approximately 10,000 ft3/s more than the 2-year recurrence flood of 2,470 ft3

/s (Soenksen and others, 1999), clearly 

indicating that the intermediate flood plain is not inundated 

by spring storm runoff processes. The highest peak stages 

on record at the Sparks stream gage commonly are associated with processes other than normal spring runoff; the most 

common are damming and breakup of winter ice. The higher 

end of the stage range of the intermediate flood plain closely 

corresponds to the range of local ice-jam elevations surveyed 

in each reach during water year 2008 (table 15) and 

is in agreement with anecdotal accounts of local 

residents. The elevations of ice indicators also 

approach the lower end of the range of elevations 

of the low terrace surfaces. These data indicate that 

landforms that appear inactive or only infrequently 

flooded by storm-related runoff processes may be 

active on a relatively frequent basis from flooding 

caused by ice jamming and associated backwater 

flooding. These data also indicate that channel ice 

may be a primary driver of channel maintenance, 

flood plain connectivity, and fluvial depositional 

processes in the river bottom. The presence of two 

sets of flood plains—one bounding a narrower 

channel associated with storm runoff processes 

and a higher flood plain bounding a wider channel 

associated with ice jams—has been reported in 

other rivers where winter ice jams recur at least 

once every 5 years (Boucher and others, 2009).
Table 15. Fluvial landforms at cross sections within four study reaches of the Niobrara National Scenic River, Nebraska.

[Cross sections are numbered in ascending order from upstream to downstream; ft, feet; ft3/s, cubic feet per second; brink is defined as minimum elevation at 

which inundation of the landform begins; Low flood plain is defined as surfaces with elevations between 0.5 to 2.0 ft.; Intermediate flood plain is defined as 

surfaces with elevations between 2.0 and 7.0 ft.; Low terraces are defined as surfaces with elevations between 7.0 and 11.0 ft.; High terraces are defined as 

surfaces with elevations greater than 11.0 ft.; all elevations are referenced to the estimated stage of median annual discharge; max., maximum; min., minimum]

Cross 

section

Elevation of 

low flood 

plain1

(ft)

Width of low 

flood plain2

(ft)

Estimated

discharge at 

brink3

(ft3/s)

Exceedance4

,

percent

Elevation of 

intermediate 

flood plain1

(ft)

Width of 

intermediate 

flood plain2

(ft)

Elevation 

of low 

terraces 

(ft)

Elevation 

of high 

terraces 

(ft)

Elevation 

of ice5

(ft)

Niobrara River upstream of Crooked Creek near Sparks, Nebraska (425429100235301)

1 -- -- -- -- 2.4 3.9 9.7 -- --

2 1.1 3.0 1,930 <0.1 -- -- -- -- --

3 .8 6.8 1,530 <.6 -- -- 8.9 -- --

4 1.3 6.4 2,150 <.01 5.1 4.9 7.3 -- --

Niobrara River at Sunny Brook Campground near Norden, Nebraska (425013100105801)

1 -- -- -- -- 4.8 38 7.6–9.7 -- 5.9–6.8

2 -- -- -- -- 4.2–5.9 37 8.9–9.6 -- 5.7–6.6

3 -- -- -- -- 6.7 22 8.3–9.3 11.1 5.6–6.4

4 -- -- -- -- 2.6–5.6 7 7.9–9.1 -- 5.3–6.2

Niobrara River at Muleshoe Creek near Norden, Nebraska (424925100083201)

1 -- -- -- -- 4.7 4.8 7.0 11.4 4.6

2 -- -- -- -- 4.0 17 7.0 18.6 4.5

3 -- -- -- -- -- -- -- 12.6–14.4 4.3

4 -- -- -- -- -- -- -- 13.9–14.6 4.2

Niobrara River at Rock Barn Campground near Norden, Nebraska (424809100065001)

1 -- -- -- -- 5.1–6.5 29 8.4 14.9 --

2 -- -- -- -- 3.1 6.3 7.2 -- --

3 -- -- -- -- 3.1–4.4 12 7.1 -- --

4 -- -- -- -- 4.1 35 7.5 -- --

Max. (ft) 1.3 6.8 -- -- 6.7 38 9.7 18.6 6.8

Min. (ft) .8 3.0 -- -- 2.4 3.9 7.0 11.1 4.2

Mean (ft) 1.1 5.4 -- -- 4.5 18 8.3 13.9 5.5

1

If two or more surfaces within range are present, values are shown as a range if elevation differences are greater than 0.1 feet and as a single, average value if 

differences are less than 0.1 feet.

2

Average width of alluvial surfaces within landform group.

3

Stage estimated using an approximate rating curve generated from stage-only gage.

4

Percent of time discharge is equaled or exceeded at Niobrara River near Sparks, Nebraska gage (06461500).

5

Ice elevations are shown as ranges when more than one ice-stage elevation marker was used.

Hydrogeomorphic Segments and Hydraulic Microhabitats 41
42 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

Bed Sediment

Sediment samples obtained in the study reaches indicate 

that the primary bed material in the active channel ranged in 

size from coarse silt (0.031 to 0.0625 mm) to coarse sand (0.5 

to 1.0 mm), and the majority of grain sizes ranged between 

about 0.2 and 0.5 mm (fine sand to medium sand) (table 16), 

similar to those reported by Colby and others (1953). Median 

grain size diameters of samples ranged from 0.10 to 0.69 mm. 

Grain-size distributions from samples also indicate that the 

bed of the Niobrara River coarsens and has increasing grainsize variability in the downstream direction (fig. 16). There 

could be several reasons for these phenomena. First, the most 

upstream study reach is approximately 5 mi downstream 

from Cornell Dam, and the dam may act as a seasonal barrier 

to coarser grain sizes. Because the sediment samples were 

obtained in the fall and late fall, several months after peak 

flows, the coarser grain sizes may have been preferentially 

trapped behind Cornell Dam. In this case, the bed sediment 

coarsening and increasing variance would be from the inputs 

of coarser sediments at tributary junctions, bank erosion, and 

landslides or other direct hillslope sediment delivery to the 

channel from the bedrock bluffs. 

Second, these phenomena could also be created from 

differences in the locations and accessibility of bed deposits 

for sampling. For example, samples obtained at the Crooked 

study reach were collected only from vegetated dunes along 

the left (north) side of the channel because the rest of the 

bed was bedrock. The uniformity of grain sizes in this case 

is likely the result of sampling of similar bedforms of similar 

size, all of which were located in approximately the same 

hydraulic environment, which should, with all other physical constraints held constant, result in a similar grain-size 

distribution from each sample. Conversely, the samples at the 

other study reaches were collected on both banks as well as 

the center of the channel where grain sizes would be expected 

to be coarser. The larger sample size of the Rock Barn study 

reach might also be expected to capture more of the sediment 

grain-size variance. However, it is unlikely that this would 

explain the downstream patterns considering Sunny Brook and 

Muleshoe had similar sample sizes and sampling strategies, 

and the pattern of increased coarsening and grain-size variance 

is still visible in the data. Furthermore, the median grain sizes 

of the samples reported here are within the ranges of those 

reported in previous studies (Colby and others, 1953; Colby 

and Hembree, 1955; Buchanan, 1981). 

Hydraulic Geometry and Hydraulics 

Values of at-a-station hydraulic geometry exponents 

indicate that the Niobrara River in the study reaches adjusts 

its geometry to changing discharges primarily through 

increases in flow depth and velocity. The Crooked study 

reach had too few measurements, over a relatively narrow 

range of discharges, to develop statistically meaningful 

hydraulic-geometry relations. Graphical summaries of study 

reach at-a-station hydraulic-geometry relations are shown in 

figure 17. Values for the exponents, coefficients, and goodness-of-fit measures associated with the at-a-station hydraulicgeometry relations are shown in table 17. Width (b) exponents 

at five of the six cross sections ranged from a negative value 

to 0.06, and four of the statistical models describing width 

adjustments indicate a lack of significance at the 90-percent 

confidence level, indicating that the Niobrara River at most 

locations in the study reaches does not typically accommodate 

flow increases through changes in channel width. 

Exponents at cross section 4 of the Muleshoe study reach 

(table 17) ranged from 0.29 to 0.37, indicating that, at least 

locally, changes in width were also an important channel 

adjustment mechanism. The higher magnitude width exponent reflects the effect of a mid-channel bedrock bar that was 

eventually inundated as discharge, and consequently stage, 

increased. This more complex hydraulic-geometry response is 

similar to those described further downstream in the BB province (table 1), and is likely representative of reaches, or short 

sections of reaches, in the CRB province where the channel 

has localized morphologic complexity associated with midchannel deposition, or variations in bedrock topography. The 

negative-width exponent was calculated for cross section 1 of 

the Muleshoe study reach, where variance in width was less 

than 4 feet over the entire range of flows (table 18). At this 

particular cross section, the banks were vertical or undercut, 

and both wading and boat measurements were made. Thus, 

the variance is likely due to slight differences in technician 

judgment of the margin of effective flow or, in the case of 

the highest discharge measurement, a slight shift (upstream 

or downstream) in the cross section measurement location. 

Depth (f) and velocity (m) exponents range in value from 0.17 

to 0.60 and 0.29 to 0.84, respectively. All fitted depth- and 

velocity-adjustment statistical models were significant at the 

90-percent confidence level. Exponent sums and coefficient 

products indicate that the statistical models generally comply 

with continuity, with 0.11 being the largest deviation from 

unity. 

The estimates of hydraulic geometry coefficients for 

some of the cross sections in the four study reaches differ in 

proportion and magnitude from those previously reported for 

the Niobrara River near Sparks, Nebr., streamflow-gaging 

station (Alexander and others, 2009). These differences in 

proportion and magnitude likely are the result of the much 

wider range and greater number of discharge values used in 

those previous models. Nonetheless, the models presented 

here indicate that, over the range of flows measured, the 

Niobrara River in the sinuous canyon and width-restricted 

valley settings accommodates increases in flow primarily 

through increases in channel depth and velocity, with deviations from this model caused by localized channel morphologic complexity. Previously reported hydraulic geometry 

relations for the Niobrara River indicate that this model of 

channel-adjustment changes as the Niobrara flows out of the 

CRB province and into the wider, more complex, braided 

reaches of the BB fluvial geomorphic province. 
Table 16. Grain-size distributions of selected bed-sediment samples from four study reaches in the Niobrara National Scenic River, 

Nebraska.

[Dn, diameter of the nth percentile of the grain-size cumulative frequency distribution in millimeters; mm, millimeters; , phi scale units defined as the negative 

base-2 logarithm of grain diameter in millimeters; MS, moderately sorted; MWS, moderately well sorted; PS, poorly sorted; WS, well sorted]

Sample 

number

D5

(mm)

D16

(mm)

D50

(mm)

D84

(mm)

D95

(mm)

Graphic mean 

(mm)

Inclusive 

graphic 

standard 

deviation ()

Sorting 

description 

(Folk, 1974)

Niobrara River upstream of Crooked Creek near Sparks, Nebraska (425429100235301)

1 0.06 0.08 0.15 0.21 0.24 0.13 0.67 MWS

2 .06 .07 .12 .20 .23 .12 .71 MWS

3 .06 .07 .13 .21 .25 .13 .71 MWS

4 .06 .07 .10 .18 .22 .10 .66 MWS

5 .06 .08 .14 .21 .24 .13 .66 MWS

6 .06 .09 .17 .24 .39 .15 .74 MS

Niobrara River at Sunny Brook Campground near Norden, Nebraska (425013100105801)

1 0.07 0.12 0.18 0.26 0.43 0.17 0.69 MWS

2 .12 .14 .22 .38 .46 .23 .64 MWS

3 .14 .17 .29 .42 .48 .27 .61 MWS

4 .13 .15 .23 .39 .46 .23 .63 MWS

5 .08 .14 .23 .40 .48 .23 .77 MS

6 .07 .13 .19 .33 .45 .20 .73 MWS

7 .06 .10 .20 .40 .56 .20 .99 MS

Niobrara River at Muleshoe Creek near Norden, Nebraska (424925100083201)

1 0.25 0.29 0.43 0.86 1.65 0.47 0.81 MS

2 .17 .26 .36 .50 .88 .36 .58 MWS

3 .14 .20 .32 .44 .49 .31 .55 MWS

4 .07 .13 .19 .34 .46 .20 .79 MS

5 .08 .14 .27 .41 .47 .25 .78 MS

Niobrara River at Rock Barn Campground near Norden, Nebraska (424809100065001)

1 0.03 0.04 0.10 0.31 0.52 0.11 1.33 PS

2 .10 .26 .40 .89 2.95 .45 1.19 PS

3 .16 .25 .35 .48 .79 .35 .59 MWS

4 .14 .18 .31 .43 .48 .29 .57 MWS

5 .14 .19 .32 .46 .68 .30 .66 MWS

6 .15 .25 .34 .45 .50 .33 .48 WS

7 .15 .25 .35 .49 .99 .25 .94 MS

8 .11 .14 .19 .29 .42 .14 1.15 PS

9 .35 .52 .69 .90 .99 .52 1.14 PS

10 .07 .10 .19 .40 .98 .12 1.42 PS

11 .06 .09 .17 .33 1.12 .11 1.59 PS

12 .16 .25 .35 .47 .78 .25 1.70 PS

Hydrogeomorphic Segments and Hydraulic Microhabitats 43
Figure 16. Bed-sediment grain-size cumulative frequency 

distributions for four study reaches within Niobrara National 

Scenic River, Nebraska.

A

B

C

D

CUMULATIVE PERCENT FINER

Median grain diameter

D50 range between 

0.10 and 0.17 mm

D50 range between 

0.18 and 0.29 mm

D50 range between 

0.19 and 0.43 mm

D50 range 

between 0.10 

and 0.69 mm

0

20

40

60

80

100

CUMULATIVE PERCENT FINER

0

20

40

60

80

100

CUMULATIVE PERCENT FINER

0

20

40

60

80

100

CUMULATIVE PERCENT FINER

0

20

40

60

80

100

0.01 0.1 1 10

GRAIN SIZE, IN MILLIMETERS

Niobrara River at Muleshoe Creek 

 near Norden, (424925100083201)

Niobrara River at Rockbarn Campground

 near Norden (424809100065001)

Niobrara River at Sunny Brook Campground 

 near Norden (425013100105801)

Niobrara River upstream of Crooked Creek 

 near Sparks (425429100235301)

EXPLANATION

D50

44 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

Hydraulic behavior over the range of flows measured was 

not consistent among all reaches, but two general modes can 

be inferred from the calculated parameters at Sunny Brook, 

Muleshoe, and Rock Barn (fig. 18). A comparable analysis 

of hydraulic behavior could not be conducted at the Crooked 

study reach because too few measurements were made. At the 

Sunny Brook and Muleshoe study reaches, average boundaryshear stress remained approximately constant for discharges 

below 900 ft3/s. Above 900 ft3/s, average boundary shear stress 

increased by approximately 20 to 30 percent (table 18). At the 

Rock Barn study reach, shear stress showed little to no change 

in the rate of increase with increasing discharge (fig. 18). 

Hydraulic resistance, as measured by the Manning’s n

(Manning’s roughness coefficient), ranged between 0.016 and 

0.049, with the highest resistance occurring at cross section 1 

of the Muleshoe study reach. Hydraulic resistance was 

observed to decrease with increasing discharge below 900 ft3/s 

at the Sunny Brook, Muleshoe, and Rock Barn study reaches. 

Above 900 ft3/s, resistance increased or stabilized at the Sunny 

Brook and Muleshoe reaches but continued to decrease at the 

Rock Barn reach. 

Unit stream power magnitudes and rates of change varied 

from reach to reach (fig. 18). Unit stream power had the 

largest magnitudes and rates of change at Muleshoe, varying 

between 0.53 and 1.28 pounds per foot-second (lb/ft-s), over 

the range of discharges measured (table 18). The magnitudes 

and rates of change in unit stream power were nearly identical 

at Sunny Brook and Rock Barn, with values ranging from 0.22 

to 0.57 lb/ft-s over the range of discharges measured (table 

18). Although not measured over the same range of discharges, 

the magnitude and rate of change of unit stream power at the 

Crooked Creek reach appear to be intermediate between those 

of Muleshoe and the lower values of Sunny Brook and Rock 

Barn. Unit stream power values calculated from the hydraulic measurements within the study reaches were comparable 

to the median values of 90th percentile unit stream power 

estimated for segments 6 and 7 using the GIS data (table 13). 

Corresponding values of unit stream power for segment 5, 

which contains the Rock Barn study reach, are lower than 

those calculated from hydraulic data measured at Rock Barn, 

although this is likely because the location of Rock Barn is 

near the upstream end of segment 7, which is discussed in 

more detail below. 

The two-mode behavior of shear stress and resistance 

at the Sunny Brook and Muleshoe reaches (fig. 18) indicates 

that the bed configuration may have changed—in particular, a 

transition from dunes (lower regime) to plane bed or antidunes 

(upper regime) may have occurred at a discharge above 

900 ft3/s. When plotted over the bedform classification results 

of Simons and Richardson (1966), which are based on experimental flume studies, the values of unit stream power for the 

range of median grain-size diameters sampled (about 0.2 mm 

to 0.4 mm) indicate that bedforms transition from dunes to 

plane bed and antidune phases between approximately 0.2 

and 0.7 lb/ft-s (fig. 19). When examined over the entire range 

of sample median diameters, the Muleshoe and Sunny Brook 
Figure 17. At-a-station hydraulic geometry relations for four study reaches in Niobrara National Scenic 

River, Nebraska, water years 2008–09, including relations between (A) discharge and wetted channel top 

width; (B) discharge and average water depth; and (C) discharge and average current velocity.

80

WETTED CHANNEL TOP WIDTH, IN FEET

1.0

AVERAGE WATER DEPTH, IN FEET

1.0

AVERAGE CURRENT VELOCITY, 

IN FEET PER SECOND 

DISCHARGE, IN CUBIC FEET PER SECOND

300 600 900 1,200 1,500

2.0

3.0

4.0

5.0

2.0

3.0

140

200

Muleshoe upstream (424925100083201)

Muleshoe downstream (424925100083201)

Rock Barn downstream (424809100065001)

Rock Barn upstream (424809100065001)

Sunny Brook upstream (425013100105801)

Sunny Brook downstream (425013100105801)

Crooked Creek section 3 (425429100235301)

Crooked Creek upstream (425429100235301)

EXPLANATION

Regression fitting lines Measurement data points

Muleshoe upstream (424925100083201)

Rock Barn upstream (424809100065001)

Sunny Brook upstream (425013100105801)

Sunny Brook downstream (425013100105801)

Muleshoe downstream (424925100083201)

Rock Barn downstream (424809100065001)

A

B

C

Hydrogeomorphic Segments and Hydraulic Microhabitats 45
Table 17. At-a-station hydraulic geometry relations for four study reaches within Niobrara National Scenic River, Nebraska.

[All stations are located in Nebraska; ft3/s, cubic feet per second; a, width coefficient; b, width exponent; c, depth coefficient; f, depth exponent; k, velocity 

coefficient; m, velocity exponent; Q, water discharge, in cubic feet per second; w, channel top width, in feet; d, average channel depth, in feet; v, mean current 

velocity in feet per second; <, less than; >, greater than; --, no data; COD, coefficient of determination for least-squares estimate of regression equation]

Exponent 

coefficient or 

statistic

Station name

Niobrara River upstream of 

Crooked Creek near Sparks 

(425429100235301)1

Niobrara River at Sunny Brook 

Campground near Norden 

(425013100105801)

Niobrara River at Muleshoe Creek near Norden 

(424925100083201)

Niobrara River at Rock Barn 

Campground near Norden 

(424809100065001)

Location within study reach2

Cross 

section 1

Cross 

section 3

Cross 

section 1

Cross 

section 4

Cross 

section 1

Cross 

section 4

Cross 

section 1

Cross 

section 4

Number of measurements used in hydraulic geometry analysis

2 3 5 5 5 5 5 5

Maximum discharge of included measurements, in ft3/s

881 649 1,250 1,260 1,320 1,330 1,200 1,190

Minimum discharge of included measurements, in ft3/s

592 501 610 574 616 574 627 621

Width coefficients and exponents (equation 1; w = aQb)

a -- -- 131 116 154 14.4 82 134

b -- -- .02 .04 –.02 .35 .06 –.01

COD -- -- .39 .98 .47 .70 .39 .11

p-value3 -- -- .26 <.01 .20 <.1 .26 0.59

Depth coefficients and exponents (equation 2; d = cQf)

c -- -- 0.03 0.09 0.12 0.13 0.20 0.72

f -- -- .60 .47 .44 .37 .37 .17

COD -- -- .84 .70 .74 .72 .85 .87

p-value3 -- -- <.1 <.1 <.1 <.1 <.1 <.1

Velocity coefficients and exponents (equation 3; v = kQm)

k -- -- 0.26 0.09 0.06 0.53 0.06 0.01

m -- -- .38 .51 .58 .29 .58 .84

COD -- -- .65 .72 .84 .83 .97 .99

p-value3 -- -- <.1 <.1 <.1 <.1 <.01 <.001

Product of coefficients

-- -- 0.98 0.89 0.99 0.98 1.00 0.98

Sum of exponents

-- -- 1.00 1.02 1.00 1.00 1.00 1.00

1

Too few data points were available to develop hydraulic geometry relations for station 425429100235301. 

2

Cross sections are numbered in ascending order from upstream to downstream and spaced approximately a single channel width apart.

3

Probability (p-value) that regression slope is zero (no correlation between discharge and geometric variable); values less than 0.10 indicate model significance at the 90-percent confidence level.

46 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
Hydrogeomorphic Segments and Hydraulic Microhabitats 47

reaches are on the margin or entirely within the transition to 

upper flow-regime (plane bed/antidune) bed phases. 

The Rock Barn study reach did not exhibit the same 

two-mode hydraulic behavior observed at the Sunny Brook 

and Muleshoe reaches. Although there may be several reasons 

for this, it was hypothesized that the difference in hydraulic 

behavior was related to two primary differences in the Rock 

Barn reach. First, the Rock Barn reach has a combination of 

lower unit stream power and coarser, less well-sorted bed sediment. When plotted over the Simons and Richardson (1966) 

bedform classification, the coarser grain sizes sampled within 

the reach indicated the bed would have been in lower regime, 

although the median and smallest grain sizes sampled would 

have been transitional or fully upper regime (fig. 19). These 

results indicate that for the ranges of grain sizes sampled, a 

plane-bed or antidunes bed state may have been present but 

not stable at the highest discharge measured. Second, and 

potentially more important, the channel more than doubles in 

total wetted width just downstream from the Rock Barn study 

reach. The width expansion downstream may have prevented 

the same type of hydraulic threshold behavior from occurring 

in the Rock Barn study reach. The expansion and contraction 

in channel width over short distances are common in the BB 

fluvial geomorphic province, which begins a short distance 

upstream from the Rock Barn reach. Because of their wider 

channel widths, the expansion zones would be expected to 

have lower unit stream power per unit discharge, and therefore, would require greater discharge to reach the same 

bedload transport rates as those in narrow reaches. 

Although channel velocities, grain sizes, and transitional 

bed-state boundaries seem to reasonably converge when 

viewed in relation to the bedform classification data of Simons 

and Richardson (1966), the Froude numbers calculated for the 

measured flows are low, indicating that the flows may have 

been dominantly lower regime (table 18). For example, Leeder 

(1999) reports that, in general, antidunes occur as stable forms 

at Froude values of 0.84 or higher. However, experimental 

data from Athaullah (1968) indicate that transitional to upperregime bedforms may occur at Froude numbers as low as 0.3 

to 0.6 for the grain sizes and channel geometries measured 

for this study (fig. 20). The median grain size used for relative 

roughness (ratio of hydraulic radius to median bed grain size) 

in figure 20 is the median D50 of all samples collected in the 

three study reaches with substantial fine sediment coverage of 

the bed—Sunny Brook, Muleshoe, and Rock Barn. Although 

the experimental data of Simons and Richardson (1966) and 

Athaullah (1968) are not in perfect agreement, both indicate 

that the bed state in the study reaches was, at a minimum, 

transitional during the higher measured discharges, and both 

indicate that the Sunny Brook and Muleshoe reaches were 

more likely to have been in an upper flow regime bed state 

than was Rock Barn. 

The coincident increase in boundary shear stress above 

900 ft3/s observed at the Sunny Brook and Muleshoe study 

reaches represents a potential hydraulic threshold above which 

bedload transport rates were likely to increase markedly. If 

the rate of change in bed shear with discharge is generally 

monotonic beyond the discharges measured, a second hydraulic shift would be expected once the stage of the river exceeds 

the height of the low flood plain. Once the stage of the flood 

plain is reached, the width of the river would be expected to 

increase rapidly, forcing a second shift in unit stream power 

values, a change in the rate of change of depth with increasing discharge, and subsequently, a shift in the rate of change 

of boundary shear stress with discharge (Leopold and others, 

1964; Richards, 1977; Bridge, 2003).

Bed Adjustment 

The seasonal bed elevation of the Niobrara River in 

the study reaches did not exhibit consistent behavior over 

the range of flows or over the season (fig. 21). The three 

reaches that were observed to have substantial coverage of 

the bed by fine sediment—Sunny Brook, Muleshoe, and 

Rock Barn—exhibited greater bed elevation variability than 

did the bedrock-dominated Crooked study reach, as would 

be expected. The upper cross sections at Sunny Brook and 

Muleshoe were both deepened (scoured) over the course of 

the season, indicating that the bed was evacuating a supply of 

sediment. Conversely, the cross sections at Rock Barn and the 

lower cross section at Sunny Brook were stable or aggrading 

sediment over the season. The upper cross section at Rock 

Barn and the lower cross section at Sunny Brook aggraded 

with increasing discharge, whereas the upper cross sections 

at Sunny Brook and Muleshoe scoured. Because the deposits 

on the bed shift frequently, especially at higher discharges, it 

is likely that these data are not temporally adequate to fully 

characterize the behavior of the river bed in the study reaches 

(Colby, 1964). Nonetheless, no consistent bed-adjustment 

pattern (scour or fill) was identified among reaches.
Table 18. Summary of channel discharge, geometry, and hydraulic parameters calculated from measurements made in water years 2008 and 2009 at four study reaches in 

Niobrara National Scenic River, Nebraska.—Continued[ft3/s, cubic feet per second; ft2, square feet; ft, feet]

Location1

Date of 

measurement Discharge (ft3/s)

Total 

hydraulic 

area 

(ft2

)

Top width 

of wetted 

channel 

(ft)

Wetted 

perimeter 

(ft)

Average 

depth2

(ft)

Hydraulic 

radius3

(ft.)

Average 

velocity4

(ft. per 

second)

Average 

slope5

(percent)

Manning 

roughness 

coefficent

Unit stream 

power 

(pounds/ftsecond)

Average 

boundary 

shear stress 

(pound-force/

ft2 )

Froude 

number 

(dimensionless)

Niobrara River upstream from Crooked Creek near Sparks, Nebraska (425429100235301)

1 4/23/2008 881 266 134 135 2.0 2.0 3.3 0.001 0.03 0.54 0.16 0.41

1 10/31/2008 592 207 125 125 1.7 1.6 2.9 .001 .03 .39 .14 .393 5/21/2008 649 211 130 131 1.6 1.6 3.1 .001 .02 .41 .13 .423 7/29/2008 501 175 128 128 1.4 1.4 2.9 .001 .02 .32 .11 .433 10/31/2008 609 201 129 130 1.6 1.6 3.0 .001 .02 .39 .13 .434 4/23/2008 837 249 134 135 1.9 1.8 3.4 .001 .02 .51 .15 .43

Niobrara River at Sunny Brook Campground near Norden, Nebraska (425013100105801)

1 4/8/2008 890 232 147 147 1.6 1.6 3.8 0.001 0.02 0.35 0.09 0.541 5/20/2008 733 240 148 149 1.6 1.6 3.1 .001 .02 .28 .09 .421 6/12/2008 1,250 320 148 149 2.2 2.1 3.9 .001 .02 .48 .12 .471 9/8/2008 633 223 147 148 1.5 1.5 2.8 .001 .02 .25 .09 .411 10/29/2008 610 183 145 146 1.3 1.3 3.3 .001 .02 .24 .07 .524 4/8/2008 889 276 153 153 1.8 1.8 3.2 .001 .02 .33 .10 .424 5/20/2008 727 292 152 154 1.9 1.9 2.5 .001 .03 .27 .11 .324 6/12/2008 1,260 419 155 158 2.7 2.7 3.0 .001 .03 .46 .15 .324 9/8/2008 681 284 151 153 1.9 1.9 2.4 .001 .03 .26 .11 .314 10/29/2008 574 276 150 151 1.8 1.8 2.1 .001 .03 .22 .10 .27

Niobrara River at Muleshoe Creek, near Norden, Nebraska (424925100083201)

1 4/9/2008 898 270 130 131 2.1 2.1 3.3 0.002 0.03 0.96 0.29 0.41 5/20/2008 714 278 130 132 2.1 2.1 2.6 .002 .04 .76 .29 .31 6/13/2008 1,200 367 129 130 2.8 2.8 3.3 .002 .04 1.29 .39 .31 9/8/2008 627 273 130 131 2.1 2.1 2.3 .002 .05 .67 .29 .31 10/30/2008 628 266 133 133 2.0 2.0 2.4 .002 .05 .66 .28 .34 4/9/2008 871 234 160 161 1.5 1.4 3.8 .002 .02 .75 .20 .54 5/20/2008 749 224 142 144 1.6 1.6 3.3 .002 .03 .73 .22 .54 6/13/2008 1,190 293 160 161 1.8 1.8 4.1 .002 .03 1.03 .25 .54 9/8/2008 660 193 142 143 1.4 1.4 3.4 .002 .03 .64 .19 .54 10/30/2008 621 180 124 124 1.5 1.4 3.4 .002 .03 .70 .20 .5

48 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
Table 18. Summary of channel discharge, geometry, and hydraulic parameters calculated from measurements made in water years 2008 and 2009 at four study reaches in 

Niobrara National Scenic River, Nebraska.—Continued[ft3/s, cubic feet per second; ft2, square feet; ft, feet]

Location1

Date of 

measurement Discharge (ft3/s)

Total 

hydraulic 

area 

(ft2)

Top width 

of wetted 

channel 

(ft)

Wetted 

perimeter 

(ft)

Average 

depth2

(ft)

Hydraulic 

radius3

(ft.)

Average 

velocity4

(ft. per 

second)

Average 

slope5

(percent)

Manning 

roughness 

coefficent

Unit stream 

power 

(pounds/ftsecond)

Average 

boundary 

shear stress 

(pound-force/

ft2 )

Froude 

number 

(dimensionless)

Niobrara River at Rock Barn Campground near Norden, Nebraska (424809100065001)

1 4/8/2008 926 288 120 122 2.4 2.4 3.2 0.001 0.02 0.41 0.13 0.4

1 5/21/2008 700 273 116 117 2.4 2.3 2.6 .001 .03 .32 .13 .31 6/11/2008 1,320 347 124 125 2.8 2.8 3.8 .001 .02 .57 .15 .41 9/9/2008 687 253 123 125 2.1 2.0 2.7 .001 .03 .30 .11 .31 10/30/2008 626 252 118 120 2.1 2.1 2.5 .001 .03 .28 .11 .34 4/8/2008 900 305 130 131 2.3 2.3 3.0 .001 .03 .37 .13 .34 5/21/2008 680 291 129 131 2.3 2.2 2.3 .001 .03 .28 .12 .34 6/11/2008 1,330 315 128 129 2.5 2.4 4.2 .001 .02 .56 .13 .54 9/9/2008 616 283 129 130 2.2 2.2 2.2 .001 .03 .26 .12 .34 10/30/2008 636 273 129 130 2.1 2.1 2.3 .001 .03 .26 .11 .3

Summary data statistics

Minimum 501 1.3 1.3 2.1 0.02 0.22 0.07Mean 803 2.0 1.9 3.0 .03 .49 .16Maximum 1330 2.8 2.8 4.2 .05 1.29 .39

1Station location refers to the location of the measurement at one of four cross sections within the reach; “1” refers to the upstream most cross section; “4” refers to the furthest downstream cross section, and “3” refers to the cross section immediately upstream from the “4” cross section.2Average depth is calculated by dividing the total hydraulic area by the top width of the wetted channel.3Hydraulic radius is calculated by dividing the total hydraulic area by the wetted perimeter.4Average velocity is calculated by dividing discharge by the total hydraulic area.5Average slope is the average of all measured water-surface slopes for all discharge measurements.

Hydrogeomorphic Segments and Hydraulic Microhabitats 49
Figure 18. Variation in selected hydraulic parameters over a range of discharges in four study reaches of 

Niobrara National Scenic River, Nebraska, water years 2008–09, including relations between (A) discharge 

and average boundary shear stress; (B) discharge and the Manning roughness coefficient; and 

(C) discharge and unit stream power.

0

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

0.45

0

0.01

0.02

0.03

0.04

0.05

0.06

0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

0 200 400 600 800 1,000 1,200 1,400

AVERAGE BOUNDARY SHEAR STRESS,

 IN POUND-FORCE PER SQUARE FOOT

DISCHARGE, IN CUBIC FEET PER SECOND

EXPLANATION

MANNING ROUGHNESS COEFFICIENT

UNIT STREAM POWER, IN FOOT-POUNDS 

PER SECOND

A

B

C

Muleshoe upstream (424925100083201)

Muleshoe downstream (424925100083201)

Rock Barn downstream (424809100065001)

Sunny Brook upstream (425013100105801) Rock Barn upstream (424809100065001)

Sunny Brook downstream (425013100105801)

Crooked Creek section 3 (425429100235301)

Crooked Creek upstream (425429100235301)

Mode 1 Mode 2

Mode 1

900 cubic feet per second

900 cubic feet per second

Mode 2

50 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
Sand

Fine Medium Coarse

Antidunes and plane bed

Transition

Dunes

Ripples

Plane bed

GRAIN SIZE, IN MILLIMETERS

0 0.2 0.4 0.6 0.8 1.0

UNIT STREAM POWER, IN POUNDS PER FOOT PER SECOND 10-2

10-3

10-1

1.0

Very fine

EXPLANATION

Minimum D50

Median D50

Maximum D50

D50 Median grain-size diameter of bed samples 

collected within each reach

Sunny Brook upstream (425013100105801)

Sunny Brook downstream (425013100105801)

Muleshoe upstream (424925100083201)

Muleshoe downstream (424925100083201)

Rock Barn upstream (424809100065001)

Rock Barn downstream (424809100065001)

Boundaries of bedform classification from Simons 

 and Richardson (1966)

Figure 19. Relation of unit stream power to median grain-size diameters sampled over the range of discharges 

measured in three study reaches of the Niobrara National Scenic River, Nebraska.

Figure 20. Relation of Froude number to dimensionless relative roughness ratio over the range of discharges measured in 

three study reaches of the Niobrara National Scenic River, Nebraska.

Sunny Brook upstream (425013100105801)

Sunny Brook downstream (425013100105801)

Muleshoe upstream (424925100083201)

Muleshoe downstream (424925100083201)

Rock Barn upstream (424809100065001)

Rock Barn downstream (424809100065001)

Transition

Upper regime

Lower regime

RATIO OF HYDRAULIC RADIUS TO MEDIAN BED GRAIN SIZE

10-1

EXPLANATION

FROUDE NUMBER 1.0

10

10 102 103 104

Boundaries of zones based on experimental 

 flume data of Athaullah (1968)

Hydrogeomorphic Segments and Hydraulic Microhabitats 51
Figure 21. Seasonal changes in bed elevation of river channel at cross sections within four study reaches of Niobrara 

National Scenic River, Nebraska. 

0

1

2

3

4

Muleshoe upstream (424925100083201)

Muleshoe downstream (424925100083201)

Rock Barn downstream (424809100065001)

Rock Barn usptream (424809100065001)

Sunny Brook upstream (425013100105801)

Sunny Brook downstream (425013100105801)

Crooked Creek 3 (425429100235301)

Crooked Creek upstream (425429100235301)

Quartiles of the bed-elevations surveyed on indicated date at each cross section

D

A

0

1

2

3

4

B

DATE

EXPLANATION

Upper quartile

Median value

Lower quartile

10/1/0712/1/07

2/1/084/1/086/1/088/1/08

10/1/08

10/1/0712/1/07

2/1/084/1/086/1/088/1/08

10/1/08

BED ELEVATION BELOW STAGE OF MEDIAN DAILY 

DISCHARGE, IN FEET

Connects median values from most upstream cross section in reach

Connects median values from most downstream cross section in reach

C

52 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

Hydraulic Microhabitats

Analysis of hydraulic microhabitats over the range 

of discharges measured at the study reaches indicates that 

some percentage of most habitat niche categories was available for at least one discharge condition, but the majority of 

hydraulic habitat available was within the intermediate-swift 

and deep-swift habitat niche categories (table 19). Deepswift conditions dominated nearly all study reaches under 

all measured discharge conditions. This is particularly so 

during median-quantile and upper-decile discharges, when 

the intermediate-swift and deep-swift hydraulic microhabitat 

niches were dominant (fig. 22). Slight differences in habitat 

distributions were observed between the three study reaches 

with substantial coverage of the bed by fine sediment (Sunny 

Brook, Muleshoe, and Rock Barn) and the bedrock-dominated 

reach (Crooked). At the Crooked reach, the intermediate-swift 

habitat category dominated the distribution during the lowest 

measured discharge (still within median-quantile frequency 

range), and the deep-swift habitat category dominated during 

the median-quantile discharge. No flows were measured at the 

Crooked reach that qualified for the upper-decile dischargefrequency category. With the exception of the Sunny Brook 

reach, the deep-swift habitat niche dominated the distribution 

for all ranges of discharges in the reaches with substantial 

amounts of sand on the bed. At Sunny Brook, the intermediate-swift habitat niche dominated during median-quantile 

discharges, but the deep-swift niche dominated during the 

lowest measurements and upper-decile categories.

The four study reaches (table 7) are located in three 

different hydrogeomorphic segments and, consequently, would 

be expected to exhibit differences in physical characteristics 

(table 13). The Crooked reach is located in segment 7, Sunny 

Brook and Muleshoe are located in segment 6, and Rock Barn 

is located in segment 5. Although these reaches occupy three 

different hydrogeomorphic segments, the habitat niche types, 

abundance of particular habitat niches, and response of microhabitat niche distributions to changing discharge conditions 
Summary 53

(fig. 22) generally were similar among all reaches. The types 

of niches and response of hydraulic habitat distributions to 

changing discharge conditions in these four reaches were most 

similar to those at the Sparks gaging station (described above), 

where the primary habitat adjustment was an increase in flow 

depth. This similarity in response was not unexpected because 

three of the four reaches are in the CRB fluvial geomorphic 

province and have similar at-a-station hydraulic geometries. 

The hydraulic geometry analysis above and in the previous 

study (Alexander and others, 2009) showed that the river in 

the CRB province mainly accommodated increasing discharge 

through increases in depth and velocity. As compared to the 

Sparks gage, the study reaches all had greater abundance 

of the deeper habitat categories over the range of discharge 

frequencies analyzed. At the Rock Barn reach, which is in the 

BB fluvial geomorphic province, the response of hydraulic 

microhabitat distribution was virtually identical to those of the 

other reaches. 

Several reasons are hypothesized for similar distributions of hydraulic microhabitat niches at each study reach 

even though they are located in differing hydrogeomorphic 

segments and fluvial geomorphic provinces. First, the study 

reaches were chosen prior to the development of the segment 

classification system and, therefore, were not chosen on the 

basis of providing physical representation of particular fluvial 

classes. Rather, reaches were primarily chosen on the basis 

of hydraulic uniformity to maximize discharge-measurement 

accuracy. Second and potentially related to the first, all reaches 

had similar channel top-widths with cross sections ranging 

in width from approximately 120 to 160 ft (fig. 17). This, in 

combination with similar discharges, produced the similarity in channel hydraulic-habitat distributions. Third, the Rock 

Barn study reach that by nominal expectation should differ 

from others because it is in a different fluvial geomorphic 

province, is located only 1.2 miles into the BB province and 

is similar in width and slope to Sunny Brook reach. Thus, 

although the reaches immediately upstream and downstream 

from Rock Barn are more characteristic of the BB province, 

the study reach itself has physical and hydraulic characteristics 

similar to those in the CRB province. To fully characterize 

the hydraulic microhabitat niche types, extents, and response 

to changing flow conditions in contrasting segments within 

and between provinces, a more elaborate field study would be 

necessary that focuses on particular hydrogeomorphic settings 

representing differing channel morphologic features. 

Summary

The Niobrara River is an ecologically and economically 

important resource in Nebraska. The Nebraska Department 

of Natural Resources’ recent designation of the hydraulically connected surface- and groundwater resources of the 

Niobrara River Basin as “fully appropriated” has emphasized 

the importance of understanding linkages between the physical 

and ecological dynamics of the Niobrara River so it can be 

sustainably managed. Numerous scientific studies have investigated the physical and hydraulic attributes of the Niobrara 

River along isolated reaches; however, none have placed these 

characteristics within a spectrum of fluvial settings at the 

basin scale. Such a study may provide the physical context for 

water-management strategies and serve as a framework for 

integrated physical and biological investigations. In cooperation with the Nebraska Game and Parks Commission, the 

U.S. Geological Survey investigated the hydrogeomorphic 

and hydraulic attributes of the Niobrara River in northern 

Nebraska. This report presents the results of an analysis of 

hydrogeomorphic segments and hydraulic microhabitats of the 

Niobrara River and its valley for the approximately 330-mi 

reach from Dunlap Diversion Dam to its confluence with the 

Missouri River. Two spatial scales were used to examine and 

quantify the hydrogeomorphic segments and hydraulic microhabitats of the Niobrara River: a basin scale and reach scale.

At the basin scale, digital spatial data and hydrologic data 

were analyzed to (1) test for differences between 36 previously 

determined longitudinal hydrogeomorphic segments; (2) quantitatively describe the hydrogeomorphic characteristics of the 

river and its valley; and (3) evaluate differences in hydraulic 

microhabitat over a range of flow regimes among three fluvial 

geomorphic provinces. 

The statistical analysis of hydrogeomorphic segments 

resulted in reclassification rates of 3 to 28 percent of the 

segments for the four descriptive geomorphic elements. The 

reassignment of classes by discriminant analysis resulted in 

a reduction from 36 to 25 total hydrogeomorphic segments 

because several adjoining segments shared the same ultimate 

class assignments among individual descriptive geomorphic elements. Virtually all of the segment mergers were in 

the CRB fluvial geomorphic province. Class reassignments 

and merger of hydrogeomorphic segments did not result 

in changes to the statistical modal class for any descriptive 

geomorphic element relative to those reported previously for 

the study area. The most frequent conditions (modal classes) 

among hydrogeomorphic segments are a width-restricted 

valley confinement condition, sinuous planview pattern, 

irregular channel width, and an alternate bar configuration. 

The class reassignments and segment mergers did, however, 

result in changes to the dominant classes per unit length of 

river, which are now the same as the modal classes.

The Niobrara River in the study area flows through a 

diversity of fluvial geomorphic settings in its traverse across 

northern Nebraska. The most distinct differences are among 

the settings found in three fluvial geomorphic provinces. In 

the Meandering Bottoms (MB) province, river discharge 

magnitudes are low, the median channel width varies from 

20 to 30 ft, but the valley is over 3,000 ft wide in places, and 

exerts little control on the channel-planview pattern. Within 

the Canyons and Restricted Bottoms (CRB) province, the river 

flows over a diversity of geologic formations, and the valley 

and river narrow and expand in approximate synchronicity, in 

some cases forming entrenched canyons, with steep channel 
Table 19. Hydraulic microhabitat distribution over a range of streamflow conditions for four study reaches in Niobrara National Scenic 

River, Nebraska.

[All references to stream discharge frequency are from the period of record of 1964 through 2007 for the Niobrara River near Sparks, Nebraska, streamflowgaging station (06461500); ft3

/s, cubic feet per second; meas., measurement; no., number; --, no data]

Discharge (ft3/s) or hydraulic 

microhabitat niche category4

(percentage of wetted channel 

width)

Upper decile1 Median quantile2 Lowest measurement3

Meas. no.5

Average

Meas. no.5

Average

Meas. no.5

Average 1 2 1 2 1 2

Niobrara River upstream of Crooked Creek near Sparks, Nebraska (425429100235301)

Discharge (ft3/s) -- -- -- 837 881 859 501 -- --

Shallow-slow -- -- -- 2.1 2.8 2.4 2.7 -- 2.7

Shallow-moderate -- -- -- .0 1.1 .6 7.0 -- 7.0

Shallow-swift -- -- -- .0 .0 .0 3.9 -- 3.9

Intermediate-slow -- -- -- .0 .0 .0 3.5 -- 3.5

Intermediate-moderate -- -- -- 6.7 4.9 5.8 3.9 -- 3.9

Intermediate-swift -- -- -- 41.4 20.9 31.2 78.9 -- 78.9

Deep-slow -- -- -- .0 .0 .0 .0 -- .0

Deep-moderate -- -- -- .0 1.5 .7 .0 -- .0

Deep-swift -- -- -- 49.8 68.8 59.3 .0 -- .0

Niobrara River at Sunny Brook Campground near Norden, Nebraska (425013100105801)

Discharge (ft3/s) 1,264 1,253 1,258 889 890 890 578 610 594

Shallow-slow 1.5 1.5 1.5 3.1 2.7 2.9 7.6 17.2 12.4

Shallow-moderate .0 .0 .0 .0 2.0 1.0 1.2 15.2 8.2

Shallow-swift .0 .0 .0 .0 11.9 6.0 .0 9.0 4.5

Intermediate-slow 2.7 .0 1.4 2.1 .0 1.1 8.6 .0 4.3

Intermediate-moderate .0 5.1 2.5 7.2 2.7 5.0 32.4 4.7 18.5

Intermediate-swift .0 42.2 21.1 63.4 46.6 55.0 6.6 28.1 17.3

Deep-slow 2.3 .0 1.1 .0 .0 .0 .0 .0 .0

Deep-moderate 13.2 1.7 7.5 2.0 .0 1.0 10.4 .0 5.2

Deep-swift 80.3 49.5 64.9 22.1 34.0 28.1 33.2 25.9 29.5

54 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

slopes, yet highly sinuous channel patterns. In the Braided 

Bottoms (BB) fluvial geomorphic province, the river primarily 

flows over Cretaceous Pierre Shale, the valley and channel are 

persistently wide, and the channel slope is generally uniform. 

The existence of vegetated islands and consequent multithread 

channel environments, indicated by a higher braided index, 

mostly coincided with reaches having gentler slopes and less 

unit stream power. Within the MB province, stream power is 

relatively low, but channel slope is persistently steeper than 

0.15 percent, and no islands were identified. Within the CRB 

province, channel slope is highly variable, braided index rarely 

exceeds 2, and islands are concentrated mainly in the reaches 

having mild slopes and lower unit stream power. In the BB 

province, braided index was, on average, higher than in the 

upstream provinces, but islands are mainly concentrated in the 

delta reach near the mouth at the Missouri River and in the 

reach immediately upstream from Spencer Dam.

Longitudinal hydrology curves indicate that the flow 

of the Niobrara River likely is dominated by groundwater 

as far downstream as Norden. Upstream from Norden, the 

mean daily, median, and 90th-percentile discharge curves 

have approximately the same longitudinal slope and have 

only minor differences in overall magnitude. Between the 

Snake River confluence and Norden, all three hydrologic 

curves begin to diverge, indicating the hydrologic regime 

becomes more variable as the river flows out of the CRB 

and into the BB province. Unit stream power values in the 

study area vary between 0 and almost 2 pounds per foot per 

second. Within the MB province, unit stream power steadily 

increases as the Niobrara gains discharge from groundwater 

inflow, and the channel slope steepens. The combination of 

steep slopes, a constrained channel width, and persistent flow 

within the CRB province results in unit stream power values 

that are between three and five times greater than those in less 
Discharge (ft3

/s) or hydraulic 

microhabitat niche category4

(percentage of wetted channel 

width)

Upper decile1 (percent) Median quantile2 (percent) Lowest measurement3 (percent)

Meas. no.5

Average

Meas. no.5

Average

Meas. no.5

Average 1 2 1 2 1 2

Niobrara River at Muleshoe Creek near Norden, Nebraska (424925100083201)

Discharge (ft3/s) 1,191 1,202 1,196 879 898 888 622 628 625

Shallow-slow .9 1.9 1.4 10.0 2.5 6.3 27.3 7.7 17.5

Shallow-moderate 12.5 .0 6.3 13.3 .0 6.6 4.0 .0 2.0

Shallow-swift .0 .0 .0 15.0 .0 7.5 6.9 .0 3.4

Intermediate-slow .6 .0 .3 .0 .0 .0 .0 2.8 1.4

Intermediate-moderate 2.5 3.1 2.8 1.6 13.1 7.3 5.3 23.4 14.3

Intermediate-swift 42.2 .0 21.1 25.6 17.3 21.5 19.4 5.3 12.4

Deep-slow .0 1.9 1.0 .0 1.9 1.0 .0 .0 .0

Deep-moderate .0 3.9 1.9 .0 .0 .0 2.6 3.8 3.2

Deep-swift 41.3 89.1 65.2 34.5 65.2 49.9 34.4 57.0 45.7

Niobrara River at Rock Barn Campground near Norden, Nebraska (424809100065001)

Discharge (ft3/s) 1,335 1,319 1,327 900 925 913 637 626 631

Shallow-slow 2.3 4.0 3.2 5.4 2.5 5.1 5.8 9.7 7.8

Shallow-moderate .0 .0 .0 .0 7.9 4.3 1.6 .0 .8

Shallow-swift .0 3.0 1.5 .0 .0 .0 .0 .0 .0

Intermediate-slow .0 .0 .0 .0 2.1 2.9 5.4 2.1 3.8

Intermediate-moderate 3.7 .0 1.9 11.2 2.7 4.4 3.9 8.5 6.2

Intermediate-swift 9.8 12.1 10.9 16.9 11.7 11.3 16.3 5.7 11.0

Deep-slow .0 .0 .0 .0 1.7 .8 .0 .0 .0

Deep-moderate 2.3 2.8 2.6 .0 1.7 5.0 12.4 4.2 8.3

Deep-swift 81.8 78.0 79.9 66.5 69.8 66.0 54.7 69.7 62.2

1

Refers to river discharges exceeded 10 percent of the time. 

2

Refers to river discharges within 25 percent of the median discharge.

3

Hydraulic microhabitat distribution at the lowest discharge measurements made during the study period.

4

Refers to the depth velocity combinations in table 6.

5

If available, two measurements were used to caclulate an average hydraulic microhabitat extent.

Table 19. Hydraulic microhabitat distribution over a range of streamflow conditions for four study reaches in Niobrara National Scenic 

River, Nebraska.—Continued

[All references to stream discharge frequency are from the period of record of 1964 through 2007 for the Niobrara River near Sparks, Nebraska, streamflowgaging station (06461500); ft3

/s, cubic feet per second; meas., measurement; no., number; --, no data]

Summary 55

confined segments with comparable or greater discharges. 

With the exception of hydrogeomorphic segment 3, which is 

affected by Spencer Dam, unit stream power values in the BB 

province are generally uniform. This consistency results from 

downstream increases in discharge that are offset by steady 

decreases in channel slope and steady increases in channel 

width downstream from Norden. Channel sinuosity values in 

the study area varied generally between 1 and 2.5, but with 

locally higher values measured in the MB province and at the 

entrenched bedrock meanders of hydrogeomorphic segment 18 

in the CRB province. Within hydrogeomorphic segment 24 

of the MB province, the Niobrara River has very little flow, 

and the channel has a two-phase meander pattern. Within 

hydrogeomorphic segment 18, the river has a highly sinuous 

pattern that is entrenched in bedrock, and the presence of 

rincons (abandoned bedrock meander bends) and the bedrock 

bed indicate that the river is cutting down through the bedrock 

at a relatively rapid rate. Channel sinuosity is lowest in the 

long, generally straight, braided reaches of the BB province.

The differences in channel morphology and hydraulic 

geometries between fluvial geomorphic provinces are evident 

in the types, relative abundance, and response of hydraulic microhabitat niches to changing discharges. The four 

gaging stations chosen for hydraulic microhabitat analysis 
Figure 22. Distribution of available hydraulic microhabitats within four study reaches of the Niobrara 

National Scenic River, Nebraska, for a range of discharges, including (A) lowest discharges measured; 

(B) median-quantile discharge; and (C) upper-decile discharge.

0

10

20

30

40

50

60

70

80

90

PERCENTAGE OF WETTED WIDTH

0

10

20

30

40

50

60

70

80

90

PERCENTAGE OF WETTED WIDTH

0

10

20

30

40

50

60

70

80

90

PERCENTAGE OF WETTED WIDTH

Shallow-slow

Shallow-moderate

Shallow-swift

Intermediate-slow

Intermediate-moderate

Intermediate-swift

Deep-slow

 Deep-moderate

Deep-swift

HYDRAULIC MICROHABITAT NICHE CATEGORY

Niobrara River at Sunny Brook Campground 

(425013100105801)

Niobrara River upstream of Crooked Creek 

(425429100235301)

Niobrara River at Muleshoe Creek (424925100083201)

Niobrara River at Rock Barn Campground 

(434809100065001)

EXPLANATION

A

C

B

56 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska
Summary 57

are distributed among three different fluvial geomorphic 

provinces: Hay Springs (MB), Cody (CRB), Sparks (CRB), 

and Verdel (BB). The hydraulic microhabitat availability was 

calculated as the average for two discharges (when available) within three discharge-duration exceedance categories—lower-decile, median-quantile, and upper-decile. At Hay 

Springs, the smaller channel and lower discharges resulted in 

the dominance of shallow and intermediate-depth hydraulic 

environments with the vast majority of hydraulic microhabitat restricted to shallow categories even during upper-decile 

discharges. At Cody and Sparks, intermediate-depth hydraulic 

conditions, particularly intermediate-swift, dominate at both 

gages over all analyzed ranges of discharge; as discharge 

increases, intermediate-depth hydraulic conditions are mainly 

exchanged for deeper hydraulic conditions. Hydraulic microhabitat conditions are most diverse in the wide, braided reach 

of Verdel, with most hydraulic microhabitat niche categories present over the entire range of discharges analyzed. 

However, as discharge increased to upper-decile flow conditions, hydraulic microhabitats were more evenly distributed, 

with no hydraulic habitat niche category covering more than 

25 percent of the total channel width. The calculated differences in hydraulic microhabitat distributions, abundance, 

and adjustments between streamflow-gaging stations are the 

result of differences in physical structure of the channel and 

consequent channel hydraulic geometry. Previous reports 

indicated that the channel of the Niobrara River at the Hay 

Springs, Cody, and Sparks streamflow-gaging stations adjusted 

to increases in discharge mainly through changes in velocity 

and depth. These adjustment mechanisms are evident in this 

hydraulic microhabitat analysis because shallower and slower 

hydraulic conditions are mainly exchanged for deeper and 

faster conditions with increasing discharge at these sites. The 

greater role of width-based adjustments at Verdel is reflected 

in the increase in abundance of intermediate- and shallowwater hydraulic conditions with increasing discharge.

At the reach scale, field measurements made in water 

years 2008 and 2009 in four study reaches within the Scenic 

Reach were used to (1) characterize the elevation and 

geomorphic processes associated with fluvial landforms, 

(2) build hydraulic geometry relations, (3) examine flow 

hydraulics over a range of discharges, and (4) examine the 

types and responses of hydraulic microhabitats to a range of 

flow magnitudes. Four landform groups were identified and 

named in order of increasing elevation as the low flood plains, 

intermediate flood plains, low terraces, and high terraces. The 

terraces were poorly characterized because the surveys did not 

extend across the full width of the alluvial valley bottom. The 

two lowest fluvial landforms are likely active in the modern 

hydroclimatic regime. The low flood plain is inundated in 

most years by the annual peak flood and may be “genetic,” in 

the sense that it is constructed of sediments transported by the 

annual spring flood regime. The discontinuous nature of the 

low flood plain is likely the result of occasional destruction or 

erosion by the higher stages of ice-jam-induced floods. The 

intermediate flood plains were identified in all study reaches 

and are between 2.4 and 6.7 ft above the stage of the median 

discharge, indicating they are not inundated by spring storm 

runoff processes. However, the higher end of the stage range 

of the intermediate flood plain closely corresponds to the 

range of local ice-jam elevations surveyed in the study reaches 

during water year 2008. Thus, the intermediate floodplain may 

be active on a relatively frequent basis from flooding caused 

by ice jamming and associated backwater flooding.

Sediment samples obtained in the study reaches indicate 

that the primary bed material in the active channel ranged in 

size from coarse silt (0.031 to 0.0625 mm) to coarse sand (0.5 

to 1.0 mm), and the majority of grain sizes ranged between 

about 0.2 and 0.5 mm. Grain-size distributions from samples 

also indicate that the bed of the Niobrara River coarsens and 

has increasing grain-size variability in the downstream direction, a pattern that likely results from inputs of coarser sediments at tributary junctions, bank erosion, and landslides or 

other direct hillslope sediment delivery to the channel.

Values of at-a-station hydraulic geometry exponents 

indicate that the Niobrara River in the study reaches adjusts its 

geometry to changing discharges primarily through increases 

in flow depth and velocity. The Crooked study reach had 

too few measurements, over a relatively narrow range of 

discharges, to develop statistically meaningful hydraulicgeometry relations. Width (b) exponents at five of the six 

cross sections were less than 0.06, and four of the statistical 

models describing width adjustments lack significance at 

the 90-percent confidence level. Depth (f) and velocity (m) 

exponents range in value from 0.17 to 0.60 and 0.29 to 0.84, 

respectively. All fitted depth- and velocity-adjustment statistical models were significant at the 90-percent confidence level. 

The hydraulic geometry relations indicate that the Niobrara 

River at most locations in the study reaches does not typically accommodate flow increases through changes in channel 

width. Exponents at one cross section in the Muleshoe study 

reach ranged from 0.29 to 0.37 indicating that, at least locally, 

changes in width were also an important channel adjustment 

mechanism. The more complex hydraulic geometry relations at the one cross section in the Muleshoe study reach 

are similar to those described further downstream in the BB 

province, and likely are representative of reaches, or short 

sections of reaches, in the CRB province where the channel 

has localized morphologic complexity associated with isolated 

mid-channel deposition, or variations in bedrock topography.

Hydraulic behavior over the range of flows measured was 

not consistent among all reaches, but two general modes can 

be inferred from the calculated parameters at Sunny Brook, 

Muleshoe, and Rock Barn. At the Sunny Brook and Muleshoe study reaches, average boundary-shear stress remained 

approximately constant for discharges below 900 ft3/s. Above 

900 ft3/s, average boundary shear stress increased by approximately 20 to 30 percent. At the Rock Barn study reach, shear 

stress showed little to no change in the rate of increase with 

increasing discharge. Hydraulic resistance was observed to 

decrease with increasing discharge below 900 ft3/s at the 

Sunny Brook, Muleshoe, and Rock Barn study reaches. Above 
58 Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska

900 ft3/s, resistance increased or stabilized at the Sunny Brook 

and Muleshoe reaches but continued to decrease at the Rock 

Barn reach. 

The two-mode behavior of shear stress and resistance 

at the Sunny Brook and Muleshoe reaches indicates that the 

bed configuration may have changed at a discharge above 

900 ft3

/s. When plotted over experimental bedform classification diagrams, the values of unit stream power for the 

range of median grain-size diameters sampled indicate that 

the Muleshoe and Sunny Brook reaches were on the margin 

or entirely within the transition to upper flow-regime (plane 

bed/antidune) bed phases. The Rock Barn study reach did not 

exhibit the same two-mode hydraulic behavior observed at the 

Sunny Brook and Muleshoe reaches. It was hypothesized that 

the difference in hydraulic behavior was related to a combination of physical differences in the Rock Barn reach, such as 

lower unit stream power, coarser, less well-sorted bed sediment, and the presence of a channel expansion zone downstream. The coincident increase in boundary shear stress above 

900 ft3

/s observed at the Sunny Brook and Muleshoe study 

reaches represents a potential hydraulic threshold above which 

bedload transport rates were likely to increase markedly. 

No consistent bed-adjustment pattern (scour or fill) was 

identified in the study reaches over the range of flows or over 

the measurement season. However, as expected, the reaches 

with substantial coverage of the bed by fine sediment—

Sunny Brook, Muleshoe, and Rock Barn—exhibited greater 

bed elevation variability than did the reach with a bedrockdominated bed, Crooked reach.

Analysis of hydraulic microhabitats over the range 

of discharges measured at the study reaches indicates that 

some percentage of most habitat niche categories was available for at least one discharge condition, but the majority of 

hydraulic habitat available was within the intermediate-swift 

and deep-swift habitat niche categories. Deep-swift conditions dominated nearly all study reaches under all measured 

discharge conditions. Slight differences in habitat distributions were observed between the study reaches with substantial coverage of the bed by fine sediment—Sunny Brook, 

Muleshoe, and Rock Barn— and the bedrock-dominated 

reach, Crooked. At the Crooked reach, the intermediate-swift 

habitat category dominated the distribution during the lowest 

measured discharge, and the deep-swift habitat category dominated during the median-quantile discharge. With the exception of the Sunny Brook reach, the deep-swift habitat niche 

dominated the distribution for all ranges of discharges in the 

reaches with substantial amounts of sand on the bed.

Although the four study reaches occupy three different 

hydrogeomorphic segments, the types, relative abundance, 

and response of hydraulic microhabitat niche distributions to 

changing discharge conditions generally were similar among 

all reaches. The types of niches and response of hydraulic 

habitat distributions to changing discharge conditions in these 

four reaches were most similar to those calculated for the 

Sparks gaging station, where the primary habitat adjustment 

was an increase in flow depth. This similarity in response was 

not unexpected because three of the four reaches are in the 

CRB fluvial geomorphic province and most cross sections 

have similar at-a-station hydraulic geometries. As compared to 

the Sparks gage, the study reaches all had greater abundance 

of the deeper habitat categories over the range of discharge 

frequencies analyzed. At the Rock Barn reach, which is in 

the BB fluvial geomorphic province, the response of hydraulic microhabitat distribution was virtually identical to those 

of the other reaches. Several reasons are hypothesized for 

similar distributions of hydraulic microhabitat niches at each 

study reach. To fully characterize the hydraulic microhabitat 

niche types, extents, and response to changing flow conditions in contrasting segments within and between provinces, 

a more elaborate field study would be necessary that focuses 

on particular hydrogeomorphic settings representing differing 

channel morphologic features. 

Acknowledgments

We thank Larry Hutchinson, Richard Holland, and Steven 

Schainost of the Nebraska Game and Parks Commission 

for their thoughtful reviews and data-collection assistance 

throughout this project; the National Park Service for their 

assistance with field measurements; the Nature Conservancy, 

U.S. Fish and Wildlife Service, and the landowners at Sunny 

Brook Camp and Rock Barn Outfitters for the gracious access 

granted to their property. Reviews and suggestions by Robert 

Meade and John Stamm greatly improved this report. Daniel 

Ginting provided valuable statistical advice.

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Back cover.  Top: section of Niobrara River showing example of braided bottoms fluvial geomorphic province.

  Photograph by Bill Hansen, National Park Service.

Center: section of Niobrara River showing example of canyons and restricted bottoms fluvial geomorphic province.

  Photograph by Ron Zelt, U.S. Geological Survey.

Bottom: section of Niobrara River showing example of meandering bottoms fluvial geomorphic province.

  Photograph by Jason Alexander, U.S. Geological Survey.
Alexander and others—Hydrogeomorphic Segments and Hydraulic Microhabitats of the Niobrara River, Nebraska—Scientific Investigations Report 2010–5141

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