U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2013–5058

Prepared in cooperation with the Northeast Texas Municipal Water District and 

the Texas Commission on Environmental Quality

Baseline Assessment of Physical Characteristics, Aquatic 

Biota, and Selected Water-Quality Properties at the Reach 

and Mesohabitat Scale for Reaches of Big Cypress, Black 

Cypress, and Little Cypress Bayous, Big Cypress Basin, 

Northeastern Texas, 2010–11
Front cover:

Top right, Cypress knees, Big Cypress Creek, Texas, July 27, 2011. Photograph taken by James B. 

Moring, U.S. Geological Survey.

Top left, Electrofishing from a barge, Big Cypress Creek, Texas, July 27, 2011. Photograph taken by Erin 

C. Sewell, U.S. Geological Survey.

Bottom right, Electrofishing from a boat, Big Cypress Creek, Texas, July 27, 2011. Photograph taken by 

Justin A. McInnis, U.S. Geological Survey.

Bottom left, Measuring physical characteristics, Big Cypress Creek, Texas, July 26, 2011. Photograph 

taken by James B. Moring, U.S. Geological Survey.

Back cover, Cypress tree near Big Cypress Creek, Texas, July 27, 2011. Photograph taken by James B. 

Moring, U.S. Geological Survey. 
Baseline Assessment of Physical 

Characteristics, Aquatic Biota, and 

Selected Water-Quality Properties at the 

Reach and Mesohabitat Scale for Reaches 

of Big Cypress, Black Cypress, and Little 

Cypress Bayous, Big Cypress Basin, 

Northeastern Texas, 2010–11

By Christopher L. Braun and James B. Moring

Prepared in cooperation with the Northeast Texas Municipal Water District and 

the Texas Commission on Environmental Quality 

Scientific Investigations Report 2013–5058

U.S. Department of the Interior

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

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2013

This and other USGS information products are available at http://store.usgs.gov/

U.S. Geological Survey

Box 25286, Denver Federal Center

Denver, CO 80225

To learn about the USGS and its information products visit http://www.usgs.gov/

1-888-ASK-USGS

Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the 

U.S. Government.

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

reproduce any copyrighted materials contained within this report.

Suggested citation:

Braun, C.L., and Moring, J.B., 2013, Baseline assessment of physical characteristics, aquatic biota, and selected 

water-quality properties at the reach and mesohabitat scale for reaches of Big Cypress, Black Cypress, and Little 

Cypress Bayous, Big Cypress Basin, northeastern Texas, 2010–11: U.S. Geological Survey Scientific Investigations 

Report 2013–5058, 90 p. 
iii

Contents

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

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

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

Description of Study Area ..................................................................................................................4

Previous Studies and Background Information ..............................................................................6

Methods .........................................................................................................................................................9

Site Selection and Environmental Flow Prescriptions ..................................................................9

Physical Characteristics ...................................................................................................................11

Aquatic Biota Collection ...................................................................................................................16

Fish Surveys ...............................................................................................................................16

Mussel Surveys .........................................................................................................................16

Selected Water-Quality Properties .................................................................................................17

Quality Assurance ..............................................................................................................................18

Physical Characteristics and Aquatic Biota at the Reach and Mesohabitat Scale for 

Reaches on Big Cypress, Black Cypress, and Little Cypress Bayous During 

Summer 2010 ..................................................................................................................................18

Physical Characteristics ...................................................................................................................18

Fish Surveys ........................................................................................................................................20

Mussel Surveys in Big Cypress Bayou and Black Cypress Bayou ............................................25

Physical Characteristics and Aquatic Biota at the Reach and Mesohabitat Scale for Big 

Cypress Bayou During Summer 2010 and Summer 2011 ........................................................32

Physical Characteristics ...................................................................................................................32

Fish Surveys ........................................................................................................................................32

Physical Characteristics and Water-Quality Properties in the Absence of Flow in 

Isolated Pools at the Reach and Mesohabitat Scale on Black Cypress and Little 

Cypress Bayous During Fall 2011 ................................................................................................34

Summary .......................................................................................................................................................37

References ...................................................................................................................................................38

Appendixes

1. Physical Habitat Measurements .............................................................................................41

2. Water-Quality Properties Measured in Samples Collected from Isolated Pools 

along Discrete Transect Lines .................................................................................................59

3. Number of Fish, Relative Abundance, and Catch Per Unit Effort ......................................65

4. Mussel Data and Habitat Descriptions ..................................................................................77

Figures

1. Map showing location of study area, Big Cypress Basin, northeastern Texas ................3

2. Map showing study reach locations and U.S. Geological Survey streamflowgaging station locations, Big Cypress Basin, northeastern Texas ......................................5

3. Graph showing daily mean discharge at U.S. Geological Survey streamflowgaging station 07346000 Big Cypress Bayou near Jefferson, Texas, August 1, 

1924–December 31, 2011 ............................................................................................................6
iv

4. Graphs showing daily mean discharge during October 1, 1979–December 31, 2011, 

at U.S. Geological Survey streamflow-gaging stations A, 07346000 Big Cypress 

Bayou near Jefferson, Texas, B, 07346045 Black Cypress Bayou at Jefferson, Tex., 

C, 07346070 Little Cypress Bayou near Jefferson, Tex., and D, measured daily 

mean discharge from stations 07346000, 07346045, and 07346070 ......................................7

5. Graphs showing daily mean discharge at U.S. Geological Survey streamflowgaging stations A, 07346000 Big Cypress Bayou near Jefferson, Texas, 

B, 07346045 Black Cypress Bayou at Jefferson, Tex., C, 07346070 Little Cypress 

Bayou near Jefferson, Tex., and D, composite depiction of measured daily 

mean discharge from stations 07346000, 07346045, and 07346070, January 1, 

2009–December 31, 2011 ............................................................................................................8

6. Map showing mesohabitat extents and channel features surveyed A, July 2010, 

and B, July 2011, at U.S. Geological Survey station 07346015 Big Cypress Bayou 

at confluence of French Creek, Jefferson, Texas ................................................................13

7. Map showing mesohabitat extents and channel features surveyed A, August 

2010, and B, October 2011, at U.S. Geological Survey station 07346044 Black 

Cypress Bayou near U.S. Highway 59 near Jefferson, Texas ............................................14

8. Map showing mesohabitat extents and channel features surveyed A, August 

2010, and B, October 2011, at U.S. Geological Survey station 07346071 Little 

Cypress Bayou near U.S. Highway 59 near Jefferson, Texas ............................................15

9. Graphs showing physical parameters in different mesohabitats collected in 2010 

from U.S. Geological Survey stations 07346015 Big Cypress Bayou at confluence 

of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near U.S. 

Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. 

Highway 59 near Jefferson, Tex. .............................................................................................19

10. Graph showing number of fish species collected by mesohabitat type from U.S. 

Geological Survey stations 07346015 Big Cypress Bayou at confluence of French 

Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., 2010 .........................................................................................................23

11. Graph showing catch per unit effort for A, darters and B, cyprinids collected by 

mesohabitat type from U.S. Geological Survey stations 07346015 Big Cypress 

Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress 

Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071Little Cypress 

Bayou near U.S. Highway 59 near Jefferson, Tex., 2010 .....................................................24

12. Graph showing catch per unit effort for A, invertivores, B, predators, and 

C, omnivores collected by mesohabitat type from U.S. Geological Survey 

stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, 

Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, 

Tex., 2010 .....................................................................................................................................26

13. Graph showing catch per unit effort for A, nest and substrate spawners and 

B, broadcast spawners collected by mesohabitat type from U.S. Geological 

Survey stations 07346015 Big Cypress Bayou at confluence of French Creek, 

Jefferson, Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near 

Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near 

Jefferson, Tex., 2010 ..................................................................................................................27

14. Graphs showing water depths associated with different mussel species 

collected from U.S. Geological Survey stations 07346017 Big Cypress Bayou 

near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at 

confluence of French Creek, Jefferson, Tex., and 07346044 Black Cypress Bayou 

near U.S. Highway 59 near Jefferson, Tex., 2010 .................................................................30
v

15. Graphs showing velocities associated with different mussel species collected 

from U.S. Geological Survey stations 07346017 Big Cypress Bayou near U.S. 

Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence 

of French Creek, Jefferson, Tex., and 07346044 Black Cypress Bayou near U.S. 

Highway 59 near Jefferson, Tex., 2010 ...................................................................................31

16. Graph showing bed sediment bulk densities at locations where mussels were 

collected from U.S. Geological Survey stations 07346017 Big Cypress Bayou 

near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at 

confluence of French Creek, Jefferson, Tex., and 07346044 Black Cypress Bayou 

near U.S. Highway 59 near Jefferson, Tex., 2010 .................................................................32

17. Graphs showing bed sediment bulk densities associated with different mussels 

collected from U.S. Geological Survey stations 07346017 Big Cypress Bayou 

near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at 

confluence of French Creek, Jefferson, Tex., and 07346044 Black Cypress Bayou 

near U.S. Highway 59 near Jefferson, Tex., 2010 .................................................................33

18. Diagram showing pool depths and cross-sectional representation of dissolved 

oxygen concentrations along surveyed transect lines on Black Cypress Bayou 

near U.S. Highway 59 near Jefferson, Texas, on October 12, 2011 ...................................35

19. Diagram showing pool depths and cross-sectional representation of dissolved 

oxygen concentrations along surveyed transect lines on Little Cypress Bayou 

near U.S. Highway 59 near Jefferson, Texas, on October 12, 2011 ...................................36

Tables

1. Study sites and sampling dates in the Big Cypress Basin, northeastern Texas, 

2010–11 ........................................................................................................................................10

2. Mesohabitat types used to describe the study reaches and physical 

characteristics measured in the Big Cypress Basin, northeastern Texas, 

during 2010–11.............................................................................................................................10

3. Low-flow prescriptions (in cubic feet per second) for Big Cypress Bayou, 

Black Cypress Bayou, and Little Cypress Bayou based upon a variety of 

ecological objectives during dry and average years ..........................................................11

4. Measured daily mean streamflows at the U.S. Geological Survey streamflowgaging stations nearest to study sites and instantaneous discharge measured 

in the field, Big Cypress Basin, Texas, 2010–11 ....................................................................12

5. Selected fish metrics from U.S. Geological Survey stations 07346015 Big Cypress 

Bayou at confluence of French Creek, Jefferson, Texas (2010–11), 07346044 Black 

Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (2010), and 07346071 

Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (2010) ..........................20

6. Presence or absence of fish species and rank abundance based on the relative 

abundance of each species collected from U.S. Geological Survey stations 

07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas 

(2010–11), 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, 

Tex. (2010), and 07346071 Little Cypress Bayou near U.S. Highway 59 near 

Jefferson, Tex. (2010) .................................................................................................................21

7. Total abundance and relative density of mussel species collected from U.S. 

Geological Survey stations 07346017 Big Cypress Bayou near U.S. Highway 59 

near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French 

Creek, Jefferson, Tex., and 07346044 Black Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., 2010 .........................................................................................................28
vi

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Length

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 0.4047 hectare (ha)

square mile (mi2

) 2.590 square kilometer (km2) 

square foot (ft2) 0.0929 square meter (m2)

Volume

gallon (gal) 3785 cubic centimeter (cm3)

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

)

Velocity

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

Flow rate

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

Mass

ounce, avoirdupois (oz) 28.4 gram (g)

ounce, avoirdupois (oz) 28,353 milligram (mg)

SI to Inch/Pound

Multiply By To obtain

Length

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

Area

hectare (ha) 2.471 acre

square kilometer (km2

) 0.3861 square mile (mi2)

square meter (m2

) 10.76 square foot (ft2) 

Volume

cubic centimeter (cm3

) 0.0002642 gallon (gal) 

cubic meter (m3

) 0.0008107 acre-foot (acre-ft) 

Flow rate

cubic meter per second (m3

/s) 35.31 cubic foot per second (ft3/s)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

milligram (mg) 0.00003527 ounce, avoirdupois (oz)
vii

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

°F=(1.8×°C)+32

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

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (mS/cm).

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) 

or micrograms per liter (μg/L). 

Baseline Assessment of Physical Characteristics, Aquatic 

Biota, and Selected Water-Quality Properties at the Reach 

and Mesohabitat Scale for Reaches of Big Cypress, Black 

Cypress, and Little Cypress Bayous, Big Cypress Basin, 

Northeastern Texas, 2010–11

By Christopher L. Braun and James B. Moring

Abstract

In 2010 and 2011, the U.S. Geological Survey (USGS), in 

cooperation with the Northeast Texas Municipal Water District 

and the Texas Commission on Environmental Quality, did a 

baseline assessment of physical characteristics and aquatic 

biota (fish and mussels) collected at the mesohabitat scale for 

reaches of Big Cypress, Black Cypress, and Little Cypress 

Bayous in the Big Cypress Basin in northeastern Texas, and 

measured selected water-quality properties in isolated pools 

in Black Cypress and Little Cypress. All of the data were 

collected in the context of prescribed environmental flows. 

The information acquired during the course of the study 

will support the long-term monitoring of biota in relation to 

environmental flow prescriptions for Big Cypress Bayou, 

Black Cypress Bayou, and Little Cypress Bayou. Data 

collection and analysis were done at mesohabitat- and reachspecific scales, where a mesohabitat is defined as a discrete 

area within a stream that exhibits unique depth, velocity, slope, 

substrate, and cover.

Biological and physical characteristic data were collected 

from two sites on Big Cypress Bayou, and one site on both 

Black Cypress Bayou and Little Cypress Bayou. The upstream 

reach of Big Cypress Bayou (USGS station 07346015 Big 

Cypress Bayou at confluence of French Creek, Jefferson, 

Texas) is hereinafter referred to as the Big Cypress 02 site. 

The downstream site on Big Cypress Bayou (USGS station 

07346017 Big Cypress Bayou near U.S. Highway 59 near 

Jefferson, Tex.) is hereinafter referred to as the Big Cypress 

01 site and was sampled exclusively for mussels. The sites on 

Black Cypress Bayou (USGS station 07346044 Black Cypress 

Bayou near U.S. Highway 59 near Jefferson, Tex.) and Little 

Cypress Bayou (USGS station 07346071 Little Cypress Bayou 

near U.S. Highway 59 near Jefferson, Tex.) are hereinafter 

referred to as the Black Cypress and Little Cypress sites, 

respectively.

A small range of streamflows was targeted for data 

collection, including a period of low flow during July and 

August 2010 and a period of very low flow during July 

2011. This scenario accounts for variability in the abundance 

and distribution of fish and mussels and in the physical 

characteristics of mesohabitats present during different flow 

conditions. Mussels were not collected from the Little Cypress 

site. However, a quantitative survey of freshwater mussels was 

conducted at Big Cypress 01.

Of the three reaches where physical habitat data were 

measured in 2010, Big Cypress 02 was both the widest and 

deepest, with a mean width of 62.2 feet (ft) and a mean depth 

of 5.5 ft in main-channel mesohabitats. Little Cypress was 

the second widest and deepest, with a mean width of 49.9 

ft and a mean depth of 4.5 ft in main-channel mesohabitats. 

Black Cypress was by far the narrowest of the three reaches, 

with a mean width of 29.1 ft and a mean depth of 3.3 ft 

in main-channel mesohabitats but it had the highest mean 

velocity of 0.42 feet per second (ft/s). Appreciably more fish 

were collected from Big Cypress 02 (596) in summer 2010 

compared to Black Cypress (273) or Little Cypress (359), 

but the total number of fish species collected among the three 

reaches was similar. Longear sunfish was the most abundant 

fish species collected from all three sites. The total number 

of fish species was largest in slow run mesohabitats at Big 

Cypress 02, fast runs at Black Cypress, and slow runs at Little 

Cypress. The catch-per-unit-effort of native minnows was 

largest in fast runs at Big Cypress 02. More species of native 

minnows, including the ironcolor and emerald shiner, were 

collected from Little Cypress relative to all other mesohabitats 

at all sites.

Fifteen species and 182 individuals of freshwater mussels 

were collected, with 69.8 percent of the individual mussels 

collected from Big Cypress 02, 23.6 percent collected from 

Big Cypress 01, and 6.6 percent collected from Black Cypress. 

Big Cypress 01was the most species rich site with 13 species, 

and washboards were the most abundant species overall. 

Mussels were not collected from Little Cypress because there 

was no flow in this stream during the targeted sampling period 

in 2011. 
2 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

On July 30, 2010, when the estimated streamflow at 

the site (based on daily mean discharge measured at the 

upstream gage in conjunction with powerplant withdrawals) 

was 45 cubic feet per second (ft3/s), Big Cypress 02 had a 

mean width of 62.2 ft and a mean depth of 5.5 ft in mainchannel mesohabitats. On July 27, 2011, when instantaneous 

streamflow at the site was 10 ft3/s, the mean width and mean 

depth in main-channel mesohabitats decreased to 49.6 ft and 

3.1 ft, respectively. Mean velocity in 2010 (0.31 ft/s) was 

approximately twice as high as 2011 (0.17 ft/s) in mainchannel mesohabitats. About 14 percent more fish were 

collected from Big Cypress 02 in 2010 relative to 2011, and 

about 18 percent fewer fish species were identified in 2011at 

this site compared to 2010. Longear sunfish, which was the 

most abundant fish species collected in 2010, was second to 

western mosquitofish in 2011. 

In the absence of flow during fall 2011, the reach at Black 

Cypress was reduced to four isolated pools, and the reach at 

Little Cypress was reduced to three isolated pools. Dissolved 

oxygen, temperature, pH, and specific conductance data 

were collected from the pools because it was hypothesized 

that these conditions would be the most limiting with respect 

to aquatic life. Dissolved oxygen concentrations ranged 

from 0.58 milligrams per liter (mg/L) to 4.79 mg/L at Black 

Cypress and from 0.24 mg/L to 5.33 mg/L at Little Cypress; 

both sites exhibited a stratified pattern in dissolved oxygen 

concentrations along transect lines, but the pattern was less 

pronounced at Black Cypress.

Introduction

In Texas, the Big Cypress Basin includes parts of 

Hopkins, Franklin, Titus, Morris, Cass, Wood, Upshur, Gregg, 

Marion, and Harrison Counties. The Big Cypress Basin in 

Texas extends from the southwestern part of Hopkins County 

to the Texas–Louisiana State line separating Harrison County, 

from Caddo Parish, Louisiana. The headwaters of the Big 

Cypress Basin include Big Cypress Creek (which turns into 

Big Cypress Bayou), Black Cypress Creek (which turns into 

Black Cypress Bayou), and Little Cypress Creek (which 

turns into Little Cypress Bayou). Whereas streamflow in Big 

Cypress Creek and Big Cypress Bayou (Big Cypress Creek 

becomes Big Cypress Bayou downstream from Lake O’ the 

Pines) has been altered by the construction of reservoirs, 

streamflows in Black Cypress Creek, Black Cypress Bayou, 

Little Cypress Creek, and Little Cypress Bayou remain largely 

unregulated. Black Cypress Creek becomes Black Cypress 

Bayou when it enters Marion County, and Little Cypress 

Creek becomes Little Cypress Bayou when it enters Harrison 

County (fig. 1). The Black Cypress Bayou has been classified 

by the State of Texas as a least-impacted reference stream 

largely on the basis of diverse fish communities found in 

this stream (Crowe and Bayer, 2005). Fish species richness 

is larger in the Big Cypress Basin compared to most other 

parts of the State (Linam and others, 2002), and as many as 

86 species of fish have been documented in the Big Cypress 

Basin (Hoover and others, 1989). Despite the relatively large 

fish species richness, some species are listed as threatened 

because of habitat alteration and degradation. For example, 

the paddlefish (Polyodon spathula) and the bluehead shiner 

(Pteronotropis hubbsi) are listed as “threatened” by the State 

of Texas (Texas Parks and Wildlife Department, 2012); the 

paddlefish has not been documented in many years, but 

populations of the bluehead shiner can be found (Thomas and 

others, 2007). 

The most threatened and declining taxon of freshwater 

organisms in the Big Cypress Basin in Texas are mussels, a 

threatened and declining taxon throughout North America. 

For example, of the 297 known species of freshwater mussels 

in the United States, 207 are extinct, federally listed as 

threatened, or considered a species of concern (Williams 

and others, 1993; Vaughn and Taylor, 1999). Factors such as 

overharvesting, pollution, and invasive species pose a threat 

to freshwater mussels in North America; their precipitous 

decline during the last century is largely a result of habitat 

loss (Layzer and others, 1993; Williams and others, 1993) 

with a major contributing factor being the widespread 

impoundment of rivers (Vaughn and Taylor, 1999, Hardison 

and Layzer, 2001). 

In the Big Cypress Basin in Texas, the Louisiana pigtoe 

(Pleurobema riddellii), documented by Mather and Bergmann 

(1994), is one of the rarest unionids (freshwater mussels of the 

family Unionidae) and is classified by the State as critically 

imperiled (State ranking of S1). Another critically imperiled 

unionid, the sandbank pocketbook (Lampsilis satura), 

also is thought to inhabit the Big Cypress Basin in Texas 

(Marsha Mays, Texas Parks and Wildlife Department, written 

commun., 2011) but has never been documented. At least 26 

species of mussels have been identified in the Big Cypress 

Basin in Texas since 1913 (Howells, 1996). 

The hydrology of a stream plays an important role in 

determining the composition, distribution, and diversity 

of aquatic communities, and a major part of instream and 

environmental flow studies is relating the biology of a stream 

to its flow regime (Bovee and others, 1998). The development 

of environmental flow recommendations or prescriptions often 

is based on recognizing the importance of the natural flows 

expressed as the stream’s quantity, timing, and variability 

in flow over time, that is, its natural flow regime (Poff and 

others, 1997; Richter and others, 2011). Mesohabitats are 

discrete areas within a stream exhibiting unique depths, 

velocities, slopes, substrates, and cover for aquatic biota 

such as undercut banks and overhanging trees (Minnesota 

Department of Natural Resources, 2012). Prescriptions 

for environmental flows have been developed by the State 

in order to help maintain sufficient flows and to support 

biodiversity in the mesohabitats of Big Cypress Basin in Texas 

(Caddo Lake Institute, 2012). Accordingly, during 2010–11, 

the U.S. Geological Survey (USGS), in cooperation with the 

Northeast Texas Municipal Water District (NETMWD) and 

the Texas Commission on Environmental Quality (TCEQ), did 
Figure 1. Location of study area, Big Cypress Basin, northeastern Texas.

£¤259

£¤59

£¤80

£¤67

£¤69

UV77

UV31 UV43

UV49

UV77

UV155

UV49

UV300

UV155

UV19

UV11

UV154

UV37

UV8

£¤271

£¤59

20

30

30

UV43

UV154

£¤80

UV11

UV155

UV154 Area shown on figure 2

Gulf of Mexico

TEXAS

Study area

CADDO

HARRISON PARISH

COUNTY

MARION

COUNTY

CASS

COUNTY

MORRIS

COUNTY

TITUS

COUNTY

FRANKLIN

COUNTY

HOPKINS

COUNTY

WOOD

COUNTY

UPSHUR

COUNTY

GREGG

COUNTY HW Pirkey

Power Plant

Base modified from U.S. Geological Survey1:24,000 quadrangle digital dataUniversal Transverse Mercator, zone 14 North American Datum of 1983

Caddo Lake

Lake O’

the Pines

Lake Bob

Sandlin

Welsh

Reservoir

Lake

Monticello

Lake Cypress

Springs

James Ba you

Black Cypress Creek

Big Cypress Bayou

Little Cy press Bayou

Little Cypress Creek

Black Cypress Bayou

Big

Cypress Creek

T E X A S

L O U I S I A N A

ARKANSAS

0 10 20 MILES

0 10 20 KILOMETERS

94°30'

95°00'

95°30'

33°00'

32°30'

94°00'

EXPLANATION

Watershed of Big Cypress Basin Big Cypress Creek and Bayou Black Cypress Creek and Bayou Little Cypress Creek and Bayou Caddo LakeBoundary of Big Cypress Basin in Texas

FERRELLS BRIDGE DAM

Sulfur

Springs

Hallsville

Mt Vernon Mt Pleasant

Kilgore

Longview

Pittsburg

Gilmer

Winnsboro

Marshall

Daingerfield Linden

Atlanta

Karnack

Jefferson

Gladewater

Mineola

Quitman
4 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

a baseline assessment to document physical characteristics, 

water-quality properties, and aquatic biota in the Big Cypress 

Basin in Texas in relation to environmental flow prescriptions 

established for the Big Cypress, Black Cypress, and Little 

Cypress Bayous. The study was done in support of the Texas 

Clean Rivers Program, “a partnership between the TCEQ and 

regional water authorities to coordinate and conduct water 

quality monitoring, assessment, and stakeholder participation 

to improve the quality of surface water within each river 

basin in Texas” (Texas Clean Rivers Program website, Texas 

Commission on Environmental Quality, 2013). 

Purpose and Scope

This report describes a baseline assessment of physical 

characteristics and aquatic biota (fish and mussels) collected 

at the mesohabitat scale for reaches of Big Cypress, Black 

Cypress, and Little Cypress Bayous in the Big Cypress 

Basin in Texas during 2010–11 in the context of prescribed 

environmental flows. Physical characteristics were measured 

in reaches of each stream to catalogue the properties of 

mesohabitats in the study area. Fish and mussel aquatic biota 

data were collected within the range of applicable low-flow 

environmental flow prescriptions. Water-quality properties 

were measured in isolated pools that remained in the Black 

Cypress and Little Cypress Bayous during no-flow conditions 

in October 2011 because the isolated pools were crucial for 

sustaining aquatic biota during periods of no flow. 

Description of Study Area

Most of the Big Cypress Basin in Texas is characterized 

by gently rolling to hilly terrain intersected by terraces and 

relatively flat flood plains. The vegetation is dominated by 

pine and mixed-pine hardwood forests with pastures and 

cultivated land, bottomland hardwood forest, and Cypress 

swamp along backwater areas and tributaries (U.S. Army 

Corps of Engineers, 1998).

There are three large impoundments on Big Cypress 

Creek upstream from Big Cypress Bayou. In addition to Lake 

O’ the Pines, flow in Big Cypress Creek also is regulated by 

Lake Cypress Springs (impounded in 1970) (Texas Parks 

and Wildlife Department, 2013) and Lake Bob Sandlin 

(impounded in 1978) (Texas State Historical Association, 

2013,) (fig. 1). In addition to impounding Big Cypress Creek, 

Lake O’ the Pines regulates flow in Big Cypress Bayou; Big 

Cypress Bayou begins where Lake O’ the Pines releases 

discharge. Construction of Ferrells Bridge Dam, which 

impounds Big Cypress Creek to form Lake O’ the Pines 

Reservoir (fig. 2), was completed in 1959. Dowell, (1964, 

p. 157) describes the history of impoundment:

Construction [of Ferrells Bridge Dam] was started 

in January 1955 and completed December 11, 

1959. The cofferdam closure was made August 21, 

1957, and water flowed through the conduits 

September 25, 1957. Deliberate impoundment began 

in August 1958, and the lake was in full use by 

December 1959. 

Since August 1957, the flow in Big Cypress Bayou has 

been characterized as completely regulated (U.S. Geological 

Survey, 2012b) and the flow regime in Big Cypress Bayou 

(monitored at U.S. Geological Survey streamflow-gaging 

station 07346000 Big Cypress Bayou near Jefferson Tex. 

[hereinafter Big Cypress Bayou gage]; figs. 2 and 3) has been 

altered. Following construction of the Lake O’ the Pines, 

the streamflow discharge record displays less variability and 

reduced streamflow amounts compared to the streamflow 

record prior to construction of the reservoir (fig. 3). Prior to 

regulation, the annual maximum daily mean discharge was 

57,100 cubic feet per second (ft3/s) on April 1, 1945, but since 

the beginning of regulation (excluding the period from January 

1, 1960, through September 30, 1979, when the Big Cypress 

Bayou gage was inactive), the highest annual maximum 

daily mean discharge has been 5,190 ft3/s (April 29, 1958) 

(U.S. Geological Survey, 2012a). The mean, maximum, and 

minimum daily mean discharges at the Big Cypress Bayou 

gage for the period from October 1, 1979, to December 31, 

2011, were 594, 3,450, and 0 ft3/s, respectively.

Whereas flows in Big Cypress Bayou are regulated, 

flows in the Black Cypress Bayou and Little Cypress Creek 

Bayou are largely unregulated. Figure 4 depicts the daily 

mean discharge measured by the Big Cypress Bayou gage, 

USGS streamflow-gaging station 07346045 Black Cypress 

Bayou at Jefferson Tex. (hereinafter Black Cypress Bayou 

gage), and USGS streamflow-gaging station 07346070 Little 

Cypress Bayou near Jefferson Tex. (hereinafter Little Cypress 

Bayou gage) for the period of record they share in common 

(October 1, 1979, to December 31, 2011).

The natural variability of the flow regime for Black 

Cypress Bayou has remained largely unchanged during the 

period of concurrent streamflow records (October 1, 1979, to 

December 31, 2011) common on all three bayous from which 

data were collected for this report. Despite being classified as 

a major perennial tributary to Big Cypress Bayou (Northeast 

Texas Municipal Water District, 2007), Black Cypress Bayou 

can become intermittent during late summer, as observed from 

June through November 2011 (figs. 4B and 5B). During the 

period from October 1, 1979, to December 31, 2011, there 

was no flow at the Black Cypress Bayou gage for a total of 

632 days. The mean, maximum, and minimum daily mean 

discharges at the Black Cypress Bayou gage for the period 

from October 1, 1979, to December 31, 2011, were 336, 

11,400, and 0 ft3

/s, respectively.

The natural variability of the flow regime for Little 

Cypress Bayou has been largely unchanged during the 

common period of record (October 1, 1979, to December 31, 

2011) with Big Cypress Bayou and Black Cypress Bayou. 

Little Cypress Bayou also is considered a major perennial 

tributary to Big Cypress Bayou (Northeast Texas Municipal 

Water District, 2007) but also can become intermittent during 

late summer, as observed from June through November 2011 
Figure 2. Study reach locations and U.S. Geological Survey streamflow-gaging station locations, Big Cypress Basin, northeastern Texas. 

Jefferson

ress Bayou

Lake

 of

 the Pines

Big Cypress Bayou

Black CypressBayou

Little Cypress Bayou

Fren

ch

Creek

UV49

£¤59

UV49

134

2208

3001

1969

729

726

1793

1324

248

728

729

MARION

COUNTY

HARRISON

COUNTY

07346000

07346045

07346070

07346044

(Black Cypress -20805)

07346015

(Big Cypress 02 - 20803)

07346017

(Big Cypress 01 - 20108)

07346071

(Little Cypress - 20804)

£¤59

Pump station for

HW Pirkey

Power Plant

FERRELLS

BRIDGE

DAM

EXPLANATION

Study reach with U.S. Geological Survey station number—Short name and Texas Commission on Environmental Quality station number in parentheses (table 1)

07346071

(Little Cypress - 20804)

07346000 U.S. Geological Survey streamflow-gaging 

 station and station number

Base modified from U.S. Geological Survey1:24,000 quadrangle digital dataUniversal Transverse Mercator projection, zone 14 North American Datum of 1983

0 1 

0 1 2 K

94°20’

32°40’32°45’32°50’

94°30’ 94°25’ 94°15’
6 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

(figs. 4C and 5C). During the period from October 1, 1979, to 

December 31, 2011, there was no flow at the Little Cypress 

Bayou gage for a total of 539 days. The mean, maximum, and 

minimum daily mean discharges at the Little Cypress Bayou 

gage for the period from October 1, 1979, to December 31, 

2011, were 526, 18,600, and 0 ft3/s, respectively.

Measured daily mean discharge values from Big Cypress 

Bayou, Little Cypress Bayou, and Black Cypress Bayou gages 

are plotted in figures 4D and 5D to demonstrate the relative 

contribution of each to flow in the Cypress Bayou Basin. 

Figure 4D shows streamflow during the common period of 

record (October 1, 1979 to December 31, 2011) for all three 

Bayous. Figure 5D shows streamflow during the course of a 

3-year period (January 1, 2009 to December 31, 2011), which 

includes a period of mean to above mean flow conditions 

(January 1, 2009 to mid-2010) as well as a period of drought 

(mid-2010 to December 31, 2011). 

Previous Studies and Background Information

This report was written in support of the Sustainable 

Rivers Project (SRP; U.S. Army Corps of Engineers, 2012) 

for Big Cypress Bayou, the Environmental Flows Project 

for Caddo Lake and its tributaries (Caddo Lake Institute, 

2012), and the Texas Commission on Environmental Quality 

(TCEQ) Clean Rivers Program. The SRP was established 

in 2002 as a partnership between the U.S. Army Corps of 

Engineers (USACE) and The Nature Conservancy to alter 

existing operations at USACE dams in order to enhance 

habitat conditions for animals and plants that depend on flows 

downstream from the dams (U.S. Army Corps of Engineers 

and The Nature Conservancy, 2012). The SRP is active in 

eight river basins across the United States, including Big 

Cypress Bayou (Konrad, 2010). 

The USACE and NETMWD are working together 

to determine the best strategy to implement prescribed 

environmental flows for Big Cypress Bayou downstream from 

the Lake O’ the Pines, which is managed by USACE. The first 

prescribed environmental flow releases from Ferrells Bridge 

Dam occurred in March 2012 (Lee Thomas, Northeast Texas 

Municipal Water District, oral commun., 2012). Reservoirs 

provide a mechanism for managing the magnitude and 

timing of river flows in order to satisfy the needs of human 

and natural communities. The SRP emphasizes the use of a 

natural flow paradigm for the determination of environmental 

flow prescriptions or recommendations (U.S. Army Corps of 

Engineers, 2012 ).

The Caddo Lake Institute website describes the 

Environmental Flows Project (Caddo Lake Institute, 2012), 

noting it was started in 2004 as a partnership between the 

Caddo Lake Institute, The Nature Conservancy, USACE, and 

NETMWD to provide adequate instream flows to sustain the 

ecological, economical, and recreational values of the Big 

Cypress Basin in Texas. Instream flow prescriptions were 

developed for different flow conditions and different parts of 

the year for Big Cypress Bayou, Black Cypress Bayou, and 

Little Cypress Bayou (Caddo Lake Institute, 2010) to describe 

the minimum desirable low flows required to maintain aquatic 

biodiversity and hydrologic connectivity between in-channel 

habitats in the form of continuous flow connecting different 

mesohabitats. 

Figure 3. Daily mean discharge at U.S. Geological Survey streamflow-gaging station 07346000 Big Cypress Bayou near Jefferson, 

Texas, August 1, 1924–December 31, 2011.

1924

1930

1940

1950

1960

1970

1980

1990

2000

2010

2011

Year

0

10,000

20,000

30,000

40,000

50,000

60,000

Daily mean discharge, in cubic feet per second
Introduction 7

Figure 4. Daily mean discharge during October 1, 1979–December 31, 2011, at U.S. Geological Survey streamflow-gaging stations 

A, 07346000 Big Cypress Bayou near Jefferson, Texas, B, 07346045 Black Cypress Bayou at Jefferson, Tex., C, 07346070 Little Cypress 

Bayou near Jefferson, Tex., and D, measured daily mean discharge from stations 07346000, 07346045, and 07346070. 

19801979 1985 1990 1995 2000 2005 2010 2011

Year

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

18,000

20,000

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

18,000

20,000

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

18,000

20,000

0

5,000

10,000

15,000

20,000

25,000

30,000

Daily mean discharge, in cubic feet per second

A

B

C

D

EXPLANATION

Measured daily mean discharge, by U.S. Geological Survey

 streamflow-gaging station number and name

 07346000 - Big Cypress Bayou near Jefferson, Texas

 07346045 - Black Cypress Bayou at Jefferson, Texas

 07346070 - Little Cypress Bayou near Jefferson, Texas
8 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Figure 5. Daily mean discharge at U.S. Geological Survey streamflow-gaging stations A, 07346000 Big Cypress Bayou near Jefferson, 

Texas, B, 07346045 Black Cypress Bayou at Jefferson, Tex., C, 07346070 Little Cypress Bayou near Jefferson, Tex., and D, composite 

depiction of measured daily mean discharge from stations 07346000, 07346045, and 07346070, January 1, 2009–December 31, 2011. Daily mean discharge, in cubic feet per second

0

2,000

4,000

6,000

8,000

10,000

12,000

0

2,000

4,000

6,000

8,000

10,000

12,000

0

2,000

4,000

6,000

8,000

10,000

12,000

0

5,000

10,000

15,000

20,000

25,000

Date

Jan.

Feb.

Mar.

Apr.

May

June

July

Aug.

Sept.

Oct.

Nov.

Dec.

Jan.

Feb.

Mar.

Apr.

May

June

July

Aug.

Sept.

Oct.

Nov.

Dec.

Jan.

Feb.

Mar.

Apr.

May

June

July

Aug.

Sept.

Oct.

Nov.

Dec.

2009 2010 2011

A

B

C

D

EXPLANATION

Measured daily mean discharge, by U.S. Geological Survey

 streamflow-gaging station number and name

 07346000 - Big Cypress Bayou near Jefferson, Texas

 07346045 - Black Cypress Bayou at Jefferson, Texas

 07346070 - Little Cypress Bayou near Jefferson, Texas

Sampling period

D

C

No flow occurred during periods shown in orange.

B

No flow occurred during periods shown in orange.

A
Methods 9

Methods 

Stream velocities were measured by using a hand-held 

acoustic Doppler velocity meter (SonTek, 2013). Standard 

USGS methods (Rantz and others, 1982; Turnipseed and 

Sauer, 2010) and methods described in the acoustic Doppler 

velocity meter operations manual (SonTek, 2003) were 

used to compute streamflow and measure stream velocities. 

Streamflow measurements were made at U.S. Geological 

Survey streamflow-gaging stations on the Big Cypress Bayou, 

Black Cypress Bayou, and Little Cypress Bayou and at the 

sites selected for aquatic biota sampling. In some cases, 

depths and velocities could not be measured at sites selected 

for aquatic-biota sampling because the water was too deep to 

use the hand-held acoustic Doppler velocity meter. In these 

instances, the depths and velocities were measured as close as 

possible to the sites selected for aquatic-biota sampling.

Aquatic biota data were collected within the range of 

applicable low-flow environmental flow prescriptions at three 

sites for fish representing different reaches on each stream 

(one site each on Big Cypress Bayou, Black Cypress Bayou, 

and Little Cypress Bayou) and three sites for mussels (two 

sites on Big Cypress Bayou and one on Black Cypress Bayou) 

in northeastern Texas. The dates and different types of data 

collected at each site in 2010 and 2011 are shown in table 1. 

Fish data were collected and analyzed at the mesohabitat and 

reach scale and mussel data were collected and analyzed at the 

reach scale. The mesohabitats characterized in this study (slow 

runs, fast runs, and various types of pools) are discrete channel 

features of relatively homogenous depth and flow that are 

distinguished from one another on the basis of localized slope, 

channel shape and structure, varying degrees of velocity, 

orientation relative to flow, and inclusion with or exclusion 

from the main channel (Hawkins and others, 2011) (table 2). 

Runs were characterized as slow or fast on the basis of relative 

stream velocity; designations as slow and fast runs were 

specific to each stream because a high velocity in one stream 

might not be characterized as a high velocity in another. Pools 

include main channel pools that are relatively deep and low 

velocity features, and margin pools (forewaters, backwaters, 

and embayments) that are low velocity features that vary 

considerably in their depth. Forewaters are oriented parallel 

and into the principal direction of flow, whereas backwaters 

are oriented parallel but in the opposite direction of the 

principal flow; embayments are oriented perpendicular to the 

principal flow direction. In this report, forewaters, backwaters, 

and embayments were collectively referred to as a “margin 

pool” mesohabitat because the physical characteristics (depth, 

velocity, and bed substrate) of the three mesohabitats were 

so similar. Because of the large variation in stream types, 

mesohabitat typing was based on relative changes in each 

stream. Each reach typically contained many or all of the 

mesohabitat types present in the entire segment; the objective 

was to categorize major habitat types present in each segment 

of stream. This type of stream habitat classification facilitates 

an understanding of biota-habitat relations that provide an 

effective approach to evaluating the effects of environmental 

change, such as changes in flow, on stream ecosystems 

(Hawkins and others, 2011). 

Site Selection and Environmental Flow 

Prescriptions

Representative reaches for use as data-collection sites 

were first identified during an initial field reconnaissance in 

2009. The upstream and downstream extent of each reach 

was determined following TCEQ’s Surface Water Quality 

Monitoring (SWQM) procedures for reach establishment 

(Texas Commission on Environmental Quality, 2007). The 

stream reaches representing data-collection sites on the Big 

Cypress, Black Cypress, and Little Cypress Bayous were 

selected in a manner consistent with TCEQ protocols (Texas 

Commission on Environmental Quality, 2007). The reach at 

each site was about 40 channel widths in length. To the extent 

possible, sites were selected near existing USGS streamflowgaging stations so that discharge obtained from these stations 

could be related to the data collected during this study (fig. 2). 

USGS station numbers and TCEQ station numbers were 

established for each site (table 1). 

The upstream site on Big Cypress Bayou (USGS station 

07346015 Big Cypress Bayou at confluence of French Creek, 

Jefferson, Tex.) is hereinafter referred to as the Big Cypress 

02 site (TCEQ station number is 20803). The downstream 

site on Big Cypress Bayou (USGS station 07346017 Big 

Cypress Bayou near U.S. Highway 59 near Jefferson, Tex.) 

is hereinafter referred to as the Big Cypress 01 site (TCEQ 

station number is 20108). The Big Cypress 01 site was 

sampled exclusively for mussels. The sites on Black Cypress 

Bayou (USGS station 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex.) and Little Cypress 

Bayou (USGS station 07346071 Little Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex.) are hereinafter referred 

to as the Black Cypress and Little Cypress sites, respectively. 

The TCEQ station numbers for the Black Cypress and Little 

Cypress sites are 20805 and 20804, respectively (fig. 2; 

table 1). 

Physical-characteristic and aquatic-biota data were 

collected at three data-collection sites (Big Cypress 02, Black 

Cypress, and Little Cypress) for selected low-flow conditions 

found within the established environmental flow prescription 

ranges for dry and average years during the July to September 

critical period that were adopted at the December 2008 

Cypress Basin Flows Workshop in Jefferson, Tex. (Caddo 

Lake Institute, 2010) for each stream. Low-flow prescriptions 

during dry and average years during the July to September 

critical period ranged from 6 to 40 ft3

/s for Big Cypress 

Bayou, 4 to 32 ft3/s for Black Cypress Bayou, and 5 to 26 ft3/s 

for Little Cypress Bayou (table 3). Physical-characteristic 

and aquatic-biota data collection was intended to include two 

sampling events targeting the higher part and lower part of 

the flow-prescription ranges (referred to herein as low flow 

and very low flow, respectively) established for each of the 
10 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Table 1. Study sites and sampling dates in the Big Cypress Basin, northeastern Texas, 2010–11.

[TCEQ, Texas Commission on Environmental Quality; ft, feet; --, no data]

Sites sampled in 2010

U.S. Geological Survey 

station number and name Short name

TCEQ 

station 

number

Reach 

length 

(ft) 

Aquatic 

habitat Fish

Estimated discharge 

based on daily mean 

discharge and power 

plant withdrawals

Mussels

07346017 Big Cypress Bayou near U.S. 

Highway 59 near Jefferson, Tex.

Big Cypress 01 20108 -- -- -- -- July 30

07346015 Big Cypress Bayou at 

confluence of French Creek, 

Jefferson, Tex. 

Big Cypress 02 20803 1,558 July 30–31 July 31 July 30–31 July 31 and 

Aug. 2

07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex. 

Black Cypress 20805 1,050 Aug. 3–4 Aug. 3–4 -- Aug. 3–4

07346071 Little Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex.

Little Cypress 20804 1,607 Aug. 18 Aug. 19 -- --1

Sites sampled in 2011

U.S. Geological Survey 

station number and name Short Name

TCEQ 

station 

number

Reach 

length 

(ft) 

Aquatic 

habitat Fish

Instantaneous 

discharge 

measured in 

the field 

Waterquality 

properties2

07346015 Big Cypress Bayou at confluence 

of French Creek, Jefferson, Tex. 

Big Cypress 02 20803 1,558 July 26–27 July 27 July 26 --

07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex.

Black Cypress 20805 1,050 -- -- -- Oct. 12

07346071 Little Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex.

Little Cypress 20804 1,607 -- -- -- Oct. 13

1

Mussels not collected because of scheduling conflicts in 2010 and an extended period of no flow in 2011. 

2

Water-quality properties: dissolved oxygen, pH, specific conductance, and temperature. 

Table 2. Mesohabitat types used to describe the study reaches and physical characteristics measured in the Big Cypress Basin, 

northeastern Texas, during 2010–11 (mesohabitat descriptions are modified from Hawkins and others, 2011).

[ft, feet; ft/s, feet per second]

Mesohabitat 

type

Main channel 

mesohabitat?

(yes or no)

Description

Slow run Yes Relatively moderate velocity feature with laminar flow and a nonturbulent surface, average and 

median depths of 5.2 ft and 4.8 ft, respectively, and average and median velocities of 0.15 ft/s and 

0.12 ft/s, respectively

Fast run Yes Relatively moderate velocity feature with laminar flow and a nonturbulent surface, average and 

median depths of 2.0 ft and 1.8 ft, respectively, and average and median velocities of 0.48 ft/s and 

0.43 ft/s, respectively

Channel pool Yes Relatively deep, low velocity feature in main channel of the stream

Margin pool

Forewater No Slackwater feature connected to the main channel, oriented into the principal direction of flow

Backwater No Slackwater feature connected to the main channel, oriented in an opposing direction to the principal 

flow direction

Embayment No Slackwater feature located adjacent to the channel and oriented perpendicular to flow

Isolated pool Yes Feature with highly variable depth and no velocity
Methods 11

three bayous. The sampling event during the July–September 

critical period in 2010 targeted the higher end of the range, 

while the sampling event during the critical period in 2011 

targeted the lower end of the range. In 2011, the study area 

was affected by the widespread severe drought in Texas 

(University of Nebraska-Lincoln, 2012). Compared to 2010, 

appreciably drier conditions prevailed during the targeted July 

through September period during 2011, with no flow during 

July–September 2011 in either Black Cypress or Little Cypress 

except for a few days during July 2011 in Little Cypress. 

Sampling was delayed until October 2011 at the Black and 

Little Cypress sites; if sustained streamflows had returned by 

October 2011, it would have enabled sampling during very 

low flow conditions. Sustained streamflow did not return to 

either site until December 2011(fig. 5), and when it did, both 

the Black and Little Cypress sites remained outside of the 

range of dry-to-average year low-flow prescriptions adopted 

by the Cypress Basin Environmental Flows Stakeholders 

group (table 3; Caddo Lake Institute, 2010); as a result, the 

second assessment in 2011 did not include sampling for fish 

and mussels at either of these sites.

Streamflows for environmental flow prescription 

classification were calculated as an average of discharge 

measurements from the USGS streamflow-gaging station 

nearest to each site where biological and physical data were 

collected during the 2-day period when biological and physical 

data were collected. In 2010, low flows ranged from an 

estimated daily mean discharge of 45 ft3

/s at Big Cypress 02 

during July 30–31, 2010, to measured daily mean discharges 

of 25 ft3/s at Black Cypress during August 3–4, 2010, and 

4.7 ft3/s at Little Cypress during August 18–19, 2010. During 

July 30–31, 2010, a daily mean discharge of 45 ft3/s was 

estimated at Big Cypress 02 as the difference between the 

daily mean discharge of 63 ft3/s measured at the Big Cypress 

Bayou gage and withdrawals of 18 ft3/s made by the H.W. 

Pirkey Power Plant in Hallsville, Tex. (fig. 1; table 4). The 

Big Cypress Bayou gage is about 5.5 miles upstream from 

the Big Cypress 02 site; the H.W. Pirkey Power Plant pump 

station (fig. 2), about 1 mile downstream from the Big Cypress 

Bayou gage, removed 1,110.19 acre-ft of water from Big 

Cypress Bayou in July 2010 (Lee Thomas, Northeast Texas 

Municipal Water District, written commun., 2012), which 

equates to a continuous 18 ft3

/s during the entire month of July 

2010 (table 4). On July 26, 2011, the instantaneous discharge 

measured at Big Cypress 02 was 10 ft3/s (table 4), which was 

characterized as a very low flow. 

Physical Characteristics

The areal extent of mesohabitats within the stream 

reach at each data-collection site was surveyed by using a 

Sokkisha Set 4A laser-operated total station (a theodolite and 

electronic distance-measurement instrument used to read slope 

distances from the instrument to a particular point) (Sokkia, 

2012). Physical characteristics, including the area of each 

mesohabitat type, were determined for each data collection 

site (appendix 1). A detailed map of the reach at each data 

collection site was produced and includes the type and area of 

each mesohabitat at Big Cypress 02, Black Cypress, and Little 

Cypress (figs. 6–8). Some of the small margin pools at Big 

Cypress 02 were not surveyed.

Representative points for physical measurements were 

selected randomly across each mesohabitat by establishing 

five transects perpendicular to the direction of flow 

(appendix 1). The five transects were intended to collectively 

represent the given mesohabitat within a reach and were 

approximately evenly spaced. When the mesohabitat was less 

than 33 ft long, three approximately evenly spaced transects 

were established perpendicular to the direction of flow. The 

transects listed in appendix 1 are not shown on figures 6–8 and 

should not be confused with the “surveyed transect points” 

used to collect to collect water-quality properties during 

October 2011 (figs.7B and 8B; appendix 2). 

Table 3. Low-flow prescriptions (in cubic feet per second) for Big Cypress Bayou, Black Cypress Bayou, and Little Cypress Bayou 

based upon a variety of ecological objectives during dry and average years (Caddo Lake Institute, 2010). 

Jan. Feb. Mar. Apr. May June July Aug. Sept. Oct. Nov. Dec.

Dry year Fish habitat Spawning habitat Maintain aquatic diversity Fish habitat

Big Cypress Bayou 90 90 218 198 114 49 13 6 6 40 90 90

Black Cypress Bayou 125 201 242 140 80 42 11 4 4 4 19 91

Little Cypress Bayou 112 186 219 158 86 38 12 5 5 5 18 68

Average year Fish habitat Benthic drift and dispersal, fish spawning Fish habitat Fish habitat

Big Cypress Bayou 268 347 390 330 150 79 35 40 40 40 90 117

Black Cypress Bayou 222 300 306 205 156 95 32 5 4 13 74 209

Little Cypress Bayou 242 471 415 287 155 96 26 10 10 19 65 144
12 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Table 4. Measured daily mean streamflows at the U.S. Geological Survey streamflow-gaging stations nearest to study sites and 

instantaneous discharge measured in the field, Big Cypress Basin, Texas, 2010–11.

[TCEQ, Texas Commission on Environmental Quality; USGS, U.S. Geological Survey; ft3/s, cubic feet per second; ft, feet; --, no data]

Sites sampled in 2010

Study sites where physical 

characteristics, aquatic biota, 

and selected water quality 

properties were collected 

(U.S. Geological Survey 

station number and name)

Short name

TCEQ 

station 

number

Date

Station 

number of 

the nearest 

USGS 

streamflowgaging 

station

Measured discharge at 

nearest USGS streamflow-gaging 

station for the specified day or 

range of days

Estimated 

discharge 

based on 

daily mean 

discharge and 

power plant 

withdrawals 

(ft3

/s)

Minimum 

discharge

(ft3

/s)

Maximum 

discharge

(ft3/s)

Mean 

discharge

(ft3/s)

07346017 Big Cypress Bayou 

near U.S. Highway 59 near Jefferson, Tex.

Big Cypress 01 20108 July 30 07346000 61 63 62 --

07346015 Big Cypress Bayou at 

confluence of French Creek, Jefferson, Tex. 

Big Cypress 02 20803 July 30–31 07346000 61 63 63 1

45

07346044 Black Cypress Bayou 

near U.S. Highway 59 near Jefferson, Tex.

Black Cypress 20805 Aug. 3–4 07346045 19 35 25 --2

07346071 Little Cypress Bayou 

near U.S. Highway 59 near Jefferson, Tex.

Little Cypress 20804 Aug. 18–19 07346070 3.7 5.8 4.7 --2

Sites sampled in 2011

Study sites where physical 

characteristics, aquatic biota, 

and selected water quality 

properties were collected

(U.S. Geological Survey 

station number and name)

Short name

TCEQ 

station 

number

Date

Station 

number of 

the nearest 

USGS 

streamflowgaging 

station

Measured discharge at 

nearest USGS streamflow-gaging 

station for the specified day or 

range of days

Instantaneous 

discharge 

measured in 

the field 

(ft3

/s)

Minimum 

discharge

(ft3

/s)

Maximum 

discharge

(ft3/s)

Mean 

discharge

(ft3/s)

07346015 Big Cypress Bayou at 

confluence of French Creek, Jefferson, Tex. 

Big Cypress 02 20108 July 26–27 07346000 26 39 32 3 10

07346044 Black Cypress Bayou 

near U.S. Highway 59 near Jefferson, Tex.

Black Cypress 20805 Oct. 12–13 07346045 0 0 0 0

07346071 Little Cypress Bayou 

near U.S. Highway 59 near Jefferson, Tex.

Little Cypress 20804 Oct. 13–14 07346070 0 0 0 0

1

Estimated as the difference between mean discharge of 62 ft3/s measured at USGS streamflow-gaging station 07346000 Big Cypress Bayou near Jefferson 

Tex. and withdrawals made by the H.W. Pirkey Power Plant. The USGS streamflow-gaging station is about 5.5 miles upstream from the data collection site; 

the H.W. Pirkey Power Plant, pump station located 1 mile downstream from the gage, removed 1,110.19 acre-ft of water from Big Cypress Bayou in July 2010, 

which equates to 18 ft3

/s (Lee Thomas, Northeast Texas Municipal Water District, written commun., 2012).

2

Instantaneous discharge not measured because the site was in close proximity to an existing USGS streamflow-gaging station.

3

Large differences in streamflow between the instantaneous discharge measured in the field and the mean discharge measured at the nearest upstream gaging 

station are largely because of the withdrawals associated with the H.W. Pirkey Power Plant.
Upstream

boundary

Down

bou

6

8

9

11

94°26'34"

94°26'30"

94°26'26"

32°44'24"

32°44'20"

94°26'32"

94°26'28"

32°44'22"

Upstream

boundary

1

2

3

5

94°26'34" 94°26'32"

94°26'30"

94°26'28"

94°26'26"

32°44'24"

32°44'22"

32°44'20"

0 50 100 METERS

0 100 200 FEET

A. July 2010

B. July 2011

EXPLANATION

Mesohabitat type (table 2) with  identifier (appendix 1) for Big Cypress 02—USGS 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas (fig. 2) Slow run Fast run Margin pool—EmbaymentCypress tree, stump, or snag

123

USGS, U.S. Geological Survey

NOTE: Not all features are shown because the areal extent of some small margin pools was not determined. 

Figure 6. Mesohabitat extents and channel features surveyed A, July 2010, and B, July 2011, at U.S. Geological Survey station 07346015 Big Cypress 

French Creek, Jefferson, Texas.
14 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Figure 7. Mesohabitat extents and channel features surveyed A, August 2010, and B, October 2011, at U.S. Geological Survey station 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Texas (Texas Commission on Environmental Quality station 20805).

Upstream

boundary

Downstream

boundary

8

11

10

9

94°21'58"

32°47'24"

32°47'22"

94°21'56"

94°21'54"

94°21'52"

Upstream

boundary

Downstream

boundary

1

4

3

2

6

5

7

A. August 2010

B. October 2011

94°21'58"

32°47'24"

32°47'22"

94°21'56"

94°21'54"

94°21'52"

0 50 100 FEET

0 25 50 METERS

EXPLANATION

Mesohabitat type (table 2) with 

 identifier (appendixes 1 and 2) for

 Black Cypress—USGS 07346044 Black 

 Cypress Bayou near U.S. Highway 59

 near Jefferson, Texas (fig. 2)

 Slow run

 Fast run

 Channel or isolated pool

 Margin pool—Backwater

Cypress tree, stump, or snag

Surveyed transect point

Center channel

Thalweg

6

2

8

5

USGS, U.S. Geological Survey
Methods 15

Figure 8. Mesohabitat extents and channel features surveyed A, August 2010, and B, October 2011, at U.S. Geological Survey station 

07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Texas (Texas Commission on Environmental Quality station 20804).

Upstream

boundary

Downstream

boundary

7

8

9

94°19'44"

32°43'16"

32°43'14"

32°43'12"

32°43'10"

32°43'08"

32°43'06"

32°43'04"

94°19'42"

94°19'42"

Upstream

boundary

Downstream

boundary

1

3

4

5

6

2

94°19'44"

32°43'16"

32°43'14"

32°43'12"

32°43'10"

32°43'08"

32°43'06"

32°43'04"

94°19'42"

94°19'42"

0 100 200 FEET

0 50 100 METERS

A. August 2010 B. October 2011

EXPLANATION

Mesohabitat type (table 2) with 

 identifier (appendixes 1 and 2) for

 Little Cypress—USGS 07346071

 Little Cypress Bayou near

 U.S. Highway 59 near Jefferson,

 Texas (fig. 2)

 Slow run

 Fast run

 Channel or isolated pool

 Margin pool—Forewater, backwater

 or embayment

Cypress tree, stump, or snag

Surveyed transect point

Center channel

Thalweg

3

2

8

1

USGS, U.S. Geological Survey
16 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Physical measurements were made at one of three 

different locations (left, center, or right) along each 

transect. At the first transect within a mesohabitat, physical 

measurements were made at a randomly selected location; 

the measurement location for each subsequent transect 

was selected based on a progression from left to right. The 

following physical measurements were made at each location: 

width, depth, velocity, dominant substrate type and size, 

and percentage of embeddedness (appendix 1). The following 

measurements also were made at the center transect of 

each mesohabitat: bankfull width and height, left and right 

bank angle; left and right bank buffer width, left and right 

bank canopy closure, left and right bank densitometer 

readings, and channel bearing at the thalweg (appendix 1). 

Fish cover types and relative abundance (appendix 1) 

were estimated for approximately a 3-ft wide buffer along 

each transect.

Aquatic Biota Collection

Fish Surveys

Fish surveys were completed following TCEQ protocols 

(Texas Commission on Environmental Quality, 2007). The 

fish surveys were done in the reaches represented by the 

Big Cypress 02, Black Cypress, and Little Cypress sites 

in 2010, and at the Big Cypress 02 site in 2011 (the Black 

Cypress and Little Cypress sites were not surveyed for fish 

during 2011 because these streams were not flowing at that 

time). In addition, reaches at each site were subsampled for 

fish at the mesohabitat scale using methods described in the 

“Texas Instream Flow Studies—Technical Overview” (Texas 

Water Development Board, 2008). Fish were collected at 

Big Cypress 02, Black Cypress, and Little Cypress from 

late July through August 2010, and again at Big Cypress 

02 in late July 2011. Fish sampling methods included boat, 

barge and backpack electrofishing, and trap netting using 

a seine. A minimum of 15 minutes (900 seconds) was 

spent electrofishing each reach. Mesohabitat boundaries 

(mapped prior to fish sampling) were marked, and each 

was electrofished in its entirety using a boat for deeper 

mesohabitats and a barge or backpack unit for shallower, 

wadeable mesohabitats. Each mesohabitat was electrofished 

twice, and the time (in seconds) was recorded, except at Big 

Cypress 02 in July 2011, when the time was inadvertently 

omitted from the field notes. The results from the two 

electrofishing surveys at each site were compiled for each 

mesohabitat. Block-netting between adjoining mesohabitats 

was used as needed to minimize fish movement between 

mesohabitats during sampling. A minimum of 10 seine hauls, 

distributed among mesohabitat types, were collected in the 

wadeable mesohabitats after completion of electrofishing. A 

3.0 by 3.0-meter (m), 0.17-centimeter (cm) mesh, flat-panel 

seine was used. All electrofishing and seining activities were 

done during daylight hours.

All collected fish were transferred to aerated holding 

tanks, and the fish collected from each mesohabitat were 

held separately. Each fish was weighed to the nearest gram 

and measured to the nearest millimeter to determine its total 

length. Fish that could be identified in the field were returned 

to the stream. Fish that could not be identified in the field 

were preserved in 10 percent buffered formalin, labeled by 

mesohabitat, and returned to the USGS Texas Water Science 

Center for preliminary identification. Fish preserved onsite 

in 10 percent formalin were transferred to 70 percent ethanol 

as soon as possible (generally within 2 weeks) for long-term 

preservation. 

Fish that were identified in the field on the day of 

sampling were identified to the lowest taxonomic level 

possible (generally species). The following information 

was recorded for each mesohabitat sampled: species, 

number of individuals by species, and mesohabitat type 

(appendix 3). A photograph was taken onsite of an individual 

fish representing each species identified in the field, and all 

photograph-vouchers are maintained by the USGS Texas 

Water Science Center in Austin. All retained fish specimens 

were preserved in 70 percent ethanol after decanting the 10 

percent buffered formalin. All retained fish, represented by at 

least one sample for each species collected at each site, were 

deposited with the Curator of Ichthyology at the University 

of Texas Natural Science Center in Austin, Tex., for species 

(taxa) verification and permanent deposition (University of 

Texas, 2012). Voucher specimens for all fish species were 

retained in accordance with the protocols detailed in TCEQ’s 

SWQM protocols (Texas Commission on Environmental 

Quality, 2007). 

Mussel Surveys

Mussels were collected from the freshwater mussel 

communities at the Big Cypress 01, Big Cypress 02, and 

Black Cypress sites in summer 2010 (appendix 4). Mussels 

were not collected from the Little Cypress site. The survey 

of freshwater mussels planned for 2010 at Little Cypress 

was not completed because of scheduling conflicts and was 

rescheduled for July–September 2011. The freshwater mussel 

survey at the Little Cypress site (rescheduled for 2011) was 

not possible because of an extended period with little to no 

flow at this site during the targeted July–September 2011 

sampling period.

Sampling involved a stratified approach using a 

0.25 square meters (m2) quadrat (Wisconsin Department 

of Natural Resources, 2005). Each study site was initially 

stratified into high- and low-density habitats based on 

preliminary mussel surveys. Stratification as high- or lowdensity habitats was based on the occurrence of distinct 

mussel beds (high density) or the lack of these beds (low 

density). Only high-density habitats were sampled at the three 

sites because the low-density habitats were too deep to sample 

using the equipment available and the preliminary surveys 

indicated mussels were more abundant in the shallower, 
Methods 17

high-density habitats. One high-density habitat was sampled 

at each site. Each high-density habitat was sampled with an 

aligned systematic sampling design utilizing three random 

starts. A systematic sampling design with multiple random 

starting points provides good spatial coverage and allows for 

the calculation of population density and variance estimates 

(Strayer, 2008). Random starting points were selected at the 

downstream end of each high density area, and subsequent 

sampling locations were located at fixed distances in both 

the upstream and transverse channel directions. The distance 

between sampling quadrats was calculated using the following 

formula:

*

/

L W d

n k =

where

d is the distance between sampling quadrats, in 

meters;

L is the strata length, in meters;

W is the mean strata width, in meters;

n is the number of quadrats sampled; and

k is the number of random starting points.

The targeted number of quadrats (“n” in the equation 

above) was 100 for each site, but the actual number of 

quadrats sampled at each site was less than 100; some quadrat 

locations could not be sampled because of in-channel debris 

such as snags or stumps. In these instances, the quadrat 

was not sampled, and the sampling crew moved to the next 

quadrat. The number of quadrats varied by site from 81 at 

Black Cypress, 77 at Big Cypress 02, and 64 at Big Cypress 

01 (appendix 4). At each site, a 0.25 m2 quadrat was placed 

on the streambed, and the streambed was searched for 

mussels by hand. The streambed was excavated to a depth of 

approximately 15 cm during the search. Mussels found alive 

were identified to the lowest taxonomic category possible 

(generally species) onsite, and total length along the long 

(anterior-posterior) axis of the valve was measured. Depth, 

velocity, and dominant substrate type were collected from the 

center of each quadrat after mussel sampling was completed 

in the same quadrat. Velocity was measured in each quadrat 

as close to the streambed as possible. Bed sediment bulk 

density was determined from the collection of a shallow 

core sample (2.5 to 10 cm deep) from the streambed directly 

below the center of the quadrat. A high-density butyrate tube 

(10.0 cm long and with a radius of 2.35 cm) was used to 

collect each core; the tube was pushed into the streambed by 

hand. The collection of sediment cores was distributed among 

the different streambed substrate types present at each site 

(appendix 4), and each core was collected in a quadrat where 

one or more live mussels were found. Therefore, there are bed 

sediment bulk density data for only a subset of mussel species 

from each site. Bed sediment bulk density was calculated 

by dividing the dry weight in grams of the sediment from 

each core by the volume in cubic centimeters of each core 

(appendix 4). Sediment dry weight was used because the wet 

weight of sediment would introduce bias depending on the 

degree of saturation of each sample. Sediment dry weight 

was determined for each core by oven-drying the sediment 

sample for 24 hours and weighing the sample to the nearest 

tenth of a gram. 

Freshwater mussels were identified in the field to species 

by a qualified biologist. Freshwater mussels are highly 

endemic organisms that are long-lived with slow growth 

rates and complex reproduction methods (Strayer, 2008). As 

a consequence, freshwater mussel populations have a slow 

recovery following population reduction. Additionally, many 

species are rare or endangered (U.S. Fish and Wildlife Service, 

2012), and therefore, each freshwater mussel species was 

vouchered by photographic documentation or by the collection 

of spent valves (valves from dead mussels) unless the species 

could not be identified in the field. Voucher photographs and 

labeled spent valves are maintained at the USGS Texas Water 

Science Center in Austin.

Selected Water-Quality Properties

Selected water-quality properties (dissolved oxygen, 

pH, specific conductance, and water temperature) were 

measured in isolated pools in Black Cypress Bayou and Little 

Cypress Bayou during October 2011 when these streams were 

not flowing by using a YSI 600XL multiparameter sonde 

(Xylem Inc., 2012). There were long periods of no flow 

during June–September 2011 in the Black Cypress and Little 

Cypress Bayous, and the targeted low flow conditions during 

June–September 2011 were unavailable in these streams. The 

isolated pools were crucial for sustaining aquatic biota during 

periods of no flow. 

The sonde was calibrated in the field each day prior to 

the measurement of water-quality properties (appendix 2). 

Water-quality properties were measured in four isolated pools 

on Black Cypress Bayou and three isolated pools on Little 

Cypress Bayou. At each pool, measurements were made 

along a transect line: midchannel, equidistant between 

midchannel and the left edge of water, and equidistant 

between midchannel and the right edge of water (except at 

transect D-D’ on Black Cypress Bayou, where data were only 

collected midchannel). Typically, water-quality measurements 

were made at three discrete depth intervals at each location 

along the stream (transect lines). When transact lines 

intersected pools that were less than 1 ft deep or less than 10 

ft wide, the water-quality properties were measured at one or 

two discrete depth intervals. At transects where water-quality 

measurements were made at three different depth intervals, 

measurements were made at the midpoint of the water column, 

a few inches above the streambed, and a few inches below 

the water surface. At measurement locations where waterquality properties were measured at a single depth interval, 

the measurements were typically made at the midpoint of the 

water column.
18 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Cross-sectional representations of dissolved oxygen 

concentrations along surveyed transect lines at the Black 

and Little Cypress sites were hand-contoured using linear 

interpolation between as many as nine measured values 

and extrapolation outside of these values. Cross-sectional 

representations of measured dissolved oxygen concentration 

were not prepared for transects C–C′ and D–D′ at the Black 

Cypress site because there were insufficient data points. 

Quality Assurance

Quality-assurance procedures for aquatic biota data 

followed the guidelines detailed in TCEQ’s SWQM protocols 

(Texas Commission on Environmental Quality, 2007). Field 

identifications were conducted by trained biologists familiar 

with the types of fish and freshwater mussel species found 

in the Big Cypress Basin in Texas with the aid of appropriate 

taxonomic keys. Unidentified fish species were provided to 

the Curator of Ichthyology at the University of Texas Natural 

Science Center in Austin, Tex., for species verification 

and permanent deposition (University of Texas, 2012). 

Unidentified mussel species were identified with the help of 

experts from Texas Parks and Wildlife. All collected voucher 

specimens (fish and mussel were labeled onsite and will be 

retained at the USGS laboratory in Austin or the University 

of Texas Natural Science Center in Austin for a minimum of 

5 years. Dissolved oxygen, pH, specific conductance, and 

water temperature were measured in the stream by using a 

calibrated water-quality sonde; calibration was done at the 

site prior to measuring water-quality properties following 

procedures described in the “National Field Manual for the 

Collection of Water-Quality Data” (U.S. Geological Survey, 

variously dated).

Physical Characteristics and Aquatic 

Biota at the Reach and Mesohabitat 

Scale for Reaches on Big Cypress, 

Black Cypress, and Little Cypress 

Bayous During Summer 2010

Physical Characteristics

Of the three stream sites, Big Cypress 02 was the widest, 

with a mean mesohabitat width across all mesohabitat types 

of 46.3 ft and a median mesohabitat width of 59.1 ft on July 

30, 2010. The mean and median widths were 62.2 and 62.3 

ft, respectively when only main channel mesohabitats were 

considered (that is, the mesohabitats adjacent to [but not part 

of] the main channel [margin pools] were excluded). The 

second widest reach was measured at the Little Cypress site, 

which during August 18–19, 2010, had mean and median 

widths across all mesohabitat types of 43.7 ft and 42.7 ft, 

respectively; the mean and median widths were 49.9 ft and 

49.2 ft, respectively, when only main-channel mesohabitats 

were considered (appendix 1). The reach at the Black 

Cypress site was the narrowest with a mean width across all 

mesohabitat types of 26.9 ft and a median width of 28.1 ft; 

mean and median widths were 29.1 ft and 28.5 ft, respectively 

when accounting for only main-channel mesohabitats.

In 2010, Big Cypress 02, on average, tended to be the 

deepest of the three sites followed by Little Cypress, and 

although the reach at Black Cypress, on average, was the 

shallowest reach, a pool in the reach at the Black Cypress 

site contained the deepest point (14.8 ft) measured from all 

three reaches. In July 2010, Big Cypress 02 had mean and 

median depths of 4.2 ft and 3.6 ft, respectively, across all 

mesohabitat types and mean and median depths of 5.5 ft and 

4.8 ft, respectively, when accounting for only main-channel 

mesohabitats. The mean and median depths at the Little 

Cypress site were 3.9 ft and 3.2 ft, respectively, across all 

mesohabitat types and mean and median depths of 4.5 ft and 

4.0 ft, respectively, when accounting for only main-channel 

mesohabitats. Black Cypress had mean and median depths of 

3.1 ft and 2.3 ft, respectively, across all mesohabitat types and 

mean and median depths of 3.3 ft and 3.0 ft, respectively when 

accounting for only main-channel mesohabitats.

Mean and median velocities in 2010 were highest at 

the Black Cypress site (0.37 and 0.33 feet per second [ft/s], 

respectively, across all mesohabitat types and 0.42 and 0.35 

ft/s, respectively, for main-channel mesohabitats, exclusively). 

Mean and median velocities were lowest at the Little Cypress 

site (0.13 and 0.09 ft/s, respectively, across all mesohabitat 

types and 0.15 and 0.10 ft/s, respectively, for main-channel 

mesohabitats, exclusively). Mean and median velocities at Big 

Cypress 02 (in 2010, 0.22 and 0.14 ft/s, respectively, across 

all mesohabitat types and 0.31 and 0.21 ft/s, respectively, 

for main-channel mesohabitats, exclusively) were between 

velocities observed at the Black Cypress and Little Cypress 

sites. Velocities exceeded 1 ft/s at only two locations within 

a single mesohabitat (the most upstream fast run in Black 

Cypress) out of all the mesohabitats where habitat data were 

collected in the three reaches.

Physical characteristics associated with the reaches 

at each site were compared on the basis of four distinct 

mesohabitat types: slow runs, fast runs, channel pools, and 

margin pools (fig. 9; table 2). Slow runs from the three reaches 

differ from one another on the basis of depths and widths, 

exhibiting relatively distinct groups among each of the three 

reaches. Fast runs in Little Cypress and Black Cypress seem 

similar on the basis of depths and widths, while fast runs 

in all three reaches seem similar on the basis of depths and 

velocities. There were insufficient data regarding the channel 

pool or margin pool mesohabitat types to draw any noteworthy 

conclusions. 
-0.20 0.2 0.4 0.6 0.8 1.0 0 1 2 3 4 5 1.2 1.4 1.6 0 0.05 0.10 0.15 0.20 0.25 0.30 0 2.5 5 7.5 10 15 0.35 -0.06 -0.04 -0.020 0.02 0.04 0.06 0 0.5 

Depth, in feet

Velocity, in feet per second

Depth, in feet 

12.5

0.400.45

-0.3-0.2-0.1

0

0.10.20.3

0 2.5 5 7.5 10 15

0.4

Depth, in feet

12.5

0.50.6

0.080.10

0

0.51.01.52.02.53.0

Depth, in feet

0 5 10 15 20 25

Wetted channel width, in feet

3.54.04.5

02468

1012

0 5 10 15 20 25

Wetted channel width, in feet

14

02468

1012

0 5 10 15 20 25

Wetted channel width, in feet

1416

30 0

0.51.01.52.02.53.0

0 2 

Wetted 

Slow runs Fast runs Channel pools M

EXPLANATION

Big Cypress 02—Big Cypress Bayou at confluence of French Creek, Jefferson, TexasBlack Cypress—Black Cypress Bayou near U.S. Highway 59 near Jefferson, TexasLittle Cypress—Little Cypress Bayou near U.S. Highway 59 near Jefferson, Texas

Figure 9. Physical parameters in different mesohabitats collected in 2010 from U.S. Geological Survey stations 07346015 Big Cypress Bayou at conflu

Jefferson, Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 n
20 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Fish Surveys

More fish were collected from Big Cypress 02 in 2010 

compared to the Black Cypress or Little Cypress sites (table 5; 

appendix 3). Five hundred and ninety-six fish were collected 

from the Big Cypress 02 site in 2010 compared to 273 fish 

at the Black Cypress site and 359 at the Little Cypress site. 

Although the number of fish collected from Big Cypress 02 

was considerably larger than the number of fish collected 

from the other two sites, the total number of fish species 

collected among the three sites was similar (table 5). Thirtyfour fish species were collected from Big Cypress 02 in 2010 

compared to 26 species from Black Cypress and 33 species 

from Little Cypress. The larger number of fish collected from 

Big Cypress 02 was influenced by the large number of sunfish 

(Centrarchidae) species, especially longear sunfish (Lepomis 

megalotis) (appendix 3). Menhinick index of species richness 

(hereinafter referred to as Menhinick index), calculated as 

the number of fish species divided by the square root of the 

total number of fish collected from each site (table 5), is a 

biological metric that expresses species diversity (Menhinick, 

1964). In general, the more species, and the fewer individuals 

per species, the greater is the diversity (Ludwig and Reynolds, 

1988). Menhinick index values were larger for Black Cypress 

(1.57) and Little Cypress (1.74) than for Big Cypress 02 (1.39 

in 2010 and 1.22 in 2011). The larger index values for Black 

Cypress and Little Cypress indicate more evenness in the 

number of species in relation to the number of individuals 

collected from these sites. 

The alteration of natural flow regimes below dams can 

reduce the diversity of native fishes and can increase the 

occurrence of introduced species (Marchetti and Moyle, 2001; 

Propst and Gido, 2004). The common carp (Cyprinus carpio), 

western mosquitofish (Gambusia affinis), and redbreast 

sunfish (Lepomis auritus) were the only species (out of 48) 

collected that were introduced species (table 6; appendix 3). 

Common carp and redbreast sunfish only occurred in Big 

Cypress 02, downstream from the Ferrells Bridge Dam on 

Lake O’ The Pines reservoir. Western mosquitofish were 

collected from both the Big Cypress site and the Black 

Cypress site. Longear sunfish (Lepomis megalotis) was the 

most abundant fish species collected from all three sites 

in summer 2010 (table 6). Species of the sunfish family 

Centrarchidae tended to be more common than other fish 

families at all sites. Blacktail shiners (Cyprinella venustus) 

were the second most abundant fish collected from Big 

Cypress 02 and fourth and ninth in rank relative abundance at 

Black Cypress and Little Cypress, respectively. The number 

of tied ranks based on relative abundance (six at Big Cypress 

02 in 2010, six at Black Cypress, and eight at Little Cypress) 

were dominated by ranks based on the collection of only a 

few individuals of several species. Low rank relative 

abundance was common for rare species like bowfin (Amia 

calva), longnose gar (Lepisosteus osseus), spotted gar 

(Lepisosteus oculatus), bullhead minnow (Pimphales vigilax), 

flathead catfish (Pylodictus olivaris), and several species 

of darters (Percidae) at all three sites. The family Percidae 

includes darters and perches; although no perches were 

collected, the category of darters and perches was used in 

this report (table 6; appendix 3). Bowfin, gar, and flathead 

catfish are op-tier large piscivorous (fish eating) fish and are 

typically less abundant in lotic (stream) ecosystems compared 

to smaller species that feed on invertebrates or algae (Dodds, 

2002).

Table 5. Selected fish metrics from U.S. Geological Survey stations 07346015 Big Cypress Bayou at confluence of French Creek, 

Jefferson, Texas (2010–11), 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (2010), and 07346071 Little Cypress 

Bayou near U.S. Highway 59 near Jefferson, Tex. (2010).

USGS 

station 

number

USGS station name Short name Date

Total 

number of 

individuals

Number 

of 

species

Total catch 

per unit of 

electrofishing 

effort1

Menhinick 

index2

07346015 Big Cypress Bayou at confluence of 

French Creek, Jefferson, Tex. 

Big Cypress 02 7/31/2010 596 34 5.08 1.39

07346015 Big Cypress Bayou at confluence of 

French Creek, Jefferson, Tex. 

Big Cypress 02 7/27/2011 525 28 Not calculated3 1.22

07346044 Black Cypress Bayou near U.S. Highway 

59 near Jefferson, Tex.

Black Cypress 8/3–4/2010 273 26 2.73 1.57

07346071 Little Cypress Bayou near U.S. Highway 

59 near Jefferson, Tex.

Little Cypress 8/19/2010 359 33 3.01 1.74

1

Catch per unit of electrofishing effort is determined by dividing the total number of individuals collected by the total time (in seconds) electrofished 

multiplied by 30 to report the catch per 30 seconds of effort. 

2

Menhinick index is calculated as the number of species divided by the square root of the total number of individuals of that species that were collected.

3

Total catch per unit effort could not be calculated because the total time electrofished was not recorded.
Physical Characteristics and Aquatic Biota at the Reach and Mesohabitat Scale for Reaches 21

Table 6. Presence or absence of fish species and rank abundance based on the relative abundance of each species collected from 

U.S. Geological Survey stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas (2010–11), 07346044 

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (2010), and 07346071 Little Cypress Bayou near U.S. Highway 59 near 

Jefferson, Tex. (2010).—Continued

[--, no individual organisms were collected, so rank abundance is not applicable]

Family Family

common name Species Species common name

Status

Rank abundance

Big 

Cypress 021

(2010)

Big 

Cypress 021

(2011)

Black 

Cypress2

(2010)

Little 

Cypress3

(2010)

Lepisosteidae Gars Lepisosteus oculatus Spotted gar Native 10 15 -- 11

Lepisosteus osseus Longnose gar Native -- 15 -- --

Amiidae Bowfin Amia calva Bowfin Native 14 15 -- 14

Clupeidae Herrings Dorosoma 

cepedianum 

Gizzard shad Native -- -- -- 7

Dorosoma petenense Threadfin shad Native 13 14 -- --

Cyprinidae Minnows Cyprinella lutrensis Red shiner Native 13 -- 11 7

Cyprinella venustus Blacktail shiner Native 2 3 4 9

Cyprinus carpio Common carp Introduced 15 -- -- --

Hybopsis amnis Pallid shiner Native -- -- -- 14

Lythrurus fumeus Ribbon shiner Native 12 -- 3 8

Notropis 

atherinoides

Emerald shiner Native -- -- -- 8

Notropis chalybaeus Ironcolor shiner Native -- -- -- 9

Notropis maculatus Taillight shiner Native 13 -- -- --

Notropis shumardi Silverband shiner Native -- -- 11 --

Notropis texanus Weed shiner Native -- -- -- 11

Pimphales vigilax Bullhead minnow Native 14 5 -- 14

Atherinopsidae Silversides Labidesthes sicculus Brooke silverside Native 12 10 5 10

Fundulidae Topminnows and 

Killifishes

Fundulus notatus Blackstripe 

topminnow

Native 7 4 4 3

Catostomidae Suckers Minytrema melanops Spotted sucker Native 14 13 9 6

Ictaluridae Catfishes Ameiurus natalis Yellow bullhead Native -- 15 -- --

Ictalurus punctatus Channel catfish Native 9 12 -- 12

Noturus gyrinus Tadpole madtom Native -- -- 11 --

Noturus nocturnus Freckled madtom Native 16 -- 11 --

Pylodictis olivaris Flathead catfish Native 14 13 -- 12

Esocidae Pickerels Esox americanus Redfin pickerel Native -- -- 10 13

Aphredoderidae Pirate perch Aphredoderus 

sayanus

Pirate perch Native 11 9 8 12

Poecilidae Mosquitofishes Gambusia affinis Western 

mosquitofish

Introduced 14 1 11 --

Table 6. Presence or absence of fish species and rank abundance based on the relative abundance of each species collected from 

U.S. Geological Survey stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas (2010–11), 07346044 

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (2010), and 07346071 Little Cypress Bayou near U.S. Highway 59 near 

Jefferson, Tex. (2010).

[--, no individual organisms were collected, so rank abundance is not applicable]
22 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Table 6. Presence or absence of fish species and rank abundance based on the relative abundance of each species collected from 

U.S. Geological Survey stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas (2010–11), 07346044 

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (2010), and 07346071 Little Cypress Bayou near U.S. Highway 59 near 

Jefferson, Tex. (2010).—Continued

[--, no individual organisms were collected, so rank abundance is not applicable]

Family Family

common name Species Species common name

Status

Rank abundance

Big 

Cypress 021

(2010)

Big 

Cypress 021

(2011)

Black 

Cypress2

(2010)

Little 

Cypress3

(2010)

Percidae Darters and 

Perches

Percina 

macrolepida

Bigscale logperch Native 15 -- 10 --

Percina sciera Dusky darter Native 14 15 11 14

Etheostoma 

asprigene

Mud darter Native 16 14 -- 14

Etheostoma 

chlorosoma

Bluntnose darter Native -- 15 11 --

Etheostoma gracile Slough darter Native -- -- -- 14

Etheostoma histrio Harlequin darter Native 15 -- 11 13

Percina maculata Blackside darter Native -- -- -- 14

Etheostoma 

proeliare

Cypress darter Native 16 15 11 14

Centrarchidae Sunfishes Lepomis 

macrochirus

Bluegill Native 3 6 2 2

Lepomis cyanellus Green sunfish Native -- -- 9 --

Micropterus 

salmoides

Largemouth bass Native 8 10 6 5

Lepomis megalotis Longear sunfish Native 1 2 1 1

Lepomis auritus Redbreast sunfish Introduced 16 -- -- --

Lepomis 

marginatus

Dollar sunfish Native 15 11 10 --

Lepomis 

microlophus

Redear sunfish Native 5 8 7 4

Lepomis miniatus Redspotted sunfish Native 4 7 7 13

Lepomis 

symmetricus

Bantam sunfish Native 16 -- -- --

Micropterus 

punctulatus

Spotted bass Native 16 13 11 9

Lepomis gulosus Warmouth Native 6 14 8 6

Pomoxis annularis White crappie Native 8 14 -- 11

Scianidae Drums Aplodinotus 

grunniens

Freshwater drum Native 14 14 -- 14

1

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex.

2

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex.

3

Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex.
Physical Characteristics and Aquatic Biota at the Reach and Mesohabitat Scale for Reaches 23

Fish data from the various mesohabitat types were 

combined into four mesohabitat categories for analysis: slow 

run, fast run, channel pool, and margin pool. Comparisons 

among sites and mesohabitat types were made by using the 

total number of species collected or catch per unit effort 

(CPUE) expressed as the number of fish collected in 30 

seconds of electrofishing. The CPUE was calculated by 

dividing the number of fish collected in a mesohabitat by the 

number of seconds electrofished in the same mesohabitat; the 

resulting quotient is then multiplied by 30 seconds. Thirty 

seconds were used because it was the shortest duration of 

electrofishing in any of the mesohabitats among all sites. 

Comparing mesohabitat fish data expressed in CPUE 

standardized the number and species collected in each 

mesohabitat regardless of differences in area sampled between 

mesohabitats. The use of CPUE to standardize fish data allows 

for direct comparisons between stream reaches or in-channel 

habitats of different size, and CPUE is a common practice 

among aquatic biologists (Nielsen and Johnson, 1983). 

Fish species richness (number of distinct species) was 

compared among the three sites by using data obtained in 

2010 when the streams at all sites were flowing. Fish species 

richness for slow runs ranged from 13 to 26 distinct species. 

Fish species richness in fast runs was less variable and 

ranged from 19 to 24 distinct species (appendix 3). The 

number of fish species was larger in margin pools at Little 

Cypress compared to this mesohabitat at the other two sites, 

and channel pools had the smallest number of fish species 

out of all mesohabitat types (fig. 10). Fast runs were 

dominated by longear sunfish, blacktail shiners, and several 

other species of sunfish and cyprinids at Big Cypress 02 

and by longear sunfish, bluegill, and blackstripe topminnows 

at Black Cypress (appendix 3). Fast runs also were dominated 

by longear sunfish and blackstripe topminnows at Little 

Cypress. 

Fish metrics that are commonly included in the 

calculation of an index of biotic integrity (IBI) for fish 

include the number of darter species, the number of native 

cyprinid species, and the number of individuals or species 

of invertivores, predators, and omnivores (Linam and 

others, 2002). These five metrics commonly used in the 

calculation of an IBI will be discussed in this report to provide 

a detailed description of the structure and function of the 

fish community at each site, but not the IBI index values 

themselves.

The fish family Percidae includes darters and perches. 

Only darters, including the darter Bigscale logperch, and no 

true perches were collected during this study. Although the 

CPUE for darters and perches in fast runs was larger at Big 

Cypress 02 (fig. 11), the number of darter species (6) was 

larger in runs in general (slow and fast runs combined) at 

Little Cypress compared to the number of darter species (5) in 

runs in Big Cypress 02. An increase in the number of fish but 

a reduction in the number of native fish species, including 

darters, is common downstream from reservoirs (Neves and 

Angermeier, 2006). 

Big Cypress Bayou at 

confluence of French 

Creek, Jefferson, Texas

(Big Cypress 02)

Black Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Texas

(Black Cypress)

Little Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Texas

(Little Cypress)

0

5

10

15

20

25

30

Total number of fish species

*

* Mesohabitat type not present.

Mesohabitat type (table 2;

 appendix 3)

 Slow runs

 Fast runs

 Channel pools

 Margin pools

EXPLANATION

Figure 10. Number of fish species collected by mesohabitat type from U.S. Geological Survey stations 07346015 Big Cypress Bayou at 

confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 

Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.
24 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Figure 11. Catch per unit effort for A, darters and B, cyprinids collected by mesohabitat type from U.S. Geological Survey stations 

07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near 

Jefferson, Tex., and 07346071Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010. Zero value Zero value Zero value Zero value Zero value

*

*

Zero value

Big Cypress Bayou at 

confluence of French 

Creek, Jefferson, Texas

(Big Cypress 02)

Black Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Texas

(Black Cypress)

Little Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Texas

(Little Cypress)

* Mesohabitat type not present.

Mesohabitat type (table 2;

 appendix 3)

 Slow runs

 Fast runs

 Channel pools

 Margin pools

EXPLANATION

0

0.2

0.4

0.6

0.8

1.0

1.2

Catch per unit effort (number of fish

collected in 30 seconds of electrofishing)

0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

A. Darters and perches

B. Native cyprinids (minnows)
Physical Characteristics and Aquatic Biota at the Reach and Mesohabitat Scale for Reaches 25

Cyprinids, as a group, are responsive to habitat 

degradation (Hughes and Gammon, 1987), and because native 

cyprinid species are so widespread in Texas, the number of 

native cyprinid species is a common metric used to evaluate 

fish communities (Linam and others, 2002). The CPUE for 

native cyprinids in fast runs at Big Cypress 02 in 2010 (1.76; 

appendix 3) was larger than the CPUE of native cyprinids 

in all other mesohabitat types at all sites. The larger CPUE 

in fast runs at Big Cypress 02 was influenced by the large 

number of one native cyprinid in particular, the blacktail 

shiner. The CPUE values for native cyprinids were more 

equally distributed among mesohabitat types in Black Cypress 

and Little Cypress (fig. 11). Four native cyprinids— pallid 

shiner, emerald shiner, ironcolor shiner, and weed shiner—

were only collected in mesohabitats in Little Cypress (table 6; 

appendix 3). 

Fish trophic metrics represented by the number of 

individuals or number of species of invertivorous, predaceous, 

and omnivorous fishes have been used as indicators of shifts 

in fish assemblage structure as influenced by degradation 

of river habitat, changes in water quality, and the presence 

of invasive fish species (Junwirth and others, 2000). In this 

study, fish classified as predators consume fish in addition to 

invertebrates and other animals. 

The CPUE for invertivores was largest in fast runs 

in Big Cypress 02 (5.56).The number of invertivores was 

also influenced by the number of native cyprinids because 

the majority of the native cyprinids are invertivorous fish 

(appendix 3). The only native cyprinids collected from all 

three sites were red shiners, blacktail shiners, and ribbon 

shiners. In slow runs, the CPUE (0.91) for predators at 

Big Cypress 02 was more than four times larger than the 

CPUE (0.20) for predators at Black Cypress, and almost 

twice as large as the CPUE (0.49) for predators at Little 

Cypress (fig. 12; appendix 3). As with native cyprinids and 

invertivores, predatory fish were fewer in number but more 

evenly distributed among mesohabitats at Black Cypress and 

Little Cypress (fig. 12; appendix 3). 

The larger CPUE for predators in slow runs at Big 

Cypress 02 was influenced by the collection of more 

individuals of species like largemouth bass and warmouth 

that were found at all three sites (appendix 3). The relatively 

small CPUE values for omnivores in slow runs were similar 

between Big Cypress 02 (0.31) and Little Cypress (0.32), and 

about three times smaller (0.10) in slow runs in Black Cypress 

(fig. 12).

Changes in the natural flow regime of a river can alter 

the composition of fish reproductive guilds by altering flow 

and temperature related spawning cues and river habitat 

(Penczak and others, 1998; Perkin and others, 2010). A 

recent comparison of the change in the relative abundance 

of nest spawners compared to broadcast spawners in Big 

Cypress Bayou between the 1950s and 2006 indicates that 

the relative abundance of nest spawners has increased by 

about 50 percent while the relative abundance of broadcast 

spawners has decreased by about 20 percent (Caddo Lake 

Institute, 2010). Nest spawners are fish that deposit eggs in a 

nest structure constructed and often guarded by one or both 

sexes of the species. Broadcast spawners release eggs into the 

water, and males and females of these species do not protect or 

nurture the eggs or develop juvenile fish in any way (Thomas 

and others, 2007). In this study, to compare reproductive 

guilds among sites and mesohabitat types, nest and substrate 

spawners were combined to form one reproductive guild 

because both types of spawners deposit eggs directly on 

some type of substrate. In contrast to nest spawners, substrate 

spawners simply deposit the eggs on a substrate without 

constructing a nest. Broadcast spawners formed the other 

reproductive guild (appendix 3), and live bearers were not 

evaluated as a category because only one live-bearing species, 

the non-native western mosquitofish, was collected. The 

CPUE of nest and substrate spawners was largest in slow and 

fast runs at Big Cypress 02 relative to the same mesohabitats 

at Black Cypress and Little Cypress (fig. 13). The larger 

CPUE values at Big Cypress 02 for nest and substrate 

spawners of 4.96 and 5.72 in slow and fast runs, respectively, 

reflect the large number of longear sunfish collected in these 

mesohabitats compared to the number of longear sunfish 

collected in the same types of mesohabitats at the other sites 

(appendix 3). In contrast, the combined broadcast spawner 

CPUE for all meoshabitats at Black Cypress and Little 

Cypress was 6.1 (Black Cypress) to 3.0 times (Little Cypress) 

the total CPUE for this reproductive guild at Big Cypress 02 

(fig. 13). Two broadcast spawners, the ribbon shiner and the 

emerald shiner, were more abundant in the mesohabitats in 

Black Cypress and Little Cypress; only six ribbon shiners 

were collected in one slow run at Big Cypress 02 (appendix 3). 

Mussel Surveys inBig Cypress Bayou and Black 

Cypress Bayou 

A quantitative survey of freshwater mussels was 

completed in the summer of 2010 at Big Cypress 01, Big 

Cypress 02, and at Black Cypress. Mussel surveys were 

done to provide baseline data on the occurrence, abundance, 

and relative density of native mussel species in support of 

an evaluation of candidate biological environmental flow 

indicators for the purpose of long-term monitoring.

A total of 182 individual freshwater mussels were 

collected, and 15 species of mussels were identified (table 7). 

Of the mussels collected, 69.8 percent (127 individuals) were 

collected from Big Cypress 02, 23.6 percent (43 individuals) 

were collected from Big Cypress 01, and 6.6 percent (12 

individuals) were collected from Black Cypress. Washboards 

(Megalonaias nervosa) were the most abundant species 

overall, with the majority of individuals of this species 

found at Big Cypress 02. Bleufers (Potamilus purpuratus), 

western pimplebacks (Quadrula mortoni), and pistolgrips 

(Tritogonia verrucosa) were the only species that occurred at 

all three sites. Big Cypress 02 was the most species rich with 

13 species of mussels, followed by Big Cypress 01 with 8 

species, and Black Cypress with 6 species. 
26 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Figure 12. Catch per unit effort for A, invertivores, B, predators, and C, omnivores collected by mesohabitat type from U.S. Geological 

Survey stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near U.S. 

Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.

*

*

*

Zero valueZero valueZero value

Zero value

Zero valueZero value

Big Cypress Bayou at 

confluence of French 

Creek, Jefferson, Texas

(Big Cypress 02)

Black Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Texas

(Black Cypress)

Little Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Texas

(Little Cypress)

* Mesohabitat type not present.

Mesohabitat type (table 2;

 appendix 3)

 Slow runs

 Fast runs

 Channel pools

 Margin pools

EXPLANATION

Catch per unit effort (number of fish

collected in 30 seconds of electrofishing)

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

0

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0

2

4

6

8

10

12

14

A. Invertivores

B. Predators

C. Omnivores
Physical Characteristics and Aquatic Biota at the Reach and Mesohabitat Scale for Reaches 27

Figure 13. Catch per unit effort for A, nest and substrate spawners and B, broadcast spawners collected by mesohabitat type from 

U.S. Geological Survey stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress 

Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.

*

*

Zero valueZero valueZero valueZero valueZero value

Big Cypress Bayou at 

confluence of French 

Creek, Jefferson, Texas

(Big Cypress 02)

Black Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Texas

(Black Cypress)

Little Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Texas

(Little Cypress)

* Mesohabitat type not present.

Mesohabitat type (table 2;

 appendix 3)

 Slow runs

 Fast runs

 Channel pools

 Margin pools

EXPLANATION

Catch per unit effort (number of fish

collected in 30 seconds of electrofishing)

0

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

2

4

6

8

10

12

14

A. Nest and substrate spawners

B. Broadcast spawners
28 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Table 7. Total abundance and relative density of mussel species collected from U.S. Geological Survey stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010

[relative density, number of quadrats with one or more individuals of a species collected relative to the total number of quadrats sampled; --, no data]

Species Species 

common name

Status

Big Cypress Bayou near 

U.S. Highway 59 

near Jefferson, Tex.

(Big Cypress 01)

Big Cypress Bayou at 

confluence of French Creek, 

Jefferson, Tex. 

(Big Cypress 02)

Black Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Tex. 

(Black Cypress)

Number 

of individuals

Number of 

quadrats 

with one 

or more 

individuals

Relative 

density

Number 

of individuals

Number of 

quadrats 

with one 

or more 

individuals

Relative 

density

Number 

of individuals

Number of 

quadrats 

with one 

or more 

individuals

Relative 

density

Amblema 

plicata

Threeridge Native -- -- -- 3 3 3.9 -- -- --

Lampsilis 

hydiana

Louisiana 

fatmucket

Native -- -- -- 2 2 2.6 -- -- --

Lampsilis teres Yellow sandshell Native 1 1 1.6 6 6 7.8 -- -- --

Leptodea 

fragilis

Fragile 

papershell

Native -- -- -- 4 4 5.2 -- -- --

Megalonaias 

nervosa

Washboard Native -- -- -- 72 32 41.6 2 2 2.5

Obliquaria 

reflexa

Threehorn 

wartyback

Native 1 1 1.6 -- -- -- -- -- --

Plectomerus 

dombevanus

Bankclimber Native 2 2 3.1 15 14 18.2 -- -- --

Potamilus 

purpuratus

Bleufer Native 1 1 1.6 8 8 10.4 1 1 1.2

Quadrula 

apiculata

Southern 

mapleleaf

Native 2 2 3.1 -- -- -- -- -- --

Quadrula 

mortoni

Western 

pimpleback

Native 8 8 12.5 2 2 2.6 1 1 1.2

Quadrula 

pustulosa

Pimpleback Native -- -- -- 6 5 6.5 2 2 2.5

Toxolasma 

texasienses

Texas lilliput1 Native -- -- -- -- -- -- 2 2 2.5

Tritogonia 

verrucosa

Pistolgrip Native 11 8 12.5 5 5 6.5 3 3 3.7

Truncilla 

truncata

Deertoe Native 16 11 17.2 1 1 1.3 -- -- --

Utterbackia 

imbecillis

Paper pondshell Native -- -- -- 1 1 1.3 -- -- --

Total 2

43 4127 212

Number of species 3

8 513 6

Total number of quadrats sampled 64 77 81

1

Preliminary identification.

2

Total includes one unidentified mussel species.

3

Total does not include unidentified mussel species.

4

Total includes a pigtoe of unidentified species and a mussel that could not be differentiated between a yellow sandshell and a fragile papershell.

5

Total includes a pigtoe of unidentified species. 
Physical Characteristics and Aquatic Biota at the Reach and Mesohabitat Scale for Reaches 29

Relative density was calculated by dividing the number 

of quadrats where one or more individuals of a species 

were collected by the total number of quadrats sampled and 

multiplying by 100 (table 7). Relative density was used as 

an indirect measure of how evenly distributed or clustered a 

mussel species is at a site, with the larger relative densities 

indicating a less clustered distribution for species because 

the more quadrats occupied by a species, the more broadly 

distributed the species is over the area sampled. Freshwater 

mussels typically occur in what are discrete isolated patches 

or subpopulations that are referred to as metapopulations 

in rivers and streams (Strayer, 2008), and these discrete 

subpopulations are patchy even at the reach scale because of 

variable meso- and microhabitat conditions related to depths, 

velocities, bed materials, and other factors that influence 

mussel occurrence and distribution at this spatial scale. At Big 

Cypress 01, relative density was largest overall for deertoes 

(17.2), pistolgrips (12.5), and western pimplebacks (12.5); 

all of which were larger than the values observed for these 

species at Big Cypress 02. At Big Cypress 02, relative density 

was largest overall for washboards (41.6), then bankclimbers 

(18.2), and bleufers (10.4). All relative densities for mussels 

at Black Cypress were comparatively low (less than 4.0) 

(table 7).

Because they are relatively immobile, freshwater 

mussels are sensitive to changes in microhabitat conditions 

related to boundary (near bed) current velocities, water 

depth, and the composition and physical characteristics of 

bed materials (Strayer, 2008). Developing adult freshwater 

mussels that inhabit rivers and streams typically are found 

in finer bed materials such as small gravels, sand, and fine 

sediments such as silts and clays. The effects of reservoirs and 

controlled releases from their dams on the downstream mussel 

community have been well documented (Benke, 1990; Yeager 

1993; Vaughn and Taylor, 1999) and include altered flow and 

temperature regimes, differences in sediment deposition, and 

changes in the transport of particulate organic matter, which 

is the food base for mussels (Vaughn and Taylor, 1999). In 

this study, velocity and water depth were collected in all 

quadrats, and a shallow sediment core of the streambed was 

collected in a subset of quadrats where at least one mussel was 

collected that represented the different shallow bed materials 

present at the site (appendix 4). Only the water depths, 

velocities, and bed sediment bulk densities obtained from 

quadrats where mussels were actually collected were used to 

compute summary statistics for the different sampling sites 

(figs. 14–17; appendix 4). 

Mussels occurred at water depths ranging from 0.6 

ft at Big Cypress 01 to 5.6 ft at Black Cypress (fig. 14; 

appendix 4). Mean depth for those species that occurred at 

all sites generally was shallowest at Big Cypress 01, and 

deepest at Black Cypress, with intermediate depths found 

at Big Cypress 02. Velocities from quadrats where mussels 

were collected ranged from -0.04 ft/s for a quadrat in Big 

Cypress 02 to 1.58 ft/s in Big Cypress 01 (a small negative 

velocity such as -0.04 ft/s is likely caused by wind blowing 

upstream over stagnant water). Mean velocities in quadrats 

where mussels were collected were highest in Big Cypress 

01 (0.93 ft/s), intermediate in Big Cypress 02 (0.41 ft/s), and 

lowest in Black Cypress (0.23 ft/s) (fig. 15; appendix 4). The 

mean velocities measured during the collection of mussels 

were different from mean velocities measured during the 

assessment of physical habitat properties (combined for all 

mesohabitats), which were higher in Black Cypress relative to 

Big Cypress 02 (appendix 1). Velocities from mussel quadrats 

were collected from as near to the streambed as possible. This 

method of measuring velocity was different from the method 

used for measuring velocities in the mesohabitats, where 

velocity was measured in accordance with standard USGS 

procedures (Rantz and others, 1982) at either 60 percent of the 

water depth or 20 percent and 80 percent of the water depth 

to compute an average velocity through the water column. 

Bankclimbers and washboards occurred over a larger range 

of velocities but at a lower mean velocity in Big Cypress 02 

than several of the smaller species, including deertoes and 

pimblebacks. At Big Cypress 02, several of the more abundant 

mussel species, such as washboards and bankclimbers, were 

collected adjacent to or just downstream from woody snags 

or stumps, which might account for the lower velocities 

associated with these species. Mussels may adapt to higher 

seasonal low flows below reservoirs compared to lower 

seasonal (for example, summer) flows in nonregulated streams 

by associating with snags and stumps where velocities may be 

moderated and the streambed may be more stable (Hardison 

and Layzer, 2001). 

Bed sediment bulk density is an indirect measure of 

the compactness of bed materials, which is influenced by 

grain-size distribution, the suspended load of sediment, flow 

conditions, and the hydraulic gradient of seepage flow in the 

hyporheic zone (Schalchli, 1992) among others factors. Bed 

compactness can influence mussel occurrence and distribution 

because mussel species vary in their ability to inhabit beds 

of varying composition and compactness (Strayer, 2008), 

and because most species spent part or all of their life cycle 

partially embedded in the streambed for stability. Higher 

mean velocities and homogenization of bed materials in rivers 

and streams below reservoirs can create more compacted 

beds, which limit mussel occurrence and distribution. Mean 

bed sediment bulk density was highest at Big Cypress 01, 

slightly lower at Big Cypress 02, and lowest at Black Cypress 

(fig. 16). Bed sediment bulk density preference was similar 

among species between Big Cypress 01 and Big Cypress 02 

(fig. 17). No pattern in bulk density preference by species was 

evident, but this could be an artifact of the small sample size 

for each species.
30 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Figure 14. Water depths associated with different mussel species collected from U.S. Geological Survey stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.

Bnkclmb Blufr Drtoe Pstlgrp SoMplf 3hrnWrty WPmbk YlSshl

Bnkclmb Blufr Drtoe FrgPshl LaFtmk Pmbk PrPnd Pstlgrp 3ridge Wshbrd WPmbk YlSshl

Blufr Pmbk Pstlgrp TxLillpt Wshbrd WPmbk

Mussel species common name

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

5.5

6.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

5.5

6.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

5.5

6.0

Water depth, in feet

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Texas

(Black Cypress)

Big Cypress Bayou near U.S. Highway 59 near Jefferson, Texas

(Big Cypress 01)

Big Cypress Bayou at confluence of French Creek, Jefferson, Texas

(Big Cypress 02)

Mean 

Measured water depth—One

 symbol may represent more

 than one value (appendix 4)

EXPLANATION

Maximum 

Minimum 

Mussel species common name

 Bankclimber

 Bleufer

 Deertoe

 Fragile papershell

 Louisiana fatmucket

 Paper pondshell

 Pimpleback

 Pistolgrip

 Southern mapleleaf

 Texas lilliput

 Threehorn wartyback

 Threeridge

 Washboard

 Western pimpleback

 Yellow sandshell

Bnkclmb

Blufr

Drtoe

FrgPshl

LaFtmk

PrPnd

Pmbk

Pstlgrp

SoMplf

TxLillpt

3hrnWrty

3ridge

Wshbrd

WPmbk

YlSshl
Physical Characteristics and Aquatic Biota at the Reach and Mesohabitat Scale for Reaches 31

Figure 15. Velocities associated with different mussel species collected from U.S. Geological Survey stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.

Bnkclmb Blufr Drtoe Pstlgrp SoMplf 3hrnWrty WPmbk YlSshl

Blufr Pmbk Pstlgrp TxLillpt Wshbrd WPmbk

Mussel species common name

Bnkclmb Blufr Drtoe FrgPshlLaFtmk Pmbk Pstlgrp 3ridgeWshbrd WPmbk YlSshl PrPnd

-0.2

0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

-0.2

0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

-0.2

0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

Velocity, in feet per second

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Texas

(Black Cypress)

Big Cypress Bayou near U.S. Highway 59 near Jefferson, Texas

(Big Cypress 01)

Big Cypress Bayou at confluence of French Creek, Jefferson, Texas

(Big Cypress 02)

Mean 

Measured velocity—One

 symbol may represent more

 than one value (appendix 4)

EXPLANATION

Maximum 

Minimum 

Mussel species common name

 Bankclimber

 Bleufer

 Deertoe

 Fragile papershell

 Louisiana fatmucket

 Paper pondshell

 Pimpleback

 Pistolgrip

 Southern mapleleaf

 Texas lilliput

 Threehorn wartyback

 Threeridge

 Washboard

 Western pimpleback

 Yellow sandshell

Bnkclmb

Blufr

Drtoe

FrgPshl

LaFtmk

PrPnd

Pmbk

Pstlgrp

SoMplf

TxLillpt

3hrnWrty

3ridge

Wshbrd

WPmbk

YlSshl
32 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Physical Characteristics and Aquatic 

Biota at the Reach and Mesohabitat 

Scale for Big Cypress Bayou During 

Summer 2010 and Summer 2011

Physical Characteristics

During July 30, 2010, the daily mean discharge at the 

USGS streamflow-gaging station (07346000 Big Cypress 

Bayou near Jefferson, Tex.) nearest to Big Cypress 02 was 

62 ft3/s (table 4), and the mean width across all mesohabitat 

types Big Cypress 02 was of 46.3 ft, and the median width was 

59.1 ft. The mean and median widths on July 30, 2010, were 

62.2 and 62.3 ft, respectively, when mesohabitats adjacent 

to the main channel and isolated from flowing water during 

low flow (margin pools) were excluded. During July 26–27, 

2011, the daily mean discharge at USGS station 07346000 

was 32 ft3/s (table 4). On July 27, 2011, Big Cypress 02 had 

a mean width across all mesohabitat types of 35.1 ft and a 

median width of 48.2 ft (appendix 1). The mean and median 

widths in 2011 were 49.6 and 46.6, respectively, if only the 

main channel mesohabitats were considered. Depths in Big 

Cypress 02 also tended to decrease between the sampling 

events of 2010 and 2011. On July 30, 2010, Big Cypress 02 

had mean and median depths of 4.2 ft and 3.6 ft, respectively, 

across all mesohabitat types and mean and median depths 

of 5.5 ft and 4.8 ft, respectively, when accounting for only 

main-channel mesohabitats; on July 27, 2011, mean and 

median depths dropped to 2.3 ft and 2.5 ft, respectively, 

across all mesohabitat types and 3.1 ft and 4.8 ft, respectively, 

when accounting for only main-channel mesohabitats. Four 

mesohabitats were mapped during each of the two sampling 

events (fig. 6), and each mesohabitat type remained the same 

between the two events.

Mean and median velocities in 2010 (0.22 ft/s and 0.14 

ft/s, respectively, across all mesohabitat types and 0.31 ft/s 

and 0.21 ft/s, respectively, for main-channel mesohabitats 

exclusively) were approximately twice as high as the 

velocities observed in 2011 (mean and medians of 0.11 

ft/s across all mesohabitat types and 0.17 ft/s and 0.11 ft/s, 

respectively, for main-channel mesohabitats exclusively). 

Mean velocities in slow runs decreased from 0.17 ft/s to 

0.08 ft/s between 2010 and 2011, while mean velocities in 

fast runs decreased from 0.58 ft/s to 0.34 ft/s during that same 

period.

Fish Surveys

About 14 percent more fish were collected from Big 

Cypress 02 in 2010 (596) relative to 2011 (525; table 5; 

appendix 3). The total number of fish species decreased by 

Figure 16. Bed sediment bulk densities at locations where mussels were collected from U.S. Geological Survey stations 07346017 Big 

Cypress Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., 

and 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.

n=6

n=5

n=7

Big Cypress Bayou at 

confluence of French 

Creek, Jefferson, Texas

(Big Cypress 02)

Big Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Texas

(Big Cypress 01)

Black Cypress Bayou 

near U.S. Highway 59 

near Jefferson, Texas

(Black Cypress)

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

2.2

2.4

2.6

2.8

Sediment bulk density, in grams per cubic centimeter

Mean 

EXPLANATION

Maximum 

Minimum 

n=5 Number of samples (appendix 4)
Physical Characteristics and Aquatic Biota at the Reach and Mesohabitat Scale 33

Figure 17. Bed sediment bulk densities associated with different mussels collected from U.S. Geological Survey stations 07346017 Big 

Cypress Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., 

and 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.

Bnkclmb Blufr Drtoe Pstlgrp SoMplf 3hrnWrty* WPmbk YlSshl*

Bnkclmb Blufr Drtoe FrgPshl LaFtmk* Pmbk PrPnd* Pstlgrp* 3ridge* Wshbrd WPmbk YlSshl*

Blufr* Pmbk Pstlgrp TxLillpt Wshbrd WPmbk

Mussel species common name

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

2.2

2.4

2.6

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

2.2

2.4

2.6

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

2.2

2.4

2.6

0.2

Sediment bulk density, in grams per cubic centimeter

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Texas

(Black Cypress)

Big Cypress Bayou near U.S. Highway 59 near Jefferson, Texas

(Big Cypress 01)

Big Cypress Bayou at confluence of French Creek, Jefferson, Texas

(Big Cypress 02)

* Bed sediment cores were not collected for sediment 

bulk density analyses at all locations. Cores were

collected from different bed types (for example sand,

gravel, sand and gravel, or woody) and in beds where 

multiple mussels were found.

Mean 

Measured sediment bulk density—

 One symbol may represent more

 than one value (appendix 4)

EXPLANATION

Maximum 

Minimum 

Mussel species common name

 Bankclimber

 Bleufer

 Deertoe

 Fragile papershell

 Louisiana fatmucket

 Paper pondshell

 Pimpleback

 Pistolgrip

 Southern mapleleaf

 Texas lilliput

 Threehorn wartyback

 Threeridge

 Washboard

 Western pimpleback

 Yellow sandshell

Bnkclmb

Blufr

Drtoe

FrgPshl

LaFtmk

PrPnd

Pmbk

Pstlgrp

SoMplf

TxLillpt

3hrnWrty

3ridge

Wshbrd

WPmbk

YlSshl
34 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

approximately 18 percent between the two sampling events 

(34 species in 2010 compared to 28 in 2011). The Menhinick 

index was larger in 2010 (1.39) than 2011 (1.22); the smaller 

Menhinick index in 2011 may be caused by lower streamflow 

in 2011 compared to 2010. 

Two introduced species (common carp and redbreast 

sunfish) were collected only in 2010. Longear sunfish, which 

was the most abundant fish species collected in 2010, was 

second to western mosquitofish in 2011 (table 6).The relative 

abundance of western mosquitofish in 2011 was based on 

a single seine haul from a shallow embayment mesohabitat 

(appendix 3). Species of the sunfish family Centrarchidae 

tended to have higher relative abundance ranks compared 

to other fish families during both sampling events. Blacktail 

shiners were the second most abundant fish collected in 2010 

and third most abundant in 2011. The lowest rank abundance 

for each date (six occurrences in 2010 and seven occurrences 

in 2011) corresponds to the collection of a single individual of 

several species. Low rank relative abundance was common in 

2010 and 2011 for several darter species.

Physical Characteristics and WaterQuality Properties in the Absence of 

Flow in Isolated Pools at the Reach 

and Mesohabitat Scale on Black 

Cypress and Little Cypress Bayous 

During Fall 2011

In the absence of flow during fall 2011, the reach at 

Black Cypress was reduced to four isolated pools (fig. 7), 

and the reach at Little Cypress was reduced to three isolated 

pools (fig. 8). The farthest downstream pool in each of the 

reaches was bisected at the previously established downstream 

boundary, and only the upper parts were analyzed in this study. 

Water depths were not measured at the same locations 

during both sampling events at Little Cypress and Black 

Cypress, so direct water-depth comparisons are not possible. 

Bathymetric maps depicting the depths of the isolated pools 

at Black Cypress and Little Cypress were generated from 

elevation data along surveyed transect lines (figs. 18–19). 

Elevation data were hand-contoured using linear interpolation 

between surveyed data points within each pool and 

extrapolation outside of these values to the surveyed pool 

perimeter. The perimeter of each pool was assigned a depth of 

zero. By overlaying the bathymetric maps from 2011 for both 

of the stream reaches on top of their respective mesohabitat 

maps from 2010 (after plotting measured water depths 

associated with the physical mesohabitat measurements), it 

was possible to estimate a difference in water depths between 

the two events. Water depths decreased by approximately 4.0 

ft at Little Cypress and approximately 2.4 ft at Black Cypress 

between 2010 and 2011.

Dissolved oxygen, temperature, pH, and specific 

conductance data were collected from pools in Little Cypress 

and Black Cypress in the absence of flow because it was 

hypothesized that these conditions would be the most limiting 

with respect to aquatic life. Dissolved oxygen and specific 

conductance did not exhibit consistent readings in the isolated 

pools at Black Cypress. Specific conductance ranged from 

98 μs/cm to 252 μs/cm and did not exhibit any consistent 

patterns with regards to depth or lateral position (appendix 2). 

However, aside from a few outliers (at transect B–B’ at the 

bottom of mid-channel and in the only reading obtained from 

transect D–D’), specific conductance was stable on a transectspecific as well as a pool-specific basis. Dissolved oxygen 

concentrations at Black Cypress ranged from 0.58 mg/L to 

4.79 mg/L and exhibited a more subtle inverse relation to 

depth compared to Little Cypress at the four transects where 

dissolved oxygen was measured at different depth intervals 

(A–A’, B–B’, E–E’, and F–F’). The stratification of dissolved 

oxygen concentrations at Black Cypress along the different 

transects is less pronounced than the stratification observed 

at Little Cypress (appendix 2), which might indicate more 

mixing at Black Cypress. Anoxic conditions (dissolved oxygen 

concentrations less than 0.5 mg/L) were not observed in any 

of the six transects at Black Cypress, but all three readings 

collected near the bottom of the water column along transect 

B–B’ were less than 1.0 mg/L. Temperature ranged from 

18.73°C to 20.43°C and in most cases, tended to be inversely 

related to water depth but did not exhibit any consistent 

patterns with regards to lateral position. The pH ranged from 

6.27 to 6.98 and tended to be relatively stable on a transectspecific basis (aside from what appears to be an anomalous 

reading of 6.98 that was collected just below the water surface 

on transect F–F’).

Other than dissolved oxygen, the other water-quality 

properties measured at Little Cypress were relatively 

consistent at all locations, particularly the measurements 

made within each individual transect (appendix 2). Specific 

conductance ranged from 217 μs/cm to 235 μs/cm and did 

not exhibit any consistent patterns with regards to water 

depth or lateral position. Temperature ranged from 19.33°C 

to 22.12°C and tended to be inversely related to water depth. 

Temperatures also tended to be lower at mid-channel relative 

to temperatures observed closer to the banks, although this 

phenomenon is likely attributable to differences in water 

depths between the locations. The pH ranged from 6.05 to 

6.91, but the range narrowed to 6.42 to 6.91 if data collected 

along A–A’ were excluded. A–A’ spans a shallow part of 

the most upstream pool that may be more heavily influenced 

by atmospheric conditions. Dissolved oxygen concentrations 

ranged from 0.24 mg/L to 5.33 mg/L and exhibited a 

consistent inverse relation to water depth, resulting in a 

stratified pattern in all five transects. The stratification 

of dissolved oxygen concentrations along the different 

transects on Little Cypress is shown in figure 19. Anoxic 

conditions were observed in two of the five transects (C–C’ 

and E–E’).
Physical Characteristics and Aquatic Biota at the Reach and Mesohabitat Scale 35

Figure 18. Diagram showing pool depths and cross-sectional representation of dissolved oxygen concentrations along surveyed 

transect lines on Black Cypress Bayou near U.S. Highway 59 near Jefferson, Texas, on October 12, 2011.

Upstream

boundary

Downstream

boundary

E'

E

F'

F

D'

D

A'

A

B'

B

C'

C

94°21'58"

32°47'24"

32°47'22"

94°21'56"

94°21'54"

94°21'52"

0 50 100 FEET

0 25 50 METERS

VERTICAL EXAGGERATION ON

CROSS SECTIONS IS 22X.

HORIZONTAL EXAGGERATION ON

CROSS SECTIONS IS 15X.

1.81 4.79 2.81

A A'

B B'

C C'

D D'

E E'

F F' 2.80 feet

3.28 feet Approximately 4.2 feet

 34.7 feet

22.8 feet

13.6 feet

8.3 feet

0.87 feet

0.42 feet

1.83 feet

14.5 feet

12.7 feet

4.62

4.79

EXPLANATION

 2.01 to 2.5

 2.51 to 3.0

 3.01 to 3.5

 3.51 to 4.0

 Greater than 4.0

Depths, in feet, for Black

 Cypress—USGS station 

 07346044 Black Cypress

 Bayou near U.S. Highway

 59 near Jefferson, Texas

 (fig. 2)

 0 to 0.5

 0.51 to 1.0

 1.01 to 1.5

 1.51 to 2.0

Dissolved oxygen, in

 milligrams per liter

 0 to 1.0

 1.01 to 2.0

 2.01 to 3.0

 3.01 to 4.0

 4.01 to 5.0

Line of section

Measured dissolved oxygen concentration,

 in milligrams per liter, for transects C–C’

 and D–D’, where contouring was not

 attempted because of insufficient data

 points—Fill color corresponds to shading

 used in all other transects

Center channel

Thalweg 

A A' USGS, U.S. Geological Survey
36 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Figure 19. Diagram showing pool depths and cross-sectional representation of dissolved oxygen concentrations along surveyed 

transect lines on Little Cypress Bayou near U.S. Highway 59 near Jefferson, Texas, on October 12, 2011.

E'

E

Upstream

boundary

Downstream

boundary

D'

D

C'

C

B'

B

A'

A

A A'

B B'

C C'

D D'

E E' 0.85 feet 2.76 feet 3.80 feet 3.71 feet

Approximately 12 feet

57.6 feet

33.8 feet

26.2 feet

25.7 feet

12.1 feet

0 100 200 FEET

0 50 100 METERS

VERTICAL EXAGGERATION ON

CROSS SECTIONS IS 36X.

HORIZONTAL EXAGGERATION ON

CROSS SECTIONS IS 18X.

94°19'44"

32°43'16"

32°43'14"

32°43'12"

32°43'10"

32°43'08"

32°43'06"

32°43'04"

94°19'42"

94°19'42"

EXPLANATION

Depth, in feet, for Little Cypress—

 USGS station 07346071 Little

 Cypress Bayou near U.S. 

 Highway 59 near Jefferson,

 Texas (fig. 2)

 0 to 0.5

 0.51 to 1.0

 1.01 to 1.5

 1.51 to 2.0

 2.01 to 2.5

 2.51 to 3.0

 3.01 to 3.5

 3.51 to 4.0

 Greater than 4.0

Dissolved oxygen, in

 milligrams per liter

 0 to 1.0

 1.01 to 2.0

 2.01 to 3.0

 3.01 to 4.0

 4.01 to 5.0

 5.01 to 6.0

Line of section

Center channel

Thalweg

A A'

USGS, U.S. Geological Survey
Summary 37

Summary

In 2010 and 2011, the U.S. Geological Survey (USGS), 

in cooperation with the Northeast Texas Municipal Water 

District and the Texas Commission on Environmental Quality, 

did a baseline assessment of physical characteristics, aquatic 

biota (fish and mussels) collected at the mesohabitat scale for 

reaches of Big Cypress, Black Cypress, and Little Cypress 

Bayous in the Big Cypress Basin in northeastern Texas, and 

measured selected water-quality properties in isolated pools 

in Black Cypress and Little Cypress. All of the data were 

collected in the context of prescribed environmental flows. 

The information acquired during the course of the study 

will support the long-term monitoring of biota in relation to 

environmental flow prescriptions for Big Cypress Bayou, 

Black Cypress Bayou, and Little Cypress Bayou. Data 

collection and analysis were done at mesohabitat- and reachspecific scales, where a mesohabitat is defined as a discrete 

area within a stream that exhibits unique depth, velocity, slope, 

substrate, and cover.

Biological and physical characteristic data were collected 

from two sites on Big Cypress Bayou, and one site on both 

Black Cypress Bayou and Little Cypress Bayou. The upstream 

reach of Big Cypress Bayou (USGS station 07346015 Big 

Cypress Bayou at confluence of French Creek, Jefferson, 

Texas) is hereinafter referred to as the Big Cypress 02 site. 

The downstream site on Big Cypress Bayou (USGS station 

07346017 Big Cypress Bayou near U.S. Highway 59 near 

Jefferson, Tex.) is hereinafter referred to as the Big Cypress 

01 site and was sampled exclusively for mussels. The sites on 

Black Cypress Bayou (USGS station 07346044 Black Cypress 

Bayou near U.S. Highway 59 near Jefferson, Tex.) and Little 

Cypress Bayou (USGS station 07346071 Little Cypress Bayou 

near U.S. Highway 59 near Jefferson, Tex.) are hereinafter 

referred to as the Black Cypress and Little Cypress sites, 

respectively.

A small range of streamflows was targeted for data 

collection, including a period of low flow during July and 

August 2010 and a period of very low flow during July 2011. 

This approach accounted for variability in the abundance 

and distribution of fish and mussels and in the physical 

characteristics of mesohabitats present during different flow 

conditions. Mussels were not collected from Little Cypress. 

However, a quantitative survey of freshwater mussels was 

completed at Big Cypress 01, Big Cypress 02, and Black 

Cypress.

Of the three reaches where physical habitat data were 

measured in 2010, Big Cypress 02 was both the widest and 

deepest, with a mean width of 62.2 ft and a mean depth of 

5.5 ft in main-channel mesohabitats. Little Cypress was the 

second widest and deepest, with a mean width of 49.9 ft and 

a mean depth of 4.5 ft in main-channel mesohabitats. Black 

Cypress was by far the narrowest of the three reaches, with 

a mean width of 29.1 ft and a mean depth of 3.3 ft in mainchannel mesohabitats, but it had the highest mean velocity of 

0.42 feet per second (ft/s). 

Appreciably more fish were collected from Big 

Cypress 02 (596) in summer 2010 compared to Black Cypress 

(273) or Little Cypress (359), but the total number of fish 

species collected among the three sites was similar. Thirtyfour fish species were collected from Big Cypress 02 in 

summer 2010 compared to 26 species from Black Cypress 

and 33 species from Little Cypress. Longear sunfish was 

the most abundant fish species collected from all three sites 

in 2010, and only 3 of the 48 fish species (common carp, 

western mosquitofish, and redbreast sunfish) collected were 

nonnative or introduced species; both occurred exclusively at 

Big Cypress 02. Fish data from the various mesohabitat types 

were combined into four mesohabitat categories for analysis: 

fast run, slow run, channel pool and margin pool (data from 

Forewaters, backwaters, and embayments were combined to 

form margin pool category for analysis). The larger number 

of fish collected from Big Cypress 02 was influenced by the 

larger abundance of sunfish (Centrarchidae) species, especially 

longear sunfish (Lepomis megalotis). Menhinick index values 

were greater for Black Cypress (1.57) and Little Cypress 

(1.74) than for Big Cypress 02 (1.39). Fish species richness 

was largest in slow run mesohabitats from Big Cypress 02 and 

Little Cypress and largest in fast runs from Black Cypress. 

Fifteen species and 182 individuals of freshwater mussels 

were collected, with 69.8 percent of the individual mussels 

collected from Big Cypress 02, 23.6 percent collected from 

Big Cypress 01, and 6.6 percent collected from Black Cypress. 

Washboards were the most abundant species overall with the 

majority of individuals found at Big Cypress 02. Big Cypress 

02 was the most species rich with 13 species, followed by 

Big Cypress 01 with 8 species, and Black Cypress with 6 

species. At Big Cypress 01, the relative density was largest 

overall for deertoes (17.2), pistolgrips (12.5), and western 

pimplebacks (12.5); all of which were higher than the values 

observed for these species at Big Cypress 02. At Big Cypress 

02, relative density was largest overall for washboards 

(41.6), then bankclimbers (18.2), and bleufers (10.4). All 

relative densities for mussels at Black Cypress were low (less 

than 4.0). Mussels occurred at water depths ranging from a 

minimum of 0.6 ft at Big Cypress 01 to a maximum of 5.6 ft 

at Black Cypress. Mean depth for those species that occurred 

at all sites generally was shallowest at Big Cypress 01, and 

deepest at Black Cypress, with intermediate depths found at 

Big Cypress 02.

About 14 percent more fish were collected from Big 

Cypress 02 in 2010 relative to 2011 (596 fish in 2010 

compared to 525 in 2011), and about 18 percent more fish 

species were identified in 2010 compared to 2011 (34 species 

in 2010 compared to 28 in 2011). The Menhinick index was 

larger in 2010 (1.39) than 2011 (1.22); the smaller Menhinick 

index in 2011 may be caused by lower streamflow in 2011 

compared to 2010. Longear sunfish, which was the most 

abundant fish species collected in 2010, was second to western 

mosquitofish in 2011.

In the absence of flow during fall 2011, the reach at Black 

Cypress was reduced to four isolated pools, and the reach at 
38 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Little Cypress was reduced to three isolated pools. Dissolved 

oxygen, temperature, pH, and specific conductance data 

were collected from the pools because it was hypothesized 

that these conditions would be the most limiting with respect 

to aquatic life. Dissolved oxygen concentrations ranged 

from 0.58 mg/L to 4.79 milligrams per liter (mg/L) at Black 

Cypress and from 0.24 mg/L to 5.33 mg/L at Little Cypress; 

both sites exhibited a stratified pattern in dissolved oxygen 

concentrations along transect lines, but the pattern was less 

pronounced at Black Cypress.

References

Benke, A.C., 1990, A perspective on American’s vanishing 

streams: Journal of the North American Benthological 

Society, v. 9, p.77–88. 

Bovee, K.D., Lamb, B.L., Bartholow, J.M., Stalnaker, C.B., 

Taylor, J., and Henriksen, J., 1998, Stream habitat analysis 

using the instream flow incremental methodology: U.S. 

Geological Survey Information and Technology Report 

1998-0004. 130 p

Caddo Lake Institute, 2010, Environmental flow regime 

and analysis recommendations report: accessed on 

June 30, 2012, at http://www.caddolakeinstitute.us/

docs/flows/8.10_Recommendations_Report/Cypress_

SB3_20100826_Main.pdf. 

Caddo Lake Institute, 2012, Environmental flows project—

Caddo Lake and its tributaries: Caddo Lake Institute, 

accessed January 3, 2012, at http://www.caddolakeinstitute.

us/flows.html.

Crowe, A.L., and Bayer, C.W., 2005, A biological, physical, 

and chemical survey of a least-impacted watershed— 

Black Cypress Bayou (creek), Texas 1998-2005: Texas 

Commission on Environmental Quality publication AS-197, 

accessed February 4, 2013 at http://www.caddolakeinstitute.

us/Docs/Black_Cypress_AS197.pdf.

Dodds, W.K., 2002, Freshwater ecology—Concepts and 

environmental applications: San Diego, Calif., Academic 

Press, p 434–435.

Dowell, C.L., 1964, Dams and reservoirs in Texas—Historical 

and descriptive information: Texas Water Commission 

Bulletin 6408, accessed June 6, 2012, at http://www.twdb.

texas.gov/publications/reports/bulletins/doc/B6408.pdf. 

Hardison, B.S., and Layzer, J.B., 2001, Relations between 

complex hydraulics and the localized distribution of mussels 

in three regulated rivers: Regulated Rivers Research and 

Management, v. 17, p. 77–84.

Hawkins, C.P., Kershner, J.L, Bisson, P.A., Bryant, M.D., 

Decker, L.M., Gregory, S.V., McCullough, D.A., Overtoin, 

C.K., Reeves, G.H., Steedman, R.J., Young, M.K., 2011, A 

hierarchical approach to classifying stream habitat features: 

Fisheries, v. 18, no. 6, p. 3–12. 

Hoover, J.J., Douglas, N.H., Kilgore, K.J., and Matthews, 

W.J., 1989, Fishes of the Cypress Bayou system in northeast 

Texas and northwest Louisiana: U.S. Army Corps of 

Engineers Waterways Experiment Station Report, 31 p. 

Howells, R.G., 1996, Preliminary survey of freshwater 

mussels of the Big Cypress Bayou system, Texas: Ingram, 

Texas, Texas Parks and Wildlife Department, 8 p.

Hubbs, C., 1957, A checklist of Texas fresh-water fishes: IF 

series Texas Game and Fish Commission, no. 3, p. 1–11. 

Hughes, R.M., and Gammon, J.R., 1987, Longitudinal changes 

in fish assemblages and water quality in the Willamette 

River, Oregon: Transactions of the American Fisheries 

Society, v. 11, no. 2, p. 196–209.

International Commission on Zoological Nomenclature, 2010, 

Standards, sense, and stability for animal names in science: 

accessed February 6, 2010, at http://www.iczn.org.

Karr, J.R., 1981, Assessment of biotic integrity using fish 

communities: Fisheries, v. 6, p. 21–27. 

Konrad, C.P., 2010, Monitoring and evaluation of 

environmental flow prescriptions for five demonstration 

sites of the Sustainable Rivers Project: U.S. Geological 

Survey Open-File Report 2010–1065, 22 p.

 Junwirth, W., Muhar, S., and Schumutz, S., 2000, Assessing 

the ecological integrity of running waters: Norwell, 

Massachusetts, Kluwer Academic Press, 487 p.

Layzer, J.B., Gordon, M.E., and Anderson, R.M., 1993, 

Mussels—The forgotten fauna of regulated rivers, a case 

study of the Caney Fork River: Research and Management, 

v. 8, nos. 1–2, p. 63–71.

Linam, G.W., Kleinsasser, L.J, and Mayes, K.B., 2002, 

Regionalization of the index of biotic integrity for Texas 

streams: Texas Parks and Wildlife Department, River 

Studies Report No. 17, 26 p.

Ludwig, J.A., and Reynolds, J.F., 1988, Statistical ecology: 

New York, John Wiley, 337 p.

Marchetti, M.P., and Moyle, P.B., 2001, Effects of flow regime 

on fish assemblages in a regulated California stream: 

Ecological Applications, v. 11, no. 2, p. 530–539.

Mather, C.M., and Bergmann, J.A.M., 1994, Freshwater 

mussels of the Cypress Bayou System, Northeast Texas: 

Malacology Data Net v. 33, nos. 5–6, p. 139–145.
References 39

Menhinick, E.F., 1964, A comparison of some speciesindividuals diversity indices applied to samples of field 

insects: Ecology, v. 45, no. 4, p. 859–861. 

Minnesota Department of Natural Resources, 2012, Minnesota 

Department of Natural Resources web site, accessed on 

June 12, 2012, at http://www.dnr.state.mn.us/watershed_

tool/glossary.html.

Neves, R.J. and Angermeier, P.L., 2006, Habitat alteration 

and its effects on native fishes in the upper Tennessee River 

system, east-central U.S.A.: Fish Biology, v. 37, p. 45–52.

Nielsen, L.A., and Johnson, D.L., 1983, Fisheries techniques: 

Blacksburg, Virginia, Southern Printing Company, 468 p.

Northeast Texas Municipal Water District, 2007, Cypress 

Creek Basin highlights report: Northeast Texas Municipal 

Water District web site, accessed on January 6, 2012, at 

http://www.netmwd.com/basinreportsmaps.html.

Penczak, T, Glowacki, L., Galicka, W., and Koszalinski, H., 

1998, A long-term study (1985–1995) of fish populations in 

the impounded Warta River, Poland: Hydrobiologia, v. 368, 

p. 157–173. 

Perkin, J., Gido, K., Johnson, E., and Tabor, V., 2010, 

Consequences of stream fragmentation and climate change 

for rare Great Plains fishes: Final report to the Great Plains 

Landscape Conservation Cooperative, 35 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. 74, no. 11, 

p. 769–784.

Propst, D.L., and Gido, K.B., 2004, Responses of native and 

nonnative fishes to natural flow regime mimicry in the San 

Juan River: Transactions of the American Fisheries Society, 

v. 133, p. 922–931.

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

of streamflow—Volumes 1 and 2: U.S. Geological Survey 

Water-Supply Paper 2175, 631 p.

Richter, B.D., Davis, M.M., Apse, C., and Konrad, C., 2011, 

A presumptive standard for environmental flow protection: 

River Research and Applications, 2011, 10 p. 

Schalchli, Ueli, 1992, The clogging of coarse gravel river beds 

by fine sediment: Hydrobiologia, v. 235/236, p. 189–197.

Sokkia, 2012, Leading manufacturer of precision surveying 

instruments: accessed on October 11, 2012, at http://www.

sokkia.com/.

SonTek, 2003, FlowTracker handheld ADV technical 

documentation: San Diego, Calif., YSI Environmental Co., 

[variously paged]. 

SonTek, 2013, FlowTracker handheld acoustic Doppler 

velocimeter: accessed on February 6, 2103, at http://www.

sontek.com/flowtracker.php. 

Strayer, D.L., 2008, Freshwater mussel ecology: Berkeley and 

Los Angeles, University of California Press, 204 p.

Texas Commission on Environmental Quality, 2007, Surface 

water quality monitoring procedures, volume 2—Methods 

for collecting and analyzing biological assemblage and 

habitat data: RG–416, 202 p.

Texas Commission on Environmental Quality, 2012, Sampling 

data query, surface water quality monitoring: Texas 

Commission on Environmental Quality, accessed on June 

30, 2012, at http://www.tceq.texas.gov/waterquality/cleanrivers/data/samplequery.html.

Texas Commission on Environmental Quality, 2013, The 

Texas clean rivers program: accessed February 4, 2013, at 

http://www.tceq.texas.gov/waterquality/clean-rivers.

Texas Parks and Wildlife Department, 2012, Nongame and 

rare species program—Federal and State listed fish species: 

Texas Parks and Wildlife Program, accessed September 

15, 2012, at https://www.tpwd.state.tx.us/huntwild/wild/

wildlife_diversity/texas_rare_species/listed_species/fish.

phtml.

Texas Parks and Wildlife Department, 2013, Lake Cypress 

Springs: accessed February 4, 2013, at http://www.tpwd.

state.tx.us/fishboat/fish/recreational/lakes/cypress_springs/.

Texas Water Development Board, 2008, Texas Instream 

Flow Studies—Technical overview: Texas Commission 

on Environmental Quality, Texas Parks and Wildlife 

Department, and Texas Water Development Board, TWDB 

Report No. 369, Austin, Tex., 147 p, accessed October 25, 

2012, at http://www.twdb.state.tx.us/publications/reports/

numbered_reports/doc/R369_InstreamFlows.pdf. 

 Thomas, C., Bonner, T.H., and Whiteside, B.G., 2007, 

Freshwater fishes of Texas: College Station, Texas, Texas 

A&M University Press, 202 p.

Turnipseed, D.P., and Sauer, V.B., 2010, Discharge 

measurements at gaging stations: U.S. Geological Survey 

Techniques and Methods, book 3, chap. A8, 87 p. (Also 

available at http://pubs.usgs.gov/tm/tm3-a8/.)

University of Nebraska-Lincoln, 2012, The Drought Monitor, 

accessed July 2012 at http://droughtmonitor.unl.edu/.

University of Texas, 2012, Ichthyology: Texas Natural Science 

Center, accessed October 29, 2012, at http://www.utexas.

edu/tmm/tnhc/fish/.

U.S. Army Corps of Engineers, and The Nature Conservancy, 

2012, Sustainable Rivers Project, accessed November 

1, 2012, at http://www.iwr.usace.army.mil/docs/

sustainablerivers/Sustainable_Rivers_Project-Status.pdf.
40 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

U.S. Army Corps of Engineers, 1998, Cypress Valley 

Watershed Texas: Reconnaissance Report accessed on 

March 15, 2013, at http://caddolakedata.us/media/1364/

cypressreport_ch2.pdf.

U.S. Fish and Wildlife Service, 2012, Listed animals: U.S. 

Fish and Wildlife Service Species Report, accessed 

September 5, 2012, at http://ecos.fws.gov/tess_public/pub/

listedAnimals.jsp.

U.S. Geological Survey, 2012a, USGS water data for Texas: 

U.S. Geological Survey National Water Information 

System, accessed September 26, 2012, at http://waterdata.

usgs.gov/tx/nwis/. 

U.S. Geological Survey, 2012b, Water-resources data for the 

United States, water year 2011: U.S. Geological Survey 

Water Data Report WDR–US–2011, accessed September 

26, 2012, at http://wdr.water.usgs.gov/. 

U.S. Geological Survey, variously dated, National field manual 

for the collection of water-quality data: U.S. Geological 

Survey Techniques of Water-Resources Investigations, 

book 9, chaps. A1–A9, accessed February 5, 2013, at 

http://pubs.water.usgs.gov/twri9A.

Vaughn, C.C., and Taylor, C.M., 1999, Impoundments and 

the decline of freshwater mussels—A case study of an 

extinction gradient: Conservation Biology, v. 13, no. 4, 

p. 912–920. 

Williams, J.D., Warren, M.L., Cummings, K.S., Harris, J.L., 

and Neves, R.J., 1993, Conservation status of freshwater 

mussels of the United States and Canada: Fisheries, v. 18, 

no. 9, p. 6–22.

Wisconsin Department of Natural Resources, 2005, Guidelines 

for sampling freshwater mussels in wadeable streams: 

Fisheries and Aquatic Sciences Research Program Report 

No. 0092–01–09, 57 p.

Xylem Inc., 2012, YSI, Monitor, analyze, and protect the 

world’s natural resources, Web Site, accessed on October 

11, 2012, at http://www.ysi.com/index.php.

Yeager, B., 1993, Impacts on warm-water streams—

Guidelines for evaluations, in Bryan, C.F. and Rutherford, 

D.A. (eds.), Dams: Little Rock, Arkansas, American 

Fisheries Society, p. 57–92.
Appendix 1—Physical Habitat Measurements

Appendix 1

Appendix 1 43

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 

59 near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; 

SA, sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date Mesohabitat 

identifier

Mesohabitat 

type1

Measurement 

location 

along transect

Transect 

number

Physical measurements

Transect 

width 

(ft)

Depth 

(ft)

Velocity 

(ft/s)

Dominant 

substrate

Embeddedness 

(percent)

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (Big Cypress 02)

7/30/2010 1 Slow run right 1 59.1 4.8 0.12 SA/W 100

7/30/2010 1 Slow run left 2 62.3 5.3 0.03 SA/W 100

7/30/2010 1 Slow run center 3 62.3 6.3 0.10 SA/W 100

7/30/2010 1 Slow run right 4 72.2 9.7 0.14 SA/W 100

7/30/2010 1 Slow run left 5 68.9 3.9 0.17 SA/W 100

7/30/2010 2 Fast run right 1 65.6 3.6 0.34 SA/W 100

7/30/2010 2 Fast run left 2 68.9 2.7 0.90 SA/W 100

7/30/2010 2 Fast run center 3 41.0 1.7 0.69 SA/W 100

7/30/2010 2 Fast run right 4 62.3 2.2 0.24 SA/W 100

7/30/2010 2 Fast run left 5 62.3 1.5 0.74 SA/W 100

7/30/2010 3 Embayment left 1 7.9 0.6 0.02 SA/W 100

7/30/2010 3 Embayment center 2 11.5 2.5 -0.04 SA/W 100

7/30/2010 3 Embayment right 3 10.5 0.6 0.06 SA/W 100

7/30/2010 4 Backwater left 1 2.3 0.2 0.00 SA 100

7/30/2010 4 Backwater center 2 3.6 0.1 0.00 SA 100

7/30/2010 4 Backwater right 3 3.9 0.6 0.00 SA 100

7/30/2010 5 Slow run left 1 65.6 6.2 0.21 SA/W 100

7/30/2010 5 Slow run center 2 68.9 11.4 0.12 SA/W 100

7/30/2010 5 Slow run right 3 59.1 6.8 0.26 SA/W 100

7/30/2010 5 Slow run left 4 59.1 12.1 0.39 SA/W 100

7/30/2010 5 Slow run center 5 55.8 4.5 0.16 SA/W 100

mean 46.3 4.2 0.22

median 59.1 3.6 0.14

mean (main-channel mesohabitats only) 62.2 5.5 0.31

median (main-channel mesohabitats only) 62.3 4.8 0.21

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 

59 near Jefferson, Tex., 2010–11.

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 
44 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Center transect measurements

Bankfull 

width 

(ft)

Bankfull 

height 

(ft)

Left 

bank 

angle 

(degrees)

Right 

bank 

angle 

(degrees)

Left 

bank 

buffer 

width 

(ft)

Right 

bank

buffer 

width 

(ft)

Left 

bank 

canopy 

closure

(degrees)

Right 

bank 

canopy 

closure

(degrees)

Left 

bank

densiometer 

reading 

(count 

from 

0 to 17)

Right 

bank 

densiometer 

reading 

(count 

from 

0 to 17)

Thalweg 

bearing 

(degrees)

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (Big Cypress 02)—Continued

7/30/2010 1 Slow run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 1 Slow run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 1 Slow run 75 16.3 42.5 15.3 >164 98 118 -- 17 17 161

7/30/2010 1 Slow run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 1 Slow run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 2 Fast run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 2 Fast run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 2 Fast run 72 7.3 20 10 >164 46 90 90 17 16 68

7/30/2010 2 Fast run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 2 Fast run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 3 Embayment -- -- -- -- -- -- -- -- -- -- --

7/30/2010 3 Embayment -- -- -- -- -- -- -- -- -- -- --

7/30/2010 3 Embayment -- -- -- -- -- -- -- -- -- -- --

7/30/2010 4 Backwater -- -- -- -- -- -- -- -- -- -- --

7/30/2010 4 Backwater -- -- -- -- -- -- -- -- -- -- --

7/30/2010 4 Backwater -- -- -- -- -- -- -- -- -- -- --

7/30/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 5 Slow run 69 10.8 32 35 >164 >164 90 90 17 17 80

7/30/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

7/30/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --
Appendix 1 45

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 

59 near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Fish cover measurements

Filamentous 

algae2

Macrophytes

Live 

trees 

or 

roots

Overhanging 

vegetation

Undercut 

banks

Coarse 

gravel

Cobble

Artificial 

substrate

Snags 

or 

logs

Large 

woody 

debris 

(>1 ft in 

diameter)3

Small 

woody 

debris 

(<1 ft in 

diameter)3

Relative abundance from 0 to 4, 0 - absent (0 percent), 

1 - sparse (<10 percent), 2 - moderate (10 to <40 percent), 

3 - heavy (40–75 percent), 4 - very heavy (>75 percent)

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (Big Cypress 02)—Continued

7/30/2010 1 Slow run 0 0 2 0 0 0 0 0 0

6 13

7/30/2010 1 Slow run 0 0 2 0 0 0 0 0 0

4 7

7/30/2010 1 Slow run 0 0 2 0 0 0 0 0 0

4 12

7/30/2010 1 Slow run 0 0 2 0 0 0 0 0 0

6 6

7/30/2010 1 Slow run 0 0 2 0 0 0 0 0 0

7/30/2010 2 Fast run 0 0 2 0 0 0 0 0 0

2 5

7/30/2010 2 Fast run 0 0 2 0 0 0 0 0 0

6 13

7/30/2010 2 Fast run 0 0 2 0 0 0 0 0 0

8 15

7/30/2010 2 Fast run 0 0 2 0 0 0 0 0 0

9 6

7/30/2010 2 Fast run 0 0 2 0 0 0 0 0 0

7/30/2010 3 Embayment 0 0 3 0 0 0 0 0 0

0 tntc

7/30/2010 3 Embayment 0 0 3 0 0 0 0 0 0

0 tntc

7/30/2010 3 Embayment 0 0 3 0 0 0 0 0 0

7/30/2010 4 Backwater -- -- -- -- -- -- -- -- --

1 3

7/30/2010 4 Backwater 0 0 0 0 0 0 0 0 0

0 3

7/30/2010 4 Backwater 0 0 0 0 0 0 0 0 0

7/30/2010 5 Slow run 0 0 2 0 0 0 0 0 0

5 4

7/30/2010 5 Slow run 0 0 2 0 0 0 0 0 0

5 4

7/30/2010 5 Slow run 0 0 2 0 0 0 0 0 0

tntc tntc

7/30/2010 5 Slow run 0 0 2 0 0 0 0 0 0

11 5

7/30/2010 5 Slow run 0 0 2 0 0 0 0 0 0
46 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 

59 near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; 

SA, sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date Mesohabitat 

identifier

Mesohabitat 

type1

Measurement 

location 

along transect

Transect 

number

Physical measurements

Transect 

width 

(ft)

Depth 

(ft)

Velocity 

(ft/s)

Dominant 

substrate

Embeddedness 

(percent)

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (Big Cypress 02)—Continued

7/27/2011 6 Slow run center 1 27.2 1.3 0.37 SA 100

7/27/2011 6 Slow run right 2 37.7 4.5 -0.03 SA 100

7/27/2011 6 Slow run left 3 46.6 2.1 0.11 SA 100

7/27/2011 6 Slow run center 4 50.9 4.4 0.02 SA 100

7/27/2011 6 Slow run right 5 55.4 4.8 0.10 SA 100

7/27/2011 7 Embayment center 1 21.7 1.2 0.09 SI 100

7/27/2011 7 Embayment right 2 16.4 0.6 -0.05 SI 100

7/27/2011 7 Embayment left 3 10.8 0.2 0.02 SI 100

7/27/2011 8 Fast run center 1 46.3 0.9 0.42 W --

7/27/2011 8 Fast run right 2 45.3 1.1 0.27 W --

7/27/2011 8 Fast run left 3 36.1 1.0 0.23 SA 100

7/27/2011 8 Fast run center 4 47.2 1.4 0.33 SA 100

7/27/2011 8 Fast run right 5 62.0 2.7 0.45 SA 100

7/27/2011 9 Embayment left 1 3.9 0.6 0.10 SA 100

7/27/2011 9 Embayment center 2 6.6 1.4 0.03 SA 100

7/27/2011 9 Embayment right 3 8.2 1.4 0.00 SA 100

7/27/2011 10 Embayment center 1 7.9 0.9 0.04 SI 100

7/27/2011 10 Embayment right 2 9.5 0.6 0.00 SI 100

7/27/2011 10 Embayment left 3 12.5 0.6 -0.11 SI 100

7/27/2011 11 Slow run right 1 53.1 3.3 0.11 SA 100

7/27/2011 11 Slow run left 2 48.2 2.3 0.01 SA 100

7/27/2011 11 Slow run center 3 56.8 8.0 0.04 SA 100

7/27/2011 11 Slow run right 4 66.9 6.0 0.02 SA 100

7/27/2011 11 Slow run left 5 64.3 3.4 0.05 SA 100

mean 35.1 2.3 0.11

median 48.2 2.5 0.11

mean (main-channel mesohabitats only) 49.6 3.1 0.17

median (main-channel mesohabitats only) 46.6 4.8 0.11
Appendix 1 47

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Center transect measurements

Bankfull 

width 

(ft)

Bankfull 

height 

(ft)

Left 

bank 

angle 

(degrees)

Right 

bank 

angle 

(degrees)

Left 

bank 

buffer 

width 

(ft)

Right 

bank

buffer 

width 

(ft)

Left 

bank 

canopy 

closure

(degrees)

Right 

bank 

canopy 

closure

(degrees)

Left 

bank

densiometer 

reading 

(count 

from 

0 to 17)

Right 

bank 

densiometer 

reading 

(count 

from 

0 to 17)

Thalweg 

bearing 

(degrees)

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (Big Cypress 02—Continued

7/27/2011 6 Slow run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 6 Slow run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 6 Slow run 72 7.9 30 25 > 98 > 98 64 78 17 17 80

7/27/2011 6 Slow run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 6 Slow run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 7 Embayment -- -- -- -- -- -- -- -- -- -- --

7/27/2011 7 Embayment -- -- -- -- -- -- -- -- -- -- --

7/27/2011 7 Embayment -- -- -- -- -- -- -- -- -- -- --

7/27/2011 8 Fast run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 8 Fast run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 8 Fast run 62 6.4 15 20 >98 >98 90 90 17 17 55

7/27/2011 8 Fast run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 8 Fast run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 9 Embayment -- -- -- -- -- -- -- -- -- -- --

7/27/2011 9 Embayment -- -- -- -- -- -- -- -- -- -- --

7/27/2011 9 Embayment -- -- -- -- -- -- -- -- -- -- --

7/27/2011 10 Embayment -- -- -- -- -- -- -- -- -- -- --

7/27/2011 10 Embayment -- -- -- -- -- -- -- -- -- -- --

7/27/2011 10 Embayment -- -- -- -- -- -- -- -- -- -- --

7/27/2011 11 Slow run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 11 Slow run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 11 Slow run 72 36.6 45 30 > 98 > 98 55 44 16 17 158

7/27/2011 11 Slow run -- -- -- -- -- -- -- -- -- -- --

7/27/2011 11 Slow run -- -- -- -- -- -- -- -- -- -- --
48 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Fish cover measurements

Filamentous 

algae2

Macrophytes

Live 

trees or 

roots

Overhanging vegetationUndercut 

banks

Coarse 

gravel

Cobble

Artificial 

substrate

Snags 

or 

logs

Large 

woody 

debris 

(>1 ft in 

diameter)3

Small 

woody 

debris 

(<1 ft in 

diameter)3

Relative abundance from 0 to 4, 0 - absent (0 percent), 

1 - sparse (<10 percent), 2 - moderate (10 to <40 percent), 

3 - heavy (40–75 percent), 4 - very heavy (>75 percent)

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (Big Cypress 02)—Continued

7/27/2011 6 Slow run 0 0 0 0 0 0 0 0 1

12 19

7/27/2011 6 Slow run 0 0 0 0 0 0 0 0 2

10 18

7/27/2011 6 Slow run 0 0 0 0 0 0 0 0 1

3 8

7/27/2011 6 Slow run 0 0 1 0 0 0 0 0 1

6 14

7/27/2011 6 Slow run 0 0 0 0 0 0 0 0 2

7/27/2011 7 Embayment 0 0 0 0 0 0 0 0 3

-- --

7/27/2011 7 Embayment -- -- -- -- -- -- -- -- -- --

--

7/27/2011 7 Embayment -- -- -- -- -- -- -- -- --

7/27/2011 8 Fast run 0 0 1 0 0 0 0 0 3

4 18

7/27/2011 8 Fast run 0 0 0 0 0 0 0 0 2

4 32

7/27/2011 8 Fast run 0 0 0 0 0 0 0 0 2

6 18

7/27/2011 8 Fast run 0 0 0 0 0 0 0 0 3

4 17

7/27/2011 8 Fast run -- -- -- -- -- -- -- -- --

7/27/2011 9 Embayment 0 0 1 0 0 0 0 0 0

0 0

7/27/2011 9 Embayment 0 0 1 0 0 0 0 0 0

0 0

7/27/2011 9 Embayment 0 0 1 0 0 0 0 0 0

7/27/2011 10 Embayment 0 0 0 0 0 0 0 0 0

1 2

7/27/2011 10 Embayment 0 0 0 0 0 0 0 0 0

0 0
Appendix 1 49

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Fish cover measurements

Filamentous 

algae2

Macrophytes

Live 

trees or 

roots

Overhanging vegetationUndercut 

banks

Coarse 

gravel

Cobble

Artificial 

substrate

Snags 

or 

logs

Large 

woody 

debris 

(>1 ft in 

diameter)3

Small 

woody 

debris 

(<1 ft in 

diameter)3

Relative abundance from 0 to 4, 0 - absent (0 percent), 

1 - sparse (<10 percent), 2 - moderate (10 to <40 percent), 

3 - heavy (40–75 percent), 4 - very heavy (>75 percent)

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (Big Cypress 02)—Continued

7/27/2011 10 Embayment 0 0 0 0 0 0 0 0 0

7/27/2011 11 Slow run 0 0 1 0 0 3 0 0 1

9 14

7/27/2011 11 Slow run 0 0 0 0 0 0 0 0 2

4 7

7/27/2011 11 Slow run 0 0 0 0 0 0 0 0 2

10 11

7/27/2011 11 Slow run 0 0 0 0 0 0 0 0 2

4 4

7/27/2011 11 Slow run 0 0 1 0 0 0 0 0 0
50 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 

59 near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; 

SA, sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date Mesohabitat 

identifier

Mesohabitat 

type1

Measurement 

location 

along transect

Transect 

number

Physical measurements

Transect 

width 

(ft)

Depth 

(ft)

Velocity 

(ft/s)

Dominant 

substrate

Embeddedness 

(percent)

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (Black Cypress)

8/3/2010 1 Fast run center 1 23.0 1.3 1.44 SA/W 100

8/3/2010 1 Fast run right 2 27.9 1.4 0.11 SA/W 100

8/3/2010 1 Fast run left 3 30.5 1.7 0.51 SA 100

8/3/2010 1 Fast run center 4 25.4 1.9 0.80 SA/W 100

8/3/2010 1 Fast run right 5 23.0 1.5 1.10 SA/W 100

8/3/2010 2 Backwater center 1 3.3 0.4 0.00 SA/W 100

8/3/2010 2 Backwater right 2 7.2 1.0 0.00 SA/W 100

8/3/2010 2 Backwater left 3 11.5 2.0 0.00 SA/W 100

8/3/2010 3 Channel pool NR 1 28.2 14.8 -0.18 SA 100

8/3/2010 3 Channel pool NR 2 29.5 6.9 0.54 SA/W 100

8/3/2010 3 Channel pool NR 3 23.6 3.8 0.37 SA/W 100

8/3/2010 4 Fast run center 1 16.7 4.1 0.50 SA/W 100

8/3/2010 4 Fast run right 2 24.6 3.4 0.26 SA/W 100

8/3/2010 4 Fast run left 3 21.3 1.5 0.91 SA/W 100

8/3/2010 4 Fast run center 4 28.5 1.3 0.72 SA/W 100

8/3/2010 4 Fast run right 5 38.1 3.3 0.10 SA/W 100

8/3/2010 5 Slow run right 1 33.8 4.0 0.20 SA/W 100

8/3/2010 5 Slow run left 2 24.3 4.0 0.32 SA/W 100

8/3/2010 5 Slow run center 3 26.9 4.9 0.31 SA/W 100

8/3/2010 5 Slow run right 4 27.9 4.9 0.22 SA/W 100

8/3/2010 5 Slow run left 5 -- -- -- -- --

8/3/2010 6 Fast run center 1 31.8 2.1 0.42 SA/W 100

8/3/2010 6 Fast run right 2 34.4 1.1 0.58 SA/W 100

8/3/2010 6 Fast run left 3 32.2 2.1 0.45 SA/W 100

8/3/2010 6 Fast run center 4 27.6 1.8 -0.06 SA/W 100

8/3/2010 6 Fast run right 5 29.5 3.6 0.35 FG/CG 100

8/3/2010 7 Slow run left 1 28.5 2.4 0.21 SA/W 100

8/3/2010 7 Slow run center 2 34.4 3.0 0.42 SA/W 100

8/3/2010 7 Slow run right 3 38.7 3.0 0.35 SA/W 100

8/3/2010 7 Slow run left 4 34.4 4.2 0.25 SA/W 100

8/3/2010 7 Slow run center 5 40.4 1.9 0.05 SA/W 100

mean 26.9 3.1 0.37

median 28.1 2.3 0.33

mean (main-channel mesohabitats only) 29.1 3.3 0.42

median (main-channel mesohabitats only) 28.5 3.0 0.35
Appendix 1 51

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, sand, 

>0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Center transect measurements

Bankfull 

width 

(ft)

Bankfull 

height 

(ft)

Left 

bank 

angle 

(degrees)

Right 

bank 

angle 

(degrees)

Left 

bank 

buffer 

width 

(ft)

Right 

bank

buffer 

width 

(ft)

Left 

bank 

canopy 

closure

(degrees)

Right 

bank 

canopy 

closure

(degrees)

Left 

bank

densiometer 

reading 

(count 

from 

0 to 17)

Right 

bank 

densiometer 

reading 

(count 

from 

0 to 17)

Thalweg 

bearing 

(degrees)

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. . (Black Cypress)—Continued

8/3/2010 1 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 1 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 1 Fast run 43 4.5 25 23 33 >164 90 90 12 16 138

8/3/2010 1 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 1 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 2 Backwater -- -- -- -- -- -- -- -- -- -- --

8/3/2010 2 Backwater -- -- -- -- -- -- -- -- -- -- --

8/3/2010 2 Backwater -- -- -- -- -- -- -- -- -- -- --

8/3/2010 3 Channel pool -- -- -- -- -- -- -- -- -- -- --

8/3/2010 3 Channel pool 39 5.0 25 38 >164 >164 140 48 0 8 --

8/3/2010 3 Channel pool -- -- -- -- -- -- -- -- -- -- --

8/3/2010 4 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 4 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 4 Fast run 39 3.9 22 10 >164 >164 90 90 17 17 35

8/3/2010 4 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 4 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 5 Slow run 43 7.8 34 30 >164 >164 90 90 14 13 90

8/3/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 6 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 6 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 6 Fast run 59 4.0 25 15 >164 >164 54 71 10 12 116

8/3/2010 6 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 6 Fast run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 7 Slow run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 7 Slow run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 7 Slow run 56 10.0 35 35 >164 >164 90 90 10 13 139

8/3/2010 7 Slow run -- -- -- -- -- -- -- -- -- -- --

8/3/2010 7 Slow run -- -- -- -- -- -- -- -- -- -- --
52 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Fish cover measurements

Filamentous 

algae2

Macrophytes

Live 

trees or 

roots

Overhanging 

vegetation

Undercut 

banks

Coarse 

gravel

Cobble

Artificial 

substrate

Snags 

or 

logs

Large 

woody 

debris 

(>1 ft in 

diameter)3

Small 

woody 

debris 

(<1 ft in 

diameter)3

Relative abundance from 0 to 4, 0 - absent (0 percent), 

1 - sparse (<10 percent), 2 - moderate (10 to <40 percent), 

3 - heavy (40–75 percent), 4 - very heavy (>75 percent)

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (Black Cypress)—Continued

8/3/2010 1 Fast run 0 0 2 0 0 0 0 0 1

4 4

8/3/2010 1 Fast run 0 0 2 0 0 0 0 0 1

1 5

8/3/2010 1 Fast run 0 0 1 0 0 0 0 0 1

2 12

8/3/2010 1 Fast run 0 0 1 1 0 0 0 0 2

0 0

8/3/2010 1 Fast run 0 0 1 2 0 0 0 0 2

8/3/2010 2 Backwater 0 0 2 1 0 0 0 0 0

0 tntc 

8/3/2010 2 Backwater -- -- -- -- -- -- -- -- --

-- --

8/3/2010 2 Backwater -- -- -- -- -- -- -- -- --

8/3/2010 3 Channel pool 0 0 0 0 0 0 0 0 2

1 1

8/3/2010 3 Channel pool 0 0 0 0 0 0 0 0 2

-- --

8/3/2010 3 Channel pool 0 0 0 0 0 0 0 0 0

8/3/2010 4 Fast run 0 0 2 2 0 0 0 0 2

5 4

8/3/2010 4 Fast run 0 0 2 0 0 0 0 0 2

1 1

8/3/2010 4 Fast run 0 0 0 0 0 0 0 0 3

3 2

8/3/2010 4 Fast run 0 0 0 2 0 0 0 0 2

5 15

8/3/2010 4 Fast run 0 0 0 2 0 0 0 0 3

8/3/2010 5 Slow run 0 0 0 0 0 0 0 0 1

1 1

8/3/2010 5 Slow run 0 0 0 1 0 0 0 0 1

1 1

8/3/2010 5 Slow run 0 0 0 0 0 0 0 0 1

1 1

8/3/2010 5 Slow run 0 0 0 0 0 0 0 0 2

-- --

8/3/2010 5 Slow run 0 0 0 0 0 0 0 0 2
Appendix 1 53

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Fish cover measurements

Filamentous 

algae2

Macrophytes

Live 

trees or 

roots

Overhanging 

vegetation

Undercut 

banks

Coarse 

gravel

Cobble

Artificial 

substrate

Snags 

or 

logs

Large 

woody 

debris 

(>1 ft in 

diameter)3

Small 

woody 

debris 

(<1 ft in 

diameter)3

Relative abundance from 0 to 4, 0 - absent (0 percent), 

1 - sparse (<10 percent), 2 - moderate (10 to <40 percent), 

3 - heavy (40–75 percent), 4 - very heavy (>75 percent)

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (Black Cypress)—Continued

8/3/2010 6 Fast run 1 0 0 0 0 0 0 0 1

4 1

8/3/2010 6 Fast run 0 0 0 1 0 0 0 0 1

1 tntc

8/3/2010 6 Fast run 0 0 0 0 0 0 0 0 3

0 tntc

8/3/2010 6 Fast run 0 0 0 0 0 3 1 0 2

0 tntc

8/3/2010 6 Fast run 2 0 0 0 0 2 1 0 2

8/3/2010 7 Slow run 0 0 0 0 0 0 0 0 2

8 5

8/3/2010 7 Slow run 0 0 0 0 0 0 0 0 2

5 8

8/3/2010 7 Slow run 0 0 0 0 0 0 0 0 2

7 9

8/3/2010 7 Slow run 0 0 0 0 0 0 0 0 2

1 1

8/3/2010 7 Slow run 0 0 0 1 0 0 0 0 1
54 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 

59 near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; 

SA, sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date Mesohabitat 

identifier

Mesohabitat 

type1

Measurement 

location 

along transect

Transect 

number

Physical measurements

Transect 

width 

(ft)

Depth 

(ft)

Velocity 

(ft/s)

Dominant 

substrate

Embeddedness 

(percent)

Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (Little Cypress)

8/18/2010 1 Slow run center 1 45.9 6.6 0.14 SA/W 100

8/18/2010 1 Slow run right 2 42.7 3.8 0.03 SA/W 100

8/18/2010 1 Slow run left 3 52.5 3.1 0.22 SA/W 100

8/18/2010 1 Slow run center 4 42.7 4.3 0.15 SA/W 100

8/18/2010 1 Slow run right 5 52.5 5.4 0.08 SA/W 100

8/19/2010 2 Forewater right 1 19.7 2.3 0.03 SA/W 100

8/19/2010 2 Forewater left 2 23.0 2.5 0.02 SA/W 100

8/19/2010 2 Forewater center 3 16.4 2.4 0.02 SA/W 100

8/19/2010 3 Fast run right 1 26.2 1.2 0.17 SA/W 100

8/19/2010 3 Fast run left 2 19.7 1.8 0.85 SA/W 100

8/19/2010 3 Fast run center 3 29.5 1.5 0.44 SA/W 100

8/19/2010 3 Fast run right 4 36.1 2.9 0.09 SA/W 100

8/19/2010 3 Fast run left 5 26.2 2.7 0.10 SA/W 100

8/19/2010 4 Forewater left 1 29.5 2.1 0.03 SA/W 100

8/19/2010 4 Forewater center 2 29.5 1.4 0.09 SA/W 100

8/19/2010 4 Forewater right 3 32.8 1.4 0.08 SA/W 100

8/19/2010 5 Slow run center 1 42.7 6.4 0.00 SA/W 100

8/19/2010 5 Slow run right 2 62.3 5.6 0.11 SA/W 100

8/19/2010 5 Slow run left 3 65.6 11.5 0.04 SA/W 100

8/19/2010 5 Slow run center 4 62.3 6.4 0.10 SA/W 100

8/19/2010 5 Slow run right 5 65.6 7.2 0.13 SA/W 100

8/19/2010 6 Channel pool center 1 65.6 3.3 0.07 SA/W 100

8/19/2010 6 Channel pool right 2 75.5 4.1 0.06 SA/W 100

8/19/2010 6 Channel pool left 3 85.3 3.5 -0.01 SA/W 100

mean 43.7 3.9 0.13

median 42.7 3.2 0.09

mean (main-channel mesohabitats only) 49.9 4.5 0.15

median (main-channel mesohabitats only) 49.2 4.0 0.10
Appendix 1 55

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 

near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Center transect measurements

Bankfull 

width 

(ft)

Bankfull 

height 

(ft)

Left 

bank 

angle 

(degrees)

Right 

bank 

angle 

(degrees)

Left 

bank 

buffer 

width 

(ft)

Right 

bank

buffer 

width 

(ft)

Left 

bank 

canopy 

closure

(degrees)

Right 

bank 

canopy 

closure

(degrees)

Left 

bank

densiometer 

reading 

(count 

from 

0 to 17)

Right 

bank 

densiometer 

reading 

(count 

from 

0 to 17)

Thalweg 

bearing 

(degrees)

Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (Little Cypress)—Continued

8/18/2010 1 Slow run -- -- -- -- -- -- -- -- -- -- --

8/18/2010 1 Slow run -- -- -- -- -- -- -- -- -- -- --

8/18/2010 1 Slow run 69 -- 27 25 164 164 82 60 7 17 47

8/18/2010 1 Slow run -- -- -- -- -- -- -- -- -- -- --

8/18/2010 1 Slow run -- -- -- -- -- -- -- -- -- -- --

8/19/2010 2 Forewater -- -- -- -- -- -- -- -- -- -- --

8/19/2010 2 Forewater -- -- -- -- -- -- -- -- -- -- --

8/19/2010 2 Forewater -- -- -- -- -- -- -- -- -- -- --

8/19/2010 3 Fast run -- -- -- -- -- -- -- -- -- -- --

8/19/2010 3 Fast run -- -- -- -- -- -- -- -- -- -- --

8/19/2010 3 Fast run 131 8.2 22 15 >164 >164 100 65 15 12 346

8/19/2010 3 Fast run -- -- -- -- -- -- -- -- -- -- --

8/19/2010 3 Fast run -- -- -- -- -- -- -- -- -- -- --

8/19/2010 4 Forewater -- -- -- -- -- -- -- -- -- -- --

8/19/2010 4 Forewater -- -- -- -- -- -- -- -- -- -- --

8/19/2010 4 Forewater -- -- -- -- -- -- -- -- -- -- --

8/19/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

8/19/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

8/19/2010 5 Slow run 102 15.2 20 20 >164 >164 54 81 17 17 342

8/19/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

8/19/2010 5 Slow run -- -- -- -- -- -- -- -- -- -- --

8/19/2010 6 Channel 

pool

-- -- -- -- -- -- -- -- -- -- --

8/19/2010 6 Channel 

pool

102 3.5 15 30 >164 >164 59 31 6 16 0

8/19/2010 6 Channel 

pool

-- -- -- -- -- -- -- -- -- -- --
56 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 

59 near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Fish cover measurements

Filamentous 

algae2

Macrophytes

Live 

trees 

or 

roots

Overhanging 

vegetation

Undercut 

banks

Coarse 

gravel

Cobble

Artificial 

substrate

Snags 

or 

logs

Large 

woody 

debris 

(>1 ft in 

diameter)3

Small 

woody 

debris 

(<1 ft in 

diameter)3

Relative abundance from 0 to 4, 0 - absent (0 percent), 

1 - sparse (<10 percent), 2 - moderate (10 to <40 percent), 

3 - heavy (40–75 percent), 4 - very heavy (>75 percent)

Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (Little Cypress)—Continued

8/18/2010 1 Slow run 0 0 1 0 0 0 0 0 0

1 3

8/18/2010 1 Slow run 0 0 1 0 0 0 0 0 0

3 6

8/18/2010 1 Slow run 0 0 1 0 0 0 0 0 0

2 0

8/18/2010 1 Slow run 0 0 1 0 0 0 0 0 0

2 6

8/18/2010 1 Slow run 0 0 1 0 0 0 0 0 0

8/19/2010 2 Forewater 0 0 1 1 0 0 0 0 1

2 4

8/19/2010 2 Forewater 0 0 1 0 0 0 0 0 1

1 2

8/19/2010 2 Forewater 0 0 1 1 0 0 0 0 1

8/19/2010 3 Fast run 0 0 1 1 0 0 0 0 3

10 20

8/19/2010 3 Fast run 0 0 1 1 0 0 0 0 3

9 25

8/19/2010 3 Fast run 0 0 1 1 0 0 0 0 3

5 17

8/19/2010 3 Fast run 0 0 1 0 0 0 0 0 2

8 12

8/19/2010 3 Fast run 0 0 1 1 0 0 0 0 1

8/19/2010 4 Forewater 0 0 1 2 0 0 0 0 2

-- --

8/19/2010 4 Forewater 0 0 1 1 0 0 0 0 2

-- --

8/19/2010 4 Forewater 0 0 0 0 0 0 0 0 1
Appendix 1 57

Appendix 1. Physical habitat measurements for USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, 

Texas, 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 

59 near Jefferson, Tex., 2010–11.—Continued

[ft, feet; ft/s, feet per second; >, greater than; <, less than; --, not measured; W, small woody debris and organic matter, regardless of size; SI, silt, <0.06 mm; SA, 

sand, >0.06 to 2 millimeters (mm); FG, fine gravel, >2 to 16 mm; CG, coarse gravel, >16 to 64 mm; NR, not recorded; tntc, too numerous to count] 

Date

Mesohabitat 

identifier

Mesohabitat 

type1

Fish cover measurements

Filamentous 

algae2

Macrophytes

Live 

trees 

or 

roots

Overhanging 

vegetation

Undercut 

banks

Coarse 

gravel

Cobble

Artificial 

substrate

Snags 

or 

logs

Large 

woody 

debris 

(>1 ft in 

diameter)3

Small 

woody 

debris 

(<1 ft in 

diameter)3

Relative abundance from 0 to 4, 0 - absent (0 percent), 

1 - sparse (<10 percent), 2 - moderate (10 to <40 percent), 

3 - heavy (40–75 percent), 4 - very heavy (>75 percent)

Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (Little Cypress)—Continued

8/19/2010 5 Slow run 0 0 1 2 0 0 0 0 1

6 7

8/19/2010 5 Slow run 0 0 1 2 0 0 0 0 2

9 11

8/19/2010 5 Slow run 0 0 1 0 0 0 0 0 1

2 2

8/19/2010 5 Slow run 0 0 1 2 0 0 0 0 1

0 0

8/19/2010 5 Slow run 0 0 1 1 0 0 0 0 1

8/19/2010 6 Channel pool 1 0 1 0 0 0 0 0 1

4 3

8/19/2010 6 Channel pool 1 0 1 1 0 0 0 0 2

3 5

8/19/2010 6 Channel pool 1 0 1 1 0 0 0 0 2

1

Forewaters, backwaters, and embayments are together referred to as margin pools. 

2

Filamentous algae present on bedrock surface. 

3

Woody debris counts were made between transects within a mesohabitat; the position of the count indicates the inverval between transects where the count 

was made.

Appendix 2

Appendix 2—Water-Quality Properties Measured in Samples 

Collected from Isolated Pools along Discrete Transect Lines

Appendix 2 61

Appendix 2. Water-quality properties measured in samples collected from isolated pools along discrete transect lines at USGS 

stations 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Texas and 07346071 Little Cypress Bayou near U.S. 

Highway 59 near Jefferson, Tex., 2011.—Continued

[mg/L, milligrams per liter; °C, degrees Celsius; μS/cm, microsiemens per centimeter at 25 degrees Celsius; --, not measured]

Mesohabitat 

identifier

Transect 

identifier Water quality

Measurement 

location in 

water column1

Left2 Center3 Right4

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. - October 12, 2011

8 A–A’ dissolved oxygen (mg/L) top 1.60 1.60 1.71

8 A–A’ dissolved oxygen (mg/L) middle 1.45 1.41 1.45

8 A–A’ dissolved oxygen (mg/L) bottom 1.43 1.45 1.40

8 A–A’ temperature (°C) top 20.07 19.88 20.21

8 A–A’ temperature (°C) middle 19.89 19.72 19.81

8 A–A’ temperature (°C) bottom 19.92 19.64 19.83

8 A–A’ pH (standard units) top 6.78 6.80 6.86

8 A–A’ pH (standard units) middle 6.79 6.82 6.89

8 A–A’ pH (standard units) bottom 6.78 6.83 6.91

8 A–A’ specific conductance (μS/cm) top 185 185 185

8 A–A’ specific conductance (μS/cm) middle 186 185 185

8 A–A’ specific conductance (μS/cm) bottom 186 188 185

9 B–B’ dissolved oxygen (mg/L) top 1.69 1.81 1.89

9 B–B’ dissolved oxygen (mg/L) middle 1.11 1.10 1.28

9 B–B’ dissolved oxygen (mg/L) bottom 0.96 0.58 0.70

9 B–B’ temperature (°C) top 19.39 19.33 19.25

9 B–B’ temperature (°C) middle 19.01 19.00 19.00

9 B–B’ temperature (°C) bottom 18.96 18.73 18.82

9 B–B’ pH (standard units) top 6.68 6.67 6.61

9 B–B’ pH (standard units) middle 6.66 6.68 6.65

9 B–B’ pH (standard units) bottom 6.63 6.50 6.52

9 B–B’ specific conductance (μS/cm) top 191 190 191

9 B–B’ specific conductance (μS/cm) middle 196 193 192

9 B–B’ specific conductance (μS/cm) bottom 205 252 218

10 C–C’ dissolved oxygen (mg/L) top -- -- --

10 C–C’ dissolved oxygen (mg/L) middle 1.81 4.79 2.81

10 C–C’ dissolved oxygen (mg/L) bottom -- -- --

10 C–C’ temperature (°C) top -- -- --

10 C–C’ temperature (°C) middle 20.14 20.22 20.16

10 C–C’ temperature (°C) bottom -- -- --

10 C–C’ pH (standard units) top -- -- --

10 C–C’ pH (standard units) middle 6.66 6.63 6.72

10 C–C’ pH (standard units) bottom -- -- --

10 C–C’ specific conductance (μS/cm) top -- -- --

10 C–C’ specific conductance (μS/cm) middle 195 193 195

10 C–C’ specific conductance (μS/cm) bottom -- -- --

Appendix 2. Water-quality properties measured in samples collected from isolated pools along discrete transect lines at USGS 

stations 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Texas and 07346071 Little Cypress Bayou near U.S. 

Highway 59 near Jefferson, Tex., 2011.

[mg/L, milligrams per liter; °C, degrees Celsius; μS/cm, microsiemens per centimeter at 25 degrees Celsius; --, not measured]

Appendix 2
62 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 2. Water-quality properties measured in samples collected from isolated pools along discrete transect lines at USGS 

stations 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Texas and 07346071 Little Cypress Bayou near U.S. 

Highway 59 near Jefferson, Tex., 2011.—Continued

[mg/L, milligrams per liter; °C, degrees Celsius; μS/cm, microsiemens per centimeter at 25 degrees Celsius; --, not measured]

Mesohabitat 

identifier

Transect 

identifier Water quality

Measurement 

location in 

water column1

Left2 Center3 Right4

11 D–D’ dissolved oxygen (mg/L) top -- -- --

11 D–D’ dissolved oxygen (mg/L) middle -- 4.62 --

11 D–D’ dissolved oxygen (mg/L) bottom -- -- --

11 D–D’ temperature (°C) top -- -- --

11 D–D’ temperature (°C) middle -- 20.43 --

11 D–D’ temperature (°C) bottom -- -- --

11 D–D’ pH (standard units) top -- -- --

11 D–D’ pH (standard units) middle -- 6.72 --

11 D–D’ pH (standard units) bottom -- -- --

11 D–D’ specific conductance (μS/cm) top -- -- --

11 D–D’ specific conductance (μS/cm) middle -- 98 --

11 D–D’ specific conductance (μS/cm) bottom -- -- --

11 E–E’ dissolved oxygen (mg/L) top 2.34 2.43 2.39

11 E–E’ dissolved oxygen (mg/L) middle 2.20 2.35 2.23

11 E–E’ dissolved oxygen (mg/L) bottom 1.97 2.09 2.16

11 E–E’ temperature (°C) top 19.54 19.61 19.61

11 E–E’ temperature (°C) middle 19.54 19.55 19.52

11 E–E’ temperature (°C) bottom 19.62 19.51 19.48

11 E–E’ pH (standard units) top 6.58 6.57 6.54

11 E–E’ pH (standard units) middle 6.57 6.56 6.52

11 E–E’ pH (standard units) bottom 6.54 6.54 6.50

11 E–E’ specific conductance (μS/cm) top 142 141 141

11 E–E’ specific conductance (μS/cm) middle 142 142 141

11 E–E’ specific conductance (μS/cm) bottom 144 142 142

11 F–F’ dissolved oxygen (mg/L) top 2.14 1.91 2.75

11 F–F’ dissolved oxygen (mg/L) middle 1.54 1.02 2.18

11 F–F’ dissolved oxygen (mg/L) bottom 1.17 1.30 1.67

11 F–F’ temperature (°C) top 19.54 19.46 19.60

11 F–F’ temperature (°C) middle 19.34 19.30 19.48

11 F–F’ temperature (°C) bottom 19.34 19.29 19.39

11 F–F’ pH (standard units) top 6.98 6.39 6.33

11 F–F’ pH (standard units) middle 6.45 6.37 6.30

11 F–F’ pH (standard units) bottom 6.43 6.35 6.27

11 F–F’ specific conductance (μS/cm) top 146 146 146

11 F–F’ specific conductance (μS/cm) middle 147 147 147

11 F–F’ specific conductance (μS/cm) bottom 148 150 147
Appendix 2 63

Appendix 2. Water-quality properties measured in samples collected from isolated pools along discrete transect lines at USGS 

stations 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Texas and 07346071 Little Cypress Bayou near U.S. 

Highway 59 near Jefferson, Tex., 2011.—Continued

[mg/L, milligrams per liter; °C, degrees Celsius; μS/cm, microsiemens per centimeter at 25 degrees Celsius; --, not measured]

Mesohabitat 

identifier

Transect 

identifier Water quality

Measurement 

location in 

water column1

Left2 Center3 Right4

Little Cypress Creek near U.S. Highway 59 near Jefferson, Tex. - October 13, 2011

7 A–A’ dissolved oxygen (mg/L) top 4.53 4.68 5.33

7 A–A’ dissolved oxygen (mg/L) middle -- 4.75 --

7 A–A’ dissolved oxygen (mg/L) bottom -- -- --

7 A–A’ temperature (°C) top 20.81 20.52 20.78

7 A–A’ temperature (°C) middle -- 20.60 --

7 A–A’ temperature (°C) bottom -- -- --

7 A–A’ pH (standard units) top 6.45 6.27 6.05

7 A–A’ pH (standard units) middle -- 6.38 --

7 A–A’ pH (standard units) bottom -- -- --

7 A–A’ specific conductance (μS/cm) top 233 233 233

7 A–A’ specific conductance (μS/cm) middle -- 232 --

7 A–A’ specific conductance (μS/cm) bottom -- -- --

7 B–B’ dissolved oxygen (mg/L) top 4.84 4.65 4.93

7 B–B’ dissolved oxygen (mg/L) middle 4.37 3.95 3.96

7 B–B’ dissolved oxygen (mg/L) bottom 2.23 0.72 3.74

7 B–B’ temperature (°C) top 20.75 20.52 20.60

7 B–B’ temperature (°C) middle 20.18 20.02 19.90

7 B–B’ temperature (°C) bottom 20.06 20.01 19.94

7 B–B’ pH (standard units) top 6.73 6.66 6.58

7 B–B’ pH (standard units) middle 6.68 6.59 6.50

7 B–B’ pH (standard units) bottom 6.61 6.52 6.42

7 B–B’ specific conductance (μS/cm) top 234 234 234

7 B–B’ specific conductance (μS/cm) middle 233 234 233

7 B–B’ specific conductance (μS/cm) bottom 234 235 234

8 C–C’ dissolved oxygen (mg/L) top 3.33 2.94 3.25

8 C–C’ dissolved oxygen (mg/L) middle 2.58 2.30 2.65

8 C–C’ dissolved oxygen (mg/L) bottom 2.32 0.35 2.10

8 C–C’ temperature (°C) top 21.04 20.60 20.94

8 C–C’ temperature (°C) middle 20.20 19.83 20.63

8 C–C’ temperature (°C) bottom 20.07 20.09 20.35

8 C–C’ pH (standard units) top 6.76 6.75 6.76

8 C–C’ pH (standard units) middle 6.74 6.74 6.75

8 C–C’ pH (standard units) bottom 6.73 6.64 6.73

8 C–C’ specific conductance (μS/cm) top 220 220 219

8 C–C’ specific conductance (μS/cm) middle 220 219 220

8 C–C’ specific conductance (μS/cm) bottom 220 223 225
64 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 2. Water-quality properties measured in samples collected from isolated pools along discrete transect lines at USGS 

stations 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Texas and 07346071 Little Cypress Bayou near U.S. 

Highway 59 near Jefferson, Tex., 2011.—Continued

[mg/L, milligrams per liter; °C, degrees Celsius; μS/cm, microsiemens per centimeter at 25 degrees Celsius; --, not measured]

Mesohabitat 

identifier

Transect 

identifier Water quality

Measurement 

location in 

water column1

Left2 Center3 Right4

9 D–D’ dissolved oxygen (mg/L) top 4.91 3.78 4.03

9 D–D’ dissolved oxygen (mg/L) middle 3.48 2.99 3.52

9 D–D’ dissolved oxygen (mg/L) bottom 2.27 1.28 3.12

9 D–D’ temperature (°C) top 22.12 21.32 21.82

9 D–D’ temperature (°C) middle 20.54 20.00 20.68

9 D–D’ temperature (°C) bottom 19.93 19.87 20.58

9 D–D’ pH (standard units) top 6.87 6.78 6.86

9 D–D’ pH (standard units) middle 6.78 6.74 6.85

9 D–D’ pH (standard units) bottom 6.76 6.73 6.91

9 D–D’ specific conductance (μS/cm) top 219 219 217

9 D–D’ specific conductance (μS/cm) middle 218 217 217

9 D–D’ specific conductance (μS/cm) bottom 217 217 218

9 E–E’ dissolved oxygen (mg/L) top 4.03 4.81 4.54

9 E–E’ dissolved oxygen (mg/L) middle 2.13 2.21 3.03

9 E–E’ dissolved oxygen (mg/L) bottom 0.24 0.64 0.28

9 E–E’ temperature (°C) top 20.90 20.91 20.97

9 E–E’ temperature (°C) middle 19.50 19.53 19.97

9 E–E’ temperature (°C) bottom 19.34 19.33 19.59

9 E–E’ pH (standard units) top 6.80 6.74 6.72

9 E–E’ pH (standard units) middle 6.75 6.66 6.68

9 E–E’ pH (standard units) bottom 6.69 6.62 6.72

9 E–E’ specific conductance (μS/cm) top 217 217 217

9 E–E’ specific conductance (μS/cm) middle 217 217 217

9 E–E’ specific conductance (μS/cm) bottom 224 223 217

1

Measurement locations within the water column were collected a few inches below the water surface (top), the midpoint of the water column (middle), or a 

few inches above the stream bed (bottom).

2

Refers to a location halfway between the midpoint of the channel and the left edge of water on the transect line.

3

Refers to a location halfway between the left edge of water and the right edge of water on the transect line.

4

Refers to a location halfway between the midpoint of the channel and the right edge of water on the transect line.
Appendix 3

Appendix 3—Number of Fish, Relative Abundance, and Catch 

Per Unit Effort

Appendix 3 67

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of 

individuals caught in 30 seconds); --, no data]

Family Family 

common name Species Species common name

Status Trophic 

group1

General 

spawning guild

Collection 

method

Lepisosteidae Gars Lepisosteus oculatus Spotted gar Native Predator Nest and substrate Electrofishing

Lepisosteus osseus Longnose gar Native Predator Nest and substrate Electrofishing

Amiidae Bowfin Amia calva Bowfin Native Predator Nest and substrate Electrofishing

Clupeidae Herrings Dorosoma cepedianum Gizzard shad Native Omnivore Nest and substrate Electrofishing

Dorosoma petenense Threadfin shad Native Omnivore Nest and substrate Electrofishing

Cyprinidae Carps and 

minnows

Cyprinella lutrensis Red shiner Native Invertivore Nest and substrate Electrofishing

Cyprinella venustus Blacktail shiner Native Invertivore Nest and substrate Electrofishing

Cyprinella venustus Blacktail shiner Native Invertivore Nest and substrate Seining

Cyprinus carpio Common carp Introduced Omnivore Nest and substrate Electrofishing

Hybopsis amnis Pallid shiner Native Invertivore NA Electrofishing

Lythrurus fumeus Ribbon shiner Native Invertivore Broadcast Electrofishing

Notropis atherinoides Emerald shiner Native Invertivore Broadcast Electrofishing

Notropis chalybaeus Ironcolor shiner Native Invertivore Nest and substrate Electrofishing

Notropis maculatus Taillight shiner Native Invertivore Nest and substrate Electrofishing

Notropis shumardi Silverband shiner Native Invertivore Broadcast Electrofishing

Notropis texanus Weed shiner Native Invertivore NA Electrofishing

Pimphales vigilax Bullhead minnow Native Invertivore Nest and substrate Electrofishing

Atherinopsidae Silversides Labidesthes sicculus Brook silverside Native Invertivore Nest and substrate Electrofishing

Labidesthes sicculus Brook silverside Native Invertivore Nest and substrate Seining

Fundulidae Topminnows and 

killifishes

Fundulus notatus Blackstripe 

topminnow

Native Invertivore Nest and substrate Electrofishing

Fundulus notatus Blackstripe 

topminnow

Native Invertivore Nest and substrate Seining

Catostomidae Suckers Minytrema melanops Spotted sucker Native Omnivore Nest and substrate Electrofishing

Ictaluridae Catfishes Ameiurus natalis Yellow bullhead Native Omnivore Nest and substrate Electrofishing

Ictalurus punctatus Channel catfish Native Omnivore Nest and substrate Electrofishing

Noturus gyrinus Tadpole madtom Native Invertivore Nest and substrate Electrofishing

Noturus nocturnus Freckled madtom Native Invertivore Nest and substrate Electrofishing

Pylodictis olivaris Flathead catfish Native Predator Nest and substrate Electrofishing

Esocidae Pickerels Esox americanus Redfin pickerel Native Predator Broadcast Electrofishing

Aphredoderidae Pirate perch Aphredoderus sayanus Pirate perch Native Invertivore Nest and substrate Electrofishing

Poecilidae Mosquitofishes Gambusia affinis Western 

mosquitofish

Introduced Invertivore Live bearing Electrofishing

Gambusia affinis Western 

mosquitofish

Introduced Invertivore Live bearing Seining

Percidae Darters and 

perches

Percina macrolepida Bigscale logperch Native Invertivore Nest and substrate Electrofishing

Percina sciera Dusky darter Native Invertivore Nest and substrate Electrofishing

Etheostoma asprigene Mud darter Native Invertivore Nest and substrate Electrofishing

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of 

individuals caught in 30 seconds); --, no data]
68 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of 

individuals caught in 30 seconds); --, no data]

Family Family 

common name Species Species common name

Status Trophic 

group1

General 

spawning guild

Collection 

method

Etheostoma 

chlorosoma

Bluntnose darter Native Invertivore Nest and substrate Electrofishing

Etheostoma gracile Slough darter Native Invertivore Nest and substrate Electrofishing

Etheostoma histrio Harlequin darter Native Invertivore Nest and substrate Electrofishing

Percina maculata Blackside darter Native Invertivore Nest and substrate Electrofishing

Etheostoma proeliare Cypress darter Native Invertivore Nest and substrate Electrofishing

Centrarchidae Sunfishes Lepomis macrochirus Bluegill Native Invertivore Nest and substrate Electrofishing

Lepomis macrochirus Bluegill Native Invertivore Nest and substrate Seining

Lepomis cyanellus Green sunfish Native Predator Nest and substrate Electrofishing

Micropterus salmoides Largemouth bass Native Predator Nest and substrate Electrofishing

Lepomis megalotis Longear sunfish Native Invertivore Nest and substrate Electrofishing

Lepomis megalotis Longear sunfish Native Invertivore Nest and substrate Seining

Lepomis auritus Redbreast sunfish Introduced Invertivore Nest and substrate Electrofishing

Lepomis marginatus Dollar sunfish Native Invertivore Nest and substrate Electrofishing

Lepomis microlophus Redear sunfish Native Invertivore Nest and substrate Electrofishing

Lepomis microlophus Redear sunfish Native Invertivore Nest and substrate Seining

Lepomis miniatus Redspotted 

sunfish

Native Invertivore Nest and substrate Electrofishing

Lepomis symmetricus Bantam sunfish Native Invertivore Nest and substrate Electrofishing

Micropterus 

punctulatus

Spotted bass Native Predator Nest and substrate Electrofishing

Lepomis gulosus Warmouth Native Predator Nest and substrate Electrofishing

Pomoxis annularis White crappie Native Predator Nest and substrate Electrofishing

Scianidae Drums Aplodinotus grunniens Freshwater drum Native Invertivore Nest and substrate Electrofishing
Appendix 3 69

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of 

individuals caught in 30 seconds); --, no data]

Species 

common name

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (July 31, 2010)

Slow run 

 (e-time 1871)

Fast run

(e-time 1312)

Embayment (Margin Pool)

(e-time 335)

Total 

relative 

abundance

Number of 

individuals

Relative 

abundance CPUE Number of individuals

Relative 

abundance CPUE Number of individuals

Relative 

abundance CPUE

Spotted gar 8 0.025 0.128 -- -- -- -- -- -- 0.013

Longnose gar -- -- -- -- -- -- -- -- -- --

Bowfin 3 0.010 0.048 -- -- -- -- -- -- 0.005

Gizzard shad -- -- -- -- -- -- -- -- -- --

Threadfin shad 5 0.016 0.080 -- -- -- -- -- -- 0.008

Red shiner -- -- -- 4 0.016 0.091 1 0.032 0.090 0.008

Blacktail shiner 2 0.006 0.032 61 0.244 1.395 -- -- -- 0.106

Blacktail shiner -- -- -- 4 0.016 0.091 -- -- -- 0.007

Common carp 2 0.006 0.032 -- -- -- -- -- -- 0.003

Pallid shiner -- -- -- -- -- -- -- -- -- --

Ribbon shiner 6 0.019 0.096 -- -- -- -- -- -- 0.010

Emerald shiner -- -- -- -- -- -- -- -- -- --

Ironcolor shiner -- -- -- -- -- -- -- -- -- --

Taillight shiner -- -- -- 5 0.020 0.114 -- -- -- 0.008

Silverband shiner -- -- -- -- -- -- -- -- -- --

Weed shiner -- -- -- -- -- -- -- -- -- --

Bullhead minnow -- -- -- 3 0.012 0.069 -- -- -- 0.005

Brook silverside 4 0.013 0.064 1 0.004 0.023 1 0.032 0.090 0.010

Brook silverside -- -- -- -- -- -- -- -- -- --

Blackstripe 

topminnow

1 0.003 0.016 12 0.048 0.274 4 0.129 0.358 0.029

Blackstripe 

topminnow

-- -- -- -- -- -- -- -- -- --

Spotted sucker 3 0.010 0.048 -- -- -- -- -- -- 0.005

Yellow bullhead -- -- -- -- -- -- -- -- -- --

Channel catfish 9 0.029 0.144 4 0.016 0.091 -- -- -- 0.022

Tadpole madtom -- -- -- -- -- -- -- -- -- --

Freckled madtom -- -- -- 1 0.004 0.023 -- -- -- 0.002

Flathead catfish 1 0.003 0.016 -- -- -- 2 0.065 0.179 0.005

Redfin pickerel -- -- -- -- -- -- -- -- -- --

Pirate perch 2 0.006 0.032 1 0.004 0.023 4 0.129 0.358 0.012

Western mosquitofish -- -- -- -- -- -- 3 0.097 0.269 0.005

Western mosquitofish -- -- -- -- -- -- -- -- -- --

Bigscale logperch 2 0.006 0.032 -- -- -- -- -- -- 0.003

Dusky darter -- -- -- 3 0.012 0.069 -- -- -- 0.005

Mud darter -- -- -- 1 0.004 0.023 -- -- -- 0.002

Bluntnose darter -- -- -- -- -- -- -- -- -- --

Slough darter -- -- -- -- -- -- -- -- -- --

Harlequin darter -- -- -- 2 0.008 0.046 -- -- -- 0.003

Blackside darter -- -- -- -- -- -- -- -- -- --

Cypress darter -- -- -- 1 0.004 0.023 -- -- -- 0.002

Bluegill 53 0.168 0.850 10 0.040 0.229 -- -- -- 0.106

Bluegill -- -- -- -- -- -- -- -- -- --

Green sunfish -- -- -- -- -- -- -- -- -- --
70 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of 

individuals caught in 30 seconds); --, no data]

Species 

common name

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (July 31, 2010)

Slow run 

 (e-time 1871)

Fast run

(e-time 1312)

Embayment (Margin Pool)

(e-time 335)

Total 

relative 

abundance

Number of 

individuals

Relative 

abundance CPUE Number of individuals

Relative 

abundance CPUE Number of individuals

Relative 

abundance CPUE

Largemouth bass 12 0.038 0.192 2 0.008 0.046 -- -- -- 0.023

Longear sunfish 119 0.378 1.908 108 0.432 2.470 8 0.258 0.716 0.394

Longear sunfish -- -- -- -- -- -- -- -- -- --

Redbreast sunfish -- -- -- 1 0.004 0.023 -- -- -- 0.002

Dollar sunfish -- -- -- 2 0.008 0.046 -- -- -- 0.003

Redear sunfish 20 0.063 0.321 10 0.040 0.229 3 0.097 0.269 0.055

Redear sunfish -- -- -- 1 0.004 0.023 -- -- -- 0.002

Redspotted sunfish 27 0.086 0.433 12 0.048 0.274 4 0.129 0.358 0.072

Bantam sunfish -- -- -- -- -- -- 1 0.032 0.090 0.002

Spotted bass 1 0.003 0.016 -- -- -- -- -- -- 0.002

Warmouth 18 0.057 0.289 1 0.004 0.023 -- -- -- 0.032

White crappie 14 0.044 0.224 -- -- -- -- -- -- 0.023

Freshwater drum 3 0.010 0.048 -- -- -- -- -- -- 0.005

Totals number 

of individuals 

and CPUE per 

mesohabitat type

315 5.051 250 5.716 31 2.776

Total number of 

species per 

mesohabitat type

22 21 10

Number of darter and 

perch species per 

mesohabitat type

1 4 0

CPUE for darters and 

perches

0.032 0.160 0

CPUE for native 

cyprinids 

(minnows)

0.128 1.761 0.090

CPUE for invertivores 3.832 5.556 2.597

CPUE for predators 0.914 0.069 0.179

CPUE for omnivores 0.305 0.091 0

CPUE for nest and 

subtrate spawners

4.955 5.716 2.507

CPUE for broadcast 

spawners

0.096 0 0

CPUE for live-bearing 0 0 0.269

CPUE for broadcast 

spawners per site 

per sampling event

0.051

Total number of 

species per site per 

sampling event

34

Total fish per site per 

sampling event

596

Total CPUE per site 

per sampling event

5.082
Appendix 3 71

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of 

individuals caught in 30 seconds); --, no data]

Species common name

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (July 27, 2011)

Slow run

(e-time not recorded)

Fast run

(e-time not recorded)

Embayment (Margin Pool)

(e-time not recorded) Total 

relative 

abundance Number of 

individuals

Relative 

abundance

Number of 

individuals

Relative 

abundance

Number of 

individuals

Relative

abundance

Spotted gar 1 0.006 -- -- -- -- 0.002

Longnose gar 1 0.006 -- -- -- -- 0.002

Bowfin 1 0.006 -- -- -- -- 0.002

Gizzard shad -- -- -- -- -- -- --

Threadfin shad 2 0.012 -- -- -- -- 0.004

Red shiner -- -- -- -- -- -- --

Blacktail shiner 14 0.087 48 0.310 6 0.029 0.130

Blacktail shiner -- -- -- -- 1 0.005 0.002

Common carp -- -- -- -- -- -- --

Pallid shiner -- -- -- -- -- -- --

Ribbon shiner -- -- -- -- -- -- --

Emerald shiner -- -- -- -- -- -- --

Ironcolor shiner -- -- -- -- -- -- --

Taillight shiner -- -- -- -- -- -- --

Silverband shiner -- -- -- -- -- -- --

Weed shiner -- -- -- -- -- -- --

Bullhead minnow 3 0.019 20 0.129 -- -- 0.044

Brook silverside 5 0.031 -- -- 1 0.005 0.011

Brook silverside -- -- -- -- 2 0.010 0.004

Blackstripe topminnow 2 0.012 7 0.045 1 0.005 0.019

Blackstripe topminnow -- -- -- -- 26 0.124 0.050

Spotted sucker 3 0.019 -- -- -- -- 0.006

Yellow bullhead -- -- 1 0.006 -- -- 0.002

Channel catfish 4 0.025 -- -- -- -- 0.008

Tadpole madtom -- -- -- -- -- -- --

Freckled madtom -- -- -- -- -- -- --

Flathead catfish 2 0.012 1 0.006 -- -- 0.006

Redfin pickerel -- -- -- -- -- -- --

Pirate perch 6 0.037 1 0.006 3 0.014 0.019

Western mosquitofish 2 0.012 -- -- -- -- 0.004

Western mosquitofish -- -- -- -- 158 0.756 0.301

Bigscale logperch -- -- -- -- -- -- --

Dusky darter 1 0.006 -- -- -- -- 0.002

Mud darter -- -- 2 0.013 -- -- 0.004

Bluntnose darter -- -- 1 0.006 -- -- 0.002

Slough darter -- -- -- -- -- -- --

Harlequin darter -- -- -- -- -- -- --
72 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of 

individuals caught in 30 seconds); --, no data]

Species common name

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (July 27, 2011)

Slow run

(e-time not recorded)

Fast run

(e-time not recorded)

Embayment (Margin Pool)

(e-time not recorded) Total 

relative 

abundance Number of 

individuals

Relative 

abundance

Number of 

individuals

Relative 

abundance

Number of 

individuals

Relative

abundance

Blackside darter -- -- -- -- -- -- --

Cypress darter -- -- -- -- 1 0.005 0.002

Bluegill 18 0.112 1 0.006 1 0.005 0.038

Bluegill -- -- 2 0.013 -- -- 0.004

Green sunfish -- -- -- -- -- -- --

Largemouth bass 8 0.050 -- -- -- -- 0.015

Longear sunfish 66 0.410 2 0.013 8 0.038 0.145

Longear sunfish -- -- 43 0.277 -- -- 0.082

Redbreast sunfish -- -- -- -- -- -- --

Dollar sunfish -- -- 6 0.039 -- -- 0.011

Redear sunfish 7 0.043 9 0.058 -- -- 0.030

Redear sunfish -- -- -- -- -- -- --

Redspotted sunfish 8 0.050 9 0.058 1 0.005 0.034

Bantam sunfish -- -- -- -- -- -- --

Spotted bass 1 0.006 2 0.013 -- -- 0.006

Warmouth 2 0.012 -- -- -- -- 0.004

White crappie 2 0.012 -- -- -- -- 0.004

Freshwater drum 2 0.012 -- -- -- -- 0.004

Totals number of individuals and CPUE 

per mesohabitat type

161 155 209

Total number of species per mesohabitat 

type

23 14 9

Number of darter and perch species per 

mesohabitat type

1 2 1

CPUE for darters and perches

CPUE for native cyprinids (minnows)

CPUE for invertivores

CPUE for predators

CPUE for omnivores

CPUE for nest and subtrate spawners

CPUE for broadcast spawners

CPUE for live-bearing

CPUE for broadcast spawners per site 

per sampling event

Total number of species per site per 

sampling event

28

Total fish per site per sampling event 525

Total CPUE per site per sampling event
Appendix 3 73

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of individuals 

caught in 30 seconds); --, no data]

Species common 

name

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (August 3–4, 2010)

Slow run 

(e-time 614)

Fast run

(e-time 2033)

Pool (Channel)

(e-time 318)

Backwater (Margin Pool)

(e-time 30) Total 

relative 

abundance

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Spotted gar -- -- -- -- -- -- -- -- -- -- -- -- --

Longnose gar -- -- -- -- -- -- -- -- -- -- -- -- --

Bowfin -- -- -- -- -- -- -- -- -- -- -- -- --

Gizzard shad -- -- -- -- -- -- -- -- -- -- -- -- --

Threadfin shad -- -- -- -- -- -- -- -- -- -- -- -- --

Red shiner -- -- -- 1 0.006 0.015 -- -- -- -- -- -- 0.004

Blacktail shiner 3 0.048 0.147 10 0.057 0.148 6 0.250 0.566 1 0.083 1.000 0.073

Blacktail shiner -- -- -- 1 0.006 0.015 1 0.042 0.094 -- -- -- 0.007

Common carp -- -- -- -- -- -- -- -- -- -- -- -- --

Pallid shiner -- -- -- -- -- -- -- -- -- -- -- -- --

Ribbon shiner 18 0.286 0.879 10 0.057 0.148 -- -- -- -- -- -- 0.103

Emerald shiner -- -- -- -- -- -- -- -- -- -- -- -- --

Ironcolor shiner -- -- -- -- -- -- -- -- -- -- -- -- --

Taillight shiner -- -- -- -- -- -- -- -- -- -- -- -- --

Silverband shiner -- -- -- 1 0.006 0.015 -- -- -- -- -- -- 0.004

Weed shiner -- -- -- -- -- -- -- -- -- -- -- -- --

Bullhead minnow -- -- -- -- -- -- -- -- -- -- -- -- --

Brook silverside 9 0.143 0.440 2 0.011 0.030 -- -- -- -- -- -- 0.040

Brook silverside -- -- -- -- -- -- -- -- -- 2 0.167 2.000 0.007

Blackstripe 

topminnow

1 0.016 0.049 17 0.098 0.251 -- -- -- 1 0.083 1.000 0.070

Blackstripe 

topminnow

-- -- -- 3 0.017 0.044 -- -- -- -- -- -- 0.011

Spotted sucker 2 0.032 0.098 3 0.017 0.044 -- -- -- -- -- -- 0.018

Yellow bullhead -- -- -- -- -- -- -- -- -- -- -- -- --

Channel catfish -- -- -- -- -- -- -- -- -- -- -- -- --

Tadpole madtom -- -- -- 1 0.006 0.015 -- -- -- -- -- -- 0.004

Freckled madtom 1 0.016 0.049 -- -- -- -- -- -- -- -- -- 0.004

Flathead catfish -- -- -- -- -- -- -- -- -- -- -- -- --

Redfin pickerel -- -- -- 2 0.011 0.030 -- -- -- -- -- -- 0.007

Pirate perch -- -- -- 7 0.040 0.103 -- -- -- -- -- -- 0.026

Western mosquitofish -- -- -- 1 0.006 0.015 -- -- -- -- -- -- 0.004

Western mosquitofish -- -- -- -- -- -- -- -- -- -- -- -- --

Bigscale logperch -- -- -- 1 0.006 0.015 -- -- -- 1 0.083 1.000 0.007

Dusky darter -- -- -- 1 0.006 0.015 -- -- -- -- -- -- 0.004

Mud darter -- -- -- -- -- -- -- -- -- -- -- -- --

Bluntnose darter -- -- -- 1 0.006 0.015 -- -- -- -- -- -- 0.004

Slough darter -- -- -- -- -- -- -- -- -- -- -- -- --

Harlequin darter -- -- -- 1 0.006 0.015 -- -- -- -- -- -- 0.004

Blackside darter -- -- -- -- -- -- -- -- -- -- -- -- --

Cypress darter -- -- -- 1 0.006 0.015 -- -- -- -- -- -- 0.004

Bluegill -- -- -- 26 0.149 0.384 -- -- -- 1 0.083 1.000 0.099

Bluegill 4 0.063 0.195 1 0.006 0.015 -- -- -- -- -- -- 0.018

Green sunfish -- -- -- 5 0.029 0.074 -- -- -- -- -- -- 0.018
74 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of individuals 

caught in 30 seconds); --, no data]

Species common 

name

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (August 3–4, 2010)

Slow run 

(e-time 614)

Fast run

(e-time 2033)

Pool (Channel)

(e-time 318)

Backwater (Margin Pool)

(e-time 30) Total 

relative 

abundance

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Largemouth bass 2 0.032 0.098 7 0.040 0.103 1 0.042 0.094 -- -- -- 0.037

Longear sunfish 12 0.190 0.586 58 0.333 0.856 12 0.500 1.132 5 0.417 5.000 0.319

Longear sunfish -- -- -- -- -- -- -- -- -- 1 0.083 1.000 0.004

Redbreast sunfish -- -- -- -- -- -- -- -- -- -- -- -- --

Dollar sunfish -- -- -- 2 0.011 0.030 -- -- -- -- -- -- 0.007

Redear sunfish 7 0.111 0.342 1 0.006 0.015 -- -- -- -- -- -- 0.029

Redear sunfish -- -- -- 1 0.006 0.015 -- -- -- -- -- -- 0.004

Redspotted sunfish 2 0.032 0.098 6 0.034 0.089 1 0.042 0.094 -- -- -- 0.033

Bantam sunfish -- -- -- -- -- -- -- -- -- -- -- -- --

Spotted bass 1 0.016 0.049 -- -- -- -- -- -- -- -- -- 0.004

Warmouth 1 0.016 0.049 3 0.017 0.044 3 0.125 0.283 -- -- -- 0.026

White crappie -- -- -- -- -- -- -- -- -- -- -- -- --

Freshwater drum -- -- -- -- -- -- -- -- -- -- -- -- --

Totals number 

of individuals 

and CPUE per 

mesohabitat type

63 3.078 174 2.568 24 2.264 12 12.000

Total number of 

species per 

mesohabitat type

13 24 5 6

Number of darter and 

perch species per 

mesohabitat type

0 5 0 1

CPUE for darters and 

perches

0 0.074 0 1.000

CPUE for native 

cyprinids 

(minnows)

1.026 0.339 0.660 1.000

CPUE for invertivores 2.785 2.273 1.887 12.000

CPUE for predators 0.195 0.251 0.377 0

CPUE for omnivores 0.098 0.044 0 0

CPUE for nest and 

subtrate spawners

2.199 2.361 2.264 12.000

CPUE for broadcast 

spawners

0.879 0.192 0 0

CPUE for live-bearing 0 0.015 0 0

CPUE for broadcast 

spawners per site 

per sampling event

0.311

Total number of 

species per site per 

sampling event

26

Total fish per site per 

sampling event

273

Total CPUE per site 

per sampling event

2.735
Appendix 3 75

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of individuals 

caught in 30 seconds); --, no data]

Species 

common name

Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (August 19, 2010)

Slow Run

(e-time 2090)

Fast Run

(e-time 834)

Pool (Channel)

(e-time 410)

Forewater (Margin Pool)

(e-time 249) Total 

relative 

abundance

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Spotted gar 4 0.022 0.057 -- -- -- -- -- -- -- -- -- 0.011

Longnose gar -- -- -- -- -- -- -- -- -- -- -- -- --

Bowfin 1 0.006 0.014 -- -- -- -- -- -- -- -- -- 0.003

Gizzard shad 9 0.050 0.129 -- -- -- -- -- -- -- -- -- 0.025

Threadfin shad -- -- -- -- -- -- -- -- -- -- -- -- --

Red shiner 6 0.033 0.086 3 0.026 0.108 -- -- -- -- -- -- 0.025

Blacktail shiner 1 0.006 0.014 6 0.052 0.216 -- -- -- -- -- -- 0.019

Blacktail shiner -- -- -- -- -- -- -- -- -- -- -- -- --

Common carp -- -- -- -- -- -- -- -- -- -- -- -- --

Pallid shiner 1 0.006 0.014 -- -- -- -- -- -- -- -- -- 0.003

Ribbon shiner 6 0.033 0.086 -- -- -- -- -- -- 2 0.049 0.241 0.022

Emerald shiner -- -- -- 8 0.069 0.288 -- -- -- -- -- -- 0.022

Ironcolor shiner 3 0.017 0.043 4 0.034 0.144 -- -- -- -- -- -- 0.019

Taillight shiner -- -- -- -- -- -- -- -- -- -- -- -- --

Silverband shiner -- -- -- -- -- -- -- -- -- -- -- -- --

Weed shiner -- -- -- -- -- -- -- -- -- 4 0.098 0.482 0.011

Bullhead minnow -- -- -- 1 0.009 0.036 -- -- -- -- -- -- 0.003

Brook silverside 3 0.017 0.043 1 0.009 0.036 -- -- -- 2 0.049 0.241 0.017

Brook silverside -- -- -- -- -- -- -- -- -- -- -- -- --

Blackstripe topminnow 7 0.039 0.100 10 0.086 0.360 -- -- -- 3 0.073 0.361 0.056

Blackstripe topminnow -- -- -- -- -- -- -- -- -- -- -- -- --

Spotted sucker 11 0.061 0.158 -- -- -- -- -- -- 1 0.024 0.120 0.033

Yellow bullhead -- -- -- -- -- -- -- -- -- -- -- -- --

Channel catfish 2 0.011 0.029 -- -- -- -- -- -- 1 0.024 0.120 0.008

Tadpole madtom -- -- -- -- -- -- -- -- -- -- -- -- --

Freckled madtom -- -- -- -- -- -- -- -- -- -- -- -- --

Flathead catfish -- -- -- 1 0.009 0.036 1 0.045 0.073 1 0.024 0.120 0.008

Redfin pickerel 1 0.006 0.014 1 0.009 0.036 -- -- -- -- -- -- 0.006

Pirate perch 2 0.011 0.029 1 0.009 0.036 -- -- -- -- -- -- 0.008

Western mosquitofish -- -- -- -- -- -- -- -- -- -- -- -- --

Western mosquitofish -- -- -- -- -- -- -- -- -- -- -- -- --

Bigscale logperch -- -- -- -- -- -- -- -- -- -- -- -- --

Dusky darter 1 0.006 0.014 -- -- -- -- -- -- -- -- -- 0.003

Mud darter 1 0.006 0.014 -- -- -- -- -- -- -- -- -- 0.003

Bluntnose darter -- -- -- -- -- -- -- -- -- -- -- -- --

Slough darter 1 0.006 0.014 -- -- -- -- -- -- -- -- -- 0.003

Harlequin darter -- -- -- 2 0.017 0.072 -- -- -- -- -- -- 0.006

Blackside darter -- -- -- 1 0.009 0.036 -- -- -- -- -- -- 0.003

Cypress darter 1 0.006 0.014 -- -- -- -- -- -- -- -- -- 0.003

Bluegill 17 0.094 0.244 4 0.034 0.144 4 0.182 0.293 3 0.073 0.361 0.078

Bluegill -- -- -- -- -- -- -- -- -- -- -- -- --

Green sunfish -- -- -- -- -- -- -- -- -- -- -- -- --

Largemouth bass 11 0.061 0.158 2 0.017 0.072 1 0.045 0.073 2 0.049 0.241 0.045

Longear sunfish 66 0.367 0.947 65 0.560 2.338 9 0.409 0.659 17 0.415 2.048 0.437
76 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 3. Number of fish, relative abundance, and catch per unit effort by species, mesohabitat type, and collection method from 

USGS stations 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas, 07346044 Black Cypress Bayou near 

U.S. Highway 59 near Jefferson, Tex., and 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[e-time, time in seconds that electrofishing was the collection method used in the mesohabitat; CPUE, catch per unit of electrofishing effort (number of individuals 

caught in 30 seconds); --, no data]

Species 

common name

Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (August 19, 2010)

Slow Run

(e-time 2090)

Fast Run

(e-time 834)

Pool (Channel)

(e-time 410)

Forewater (Margin Pool)

(e-time 249) Total 

relative 

abundance

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Number 

of individuals

Relative 

abundanceCPUE

Longear sunfish -- -- -- -- -- -- -- -- -- -- -- -- --

Redbreast sunfish -- -- -- -- -- -- -- -- -- -- -- -- --

Dollar sunfish -- -- -- -- -- -- -- -- -- -- -- -- --

Redear sunfish 7 0.039 0.100 1 0.009 0.036 6 0.273 0.439 3 0.073 0.361 0.047

Redear sunfish -- -- -- -- -- -- -- -- -- -- -- -- --

Redspotted sunfish -- -- -- 2 0.017 0.072 -- -- -- -- -- -- 0.006

Bantam sunfish -- -- -- -- -- -- -- -- -- -- -- -- --

Spotted bass 4 0.022 0.057 1 0.009 0.036 1 0.045 0.073 1 0.024 0.120 0.019

Warmouth 9 0.050 0.129 2 0.017 0.072 -- -- -- 1 0.024 0.120 0.033

White crappie 4 0.022 0.057 -- -- -- -- -- -- -- -- -- 0.011

Freshwater drum 1 0.006 0.014 -- -- -- -- -- -- -- -- -- 0.003

Totals number 

of individuals 

and CPUE per 

mesohabitat type

180 2.584 116 4.173 22 1.610 41 4.940

Total number of 

species per 

mesohabitat type

26 19 6 13

Number of darter and 

perch species per 

mesohabitat type

4 2 0 0

CPUE for darters and 

perches

0.057 0.108 0 0

CPUE for native 

cyprinids (minnows)

0.244 0.791 0 0.723

CPUE for invertivores 1.780 3.921 1.390 4.096

CPUE for predators 0.488 0.252 0.220 0.602

CPUE for omnivores 0.316 0 0 0.241

CPUE for nest and 

subtrate spawners

2.483 3.849 1.610 4.699

CPUE for broadcast 

spawners

0.100 0.324 0 0.241

CPUE for live-bearing 0 0 0 0

CPUE for broadcast 

spawners per site 

per sampling event

0.151

Total number of 

species per site per 

sampling event

33

Total fish per site per 

sampling event

359

Total CPUE per site 

per sampling event

3.006

1

 Taxon (refers to a genetically related group or groups of one or more organisms with common characteristics that differentiated them as a unit. From 

International Commission on Zoological Nomenclature. 

1

Fish species classified as predators consume other fish more than other organisms.
Appendix 4

Appendix 4—Mussel Data and Habitat Descriptions

Appendix 4 79

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

Big Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (random starting point no. 1) - 7/30/2010

1 1 NF NA NA 2.5 0.82 SA -- 8.0 2.35 138.8 278.1 262.9 1.9

1 2 NF NA NA 0.7 0.02 SA -- -- -- -- -- -- --

2 3 NF NA NA 1.3 1.45 CG -- -- -- -- -- -- --

3 4 Pistolgrip L 50 1.4 0.67 SA -- -- -- -- -- -- --

3 4 Pistolgrip L 84 1.4 0.67 SA -- -- -- -- -- -- --

3 5 NF NA NA 1.1 0.98 CG -- 3.0 2.35 52.0 112.8 93.0 1.8

4 6 NF NA NA 1.4 0.84 SA -- -- -- -- -- -- --

4 7 Deertoe L 48 1.5 0.74 SA -- 4.0 2.35 69.4 129.6 105.5 1.5

4 7 Deertoe L 47 1.5 0.74 SA -- 4.0 2.35 69.4 129.6 105.5 1.5

4 8 NF NA NA 1.3 0.00 H -- -- -- -- -- -- --

4 9 NF NA NA 1.1 1.00 SA -- -- -- -- -- -- --

5 10 NF NA NA 1.3 0.45 SA/G -- -- -- -- -- -- --

5 11 Bankclimber L 73 1.1 0.61 CG -- 2.5 2.35 43.4 94.8 83.8 1.9

5 11 Southern 

mapleleaf

L 40 1.1 0.61 CG -- 2.5 2.35 43.4 94.8 83.8 1.9

5 12 NF NA NA 0.9 0.86 FG -- -- -- -- -- -- --

5 13 NF NA NA 0.7 0.63 SA -- 4.0 2.35 69.4 135.9 110.9 1.6

5 14 NF NA NA 1.2 0.74 SA/FG -- -- -- -- -- -- --

6 15 NF NA NA 2.2 0.14 SA -- -- -- -- -- -- --

6 16 NF NA NA 1.5 0.67 SA -- -- -- -- -- -- --

6 17 NF NA NA 1.5 0.67 H -- -- -- -- -- -- --

6 18 NF NA NA 2.0 0.01 SA/O -- -- -- -- -- -- --

6 19 NF NA NA 1.9 0.62 SA/CG -- -- -- -- -- -- --

6 20 NF NA NA 2.3 0.94 CG -- 4.0 2.35 69.4 157.0 139.3 2.0

6 21 NF NA NA 1.0 0.25 SA/W -- -- -- -- -- -- --

Big Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (random starting point no. 2) - 7/30/2010

1 22 NF NA NA 2.1 0.00 SA/O -- -- -- -- -- -- --

1 23 NF NA NA 2.8 0.28 SA -- 8.0 2.35 139 394.3 338.3 2.4

1 24 NF NA NA 1.9 0.39 VCG -- -- -- -- -- -- --

2 25 Threehorn 

wartyback

L 39 1.2 0.25 SA/CG -- -- -- -- -- -- --

2 25 Bankclimber D 65 1.2 0.25 SA/CG -- -- -- -- -- -- --

2 25 Deertoe D 50 1.2 0.25 SA/CG -- -- -- -- -- -- --

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]
80 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

2 25 Deertoe D 45 1.2 0.25 SA/CG -- -- -- -- -- -- --

2 25 Deertoe D 46 1.2 0.25 SA/CG -- -- -- -- -- -- --

2 26 NF NA NA 1.4 1.47 CG -- -- -- -- -- -- --

3 27 Western 

pimpleback

L 35 1.5 0.82 SA/G -- 8.0 2.35 139 332.1 288.8 2.1

3 28 Deertoe L 35 1.4 1.52 SA -- -- -- -- -- -- --

3 28 Western 

pimpleback

L 34 1.4 1.52 SA -- -- -- -- -- -- --

3 28 Deertoe L 36 1.4 1.52 SA -- -- -- -- -- -- --

4 29 Western 

pimpleback

L 38 1.3 1.08 SA/G -- -- -- -- -- -- --

4 29 Deertoe L 47 1.3 1.08 SA/G -- -- -- -- -- -- --

4 30 Pistolgrip D 80 1.2 1.1 SA/CO -- -- -- -- -- -- --

4 31 NF NA NA 1.3 0.94 B 

Covered 

by SA

-- -- -- -- -- -- --

4 32 NF NA NA 1.0 0 B 

Covered 

by SA

-- -- -- -- -- -- --

5 33 NF NA NA 1.3 0.67 SA -- -- -- -- -- -- --

5 34 Deertoe L 49 1.1 1.05 SA/CG -- 5.0 2.35 86.7 229.9 218.5 2.5

5 35 Western 

pimpleback

L 23 1.2 0.86 SA/CG -- -- -- -- -- -- --

5 36 Pistolgrip L 43 0.6 0.96 SA/FG -- -- -- -- -- -- --

6 37 NF NA NA 2.1 0.38 CG -- -- -- -- -- -- --

6 38 NF NA NA 1.5 0.74 SA -- -- -- -- -- -- --

6 39 NF NA NA 1.2 0.86 B -- -- -- -- -- -- --

6 40 NF NA NA 1.1 0.06 CG -- -- -- -- -- -- --

7 41 NF NA NA 2.5 0.31 SA/W -- -- -- -- -- -- --

7 42 NF NA NA 1.7 0.27 SA/O -- -- -- -- -- -- --

7 43 NF NA NA 1.4 0.68 B -- -- -- -- -- -- --

7 44 NF NA NA 2.1 0.66 SA/FG -- -- -- -- -- -- --

Big Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (random starting point no. 3) - 7/30/2010

1 45 NF NA NA 2.3 0.18 SA -- -- -- -- -- -- --

1 46 Deertoe L 53 2.7 1.04 SA -- -- -- -- -- -- --
Appendix 4 81

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

2 47 Pistolgrip L 60 1.8 1.35 SA/FG -- 6.0 2.35 104 246.4 211.7 2.0

2 47 Deertoe L 44 1.8 1.35 SA/FG -- 6.0 2.35 104 246.4 211.7 2.0

2 47 Pistolgrip L 72 1.8 1.35 SA/FG -- 6.0 2.35 104 246.4 211.7 2.0

2 47 Unknown L 49 1.8 1.35 SA/FG -- 6.0 2.35 104 246.4 211.7 2.0

2 48 NF NA NA 1.0 1.05 CG -- -- -- -- -- -- --

3 49 Western 

pimpleback

L 34 1.7 1.45 CG -- -- -- -- -- -- --

3 49 Pistolgrip L 75 1.7 1.45 CG -- -- -- -- -- -- --

3 49 Deertoe L 46 1.7 1.45 CG -- -- -- -- -- -- --

3 49 Deertoe L 28 1.7 1.45 CG -- -- -- -- -- -- --

3 50 Yellow 

sandshell

L 74 1.0 1.58 CG -- -- -- -- -- -- --

4 51 Pistolgrip L 70 1.3 1.37 SA/CG -- -- -- -- -- -- --

4 52 NF NA NA 1.1 1.24 SA/ CG -- -- -- -- -- -- --

4 53 NF NA NA 1.2 0.85 CG -- -- -- -- -- -- --

5 54 NF NA NA 1.1 0.79 SA -- 6.0 2.35 104 260.9 218.6 2.1

5 55 Western 

pimpleback

L 37 1.3 0.79 SA -- -- -- -- -- -- --

5 55 Southern 

mapleleaf

L 25 1.3 0.79 SA -- -- -- -- -- -- --

5 55 Deertoe L 27 1.3 0.79 SA -- -- -- -- -- -- --

5 56 Bleufer L 116 1.6 0.74 SA -- 5.0 2.35 86.7 164.3 136.2 1.6

5 56 Deertoe L 39 1.6 0.74 SA -- 5.0 2.35 86.7 164.3 136.2 1.6

5 57 Pistolgrip L 71 0.6 0.79 SA/CG -- -- -- -- -- -- --

5 57 Pistolgrip L 45 0.6 0.79 SA/CG -- -- -- -- -- -- --

5 57 Western 

pimpleback

L 33 0.6 0.79 SA/CG -- -- -- -- -- -- --

6 58 NF NA NA 1.9 0.7 SA/CO -- -- -- -- -- -- --

6 59 NF NA NA 1.2 0.81 SA -- -- -- -- -- -- --

6 60 NF NA NA 1.1 0.94 CG -- -- -- -- -- -- --

6 61 Deertoe D 27 1.0 0.66 CG -- -- -- -- -- -- --

6 61 Western 

pimpleback

L 52 1.0 0.66 CG -- -- -- -- -- -- --

7 62 Pistolgrip D 61 1.8 0.28 SA -- -- -- -- -- -- --

7 63 NF NA NA 1.7 0.85 B -- -- -- -- -- -- --
82 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

7 64 NF NA NA 1.8 0.94 CG -- -- -- -- -- -- --

Mean depth and velocity in quadrats where 

mussels were collected

1.4 0.93

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (random starting point no. 1) - 7/31/2010

1 1 Bankclimber D 113 3.1 0.05 SA 0 7.5 2.35 1301 283.9 231.9 1.8

1 1 Washboard L 155 3.1 0.05 SA 1.0 7.5 2.35 130 283.9 231.9 1.8

1 2 Washboard L 160 4.3 0.00 SA 0 -- -- -- -- -- --

1 2 Washboard L 145 4.3 0.00 SA 1.0 -- -- -- -- -- --

1 2 Washboard L 167 4.3 0.00 SA 2.0 -- -- -- -- -- --

1 2 Washboard L 167 4.3 0.00 SA 3.0 -- -- -- -- -- --

1 3 Pimpleback L 30 3.4 -0.04 SA/O 0.3 -- -- -- -- -- --

2 4 Bankclimber L 113 2.9 0.50 SA -- -- -- -- -- -- --

2 4 Washboard L 174 2.9 0.50 SA -- -- -- -- -- -- --

2 4 Washboard L 160 2.9 0.50 SA -- -- -- -- -- -- --

2 5 Bankclimber L 117 2.5 0.02 SA 0.3 -- -- -- -- -- --

2 5 Washboard L 166 2.5 0.02 SA 1.3 -- -- -- -- -- --

3 6 Washboard L 148 1.8 0.65 SA -- 10.0 2.35 174 421.2 345.5 2.0

3 6 Bankclimber L 113 1.8 0.65 SA -- 10.0 2.35 174 421.2 345.5 2.0

3 7 NF NA NA 1.6 0.13 SA/O >5 -- -- -- -- -- --

4 8 Washboard L 172 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Washboard L 163 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Washboard L 155 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Washboard L 172 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Yellow 

sandshell 

or fragile 

papershell

L 83 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Bankclimber L 112 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Washboard L 174 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Washboard L 175 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Washboard L 157 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Washboard L 155 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Bankclimber L 111 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Washboard L 174 2.2 0.21 SA 0 -- -- -- -- -- --
Appendix 4 83

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

4 8 Washboard L 166 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Washboard L 167 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Washboard L 168 2.2 0.21 SA 0 -- -- -- -- -- --

4 8 Yellow 

sandshell

L 98 2.2 0.21 SA 0 -- -- -- -- -- --

4 9 NF NA NA 0.8 0.58 SA -- -- -- -- -- -- --

5 10 Washboard L 167 1.5 0.52 SA -- -- -- -- -- -- --

5 11 NF NA NA 2.1 0.43 SA/O -- 3.0 2.35 52.0 76.2 57.0 1.1

6 12 NF NA NA 1.2 0.44 SA -- -- -- -- -- -- --

6 13 Bleufer L 141 2.7 0.43 SA/O 0.5 -- -- -- -- -- --

6 13 Washboard L 184 2.7 0.43 SA/O 0.5 -- -- -- -- -- --

6 13 Washboard L 165 2.7 0.43 SA/O 0.5 -- -- -- -- -- --

6 13 Threeridge D 114 2.7 0.43 SA/O 0.5 -- -- -- -- -- --

6 13 Pistolgrip L 110 2.7 0.43 SA/O 0.5 -- -- -- -- -- --

6 14 NF NA NA 1.2 0.30 SA/O -- -- -- -- -- -- --

7 15 Fragile 

papershell

L 81 1.9 0.68 SA/O >5 -- -- -- -- -- --

7 15 Washboard D 151 1.9 0.68 SA/O >5 -- -- -- -- -- --

7 16 Washboard L 167 3.3 0.21 SA/O >5 -- -- -- -- -- --

7 16 Bleufer L 148 3.3 0.21 SA/O >5 -- -- -- -- -- --

7 17 NF NA NA 1.1 0.00 O -- -- -- -- -- -- --

8 18 NF NA NA 1.9 0.90 SA -- -- -- -- -- -- --

8 19 Washboard L 153 1.8 0.40 SA/O -- -- -- -- -- -- --

8 19 Washboard L 158 1.8 0.40 SA/O -- -- -- -- -- -- --

9 20 Washboard L 146 1.9 0.47 SA/O -- -- -- -- -- -- --

9 21 Washboard L 157 2.0 0.27 SA/O 0.5 -- -- -- -- -- --

9 21 Pistolgrip D 114 2.0 0.27 SA/O 0.5 -- -- -- -- -- --

9 21 Bankclimber D 112 2.0 0.27 SA/O 0.5 -- -- -- -- -- --

9 21 Washboard D 178 2.0 0.27 SA/O 0.5 -- -- -- -- -- --

9 21 Washboard D 165 2.0 0.27 SA/O 0.5 -- -- -- -- -- --

9 22 NF NA NA 1.0 0.00 SA/

CL/O

-- -- -- -- -- -- --

10 23 Bankclimber L 118 1.7 1.32 SA/O -- -- -- -- -- -- --

10 23 Washboard L 168 1.7 1.32 SA/O -- -- -- -- -- -- --
84 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

10 23 Washboard L 156 1.7 1.32 SA/O -- -- -- -- -- -- --

10 23 Washboard D 159 1.7 1.32 SA/O -- -- -- -- -- -- --

10 23 Washboard D 157 1.7 1.32 SA/O -- -- -- -- -- -- --

10 24 Yellow 

sandshell

L 105 2.5 0.49 -- 0 -- -- -- -- -- --

10 25 NF NA NA 1.5 0.37 SA/O -- -- -- -- -- -- --

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (random starting point no. 2) - 7/31/2010

1 26 Washboard L 163 1.0 0.29 SA/O 0 5.0 2.35 86.7 160.4 121.5 1.4

1 26 Washboard L 173 1.0 0.29 SA/O 0 5.0 2.35 86.7 160.4 121.5 1.4

1 26 Washboard L 156 1.0 0.29 SA/O 0 5.0 2.35 86.7 160.4 121.5 1.4

1 26 Washboard L 161 1.0 0.29 SA/O 0 5.0 2.35 86.7 160.4 121.5 1.4

1 26 Washboard L 175 1.0 0.29 SA/O 0 5.0 2.35 86.7 160.4 121.5 1.4

1 26 Fragile 

papershell

L 82 1.0 0.29 SA/O 0 5.0 2.35 86.7 160.4 121.5 1.4

1 27 NF NA NA 1.0 0.29 SA/O 0 -- -- -- -- -- --

1 28 Washboard L 157 3.7 0.69 SA 2.5 -- -- -- -- -- --

1 28 Washboard L 152 3.7 0.69 SA 2.5 -- -- -- -- -- --

1 28 Washboard L 154 3.7 0.69 SA 2.5 -- -- -- -- -- --

1 28 Washboard L 161 3.7 0.69 SA 2.5 -- -- -- -- -- --

2 29 Louisiana 

fatmucket

NA 108 1.8 0.67 SA 4.4 -- -- -- -- -- --

2 30 NF NA NA 1.1 0.24 SA/O -- -- -- -- -- -- --

2 31 Washboard L 162 1.8 0.59 SA 2.2 6.0 2.35 104 247.9 201.4 1.9

2 31 Bankclimber L 114 1.8 0.59 SA 2.2 6.0 2.35 104 247.9 201.4 1.9

2 31 Deertoe L 47 1.8 0.59 SA 2.2 6.0 2.35 104 247.9 201.4 1.9

2 31 Western 

pimpleback

D 63 1.8 0.59 SA 2.2 6.0 2.35 104 247.9 201.4 1.9

3 32 NF NA NA 1.3 0.52 SA/O -- -- -- -- -- -- --

3 33 Washboard L 178 2.4 0.39 SA -- -- -- -- -- -- --

3 33 Western 

pimpleback

L 35 2.4 0.39 SA 1.0 -- -- -- -- -- --

3 33 Fragile 

papershell

D 90 2.4 0.57 SA -- -- -- -- -- -- --

3 34 NF NA NA 0.8 0.57 SA -- -- -- -- -- -- --

4 35 NF NA NA 0.6 0.37 SA -- -- -- -- -- -- --

4 36 Washboard L 154 2.8 0.68 SA 2.5 -- -- -- -- -- --
Appendix 4 85

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

5 37 NF NA NA 0.9 0.29 SA/O -- -- -- -- -- -- --

5 38 Bleufer L 140 2.8 0.11 SA/O -- 8.0 2.35 139 286.4 227.4 1.6

5 38 Washboard L 153 2.8 0.11 SA/O -- 8.0 2.35 139 286.4 227.4 1.6

6 39 NF NA NA 1.3 0.52 SA -- -- -- -- -- -- --

6 40 Washboard L 162 2.9 0.47 SA/O 2.2 -- -- -- -- -- --

6 40 Washboard L 171 2.9 0.47 SA/O 2.2 -- -- -- -- -- --

6 40 Washboard L 151 2.9 0.47 SA/O 2.2 -- -- -- -- -- --

6 40 Washboard L 149 2.9 0.47 SA/O 2.2 -- -- -- -- -- --

6 40 Washboard L 156 2.9 0.47 SA/O 2.2 -- -- -- -- -- --

6 40 Washboard L 147 2.9 0.47 SA/O 2.2 -- -- -- -- -- --

6 41 Bankclimber L 106 2.7 0.24 SA/O 1.3 -- -- -- -- -- --

6 41 Washboard L 161 2.7 0.24 SA/O 1.3 -- -- -- -- -- --

7 42 Yellow 

sandshell

L 46 1.6 0.53 SA 0 -- -- -- -- -- --

7 43 Washboard L 175 2.8 0.06 SA/W 0 -- -- -- -- -- --

7 43 Bleufer L 141 2.8 0.06 SA/W 0 -- -- -- -- -- --

7 44 NF NA NA 1.6 0.01 SA/W -- -- -- -- -- -- --

8 45 Pistolgrip D 133 1.9 0.50 SA/W 0 -- -- -- -- -- --

8 45 Pigtoe1 D 73 1.9 0.50 SA/W 0 -- -- -- -- -- --

8 46 NF NA NA 1.5 0.59 SA/W -- -- -- -- -- -- --

8 46 Paper 

pondshell

L 44 1.5 0.59 SA/W -- -- -- -- -- -- --

8 46 Pistolgrip D 147 1.5 0.59 SA/W -- -- -- -- -- -- --

8 47 Bleufer L 52 1.8 0.24 SA/O 0.5 -- -- -- -- -- --

8 47 Yellow 

sandshell

-- 107 1.8 0.24 SA/O -- -- -- -- -- -- --

9 48 Washboard L 160 1.2 0.65 SA >5 10.0 2.35 1745 412.4 341.3 2.0

9 49 Bankclimber L 101 1.6 0.12 SA/O 1.0 -- -- -- -- -- --

9 50 Bleufer D NA 1.2 0.17 SA -- -- -- -- -- -- --

Big Cypress Bayou at confluence of French Creek, Jefferson, Tex. (random starting point no. 3) - 7/31/2010

1 51 Washboard L 155 1.8 0.34 -- 3.0 -- -- -- -- -- --

1 51 Bankclimber D 76 1.8 0.34 -- 3.0 -- -- -- -- -- --

1 51 Threeridge D 106 1.8 0.34 SA 3.0 -- -- -- -- -- --

1 52 NF NA NA 0.5 0.19 SA/O 0 -- -- -- -- -- --
86 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

1 53 NF NA NA 1.8 -0.01 SA/W/R -- -- -- -- -- -- --

1 54 NF NA NA 1.2 0.02 SA/W/R -- -- -- -- -- -- --

2 55 Yellow 

sandshell

L 102 1.3 0.43 SA/W 0 -- -- -- -- -- --

2 56 Bankclimber L 117 1.4 0.49 SA 0 -- -- -- -- -- --

2 56 Pimpleback L 67 1.4 0.49 SA 1 -- -- -- -- -- --

2 57 NF NA NA 2.2 -0.09 SA/O -- -- -- -- -- -- --

3 58 NF NA NA 1.7 0.28 SA -- -- -- -- -- -- --

4 59 Pimpleback L 67 2.4 0.70 SA 2.0 7.5 2.35 130 313.4 257.4 2.0

4 59 Pimpleback L 29 2.4 0.70 SA 2.0 7.5 2.35 130 313.4 257.4 2.0

4 59 Bleufer L 143 2.4 0.70 SA 2.0 7.5 2.35 130 313.4 257.4 2.0

4 60 Louisiana 

fatmucket

L 102 1.6 0.41 SA -- -- -- -- -- -- --

4 60 Pimpleback L 32 1.6 0.41 SA -- -- -- -- -- -- --

5 61 Pimpleback L 34 2.6 0.39 SA 2.0 -- -- -- -- -- --

5 61 Washboard L 169 2.6 0.39 SA -- -- -- -- -- -- --

5 61 Washboard L 158 2.6 0.39 SA -- -- -- -- -- -- --

5 62 Washboard L 149 1.5 0.63 SA -- -- -- -- -- -- --

5 62 Washboard L 150 1.5 0.63 SA -- -- -- -- -- -- --

5 62 Threeridge L 103 1.5 0.63 SA -- -- -- -- -- -- --

5 62 Yellow 

sandshell

L 70 1.5 0.63 SA -- -- -- -- -- -- --

6 63 NF NA NA 1.0 0.37 SA/O -- 5.0 2.35 86.7 145.8 109.4 1.3

6 64 NF NA NA 2.4 0.27 SA -- -- -- -- -- -- --

6 65 Bleufer L 142 1.6 0.29 SA/O 0 -- -- -- -- -- --

7 66 NF NA NA 1.5 1.80 SA/S/

CL

-- -- -- -- -- -- --

7 67 Washboard L 156 3.0 0.21 SA/W >5 -- -- -- -- -- --

7 67 Washboard L 154 3.0 0.21 SA/W >5 -- -- -- -- -- --

7 67 Washboard L 145 3.0 0.21 SA/W >5 -- -- -- -- -- --

7 67 Washboard L 143 3.0 0.21 SA/W >5 -- -- -- -- -- --

7 67 Bankclimber D 112 -- -- -- -- -- -- -- -- -- --

7 68 NF NA NA 1.9 0.15 SA/W -- -- -- -- -- -- --

7 69 NF NA NA 1.0 0.40 SA/O -- -- -- -- -- -- --
Appendix 4 87

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

8 70 Washboard -- 152 1.6 0.48 SA/O 1.7 -- -- -- -- -- --

8 70 Washboard -- 153 1.6 0.48 SA/O 1.7 -- -- -- -- -- --

8 70 Fragile 

papershell

D 106 1.6 0.48 SA/O 1.7 -- -- -- -- -- --

8 71 NF NA NA 1.7 0.23 SA/W -- -- -- -- -- -- --

9 72 Washboard D 172 1.2 0.67 SA -- -- -- -- -- -- --

9 72 Bankclimber D 69 1.2 0.67 SA -- -- -- -- -- -- --

9 73 NF NA NA 2.1 0.36 SA -- -- -- -- -- -- --

9 74 NF NA NA 1.4 0.23 SA/W -- -- -- -- -- -- --

10 75 NF NA NA 0.6 0.39 SA -- -- -- -- -- -- --

10 76 Washboard L 165 1.3 0.39 SA/W 0 -- -- -- -- -- --

10 76 Pistolgrip L 150 1.3 0.39 SA/W 1 -- -- -- -- -- --

10 77 Washboard L 146 2.2 0.56 SA/O 0.5 -- -- -- -- -- --

Mean depth and velocity in quadrats where 

mussels were collected

2.2 0.41

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (random starting point no. 1) - 8/3/2010

1 1 NF NA NA 1.9 0.04 RM -- -- -- -- -- -- --

3 2 NF NA NA -- -- SI/RM -- -- -- -- -- -- --

4 1 NF NA NA 1.5 -0.03 SI/RM -- -- -- -- -- -- --

4 2 NF NA NA 5.9 0.01 SI -- -- -- -- -- -- --

4 3 NF NA NA 3.9 0.27 SA/O -- -- -- -- -- -- --

5 4 NF NA NA 1.1 0.14 SA/W -- -- -- -- -- -- --

5 5 NF NA NA 2.8 0.77 SA/W -- -- -- -- -- -- --

5 6 NF NA NA 1.3 0.50 SA/RM -- -- -- -- -- -- --

6 7 NF NA NA 2.0 -0.05 CG -- -- -- -- -- -- --

6 8 NF NA NA 3.4 0.29 SA/W -- -- -- -- -- -- --

6 9 NF NA NA 1.1 0.33 W/RM -- -- -- -- -- -- --

7 10 NF NA NA 2.8 0.41 LCO -- -- -- -- -- -- --

7 11 Pistolgrip D 57 3.8 0.21 LCO -- 3.0 2.35 52.0 99.8 73.3 1.4

8 12 NF NA NA 2.1 0.22 SA/S -- -- -- -- -- -- --

8 13 NF NA NA 2.3 0.27 SA/O -- 3.0 2.35 52.0 79.6 51.6 1.0

9 14 NF NA NA 2.1 0.07 SA -- -- -- -- -- -- --

9 15 NF NA NA 4.6 0.04 SA/O -- -- -- -- -- -- --
88 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

10 16 NF NA NA 3.8 0.16 RM -- -- -- -- -- -- --

10 17 Pistolgrip L 63 5.6 0.03 SA/W -- -- -- -- -- -- --

10 17 Washboard L 91 5.6 0.03 SA/W -- -- -- -- -- -- --

11 18 NF NA NA 1.5 0.52 SA/O -- -- -- -- -- -- --

11 19 NF NA NA 3.8 0.64 SA/O -- -- -- -- -- -- --

12 20 NF NA NA 2.2 0.16 O -- -- -- -- -- -- --

13 21 NF NA NA 1.4 -0.05 O -- -- -- -- -- -- --

13 22 NF NA NA 2.4 0.33 SA/W -- -- -- -- -- -- --

14 23 NF NA NA 1.3 0.61 SA/W -- -- -- -- -- -- --

14 24 NF NA NA 1.3 0.62 SA -- 11.0 2.35 191 334.3 229.8 1.2

15 25 NF NA NA 1.8 0.53 SA/O -- -- -- -- -- -- --

15 26 NF NA NA 2.8 0.60 SA/W -- -- -- -- -- -- --

16 27 NF NA NA 1.9 0.29 SA -- -- -- -- -- -- --

16 28 Western 

pimpleback

L 23 1.6 0.45 SA/W -- 5.0 2.35 86.7 171.8 127.4 1.5

17 29 NF NA NA 1.2 0.39 O -- -- -- -- -- -- --

17 30 Bleufer L 49 4.0 0.45 SA -- -- -- -- -- -- --

18 31 NF NA NA 1.2 0.28 SA/O -- -- -- -- -- -- --

18 32 NF NA NA 1.9 1.14 SA/W -- -- -- -- -- -- --

19 33 NF NA NA 2.0 0.00 SA/W -- -- -- -- -- -- --

19 34 NF NA NA 2.3 1.02 SA/W -- -- -- -- -- -- --

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (random starting point no. 2) - 8/3/2010

4 35 NF NA NA 3.2 -0.12 SA/O -- -- -- -- -- -- --

4 36 NF NA NA 5.6 0.25 SA/O -- -- -- -- -- -- --

5 37 NF NA NA 1.3 0.12 SA/RM -- -- -- -- -- -- --

5 38 Pimpleback D 45 4.0 0.17 SA -- 4.0 2.35 69.4 102.5 64.7 0.9

6 39 NF NA NA 2.5 -0.02 RM -- -- -- -- -- -- --

6 40 NF NA NA 3.0 0.54 SA/O -- -- -- -- -- -- --

7 41 NF NA NA 1.2 0.57 B -- -- -- -- -- -- --

7 42 NF NA NA 3.4 0.08 FG -- 5.0 2.35 86.7 169.7 118.8 1.4

8 43 Texas lilliput2 L 42 2.2 0.43 SA -- -- -- -- -- -- --

8 44 NF NA NA 1.6 0.30 SA/W -- -- -- -- -- -- --

9 45 NF NA NA 4.4 0.16 SA/W -- -- -- -- -- -- --

9 46 NF NA NA 2.9 0.19 SA/O -- -- -- -- -- -- --
Appendix 4 89

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

10 47 NF NA NA 3.5 0.19 SA/O -- -- -- -- -- -- --

10 48 NF NA NA 4.1 0.02 O -- -- -- -- -- -- --

11 49 Pimpleback D 42 1.4 0.47 SA/O -- -- -- -- -- -- --

11 50 Texas lilliput2 L 43 3.4 -0.01 SA/O -- 5.0 2.35 86.7 93.9 36.6 0.4

13 51 NF NA NA 1.2 0.57 SA/O -- -- -- -- -- -- --

13 52 NF NA NA 3.2 0.41 SA -- -- -- -- -- -- --

14 53 NF NA NA 1.5 0.62 SA/W -- -- -- -- -- -- --

14 54 NF NA NA 0.9 0.57 SA -- 6.0 2.35 104 161.5 115.0 1.1

15 55 NF NA NA 1.6 0.71 SA/O -- -- -- -- -- -- --

15 56 Unknown -- 62 1.0 -0.02 SA/O -- -- -- -- -- -- --

16 57 NF NA NA 1.5 0.71 SA/W -- -- -- -- -- -- --

16 58 NF NA NA 1.2 0.48 SA -- -- -- -- -- -- --

17 59 NF NA NA 2.1 0.51 SA/O -- -- -- -- -- -- --

17 60 NF NA NA 3.0 0.27 SA -- 9.0 2.35 156 313.3 246.4 1.6

18 61 NF NA NA 1.2 0.23 SA/W -- -- -- -- -- -- --

18 62 NF NA NA 3.1 0.17 SA/W -- -- -- -- -- -- --

19 63 NF NA NA 1.9 0.41 SA -- -- -- -- -- -- --

Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex. (random starting point no. 3) - 8/3/2010

1 64 NF NA NA 4.1 0.09 SA -- -- -- -- -- -- --

1 65 NF NA NA 3.5 0.06 SA/RM -- -- -- -- -- -- --

2 66 NF NA NA 3.9 -0.03 SA -- -- -- -- -- -- --

2 67 NF NA NA 3.9 0.22 SA/W -- -- -- -- -- -- --

3 68 NF NA NA 2.4 -0.04 SA/W -- -- -- -- -- -- --

4 69 Washboard L 127 3.5 0.02 CG -- 4.0 2.35 69.4 145.5 105.8 1.5

5 70 NF NA NA 2.9 0.12 W -- -- -- -- -- -- --

6 71 NF NA NA 3.3 0.31 SA/W -- 5.0 2.35 86.7 186.7 133.7 1.5

7 72 NF NA NA 3.6 0.32 SA -- -- -- -- -- -- --

8 73 NF NA NA 2.8 -0.15 SA/W -- -- -- -- -- -- --

8 74 NF NA NA 1.0 0.12 O -- -- -- -- -- -- --

9 75 NF NA NA 5.2 0.27 SA -- -- -- -- -- -- --

11 76 NF NA NA 1.3 0.35 SA -- 9.0 2.35 156 307.6 238.6 1.5

12 77 NF NA NA 1.0 0.85 SA -- -- -- -- -- -- --

13 78 NF NA NA 1.1 0.43 RM -- -- -- -- -- -- --
90 Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties

Appendix 4. Mussel data and habitat descriptions, including bed sediment bulk densities from USGS stations 07346017 Big Cypress 

Bayou near U.S. Highway 59 near Jefferson, Texas, 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Tex., and 

07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex., 2010.—Continued

[L, alive; D, dead; mm, millimeters; ft, feet; ft/s, feet per second; m, meters; cm, centimeters; cm3, cubic centimeters; g, grams; g/cm3, grams per cubic 

centimeter; NF, no mussels were found in this quadrat; NA, not applicable; --, not measured or determined; SA, sand; CG, coarse gravel; H, hardpan; G, gravel; 

FG, fine gravel; O, organic matter; W, woody debris; VCG, very coarse gravel; B, bedrock; G, gravel; CO, cobble; CL, clay; R, root; RM, root mass; SI, silt; >, 

greater than; Starting points no. 1, 2, and 3 refer to the random starting points for each of the three quadrat surveys per site; no., number]

Transect Quadrat

Common 

species

name

Condition 

(L/D)

Length 

(mm)

Depth 

(ft)

Velocity 

(ft/s)

Substrate 

description

Distance 

to woody 

debris 

(m)

Properties of bed sediment bulk density cores

Length 

(cm)

Radius 

(cm)

Volume 

(cm3

)

Final 

wet 

weight 

(g)

Final 

dry 

weight 

(g)

Bulk 

density 

(g/cm3

)

14 79 Pistolgrip L 89 2.6 0.55 SA/RM -- -- -- -- -- -- --

15 80 NF NA NA 5.1 -- SA -- -- -- -- -- -- --

16 81 NF NA NA 1.3 0.85 SA/W -- -- -- -- -- -- --

Mean depth and velocity in quadrats where 

mussels were collected

3.2 0.23

1

Unidentified species.

2

Preliminary identification.

Publishing support provided by

Lafayette Publishing Service Center

Information regarding water resources in Texas is available at 

http://tx.usgs.gov/
Braun and Moring—Baseline Assessment of Physical Characteristics, Aquatic Biota, and Selected Water-Quality Properties—SIR 2013–5058

Printed on recycled paper

I SBN 978- 1- 4113-3581- 3

9 7 8 1 4 11 335813