Physical Stream Habitat 

Dynamics in Lower Bear Creek, 

Northern Arkansas 

Biological Science Report 

USGS/BRD/BSR–2003-0002 

U.S. Department of the Interior Prepared in cooperation with the National Park Service, Water 

U.S. Geological Survey Resources Division and the Buffalo National River 
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Cover photo: Riffle in the Crane Bottom study area, Lower Bear Creek. 

NOTE: The mention of trade names are for information purposes only and are not an endorsement of the U.S. 

Geological Survey or the Federal Government. 
Physical Stream Habitat Dynamics 

in Lower Bear Creek, Northern 

Arkansas 

Biological Science Report 

USGS/BRD/BSR-2003—0002 

July 2003 

By Joanna M. Reuter1, Robert B. Jacobson1, Caroline M. Elliott2 

Prepared in coperation with the National Park Service, Water Resources Division and the Buffalo 

National River. 

U.S. Geological Survey, Biological Resources Division, Columbia Environmental Research Center, 4200 New Haven Road, Columbia, MO 65201 2

AScI Corporation, Columbia Environmental Research Center, 4200 New Haven Road, Columbia, MO 65201 

1
Contents 

Page 

Abstract...........................................................................................................................................................................i

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

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

Acknowledgments..........................................................................................................................................................2

Background....................................................................................................................................................................3

Stream Geomorphology and Physical Habitat........................................................................................................3

Geomorphic Context of Ozarks Streams................................................................................................................5

Physical Setting of Bear Creek and Crane Bottom................................................................................................6

Approach.......................................................................................................................................................................9

Hydrology of Bear Creek at Crane Bottom.................................................................................................................11

Methods.................................................................................................................................................................11

Flow duration........................................................................................................................................................12

Peak flows.............................................................................................................................................................14

Backwater..............................................................................................................................................................14

Geomorphic Dynamics and Habitat.............................................................................................................................20

Methods.................................................................................................................................................................20

Results...................................................................................................................................................................24

Bed Particle Size Distributions......................................................................................................................24

Geomorphic Change at Cross Sections.........................................................................................................24

Scour and Fill Measured with Scour Chains.................................................................................................31

Sediment Transport Measured with Painted Rocks.......................................................................................31

Hydrologic Dynamics and Habitat...............................................................................................................................31

Methods.................................................................................................................................................................31

Input Data and Parameters.............................................................................................................................33

Calibration and Validation.............................................................................................................................35

Habitat Classification.....................................................................................................................................37

Hydrodynamic Habitat Modeling Results............................................................................................................37

Streambed Mobility......................................................................................................................................................39

Methods.................................................................................................................................................................39

Results...................................................................................................................................................................39

Discussion: Sources of Physical Stream Habitat Variability......................................................................................44

Summary and Conclusions...........................................................................................................................................45

References Cited..........................................................................................................................................................47

Appendix 1 - Cross section Monitoring Data..............................................................................................................51

Appendix 2 - Hydraulic Model Maps..........................................................................................................................83

ii 
Tables 

Page

Table 1. Information on streamgaging station data used in this report..................................................................14

Table 2. Peak discharges, exceedance probabilities, and approximate recurrence intervals for four floods

Table 5. Total annual and net annual geomorphic change at Bear Creek and Crane Bottom compared with

.........16

Table 3. Locations and descriptions of monumented cross sections used in this study.........................................21

Table 4. Volumetric change at Crane Bottom site measured from cross section resurveys...................................28

seven other sites in the Ozarks..................................................................................................................29

Table 6. Information on scour chains installed in September 2001.......................................................................32

Table 7. Modeled discharges, habitat areas, flow-duration, and flood-frequency data for Crane Bottom............34

Figures

Figure 1. Location of Bear Creek and Buffalo River basins....................................................................................1

Figure 2. Location of the Crane Bottom study reach in the Bear Creek drainage basin, and locations of

U.S. Geological Survey streamflow gaging stations on the Buffalo River and Bear Creek.......................2

Figure 3. Typical arrangement of physical stream habitat units in Ozark Streams..................................................3

Figure 4. General physical stream habitat unit (meso-scale) classification systems for Ozarks streams.................4

Figure 5. Maps of the Bear Creek drainage basin.....................................................................................................7

Figure 6. Detailed map of the Crane Bottom study reach, boundaries of the Buffalo National River,

and locations of the stage gages operated at Crane Bottom......................................................................8

Figure 7. Detailed map of Crane Bottom study reach showing cross section locations and 

physiographic details..................................................................................................................................8

Figure 8. Photographs of vegetation at Crane Bottom..............................................................................................9

Figure 9. Climatological data from Marshall, Arkansas.........................................................................................10

Figure 10. Hydrologic record and survey dates, Bear Creek near Silver Hill, Arkansas.........................................10

Figure 11. Locations of streamflow gaging stations used in hydrologic analysis....................................................12

Figure 12. Flow duration data for Bear Creek at Crane Bottom and reference streamgages...................................13

Figure 13. Frequency hydrographs for streamgaging stations..................................................................................15

Figure 14. Flood frequency analyses showing annual exceedance probabilities......................................................17

Figure 15. Hydrographs showing stages at Buffalo River near St. Joe, Arkansas and Bear Creek, near Silver

Hill Arkansas, and backwater effects at Crane Bottom...........................................................................18

Figure 16. Discharge, stage, and water-surface slopes at Crane Bottom illustrating backwater conditions............19

Figure 17. Map of study reach at Crane Bottom showing locations of cross sections, scour chains and 

painted rock experiment...........................................................................................................................23

Figure 18. Schematic diagram showing how scour chains are used to document erosion and redeposition...........24

Figure 19. Particle-size data from pebble counts, Bear Creek at Crane Bottom......................................................25

Figure 20. Net erosion and deposition by cross section for three survey intervals and for entire monitoring

period, Bear Creek at Crane Bottom.......................................................................................................27

Figure 21. Change in cross section area for two survey intervals compared to February 2002 cross 

section area...............................................................................................................................................30

Figure 22. Photographs of rhizomes of water willow at surface of stable gravel bar..............................................33

Figure 23. Model input data grids for Crane Bottom................................................................................................35

Figure 24. Finite element mesh used for 2-dimensional hydraulic modeling at Crane Bottom reach 

of Bear Creek...........................................................................................................................................36

Figure 25. Regression relation between Bear Creek discharge measured by U.S. Geological Survey near Silver

Hill, Arkansas and discharge measured by National Park Service at Crane Bottom study reach..........36

Figure 26A.Water-surface elevation data plotted along study reach showing modeled, calibration, and 

validation water-surface elevations..........................................................................................................37

Figure 26B.Water-surface elevation data plotted along study reach, showing modeled, calibration, and

validation water-surface elevations..........................................................................................................38

Figure 27. Scheme used for classifying model output into habitat units.................................................................39

Figure 28. Relations between discharge and area of habitat units, and Shannon-Wiener diversity index...............40

Figure 29. Time series of modeled habitat areas, diversity index, and discharge at Crane Bottom.........................42

Figure 30. Maps of relative ranges of boundary shear stresses showing shift of maximum shear stress

from riffles to pools.................................................................................................................................43

Figure 31. Relations between discharge and calculated percent of bed entrained, and discharge and 

magnitude x frequency product................................................................................................................44

iii 
Abstract


We evaluated the roles of geomorphic and hydrologic dynamics in determining physical stream habitat in Bear 

Creek, a stream with a 239 km2 drainage basin in the Ozark Plateaus (Ozarks) in northern Arkansas. During a relatively wet 12-month monitoring period, the geomorphology of Bear Creek was altered by a series of floods, 

including at least four floods with peak discharges exceeding a 1-year recurrence interval and another flood with 

an estimated 2- to 4-year recurrence interval. These floods resulted in a net erosion of sediment from the study 

reach at Crane Bottom at rates far in excess of other sites previously studied in the Ozarks. The riffle-pool framework of the study reach at Crane Bottom was not substantially altered by these floods, but volumes of habitat in 

riffles and pools changed. The 2- to 4-year flood scoured gravel from pools and deposited it in riffles, increasing 

the diversity of available stream habitat. In contrast, the smaller floods eroded gravel from the riffles and deposited it in pools, possibly flushing fine sediment from the substrate but also decreasing habitat diversity. 

Channel geometry measured at the beginning of the study was used to develop a two-dimensional, finite-element hydraulic model to assess how habitat varies with hydrologic dynamics. Distributions of depth and velocity 

simulated over the range of discharges observed during the study (0.1 to 556 cubic meters per second, cms) were 

classified into habitat units based on limiting depths and Froude number criteria. The results indicate that the areas 

of habitats are especially sensitive to discharge at low to medium flows. Races (areas of swift, relatively deep 

water downstream from riffles) disappear completely at the lowest flows, and riffles (areas of swift, relatively shallow water) contract substantially in area. Pools also contract in area during low flow, but deep scours associated 

with bedrock outcrops sustain some pool area even at the lowest modeled flows. Modeled boundary shear stresses 

were used to evaluate which flows are responsible for the most mobilization of the bed, and therefore, habitat 

maintenance. Evaluation of the magnitude and frequency of bed-sediment entrainment shows that most of habitat 

maintenance results from flows that occur on average about 4 to 7 days a year. 

Our analysis documents the geomorphic and hydrologic dynamics that form and maintain habitats in a 

warmwater stream in the Ozarks. The range of flows that occurs on this stream can be partitioned into those that 

sustain habitat by providing the combinations of depth and velocity that stream organisms live with most of the 

time, and those flows that surpass sediment entrainment thresholds, alter stream geomorphology, and therefore 

maintain habitat. The quantitative relations show sensitivity of habitats to flow variation, but do not address how 

flow may vary in the future, or the extent to which stream geomorphology may be affected by variations in sediment supply. 

Keywords: aquatic habitat, geomorphology, hydrology, Ozarks, Arkansas 

Suggested Citation: 

Reuter, J.M.; Jacobson, R.B., and Elliott, C.M., 2003, Physical Stream Habitat Dynamics in Lower Bear Creek, 

Northern Arkansas, USGS/BRD/BSR–2003-0002, 49 p. 

iv 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 1 

Introduction 

Like many streams, Bear Creek in northern 

Arkansas (fig. 1) is subject to competing demands for 

its available discharge. Changes in water use, land 

use, or climate would have the potential to alter the 

quantity and timing of discharge in Bear Creek. A 

general question in many streams is how changes in 

hydrology can affect the processes that create, maintain, and sustain physical stream habitat, the template 

upon which biologic communities are built (Plafkin 

and others, 1989). 

Streams of the Ozark Plateaus (Ozarks; fig. 1) 

drain rural landscapes dominated by forest and agricultural lands, with scattered, small, urbanized areas. 

Because of generally low land-use stress and substantial contributions of spring flow from karst aquifers, 

Ozarks streams have generally good water quality. 

Nutrients and bacteria are elevated in agricultural 

drainage basins but they rarely exceed drinking water 

standards (Petersen and others, 1998). Probably 

because of the generally high water quality and low 

levels of habitat disturbance, Ozarks streams maintain 

high biological diversity, hosting approximately 175 

fish species (Petersen, 1998). Thirty species of fish 

have been identified in Bear Creek (Petersen, 2002, 

pers. comm.; Magoulick, 2002, pers. com). 

Bear Creek is a tributary to the Buffalo River, a 

National River managed by the National Park Service. 

Preservation of the aquatic ecosystem of the Buffalo 

River is a substantial challenge for the National Park 

Service because it owns only a corridor along the 

river, amounting to 11 percent of the Buffalo River 

drainage area. Hence, the National Park Service has 

an interest in understanding how changes in water and 

watershed management affect physical stream habitats, and in understanding biological responses to 

habitat change. 

Figure 1. Location of Bear Creek and Buffalo River basins. 
Acknowledgments

2 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

In 1997, a site in the upper Bear Creek drainage 

basin (fig. 2) was proposed for construction of a 

water-supply reservoir. A dam at the proposed location would impound approximately 11 per cent of the 

drainage area of Bear Creek. Assessment of the 

potential effects of such an impoundment requires a 

quantitative understanding of how flow changes 

would affect the physical habitat template, and the 

stream ecosystem. 

Purpose and Scope 

The purpose of this report is to document and 

analyze sensitivity of physical stream habitat on Bear 

Creek to geomorphic and hydrologic dynamics. The 

scope includes two components: evaluation of habitat 

sensitivity to erosion and deposition events and 

assessment of habitat sensitivity to hydrologic variation. 

The first component was addressed through monitoring of geomorphic change over a 12-month period, 

evaluation of channel scour, a painted rock experiment, and modeling of bed-material entrainment. 

Although measurement of geomorphic change over a 

short time period cannot address the possible longterm effects of erosion and deposition, it can provide 

useful estimates of rates and observations of processes. In addition, measurements and modeling are used 

to estimate threshold conditions for bed-material 

entrainment to indicate which flows are necessary to 

maintain physical habitat. 

The second component was addressed through 

hydraulic modeling of habitats resulting from a range 

of discharges while keeping channel morphology constant. The approach is typical of instream flow studies wherein a two-dimensional (depth-averaged) 

hydraulic model is used to simulate depth and velocity 

distributions with discharge. The modeled results are 

then summarized in terms of hydraulic habitats as 

defined by Panfil and Jacobson (1999). A three-year 

record of flows on Bear Creek is used to evaluate 

flow exceedances and flood frequencies associated 

with modeled discharges. 

Habitat availability and geomorphic dynamics in 

Bear Creek ultimately need to be addressed over time 

frames longer than the available three-year hydrologic 

record. Evaluation of how habitats in Bear Creek 

might respond to hydrologic alterations within the 

Bear Creek drainage basin will require either longterm hydrologic records or results of basin-scale 

hydrologic simulation models. In addition, changes in 

sediment supply as a result of contemporary land-use 

practices, or ongoing adjustment of the drainage basin 

to historical land uses, could substantially alter geomorphology of reaches of Bear Creek in the future. 

Figure 2. Location of the Crane Bottom study reach in the Bear 

Creek drainage basin, and locations of U.S. Geological Survey 

streamflow gaging stations on the Buffalo River and Bear Creek. 

We acknowledge the Buffalo National River and 

the Water Resources Division of the National Park 

Service for monetary and logistical support. We are 

especially grateful to Park Service employees David 

Mott, Jessica Caplinger, Faron Usrey, John Petty, and 

Greg Comer for help in field work. Harold Johnson 

and Gary D’Urso (U.S. Geological Survey) contributed to field surveys. Terry Waddle (U.S. 

Geological Survey) and Peter Steffler (University of 

Alberta) provided guidance in hydraulic modeling. 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 3 

Background 

Streams respond to changes in their drainage 

basins in inherently complex ways (Jacobson and others, 2001). The interactions of hydrology, sediment 

supply, sediment routing, water quality, and thresholds 

of stream instability typically result in only broadly 

predictable trends in physical habitats. In addition to 

the uncertainties of stream-habitat responses, biological responses are subject to interactions among food 

webs, population dynamics, predator/prey relations, 

and competition. Assessment and prediction of stream 

ecological responses depend fundamentally on an 

understanding of the physical and biological context 

of the stream system. 

Stream geomorphology and physical habitat 

Habitat is defined, in general, as the three-dimensional structure in which organisms live (Gordon and 

others, 1992). Stream habitat typically is defined to 

include physical and chemical attributes of the volume 

occupied by specific stream or riparian organisms. 

Physical stream habitat is used here to describe depth, 

velocity, and substrate available to all stream organisms. Physical stream habitat results from interaction 

of water with the morphology of the stream channel 

and adjacent flood plains. Stream hydrology determines how much water is in the channel and when. 

Stream morphology determines how the water is distributed across the channel, and therefore the spatial 

distribution of depth, velocity, and substrate. 

Physical stream habitat characteristics vary 

through time because of changes in river discharge 

and because erosion and deposition alter the morphology of the river. Stream habitat dynamics can be 

divided into two general time domains: those associated solely with hydrologic variation (hydrologic 

dynamics and habitat-sustaining flows) and those 

associated with erosional and depositional changes to 

topography (geomorphic dynamics and habitat formation and maintenance flows). These two domains 

overlap at discharges where significant sediment transport takes place. 

Although physical stream habitats are highly 

dynamic, low-flow classification systems typically are 

used to organize data and facilitate communication. 

The hydraulic habitat (meso-scale habitat) classification system used in this report (figs. 3, 4) is modified 

from McKenney (1997). This hierarchical classification system was developed particularly to optimize 

description of low-gradient, cobble-gravel streams 

typical of the Ozarks. The highest level of the classification separates units based on whether they are in 

the main flow (longitudinal units) or at the margins. 

Figure 3. Typical arrangement of physical stream habitat units in Ozarks streams, after McKenney (1997), Panfil and Jacobson 

(2001). A. Planview showing longitudinal and marginal habitats. B. Longitudinal view along thalweg. See figure 4 for additional descriptions. 
4 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 4. General physical stream habitat unit (meso-scale) classification system for Ozarks streams (from McKenney 1997). Not all 

units are present at Crane Bottom. 

The system further subsets according to gradient, persistence (sensitivity to discharge), and morphology 

(fig. 4). 

Ultimately, most management, social, and ecological interests focus on the biological endpoints of 

altered ecosystems, rather than the physical habitat 

template. Although this report focuses on physical 

stream habitat, the fundamental role of physical 

processes in structuring stream ecosystems allows 

some ecological inference. 

At a very basic level, ecologists generally accept 

that habitat diversity is associated with biological 

diversity because a greater range of physical environments potentially allows more species to thrive in the 

stream channel (Gorman and Karr, 1978; Schlosser, 

1987; Jeffries and Mills, 1990). Physically, greater 

diversity of elevations within a stream reach assures 

that during low-flow periods, more wetted area will be 

available. At high flows, greater physical diversity 

will create refuge areas for fish to escape high velocities and shear stresses. Therefore, physical processes 

that homogenize habitat by filling pools or eroding riffles, for example, would be considered to diminish 

habitat diversity. 

More specifically, physical habitats of Ozarks 

streams have been shown to be highly associated with 

specific ecological processes, individual species, or 

assemblages of species. For example, net community 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 5 

productivity has been found to be significantly higher 

in riffles and glides than in pools (Whitledge and 

Rabeni, 2000). Peterson and Rabeni (2001) found that 

long-ear sunfish (Lepomis megalotis), smallmouth 

bass (Micropterus dolomieu), and shadow bass 

(Ambloplites ariommus) were associated with pools in 

Ozarks streams, whereas species such as rainbow 

darter (Etheostoma caeruleum) and Ozark minnow 

(Notropis nubilus) were associated with higher velocities in riffles and races. These authors also found that 

habitat affinities varied by season and size of streams. 

Similarly, Doisy and Rabeni (2001) documented that 

benthic invertebrate community composition, diversity, and functional groups in an Ozarks stream correlated with basic hydraulic descriptors, including Froude 

number (a dimensionless hydraulic variable), indicating a strong physical habitat control on benthic communities. 

While fish species can swim to take advantage of 

habitats that move from place to place because of erosion and deposition, benthic invertebrates in general 

are more dependent on stability of the substrate that 

comprises their habitat. Some organisms, like mussels, require relatively stable substrate over periods of 

seasons to decades, whereas many benthic insects 

depend on stability for a year or less (Barbour and 

others, 1999). For maintenance of habitats for the less 

mobile benthic invertebrates, the stream should contain patches of substrate that are subject to neither 

deposition nor erosion. Absolute stability, however, 

usually is not considered desirable since accumulation 

of fine sediment may diminish the volume and quality 

of benthic habitat. Periodically, flows capable of 

entraining the bed are needed to flush fine sediments 

and rejuvenate the substrate (Milhous, 1982). 

Physical habitat also varies over time as hydrologic variations influence environmental variables 

such as temperature, dissolved oxygen, and turbidity. 

Life stages of aquatic species may be synchronized to 

periods of high or low flow because of the associated 

environmental variables (Poff and others, 1997). For 

example, smallmouth bass are known to spawn only 

when temperatures reach 16-19 O

C (Scott and 

Crossman, 1973); therefore, they need flow over gravel substrate at that temperature for successful reproduction. Because life histories are related to flow, 

temperature, and habitat in complex ways, a simplified approach to assessing the effects of flow alteration is to compare the altered hydrograph to a nonregulated hydrograph (Richter and others, 1997) rather 

than to consider individual species requirements. In 

limiting cases the effects of flow variation can be 

quite clear. For example, flow alteration that would 

dry up perennial riffles and pools would have significant effects on the stream ecosystem. 

Geomorphic context of Ozarks streams 

Previous studies on streams of the Ozark Plateaus 

have documented that Ozarks streams have always 

carried a large volume of gravel-cobble size bed load 

(Jacobson and Pugh, 1992; Jacobson, in press). 

Stratigraphic and historical studies have also documented that Ozarks streams have responded to historical land-use disturbances by releasing large quantities 

of excess bed load that are now in transit through 

stream systems (Jacobson, 1995; Jacobson and Primm, 

1997; Jacobson and Gran, 1999). Waves of bed-material sediment with wavelengths measured in tens of 

meters to kilometers are a persistent, slowly traveling 

source of geomorphic disturbance. Rates and processes of geomorphic dynamics, and implications for 

stream habitats, have been addressed in a related 

series of studies (McKenney and others, 1995; 

McKenney and Jacobson, 1996; McKenney, 1997; 

Jacobson and Pugh, 1997; and McKenney, 2001). 

These studies refined a classification of Ozarks stream 

habitats and documented spatial variability in geomorphic processes of habitat alteration. In particular, 

these authors determined: 1) lateral erosion processes 

on Ozarks streams are concentrated in discrete disturbance reaches separated by stable reaches; 2) long, 

straight stable reaches are efficient transporters of bed 

load, whereas bed load is deposited and episodically 

removed from disturbance reaches; 3) vertical, transient aggradation in pools proceeds from downstream 

to upstream, resulting in alteration of pools into 

glides; 4) deposition of excess bed load in wave-like 

forms can create transient riffles, resulting in high 

variability in riffle spacing. 

The sensitivity of habitats to hydrologic variation 

was assessed by Panfil and Jacobson (1999) on Jacks 

Fork, Missouri. This study implemented a two-dimensional hydraulic model for a 500 m reach of Jacks 

Fork where the drainage area upstream of the reach 

was 422 km2

. The authors assessed potential biologic 

importance of modeled flows by defining habitat 

fields (combinations of depth and velocity) based on 

depth criteria and Froude number. 

F = v

g * d

where, F = Froude number, v = depth averaged water 

velocity, g = gravitational acceleration constant, and d 

= water depth. 

By modeling a range of discharges that did not 

involve significant sediment transport, Panfil and 

Jacobson (1999) determined that areas of races (concentrated flow downstream of riffles) and riffles were 

most sensitive to changing discharge; both habitats 

increased substantially in area with increasing 
6 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

discharge. Pool area at their study site was relatively 

insensitive to hydrologic variation because bedrock 

bluffs created favorable hydraulic conditions for deep 

scour, resulting in areas of deep, slow flow that persisted over a wide range of discharges. 

A series of additional studies have addressed 

Ozarks physical stream habitats at the scale of 

drainage basins. These are associative studies that 

explore the synoptic spatial relations between stream 

habitats and characteristics of their drainage basins. 

In an associative study of stream habitats of 41 sites in 

the Ozarks, Femmer (1997) found that stream morphology variation was associated mostly with physiography and drainage-basin size; land-use factors 

were more important at the scale of individual reaches 

where riparian land use in the stream corridor controlled shading and seemed to be related to bank erosion. Petersen (1998) worked with a subset of the 

same habitat data plus fish community samples from 

the reaches, and concluded that fish communities were 

influenced primarily by elevated nutrients and greater 

canopy openness (resulting in more sunlight and periphyton growth) in agricultural drainage basins compared to forested drainage basins. Petersen (1998) 

also noted some relations between fish communities 

and geomorphic factors including channel sinuosity, 

channel width, channel depth, width:depth ratio and 

drainage area. Panfil and Jacobson (2001) used a 

refined habitat-assessment protocol to explore relations between drainage-basin conditions and stream 

morphology in 19 tributary streams to the Buffalo 

River in Arkansas and 24 tributaries to the Current 

River, Missouri. They concluded that physiography 

and drainage-basin size were dominant influences on 

physical stream habitat; however, when subset by river 

and physiographic unit, subtle land-use associations 

could be detected. Two confounding factors in associative studies are: a) that transport of sediment 

through drainage basins requires years to hundreds of 

years and so physical stream habitats have lagged 

responses to land-use effects (Jacobson and others, 

2001); and b) many landscape-scale variables are covariant, resulting in obscured cause and effect links. 

The general geomorphic context of the Ozarks 

indicates that physical stream habitats in Bear Creek 

can be expected to vary with time according to 

hydrology and geomorphology. The history of geomorphic adjustments of Ozarks streams (Jacobson, 

1995; Jacobson and Primm, 1997; Jacobson and Gran, 

1999) indicates that habitats in Bear Creek have been 

and probably will be affected by waves of land-usederived bed load moving through the stream network. 

These waves would be expected to affect reaches of 

Bear Creek by filling in the downstream ends of pools 

– and in severe cases – resulting in transient riffles 

due to episodic bed load accumulation. Effects of 

future hydrologic alterations in the drainage basin 

would occur within the context of ongoing geomorphic adjustments. 

Physical setting of Bear Creek and Crane 

Bottom 

The Buffalo River drainage basin lies within the 

Ozark Plateaus physiographic province (fig. 1), a 

region dominated by relatively flat-lying Paleozoic 

sedimentary rocks. Physiographically, the Buffalo 

River drains portions of the Boston Mountains, 

Springfield Plateau, and Salem Plateau. The Buffalo 

River’s largest tributaries flow into the Buffalo from 

the south, where the high relief Boston Mountains are 

most prominent. 

Bear Creek flows northward for a distance of 

approximately 45 kilometers from its headwaters to its 

junction with the Buffalo National River near the town 

of Gilbert. At the junction, Bear Creek has a drainage 

area of 239 km2

, making it the fifth largest of the 

Buffalo River’s tributaries. The headwaters are in the 

rugged Boston Mountains, which are dominated by 

sandstone and shale bedrock formations of 

Pennsylvanian age. For much of its length, Bear 

Creek flows through a wide, flat valley that is heavily 

used as pasture land (fig. 5). The wide valleys are 

preferentially formed on the Mississippian Boone 

Formation, a highly permeable formation composed of 

soluble limestone and non-soluble chert. This chert 

tends to break into gravel-size pieces and is a major 

bed sediment source. For the 10 km just upstream of 

the junction with Buffalo River, Bear Creek flows in a 

valley floored by less permeable carbonate and sandstone of Ordovician age. 

Approximately two kilometers before flowing 

into the Buffalo River, Bear Creek crosses the park 

boundary of the Buffalo National River (figs. 1, 2). 

The reach selected for this study (known as Crane 

Bottom) is the uppermost one kilometer of Bear Creek 

within the Buffalo National River boundary (fig. 6). 

The reach is entrenched and bordered on the river left 

(left bank when facing downstream) over most of its 

length by a steep bedrock bluff and on the river right 

by fluvial terraces. The presently forming flood plain 

of Bear Creek is composed of gravel bars and partially 

vegetated surfaces inset at elevations 3-4 m below the 

general elevation of the fluvial terraces. 

The Crane Bottom reach has a representative 

selection of hydraulic habitat units. The upstream end 

is a long glide with scattered boulders in the middle 

and left of the channel. At cross section 26 (fig. 7), 

Bear Creek bends to the right, forming a pool against 

the bedrock bluff. Downstream of cross section 26, 

Bear Creek has three riffle-race-pool sequences. At 

cross section 2, Bear Creek has another bluff pool as 

the channel bends to the left. 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 7 

Figure 5. Maps of the Bear Creek drainage basin. A. Land use map showing major land-use categories. B. Geologic map on shaded relief, showing the steep slopes of the upper basin and the wide valley of Bear Creek cut into the Boone Formation. 

vation model from U.S. Geological Survey (2000a). Land-cover data from U.S. Geological Survey (2000b); geology data from Hofer 

and others (1995). 

Digital eleThe high banks of the fluvial terraces are dominantly composed of particles sand size and smaller, 

with minor lenses of gravel-cobble sized material. 

The active channel is dominated by gravel and cobble, 

with patches of boulders and bedrock. 

Local vegetation communities on the gravel-cobble bars include monocultures of perennial water willow (Justicia americana), patches of more diverse 

herbaceous vegetation including grasses, and, on higher bars, young trees, dominantly American sycamore 

(Platanus occidentalis) (fig. 8). The steep banks, as 

well as a buffer zone extending from the top of the 

steep banks to cleared fields, are vegetated with a 

combination of deciduous trees, herbaceous vegetation, and local stands of cane (Arundinaria gigantea). 

The cleared areas on the terraces are maintained as 

hay fields, and are therefore free of woody vegetation. 

The climate of Bear Creek is humid, temperate 

with a mean annual temperature of 14.7 o

C (58.5 oF) 

and mean annual precipitation of 1110 mm (43.7 in) 

(Marshall, Arkansas weather station, National Oceanic 

and Atmospheric Administration, 2002). Peaks in the 

seasonal distribution of precipitation occur in MarchMay and in November (fig. 9). Although measurable 

snowfall occurs in almost every year, snowfall is a 

minor component of total precipitation and rarely 

remains more than a few days. 

Bear Creek is gaged at U.S. Highway 65 where 

the drainage area is 212.7 km2 (83.1 mi2

), or approximately 91% of the total drainage of Bear Creek 

upstream of the junction with Buffalo River (Petersen 

and others, 2002; fig. 2). This streamgage was 

installed by the U.S. Geological Survey in January 

1999 and has been operated to the present (2003). 

Streamflow is highly variable, reflecting the combined 

effects of high runoff and highly variable meteorological inputs (fig. 10). Mean daily stream discharge for 

the period of record (January 22, 1999 – July 15, 

2002) is 2.94 cubic meters per second (cms). This 

value is considerably higher than 1.58 – 1.78 cms values cited in Petersen and others (2002) because it is 

averaged over a longer time period and includes large 
8 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 6. 

gages operated at Crane Bottom. 

Detailed map of the Crane Bottom study reach, boundaries of the Buffalo National River, and locations of the stage 

Figure 7. Detailed map of Crane Bottom study reach showing cross section locations and physiographic details. 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 9 

discharges in calendar years 2001 – 2002. 

Bear Creek has high concentrations of 

nutrients, dissolved organic carbon, fecalindicator bacteria, and suspended sediment 

relative to the Buffalo River mainstem and 

other lowland-use-impact reference basins 

in the Ozarks; however, nutrient 

concentrations in Bear Creek were considerably lower than those found in the 

Illinois River (Arkansas), a river affected 

by waste-water treatment outfalls, extensive pastureland, and poultry waste 

(Petersen and others, 2002). 

Approach 

This study used a combination of 

field- and modeling-based analytical tools. 

Field-based data collection was used to 

document and quantify geomorphic 

changes and to collect data for construction, calibration, and validation of 

hydraulic models. Two-dimensional modeling was used to assess habitat variation 

with discharge as well as bed-material 

entrainment flows. 

We addressed geomorphic 

dynamics–the rates and processes of erosion and deposition that change channel 

and flood-plain topography–by measuring 

geomorphic change in three ways. The 

most fundamental measure of geomorphic 

change was obtained by resurveys of thirty-one channel cross sections and by direct 

calculation of erosion and deposition 

between surveys. A pair of cross-section 

surveys can reveal net surface topographic 

change, but in cases of erosion followed by 

deposition, the total amount of change cannot be detected by cross-section surveys 

alone. To address this, we used scour 

chains to assess whether scour and fill took 

place in the channel. Finally, we attempted 

to use painted rocks to identify flow conditions that are sufficient to initiate sediment 

movement. 

We constructed, calibrated, and validated a two-dimensional, finite-element 

hydraulic model based on field measurements of topography, vegetation, particle- Figure 8. Photographs of vegetation at Crane Bottom. A. View of Bear Creek at size distributions, and water-surface eleva­ stream level showing gravel bars with water willow and deciduous woody vegeta- tions. Results of the model were analyzed tion on banks. View is looking upstream near cross section 23. B. View of downstream pool at cross section 1 showing sparse vegetation on gravel bar. C. in a geographic information system (GIS) 

Overview of Crane Bottom looking to the west and upstream, just after an over- to quantify habitat classes that exist during

bank flood, March 19, 2002. Foreground is downstream low terrace, cross sec- a range of discharges. The timing and 

tions 5-12. Banks have deciduous woody vegetation and terrace surfaces are in duration of habitat availability were 

grass. 
10 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 9. Climatological data from Marshall, Arkansas. A. Monthly average temperature. B. Monthly average 

precipitation. Data from National Oceanic and Atmospheric Administration (2002). 

Figure 10. Hydrologic record of 30-minute discharge values. U.S. Geological Survey streamflow gaging station Bear Creek 

near Silver Hill, Arkansas, and dates of cross section surveys at Crane Bottom. 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 11 

quantified using discharge data from the U.S. 

Geological Survey streamgage on Bear Creek. The 

frequency of bed-material entrainment events were 

assessed from the monitoring data and from simple 

boundary shear-stress calculations from the twodimensional hydraulic model. The model shear stress 

calculations are compared with particle-size distributions on the bed of Bear Creek to determine the frequencies of flows that are capable of initiating movement of bed material and maintaining habitats under 

present-day conditions. 

These analyses quantify physical habitat dynamics under the prevailing, baseline hydrologic conditions. This understanding is important background for 

assessing potential effects of future hydrologic alterations on habitat sustaining and maintaining flows. 

Prediction of actual differences attributable to flow 

alterations on Bear Creek, however, would require 

synthesis of a hydrologic time series for the altered 

future conditions; this level of analysis is beyond the 

scope of this report. 

Analysis of the quantity of habitat available at 

various discharges depends on the assumption that 

channel morphology does not change with discharge. 

This is a common assumption for instream flow studies and many hydraulic modeling efforts, but the 

assumption limits ability to address the role of high 

flows in creating and maintaining habitat through erosion and deposition. Conventionally, instream flows 

are separated into those that provide habitat for stream 

organisms most of the time (and with emphasis on 

minimum low flows) and those that maintain habitat, 

or so-called flushing flows (Gordon and others, 1992). 

In reality, there is a continuum among flows because 

morphology is subject to alteration as soon as sediment transport begins. In rivers where substrate is 

dominated by coarse bed material, sediment transport 

may initiate over a narrower range of flows (compared 

to rivers with mixed-size bed material) and the 

assumption of distinctly different flows regimes would 

be better justified. In this report, habitat availability is 

calculated for the entire range of modeled discharges, 

but reliability of habitat estimates is considered less 

for sediment-transporting discharges near or above 

bankfull. 

The following sections of this report present 

information on: 

• Hydrology of Bear Creek at the Crane 

Bottom study reach. 

• The effects of geomorphic dynamics on 

habitats measured from cross section 

monitoring, scour chains, and painted 

rocks experiments. 

• The effects of hydrologic dynamics on 

habitats assessed through hydraulic 

modeling. 

• Analysis of sediment transport potential 

from hydraulic modeling. 

The specific methods used in each study component 

are presented with the results. 

Hydrology of Bear Creek at Crane Bottom 

Understanding of stream habitat dynamics of Bear 

Creek at Crane Bottom requires an understanding of 

the magnitude, frequency, duration, and sequence of 

flows that sustain and maintain habitats. This section 

presents information on the hydrology of Bear Creek 

as measured at Silver Hill, Arkansas, and extended to 

the Crane Bottom study site (fig. 2). 

Methods 

Crane Bottom does not have a discharge-rated 

streamgage with a record of sufficient length for 

understanding variability of flow over time; therefore 

we developed our understanding of hydrology at 

Crane Bottom by reference to the U.S. Geological 

Survey streamflow gaging station record for Bear 

Creek near Silver Hill, Arkansas. We used data from 

this streamgage for the period from January 1999 

(when the streamgage was installed) to July 2002 (the 

end of active data collection for this study). Because 

the Silver Hill streamflow record is only about 3.5 

years long, however, we also used additional streamgage records for reference (fig. 11). Ideally, these 

records would be from drainage basins that are located 

near Bear Creek, drain similar physiographic terrain, 

are of comparable drainage area, and cover the same 

period of record as the Silver Hill streamgage but 

extend further back in time. These conditions cannot 

all be met; reference gages are listed in table 1 and 

shown in figure 11. 

Two pressure transducers and data loggers were 

installed to document water-surface elevations at the 

upstream and downstream ends of the Crane Bottom 

reach (fig. 7). The pressure transducers were surveyed 

into the coordinate system used for cross section surveys. The loggers were set to record water depths at 

15-minute intervals. Discharge measurements were 

made by National Park Service personnel at Crane 

Bottom in conjunction with routine water-quality sampling, using standard streamgaging techniques for 

wading measurements. These discharge measurements are used to construct stage-discharge relations 

for low flows at the site and to evaluate relations 

between discharge at Crane Bottom and discharges 

measured upstream at the U.S. Geological Survey 

streamgaging station at Silver Hill. 
12 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 11. Locations of streamflow gaging stations used in hydrologic analysis. 

Flow duration 

The time period during which channel morphology was monitored at Crane Bottom (June 2001 – June 

2002) was wet relative to the average. Five rain gages 

maintained by the National Park Service in the Bear 

Creek drainage basin vicinity received totals of 1473, 

1610, 1422, 1671, and 1547 mm (millimeters) of rainfall June 1, 2001 – May 30, 2002 (National Park 

Service, Harrison, Arkansas, unpublished data), compared to the annual average rainfall of 1110 mm, 1971 

– 2000 (National Oceanic and Atmospheric 

Administration, 2002). Daily mean discharge for 

Buffalo River near St. Joe during 6/1/2001 – 

6/30/2002 was 44.6 cms compared to a long-term 

daily mean discharge (1940 – 2002) of 30.0 cms (U.S. 

Geological Survey, 2003). Furthermore, the periods 

of higher-than-normal rain were concentrated in the 

winter and early spring months. Hence, during the 

study period Bear Creek probably had higher flows 

and more geomorphic activity than average. 

The percent of time that given flows are equaled 

or exceeded is a basic reference for the temporal distribution of flow. In this report, flow exceedance values are referenced to the percent of the total period of 

record of each gage; for short records that do not sample average hydroclimatic conditions, these 

exceedance values could be biased. Flow exceedances 

– using daily mean flows, undifferentiated by season 

or year – for Bear Creek at Crane Bottom (as stages), 

Bear Creek near Silver Hill, Buffalo River near 

Boxley, and North Sylamore River near Fifty Six 

show that most of the time flow in these small 

drainage basins is constant and low (fig. 12). The 

interquartile range of stages (stages equaled or 

exceeded between 25 and 75 percent of the time) was 

only 23 cm at the upstream streamgage and 32 cm at 

the downstream streamgage at Crane Bottom (fig. 

12A); flows with stages in excess of 2 m above the 

lowest stages occur only 1-2 percent of the time, or 3­

7 days per year. 

Discharge-rated streamgaging stations on similar 

streams show similar variation. Despite substantial 

differences in drainage area, North Sylamore Creek, 

Buffalo River at Boxley, and Bear Creek near Silver 

Hill have similar flow-duration curves (fig. 12B, C). 

Compared to Buffalo River at Boxley and North 

Sylamore Creek, Bear Creek at Silver Hill has a more 

constant baseflow discharge; North Sylamore Creek is 

somewhat flashier than the other two streams at flows 

greater than the median. The interquartile ranges of 

discharges on Bear Creek near Silver Hill, Buffalo 

River near Boxley, and North Sylamore Creek are 2.1, 

2.7, and 0.8 cms. These comparisons should be evaluated cautiously because of the relatively short record 

lengths for Bear Creek near Silver Hill and Buffalo 

River near Boxley (table 1). 

Seasonality of flows is especially important to 

aquatic biota whose life cycles are synchronized to 

characteristics like seasonal habitat availability, water 

temperature, or length of day. Seasonality and flow 

duration were addressed using frequency hydrographs 

for two gages with sufficient record lengths, North 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 13 

Figure 12. Flow duration data for Bear Creek at Crane Bottom and reference streamgages. A. Elevation durations at two 

stage gages, Crane Bottom. B. Flow durations for Buffalow River near Boxley, Bear Creek near Silver Hill, and North 

Sylamore Creek near Fifty Six. C. Flow duration data for three gages above, using a logarithmic plot. 
14 

1

BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002 

Table 1. Information on streamgaging station data used in this report 

Drainage area, 

USGS square 

Gage number kilometers Length of record, notes 

Bear Creek near Silver Hill, 

Arkansas 07056515 212.7 

Daily streamflow, 1/22/1999 to 

present1 

Annual peak flow, 3 events 

Buffalo River near St. Joe, 

Arkansas 07056000 2122.2 Daily streamflow, 10/1/1939 to present Annual peak flow, 64 events 

Buffalo River near Boxley, 

Arkansas 07055646 146.9 Daily streamflow, 4/17/1993 to present Annual peak flow, 8 events 

North Sylamore Creek near 

Fifty-Six, Arkansas 07060710 148.7 Daily streamflow, 12/9/1965 to present Annual peak flow, 36 events 

 present = July 2002; streamgaging continues at these gages. 

Sylamore near Fifty Six and Buffalo River near St. Joe 

(fig. 13). These diagrams include a cumulative frequency analysis of flow for every day of the year during the period of record. When the frequencies are 

plotted by day of year, the seasonal variability is 

apparent in variation along the x-axis and inter-annual 

variation is apparent in variation along the y-axis. 

As representatives of drainage basins in northern 

Arkansas, these two records show the broad seasonality of increased discharge March-May and low flow 

August – November. The lowest flows occur in 

September. The period November – December is 

characterized by large inter-annual variability. The 

highest flows during the year can occur any time during September – June. 

Peak flows 

Flows capable of transporting large quantities of 

sediment are typically considered floods. Geomorphic 

theory supports the idea that the floods that are most 

effective at maintaining the channel and transporting 

sediment are bankfull flows, with typical recurrence 

intervals of 1.5 – 2.0 years (Wolman and Miller, 1960; 

Andrews, 1984). The length of record for Bear Creek 

at Silver Hill is insufficient for flood frequency analysis, so the probabilities of floods on Bear Creek during 

the course of this study were assessed by reference to 

probabilities calculated for North Sylamore near Fifty 

Six, Buffalo River near Boxley, and Buffalo River 

near St. Joe (table 2). This analysis used the annual 

series of peak discharges, fit to a Log Pearson Type III 

curve following the guidelines of the Interagency 

Advisory Committee on Water Data (1982); the U.S. 

Geological Survey software PEAKFQ v. 4.1 (Thomas 

and others, 1998) was used in this analysis. 

A short record of peak flows (eight years) on 

Buffalo River near Boxley results in wide 95% confidence intervals for flood probabilities (fig. 14A). The 

longer record at North Sylamore (fig. 14B) provides a 

more accurate estimate of flood frequency in drainage 

basins of this size; the record of Buffalo River near St. 

Joe (fig. 14C) may be somewhat unrepresentative of 

flood frequencies on Bear Creek because the drainage 

area is so much larger (table 1). 

By comparing probabilities (or recurrence intervals) for the same floods – and noting similarities or 

differences – in peak flows per unit drainage area (unit 

peak discharges) the Bear Creek floods can be put into 

context. Unit peak discharges generally decrease with 

increasing drainage area because of decreasing probabilities of receiving uniformly intense rainfall over 

larger drainage basins. Hence, unit peak discharges 

would be expected to be larger for floods of comparable recurrence on North Sylamore and Buffalo River 

near Boxley, compared to Bear Creek. Conversely, 

unit peak discharges on Buffalo River near St. Joe 

would be expected to be smaller for floods of the 

same probability. Based on these references, the 

floods of 2/16/2001 and 3/19/2002 were estimated to 

have recurrence intervals close to one year, whereas 

the flood of 12/16/2001 was estimated at slightly 

higher, 1-2 years. The flood of 1/31/2002 was estimated at between 2 and 4 years recurrence based on 

the high unit discharge and National Park Service precipitation records that indicated the Bear Creek basin 

received considerably more precipitation than the 

upper Buffalo River near Boxley. 

Backwater 

Flows at Crane Bottom are affected at times by 

high water on the mainstem Buffalo River, nearly 1 

km downstream. For example, during the flood of 

December 2001, the mainstem Buffalo River streamgage (approximately 9 km upstream from the Bear 

Creek junction) peaked at a stage of 8.5 m, 12 hours 

after Bear Creek. The first rise from this flood on 

Bear Creek at Crane Bottom occurred at about midnight, but a second peak occurred 6 hours later, simultaneous with the peak on the Buffalo River. The second peak was higher at the downstream stage gage at 

Crane Bottom than at the upstream stage gage at 

Crane bottom (fig. 15A.). Hence, this backwater substantially decreased the slope of Bear Creek in the 

study reach. 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 15 

Figure 13. Frequency hydrographs for streamgaging stations at: A. North Sylamore Creek near Fifty Six, Arkansas and 

B. Buffalo River near St. Joe, Arkansas. 
16 

Table 2. Peak discharges, exceedance probabilities, and approximate recurrence intervals for four floods, February 2001 - March 2002. Three reference gages show comparable 

values for the same flood. Probabilities were calculated from U.S. Geological Survey peak-flow files, using the recommended "Bulletin 17-B" guidelines with regional skew coefficients (Interagency Advisory Committee, 1982).

[km2, square kilometers; cms, cubic meters per second; est., estimated] 

Approximate 

Unit peak annual Recurrence 

Drainage Peak, discharge, exceedance interval, 

Approximate 

Unit peak annual Recurrence 

Peak, discharge, exceedance interval, 2 2 2 Gage area, km cms cms/km probability years cms cms/km probability years 

2/16/2001 12/16/2001 

Bear Creek near Silver Hill 123 220 1.79 est.: 1 310 2.52 est.: 1-2Buffalo River nearBoxley 147 130 0.88 0.9 1.1 290 1.97 0.44 2.3Buffalo River near St.Joe 2,122 820 0.39 0.6 1.7 1200 0.57 0.44 2.3North SylamoreCreek near Fifty Six 149 80 0.54 0.68 1.5 150 1.01 0.42 2.4

1/31/2002 3/19/2002 

Bear Creek near Silver Hill 123 460 3.74 est.: 2-4 200 1.63 est.: 1

Buffalo River nearBoxley 147 150 1.02 0.88 1.1 200 1.36 0.75 1.3Buffalo River near St.Joe 2,122 920 0.43 0.56 1.8 1530 0.72 0.32 3.1North SylamoreCreek near Fifty Six 149 220 1.48 0.28 3.6 100 0.67 0.58 1.7

BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 17 

Figure 14. 

Arkansas, B. Buffalo River near St. Joe, Arkansas, and C. North Sylamore Creek near Fifty Six, Arkansas. 

Flood frequency analyses showing annual exceedance probabilities for A. Buffalo River near Boxley, 
18 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

In comparison, the flood of January 24, 2002 was 

of smaller magnitude on Buffalo River, and the flow 

of Bear Creek at Crane Bottom was unaffected by 

backwater (fig. 15B). The flood of January 31, 2002 

(fig. 15C) was intermediate on the Buffalo River 

(about 5 m rise), and affected water-surface elevations 

on Bear Creek, but to a lesser extent compared to the 

December flood. 

These examples indicate that backwater can affect 

flood flows at Crane Bottom when stages of about 5 

m or greater occur on the mainstem within about 24 

hours of peaks on Bear Creek. Because flows on the 

Buffalo River and Bear Creek generally result from 

the same weather systems, backwater is a possibility 

when Buffalo River is in flood. Small, concentrated 

storm cells over the Bear Creek drainage basin could 

possibly cause floods on Bear Creek without corresponding floods on Buffalo River. It is also possible 

that backwater from floods on the mainstem could 

affect Bear Creek at Crane Bottom when flows are 

Figure 15. Hydrographs showing stages at Buffalo River near St. Joe, Arkansas and Bear Creek, 

near Silver Hill, Arkansas, and backwater effects at Crane Bottom. The Crane Bottom stages are 

graphed on the same arbitrary datum; the stages for Buffalo River and Bear Creek near Silver Hill 

have been shifted vertically for ease of comparison. A. Flood of December 16-20, 2001. B. Flood of 

January 23-27, 2002. C. Flood of January 31-February 4, 2002. 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 19 

low on Bear Creek. 

Water-surface slope serves as an indicator of 

backwater at Crane Bottom. Under normal variation 

of flows without backwater effects, the water-surface 

slope of Bear Creek tends to decrease with increasing 

discharge (fig. 16A). The relation between slope and 

discharge developed from estimated discharges at 

Crane Bottom and measured slopes between the two 

stage gages indicates that slope decreases rapidly from 

0.002 to 0.0016 as discharge increases from 0 to about 

15 cms. Water-surface slope then decreases less rapidly to a minimum value of 0.0013 at 556 cms (about 

4-year recurrence flow). 

During a flood event affected by backwater, however, water-surface slopes can be substantially 

decreased. For example, the flood of 12/16 – 

12/18/2001 exhibited an expected decrease in slope 

with increasing discharge during the non-backwater 

part of the flood (figs.15, 16B). About mid-day on 

12/17/2001, however, flow on the Buffalo River 

Figure 16. Discharge, stage, and water-surface slopes at Crane Bottom illustrating backwater conditions. A. Water-surface slope and estimated discharge for Bear Creek at Crane Bottom for non-backwater conditions. B. Relation between upstream stage and water-surface slope calculated between 

upstream and downstream gages at Crane Bottom, showing effects of backwater from the Buffalo River 

mainstem on water-surface slope at Crane Bottom. 
20 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

mainstem began to create a backwater effect at Crane 

Bottom, and slopes decreased to as low as 0.00014 

before recovering on 12/18/2001 as the backwater 

effect diminished. 

The temporal distribution of backwater effects 

was assessed by evaluating how often water-surface 

slopes decreased below 0.0013 at the study site; a 

slope of 0.0013 would still maintain flow through the 

reach, so this slope is a conservative threshold that 

indicates a slowing of velocities rather than a zerovelocity backwater conditions. The cumulative frequency distribution of water-surface slopes at Crane 

Bottom for the period from May 2001 to July 2002 

(approximately 340 days when both gages were operating) shows that water-surface slopes were in excess 

of 0.0013 92% of the time. 

Although backwater conditions are infrequent, 

they have the potential to alter sedimentation patterns, 

and hence habitat characteristics. Because backwater 

conditions typically occur toward the end of the flood 

events on Bear Creek, high shear stresses and bedmaterial entrainment conditions are followed by low 

water-surface slopes, low shear stresses, and conditions favorable to deposition of sediment. Backwater 

events have the potential, therefore, to deposit finer 

sediment and perhaps more sediment than would be 

deposited without the backwater conditions. 

However, the riffle-pool framework of fluvial habitats 

is presumably maintained by the non-backwater peak 

flows that typically occur before the onset of backwater conditions. Because this study is concerned with 

habitats that exist most of the time for stream organisms, the hydraulic model to evaluate sensitivity of 

habitats to flow ignores backwater effects. Our analysis of habitat maintaining flows concentrates on the 

sediment-transporting capabilities of peak flows 

exclusive of backwater conditions because understanding of the functions of these flows is applicable 

to most of the length of Bear Creek that is not subject 

to backwater effects. 

Geomorphic Dynamics and Habitat 

Geomorphic dynamics refers to the changes in physical habitat template that occur because of erosion and 

deposition. We evaluated geomorphic dynamics using 

field measurements of channel changes. 

Methods 

A modified “Wolman” pebble count (Wolman, 

1954) was performed at cross sections in June 2001 to 

document substrate size in the Crane Bottom reach. 

The technique follows that of Panfil and Jacobson 

(2001) in which 100 particles were randomly selected 

from the bed and measured with calipers (or if too 

large, with an engineer’s ruler). This protocol samples 

along a cross-section, and approximately 5 m 

upstream and downstream, between the estimated 

bankfull elevations of both banks. The particle size 

data were used in statistical descriptions of stream 

substrate and as an aid to estimating roughness height 

values for hydraulic modeling. 

Thirty-one topographic cross sections were 

benchmarked during June 2001 to document geomorphic change and to aid in construction of a 

topographic mesh for hydraulic modeling (fig. 7; table 

3). Cross-section endpoints were established with 

pieces of 13 mm diameter rebar that were driven into 

the ground and tagged. Endpoints were located at elevations above anticipated flows, typically at elevations 

consistent with the alluvial terraces on the right bank. 

When possible, the rebar was placed just downstream 

of a large tree to reduce the chance of disturbance, as 

well as to help in finding the cross sections for subsequent surveys. 

The cross sections were surveyed with a total station, and data were automatically logged into commercial software. Cross sections were referenced to an 

arbitrary local coordinate system that was used 

throughout the survey and modeling process. Each 

surveyed cross-section point was also classified 

according to the dominant particle size class (that is, 

the particle size class that is most dominant in the 1-m 

radius area around the point). Points along the cross 

sections were positioned on significant topographic 

breaks and were spaced no more than 5 m; most point 

spacings were on the order of 2 m except in very uniform topography. Cross sections had an average of 35 

points per survey. Reproducibility of topographic 

cross-section surveys are limited mainly by point 

spacing and depth to which a surveying prism pole 

will sink into the ground, or around soil and sediment 

particles (DeVries and Goold, 1999). Sediment and 

soil material along these cross sections ranged from 

mud (0 – 0.05 mm) to large boulders (greater than 512 

mm). Most of the materials that were eroded or 

deposited during the course of this project were in the 

sand to small-cobble size range (2-128 mm); accordingly, rod-placement error is estimated to be no more 

than 128 mm. 

Cross sections were surveyed four times during 

the course of the study (June 2001, December 2001, 

February 2002, and June 2002). For each survey, a 

tag line was strung between the rebar endpoints to 

ensure that the original, straight cross section was surveyed. Geomorphic changes at each cross section 

were calculated by importing survey data (horizontal 

position and elevation) into a GIS, constructing polygons in the plane of the cross section, and intersecting 

data from subsequent dates to produce polygons of 

erosion or deposition. Net change was calculated as 

depositional area minus erosional area. Total 
21 

Table 3. Locations and descriptions of monumented cross sections used in this study [c.s., cross section; diam., diameters; cm, centimeter; m, meter; d.s., downstream; u.s., upstream; lb, left bank; rb, right bank; n/a, not applicable]

Approximate Cross distance to Dominant Location of rebar 

section next c.s., in habitat number meters Left bank Right bank 

1 RB--25; LB--0 Pool In shrubs, shared with C.S. 2. 2 18 Pool In shrubs, shared with C.S. 1. 

Near top of high bank; at base of roots of 46 cm box elder on u.s. side of 

3 21 Pool tree.

Top of high bank just d.s. of 10” diam. dead tree and behind very large 4 38 Race box elder. At top of high bank, not near tree (except poison ivy). 5 20 Riffle Top of high bank just d.s. of paw paw (3 small trunks all less than or 6 31 Riffle equal to 2.5 cm diam.). On high bank, just d.s. of a small spicebush with multiple stems and near 7 21 Riffle a couple of small paw paws. Top of high bank, lower terrace; just d.s. of 5 cm diam. redbud; uphill 

8 28 Glide from 20 cm diam. ash (also flagged). 

Top of high bank, lower terrace, just before rise to upper terrace; approximately 60 cm d.s. of dead 3 cm diam. tree; a leaning box elder 9 45 Glide approximately in line with stake and approximately 1⁄2 way down bank 

also flagged. 

Approximately 3 m d.s. of an 20 cm diam. locust. 10 54 Pool Top of high bank, not by a tree; an 20 cm diam. elm part way down bank 11 38 Pool and slightly d.s. of c.s. was flagged. Top of high bank; not near any large trees, but a lot of small shrubs; a 

12 41 Pool box elder (approximately 30 cm diam.) at base of high bank flagged--it is 

slightly u.s. of c.s. line. Barbed wire near base of high bank. Top of high bank, approximately 1 m d.s. of post oak with 3 trunks 

13 17 Race (approximately 30 cm, 25 cm, and 15 cm). 

Top of high bank d.s. from approximately 13 cm diam. locust; among cane and other thick vegetation. 

14 24 Riffle 

Just d.s. of 8 cm diam. osage orange with vine growing on it; vegetation 16 20 Riffle is very dense. In a thicket at very roughly the same elevation as right bank--go up slope 

17 29 Glide at slab of rock that is against base of high bank; the elm tree next to this 

rock is flagged. 

Along pressure transducer pipe near bend. 

Upper bench near valley wall, just d.s. from 1 ft diam. mulberry 

Top of high bank, not next to a tree; about 1 m back from edge of steep bank; about 3 m u.s. from 5 cm diam. box elder; near trail to gage. On high bank just u.s. of 8 cm diam. box elder; very close to corner of field.

Top of high bank just u.s. of small hackberry (approximately 5 cm 

diam. trunk is broken off near ground); fairly thick low vegetation. 

Top of high bank, not near a big tree; behind a fallen tree and in cane. Between 2 grape vines, just u.s. of 25 cm diam. elm. Top of high bank; approximately 60 cm d.s. of a box elder with several small trunks (mostly < 2 cm diam.); nearest big tree is 38 cm diam. elm--this is about 6 m d.s. and slightly down bank. Top of high bank, approximately 2 m d.s. of locust with twisted vines; small hackberry towards stream and d.s. of rebar also flagged. 

Top of high bank; in cane, not near a big tree; a 30 cm diam. elm near 

top of bank and approximately 1 m d.s. of c.s. also flagged. 

Top of high bank; through thicket of cane, immediately d.s. of dead tree (diam. > 30 cm); several other large trees nearby. Just d.s. and slightly up bank of 38 cm box elder; approximately 1.5 vertical meters below top of high bank. Top of high bank, approximately 2 ft u.s. of 46 cm diam. post oak; almost to u.s. edge of lower field. Original stakes washed out, replaced further along section. Top of high bank, just off corner of lower field and approximately in line with location where road drops down to the lower field; hackberry with 2 trunks that is leaning out over bank is approximately 2.5 m from rebar (approximately along c.s.). Original stakes washed out, replaced further along section. Just d.s. of 30 cm diam. hackberry (2 large hackberries growing close together--the rebar is by the one that is set back farther from the bank). Top of high bank just d.s. of 30 cm diam. elm; back from edge of bank a few meters; separated from upper field by cane. 

PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 
22 

Table 3. Locations and descriptions of monumented cross sections used in this study --Continued[c.s., cross section; diam., diameters; cm, centimeter; m, meter; d.s., downstream; u.s., upstream; lb, left bank; rb, right bank; n/a, not applicable]

Approximate Cross distance to Dominant Location of rebar 

section next c.s., in habitat number meters Left bank Right bank 

In thicket; not near any big trees; some small boulders present at base of 

18 29 bank; an elm tree approximately 18 cm diam. is growing at base of bank 

approximately 2 or 3 m above c.s.--this elm is also flagged. 1 m d.s. of 10 cm diam. persimmon; another persimmon down the bank 19 46 Glide and along the c.s. is also flagged. Just d.s. of 20 cm diam. cedar that is at top of lowest ledge of bluff; just 20 48 Riffle d.s. of first major bluff outcrop at stream level. In thicket, not near a big tree; on bench at top of eroding steep bank; 

21 51 Pool below the bluff. 

At base of ash (15 cm diam.) and elm (25 cm diam.) growing together; 

22 50 Race approximately 1⁄2 way between stream level and rock bluff above. 

Just d.s. of approximately 30 cm diam. hop hornbean w/ poison ivy vine; 23 32 Riffle approximately 3⁄4 of way between stream level and bluff line. Below and d.s. of cave entrance (cave has large metal fence); at top of 

24 56 Riffle eroding bank; just u.s. of runoff channel from cave; a small (4 cm diam.) 

hickory approximately 2 m down slope along c.s. flagged. Biggest tree downslope of the u.s. cave fence is a red oak (close to 60 cm 25 64 Riffle diam.); rebar is just u.s. of red oak. 

26 RB--44; LB--67 Pool D.s. and approximately 2 m uphill of 45 cm diam. dead tree; c.s. crosses large slab of rock. 

3 m uphill of 5 cm diam. paw paw; a large ash is leaning out over the 27 58 Glide water approximately 5 m d.s. of c.s. line. Top of high bank, just d.s. of 45 cm diam. dead (?) tree with lots of vines; 28 42 Glide view to field obscured by cane and other vegetation. 30 cm d.s. from 30 cm diam. maple. 29 27 Glide 45 cm d.s. from 15 cm diam. elm. 

30 36 Glide 

n/a Glide Between 2 paw paws, each approximately 5 cm diam. 31 

Top of high bank, back from edge of bank approximately 10 m; d.s. of 5 cm diam. hackberry; a hornbean approximately in line w/ c.s. and part way down bank is also flagged. Top of high bank (but not the higher terrace); d.s. of 5 cm diam. box elder which is growing within 15 cm of a 25 cm diam. redbud. Top of high bank (lower terrace); just d.s. of 25 cm diam. honey locust Top of high bank, separated from field by stand of cane; just u.s. of 2 honey locusts, each 3 cm diam.; a hackberry part way down bank and approximately 1.5 m d.s. of c.s. also flagged Top of high bank, just d.s. of group of 3 osage orange trunks (approximately diam.: 15 cm, 10 cm, 5 cm); approximately 2 m back from steep slope. Top of high bank, a few m back from drop off; in cane thicket, no big trees nearby. Top of high bank; approximately 45 cm d.s. of 2 cm diam. elm; a small box elder in line with c.s. and part way down bank also flagged. Top of high bank, just d.s. of 15 cm diam. locust (visible from field); back from edge of steep bank approximately 2 m. Top of high bank, not immediately next to big tree; u.s. 6 m from dead tree covered in vines; thick low vegetation. Below top of high bank; 5 m uphill of 20 cm diam. ash; approximately 30 cm d.s. of 2 cm diam. hackberry. Near base of 10 cm diam. paw paw 

Top of high bank, middle of slump; just d.s. of 38 cm diam. honey 

locust. 

Top of high bank, approximately 1.5 m back from edge of bank; a 10 

cm diam. hackberry u.s. of stake and at edge of steep bank also flagged. 

Top of high bank, d.s. 45 cm from 15 cm diam. mulberry; dead log 

that is hiding pressure transducer pipe; leads to mulberry tree. 

BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 23 

depositional, erosional, and net-change volumes for 

the three time periods were calculated by multiplying 

cross section area changes by channel lengths (onehalf of the distance to the upstream and downstream 

cross sections). 

In addition to the erosion and deposition calculation for the entire cross section, we calculated the erosion and deposition that occurred in the portion of the 

channel below the water surface elevation as surveyed 

on December 13, 2001, when the discharge was 

approximately 6.2 cms, the flow equaled or exceeded 

only 10% of the time. This reference water-surface 

elevation serves several purposes: 

1) Cross-section re-survey errors tend to 

be greatest on steep banks where the 

cross sections intersect large boulders 

or slump blocks, or pass through 

dense vegetation; consideration of 

data below the reference elevation 

minimizes these errors. 

2) Use of the reference water-surface 

elevation provides a subset of geomorphic change measurements for the 

portion of the frequently wetted channel that is more directly relevant to 

stream organisms. 

3) Calculations relative to this fixed 

water-surface elevation are consistent 

for all cross sections and dates. 

4) Calculations relative to this fixed 

water-surface elevation are not biased 

by large erosional and depositional 

volumes associated with slumps of 

the high bank that occurred during 

the monitoring period. 

As with the calculation for the whole cross section, 

the reference channel calculation was accomplished 

by intersecting polygons of subsequent survey dates. 

Scour chains were installed at 18 sites (fig. 17) in 

September 2001 to evaluate how much of the bed was 

disturbed during sediment-transporting events. Each 

scour chain consisted of a length of “dog chain” that 

was attached to an anchoring device and driven vertically into the streambed (fig. 18). The chain was 

trimmed at the bed surface and the location was surveyed with a total station to help with recovery. Total 

length of chain depended on bed conditions; most 

were 45 – 60 cm long. We attempted to locate scour 

chains in February and June 2002 by resurveying 

locations and using a metal detector. When located, 

the chain was excavated to note the depth at which the 

chain had been reoriented to a near-horizontal position, thereby indicating the maximum depth of scour. 

An additional sediment transport experiment was 

carried out using painted rocks as tracers. This experiment was intended to document a threshold of bedmaterial entrainment and, possibly, average transport 

distance of particles. During a period of low flow, on 

December 14, 2001, we placed painted rocks of two 

size classes in the bed of the stream just downstream 

of cross section 18 (fig. 17). Approximately 2000 

particles sieved to the 16-32 mm size range (coarse 

gravel) and painted neon green were placed in a line 

about 20 meters in length, extending across a gravel 

bar from near the base of the high right bank to 

approximately one-half of the channel width. 

Figure 17. Map of study reach at Crane Bottom showing locations of cross sections, scour chains, and 

painted rock experiment. 
24 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 18. Schematic diagram showing how scour chains are used to document erosion and redeposition. 

Approximately 5000 particles sieved to the 8-16 mm 

size range (medium gravel) and painted neon orange 

were placed in a line parallel to and just upstream of 

the first group. All particles were above the summer 

low flow water level, although some were placed as 

much as 10 cm under the water surface. 

Results 

Bed Particle Size Distributions 

Particle-size distributions by cross section are 

shown in figure 19. Generally, particle size varies 

with habitat units, with pools being noticeably finer 

than riffles and races (fig. 19A). Because pebble 

counts sample only the top layer of sediment, they 

reflect only the most recent deposition. Fine sediment 

in pools may therefore record deposition from slack 

current on the receding limb of flood hydrographs, 

rather than relating to maximum velocities in pools 

during peak flows. 

Cross section 24 (figs. 19B, C) stands out as 

being substantially coarser than other cross sections. 

This riffle is just downstream of a deep pool on a 

bedrock-defended bend; the coarse sediment size may 

be relict from a large flood that scoured the pool and 

left a lag of very large substrate on the next riffle 

downstream. 

Geomorphic Change at Cross Sections 

Cross sections were installed in June 2001 and 

resurveyed three times, thereby allowing calculation 

of change in three transitions (fig. 20): June – 

December 2001; December 2001 – February 2002; 

February 2002 – June 2002. Cross section locations 

are on figure 7 and the surveys are shown in Appendix 

1. Some cross sections were affected by large bank 

slumps of alluvial terrace sediments along the right 

bank. The volume of these slump features dominated 

some aspects of geomorphic change calculations; 

although they represent important parts of the sediment budget, the slump volumes obscure the geomorphic changes to in-channel habitats. Hence, two sets 

of calculations are provided; one set is based upon the 

full, surveyed cross sections, while the other set of 

calculations is limited to geomorphic changes below a 

reference elevation at each cross section (table 4). 

Calculated geomorphic change was highly variable over the three transition periods. When change 

was substantial, it varied systematically along the 

study reach (fig. 20). From June 2001 to December 

12, 2001 (when the December survey was completed), 

the largest daily mean flow of Bear Creek at Silver 

Hill was only 10.6 cms. The resulting geomorphic 

change was very small with no clear spatial pattern 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 25 

Figure 19. Particle-size data from pebble counts, Bear Creek at Crane Bottom. A. D84 (84th percentile), D50 (50th 

percentile), and D16 (16th percentile) plotted by cross section. B. Particle-size classes for each cross section. 
The net geomorphic change was –216 3 3

26 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 19 (cont.) Particle-size data from pebble counts, Bear Creek at Crane Bottom. C. Cumulative particle-size distributions 

for pebble counts at cross sections. 

m

(figure 20A). 

3 in the entire channel area, and +34 m in the reference channel (table 4). 

Between December 12, 2001 and February 11, 

2002 Bear Creek experienced a flood of about 310 

cms followed by the largest flood of the study period 

with about 460 cms (discharges measured at the Silver 

Hill streamgage) with an estimated 2- to 4-year recurrence interval (table 2). These floods were responsible 

for a net geomorphic change of –2,652 m3 based on 

the full cross-section calculations and -2,770 m3 within the reference channel. In the reference channel, 

erosion dominated over deposition by a factor of 

about 3. The total change in the reference channel 

was 6.4 times greater than the total reference-channel 

change in the previous survey period. Erosion was 

clearly focused in glides and pools and deposition 

occurred in riffles and races (fig. 20B). By eroding 

from pools and depositing in riffles, this flood was 

responsible for enhancing habitat variability and 

hydraulic diversity. 

Between February 2002 and June 2002, Bear 

Creek experienced four floods in excess of 60 cms 

(fig. 10). The flood of March 19, 2002 was estimated 

to have a recurrence interval of about 1 year (table 2). 

In contrast to the previous period, erosion and deposition in the reference channel were nearly equal, with a 

net deposition of 107 m . Total change to the reference channel in this period was only 3,927 m3 

compared to 5,570 m3 in the previous period. When considering the total cross-sectional area, erosion outbalanced deposition by 3,506 m3 

to 2,979 m3. Total-area 

calculations included some large slump blocks on the 

right bank that eroded during this period. Also in contrast to the previous survey period, the locations of 

erosion and deposition were reversed, with the bulk of 

erosion occurring in riffles and races and the bulk of 

deposition occurring in pools and glides (fig. 20C). 

For the entire monitoring period June 2001 – June 

2002, the net change based on the full cross sections 

was –3,397 m3

, indicating a net erosive period. For 

the reference channel, the period was also dominated 

by erosion, with net change of –2,630 m3 (table 4). 

By habitat unit, the net change during this time period 

was dominated by erosion in pools and glides (fig. 

20D). 

The amount of geomorphic change experienced in 

the Crane Bottom reach during this study was large, 

probably due in part to the unusually high number of 

large floods. Annual total and net volumetric changes 

per unit drainage area at Crane Bottom were 8-40 

times greater than similar erosion calculations 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 27 

Figure 20. Net erosion and deposition by cross section for three survey intervals and for entire monitoring period, Bear 

Creek at Crane Bottom. 
28 

Table 4. Volumetric change at Crane Bottom site measured from cross section resurveys. Areal change at cross sections was multiplied by one half of distance to next 

cross section upstream and downstream to obtain volume. 

Volumetric change

June 2001 - Dec 2001 - Feb 2002 - June 2001 -

Dec 2001 Feb 2002 June 2002 June 2002 

Erosion, cubic meters 1,297.4 5,278.0 3,506.4 5,377.4 

Deposition, cubic meters 1,081.0 2,625.5 2,978.7 1,980.8 Total change, cubic meters 2,378.5 7,903.5 6,485.1 7,358.1 

Net change, cubic meters -216.4 -2,652.5 -527.7 -3,396.6 

Total area Total change per unit channel length, cubic meters/meter 2.2 7.2 5.9 6.7 

Net change per unit channel length, cubic meters/meter -0.2 -2.4 -0.5 -3.1 

Total change per unit drainage basin area, cubic meters/square kilometer 10.0 33.2 27.2 30.9 

Net change per unit drainage basin area, cubic meters/square kilometer -0.9 -11.1 -2.2 -14.3 

Erosion, cubic meters 414.8 4,170.8 1,910.0 3,584.5 Deposition, cubic meters 448.5 1,400.0 2,017.1 954.4 Total change, cubic meters 863.3 5,570.8 3,927.1 4,538.8 

Net change, cubic meters 33.6 -2,770.8 107.1 -2,630.1 

Reference channel area Total change per unit channel length, cubic meters/meter 0.8 5.1 3.6 4.1 

Net change per unit channel length, cubic meters/meter 0.0 -2.5 0.1 -2.4 Total change per unit drainage basin area, cubic meters/square kilometer 3.6 23.4 16.5 19.1 

Net change per unit drainage basin area, cubic meters/square kilometer 0.1 -11.6 0.4 -11.1 

BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002
29 

Table 5. Total annual and net annual geomorphic change at Bear Creek at Crane Bottom compared with seven other sites in the Ozarks (McKenney and Jacobson, 1996). [km, kilometer; m, 

meter] 

Total volumetric change

Annual Annual 

change per change per Annual change 

unit unit per channel

Basin Reach Annual drainage channel length, per unit

area, length, geomorphic area, length, drainage area, 

Net volumtetric change, deposition minus erosion 

Annual 

Annual 

change per change per Annual change 

unit unit per channel

Annual drainage channel length, per unit

change, area, length, drainage area,

2 3 3 2 3 3 2 3 3 2 3 3 2 Study Reach km m change, m m /km m /m m /m/km m m /km m /m m /m/km

Bear Creek at Crane Bottom, total area 238 1096 7,358 30.9 6.7 0.0282 -3,397 -14.3 -3.1 -0.0130Bear Creek at Crane Bottom, bankfull channel 238 1096 4,539 19.1 4.1 0.0174 -2,630 -11.1 -2.4 -0.0101Little Piney Creek at Hickory Point, Missouri 380 760 818 2.2 1.1 0.0028 -347 -0.9 -0.5 -0.0012

Jacks Fork at Fox Farm, Missouri 87 350 286 3.3 0.8 0.0094 -34 -0.4 -0.1 -0.0011

Jacks Fork at Ratcliff Ford, Missouri 422 560 1,457 3.5 2.6 0.0062 154 0.4 0.3 0.0007Jacks Fork at Burnt Cabin, Missouri 789 940 3,520 4.5 3.7 0.0047 -1,359 -1.7 -1.4 -0.0018Buffalo River at Wilderness Boundary, Arkansas 150 470 241 1.6 0.5 0.0034 -173 -1.2 -0.4 -0.0025Buffalo River at Blue Hole, Arkansas 1020 840 1,042 1.0 1.2 0.0012 -421 -0.4 -0.5 -0.0005Buffalo River at Shineeye, Arkansas 2150 800 3,349 1.6 4.2 0.0019 -2,434 -1.1 -3.0 -0.0014Source for other streams: McKenney, R. and Jacobson, R.B., 1996, Erosion and deposition at the riffle-pool scale in gravel-bed streams, Ozark Plateaus, Missouri and 

Arkansas, 1990-95: U.S. Geological Survey Open-File Report 655-A. 

PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 
30 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

elsewhere in the Ozarks over different time periods 

(McKenney and Jacobson, 1996; table 5). Three of 

the sites listed in table 5 are from the Buffalo River 

and three of the sites are from Jacks Fork, Missouri. 

The Jacks Fork sites experienced an estimated 50-year 

recurrence interval flood during the monitoring period. 

In addition to temporal and physiographic differences 

among sites, the comparison data in table 5 differ 

from the Crane Bottom study in that they were calculated from annual surveys over 3 to 7 years. Even 

with variations that might result from differences 

among sites and monitoring times, the large rates of 

volumetric change on Bear Creek are notable. 

Different habitat units responded differently to 

sediment transporting events during the monitoring 

period. Of particular interest was the tendency of riffles and races to experience deposition during the 

December 2001 – February 2002 period and then to 

experience erosion during the succeeding February 

2002 – June 2002 period, with pools and glides experiencing the opposite effects (fig. 21). Cross sections 

that had small reference-channel area in June 2001 

(that is, mostly riffles and races) decreased in area 

from December 2001 – February 2002 because of 

deposition whereas cross sections that had large reference-channel area increased in area in the same time 

period because of erosion. The trend is opposite for 

the time period February 2002 – June 2002 when riffle-race cross sections increased in areas because of 

erosion and glides and pools decreased in area 

because of deposition. 

The implication of these changes is that floods of 

varying magnitude can have very different effects on 

the quantity and quality of stream habitat. The largest 

Figure 21. Change in cross section area for two survey intervals compared to February 2002 cross section area. 

Small cross section areas in February 2002 are riffles and large areas are pools. The 2-4 year flood between 

February 2002 and December 2001 increased areas of pools and decreased areas of riffles. The 1-year flood 

between February 2002 and June 2002 decreased the area of pools and increased the area riffles. 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 31 

flood in the December 2001 – February 2002 period 

was estimated to have a 2- to 4-year recurrence interval whereas the largest flood in the February 2002 – 

June 2002 period was at most a 1-year event. 

Although the estimated frequencies of these two 

floods are not very different, they had opposite effects 

on stream habitat maintenance, suggesting that some 

threshold exists in the maintenance processes. This 

idea is consistent with the theory of velocity reversal 

(Keller, 1971), which holds that as discharge increases 

and water-surface slope equalizes between pools and 

riffles, a threshold is reached at which average velocities in pools become greater than the average velocities in riffles. The monitoring results from Bear Creek 

may support this idea: that at some range of discharge 

the shear stresses and sediment transport capacity in 

pools exceeds that of riffles, causing erosion in the 

pools and deposition in riffles. Possibly, however, the 

additional smaller floods during the survey periods, 

the sequence of floods, backwater effects, or varying 

sediment supply could also influence the observed 

geomorphic change. Calculation of boundary shear 

stresses from hydraulic model results, as discussed in 

a later section, provide further insight into the idea of 

a velocity reversal. 

Scour and Fill Measured with Scour Chains 

Excavation of scour chains confirmed that substantial scour does occur on Bear Creek; that is, 

changes in the surface topography measured in cross 

sections is a minimum measure of the volume of sediment moving through the system. Moreover, because 

water depths limited scour-chain installation to glides 

and riffles, these scour chain measurements do not 

necessarily measure the maximum amount of scour 

possible in this stream. In some cases, scour chains 

were not recoverable after the flood events, with the 

implication that they were completely removed by 

scour equal to at least the length of the chain (table 6). 

In other cases, the chains were recovered and the 

length of the chain that was bent over was used as an 

indicator of maximum scour. 

Measured scour in the 15 locations varied from 0 

to greater than 64 cm. The only chains that did not 

experience scour were in dense thickets of water willow on gravel-cobble bars (fig. 22). The water willow’s dense network of rhizomes and roots provides 

resistance to erosion. Some areas of water willow did 

experience erosion, but primarily through undercutting 

of the plants. For example, the scour chain in the 

middle of the cross section downstream of CS25 (fig. 

17) was installed in a stand of water willow. By June 

2002, 24 cm of the chain was free in the water. A 

scarp capped in water willow remained adjacent to the 

chain indicating the former surface elevation; such 

scarps were apparent in several locations in the vicinity. 

Scour chain results indicate that substantial erosion and redeposition are possible on Bear Creek. 

Geomorphic change measured in cross sections, therefore, is a minimum evaluation of total geomorphic 

change between surveys. 

Sediment Transport Measured with Painted Rocks 

In the best-case scenario, the painted rock experiment would have been able to evaluate the minimum 

discharge required to transport the rocks. Instead of a 

flood that was just capable of transporting the experimental rocks, however, Bear Creek experienced a 

peak discharge estimated to have a 1-2 year recurrence 

interval (310 cms at Silver Hill streamgage, December 

16, 2001), immediately after the rocks were emplaced. 

No painted rocks were found at their original locations 

during a visit to the site on December 19. Moreover, 

all herbaceous vegetation had been removed from the 

gravel-bar location where the rocks had been placed. 

The high flows in December 2001 were followed by 

additional high flows in January and February 2002. 

Because flood discharges during the experiment were 

far in excess of the minimum needed to transport 

gravel, the painted rock experiment was not effective 

in identifying an entrainment threshold. However, the 

experiment was successful in confirming that a 1-2 

year recurrence flood on Bear Creek is capable of substantial entrainment of 8-32 mm gravel. 

The frequent, high magnitude floods during the 

winter and spring of 2001-2002 contributed to an 

extremely low recovery rate for assessing transport 

distance. Only one painted rock was recovered during 

a survey on February 15, 2002. This was an orange 

rock (b axis of 15 mm), recovered approximately 320 

m downstream of its original location. 

Hydrologic Dynamics and Habitat 

We assessed habitat dynamics resulting from 

hydrologic variation using a two-dimensional 

hydraulic model of Bear Creek. The model is useful 

for inventorying habitat quantities over a wide range 

of discharges. The relation between habitat availability and discharge can then be combined with the time 

series of discharges to assess the temporal distribution 

of habitat. 

Methods 

The two-dimensional hydraulic model we used 

solves the shallow-water, depth-averaged equations to 

balance mass and momentum on a finite element 

mesh. Results from a two-dimensional model provide 

a map view of depth and depth-averaged velocity for a 

given, steady discharge. The maps of continually 

varying depth and velocity can be used to inventory 
32 

Table 6. Information on scour chains installed in September 2001. [ds, downstream; us, upstream; cm, centimeter] 

Approximate surface 

elevation change, in cm (+ Estimate of 

for deposition, - for erosion) depth of 

Location Scour scour relative Scour

Cross oncross chain Date of Sept. 2001 to Sept. 2001 to to September chain 

section Habitat section length, cm search Feb. 2002 June 2002 2001 surface found? Comments 

777

8

8816 16 16 17 17 17 ds of 25 ds of 25 

ds of 25 

us of 25 

us of 25 

us of 25 

Riffle Riffle Riffle 

Glide 

Glide Glide 

Riffle 

Riffle Riffle 

Glide 

Glide Glide 

Riffle 

Riffle 

Riffle 

Glide 

Glide 

Glide 

Left 

Middle 

Right 

Left 

Middle 

Right 

Left 

Middle 

Right 

Left 

Middle 

Right 

Left 

Middle 

Right 

Left 

Middle 

Right 

43 Feb. 15, 2002 

60 Feb. 15, 2002 

52 Feb. 15, 2002 

64 Feb. 15, 2002 60 Feb. 15, 2002 

50 Feb. 15, 2002 

63 June 20, 2002 

69 June 20, 2002 

42 June 20, 2002 

65 June 20, 2002 

62 June 20, 2002 

72 June 20, 2002 

63 June 23, 2002 

45 June 23, 2002 

49 Feb. 14, 2002 

June 23, 2002 

61 Feb. 14, 2002 

63 Feb. 14, 2002 

June 23, 2002 

46 Feb. 14, 2002 

June 23, 2002 

-45 

-28 

-1 

-6 

-4 

-32 

2

19 

19 

22 

10

14

-6

-19 

6

26

2

-24

3

64 

45 cm 

at least 60 cm 

> 52 cm ? 

> 64 cm ? 

> 60 cm ? 

> 50 cm ? 

30 cm 

> 19 cm 

33 cm 

0

24 cm 

0

0

40-50 cm ? 

< 8 cm 

12 cm 

< 16 cm 

22 cm 

No 

No 

No 

No 

No 

No 

No 

Yes 

No 

Yes 

Yes 

No 

Yes 

Yes 

Yes 

Yes 

Yes 

Yes 

Yes 

Yes 

Yes 

Bedrock exposed at former location of scour chain.

Dug to bedrock without finding chain.

Vegetation was present when chain was installed; no remaining 

roots in February. Maximum depth of search was about 30 cm.

No metal detector signal.

Maximum depth of search was 20 cm below September surface 

level. No metal detector signal.

Maximum depth of search was 35 cm below September surface 

level. No metal detector signal.

No metal detector signal.

Maximum depth of search was 22 cm below September surface 

level.

Angled downstream and slightly to right bank.

Maximum depth of search was 47 cm below September surface 

level.

Chain found in ambiguous position.

Angled downstream and slightly to left bank.

Maximum depth of search was 47 cm below September surface 

level.

Dense water willow roots still intact.

Originally in water willow. 24 cm of chain loose in water and 

adjacent to scarp of intact water willow plants.

Dense water willow roots still intact.

Dense water willow roots still intact.

Unchanged to within 2 links (8 cm) of top of chain. Reburied 

chain vertically.

Unchanged to within 4 links (16 cm) of top of chain. Reburied 

chain vertically.

BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 33 

Figure 22. Photographs of rhizomes of water willow at surface of stable gravel bar. 

areas and spatial characteristics of habitats over the 

range of modeled discharges. To model flow conditions, we used River2D (version 0.90, July 23, 2002) 

and its supporting programs, R2D_Bed and 

R2D_Mesh1. This two-dimensional hydrodynamic 

model code has several features that make it well suited for simulating flow of rivers and streams such as 

Bear Creek. River2D handles wetting and drying by 

converting to ground-water flow equations for subsurface flow, and it explicitly handles transitions between 

sub- and supercritical flow (Steffler and Blackburn, 

2001). 

We modeled steady discharges from 0.13 to 556 

cms. This range corresponds to the observed range of 

flows during the study period, 99% exceedance to 

approximately a 1 in 4 year probability flood (table 7). 

Input data and parameters 

The topographic map of Crane Bottom (fig. 23A) 

is based on cross-section survey data from June 2001, 

augmented with additional data points as needed to 

define the major topographic features for the entire 

study reach. We used a contouring program (Surfer®, 

Golden Software, Golden, Colorado) and GIS software (ArcView®, ESRI, Redlands, California) to aid in 

contouring the data points and developing the onemeter grid that was used as model input. For the purpose of modeling, the topography was extended 

upstream and downstream of the surveyed reach by 

adding fictitious inflow and outflow chutes; this minimized problems with flow recirculation across the 

boundary and moved the boundary conditions away 

from the area used to inventory habitats. 

The substrate map of the reach is based on dominant particle size data collected at survey points during the June 2001 survey. This substrate map was 

used to generalize and assign roughness height, the 

resistance parameter used by River2D (fig. 23B). D84 

values (the 84th percentile of the cumulative particlesize distribution) calculated from the cross-section 

pebble-count data provided a preliminary guide for 

appropriate roughness height values, but final roughness height values are a product of calibration. 

The mesh in figure 24 was used for the full range 

of flows with only minor alterations to either improve 

model stability (generally by increasing local mesh 

density) or to reduce computational effort (by trimming part of the mesh at high elevations for low 

flow). The boundary line, breaklines, and preliminary 

nodes were generated in ArcView®, and the mesh was 

refined in R2D_Mesh and River2D. The mesh density 

provides a suitable number of elements across the 

channel at the lowest flows. 

Boundary conditions necessary to run this model 

are discharge at the upstream end of the reach and a 

fixed stage at the downstream end. Thirty-two discharges were selected to represent the range of flows 

observed during the study period (table 7). Because 

discharge data are available at Silver Hill, flow 

exceedance and flood-frequency analyses was 

1

The River 2D programs are freely available from University of Alberta: <http://www.river2d.ualberta.ca.> June, 2003. 
34 

1

BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002 

Table 7. Modeled discharges, habitat areas, flow-duration, and flood-frequency data for Crane Bottom. Exceedance data are based on 

daily mean discharges for the period of record; flood frequency data are based on annual peak flows. 

Habitat Area, in Square Meters 

Discharge at 

Crane 

Bottom, in Edgecms water Glide Pool Race 

Discharge 

non- Discharge 

Total exceedance exceedance 

wetted relative Relative Exceedance 

Riffle habitat frequency frequency days per year 

0.10 4,941 8,082 550 0 368 13,941 1% 99% 360.3 

0.13 4,859 8,271 593 0 481 14,204 4% 96% 351.1 

0.14 4,785 8,390 634 0 568 14,376 6% 94% 344.6 

0.18 4,710 8,508 675 0 655 14,548 11% 90% 326.7 

0.22 4,550 8,642 752 0 851 14,795 16% 84% 307.7 

0.27 4,521 8,816 818 1 948 15,104 20% 80% 290.9 

0.31 4,456 8,925 894 3 1,068 15,346 25% 75% 273.0 

0.38 4,402 9,015 973 14 1,253 15,657 33% 67% 243.8 

0.41 4,379 9,016 990 24 1,344 15,753 37% 63% 230.7 

0.51 4,426 9,146 1,110 55 1,530 16,267 40% 60% 219.4 

0.62 4,506 9,212 1,260 112 1,694 16,784 45% 55% 200.0 

0.82 4,741 9,486 1,710 257 1,369 17,563 50% 50% 181.8 

1.0 4,759 9,434 1,987 447 1,561 18,188 55% 45% 165.0 

1.3 4,626 9,306 2,284 717 1,793 18,726 60% 40% 145.3 

1.8 4,441 9,132 2,649 1,070 2,118 19,410 65% 35% 127.8 

2.2 4,138 9,073 2,763 1,563 2,485 20,022 70% 30% 109.9 

2.8 3,806 9,236 2,333 2,237 2,936 20,548 75% 25% 91.3 

3.6 3,521 9,564 1,820 2,915 3,358 21,178 80% 20% 73.4 

5.0 2,848 9,396 1,596 3,960 4,031 21,831 85% 15% 54.0 

7.1 2,304 8,273 1,529 5,635 4,906 22,647 90% 10% 36.5 

8.3 2,187 7,546 1,594 6,680 5,152 23,159 92% 8% 29.2 

10.6 2,026 6,502 1,444 8,103 5,809 23,884 94% 6% 21.9 

13.1 1,862 6,104 1,341 8,926 6,319 24,552 96% 4% 14.6 

25.2 1,236 5,330 1,872 9,327 8,662 26,427 98% 2% 7.3 

39.9 958 5,012 2,252 8,904 10,698 27,824 99% 1% 3.7 

69.0 848 4,543 3,272 7,750 13,465 29,878 99% 1% 3.3 

98.0 802 4,476 3,723 7,118 15,364 31,483 99% 1% 2.2 

156 823 4,630 2,736 7,738 18,131 34,058 100% 0% 0.0 1 Estimated Recurrence Interval

242 1,182 4,282 1,577 6,046 24,138 37,225 1 

290 4,833 7,579 2,991 10,703 21,387 47,493 1-2 

340 9,232 19,477 14,591 24,729 15,116 83,145 1-2 

450 7,082 24,437 11,487 21,589 26,174 90,769 2-4 

556 4,671 27,590 10,271 23,836 44,192 110,560 2-4 

Recurrence intervals are estimated from comparisons with recurrence intervals calculated for the same floods at other streamgages with longer records. 

See table 2. Discharges at Crane Bottom are estimated by regression model between measured discharges at Silver Hill and Crane Bottom for flows less 

than 160 cms. For flows greater than 160 cms, unit area discharges at Silver Hill were multiplied by drainage area at Crane Bottom to estimate discharge at 

Crane Bottom. 

completed on this dataset to select discharges. A 

regression between the Silver Hill discharge and the 

available Crane Bottom discharge measurements (fig. 

25) was used to determine the Crane Bottom discharge 

for the desired exceedance and probability values. To 

determine the downstream fixed stage values at the 

Crane Bottom modeling reach associated with the 

desired discharges, we used a regression between the 

stage at Silver Hill and the downstream Crane Bottom 

stage, taking into account the time lag between the 

peak flows at Silver Hill and Crane Bottom. We 

selected only stages that were not influenced by rapidly changing discharges or by backwater to construct 

the regression. 

Other parameters required by River2D include ,1 

and ,2 (coefficients used to calculate eddy viscosity), 

an upwinding coefficient to parameterize the finite 

element solving scheme, and ground-water transmissivity and minimum depth coefficients for aiding in 

wetting and drying calculations at the wetted 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 35 

Figure 23. Model input data grids for Crane Bottom. The input map grids were used to parameterize the finite element 

mesh bed file. A. Elevation grid. B. Bed roughness height (ks) grid. 

boundary. Eddy viscosity and upwinding parameters 

were kept as default values (0, 0.5, and 0.5). Groundwater transmissivity was set at 0.01 to minimize 

ground-water discharge for flows of 0.1 – 0.6 cms, but 

was increased to the recommended default value of 

0.1 for flows 0.6 – 556 cms. The minimum depth for 

ground-water flow determines the water depth at 

which the model treats discharge as ground-water flow 

rather than surface water. Stable models were 

achieved when this value was set to 0.05 for discharges 0.1 – 0.6 cms, and 0.1 for discharges 0.6 – 

556 cms. 

Calibration and validation 

Because water-surface-elevation profiles were 

available over a range of discharge from a relatively 

low summer flow to a 2- to 4-year flood, these profiles were used as the primary means of calibration. 

Water surface elevations for bankfull flows and below 

were measured directly, while the overbank water-surface elevations were based on high-water marks after 

the floods. The water surface elevations from the 

model were extracted from the center of each cross 

section to compare to the water-surface elevations 

measured in the field. 

Figure 26 shows measured and modeled water 

surface elevations. Water-surface elevations from 

June 2001 (0.45 cms), and December 2001 (3.5 cms 

and 340 cms) were used to calibrate the model and 

water-surface elevations from 0.18 to 570 cms (fig. 

26A, B) were used to validate model performance. 

Water-surface elevations were chosen to minimize 

backwater effects. Measured water-surface elevations 

from late December 2001 (23.5 cms) and February 

2002 show substantial deviations from the model 

because these flows occurred after the streambed was 

altered by high flows in December 2001 and January 

2002. 

In addition to close agreement between measured 

and modeled water-surface elevations, models were 

considered successful if they achieved a low net outflow (less than 5% of the flow was unaccounted by 

the model) over run times sufficient to achieve a 

steady state (usually greater than 10,000 time steps). 
36 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 24. Finite element mesh used for 2-dimensional hydraulic modeling at Crane Bottom reach of Bear Creek. 

Figure 25. Regression relation between Bear Creek discharge measured by U.S. Geological Survey near Silver Hill, Arkansas and 

discharge measured by National Park Service at Crane Bottom study reach. CB is Crane Bottom discharge; SH is Silver Hill 

discharge. 

Model results were also evaluated for whether they field were accepted if they affected only small areas 

realistically reproduced known flow patterns – such as and did not substantially affect habitat area calculaa large eddy near an embayment in the bank at cross tions. 

section 29 (as inferred from field observations). In 

some cases, modeled local instabilities in the flow 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 37 

Figure 26A. 

datasets. Entire range of flows. 

Water-surface elevation data plotted along study reach showing modeled, calibration, and validation water-surface elevation 

Habitat classification: 

We used the habitat classification system developed by Panfil and Jacobson (1999), which is based 

on depth and Froude number (fig. 27). To apply the 

habitat classification, data were extracted from 

River2D on a one-meter grid. A script was used to 

read the depth and Froude number data files, apply the 

classification scheme, and produce output files with 

the coordinate and habitat data. These output files 

were converted to grids in ArcView® for further analysis. 

Hydrodynamic Habitat Modeling Results 

Maps of depth, velocity, Froude number, and 

habitat classification are included in Appendix 2; figures 28A-C show variation in habitat areas with 

discharge. Habitats classified at high flows need to be 

evaluated with caution. For example, at high flows, 

areas that classify as riffles have fast, relatively shallow water and high Froude numbers where the water 

is running over grassy substrate on the terraces. 

Because of the lack of gravel/cobble substrate, these 

areas would not have the same habitat value as riffles 

within the channel. Similarly, areas that classify as 

edgewater habitats (with shallow depths and low 

velocities) will have very different substrates during 

high discharges than those that classify as edgewater 

during low discharges. Because the high-flow habitats 

exist for short periods of time relative to low-flow 

habitats, they probably have substantially different 

influences on stream ecosystem functions. At high 

flows, the importance of riffles and races may be that 

they are high-energy areas whereas edgewaters and 

pools are relative energy refugia. At flows above 10% 

exceedance, the areas of edgewaters and pools are relatively stable, indicating little change in availability of 

energy refugia (fig. 28B). 

From the minimum to median flows (approximately 0 to 0.9 cms), habitat areas are quite variable. 

At the lowest flows modeled in this study, riffles are 

mostly dry, leaving disconnected pool and glide areas. 

At these low flows, there is abundant edgewater 
38 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 26B. Water-surface elevation data plotted along study reach, showing modeled, calibration, and validation water-surface elevation 

datasets. Discharges limited to 69 cubic meters per second and less. 

habitat on the margins of the channel and pools area is 

at a minimum. Race habitats are missing completely 

until a discharge of about 0.3 cms (70% flow 

exceedance). As discharge increases, riffle, pool, race, 

and glide areas increase, whereas edgewaters 

decrease. Race area stays extremely small until nearly 

the median flow (0.8 cms). 

An integrated measure of habitat diversity was 

calculated using the Shannon-Wiener diversity index 

(Shannon and Weaver, 1949): 

m

SDI = −¦( P ln * P ) i i

i=1 

where SDI = Shannon-Weiner Diversity Index, P = 

proportion of area in habitat class i, and m = number 

of habitat classes. The SDI increases with number of 

habitat classes and with the evenness of the distribution of area among the habitat classes. For this stream 

reach, SDI of habitat classes increases rapidly from 

minimum flow to the median flow (50% flow 

exceedance), then increases more slowly to an asymptotic value at about 25% exceedance. As an integrated 

measure of habitat diversity, the SDI shows that Bear 

Creek habitat diversity is particularly sensitive to low 

flows (fig. 28A-C). 

Habitat areas and diversity index values can be 

calculated for any discharge value by interpolating 

values between modeled discharges. Habitat unit time 

series can then be calculated for any time series of 

flows on Bear Creek (fig 29). 

Because the habitat diversity index increases rapidly from the minimum to the median flow, periods of 

moderate discharge in winter to early summer are 

characterized by relatively high habitat diversity values, whereas late-summer and fall values are very low 

(fig. 29). Since January 1999, the most substantial 

habitat variation at Crane Bottom has been in area of 

riffles and races. In particular, the area of race habitat 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 39 

Figure 27. Scheme used for classifying model output into habitat 

units (Panfil and Jacobson, 1999). 

is sensitive to low flows, diminishing to zero below 

about 0.3 cms. Races were completely absent at 

Crane Bottom for nearly one half of the modeled time 

period. Areas of glides, pools, and edgewaters are 

more consistent over time, and are substantial even 

during periods of low flow in late summer and fall. 

Streambed Mobility 

Modeled depths and water-surface elevations can 

be used to calculate estimates of boundary shear stress 

on the bed, and to explore how much of the bed is 

potentially mobilized at various flows. The product of 

flow frequency and percentage of the bed mobilized 

by each flow is a measure of geomorphic work 

accomplished by each flow (following Wolman and 

Miller, 1960). An understanding of which flows are 

responsible on average for most of the bed mobilization on Bear Creek will help in evaluating flows necessary for habitat maintenance. 

Methods 

Bed mobilization can be estimated by comparing 

boundary shear stress with critical shear stress necessary to entrain bed material. Spatially distributed 

boundary shear stresses can be calculated using modeled water-surface elevation and depth outputs from 

the hydraulic models, using the total boundary shear 

stress equation (Chow, 1959): 

τ = ρgdS b

where, Jb = boundary shear stress in newtons per 

square meter (N/m2), D = unit weight of water (kg/m3, 

1000 kg/m3), g = gravitational acceleration constant 

(9.8 m/s2

), d = depth in meters, and S is the energy 

slope, approximated here by the water-surface slope. 

A map of water-surface slope was constructed by calculating slope on a cell-by-cell basis from the modeled water-surface elevations. This slope map was 

then smoothed by calculating a 7 m x 7 m moving 

average; smoothing helped eliminate extreme slope 

values resulting from small instabilities in the modeled flow field. The boundary shear stress map was 

created by multiplying the constants by slope and 

depth on a cell-by-cell basis. 

The shear stress necessary to initiate movement of 

the bed was estimated by calculating the critical shear 

stress to mobilize the median of the particle-size distribution (Shields, 1936): 

τ c = θ (ρ s − ρ )gD50 

where Jc = critical shear stress in N/m2

, 2= Shields 

dimensionless critical shear stress, D = unit weight of 

water (taken as 1000 kg/m3), Ds = unit weight of sediment (taken as 2650 kg/ m3

), g = the gravitational constant, and D50 = median particle size, in meters. 

The dimensionless critical shear stress varies with 

flow turbulence and characteristics of the particle-size 

distribution, including shape and packing of particles. 

We assumed fully hydraulically rough conditions and 

used a generally accepted value for gravel-cobble 

streambeds, 0.04 (Yalin and Karahan, 1979). For D50, 

we used the median of the entire pebble-count dataset 

(0.029 m, n = 2,964) for the Crane Bottom reach. By 

using the lumped, median value, our analysis focuses 

on the stability of the entire reach, and may therefore 

under or overestimate stability of areas within the 

reach. 

Incipient motion of the bed occurs when Jb/Jc = 1. 

As a general approximation, overall bed mobility 

occurs when the boundary shear stress is twice the 

critical shear stress, or Jb/Jc = 2 (Wilcock and 

McArdell, 1993). Subsequent analysis uses both of 

these conditions. 

Results 

The hydraulic models predict that boundary shear 

stresses are at maxima in riffles during flows ranging 

from about 0.1 – 13.1 cms and begin to relocate to 

pools by about 25.2 cms (fig. 30A-C). When flows 

reach 30.9 cms, the shear stress maxima are spread 

more uniformly in the reach and are no longer concentrated in the low-flow riffles (fig. 30D). At flows of 

240 cms and higher, models predict that shear stress 

maxima are concentrated in the pools (figs. 30D, E), a 

result that is consistent with the velocity reversal 

hypothesis (Keller, 1971). The velocity reversal 

hypothesis states that the locations of maximum 

velocity in a river shift from riffles to pools when 

discharge exceeds a threshold, resulting in scour of 
40 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 28. Relations between discharge and area of habitat units, and Shannon-Wiener diversity index. The three 

graphs are of the same data but over varying ranges of discharge. 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 41 

pools and deposition in riffles. However, the change 

from deposition to erosion in pools in Bear Creek, 

measured as geomorphic change in the cross sections, 

occurs at flows that are much less frequent than 20 

cms: the modeled shear stress reversal occurs at flows 

that are equaled or exceeded about 7 days per year 

whereas the survey data indicate that flows that 

change from pool-filling to pool-scouring occur 

between once a year to once every 2- to 4-years. It is 

possible that although shear stress maxima occur in 

pools at discharges greater than 20 cms, critical shear 

stresses for the total bed material mobilization in the 

pools are not achieved until discharges are much higher. 

Maps of boundary shear stress can be compared 

to reach-median particle size to calculate the proportion of the bankfull channel bed that can be mobilized 

by different discharges. The modeling results predict 

that less than 30% of the bed is fully mobilized until 

discharges exceed about 40 cms, a flow that is equaled 

or exceeded only about 1 percent of the time during 

the year (that is, 3-4 days per year). From 40 to about 

100 cms there is a sharp, linear increase in the proportion of the bed mobilized, followed by a gentle rise to 

an asymptote at about 290 cms. By 450 cms the 

model predicts that 100% of the bed will be fully 

mobilized (fig. 31). 

The percent of the bed mobilized by a given 

discharge (magnitude) can be multiplied by the frequency of that discharge to calculate the magnitude x 

frequency product, a measure of geomorphic work 

(Wolman and Miller, 1960). According to this theory, 

when the product of magnitude and frequency is plotted against discharge, the peak of the curve occurs at 

the discharge that transports most of the sediment, or 

in this case, is responsible for the most bed mobilization and habitat maintenance. The magnitude frequency product curve for Crane Bottom has a distinct peak 

at 13-25 cms, flows that attain incipient entrainment 

for about 20-40% the bed (fig. 31). The magnitude 

frequency curve for full entrainment peaks at 25 - 40 

cms, a flow that is predicted to fully mobilize about 

17 - 30% of the bed. 

The flows predicted to do the most geomorphic 

work in terms of mobilizing the bed of Bear Creek at 

Crane Bottom are relatively frequent, occurring multiple days per year on average. Theory holds that the 

flows that generally do the most geomorphic work in 

terms of stream sediment transport – often referred to 

as dominant discharges —should be around bankfull 

stage, with recurrence intervals on the order of 1 – 1.5 

years on the annual maximum series (Wolman and 

Miller, 1960; Andrews, 1980). Other authors have 

pointed out that the peak of the magnitude frequency 

relation will vary with the shape of the sediment transport curve, the shape of the flow frequency curve, and 

the caliber of sediment under consideration (Nash, 

1994). In this analysis, several factors may be responsible for the relatively high frequency of flows that are 

dominant in bed mobilization. 

• We have used the area of the bed mobilized as an indicator of geomorphic 

work that rejuvenates benthic habitats 

by flushing sediment. This measure of 

work is likely to have a discharge-mag 

nitude relation that rises and reaches an 

asymptote more quickly with increasing 

discharge than a bed-load transport 

curve. Bed load transport curves are 

unlikely to reach an asymptote as long 

as sediment is available. 

• The frequency distribution of daily 

mean discharges on Bear Creek is dominated by low flows. This skews the 

calculation of dominant discharge to 

low discharge values. 

• The relatively high slope (typically 

0.2%) and abundant bed material in the 

coarse gravel size range contribute to 

high rates of bed mobilization. 

The 13 – 40 cms discharge is the best available 

estimate of the flow that is required to maintain Bear 

Creek stream habitats by transporting sediment and 

flushing fine sediment from the substrate. The geomorphic data, however, suggest that flows as much as 

twice as large (comparable to the January 31, 2002 

flood) may be necessary to redistribute substantial 

quantities of sediment among pools and riffles (table 

4, fig. 20). 

These calculations illustrate the function of large 

flows in rejuvenating habitats by entraining and transporting sediment. The specific relations between 

discharge and percent of the bed entrained (fig. 31) 

are highly dependent on accuracy of the hydraulic 

model, choice of the Shield’s parameter value, the 

assumption that full mobilization occurs when Jb/Jc = 

2, and the assumption that bed material particle size is 

uniform in the reach. Variation in these factors can 

change the shape of the relation between discharge 

and bed entrainment. Documented changes in channel 

morphology during the course of this study support 

the idea that these calculations are a conservative 

(minimum) estimate of the mobility of the Bear Creek 

bed (table 4, fig. 20). The shape of the magnitude frequency product curve, however, is relatively insensitive to the Jb/Jc calculation; even if the Shields parameter varies by +/- 40% the peak of the relation remains 

at a discharge of 25 - 40 cms. 

Bed mobilization and habitat alteration may be 

affected by other factors not taken into account in this 
42 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 29. A. Riffles 

and races. D. Daily mean discharge. 

Time series of modeled habitat areas, diversity index, and discharge at Crane Bottom. 

B. Glides, pools, and edgewaters. C. Shannon-Wiener diversity index. 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 43 Figure 30. Maps of relative ranges of boundary shear stresses showing shift of maximum shear stress from riffles to pools. A. 10.6 cubic meters per second. B. 13.1 cubic meters per second. C. 25.2 cubic meters per second. D. 39.9 cubic meters per second. E. 242 cubic meters per second. F. 556 cubic meters per second. Riffle and pool locations refer to low-flow positions. 
44 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Figure 31. Relations between discharge and calculated percent of bed entrained, and discharge and magnitude x frequency product. Calculations include proportion of bed entrained assuming incipient motion (boundary shear stress is 

equal to critical shear stress) and assuming full mobilization (boundary shear stress is 2 times critical shear stress). 

modeling exercise. In particular, emergent aquatic 

vegetation – primarily water willow – is clearly a stabilizing influence on these gravel bars, and would 

impart a substantial transport threshold. The threshold 

effect could substantially change the calculated relation in fig. 31. 

Discussion: Sources of Physical Stream Habitat Variability 

Physical stream habitats in Bear Creek vary with 

discharge (hydrologic dynamics) and with sediment 

transporting events (geomorphic dynamics). The 

monitoring period for this study was relatively wet, 

and high flow events convincingly demonstrated that 

substantial geomorphic changes in physical habitats 

are possible on Bear Creek. The hydraulic modeling 

of habitats served to simulate sensitivity of habitats to 

hydrologic variation alone. 

The broadest aspects of physical habitat at Crane 

Bottom did not change during the study period: the 

framework pool-riffle sequence persisted, and the 

pools and riffles maintained their positions and relative areas. The greatest alteration to the broad-scale 

framework involved a few 10’s of meters of migration 

of the crest of the downstream riffle (near cross section 7) and some movement of transient, bed-materialwave riffles near cross sections 18 and 20 during the 

monitoring period. 

At the same time, changes in the elevations of 

some habitats, and evidence of scour, demonstrate that 

the Bear Creek stream habitats are susceptible to substantial geomorphic change, largely in the vertical 

dimension. The series of floods monitored during this 

study were responsible for approximately 2.4 m3 of 

net erosion per meter of channel length in the reference channel (table 5). This value is nearly an order 

of magnitude greater than many other monitored sites 

in the Ozarks, a fact that might be explained in part by 

the abnormally high discharges during the monitoring 

period. Large amounts of geomorphic change might 

also be associated with passage of waves of sediment 

that have been liberated by land-use disturbances 

upstream and are moving slowly through the drainage 

basin (Jacobson and Gran, 1999). 

Like six of seven of the reference monitoring sites 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 45 

in the Ozarks (table 5), Crane Bottom was characterized by net erosion during this monitoring period. 

This might be a coincidence, or it might be that, as 

argued by Jacobson (1995), most small drainage 

basins in the Ozarks are currently exporting sediment 

to downstream reaches. Without establishing a 

detailed history of the Bear Creek drainage basin it is 

impossible to evaluate the extent to which the Crane 

Bottom reach has been affected by historical land use. 

Different floods had substantially different effects 

on where erosion and deposition occurred. The largest 

monitored flood (with an estimated 2- to 4-year recurrence interval) scoured pools and deposited gravel and 

cobbles in riffles whereas floods of an estimated 1­

year recurrence interval deposited sediment in pools 

and eroded riffles. Essentially, the larger flood 

increased habitat depth diversity whereas the 1-year 

flood tended to homogenize habitat depths. The specific effects of these habitat changes on biota in Bear 

Creek are unknown. Certainly, all the floods in excess 

of 1-year recurrence interval transported sediment 

over substantial areas of the streambed, processes that 

could disturb benthic invertebrate populations, and/or 

rework particle-size characteristics of the bed, and 

therefore had potential to influence stream communities. Perhaps the most important function of geomorphic dynamics is the deepening of pool habitats by 

large floods, a process that maintains deep-water areas 

during subsequent periods of low flows. 

Estimates of thresholds of change from shear 

stress modeling suggest that the bed material of Bear 

Creek can be mobilized by relatively frequent flows, 

with as much as 60% of the bed being mobilized by 

flows that occur, on average, 3 days per year. Over 

the long term, flows that occur 4-7 days per year are 

responsible for mobilizing the greatest proportion of 

the bed area, and are therefore presumably responsible 

for most rejuvenation of benthic habitats. Vegetation 

on gravel bars – principally water willow – seems to 

increase entrainment thresholds and serves to stabilize 

gravel bars. Decreases in gravel transport due to vegetation are not quantified, but field observations support the idea that emergent aquatic vegetation is an 

important factor in channel stability in the Ozarks. 

Hydraulic modeling provides a basis for evaluating sensitivity of physical habitats to variations in 

discharge in Bear Creek. Glides and edgewaters are 

relatively abundant and insensitive to changes in 

discharge. Pools have residual area of about 4 percent 

of the total habitat area at the lowest flow modeled, 

and increase substantially to a peak area at discharges 

between 50 and 25% exceedance. An even higher 

peak in pool area occurs at overbank discharge (about 

340 cms; fig. 28C) because of large areas of deep, 

slow water on the flood plain; however, these pool 

areas exist very infrequently. Riffles and races occupy 

very small areas at the lowest discharges and increase 

rapidly with increasing discharge. Races are the most 

sensitive to discharge because they disappear at discharges below 70% exceedance. 

As a general measure of ecological value, the 

diversity of habitat is very sensitive to discharge from 

100 to 50% exceedance, and fairly sensitive up to 

25% exceedance, at which point diversity declines 

slowly with increasing discharge to a minimum when 

flow goes overbank at about 225 cms (fig. 28). At 

discharges greater than the top of the bank, diversity 

increases with increasing discharge as broader areas of 

the flood plain and terraces are inundated. The sensitivity of the Shannon-Wiener diversity index to 

discharge variation indicates that alterations to low 

flows on Bear Creek may be expected to cause substantial changes in ecological structure. 

Specific biological effects of varying discharge 

are more difficult to quantify and were not the subject 

of this study. However, some information from the 

literature is available to evaluate potential linkages. 

Pool area is restricted at the very smallest discharges, 

which could affect pool-dwelling species such as sunfish and smallmouth bass (Peterson and Rabeni, 

2001). Potentially more important, however, is the 

complete loss of race and riffle habitat that occurs at 

very low flows (fig. 28A). These habitats are generally used by benthic fish species such as the rainbow 

darter and the Ozark minnow. Loss of these habitats 

for extended periods of time could displace or extirpate these species. 

Summary and Conclusions 

We investigated the physical stream habitat of 

Bear Creek, northern Arkansas, to document and analyze sensitivity of habitats to geomorphic and hydrologic dynamics. Like most streams in the Ozarks, 

Bear Creek has had a history of land-use disturbance 

that has mobilized excess gravel bedload. Continued 

downstream movement of gravel bedload through the 

channel network can be expected to cause persistent 

geomorphic disturbance, which will act as a background to any additional hydrologic alterations. 

The study reach selected for monitoring and modeling of Bear Creek is Crane Bottom, about 1 km 

upstream of the junction of Bear Creek with the 

Buffalo River. The reach consists of three riffle-pool 

sequences and has a representative selection of 

hydraulic habitat units. We installed 31 cross sections 

for monitoring geomorphic changes; the cross sections 

were resurveyed three times in a one-year period to 

document erosion and deposition. Cross-section monitoring was supplemented with particle tracer experiments and re-excavation of scour chains. We used a 

two-dimensional, finite-element hydraulic model to 
46 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

quantify areas of physical habitat available at a range 

of discharges from low flows to 2- to 4-year recurrence interval floods. The results of the modeling 

were used to assess sensitivity of habitat availability 

to flow alterations, and to evaluate the frequency of 

flows capable of initiating bed material movement. 

The time period selected for this study was relatively wet. Rainfall in the Bear Creek drainage basin 

was approximately 140% of normal during this time. 

Seven individual floods of approximate bankfull stage 

were recorded; the largest was estimated to have a 2­

to 4-year recurrence interval. 

Monitoring of geomorphic change at Bear Creek 

during this period documented that relatively frequent 

floods – those that occur several times per year to 

those that occur on average once every 2 to 4 years – 

are instrumental in maintaining diversity of physical 

habitats through erosion and deposition of gravel. 

These floods create the geomorphic framework that 

determines depths and velocities produced by lower 

discharges. Modeling of the critical shear stresses 

necessary to initiate sediment movement indicates that 

most of the bed mobilization that maintains benthic 

habitat is accomplished by flows that occur 4-7 days 

per year. 

For a range of flows that do not transport appreciable sediment, habitat availability is determined by 

hydraulic controls on depth and velocity. Habitat 

availability was modeled using a depth-averaged, 

finite-element, 2-dimensional hydraulic model, calibrated to measured flows. This class of model can 

develop inventories of habitat areas, but depends on 

the assumption that the channel morphology does not 

change during the range of flows. 

Areas of hydraulically defined physical habitats in 

Bear Creek vary substantially with discharge, especially for flows that are equaled or exceeded 100-50% 

of the time. An index of diversity of habitat also 

varies substantially over this range of discharge, indicating that alteration of low flows may be expected to 

cause changes in the structure of the stream ecosystem. Among hydraulic habitat units, areas of races 

and riffles are the most sensitive to discharge. These 

habitats diminish substantially as discharge decreases 

from 50% to 75% flow exceedance; races disappear 

completely at about 70% flow exceedance. 

This analysis establishes the roles of high and low 

flows in maintaining and sustaining physical habitat 

on Bear Creek. Different flows have different roles: 

high flows determine the geomorphic template by 

scouring pools, transporting sediment, rejuvenating 

benthic habitat, and depositing sediment in riffles; low 

flows that prevail most of the time combine with the 

geomorphic template to create habitat. How habitat 

might change in the future, however, is dependent on 

factors that have not been measured as part of this 

study. Like most Ozarks streams, Bear Creek is subject to ongoing geomorphic changes as waves of bedmaterial load migrate downstream through the river 

basin. These waves could significantly vary sediment 

supplied to discrete reaches of Bear Creek, and thereby alter sediment transport and the resulting template 

of channel morphology. In addition, changes in 

hydrology in the basin could result from land-use 

change, water resource development, or climate 

change. Changes in hydrologic budget may change 

the frequency and magnitude of habitat-maintaining 

events, and may change the seasonal distribution of 

low flows and associated habitats. The results of this 

study document the dependence of physical habitat on 

the entire spectrum of flows. 

Alteration of the availability of physical habitat 

could be expected to affect ecological communities of 

Bear Creek. Physical habitats of Ozarks streams are 

known to be highly associated with specific ecological 

processes, individual species, or assemblages of 

species. The high sensitivity of races and riffles in 

Bear Creek to variability of low flows indicates that 

benthic, riffle- and race-dwelling species such as the 

rainbow darter (Etheostoma caeruleum) and Ozark 

minnow (Notropis nubilus) could be at risk if low 

flows were significantly altered. Similarly, pooldwelling species such as smallmouth bass 

(Micropterus dolomieu) and Ozark bass (Ambloplites 

constellatus) could be at risk if decreases in peak 

flows favored sedimentation in pools. 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 47 

References Cited 

Andrews, E.D., 1980, Effective and bankfull discharges of streams in the Yampa river basin, 

Colorado and Wyoming: Journal of 

Hydrology, v. 46, p. 311-330. 

Andrews, E.D., 1984, Bed-material entrainment and 

hydraulic geometry of gravel-bed rivers in 

Colorado: Geological Society of America 

Bulletin, v. 95, p. 371-378. 

Barbour, M.T., Gerritsen, J., Snyder, B.D., and 

Stribling, J.B., 1999, Rapid bioassessment 

protocols for use in streams and wadeable 

rivers – Periphyton, benthic macroinvertebrates, and fish (2nd ed.): U.S. Environmental 

Protection Agency, Office of Water, EPA 841-

B—99-002. 

Chow, V.T., 1959, Open-channel hydraulics: New 

York, McGraw-Hill, Inc., 680 p. 

DeVries, P. and Goold, D.J., 1999, Leveling rod base 

required for surveying gravel river bed elevations: Water Resources Research, v. 35, p. 

2877-2879. 

Doisy, K.E. and Rabeni, C.F., 2001, Flow conditions, 

benthic food resources, and invertebrate community composition in a low-gradient stream 

in Missouri: Journal of the North American 

Benthological Society, v. 20, p. 17-32. 

Femmer, S.R., 1997, Water-quality assessment of the 

Ozark Plateaus study unit, Arkansas, Kansas, 

Missouri, and Oklahoma — Habitat data and 

characteristics at selected sites, 1993-95: 

U.S. Geological Survey, Open-File Report 

97-236, 44 p. 

Gordon, N. D., McMahon, T. A., and Finlayson, B. L., 

1992, Stream Hydrology: An introduction for 

ecologists: Chichester, England, John Wiley 

and Sons, 526 p. 

Gorman, O.T., and Karr, J.R., 1978, Habitat structure 

and stream fish communities: Ecology, v. 59, 

p. 507-515.

Hofer, K.R., Scott, H.D., and Mckimmey, J.M., 1995, 

Spatial distribution of the surface geology 

and 1992 land use of the Buffalo River 

Watershed: Arkansas Water Resources Center 

Publication, no. 174, pg.43. 

Interagency Advisory Committee on Water Data, 

1982, Guidelines for determining flood-flow 

frequency: Bulletin 17B of the Hydrology 

Subcommittee, Office of Water Data 

Coordination, U.S. Geological Survey, 

Reston, Virginia., 183 p. 

Jacobson, R.B., 1995, Spatial controls on patterns of 

land-use induced stream disturbance at the 

drainage-basin scale—an example from gravel-bed streams of the Ozark Plateaus, 

Missouri: Costa, J.E., Miller, A.J., Potter, 

K.W., and Wilcock, P.R., eds., AGU 

Geophysical Monograph 89, The Wolman 

Volume, p. 219-239. 

Jacobson, R.B., in press, Downstream effects of timber harvest in the Ozarks of Missouri: in, 

Flader, S., ed., Toward Sustainability for 

Missouri Forests, U.S. Forest Service NC 

Research Station General Technical Report. 

Jacobson, R.B., Femmer, S.F., and McKenney, R., 

2001, Land-Use Changes and the Physical 

Habitat of Streams: U.S. Geological Survey 

Circular 1175, 63 p. 

Jacobson, R.B. and Gran, K.B., 1999, Gravel routing 

from widespread, low-intensity landscape 

disturbance, Current River Basin, Missouri: 

Earth Surface Processes and Landforms, v. 

24, 897-917. 

Jacobson, R.B., and Primm, A.T., 1997, Historical 

land-use changes and potential effects on 

stream disturbance in the Ozark Plateaus, 

Missouri: U.S. Geological Survey WaterSupply Paper 2484, (reprint of Open-File 

Report 94-333). 95 p. 

Jacobson, R.B., and Pugh, A.L., 1992, Effects of land 

use and climate shifts on channel instability, 

Ozark Plateaus, Missouri, U.S.A.: 

Proceedings of the workshop on the effects of 

global climate change on hydrology and 

water resources at the catchment scale, 

February 3-6, 1992, Tsukuba, Japan, JapanU.S. Committee on Hydrology, Water 

Resources and Global Climate Change, p. 

423-444. 

Jacobson, R.B., and Pugh, A.L., 1999, Riparian vegetation controls on the spatial pattern of 

stream-channel instability, Little Piney Creek, 

Missouri: U.S. Geological Survey WaterSupply Paper 2494. 33 p. 

Jeffries, M., and Mills, D., 1990, Freshwater Ecology: 

Principles and Applications: Belhaven Press, 

N.Y., 285 p. 

Keller, E.A., 1971, Areal sorting of bedload material, 

the hypothesis of velocity reversal: 

Geological Society of America Bulletin, v. 

82, p. 279-280. 

McKenney, R., 1997, Formation and Maintenance of 

Hydraulic Habitat Units in the Streams of the 

Ozark Plateaus: unpublished Ph.D. 

Dissertation, Pennsylvania State University, 

State College, Pennsylvania, 340 p. 

McKenney, R., 2001, Channel changes and habitat 

diversity in a warm-water, gravel-bed stream, 

in, Dorava, J., Montgomery, D., Palcsak, B., 

and Fitzpatrick, F., Geomorphic Processes 

and Riverine Habitat, American Geophysical 
48 BIOLOGICAL SCIENCE REPORT USGS/BRD/BSR-2003-0002

Union, Water Science and Application Series, 

v. 4. p. 57-72.

McKenney, R., and Jacobson, R.B., 1996, Erosion and 

deposition at the riffle-pool scale in gravelbed streams, Ozark Plateaus, Missouri and 

Arkansas, 1990-95: U.S. Geological Survey 

Open-File Report 655-A. 

McKenney, R., Jacobson, R.B., and Wertheimer, R.C., 

1995, Woody vegetation and channel morphogenesis in low-gradient, gravel-bed 

streams in the Ozarks Region, Missouri and 

Arkansas: Geomorphology, v. 13, p. 175-198. 

Milhous, R.T., 1982, Effect of sediment transport and 

flow regulation on the ecology of gravel-bed 

rivers, in Hey, R.D., Bathhurst, J.C., and 

Thorne, C.R., eds., Gravel-bed rivers: 

Chichester, England, John Wiley and Sons, p. 

819-842. 

Nash, D.B., 1994, Effective sediment-transporting 

discharge from magnitude-frequency analysis: Journal of Geology, v. 102, p. 79-95. 

National Oceanic and Atmospheric Administration, 

2002, Climatography of the United States No. 

81, Monthly Station Normals of Temperature, 

Precipitation, and Heating and Cooling 

Degree Days 1971 – 2000, Arkansas: 

Asheville, North Carolina, National 

Environmental Satellite, Data, and 

Information Service, National Climatic Data 

Center, 26 p. 

Panfil, M.S. and Jacobson R.B., 1999, Hydraulic modeling of in-channel habitats in the Ozark 

Highlands of Missouri: Assessment of habitat 

sensitivity to environmental change. View 

this document online at: 

<http:/www.cerc.usgs.gov/rss/rfmodel/> 

Panfil, M.S., and Jacobson, R.B., 2001, Relations 

among geology, physiography, land use, and 

stream habitat conditions in the Buffalo and 

Current river systems, Missouri and 

Arkansas: U.S. Geological Survey, Biological 

Sciences Report, BSR-2001-0005, 111 p. 

online at: 

<http://www.cerc.usgs.gov/pubs/center/pdfDo 

cs/BSR2001-0005.pdf> 

Petersen, J.C., Adamski, J.C., Bell, Davis, J.V., 

Femmer, S.R., Freiwald, D.A., and Joseph, 

R.L., 1998, U.S. Geological Survey Circular 

1158, online at: 

<http://water.usgs.gov/pubs/circ1158>, updated April 3, 1998 

Petersen, J.C., Haggard, B.E., and Green, W.R., 2002, 

Hydrologic characteristics of Bear Creek near 

Silver Hill and Buffalo River near St. Joe, 

Arkansas, 1999-2000: U.S. Water-Resources 

Investigations Report 02-4024, 36 p. 

Petersen, J.C., 1998, Water-Quality Assessment of the 

Ozark Plateaus Study Unit, Arkansas, 

Kansas, Missouri, and Oklahoma — Fish 

Communities in Streams and their Relations 

to Selected Environmental Factors: U.S. 

Geological Survey, Water-Resources 

Investigations Report 98-4155, 32 p. 

Peterson, J.T., and Rabeni, C.F., 2001, The relation of 

fish assemblages to channel units in an Ozark 

stream: Transactions of the American 

Fisheries Society, v. 130, p. 911-926. 

Planking, J.L., Barbour, M.T., Porter, K.D., Gross, 

S.K., and Hughes, R.M., 1989, Rapid 

bioassessment protocols for use in streams 

and rivers: U.S. Environmental Protection 

Agency, EPA/444/4-89-001, 176 p. 

Poff, N.L., Allan, J.D., Bain, M.B., Karr, J.R., 

Prestegaard, K.L., Richter, B.D., Sparks, 

R.E., and Stromberg, J.C., 1997, The natural 

flow regime: BioScience, v. 47, p. 769-784. 

Richter, B.D., Baumgartner, J.V., Wigington, R., and 

Brau, D.P., 1997, How much water does a 

river need? Freshwater Biology, v. 37, p. 231­

249. 

Schlosser, I.J., 1987, A conceptual framework for fish 

communities in small warmwater streams, in, 

Matthews, W. J., and Heins, D. C., eds., 

Community and Evolutionary Ecology of 

North American Stream Fishes: Norman, 

University of Oklahoma Press, p. 17-24, 

269-299. 

Scott, W.B., and E.J. Crossman. 1973. Freshwater 

fishes of Canada. Bull. Fish. Res. Board Can. 

184. 966 pp. 

Shannon, C.E., and Weaver, W., 1949, The mathematical theory of communication: Urbana, Ill., 

The Univ. of Illinois Press, p. 19-27, 82-83, 

104-107. 

Shields, A., 1936, Application of similarity principles 

and turbulence research to bedload, in, 

Anwendung der Aehnlichkeitsmechanik und 

der Turbulezforschung auf die 

Geschiebewegung: Mitteilun Preussischen 

Versuchanstalt fur Wasserbau und Schiffbau, 

Berlin, No. 26, by Ott., W.P. and van 

Uchelen, J.C., California Institute of 

Technology Hydrodynamics, Pasadena, 

California, Report 167, 43 p. 

Steffler, P. and Blackburn, J., 2001, River2D - TwoDimensional Depth Averaged Model of River 

Hydrodynamics and Fish Habitat, 

Introduction to Depth Averaged Modeling 

and User’s Manual: University of Alberta, 89 

p. 

Thomas, W.O., Jr., Lumb, A.M., Flynn, K.M., and 

Kirby, W.H., 1998, User’s manual for 
PHYSICAL STREAM HABITAT DYNAMICS IN LOWER BEAR CREEK 49 

program PEAKFQ, annual flood frequency 

analysis using Bulletin 17B guidelines, written communication, unpublished ms, 89 p. 

U.S. Geological Survey, 2003, Daily streamflow for 

Missouri: Online digital hydrologic data, 

URL: http://waterdata.usgs.gov/mo/nwis. 

U.S. Geological Survey, 2000a, US GeoData Digital 

Elevation Models, Fact Sheet 040-00, 

<http://mapping.usgs.gov/mac/isb/pubs/factsheets/fs07099.html>. 

U.S. Geological Survey, 2000b, National Land Cover 

Data, 30-meter resolution, 

<http://edcsgs9.cr.usgs.gov/programs/lccp/nat 

ionallandcover.html>. 

Whitledge, G.W., and Rabeni, C.F., 2000, Benthic 

community metabolism in three habitats in an 

Ozark stream: Hydrobiologia: v. 437, p. 165­

170. 

Wilcock, P.R., and McArdell, B.W., 1993, Surfacebased fractional transport rates – 

Mobilization thresholds and partial transport 

of a sand-gravel sediment: Water Resources 

Research, v. 29, p. 1297-1312. 

Wolman, M.G., 1954, A method of sampling coarse 

river bed material: American Geophysical 

Union Transactions, v. 35, p. 951-956. 

Wolman, M.G., and Miller, J.P., 1960, Magnitude and 

frequency of forces in geomorphic processes: 

Journal of Geology, v. 68, p. 54-74. 

Yalin, M.S. and Karahan, E., 1979, Inception of sediment transport: Journal Hydraulics Div., 

American Society of Civil Engineers, v. 105, 

p. 1433-1443.


REPORT DOCUMENTATION PAGE Form Approved 

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1. AGENCY USE ONLY (Leave Blank) 2. REPORT DATE 

July 2003 

3. REPORT TYPE AND DATES COVERED 

Biological Science Report 

4. TITLE AND SUBTITLE 

Physical Stream Habitat Dynamics in Lower Bear Creek, Northern Arkansas 5. FUNDING NUMBERS 

6.AUTHOR(S) 

Joanna M. Reuter, Robert B. Jacobson, and Caroline M. Elliot 

7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 

U.S. Department of the Interior 

U.S. Geological Survey, Biological Resources Division 

Columbia Environmental Research Center 

4200 New Haven Road 

Columbia, MO 65201 

8. PERFORMING ORGANIZATION 

 REPORT NUMBER 

USGS/BRD/BSR--2003-0002 

9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 

U.S. Department of the Interior 

U.S. Geological Survey 

Biological Resources Division 

Reston, VA 20192 

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 AGENCY REPORT NUMBER 

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12b. DISTRIBUTION CODE 

13. ABSTRACT (Maximum 200 words) We evaluated the roles of geomorphic and hydrologic dynamics in determining physical stream habitat in 

Bear Creek, a 239 km2 watershed in the Ozarks, northern Arkansas. During a relatively wet 12-month period, Bear Creek was altered by a 

series of floods, including four with discharges exceeding a 1-year recurrence interval and one with an estimated 2- to 4-year recurrence 

interval. These floods eroded sediment from the study reach at rates in excess of other sites previously studied in the Ozarks. The 2- to 4-

year flood scoured gravel from pools and deposited it in riffles. The smaller floods eroded gravel from the riffles and deposited it in pools. A 

two-dimensional hydraulic model was compiled to assess habitat variation with hydrology. Depths and velocities simulated for discharges of 

0.1 to 556 cubic meters per second were classified into habitats using hydraulic criteria. Races disappear completely at the lowest flows; 

riffles contract substantially. Pools also contract during low flow, but deep scours adjacent to bedrock outcrops sustain some pool area even 

at the lowest flows. Magnitude and frequency of bed-sediment entrainment show that most habitat maintenance results from flows that occur 

about 4-7 days a year. 

14. SUBJECT TERMS: aquatic habitat, geomorphology, hydrology, Ozarks, Arkansas 15. NUMBER OF PAGES 

49 pages +appendices 

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