Prepared in cooperation with National Park Service, Whiskeytown National Recreation Area

Upper Clear Creek Watershed Aquatic Chemistry and Biota 

Surveys, 2004–5, Whiskeytown National Recreation Area, 

Shasta County, California

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2012–1173

Upper Clear Creek Watershed Aquatic 

Chemistry and Biota Surveys, 2004–5, 

Whiskeytown National Recreation Area, 

Shasta County, California

By Marissa L. Wulff, Jason T. May, and Larry R. Brown

Prepared in cooperation with National Park Service, 

Whiskeytown National Recreation Area

Open-File Report 2012–1173

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2012

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Suggested citation:

Wulff, M.L., May, J.T., and Brown, L.R., 2012, Upper Clear Creek watershed aquatic chemistry and biota surveys, 

2004–5, Whiskeytown National Recreation Area, Shasta County, California: U.S. Geological Survey Open-File Report 

2012–1173, 8 p.
iii

Contents

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

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

Study Area..............................................................................................................................................1

Methods...........................................................................................................................................................2

Water Samples......................................................................................................................................2

Bed Sediment for Chemical Analyses...............................................................................................3

Algal Assemblage Samples ................................................................................................................3

Benthic Macroinvertebrate Assemblage Samples.........................................................................3

Fish and Amphibian Samples..............................................................................................................4

Stream Habitat Characterization........................................................................................................4

Results and Discussion.................................................................................................................................5

References Cited............................................................................................................................................6

Tables .............................................................................................................................................................8

Figures

1. Map of location of survey sites within Whiskeytown National Recreation Area,

Shasta County, California .................................................................. 2

Tables

1. Sites sampled during collection of biological inventory for Whiskeytown

National Recreation Area, Shasta County, California, 2004–5, including site code,

latitude and longitude, official U.S. Geological Survey (USGS) site name, and

USGS station ID.............................................................................. 8

2. Major ions and water-quality measurements, including pH and specific

conductance, analyzed by the U.S. Geological Survey National Water Quality

Laboratory, schedule 1210, for Whiskeytown National Recreation Area, Shasta

County, California, 2004–5 .................................................................. 8

3. Major ions and water-quality measurements, including pH and specific

conductance, analyzed by the University of Montana Biogeochemistry

Laboratory for water samples from the Whiskeytown National Recreation Area,

Shasta County, California, 2005 ............................................................ 8

4. Trace Metals in filtered water analyzed by USGS National Water-Quality

Laboratory, schedule 2710, for the Whiskeytown National Recreation Area,

Shasta County, California, 2004–5 ......................................................... 8

5. Trace metals in water samples from Whiskeytown National Recreation Area,

Shasta County, California, analyzed by the University of Montana

Biogeochemistry Laboratory, 2005 ...................................................... 8
iv

6. Nutrients in surface-water samples from the Whiskeytown National Recreation

Area, Shasta County, California, analyzed by the U.S. Geological Survey National

Water-Quality Laboratory, schedule 2711, 2004–5 ....................................... 8

7 Major and trace inorganic elementsin bed-sediment samples from Whiskeytown

National Recreation Area, Shasta County, California, analyzed by the University

of Montana Environmental Biogeochemistry Laboratory, 2004–5 ..................... 8

8. Count of diatom valves by taxa from samples taken at sites in the Whiskeytown

National Recreation Area, California, 2004–5. A total of 600 diatom valves (300

diatom frustules or cells) were enumerated and identified at 1000X magnification

under a microscope ........................................................................ 8

9. Genera of soft algae, and abundance of live and dead diatoms, for samples?

collected from sites in the Whiskeytown Recreation Area, Shasta County,

California, 2004–5 ........................................................................... 8

10. Average ash-free dry mass, total chlorophyll-a, and total pheophytin for samples

collected from the Whiskeytown National Recreation Area, Shasta County,

California, 2004 and 2005 .................................................................. 8

11. Taxa list, following the scientific hierarchy of Ode (2003), for macroinvertebrates

collected from stream sites in Whiskeytown National Recreation Area, Shasta

County, California, 2004–5 .................................................................. 8

12. Selected macroinvertebrate metrics from the Northern California IBI, by Rehn

and others (2005), for macroinvertebrate samples collected from stream sites in

the Whiskeytown Recreation Area, Shasta County, California, 2004–5............... 8

13. Proportional abundance of macroinvertebrates in targeted riffle samples

collected from the Whiskeytown National Recreation Area, Shasta County,

California, 2004–5 ........................................................................... 8

14. Proportional abundance of macroinvertebrates in reach-wide samples collected

from the Whiskeytown National Recreation Area, Shasta County, California, 2004–5 8

16. Field measurements for fish and amphibians captured at sites in Whiskeytown

National Recreation Area, Shasta Country, California, during fall, 2004 and 2005... 8

17. Summary of length and weight data for fish and salamanders captured at sites

in Whiskeytown National Recreation Area, Shasta County, California, during fall,

2004 and 2005................................................................................. 8

18. Sample-reach lengths, elevations, and selected habitat characteristics for sites

sampled in Whiskeytown National Recreation Area, Shasta Country, California,

during fall, 2004–5 ........................................................................... 8

19. Substrate-size characterization summarized by site for the Whiskeytown

National Recreation Area, Shasta Country, California, 2004–5 ........................ 8

Tables—Continued
v

Conversion Factors

SI to Inch/Pound

Multiply By To obtain

Length

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

Area

square meter (m2) 0.0002471 acre 

Flow rate

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

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

kilogram (kg) 2.205 pound avoirdupois (lb)

Volume

mililiter (mL) 0.03382 ounce, fluid (fl. oz)

mililiter (mL) 0.002113 pint (pt)

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

°F=(1.8×°C)+32

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

°C=(°F-32)/1.8

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 

25°C).

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

or micrograms per liter (μg/L).

Abbreviations

CSBP California Bioassessment Procedure

DFG-ABL California Department of Fish and Game Aquatic Biological Assessment Laboratory

EPA Environmental Protection Agency

IBI Index of biotic integrity

NPS National Park Service

QA/QC Quality assurance/ quality control

USGS U.S. Geological Survey

WHIS Whiskeytown National Recreation Area
vi

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Abstract

The U.S. Geological Survey, in cooperation with the 

National Park Service and Whiskeytown National Recreation 

Area, performed a comprehensive aquatic biota survey of 

the upper Clear Creek watershed, Shasta County, California, 

during 2004-5. Data collected in this study can provide 

resource managers with information regarding aquatic 

resources, watershed degradation, and regional biodiversity 

within Whiskeytown National Recreation Area. Surveys of 

water chemistry, bed-sediment chemistry, algae assemblages, 

benthic macroinvertebrate assemblages, aquatic vertebrate 

assemblages, in-stream habitat characteristics, and sediment 

heterogeneity were conducted at 17 stream sites during 

both 2004 and 2005, with an additional 4 sites surveyed in 

2005. A total of 67 bed-sediment samples were analyzed 

for major and trace inorganic element concentrations. 

Forty-six water samples were analyzed for trace metals and 

nutrients. A total of 224 taxa of invertebrates were collected 

during these surveys. Eleven fish species, seven of which 

were native, and two species of larval amphibians, were 

collected. A total of 24 genera of soft algae and 159 taxa of 

diatoms were identified. To date, this survey represents the 

most comprehensive inventory of aquatic resources within 

Whiskeytown National Recreation Area, and this information 

can serve as a baseline for future monitoring efforts and to 

inform management decisions.

Introduction

The purpose of this report is to document the results of 

a biotic and abiotic inventory of the assemblages of resident 

aquatic biota, instream habitat, and water-quality conditions 

in the streams of the upper Clear Creek watershed, Shasta 

County, California (fig. 1). The primary objective of the study 

was to document the aquatic biodiversity supported by the 

streams in the area so that local resource managers can make 

informed decisions regarding aquatic resources. 

Study Area

The study area is located in northwestern California 

in the upper Clear Creek watershed, primarily within the 

Whiskeytown National Recreation Area (WHIS; fig. 1). 

The watershed extends across many private and public 

lands, including National Park Service, Bureau of Land 

Management, and U.S. Forest Service lands. 

Whiskeytown National Recreation Area is located at the 

convergence of three physiographic provinces: the Cascade 

Range, the Coast Range, and the Sacramento Valley. The 

area has a Mediterranean climate characterized by hot, dry 

summers and cool winters with moderate rainfall. Mean 

annual rainfall in the area is approximately 1,500 millimeters 

(mm). The study area lies within the Klamath-Siskiyou 

ecoregion, which is an area of significant biodiversity, 

especially for terrestrial plants (DellaSala and others, 

1999). In the context of fish zoogeography, it lies within the 

Central Valley sub-province of the larger Sacramento-San 

Joaquin Province. The Central Valley fish fauna includes 

28 native species, many of them endemic to California, and 

40 non-native species (Moyle, 2002). The region’s moderately 

rich herptofauna of 38 species is attributed to the overlap 

between northern and southern taxa and the presence of 

appropriate, complex habitat (Bury and Pearl, 1999). 

 There is a long history of human disturbance in the area. 

The Clear Creek watershed, historically, was the scene of 

extensive mining operations and timber harvests, primarily in 

the mid to late 1800s. Mining activities left numerous dredge 

tailing piles, pits, tunnels, roads, and acid mine drainage. 

Runoff from abandoned mine lands has resulted in elevated 

levels of metals in the stream sediments (Moore, 2002). 

Upper Clear Creek Watershed Aquatic Chemistry and 

Biota Surveys, 2004–5, Whiskeytown National Recreation 

Area, Shasta County, California

By Marissa L. Wulff, Jason T. May, and Larry R. Brown
2 Upper Clear Creek Watershed Aquatic Chemistry and Biota Surveys, 2004-5, Whiskeytown National Recreation Area, California

Methods

Seventeen sites were sampled during the fall (September) 

of 2004. In fall of 2005, the same 17 sites were sampled, as 

well as 4 additional sites (table 1; fig. 1). Sampled reaches 

on the mainstem of Clear Creek were 400 meters (m) long, 

whereas sampled reaches on the smaller tributary streams were 

100-150 m long, depending on channel width. Reach length 

was roughly 20 times the mean wetted channel width.

Water Samples

Water samples were collected by using a mid-stream grab 

method. One replicate sample and one equipment blank were 

collected during each year of the study period. Equipment 

blanks were collected according to U.S. Geological Survey’s 

(USGS) protocol as described in Wilde et al. (1999). Blank 

samples were collected in order to identify potential sources 

of sample contamination during collection and processing. 

Paige-Boulder Creek

Grizzly Gulch

Willow Creek

California

Study

Area

Whiskeytown

 Lake

122°42' 122°39' 122°36' 122°33'

40°

33'

40°

36'

40°

39'

40°

42'

0 1 2 Miles

0 1 2 Kilometers

Whiskeytown National

Recreation Area

BRAN1

BRAN2

PGBCR1

WKCR1

BOCR1

BOCR2

CYCR1

CLCR3

CYCR3

WLCR2

MLCR

CARR GZGL

CLN1

CLN2 SCRP

RTGL CLCR4

FRGL

Clear Creek

Clear Creek

Crystal Creek

Whiskey Creek

Cline Gulch

Brandy Creek

Boulder Creek

Mill Creek

French Gulch

CLCR1

CLCR2

Figure 1. Location of survey sites within Whiskeytown National Recreation Area, Shasta 

County, California.
Methods 3

Samples were analyzed for nutrients, major ions, and trace 

metals at the USGS National Water-Quality Laboratory 

in Denver, Colorado. Nutrients were determined from 

0.45-micrometer (μm) filtered and unfiltered samples by 

using methods of Patton and Kryskalla (2003) and Fishman 

(1993). Major ions were determined from filtered water 

samples by using the methods of Hoffman and others (1996), 

Garbarino and Struzeski (1998), and Fishman and Friedman 

(1989). Trace metals were also determined from filtered 

samples by using the methods of Garbarino and others (2006), 

Garbarino (1999), and Fishman and Friedman (1989). Selected 

samples were analyzed for major ions and trace metals at the 

University of Montana’s Environmental Biogeochemistry 

Laboratory. Methods of analysis were Environmental 

Protection Agency (EPA) 300.0 (U.S. Environmental 

Protection Agency, 1993) and EPA 6020 (U.S. Environmental 

Protection Agency, 1994), which were similar to those used at 

the USGS National Water-Quality Laboratory. 

Bed Sediment for Chemical Analyses

Bed-sediment samples were collected for metals 

analysis by using methods described by Moore (2002). This 

method uses a partial acid digestion to estimate the biological 

availability of metals in sediments. Generally, one composite 

sample was collected per site. At selected sites, composite 

samples were collected in triplicate to assess the variability of 

chemical concentrations in bed sediments. 

Samples of fine-grain sediments were collected by 

using a plastic spoon and were sieved with a 63-μm mesh 

nylon-sieve cloth directly into a sample jar. A composite 

sample consisted of sediment from 5 to 10 locations within the 

study reach. Samples were placed on dry ice and frozen prior 

to shipment to the Murdock Environmental Geochemistry 

Laboratory at the University of Montana for chemical 

analyses. Sample collection and processing equipment 

were cleaned between each sampling site by using methods 

described by Shelton and Capel (1994). 

Algal Assemblage Samples

Algal sampling, including quality assurance and quality 

control (QA/QC) procedures, was conducted according to 

standard USGS protocols (Moulton and others, 2002) as 

applied by Brown and others (2008). At each site, from three 

to five rocks at each of five locations within the study reach 

were collected and the benthic algae were removed with a 

stiff brush. All benthic algae were combined into a single 

composite sample. Sample areas were measured by cutting 

an aluminum foil template to the size of each brushed area. 

The areas of the templates were determined in the laboratory 

by using a digitizing tablet and then were summed for each 

site to provide the total area sampled. Triplicate 5-milliter 

(mL) subsamples were taken from the composite sample for 

determination of chlorophyll-a concentrations. Triplicate 5-mL 

subsamples were also taken from the composite sample for 

determination of ash-free-dry mass. Each 5-mL subsample 

was filtered onto a 0.47-mm glass fiber filter and then 

macroinvertebrates, detritus, and large substrate particles were 

removed with forceps. The filter was then folded into quarters, 

wrapped in foil, placed in a labeled plastic bag, and frozen on 

dry ice. Samples were kept frozen in a freezer until analyzed 

(Wetzel and Likens, 1978). The remaining portion of the 

composite sample was used for identification and enumeration 

of algae taxa. Chlorophyll-a analysis, ash-free-dry mass 

determination, identification, and enumeration of algae were 

completed at Portland State University, Oregon, under the 

direction of Dr. Yangdong Pan.

Soft-body algae (live non-diatom algae) were identified 

and enumerated in a Palmer counting chamber at 400X 

magnification by using a microscope. A total of 300 algal 

counting units (live soft-body algae and diatoms) were 

identified and enumerated. For colonial algae, each colony 

was counted as one algal unit. For thin filamentous blue‐green 

algae in which cross-walls are often difficult to detect, a 

10-μm length of trichomes was counted as one algal unit. 

Counting units were then converted to cell densities. 

For diatom analysis, samples were processed with 

concentrated sulfuric acid and potassium dichromate (Patrick 

and Reimer, 1966). After numerous rinses with distilled water, 

cleaned diatom frustules were placed in mounting medium 

to make permanent slides. A total of 600 diatom valves 

(300 diatom frustules or cells) were enumerated and identified 

at 1000X magnification under a microscope. Diatoms were 

identified to the species level, whenever possible, by using 

current taxonomic references. Laboratory processing for all 

algal samples adhered to QA/QC methods as described in Pan 

and Stevenson (2001).

Benthic Macroinvertebrate 

Assemblage Samples

Benthic macroinvertebrates were collected by using 

two methods. We collected a targeted riffle sample, or a 

sample from a relatively shallow and coarse-bedded area 

over which water flows at a relatively higher velocity and 

greater turbulence than elsewhere in the stream, by using 

methods similar to those of the California State Bioassessment 

Procedure (CSBP) described by Harrington (1996). The 

standard CSBP includes collection of three replicate kick-net 

samples (D-frame net with 500-micron mesh) from each 

of three separate riffles. Also, a reach-wide quantitative 

multihabitat sample was collected by using methods similar to 

the U.S. Environmental Protection Agency’s Environmental 

Monitoring and Assessment Program (Peck and others, 

2006). Samples were sieved through a 0.5 mm sieve and then 

preserved with 95 percent ethanol solution. Both reach-wide 

and targeted riffle sampling were done during this survey to 

help the National Park Service (NPS) decide which method 

would be best for their agency to use for future monitoring. 
4 Upper Clear Creek Watershed Aquatic Chemistry and Biota Surveys, 2004-5, Whiskeytown National Recreation Area, California

The NPS also wanted to build their inventory of species 

presence as much as possible, which is an area where 

reach-wide sampling can be very useful.

Samples were analyzed at the California Department of 

Fish and Game Aquatic Biological Assessment Laboratory 

(DFG-ABL) during 2004 and at Rhithron Associates, Inc., 

during 2005. The DFG-ABL adhered to QA/QC procedures 

detailed in Harrington (2003). Rhithron Associates, Inc., 

adhered to QA/QC procedures detailed in Rhithron (2002). 

Organisms were classified to the lowest practical taxon, which 

was usually genus for well-known groups or some higher 

taxonomic level for some of the lesser known or difficult to 

identify taxa. Macroinvertebrates were also summarized as 

percentage abundance at the genus level or higher taxonomic 

level for some of the lesser known or difficult to identify 

taxa. The percentage-abundance format was used because 

it standardizes counts to a common scale (percentage), 

provides an easily understood measure of relative abundance 

for comparison within and between stations, and is a 

format commonly used for statistical analyses. Invertebrate 

species were given a tolerance value to pollution based on 

a 0 to 10 scale, where 0 is the most sensitive to pollution 

(Ode, 2003).

Invertebrate sample metrics that are part of the northern 

California index of biotic integrity (IBI) were generated, and 

IBI scores were calculated for both sample types by methods 

described in Rehn and others (2005). These IBI scores are 

intended to give a relative assessment of the stream condition 

on the basis of a regional indicator.

Fish and Amphibian Samples

Sampling procedures and QA/QC methods were followed 

per Walsh and Meador (1998). Fish and larval amphibians 

were collected with backpack electrofishing by using a 

Smith‐Root Type XII electrofisher. All sites were sampled with 

at least a single pass of the shocker. Some sites were sampled 

with three passes, as part of an associated study. Total length 

in millimeters was measured for fish and larvae of tailed frogs 

(Ascaphus truei). Snout-vent length was measured (in mm) 

on Pacific giant salamander larvae (Dicamptodon tenebrosus). 

Adult amphibians were noted visually but were not collected. 

A minimum of the first 30 individuals of each species were 

measured to the nearest 0.1 gram (g) on an electronic balance, 

with the exception of very small individuals that were 

sometimes weighed in batches. Length-weight relationships 

were derived for each site so that weights could be assigned to 

unweighed individuals. The two Clear Creek sites downstream 

from the dam (CLCR1, CLCR2) were sampled for fish 

and amphibians by visual observation while snorkeling. 

Electrofishing was not done on these sites because of high or 

deep flows and permitting issues for state and federally listed 

species. Snorkel observations began at the downstream end of 

the reach and were completed in a single upstream pass. Fish 

sampling was conducted in accordance with USGS protocols 

for sample collection (Moulton and others, 2002) and QA/QC 

(Walsh and Meador, 1998). Snorkeling is an accepted method 

in fisheries biology but can underrepresent cryptic species, 

such as sculpins (Schreck and Moyle, 1990). In this study, a 

snorkeler near each bank proceeded upstream only counting 

fish as they moved downstream past the snorkelers. Snorkelers 

communicated with each other to prevent double counts. Both 

snorkelers (LRB and JTM) were experienced and familiar with 

all of the species observed in this study. In addition, LRB is 

the designated USGS fish taxonomic specialist for California, 

as outlined in Walsh and Meador (1998). Fish and amphibians 

were identified to species level and counted. In 2004, fish 

lengths were estimated visually and recorded. Snorkel 

surveying in 2005 collected counts of the total number of each 

species observed. 

Stream Habitat Characterization

In-stream habitat measurements were taken at each 

site according to the National Water-Quality Assessment 

Program stream habitat protocol (Fitzpatrick and others, 

1998). The stream sampling reach length was set at 20 times 

the wetted-channel width. Habitat variables were measured 

for 11 transects separated at equally spaced intervals within 

each reach. Stream width (wetted channel) was measured 

directly from a transect tape, and open canopy was measured 

at midstream with a clinometer. A densiometer was used to 

calculate canopy cover. Percentage area of habitat features, 

such as woody debris and overhanging vegetation, were 

visually estimated within a section of the stream extending 

2-m upstream and downstream of the transect tape. Depth, 

velocity, and substrate were measured at a minimum of three 

points on each transect. Depth was measured with a wading 

rod, and velocity with an electronic meter (Marsh-McBirney) 

at 60 percent of total depth as measured from the bottom. 

The dominant substrate was classified at each transect point. 

Habitat variables were computed as the geometric mean of the 

11 transect values or the geometric mean of the 33, or more, 

point values. 

In addition, a more detailed characterization of sediment 

size classes was conducted at each site. Substrate was 

clasifyed by size ranging from fine sand (< 2 mm) to large 

boulder (>512 mm) and bedrock. A minimum of 20 substrate 

size measurements were collected for each transect, resulting 

in approximately 200 individual substrate size measurements 

for each survey site. The substrate size data were collected to 

allow assessment of changes in fine sediment resulting from 

future runoff events. 
Results and Discussion 5

Results and Discussion

Metal and nutrient results for water samples are 

presented in tables 2 through 6. The highest levels of copper, 

10.8 micrograms per liter (μg/L), and zinc, 51.9 μg/L, were 

both found in Willow Creek (WLCR2). Scorpion Creek 

(SCRP) had the highest level of selenium at 0.98 μg/L and 

arsenic at 25.9 μg/L, whereas Clear Creek (CLCR1) had 

the highest level of nickel at 2.54 μg/L. The range of results 

across all sites for metals of ecological importance is reported 

alphabetically as follows: arsenic, 25.9 – less than 0.1 μg/L; 

copper, 10.8 – lass than 0.1μ g/L; nickel, 2.54 – less than 

0.06 μg/L; selenium, 0.98 – less than 0.01 μg/L; and zinc, 

51.9 –  less than 0.6 μg/L.

Results for bed-sediment samples are presented in 

table 7. Of all the sites sampled, Scorpion Creek (SCRP) 

had the highest concentrations of arsenic,440.2 milligrams 

per kilogram (mg/kg); mercury, 2.8 mg/kg; and lead, 

133.0 mg/kg. Willow Creek (WLCR2) had the highest levels 

of both copper, 1,190.0 mg/kg, and zinc, 1,224.0 mg/kg. 

Whiskey Creek (WKCR1) had the highest concentration of 

cadmium, 11.0 mg/kg, and Clear Creek (CLCR1) had the 

highest level of nickel, 91.1 mg/kg. 

Forty-eight genera of diatoms were identified across all 

sites during the two sample years (table 8). Also, 10 genera 

of blue-green algae, 12 genera of green algae, 1 genus of 

red algae, and 1 genus of yellow-green algae were identified 

(table 9). The blue-green algae, Anabaena and Oscillatoria,

were the most common genera found in the samples across 

all sites. Brandy Creek (BRAN1) had the greatest number 

of soft algae, most of which were in the genus Oscillatoria. 

Clear Creek (CLCR1) and Cline Gulch (CLN2) also had high 

numbers of algae compared to the rest of the sites. Ash free 

dry mass, uncorrected chlorophyll-a, corrected chlorophyll-a 

(concentration of pheophytin subtracted), and total pheophytin 

for the three subsamples from each site are presented for both 

years (table 10). Some chlorophyll-a values could not be 

corrected for the contribution of pheophytin because negative 

values were obtained for the concentration of pheophytin in 

some samples. Negative values can be caused by interference 

from similar compounds in the sample. Although this was 

not the case for all of the samples, uncorrected chlorophyllvalues should be used when comparing data among sites or 

between years.

Benthic macroinvertebrate taxa collected at all 

sites from both years are presented in table 11. Benthic 

macroinvertebrate metrics that are part of the Northern 

California IBI (Rehn and others, 2005) and IBI scores are 

presented in table 12. Metric results of individual samples for 

major taxonomic groups for both reach wide and targeted riffle 

samples were averaged for all sites and are presented here as 

mean (M), standard deviation (SD), and range (R: max- min): 

Coleoptera taxa (M:5, SD:2, R:11), Diptera taxa (M:20, 

SD:4, R:19), percentage intolerant (M:23, SD:11, R: 45), 

percentage non-gastropoda scrapers (M:16, SD:12, R:64), 

percentage predator taxa (M:14, SD:7, R:32), percentage 

shredder taxa (M:10, SD:4, R:20), percentage non-insecta taxa 

(M:14, SD:5, R:24), northern California IBI scores for targeted 

riffle samples (M:68, SD:11, R:36), northern California IBI 

scores for reach-wide samples (M:68, SD:11, R:58), and the 

number of individuals counted per sample (M:542, SD:47, 

R:242). Sixty-eight percent of Northern California IBI scores 

for WHIS scored in the ‘good’ and above range. Willow Creek 

(WLCR2) had consistently low IBI scores. Boulder Creek 

(BOCR1), Brandy Creek (BRAN1), Cline Gulch (CLN1), 

Crystal Creek (CYCR1), Mill Creek (MLCR1), Scorpion 

Creek (SCRP) and Whiskey Creek (WKCR1) had at least 

one score in the “very good” range. Eight out of the nine 

“very good” assessments occurred in 2004. The percentage 

abundance of macroinvertebrate taxa collected during the fall 

of 2004 and 2005 are presented for targeted riffle samples and 

reach-wide samples in tables 13 and 14, respectively.

A total of 11 fish species and 4 species of amphibians 

were collected during the study (table 15). A summary of 

all field measurements, including length and weight of each 

fish and amphibian collected during the study, is presented 

in table 16. Rainbow trout were found in the most samples, 

but riffle sculpin was the most abundant species. Larval 

lampreys were captured but not identified because key 

adult morphological characteristics are required for species 

identification. Of the 11 fish taxa, only 4 were non-native 

species, and of the non-native fish species, only brook trout 

was found in more than one sample. Brook trout accounted 

for less than 1 percent of the total number of fish captured. 

One adult of the non-native bullfrog (Rana catesbeiana) was 

captured at the Whiskey Creek site, which was also the site 

where the non-native green sunfish and largemouth bass were 

collected. Pacific giant salamander larvae were captured at 

almost every site, except in the mainstem of Clear Creek. 

Tailed-frog larvae were only observed at the upper sites on 

Brandy, Boulder, and Crystal Creeks, where riffle sculpin were 

absent. Adult foothill yellow-legged frogs (Rana boylii) were 

observed in Cline Gulch, Grizzly Creek, Scorpion Gulch, Mill 

Creek, Paige-Boulder Creek, and Willow Creek. Total weight 

and length data for commonly captured (found in five or more 

sites) fish and amphibians are presented in table 17. Mean and 

range data for adult tailed frog, tailed frog larvae, bullfrog, 

foothill yellow-legged frog, green sunfish, hardhead, Kokanee 

salmon, largemouth bass, and Pacific lamprey were not 

calculated because they were considered rare in the dataset. 
6 Upper Clear Creek Watershed Aquatic Chemistry and Biota Surveys, 2004-5, Whiskeytown National Recreation Area, California

Habitat characteristics, including reach length, elevation, 

gradient, discharge, percent riffle, mean wetted width, 

mean open canopy, mean riparian shade, mean depth, mean 

water velocity, and dominant substrate, were assessed in 

both years for each site (table 18). Clear Creek was the 

largest, lowest gradient river sampled. Headwater portions 

of Boulder and Crystal Creeks were quite steep (gradient 

greater than10 percent). Clear Creek 1 and 2 are both located 

downstream from the reservoir and are affected by reservoir 

releases. These sites have some of the largest recorded 

flows of all the sites. Substrate size and heterogeneity are 

summarized by site and year in table 19. 

This survey represents the most comprehensive effort to 

date to document and inventory the status of aquatic resources 

within upper Clear Creek and WHIS. This information can 

serve as a baseline for future monitoring efforts and inform 

future management decisions.

References Cited

Brown, L.R., May, J.T., and Hunsaker, C.T., 2008, Species 

composition and habitat associations of benthic algal 

assemblages in headwater streams of the Sierra Nevada, 

California: Western North American Naturalist v. 68, 

p. 194–209.

Bury, R.B., and Pearl, C.A., 1999, Klamath-Siskiyou 

Herpetofauna: Biogeographic Patterns and Conservation 

Strategies: Natural Areas Journal, v. 19, p. 341–350.

DellaSala, D.A., Reid, S.B., Frest, T.J., Strittholt, J.R., and 

Olson, D.M., 1999, A global perspective on the biodiversity 

of the Klamath-Siskiyou ecoregion: Natural Areas Journal, 

v.19, p. 300–319.

Fishman, M.J., ed., 1993, Methods of analysis by the U.S. 

Geological Survey National Water Quality Laboratory– 

Determination of inorganic and organic constituents in 

water and fluvial sediments: U.S. Geological Survey 

Open-File Report 93-125, 217 p.

Fishman, M.J., and Friedman, L.C., 1989, Methods for 

determination of inorganic substances in water and fluvial 

sediments: U.S. Geological Survey Techniques of WaterResources Investigations, book 5, chap. A1, 545 p.

Fitzpatrick, F.A., Waite, I.R., D’Arconte, P.J., Meador, M.R., 

Maupin, M.A., and Gurtz, M.E., 1998, Revised methods for 

characterizing stream habitat in the National Water-Quality 

Assessment Program: Water-Resources Investigations 

Report 98-4052, 77 p.

Garbarino, J.R., 1999, Methods of analysis by the U.S. 

Geological Survey National Water Quality Laboratory– 

Determination of dissolved arsenic, boron, lithium, 

selenium, strontium, thallium, and vanadium using 

inductively coupled plasma-mass spectrometry: U.S. 

Geological Survey Open-File Report 99-093, 31 p.

Garbarino, J.R., Kanagy, L.K., and Cree, M.E., 2006, 

Determination of elements in natural-water, biota, sediment 

and soil samples using collision/reaction cell inductively 

coupled plasma-mass spectrometry: U.S. Geological Survey 

Techniques and Methods, book 5, sec. B, chap.1, 88 p.

Garbarino, J.R., and Struzeski, T.M., 1998, Methods of 

analysis by the U.S. Geological Survey National Water 

Quality Laboratory– Determination of elements in wholewater digests using inductively coupled plasma- optical 

emission spectrometry and inductively coupled plasmamass spectrometry: U.S. Geological Survey Open-File 

Report 98-165, 101 p.

Harrington, J.M., 1996, California stream bioassessment 

procedure: California Department of Fish and Game, Water 

Pollution Control Laboratory, Rancho Cordova, California, 

11 p.

Harrington, J.M., 2003, Quality assurance project plan for 

the California stream bioassessment procedure: California 

Department of Fish and Game, Water Pollution Control 

Laboratory, Rancho Cordova, California, 116 p.

Hoffman, G.L., Fishman, M.J., and Garbarino, J.R., 1996, 

Methods of analysis by the U.S. Geological Survey National 

Water Quality Laboratory– In-bottle acid digestion of 

whole-water samples: U.S. Geological Survey Open-File 

Report 96-225, 28 p.

Meffe, G.K., Nielsen, L.A., Knight, R.L., and Schenborn, 

D.A., 2002, Ecosystem Management: Adaptive, community 

based conservation: Island Press, Washington DC, 336 p.

Moore, J.C., 2002, Trace metals in sediments from mineimpacted rivers: Clear Creek, California: Final Contract 

Report 02WRAG001, University of Montana, 133 p.

Moulton, S.R.II, Kennen, J.G., Goldstein, R.M., and 

Hambrook, J.A., 2002, Revised protocols for sampling 

algal, invertebrate, and fish communities as part of National 

Water-Quality Assessment Program: U.S. Geological 

Survey, Open File Report 02-150, 87 p.

Moyle, P.B., 2002, Inland Fishes of California: University of 

California Press, Berkeley, 517 p.

Moyle, P.M., and Moyle, P.R., 1995, Endangered fishes and 

economics: intergenerational obligations: Environmental 

Biology of Fishes, v. 43, p. 29–37. 
References Cited 7

Ode, P., 2003, List of Californian Macroinvertebrate Taxa 

and Standard Taxonomic Effort: Aquatic Bioassessment 

Laboratory, Rancho Cordova, California, 45 p. 

Pan, Y., and Stevenson, R.J., 2001, QAPP for Evaluation of 

Periphyton-Environmental Gradients in Western Streams: 

Portland State University, Portland, Oregon, 8 p.

Patrick, R., and Reimer, C.W., 1966, The diatoms of the 

United States: Monograph 13, v. 1, Academy of Natural 

Sciences of Philadelphia, 688 p.

Patton, C.J., Kryskalla, J.R., 2003, Methods of Analysis 

by the U.S. Geological Survey National Water Quality 

Laboratory: Evaluation of Alkaline Persulfate Digestion 

as an Alternative to Kjeldahl Digestion for Determination 

of Total and Dissolved Nitrogen and Phosphorus in Water, 

Water-Resources Investigations Report 03-4174, 33p.

Peck, D.V., Herlihy, A.T., Hill, B.H., Hughes, R.M., 

Kaufmann, P.R., Klemm, D.J., Lazorchak, J.M., 

McCormick, F.H., Peterson, S.A., Ringold, P.L., Magee, T., 

and Cappaert, M.R., 2006, Environmental Monitoring and 

Assessment Program – Surface Waters Western Pilot Study: 

Field Operations Manual for Wadeable Streams: EPA 620/

R-06/003. U.S. Environmental Protection Agency Office of 

Research and Development, Washington, D.C, 332 p.

Rehn, A.C., Ode, P.R., and May, J.T., 2005, Development of 

a Benthic Index of Biotic Integrity (B-IBI) for Wadeable 

Streams in Northern Coastal California and its Application 

to Regional 305(b) Assessment. California Surface Water 

Ambient Monitoring Program, Sacramento, CA, 40 p. 

Available at http://www.swrcb.ca.gov/water_issues/

programs/swamp/reports.shtml)

Rhithron Associates, Inc., 2002, Statement of Qualifications, 

Missoula, MT, 30 p. 

Schreck, C.B., and Moyle, P.B., eds, 1990, Methods for Fish 

Biology: American Fisheries Society, Bethesda, 704 p.

Shelton, L.R., and Capel, P.D., 1994, Guidelines for Collecting 

and Processing Samples of Stream Bed Sediment for 

Analysis of Trace Elements and Organic Contaminants 

for the National Water-Quality Assessment Program: U.S. 

Geological Survey Open-File Report 94-458, 20 p.

U.S. Environmental Protection Agency, 1993, Method 300.0: 

Methods for the Determination of Inorganic Substances in 

Environmental Samples (EPA/600/R-93/100). http://www.

epa.gov/nscep/index.html.

U.S. Environmental Protection Agency, 1994, Method 6020: 

Inductively Coupled Plasma Mass Spectrometry. http://

www.epa.gov/region8/water/biosolids/analyticalmethods.

html.

U.S. Geological Survey, 2006, Collection of water 

samples (ver. 2.0): U.S. Geological Survey Techniques 

of Water-Resources Investigations, book 9, chap. A4, 

September 2006, accessed [September 15, 2012], at http://

pubs.water.usgs.gov/twri9A4/.

Walsh, S.J., and Meador, M.R., 1998, Guidelines for quality 

assurance and quality control of fish taxonomic data 

collected as part of the National Water Quality Assessment 

Program: U.S. Geological Survey Water Resources 

Investigations Report 98-4239, 39 p. 

Wetzel, R.G., and Likens, G.E., 1978, Limnological 

Analyses: W.B. Saunders Company, Philadelphia, 429 p.
8 Upper Clear Creek Watershed Aquatic Chemistry and Biota Surveys, 2004-5, Whiskeytown National Recreation Area, California

Table 1. Sites sampled during collection of biological inventory for Whiskeytown National Recreation Area, Shasta County, California, 

2004–5, including site code, latitude and longitude, official U.S. Geological Survey (USGS) site name, and USGS station ID.

Table 2. Major ions and water-quality measurements, including pH and specific conductance, analyzed by the U.S. Geological Survey 

National Water Quality Laboratory, schedule 1210, for Whiskeytown National Recreation Area, Shasta County, California, 2004–5.

Table 3. Major ions and water-quality measurements, including pH and specific conductance, analyzed by the University of Montana 

Biogeochemistry Laboratory for water samples from the Whiskeytown National Recreation Area, Shasta County, California, 2005.

Table 4. Trace Metals in filtered water analyzed by USGS National Water-Quality Laboratory, schedule 2710, for the Whiskeytown 

National Recreation Area, Shasta County, California, 2004–5.

Table 5. Trace metals in water samples from Whiskeytown National Recreation Area, Shasta County, California, analyzed by the 

University of Montana Biogeochemistry Laboratory, 2005.

Table 6. Nutrients in surface-water samples from the Whiskeytown National Recreation Area, Shasta County, California, analyzed by 

the U.S. Geological Survey National Water-Quality Laboratory, schedule 2711, 2004–5.

Table 7. Major and trace inorganic elementsin bed-sediment samples from Whiskeytown National Recreation Area, Shasta County, 

California, analyzed by the University of Montana Environmental Biogeochemistry Laboratory, 2004–5

Table 8. Count of diatom valves by taxa from samples taken at sites in the Whiskeytown National Recreation Area, California, 2004–5. 

A total of 600 diatom valves (300 diatom frustules or cells) were enumerated and identified at 1000X magnification under a microscope.

Table 9. Genera of soft algae, and abundance of live and dead diatoms, for samples? collected from sites in the Whiskeytown 

Recreation Area, Shasta County, California, 2004–5.

Table 10. Average ash-free dry mass, total chlorophyll-a, and total pheophytin for samples collected from the Whiskeytown National 

Recreation Area, Shasta County, California, 2004 and 2005.

Table 11. Taxa list, following the scientific hierarchy of Ode (2003), for macroinvertebrates collected from stream sites in Whiskeytown 

National Recreation Area, Shasta County, California, 2004–5.

Table 12. Selected macroinvertebrate metrics from the Northern California IBI, by Rehn and others (2005), for macroinvertebrate 

samples collected from stream sites in the Whiskeytown Recreation Area, Shasta County, California, 2004–5.

Table 13. Proportional abundance of macroinvertebrates in targeted riffle samples collected from the Whiskeytown National 

Recreation Area, Shasta County, California, 2004–5.

Table 14. Proportional abundance of macroinvertebrates in reach-wide samples collected from the Whiskeytown National Recreation 

Area, Shasta County, California, 2004–5.

Table 16. Field measurements for fish and amphibians captured at sites in Whiskeytown National Recreation Area, Shasta Country, 

California, during fall, 2004 and 2005.

Table 17. Summary of length and weight data for fish and salamanders captured at sites in Whiskeytown National Recreation Area, 

Shasta County, California, during fall, 2004 and 2005.

Table 18. Sample-reach lengths, elevations, and selected habitat characteristics for sites sampled in Whiskeytown National 

Recreation Area, Shasta Country, California, during fall, 2004–5.

Table 19. Substrate-size characterization summarized by site for the Whiskeytown National Recreation Area, Shasta Country, 

California, 2004–5.

Tables

These Whiskeytown National Recreation Area (WHIS) Inventory tables are available in a Microsoft© workbook for 

download at http://pubs.usgs.gov/ofr/2012/1173.
Publishing support provided by the U.S. Geological Survey Science

Publishing Network, Sacramento and TacomaPublishing Service Centers

For more information concerning the research in this report, contact the

 Director, California Water Science Center

U.S. Geological Survey

6000 J Street, Placer Hall

Sacramento, California 95819

http://ca.water.usgs.gov
Printed on recycled paper

Wulff and others— Upper Clear Creek Watershed Aquatic Chemistry and Biota Surveys, 2004-5, Whiskeytown National Recreation Area, California—Open-File Report 2012–1173