Periphyton and Macroinvertebrate 

Communities at Five Sites in the 

San Joaquin River Basin, California, 

during June and September, 2001

By Larry R. Brown and Jason T. May

In cooperation with the Central Valley Regional Water Quality Control Board

Scientific Investigations Report 2004-5098

U.S. Department of the Interior

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

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia: 2004

For sale by U.S. Geological Survey, Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

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Telephone: 1-888-ASK-USGS

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Any use of trade, product, or firm names in this publication 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:

Brown, L.R., and May, J.T., 2004, Periphyton and macroinvertebrate communities at five sites in the San Joaquin River 

Basin, California, during June and September, 2001: U.S. Geological Survey Scientific Investigations Report 2004-

5098, 43 p.
iii

Figures

Figure 1. Locations of sampling sites and drainage basins in the San Joaquin River Basin, 

California ....................................................................................... 3

Figure 2. Graph showing discharge records from March through April for sampling sites 

in the San Joaquin River Basin, California ................................................ 6

Figure 3. Cluster dendrogram showing the results of a group average linkage cluster 

analysis of periphyton presence–absence data .......................................... 7

Figure 4. Graph showing plots of site scores and taxa scores on the first two axes of a 

detrended correspondence analysis of periphyton abundance data .................. 8

Figure 5. Graph showing plots of periphyton detrended correspondence analysis 

axis 1 site scores with selected environmental variables .............................. 10

Figure 6. Cluster dendrogram showing the results of a group average linkage cluster 

analysis of macroinvertebrate presence–absence data ................................. 11

Figure 7. Graph showing plots of site scores and taxa scores on the first two axes of a 

detrended correspondence analysis of macroinvertebrate abundance data ......... 12

Figure 8. Graph showing plots of macroinvertebrate detrended correspondence 

analysis axis 1 site scores with selected environmental variables ..................... 13

Contents

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

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

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

Study Area .......................................................................................... 2

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

Sampling Design .................................................................................... 2

Periphyton .......................................................................................... 2

Benthic Macroinvertebrates ..................................................................... 5

Data Analysis ....................................................................................... 5

Results and Discussion ................................................................................. 7

Environmental Variables ........................................................................... 7

Periphyton .......................................................................................... 7

Macroinvertebrates ................................................................................. 9

Summary and Conclusion .............................................................................. 14

References ................................................................................................ 14
iv

Tables

Table 1. Sites sampled in 2001 in the San Joaquin River Basin, California ..................... 4

Table 2. Physical habitat variables measured in June and September 2001 at five sites in the 

San Joaquin River Basin, California ......................................................... 4

Table 3. Values for environmental variables measured during June and September 2001 

at five sites in the San Joaquin River Basin, California ................................. 16

Table 4. Discharge statistics for the periods from March 1, 2001 to the date of the 

June 2001 sample (spring) and from the June sample to the September 2001 

sample (summer) .............................................................................. 9

Table 5. Periphyton taxa collected from each of five sites in June and September 2001 in the 

San Joaquin River Basin, California ......................................................... 18

Table 6. Periphyton taxa from richest targeted habitat samples collected from snag habitat 

at five sites in the San Joaquin River Basin, California ................................. 28

Table 7. Macroinvertebrate taxa collected from each of five sites in June and 

September 2001 in the San Joaquin River Basin, California .............................. 34

Table 8. Macroinvertebrate taxa from richest targeted habitat samples collected from 

snag habitat at five sites in the San Joaquin River Basin, California .................. 40

Conversion Factors, Abbreviations, and Acronyms

Multiply By To obtain

centimeter (cm) 0.3937 inch (in.)

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

inch (in.) 2.54 centimeter (cm)

kilometer (km) 0.6214 mile (mi)

liter (L) 1.057 quart (qt)

meter (m) 3.281 foot (ft) 

mile (mi) 1.609 kilometer (km)

millimeter (mm) 0.03937 inch (in.)

square centimeter (cm2) 0.1550 square inch (in2)

square meter (m2) 0.0002471 acre 

square mile (mi2) 2.590 square kilometer (km2) 

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

 °F=(1.8×°C)+32

Abbreviations and Acronyms

CVRWQCB Central Valley Regional Water Quality Control Board

dca Detrended Correspondence Analysis

dth Depositional Targeted Habitat

NAWQA National Water Quality Assessment Program

PNAS Philadelphia National Academy of Science

qmh Qualitative Multihabitat

rth Richest Targeted Habitat

tmdl Total Maximum Daily Load

USGS U.S. Geological Survey

μm micrometer
Periphyton and Macroinvertebrate Communities at Five 

Sites in the San Joaquin River Basin, California, during 

June and September, 2001

By: Larry R. Brown and Jason T. May

Abstract

The effects of agriculture, particularly from the use of 

pesticides, on aquatic ecosystems in the San Joaquin River 

Basin concern many aquatic resource managers, water quality 

managers, and water users. A total of five sites were sampled 

once in June 2001 and once in September 2001 to document the periphyton (attached algae) community, the benthic 

macroinvertebrate (insects and non-insects) community, and 

stream habitat conditions. The purposes of the study were to 

document existing conditions and, to the extent possible, relate 

the periphyton and macroinvertebrate community condition to 

environmental conditions.

A total of 161 taxa of algae were collected during the 

study. Samples from the richest targeted habitat, woody debris, 

included 109 taxa. In both the June and September samples, 

greater than 95 percent of the taxa collected were diatoms. 

Cluster analysis and detrended correspondence analysis of 

sample data showed that Orestimba Creek had a very different 

periphyton community than the Merced and Tuolumne Rivers. 

Salt Slough and the San Joaquin River had community compositions that were intermediate between the two extremes. A 

total of 126 taxa of macroinvertebrates were collected during 

the study. Samples from woody debris included 59 taxa. The 

samples included a variety of both insect and non-insect taxa. 

Cluster analysis and detrended correspondence analysis of 

sample data showed that Orestimba Creek was very different from the Merced River and Tuolumne River, similar to 

the results for periphyton. Orestimba Creek was dominated 

by non-insects, while the Merced and Tuolumne Rivers 

were dominated by insects. Salt Slough was more similar to 

Orestimba Creek because of the abundance of non-insects. 

The San Joaquin River was more similar to the Merced and 

Tuolumne Rivers.

There was no evidence of major differences between June 

and September samples for either the periphyton or macroinvertebrate communities. Specific conductance (a surrogate for 

salinity) and several habitat measures were associated with differences in the periphyton and macroinvertebrate communities 

at the five sites. Additional sampling at more sites over a longer period of time will likely be necessary before the effects of 

water quality and habitat conditions on aquatic communities 

are fully understood in the San Joaquin River Basin.

Introduction

Agriculture in California’s San Joaquin Valley is both 

productive and valuable. The availability of water for irrigation, the Mediterranean climate, and the long growing season 

have combined to make the valley one of the most intensively 

farmed and economically important agricultural regions in 

the United States. In 2000, California’s agricultural industry 

produced a gross cash income of 27 billion dollars and supplied more than half of the nation’s fruits, nuts, and vegetables 

(California Department of Food and Agriculture 2001). The 

San Joaquin Valley accounted for most of this production.

This agricultural activity includes widespread and intensive use of various pesticides. The occurrence and concentrations of these compounds and their effects on water quality 

have been a long-standing concern in the region (Domagalski 

and others, 1997; Panshin and others, 1998; Kratzer, 1999; 

Kratzer and others, 2002; Domagalski and Munday, 2003; 

Zamora and others, 2003). The potential toxicity of dissolved 

pesticides to aquatic organisms has been a particular concern 

(Foe and Connor, 1991; Foe, 1995; Kuivila and Foe, 1995). 

Studies addressing the potential toxicity have focused on the 

results of laboratory toxicity tests (Foe and Connor, 1991; 

Foe, 1995; Kuivila and Foe, 1995). Toxicity to the invertebrate 

Ceriodaphnia dubia has often been observed in these studies, 

and the toxicity was linked to several dissolved pesticides. 

However, the effects of dissolved pesticides on the resident 

aquatic communities of affected water bodies have not been 

evaluated in detail.

The Central Valley Regional Water Quality Control 

Board (CVRWQCB) is in the process of formulating and 

applying pesticide total maximum daily loads (TMDLs) in 

various water bodies of the San Joaquin River Basin. As part 

of this process, biological assessments (hereinafter, bioassessments) have been identified as an important tool for assessing 

the success of the TMDLs in protecting or improving beneficial uses of these water bodies. Most existing bioassess-
2 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001

ment procedures have been developed for small wadeable 

streams with riffles. These procedures are difficult to apply in 

most Central Valley streams, which tend to have fine grained 

bottoms and few, if any, riffles. Protocols developed by the 

National Water Quality Assessment Program (NAWQA) for 

bioassessment of macroinvertebrate and algae communities 

(Moulton and others, 2002) have been successfully used by 

U.S. Geological Survey (USGS) personnel in the San Joaquin 

River and its tributaries (Brown and May, 2000a,b; Leland and 

others, 2001). A detailed NAWQA protocol for characterization of stream habitat also has been developed (Fitzpatrick and 

others, 1998).

Purpose and Scope

The purpose of this report is to present the results of 

bioassessments of macroinvertebrate and periphyton communities, using NAWQA protocols, in selected water bodies 

of the San Joaquin River Basin. The results of stream habitat 

assessments conducted in support of the bioassessments are 

also reported. These results will be used to document existing conditions in the selected water bodies. The importance 

of habitat quality and water quality in determining the community structure of the resident macroinvertebrate and algae 

communities also was assessed.

Study Area

The perennial San Joaquin River Basin drains a total area 

of 7,345 mi2. Of this area, 59 percent lies in the Sierra Nevada, 

11 percent in the Coast Ranges, and 30 percent in the San 

Joaquin Valley. The Sierra Nevada and Coast Ranges portions 

of the drainage are predominantly forested land. Virtually all 

irrigated agriculture and most pesticide applications occur in 

the San Joaquin Valley portion of the drainage; thus, this study 

focuses on the San Joaquin Valley portion of the perennial San 

Joaquin River Basin (fig. 1).

The climate in the San Joaquin Valley is arid-to-semiarid, 

characterized by hot, dry summers and cool, wet winters. Most 

precipitation falls during November through April. The average annual precipitation ranges from 13 to 40 cm in the valley 

and increases to amounts ranging from 102 to more than 

228 cm at the higher altitudes in the Sierra Nevada (Gronberg 

and others, 1998; Panshin and others, 1998). Precipitation is 

highly variable from year to year. The year that was sampled 

in this study, 2001, was classified as dry on the basis of a 

water availability index with the categories—wet, above normal, below normal, dry, and critical (California Department of 

Water Resources, 2003). Most of the precipitation in the San 

Joaquin River Basin occurs as snow in the Sierra Nevada.

The surface-water hydrology of the San Joaquin River 

drainage has been substantially altered to store and distribute 

water derived from snowmelt in the Sierra Nevada. Every 

major river in the study area has one or more reservoirs. This 

water is subsequently used for irrigated agriculture and a 

variety of other urban and environmental uses. USGS streamflow records for 1951 to 1995 show 66 percent of the flow of 

the perennial San Joaquin River was contributed by the three 

large eastern tributaries: the Merced River (15 percent), the 

Tuolumne River (30 percent), and the Stanislaus River (21 percent). Bear Creek, Mud and Salt Sloughs, ephemeral streams 

draining the Coast Ranges, drainage canals that flow directly 

to the San Joaquin River and occasionally the upper San 

Joaquin River upstream of Bear Creek, contributed the remaining 34 percent of streamflow.

Methods

Sampling Design

The CVRWQCB helped identify five sites to be 

sampled in the study (table 1, fig. 1). Each site was sampled 

twice, once in June 2001 and once in September 2001. The 

sites were sampled twice to determine if there were any 

major differences in periphyton or benthic macroinvertebrate 

communities related to spring (June) or summer (September) sampling. All sampling activity was conducted within a 

reach of stream defined as 20 times the mean channel width, 

and within the range of 150 m to 1,000 m long. Habitat 

variables were assessed according to Fitzpatrick and others 

(1998) during both visits. The habitat variables and methods 

of measurement are given in table 2. Individual habitat variables at a reach were measured at one of three scales—the 

entire reach, at 11 equidistant transects across the stream, or 

at three points each on each of the 11 equidistant transects 

(table 2). We also used daily flow records to evaluate flow 

variability at the sites. Data were obtained from either USGS 

or California Department of Water Resources gaging stations.

Periphyton

Three different types of periphyton samples were collected—richest targeted habitat (RTH), depositional targeted 

habitat (DTH), and qualitative multihabitat (QMH) (Moulton 

and others, 2002). The RTH sample represents a habitat that is 

found at all sites, and that is expected to have a high diversity 

of species. From previous studies (Leland and others, 2001), 

large woody debris (snags) was selected as the RTH habitat. 

The DTH sample was taken from low velocity areas with fine 

substrate. The QMH sample was collected from all available 

habitat types with the purpose of assembling a complete species list for the site. All sampling procedures are described in 

detail in Moulton and others (2002).

The RTH sample was collected by removing a snag from 

the water and scraping a small area from the top of the snag 

with a knife. All the material removed was placed in a sample 

bottle and the area scraped was measured with a ruler. One 

snag was sampled at each of five different locations within the 

sampling reach. All samples were composited into a single 
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Figure 1. Locations of sampling sites and drainage basins in the San Joaquin River Basin, California.

Methods 3
USGS 

Station 

Number

Site 

number Station name

Total 

basin 

area1

(mi2)

Valley- portion 

of basin area2

(mi2)

Dates sampled

11261100 1 Salt Slough at Highway 165 near Stevinson 492 492 June 27 and September 19, 2001

11273500 2 Merced River at River Road near Newman 1,276 321 June 26 and September 18, 2001

11274538 3 Orestimba Creek at River Road near Crows Landing 196 11 June 25 and September 17, 2001

11290200 4 Tuolumne River at Shiloh Road Bridge near Grayson 1,897 319 June 28 and September 20, 2001

11303500 5 San Joaquin River near Vernalis 13,536 7,395 June 29 and September 21, 2001

1

 Topographical drainage basin.

2

 Portion of the topographical drainage basin on the valley floor with perennial flow.

Table 1. Sites sampled in 2001 in the San Joaquin River Basin, California.

[mi2, square mile]

Variable (units) How measured Equipment used

Reach length (m) Mid-channel distance from top to bottom of sampling reach Laser rangefinder

Reach water-surface gradient (m/km) Vertical drop from top to bottom of sampling reach Surveying level and surveying rod

Geomorphic channel units (m) Percentage of reach distance consisting of pool, riffle, and 

run

Laser rangefinder or measuring tape

Wetted channel width (m) Width of wetted channel at 11 equidistant transects Laser rangefinder or measuring tape

Bankfull channel width1 (m) Channel width from top of left bank to top of right bank, at 

each of 11 equidistant transects

Laser rangefinder or measuring tape

Canopy angles (degrees) Degrees of open sky, measured from the midpoint of each of 

11 equidistant transects

Clinometer

Riparian canopy closure (percent) Percentage of canopy at the left bank and the right bank, 

measured at each of 11 equidistant transects

Densiometer

Bank angle (degrees) Horizontal angle (degrees) of the bank at the left bank 

and the right bank, measured at each of 11 equidistant 

transects

Clinometer

Bank height (m) Vertical distance from the deepest part of the channel to the 

top of the bank, measured for the left and right bank at 

each of 11 equidistant transects

Hand level and surveying rod

Bank substrate2 Dominant bank substrate at left and right bank at each of 11 

equidistant transects

Visual estimate

Depth (m) Depth at thalweg (deepest point) and two additional evenly 

spaced points, at each of 11 equidistant transects

Calibrated wading rod, or depth 

sounder

Water velocity (m/s) Water velocity at thalweg (deepest point) and two additional 

evenly spaced points, at each of 11 equidistant transects

Marsh-McBirney electronic flow 

meter

Bed substrate2 Dominant substrate at thalweg (deepest point) and two additional evenly spaced points, at each of 11 equidistant 

transects

Visual estimate

1

 In regulated rivers, the traditional concept of bank (channel formed by the 1.5 to 2 year flood) is difficult to apply. For these measurements we used visible 

water marks, erosion, trash lines, and vegetation as indicators of “bank” position.

2

 The dominant substrate was characterized as: 1, concrete; 2, silt, mud, or detritus; 3, sand (>0.063–2 mm); 4, fine/medium gravel (>2–16 mm); 5, coarse 

gravel (>16–32 mm); 6, very coarse gravel (>32–64 mm); 7, small cobble (>64–128 mm); 8, large cobble (>128–256 mm); 9, small boulder (>256–512 mm); 

10, large boulder, irregular bedrock, irregular hardpan, or irregular artificial surface.

Table 2. Physical habitat variables measured in June and September 2001 at five sites in the San Joaquin River Basin, California.

[m, meter; m/km, meter per kilometer; m/s, meter per second; mm, milimeter]

4 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Methods 5

bottle and preserved in a solution of 4 percent buffered formalin.

The DTH sample was collected using the inverted petridish method. The lid of a 47-mm petri dish is placed underwater and all air bubbles removed from the underside. The 

petri dish is then carefully pressed into the substrate, edge-side 

down. A spatula is then slid under the lid and sealed against 

the edge of the petri dish. This shallow core is then removed 

and the material scraped and washed into the sample bottle. 

As with the RTH samples, one petri-dish sample was taken at 

each of five different locations within the sampling reach. All 

samples were composited into a single bottle and preserved 

with 4 percent buffered formalin.

The QMH sample was collected with a variety of methods including the scraping of woody debris and the petridish method. In addition, a turkey baster was used to sample 

periphyton from sand, aquatic macrophytes, and filamentous 

algae. All the samples were composited into a single bottle 

and preserved in a solution of 4 percent buffered formalin. 

Periphyton were identified and enumerated at the 

Philadelphia National Academy of Science (PNAS) according 

to Charles and others (2002).

Benthic Macroinvertebrates

Two types of macroinvertebrate samples were collected, 

an RTH and a QMH. Similar to periphyton, the RTH sample 

was collected from woody debris. A section of woody debris 

was removed from a larger piece using pruning shears or a 

saw. The pieces were then gently removed from the water and 

placed in a bucket. A 500-μm mesh net was held downstream 

of the snag to capture organisms that were dislodged during 

snag removal. One sample was taken from a single snag at 

each of five different locations within the sampling reach. The 

associated macroinvertebrates were then removed by gently 

brushing and hand picking with forceps. All organisms from 

the snags and net were then rinsed in a 500-μm sieve. All 

organisms were combined in a single bottle and preserved in 

a solution of 10 percent buffered formalin. The length and 

average diameter of each snag was measured for calculation of 

sample areas.

The QMH sample was collected from all available habitat 

types within the reach. All sampling was conducted with a 

500-μm mesh D-frame net. Woody debris and other hard substrates (concrete and rock) were sampled by brushing material 

into the net. The net was swept through aquatic macrophytes, 

filamentous algae, overhanging terrestrial vegetation and areas 

with fine substrates. All organisms from the net were then 

rinsed in a 500-μm sieve. All organisms were combined in a 

single bottle and preserved in a solution of 10 percent buffered 

formalin.

Macroinvertebrates were identified and enumerated at the 

USGS’s National Water Quality Laboratory using the procedures of Moulton and others (2000).

Data Analysis

Habitat variables were summarized as mean and standard deviation for each sampling event at each site. Daily 

flow records were summarized graphically, and as mean, 

standard deviation, and coefficient of variation. Periphyton 

and macroinvertebrate species lists were constructed using all 

taxa collected in all sample types. Quantitative analyses (see 

below) were conducted on RTH algae data (cells/cm2) and 

RTH macroinvertebrate data (organisms/m2). DTH algae data 

were not analyzed quantitatively (see below) because accurate counts of diatoms were not possible in the samples from 

Orestimba Creek. A combination of low diatom density and 

excessive fine sediment in Orestimba Creek made it unfeasible to concentrate the sample to the extent needed to obtain 

accurate diatom counts. The taxa present in the DTH samples 

from sites other than Orestimba Creek were included in the 

taxa lists for those sites. 

RTH macroinvertebrate and RTH algae data were analyzed using cluster analysis and ordination (detrended correspondence analysis). Data were analyzed as presence–absence 

and as densities. Only species found at two or more sites were 

included in these analyses. This was a compromise between 

the value of rare species in characterizing sites (Cao and others, 2001), and the uncertainty regarding the capability of sampling procedures to detect rare species. Presence–absence data 

were analyzed using Jaccards similarities followed by a group 

average linkage method cluster analysis. Jaccards similarity is 

calculated as, 2C/(A + B + C), where A is the number of taxa 

found only at site 1, B is the number of taxa found only at site 

2, and C is the number of taxa found at both sites. Jaccards 

similarity varies from 1 (all taxa shared) to 0 (no taxa shared). 

Clustering, in general, is a group of methods that produce a 

hierarchical arrangement of samples that are based on similarities between samples (see Gauch, 1982). The method starts 

with each sample assigned to a cluster with a single member 

and then uses a distance measure to group similar clusters 

into larger clusters until a final single cluster contains all the 

samples. Thus, more similar sites are closer in distance and 

cluster together. The results are portrayed graphically as a 

dendrogram (see fig. 3 as an example). The similarity of different groups can be assessed by observing the “percentage of 

information remaining” at branching points. All information is 

present when individual sites are considered and no information remains when all sites have been combined into a single 

group.

Detrended correspondence analysis (DCA), a special case 

of correspondence analysis, is an indirect ordination technique. This means that community structure at specific sites 

(the group of taxa found there) is determined independently 

of environmental variables. The basic idea behind correspondence analysis is that species are assigned weighted scores 

depending on their interrelationships and then the samples are 

scored on the basis of the abundance of each species in that 

sample. The result of the analysis is a set of species scores and 
Figure 2. Discharge records from March through April for sampling sites in the San Joaquin River Basin, California. Some site names 

are abbreviated from those in table 1. The Tuolumne River at Shiloh Road site is replaced by the Tuolumne River at Modesto site 

USGS gaging station 11290000), which is located several miles upstream from the Tuolumne River at Shiloh Road site. Periods when 

the gage at the Merced River site was not operating properly are indicated by the broken line.

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6 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Results and Discussion 7

a set of sample scores that can be used to understand ecological relationships between species and samples (see fig. 4 as 

an example). Relationships of communities to environmental 

variables must be determined after the ordination, for example, 

by correlating sample scores with values for environmental 

variables, such as specific conductance. 

Relationships of RTH algae and RTH invertebrate communities to environmental variables were explored using correlation analysis. Pearson product-moment correlations were 

calculated between the environmental variables and the sample 

scores on DCA axis 1. Data were then plotted for all correlations with r > 0.5. Significance values are not reported because 

the data likely violate several assumptions of correlation. 

Most importantly, the June and September samples collected 

from each site would not be expected to be independent. Taxa 

present in June have a high probability of also being present in 

September. However, the plots might be useful in identifying 

variables of interest for future studies.

Results and Discussion 

Environmental Variables

The sites sampled ranged from a small agricultural drain, 

Orestimba Creek, to a large river, the San Joaquin River, and 

these differences are reflected in the values for habitat variables (table 3, at back of report). Orestimba Creek is notable 

for having a much steeper gradient, steeper banks, and a more 

closed canopy than the other sites (table 3).

There are differences between June and September for 

several sites, related to discharge (table 3). Discharge was 

similar in June and September at the Merced River, Tuolumne 

River, and San Joaquin River sites. September discharge was a 

quarter or less of June discharge at Salt Slough and Orestimba 

Creek. These changes in discharge were associated with 

declines in mean water depth and water velocity (table 3). 

There were some differences in specific conductance between 

June and September, especially for Salt Slough and Orestimba 

Creek, both of which had increases of about 50 percent from 

June to September (table 3). 

There are also differences in discharge patterns among 

the sites (fig. 2 and table 4). All the streams exhibited an early 

March high flow, likely related to rainfall. All sites except 

Salt Slough, had elevated flows from mid-April to mid-May 

related to water releases made for salmon management activities in the San Joaquin River. Flows in the Merced, Tuolumne, 

and San Joaquin Rivers were relatively constant during June 

through September. Flows in Salt Slough and Orestimba Creek 

were more variable during this time (table 4). Orestimba 

Creek was the most variable stream during the summer, with a 

coefficient of variation of 51 percent. Flow at Orestimba Creek 

varied between 1 and 41 ft3/s.

Periphyton

A total of 161 taxa of algae were collected during the 

study (table 5, at back of report). All but three taxa were 

identified to species. Two of the three taxa are the cyanophytes 

(bluegreen algae) Oscillatoria and Lyngbya, and the third is 

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Figure 3. Cluster dendrogram showing the results of a group average linkage cluster analysis of periphyton presense–absense data. 

The first two letters of the site codes refer to the river (OC, Orestimba Creek; SS, Salt Slough; SJ, San Joaquin River; MR, Merced 

River; TR, Tuolumne River). The third letter indicates the month of sampling (J, June; S, September).
Figure 4. Plots of site scores and taxa scores on the first two 

axes of a detrended correspondence analysis (DCA) of periphyton abundance data. The first two letters of the site codes refer 

to the river (OC, Orestimba Creek; SS, Salt Slough; SJ, San 

Joaquin River; MR, Merced River; TR, Tuolumne River). The third 

letter indicates the month of sampling (J, June; S, September). 

Taxa codes are listed in table 6. (A) Site scores. (B) Taxa scores.

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8 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001

an unidentified diatom in the genus Caloneis. The periphyton 

were dominated by diatoms. Of the 161 taxa collected, 155 

(96 percent) were diatoms. Many of the taxa were rare, with 

67 (42 percent) found in only one sample. The number of taxa 

found in each sample varied from 39 to 67. Orestimba Creek 

had the lowest number of taxa, with 39 in June and 40 in September. Salt Slough had more taxa than Orestimba Creek (52 

in June and 50 in September) but fewer than the other sites, 

which ranged from 58 to 67 taxa. The differences between 

seasons were minor, with a maximum difference of four taxa 

at the San Joaquin River site. The low number of taxa found at 

Orestimba Creek was at least partially due to the low density 

of algae cells in the DTH sample. The high concentration of 

fine sediment in these samples made it unfeasible to concentrate the samples so that accurate counts could be conducted; 

however, the PNAS did state that there were very few algae of 

any kind in these samples.

The RTH samples collected from snag habitat included 

109 taxa, including 106 species of diatoms (97 percent) 

(table 6, at back of report). In addition, the samples included 

one species of Chlorophyta (green algae) and two taxa of 

Cyanophyta (blue-green algae). Forty-eight taxa (43 percent) 

were found in only one sample and were not included in the 

quantitative analyses.

Jaccards similarities vary from 0.255 to 0.636 among 

the samples. This means that after removing the taxa found in 

only one sample, any two samples shared from 25 percent to 

63 percent of the total taxa found in those two samples. The 

cluster analysis (fig. 3) indicates that samples collected from 

the same site in June and September tend to be more similar to 

each other than to samples collected from other sites; however, there are some exceptions. The highest similarity (0.636) 

is found between the June sample from the Tuolumne River 

and the September sample from the Merced River. The June 

sample from the San Joaquin River is more similar to the two 

Salt Slough samples (0.535 and 0.512) than to the September 

sample from the San Joaquin River (0.413).

The first four axes of the DCA explain 28, 7, 4, and 1 percent of the variance, respectively. A plot of sample scores on 

the first two DCA axes (fig. 4) generally supports the results of 

the cluster analysis. Scores on DCA axis 1 of samples from the 

same site tend to be similar between the two months sampled. 

DCA axis 1 scores show that Orestimba Creek was most different from the Merced and Tuolumne Rivers with Salt Slough 

(SSJ and SSS on fig. 4A) and the San Joaquin River (SJJ and 

SJS) having intermediate scores (fig. 4A). DCA axis 2 mainly 

separates samples from different months (fig. 4A). September 

samples tend to have higher scores on DCA axis 2 compared 

with June samples, except for Orestimba Creek, which has the 

opposite pattern.

Interpretation of the taxa score plot (fig. 4B) is difficult 

because there are few environmental preference and tolerance 

data available for species of algae. Basically, taxa located to 

the left in the taxa plot (fig. 4B) tend to be more abundant 

in samples with low scores on DCA axis 1 (fig. 4A), and 

taxa located to the right in the taxa plot (fig. 4B) tend to be 

more abundant in samples with higher scores on DCA axis 1 

(fig. 4A).

Specific conductance, water temperature, and several 

habitat variables appear to be related to periphyton DCA axis 

1 site scores (fig. 5). The habitat relationships of gradient, 

open canopy, and shade are dependent on Orestimba Creek 

being very different from the other sites (fig. 5). High variability in flow (tables 3 and 4) at Orestimba Creek is probably 

also an important factor affecting ecological communities, 
Station name Time

period

Minimum

discharge 

(ft3/s)

Maximum

discharge 

(ft3/s)

Mean

discharge 

(ft3/s)

Standard

deviation

Coefficient

of variation

Salt Slough at Highway 165 near Stevinson Spring 106 717 241 120 50

Summer 48 223 53 53 38

Merced River at River Road near Newman1 Spring 150 1,284 440 317 72

Summer 38 176 110 29 27

Orestimba Creek at River Road near Crows Landing Spring 1 488 47 59 126

Summer 1 41 13 7 51

Tuolumne River at Shiloh Road Bridge near Grayson1 Spring 182 2,670 732 495 68

Summer 178 329 268 37 14

San Joaquin River near Vernalis Spring 1,310 5,900 2,900 1,232 42

Summer 1,150 1,600 1,365 86 6

1

 Discharge calculated from data provided by the California Department of Water Resources.

Table 4. Discharge statistics for the periods from March 1, 2001 to the date of the June 2001 sample (spring) and from the June sample 

to the September 2001 sample (summer).

[ft3/s, cubic feet per second]

Results and Discussion 9

especially because the low flows probably resulted in much 

of the habitat for periphyton and invertebrates being exposed 

to air for some amount of time. Bank angle could be related 

to the degree of shading as indicated by a low value for open 

canopy angle and a high percent canopy cover (table 3). It is 

unclear how bank substrate would directly affect periphyton 

communities on woody debris. It seems likely that bank angle, 

water temperature, and the other habitat variables simply 

indicate that Orestimba Creek is a unique habitat among the 

five sites—a relatively steep, incised stream receiving mainly 

agricultural drainage water—which favors a different periphyton community compared with the other sites. It is unclear 

whether inclusion of a wider variety of water bodies in the 

analysis, with a wider range of habitat characteristics, would 

strengthen or weaken these habitat relationships.

Leland and others (2001) found that specific conductance 

(a surrogate for salinity) was a major determinant of periphyton community structure in the lower San Joaquin River drainage. In addition, dissolved inorganic nitrogen concentration 

was found to be a good predictor of periphyton communities 

as long as sufficient numbers of tributary sites with low concentrations of inorganic nitrogen were included in the model 

(Leland and others, 2001). The importance of specific conductance in structuring the periphyton community is supported by 

the plot of DCA axis 1 site scores against specific conductance 

(fig. 5). We did not collect nutrient data as part of this study; 

therefore, we cannot comment on the potential effects of inorganic nitrogen on the periphyton community.

Macroinvertebrates

A total of 126 taxa of macroinvertebrates were identified 

from a least one sample during the study (table 7, at back of 

report). Specimens were reported at a variety of taxonomic 

levels for various reasons. Most often, small or damaged 

individuals of insect larvae could not be identified to species. 

Some non-insect taxa are also difficult to identify because of 

size, or poorly known or difficult taxonomy.

A total of 59 taxa were found in the RTH samples collected from snag habitat (table 8, at back of report). Twenty 

taxa were found in only one sample. Taxa per sample ranged 

from 10 in the September sample from Salt Slough to 27 in the 

September sample from Merced River. Orestimba Creek and 

Salt Slough had fewer species in September compared with 

June. The Merced, Tuolumne, and San Joaquin Rivers had the 

same or more species in the September samples compared to 

the June samples (table 8).

Jaccards similarities vary from 0.115 to 0.652 among the 

samples. This means that after removing the taxa found in only 

one sample, any two samples shared from 11 to 65 percent 

of the total taxa found at those two sites. The cluster analysis 

(fig. 6) indicates that the June and September samples from 

Orestimba Creek are very similar to each other and the June 

and September samples from Salt Slough are very similar to 

each other. The macroinvertebrate communites of Orestimba 

Creek and Salt Slough were very different from each other and 

from the other sites. In contrast, June samples from the Merced and Tuolumne Rivers have the highest similarity (0.636), 

and September samples from these sites have the second 

highest similarity (0.630). The San Joaquin River samples are 

more similar to the Merced and Tuolumne River samples than 

to the Orestimba Creek and Salt Slough samples (fig. 6). The 

June sample from the San Joaquin River is more similar to 

the Merced and Tuolumne River samples than the September 

sample from the San Joaquin River.

The first four axes of the DCA explain 32, 9, 3, and 

1 percent of the variance, respectively. A plot of sample scores 

on the first two DCA axes (fig. 7A) generally supports the 
10 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001

Figure 5. Plots of periphyton detrended correspondence analysis (DCA) axis 1 site scores with selected environmental variables. 

The first two letters of the site codes refer to the river (OC, Orestimba Creek; SS, Salt Slough; SJ, San Joaquin River; MR, Merced 

River; TR, Tuolumne River). The third letter indicates the month of sampling (J, June; S, September). For bank substrate, 2 = silt and 

3 = sand.

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Figure 6. Cluster dendrogram showing the results of a group average linkage cluster analysis of macroinvertebrate presence–

absence data. The first two letters of the site codes refer to the river (OC, Orestimba Creek; SS, Salt Slough; SJ, San Joaquin River; 

MR, Merced River; TR, Tuolumne River). The third letter indicates the month of sampling (J, June; S, September).

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Results and Discussion 11

results of the cluster analysis. DCA axis 1 scores show that 

samples from Orestimba Creek and Salt Slough are distinct 

from samples from the other streams. The more intermediate 

position of the September San Joaquin River sample is consistent with the position of this sample in the cluster dendrogram (fig. 6). There is no obvious pattern to the distribution of 

samples along DCA axis 2 (fig. 7A). 

Examination of the taxa plot (fig. 7B) shows two groups 

of taxa, similar to the two groups of sample scores. One group, 

with scores of less than one, is dominated by non-insect taxa, 

except for several groups of dipterans including ceratopogonids (21), dolichopodids (39), and several genera of chironomids (29 and 30). The group with scores greater than one 

is dominated by insects with the only non-insects being the 

amphipod, Hyallela azteca (13), and the water mites (11). The 

two plots together show that samples from Orestimba Creek 

and Salt Slough were characterized by high abundances of 

non-insects. Samples from the Merced, Tuolumne, and San 

Joaquin Rivers were characterized by high abundances of 

insects.

These results are consistent with earlier work in the 

Central Valley. Brown and May (2000a,b) found that environmentally stressful agricultural drains and urban streams 

were dominated by the same tolerant non-insect taxa observed 

in this study. Brown and May (2000a) found that tributaries draining the Sierra Nevada (including the Stanislaus, 

Tuolumne, and Merced Rivers) had similar benthic macroinvertebrat communities characterized by high abundances of 

insects. Brown and May (2000a) defined two groups of “drain 

sites” that included samples from agricultural drains, including Orestimba Creek and an urban stream. Further analysis 

by Brown and May (2000a) found that specific conductance 

and the percentage of agricultural and urban land use in the 

basins are important variables that explain the differences in 

macroinvertebrates among sites, with the drain sites representing the most stressful environments and the tributary sites 

representing the least stressful environments. Similarly, Leland 

and Fend (1998) found that tributary rivers—Stanislaus, 

Tuolumne, and Merced Rivers—had different macroinvertebrate communities than sloughs or sections of the San Joaquin 

River influenced by large inputs of agricultural drainage water. 

Leland and Fend (1998) also identified salinity as an important 

explanatory variable for understanding benthic macroinvertebrate communities in the Central Valley.
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Figure 7. Plots of site scores and taxa scores on the first two 

axes of a detrended correspondence analysis (DCA) of macroinvertbrate abundance data. The first two letters of the site codes 

refer to the river (OC, Orestimba Creek; SS, Salt Slough; SJ, San 

Joaquin River; MR, Merced River; TR, Tuolumne River). The third 

letter indicates the month of sampling (J, June; S, September). 

Taxa codes are listed in table 8. (A) Site scores. (B) Taxa scores.

12 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001

Examination of plots of DCA axis 1 scores against environmental variables (fig. 8) supports the importance of specific 

conductance, a surrogate for salinity. Similar to the results 

for periphyton, values for Orestimba Creek samples appear 

to be responsible for the relationships between DCA axis 1 

and water temperature, gradient, shade, and open canopy. 

The differences in bank substrate are small, basically indicating a slightly higher occurrence of silt (a score of 2) along 

with sand (a score of 3) at Orestimba Creek and Salt Slough 

compared with the other sites. As noted earlier for periphyton, 

the relationship of DCA axis 1 to bank angle may be related to 

canopy cover. Channel width and bankfull width (not plotted, 

but similar to channel width) also appear to have relationships 

to DCA axis 1 sample scores; however, it seems unlikely this 

relationship is real because the widest channel at the San Joaquin River site actually had intermediate DCA axis 1 scores. 

As mentioned earlier for periphyton, flow fluctuation and low 

flows at Orestimba Creek (table 3) are also probably important 

in determining composition of the periphyton and macroinvertebrate communities.

We did not sample pesticides in this study, despite 

concerns regarding potential toxicity of dissolved pesticides 

to aquatic life (Foe and Connor, 1991; Foe, 1995; Kuivila and 

Foe, 1995). However, dissolved pesticide concentrations were 

measured at these sites as part of another study, covering the 

period from April to August 2001 (Domagalski and Munday, 

2003). In general, dissolved pesticides were most frequently 

detected and at the highest concentrations at Orestimba Creek. 

Unfortunately, Orestimba Creek also had the most unique 

habitat, so the relative effects of dissolved pesticides and 

other habitat and water-quality variables, particularly specific 

conductance, cannot be separated. This is a common problem 

when evaluating bioassessment data (Brown and others, 1999). 

Further, the ecological risks associated with dissolved pesticides are typically assessed for single pesticides (Giddings and 

others, 2000) rather than for complex mixtures found in San 

Joaquin Basin streams.
Results and Discussion 13

Figure 8. Plots of macroinvertebrate detrended correspondence analysis (DCA) axis 1 site scores with selected environmental 

variables. The first two letters of the site codes refer to the river (OC, Orestimba Creek; SS, Salt Slough; SJ, San Joaquin River; MR, 

Merced River; TR, Tuolumne River). The third letter indicates the month of sampling (J, June; S, September). For bank substrate, 

2 = silt and 3 = sand.

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References

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River drainages, California: Environmental Monitoring and 

Assessment, v. 64, p. 311–329.

Brown, L.R,. and May, J.T., 2000b, Benthic macroinvertebrate 

assemblages and their relations with environmental variables in the Sacramento and San Joaquin River drainages, 

California, 1993–1997: U.S. Geological Survey WaterResources Investigations Report 00-4125.

Brown, L.R., Kratzer, C.R., and Dubrovsky N.M., 1999, Integrating chemical, water quality, habitat, and fish assemblage 

data from the San Joaquin River drainage, California, in

Scow, K.M., and others, eds., Integrated assessment of ecosystem health: Boca Raton, Fla., Lewis Publishers, p.25–62.

Cao, Y., Larsen, D.P., and Thorne, R. St.-J., 2001, Rare species 

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14 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001

Summary and Conclusion

The widespread and intensive use of agricultural pesticides in the San Joaquin River Basin is a long standing 

concern in relation to potential toxicity to aquatic organisms. 

Data on the periphyton and macroinvertebrate communities 

and physical habitat were collected at five sites in the San 

Joaquin River Basin in June and September 2001 to provide 

background on existing conditions and to provide initial 

information on environmental factors that might be affecting 

the communities. A total of 161 taxa of algae and 126 taxa 

of macroinvertebrates were collected. Cluster analyses and 

detrended correspondence analysis of the data showed that the 

periphyton community of Orestimba Creek was different from 

the periphyton communities of the Merced and Tuolumne Rivers. Periphyton communites of Salt Slough and the San Joaquin River had compositions that were intermediate between 

Orestimba Creek and the Merced and Tuolumne Rivers. With 

regard to macroinvertebrates, community composition of Salt 

Slough was similar to Orestimba Creek, and community composition of the San Joaquin River was similar to the Merced 

and Tuolumne Rivers.

Examination of data plots suggested that specific conductance, a surrogate for salinity, might be an important variable 

affecting the composition of periphyton and macroinvertebrate 

communities, as had been found in earlier studies. Several 

physical measures of the environment also appeared to be 

related to the composition of periphyton and macroinvertebrate 

communities; however, several of these apparent relationships 

were mainly related to the unique communities and habitat 

conditions in Orestimba Creek. Orestimba Creek also had very 

different flow characteristics from the other sites. This study 

did not include extensive measures of water quality, including 

pesticides, that might also be influencing biological communities. Data from another study indicated that Orestimba Creek 

was the stream most affected by dissolved pesticides; however, 

there is no way to separate the effects of pesticides from those 

of other water quality and habitat variables.

This study provides valuable baseline data for the San 

Joaquin River Basin. However, the data collected have a limited temporal and spatial scope. Continued sampling at more 

sites over several years will likely be needed to more fully 

understand the composition of periphyton and macroinvertebrate communities in the San Joaquin River Basin. Habitat and 

water quality assessments should be conducted in concert with 

biological sampling to provide the necessary data to better 

understand the effect of land and water use on those communities.
Fitzpatrick, F.A., Waite, I.R., D’Arconte, P.J., Meador, M.R., 

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

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Foe, C.G., and Connor, Valerie, 1991, San Joaquin watershed 

bioassay results, 1988–1990: Sacramento, Calif., Central 

Valley Regional Water Quality Control Board Staff Memorandum, 79 p.

Foe, C.G., 1995, Insecticide concentrations and invertebrate 

bioassay mortality in agricultural return water from the San 

Joaquin Basin: Sacramento, Calif., Central Valley Regional 

Water Control Board, 190 p.

Gauch, H.G., 1982, Multivariate analysis in community ecology: Cambridge, UK, Cambridge University Press, 314 p.

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Ecological risks of diazinon from agricultural use in the 

Sacramento–San Joaquin River Basins, California: Risk 

Analysis, v. 20, no. 5, p. 545–572.

Gronberg, J.M., Dubrovsky, N.M., Kratzer, C.R., Domagalski, 

J.L., Brown, L.R., and Burow, K.R., 1998, Environmental setting of the San Joaquin–Tulare Basins, California, 

1992–1995: U.S. Geological Survey Water-Resources 

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Kratzer, C.R., 1999, Transport of diazinon in the San Joaquin 

River Basin, California: Journal of the American Water 

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Kratzer, C.R., Zamora, Celia, and Knifong, D.L., 2002, Diazinon and chlorpyrifos loads in the San Joaquin River Basin, 

California, January and February 2000: U.S. Geological 

Survey Water-Resources Investigations Report 02-4013, 

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Kuivila, K.M., and Foe, C.G., 1995, Concentrations, transport 

and biological effects of dormant spray pesticides in the San 

Francisco Estuary: Environmental Toxicology and Chemistry, v.14, p. 1141–1150.

Leland, H.V, and Fend, S.V., 1998, Benthic invertebrate distributions in the San Joaquin River, California, in relation to 

physical and chemical factors: Canadian Journal of Fisheries and Aquatic Sciences, v. 55, p. 1051–1067.

Leland, H.V., Brown, L.R., and Mueller, D.K., 2001, Distribution of algae in the San Joaquin River, California, in relation 

to nutrient supply, salinity, and other environmental factors: 

Freshwater Biology, v. 46, p. 1139–1167.

Moulton, S.R., II, Carter, J.L., Grotheer, S.A., Cuffney, T.F., 

and Short, T.M., 2000, Methods of analysis by the U.S. 

Geological Survey National Water Quality Laboratory—

Processing, taxonomy, and quality control of benthic macroinvertebrate samples: U.S. Geological Survey Open-File 

Report 00-212, 49 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 the 

National Water-Quality Assessment Program: U.S. Geological Survey Open-File Report 02-150, 75 p.

Panshin, S.Y., Dubrovsky, N.M., Gronberg, J.M., and 

Domagalski, J.L., 1998, Occurrence and distribution of dissolved pesticides in the San Joaquin River Basin, California: 

U.S. Geological Survey Water-Resources Investigations 

Report 98-4032, 88 p.

Zamora, Celia, Kratzer, C.R., Majewski, M.S., and Knifong, 

D.L., 2003, Diazinon and chlorpyrifos loads in precipitation and urban and agricultural storm runoff during January 

and February 2001 in the San Joaquin Basin, California: 

U.S. Geological Survey Water-Resources Investigations 

Report 03-4091, 56 p.

References 15
Station name

Reach 

length

(m, n=1)

Discharge

(ft3/s, 

n=1)

Water

temperature

(°C, n=1)

pH

(n=1)

Specifc

conductance

(μS/cm, 

n=1)

Dissolved

oxygen

(mg/L, 

n=1)

Reach

water-surface

gradient

(m/km, n=1)

Water

depth

(m, n=33)

Water

velocity

(m/s, n=33)

June 2001

Salt Slough at Highway 165 

near Stevinson

600 204 24.4 7.3 1,009 7.5 0.14 0.99 ± 0.49 0.36 ± 0.14

Merced River at River Road 

near Newman

600 2251 28.7 7.4 322 8.8 0.31 0.57 ± 0.29 0.30 ± 0.13

Orestimba Creek at River 

Road near Crows Landing

150 29 23.6 7.7 715 8.2 2 0.42 ± 0.17 0.47 ± 0.19

Tuolumne River at Shiloh 

Road Bridge near Grayson

500 2241 26.5 7.5 342 8.2 0.17 0.60 ± 0.22 0.35 ± 0.09

San Joaquin River near 

Vernalis

1,000 1,510 25.6 8.3 667 12 0.19 0.91 ± 0.45 0.47 ± 0.12

September 2001

Salt Slough at Highway 165 

near Stevinson

600 52 26.5 8.1 1,630 9.4 — 0.59 ± 0.33 0.21 ± 0.08

Merced River at River Road 

near Newman

600 1761 24.8 7.5 212 9.5 — 0.62 ± 0.23 0.38 ± 0.15

Orestimba Creek at River 

Road near Crows Landing

150 6 21.7 8 1,071 9.7 — 0.26 ± 0.13 0.24 ± 0.20

Tuolumne River at Shiloh 

Road Bridge near Grayson

500 2871 23.9 7.7 263 9.2 — 0.75 ± 0.25 0.36 ± 0.10

San Joaquin River near 

Vernalis

1,000 1,370 25.6 8.3 667 12 — 0.94 ± 0.53 0.39 ± 0.14

1

 Discharge calculated from data provided by the California Department of Water Resources.

Table 3. Values for environmental variables measured during June and September 2001 at five sites in the San Joaquin River Basin, 

California.

[Values are mean ± standard deviation unless n = 1; m, meter; n, sample size; ft3/s, cubic feet per second; °C, degrees Celsius; μS/cm, microsiemens per centimeter; m/km, meter per kilometer; mg/L, milligram per liter; m/s, meter per second; —, not measured]

16 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Tables 17

Station name

Bed

substrate

(n=33)

Pool

(percent)

Run

(percent)

Riffle

(percent)

Wetted

channel

width

(m, n=11)

Bankfull

channel

width

(m, n=11)

Canopy

angle

(degrees, 

n=11)

Riparian

canopy

closure

(percent)

Bank

angle

(degrees, 

n=22)

Bank

height

(m, n=22)

Bank

substrate

(n=22)

June 2001

Salt Slough at 

Highway 165 

near Stevinson

2.0 ± 0 0 100 0 19.6 ± 1.8 21.7 ± 1.8 151 ± 9 29 ± 31 38 ± 27 0.33 

± 0.09

2.7 

± 2.3

Merced River at 

River Road near 

Newman

3.0 ± 0 0 100 0 29.5 ± 5.6 30.3 ± 5.6 141 ± 21 15 ± 22 28 ± 22 0.42 

± 0.08

3.0 ± 0

Orestimba Creek at 

River Road near 

Crows Landing

3.5 ± 1.0 13 84 3 6.7 ± 1.4 7.3 ± 1.4 45 ± 42 78 ± 23 60 ± 28 0.29 

± 0.05

2.0 ± 0

Tuolumne River 

at Shiloh Road 

Bridge near 

Grayson

3.0 ± 0 0 100 0 42.3 ± 4.7 43.5 ± 4.9 148 ± 16 27 ± 22 22 ± 17 0.52 

± 0.06

2.7 

± 2.3

San Joaquin River 

near Vernalis

3.1 ± 0.3 0 100 0 109.6 

± 18.6

112.0 ± 18.5 165 ± 3 2 ± 4 30 ± 25 0.59 

± 0.11

3.0 ± 0

September 2001

Salt Slough at 

Highway 165 

near Stevinson

2.6 ± 1.4 0 100 0 13.9 ± 3.0 20.4 ± 2.9 141 ± 13 19 ± 16 47 ± 32 0.58 

± 0.06

2.4 

± 1.7

Merced River at 

River Road near 

Newman

3.0 ± 0 0 100 0 29.6 ± 5.9 46.4 ± 12.2 145 ± 18 21 ± 26 27 ± 27 0.61 ± 0.1 3.0 ± 0

Orestimba Creek at 

River Road near 

Crows Landing

3.4 ± 1.0 13 84 3 6.1 ± 2.4 8.6 ± 2.3 53 ± 38 74 ± 24 52 ± 16 0.69 

± 0.06

2.4 

± 1.7

Tuolumne River 

at Shiloh Road 

Bridge near 

Grayson

3.0 ± 0 0 100 0 43.2 ± 5.1 47.6 ± 3.9 149 ± 16 42 ± 32 28 ± 17 0.70 

± 0.09

3.3 

± 1.5

San Joaquin River 

near Vernalis

3.0 ± 0 0 100 0 112.5 

± 23.3

115.7 ± 22.9 163 ± 5 6 ± 11 32 ± 24 0.69 

± 0.24

3.0 ± 0

1

 Discharge calculated from data provided by the California Department of Water Resources.

Table 3. Values for environmental variables measured during June and September 2001 at five sites in the San Joaquin River Basin, 

California—Continued.

[Values are mean ± standard deviation unless n = 1; m, meter; n, sample size; ft3/s, cubic feet per second; °C, degrees Celsius; μS/cm, microsiemens per centimeter; m/km, meter per kilometer; mg/L, milligram per liter; m/s, meter per second; —, not measured]
Table 5. Periphyton taxa collected from each of five sites in June and September 2001 in the San Joaquin River Basin, California.

[Frequency of occurrence refers to the number of samples in which a taxon was found. ”?” denotes unidentified species]

Taxon Frequency of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Total taxa per sample: 52 50 67 64 39 40 61 58 63 59Chlorophyta (Green algae)Cosmarium margaritatum 

(Lund) Roy & Bissett

1 0 0 1 0 0 0 0 0 0 0

Netrium digitus Ehrenberg 1 0 0 1 0 0 0 0 0 0 0Scenedesmus quadricauda var. 

longispina fo. assymmetricus (Hortobágyi) Uherkovich

5 0 0 1 1 0 0 1 0 1 1

Chrysophyta (Golden algae, 

only diatoms listed)

Achnanthes lanceolata var. haynaldii (Schaarschmidt) Cleve

1 1 0 0 0 0 0 0 0 0 0

Achnanthes oblongella Østrup 1 0 0 0 1 0 0 0 0 0 0Achnanthes subhudsonis var. 

kraeuselii (Cholnoky) Cholnoky

5 0 1 1 0 0 0 1 0 1 1

Achnanthidium exiguum var. 

heterovalvum (Krasske) Czarnecki

6 0 1 1 1 0 0 1 1 0 1

Achnanthidium minutissimum 

(Kützing) Czarnecki

10 1 1 1 1 1 1 1 1 1 1

Achnanthidium pyrenaicum 

(Hustedt) Kobayasi

5 0 0 1 1 0 0 1 1 1 0

Actinocyclus normanii (Gregory) 

Hustedt

3 0 0 0 1 0 0 1 1 0 0

Adlafia bryophila (Petersen) 

Lange-Bertalot

3 0 0 0 0 0 0 1 1 1 0

Amphora acutiuscula Kützing 1 0 0 0 0 0 0 0 0 0 1Amphora inariensis Krammer 4 0 0 0 0 1 1 0 1 1 0Amphora ovalis (Kützing) Kützing

1 0 0 0 0 0 0 1 0 0 0

Amphora veneta Kützing 7 0 1 0 1 0 1 1 1 1 1

18 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Taxon Frequency of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Aulacoseira granulata (Ehrenberg) Simonsen 3 0 1 0 0 0 0 1 0 0 1Bacillaria paradoxa Gmelin 10 1 1 1 1 1 1 1 1 1 1Brachysira serians (Brebisson) 

Round et Mann

1 0 0 0 0 0 1 0 0 0 0

Caloneis bacillum (Grunow) 

Cleve

1 0 0 0 1 0 0 0 0 0 0

Caloneis sp. 1 ? 1 0 0 0 0 0 1 0 0 0 0Cavinula jaernefelti (Hustedt) 

Mann and Stickle

4 0 0 1 1 0 0 1 1 0 0

Cocconeis cf. neothumensis 

Krammer

1 0 0 1 0 0 0 0 0 0 0

Cocconeis disculus (Schumann) 

Cleve

1 1 0 0 0 0 0 0 0 0 0

Cocconeis pediculus Ehrenberg 1 1 0 0 0 0 0 0 0 0 0Cocconeis placentula var. lineata 

(Ehrenberg) Van Heurck

7 0 1 1 1 0 0 1 1 1 1

Craticula accomoda (Hustedt) 

Mann

1 0 0 0 0 0 0 0 0 0 1

Craticula citrus (Krasske) 

Reichardt

1 1 0 0 0 0 0 0 0 0 0

Craticula cuspidata (Kützing) 

Mann

2 0 0 1 0 0 0 1 0 0 0

Craticula molestiformis 

(Hustedt) Lange-Bertalot

8 0 1 0 1 1 1 1 1 1 1

Craticula submolesta (Hustedt) 

Lange-Bertalot

1 0 0 0 0 1 0 0 0 0 0

Cyclostephanos invisitatus 

(Hohn et Hellerman) Theriot, Stoermer et Håkansson

1 0 0 0 0 0 0 0 0 1 0

Cyclotella atomus Hustedt 7 1 1 1 0 0 1 1 0 1 1Cyclotella meneghiniana Kützing 10 1 1 1 1 1 1 1 1 1 1Cyclotella ocellata Pantosek 1 0 0 0 0 0 0 0 0 0 1

Table 5. Pe [Frequency of occurrence refers to the number of samples in which a taxon was found. ”?” denotes unidentified species]

Tables 19
Taxon Frequency of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Cyclotella pseudostelligera 

Hustedt

1 0 0 0 0 0 0 1 0 0 0

Cymbella affinis Kützing 1 0 0 0 0 0 0 0 0 0 1Cymbella laevis Naegeli ex 

Kützing

1 0 0 0 0 0 1 0 0 0 0

Cymbella turgidula Grunow 2 0 0 0 0 0 0 1 1 0 0Diadesmis confervacea Kützing 5 1 0 0 1 0 0 1 1 1 0Diatoma vulgaris Bory 3 0 0 1 0 0 0 0 0 1 1Diploneis elliptica (Kützing) 

Cleve

1 1 0 0 0 0 0 0 0 0 0

Diploneis oblongella (Naegeli ex 

Kützing) Ross

3 1 1 0 1 0 0 0 0 0 0

Diploneis parma Cleve 1 1 0 0 0 0 0 0 0 0 0Diploneis smithii (Brébisson ex 

Smith) Cleve

1 0 0 0 1 0 0 0 0 0 0

Encyonema lunatum (Smith) Van 

Heurck

2 0 0 1 0 0 1 0 0 0 0

Encyonema minutum (Hilse) 

Mann

7 0 0 1 1 1 1 0 1 1 1

Encyonema prostratum (Berkeley) Kützing

1 0 0 0 0 1 0 0 0 0 0

Encyonema silesiacum (Bleisch) 

Mann

2 0 0 1 0 0 0 0 0 1 0

Epithemia sorex Kützing 2 1 1 0 0 0 0 0 0 0 0Eunotia incisa Smith ex Gregory 2 0 0 0 1 0 0 1 0 0 0Eunotia pectinalis var. minor 

(Kützing) Rabenhorst

3 1 0 1 1 0 0 0 0 0 0

Eunotia tenella (Grunow) Cleve 1 0 0 0 0 0 0 0 1 0 0Fallacia pygmaea (Kützing) 

Stickle et Mann

5 1 1 0 0 0 1 0 0 1 1

Fallacia tenera (Hustedt) Mann 1 0 0 1 0 0 0 0 0 0 0Fragilaria capucina 

Desmazières

1 0 0 0 0 0 0 0 0 0 1

Table 5. Pe [Frequency of occurrence refers to the number of samples in which a taxon was found. ”?” denotes unidentified species]

20 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Taxon Frequency of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Fragilaria capucina var. 

rumpens (Kützing) LangeBertalot

6 1 0 1 1 1 0 0 1 1 0

Fragilaria crotonensis Kitton 1 0 0 1 0 0 0 0 0 0 0Fragilariforma constricta (Ehrenberg) Williams et Round 1 0 0 0 0 0 0 1 0 0 0Fragilariforma virescens (Ralfs) 

Williams et Round

1 0 0 0 0 0 0 1 0 0 0

Frustulia rhomboides (Ehrenberg) De Toni 1 0 0 0 0 0 0 0 1 0 0Gomphonema kobayasii Kociolek & Kingston 6 1 1 1 1 1 0 0 0 0 1Gomphonema mexicanum Grun. 

in V. H.

1 0 0 0 0 0 0 1 0 0 0

Gomphonema parvulius (LangeBertalot et Reichardt) LangeBertalot et Reichardt 2 0 0 0 0 1 0 0 1 0 0Gomphonema parvulum (Kütz.) 

Kütz.

9 1 1 1 1 1 1 1 1 1 0

Gomphonema rhombicum Fricke 2 0 0 1 0 0 0 0 1 0 0Gyrosigma spencerii (Quek.) 

Griff. & Henfr.

6 1 1 1 1 0 1 0 1 0 0

Hippodonta capitata (Ehrenberg) 

Lange-Bertalot, Metzeltin et Witkowski

8 1 1 1 1 0 0 1 1 1 1

Karayevia clevei (Grunow) 

Kingston

1 0 0 0 0 0 0 0 1 0 0

Luticola goeppertiana (Bleisch) 

Mann

4 1 0 0 1 0 1 1 0 0 0

Luticola mutica (Kutz.) Mann 2 1 0 0 0 1 0 0 0 0 0Luticola nivalis (Ehrenberg) 

Mann

2 0 0 0 0 1 1 0 0 0 0

Mayamaea agrestis (Hustedt) 

Lange-Bertalot

2 0 0 0 0 0 0 1 0 1 0

Table 5. Pe [Frequency of occurrence refers to the number of samples in which a taxon was found. ”?” denotes unidentified species]

Tables 21
Taxon Frequency of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Mayamaea atomus (Kützing) 

Lange-Bertalot

7 0 1 1 0 1 0 1 1 1 1

Melosira varians Ag. 8 1 1 1 1 0 0 1 1 1 1Meridion circulare (Grev.) Ag. 4 0 1 1 1 0 0 0 0 0 1Navicula absoluta Hustedt 1 0 0 0 0 0 0 0 0 0 1Navicula arvensis fo. major 

Mang.

1 0 0 0 0 0 0 1 0 0 0

Navicula arvensis Hustedt 5 0 1 1 1 0 1 0 1 0 0Navicula capitatoradiata Germain

3 0 0 1 0 0 0 0 0 1 1

Navicula cincta (Ehr.) Ralfs 1 0 0 0 0 1 0 0 0 0 0Navicula cryptocephala Kützing 1 0 0 0 0 0 0 0 1 0 0Navicula cryptotenella L.B. in 

Kramm. & L.-B.

9 1 1 0 1 1 1 1 1 1 1

Navicula erifuga Lange-Bert. 1 0 0 0 0 1 0 0 0 0 0Navicula exigua var. capitata 

Patr.

1 0 0 0 1 0 0 0 0 0 0

Navicula festiva Krass. 1 0 0 0 0 0 0 1 0 0 0Navicula gregaria Donk. 10 1 1 1 1 1 1 1 1 1 1Navicula hustedtii Krass. 3 0 0 0 1 0 0 1 1 0 0Navicula integra (W. Sm.) Ralfs 1 0 1 0 0 0 0 0 0 0 0Navicula menisculus Schum. 1 0 0 0 0 0 0 0 0 1 0Navicula minima Grunow 7 0 0 1 1 1 1 1 1 1 0Navicula notha Wallace 3 0 0 0 0 1 1 0 0 0 1Navicula praeterita Hustedt 1 0 1 0 0 0 0 0 0 0 0Navicula radiosa Kützing 10 1 1 1 1 1 1 1 1 1 1Navicula recens Lange-Bert. 10 1 1 1 1 1 1 1 1 1 1Navicula rostellata Kützing 2 0 0 1 0 0 0 0 1 0 0Navicula sanctaecrucis Østrup 6 1 0 1 1 0 0 1 1 0 1Navicula schroeteri var. escambia Patr. 10 1 1 1 1 1 1 1 1 1 1

Table 5. Pe [Frequency of occurrence refers to the number of samples in which a taxon was found. ”?” denotes unidentified species]

22 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Taxon Frequency of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Navicula subminuscula Mang. 10 1 1 1 1 1 1 1 1 1 1Navicula tenelloides Hustedt 1 1 0 0 0 0 0 0 0 0 0Navicula tripunctata (O. F. 

Müll.) Bory

4 1 0 1 0 0 1 0 0 1 0

Navicula trivialis Lange-Bertalot 1 0 0 0 0 0 0 0 0 1 0Navicula veneta Kützing 2 0 0 0 0 1 0 1 0 0 0Navicula viridulacalcis (Hustedt) Lange-Bertalot 7 0 1 1 1 0 1 1 1 1 0Neidium ampliatum (Ehr.) 

Kramm.

1 0 0 1 0 0 0 0 0 0 0

Nitzschia aequorea Hustedt 2 0 1 0 1 0 0 0 0 0 0Nitzschia amphibia Grunow 10 1 1 1 1 1 1 1 1 1 1Nitzschia cf. acidoclinata 1 0 0 0 1 0 0 0 0 0 0Nitzschia cf. rosenstockii LangeBert. 1 0 0 0 1 0 0 0 0 0 0Nitzschia clausii Hantz. 3 0 0 0 0 1 1 0 0 0 1Nitzschia dissipata (Kützing) 

Grunow

8 1 1 1 0 1 1 0 1 1 1

Nitzschia filiformis (W. Sm.) 

V. H.

1 0 0 0 0 0 0 0 0 0 1

Nitzschia flexa Schum. 2 0 0 0 0 1 1 0 0 0 0Nitzschia fonticola Grunow 10 1 1 1 1 1 1 1 1 1 1Nitzschia heufleriana Grunow 1 0 0 0 1 0 0 0 0 0 0Nitzschia inconspicua Grunow 10 1 1 1 1 1 1 1 1 1 1Nitzschia intermedia Hantz. ex 

Cl. et Grun.

1 0 0 0 0 0 0 0 0 1 0

Nitzschia lanceolata W. Sm. 1 0 0 0 0 0 0 0 0 1 0Nitzschia linearis (Ag. ex W. 

Sm.) W. Sm.

4 1 1 1 0 0 0 0 0 1 0

Nitzschia nana Grun. in V. H. 1 0 0 0 0 1 0 0 0 0 0Nitzschia palea (Kützing) Smith 10 1 1 1 1 1 1 1 1 1 1Nitzschia reversa W. Sm. 8 1 1 1 0 1 1 1 0 1 1

Table 5. Pe [Frequency of occurrence refers to the number of samples in which a taxon was found. ”?” denotes unidentified species]

Tables 23
Taxon Frequency of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Nitzschia sigma (Kütz.) W. Sm. 2 0 0 0 0 0 1 0 0 1 0Nitzschia siliqua Arch. 1 0 1 0 0 0 0 0 0 0 0Nitzschia sinuata var. tabellaria 

(Grun.) Grun. in V.H.

2 0 0 0 0 0 0 1 0 0 1

Pinnularia intermedia (Lagerst.) 

Cl.

1 1 0 0 0 0 0 0 0 0 0

Placoneis clementis (Grun) Cox 7 1 0 1 1 0 0 1 1 1 1Placoneis elginensis (Greg.) Cox 1 0 0 0 0 0 0 1 0 0 0Plagiotropis lepidoptera var. 

proboscidea (Cl.) Reim.

1 0 0 0 0 0 0 0 0 0 1

Planothidium apiculatum (Patrick) Lange-Bertalot

4 0 0 1 1 0 0 0 1 0 1

Planothidium biporomum (Hohn 

et Hellerman) Lange-Bertalot

2 0 0 1 1 0 0 0 0 0 0

Planothidium delicatulum (Kützing) Round et Bukhtiyarova

1 0 0 0 0 0 0 0 0 1 0

Planothidium lanceolatum 

(Brébisson ex Kützing) Lange-Bertalot

8 1 1 1 1 0 0 1 1 1 1

Planothidium rostratum (Østrup) 

Lange-Bertalot

4 0 0 1 1 0 0 1 1 0 0

Pleurosigma salinarum Grunow 1 0 0 0 0 0 0 0 0 0 1Pleurosira laevis (Ehrenberg) 

Compere

2 0 0 0 0 0 0 0 1 1 0

Psammothidium bioretii (Germ.) 

Bukht. et Round

1 0 0 0 1 0 0 0 0 0 0

Pseudostaurosira brevistriata 

(Grun. in V.H.) Williams & Round

3 1 0 1 0 0 0 0 0 1 0

Reimeria sinuata (Greg.) Kociolek & Stoermer

3 0 0 1 0 0 0 0 0 1 1

Rhoicosphenia abbreviata 

(Agardh) Lange-Bertalot

7 1 1 1 0 0 0 1 1 1 1

Table 5. Pe [Frequency of occurrence refers to the number of samples in which a taxon was found. ”?” denotes unidentified species]

24 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Taxon Frequency of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Rhopalodia operculata (C. Ag.) 

Häkens.

1 0 0 0 0 0 0 0 1 0 0

Sellaphora bacillum (Ehr.) Mann 3 0 0 1 1 0 0 0 0 1 0Sellaphora pupula (Kütz.) 

Meresckowsky

9 1 1 1 1 1 0 1 1 1 1

Sellaphora rectangularis (Greg.) 

Lange-Bertalot & Metzeltin

1 0 0 0 0 0 0 1 0 0 0

Sellaphora seminulum (Grun.) 

Mann

8 0 0 1 1 1 1 1 1 1 1

Skeletonema potamos (Weber) 

Hasle

2 1 0 0 0 0 0 0 0 0 1

Staurosira construens var. venter 

(Ehr.) Hamilton

10 1 1 1 1 1 1 1 1 1 1

Staurosirella pinnata (Ehrenberg) Williams et Round 8 1 1 1 1 0 0 1 1 1 1Surirella brebissonii Kramm. & 

Lange-Bert.

3 1 1 0 0 0 0 0 0 1 0

Surirella minuta Bréb. 1 0 0 1 0 0 0 0 0 0 0Surirella tenera Greg. 1 0 0 0 1 0 0 0 0 0 0Synedra ulna (Nitz.) Ehr. 6 1 1 1 1 0 0 1 1 0 0Tabellaria flocculosa (Roth) 

Kütz.

1 0 1 0 0 0 0 0 0 0 0

Tabularia tabulata (C. A. Ag.) 

Snoeijs

1 0 0 0 0 0 0 0 1 0 0

Thalassiosira pseudonana Hasle 

& Heimdal

1 0 1 0 0 0 0 0 0 0 0

Thalassiosira weissflogii (Grun.) 

Fryxell & Hasle

3 0 0 0 1 0 0 0 0 1 1

Tryblionella apiculata Greg. 4 1 1 0 0 0 0 0 0 1 1Tryblionella calida (Grun.) 

Mann

3 0 0 0 0 1 1 0 0 1 0

Tryblionella levidensis Wm. Sm. 2 0 0 0 1 0 0 0 1 0 0Cyanophyta (Blue-green algae)

Table 5. Pe [Frequency of occurrence refers to the number of samples in which a taxon was found. ”?” denotes unidentified species]

Tables 25
Taxon Frequency of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Lyngbya sp. 2 0 0 1 1 0 0 0 0 0 0Microcystis aeruginosa Kützing 2 0 1 0 0 0 0 0 0 0 1Oscillatoria sp. 6 1 0 1 1 0 0 1 0 1 1

Table 5. Pe [Frequency of occurrence refers to the number of samples in which a taxon was found. ”?” denotes unidentified species]

26 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Scientific Name Taxa code Salt Slough Merced River Orestimba CreeK Tuolumne River San Joaquin River June September June September June September June September June September

Chlorophyta (Green algae)Scenedesmus quadricauda var. 

longispina fo. assymmetricus (Hortobágyi) Uherkovich

52 0 0 0 141,608 0 0 0 0 0 31,859

Chrysophyta (Golden algae, all 

taxa listed are diatoms)

Achnanthes oblongella Østrup — 0 0 0 14,373 0 0 0 0 0 0Achnanthes subhudsonis var. 

kraeuselii (Cholnoky) Cholnoky

1 0 0 13,561 0 0 0 14,387 0 0 0

Achnanthidium exiguum var. heterovalvum (Krasske) Czarnecki 2 0 21,287 0 57,491 0 0 14,387 59,814 0 0Achnanthidium minutissimum (Kützing) Czarnecki 3 0 0 23,248 0 50,107 5,569 0 99,690 0 0Achnanthidium pyrenaicum (Hustedt) Kobayasi 4 0 0 11,624 28,746 0 0 43,160 19,938 0 0Adlafia bryophila (Petersen) LangeBertalot — 0 0 0 0 0 0 0 19,938 0 0Amphora acutiuscula Kützing — 0 0 0 0 0 0 0 0 0 31,753Amphora inariensis Krammer 5 0 0 0 0 15,418 11,137 0 0 7,086 0Amphora ovalis (Kützing) Kützing — 0 0 0 0 0 0 28,773 0 0 0Amphora veneta Kützing 6 0 10,644 0 0 0 5,569 0 39,876 35,432 841,452Bacillaria paradoxa Gmelin 7 5,202 138,369 7,749 43,118 0 0 14,387 0 7,086 0Brachysira serians (Brebisson) 

Round et Mann

— 0 0 0 0 0 5,569 0 0 0 0

Caloneis sp. 1 ? — 0 0 0 0 0 5,569 0 0 0 0Cavinula jaernefelti (Hustedt) Mann 

and Stickle

— 0 0 0 14,373 0 0 0 0 0 0

Cocconeis cf. neothumensis Krammer — 0 0 1,937 0 0 0 0 0 0 0Cocconeis disculus (Schumann) 

Cleve

— 226 0 0 0 0 0 0 0 0 0

Cocconeis pediculus Ehrenberg — 226 0 0 0 0 0 0 0 0 0

Table 6. Periphyton ta [Periphyton taxa units are density in cells/cm2. Taxa codes were only assigned to species occurring in more than one sample. —, no code assigned; “?” denotes unidentified species]

Tables 27
Scientific Name Taxa code Salt Slough Merced River Orestimba CreeK Tuolumne River San Joaquin River June September June September June September June September June September

Cocconeis placentula var. lineata 

(Ehrenberg) Van Heurck

8 0 10,644 81,367 57,491 0 0 374,055 199,379 42,519 79,382

Craticula accomoda (Hustedt) Mann

— 0 0 0 0 0 0 0 0 0 15,876

Craticula cuspidata (Kützing) Mann 9 0 0 1,937 0 0 0 14,387 0 0 0Craticula molestiformis (Hustedt) 

Lange-Bertalot

10 0 21,287 0 0 15,418 16,706 0 19,938 14,173 0

Craticula submolesta (Hustedt) 

Lange-Bertalot

— 0 0 0 0 3,854 0 0 0 0 0

Cyclostephanos invisitatus (Hohn et 

Hellerman) Theriot, Stoermer et Håkansson

— 0 0 0 0 0 0 0 0 21,259 0

Cyclotella atomus Hustedt 11 2,488 0 0 0 0 44,549 0 0 106,297 190,517Cyclotella meneghiniana Kützing 12 6,558 478,968 1,937 0 0 5,569 0 39,876 552,742 571,552Cyclotella pseudostelligera Hustedt

— 0 0 0 0 0 0 28,773 0 0 0

Cymbella affinis Kützing

— 0 0 0 0 0 0 0 0 0 31,753

Cymbella laevis Naegeli ex Kützing

— 0 0 0 0 0 5,569 0 0 0 0

Diadesmis confervacea Kützing 13 452 0 0 0 0 0 0 0 35,432 0Diatoma vulgaris Bory 14 0 0 7,749 0 0 0 0 0 7,086 0Diploneis oblongella (Naegeli ex 

Kützing) Ross

— 0 10,644 0 0 0 0 0 0 0 0

Diploneis parma Cleve

— 452 0 0 0 0 0 0 0 0 0

Encyonema lunatum (Smith) Van 

Heurck

15 0 0 1,937 0 0 5,569 0 0 0 0

Encyonema minutum (Hilse) Mann 16 0 0 13,561 14,373 3,854 11,137 0 19,938 0 15,876Encyonema prostratum (Berkeley) 

Kützing

— 0 0 0 0 3,854 0 0 0 0 0

Eunotia incisa Smith ex Gregory

— 0 0 0 14,373 0 0 0 0 0 0

Fallacia pygmaea (Kützing) Stickle 

et Mann

17 905 10,644 0 0 0 5,569 0 0 7,086 79,382

Fragilaria capucina Desmazières

— 0 0 0 0 0 0 0 0 0 15,876

Fragilaria capucina var. rumpens 

(Kützing) Lange-Bertalot

18 226 0 5,812 0 3,854 0 0 0 7,086 0

Table 6. Periphyton taxa from r [Periphyton taxa units are density in cells/cm2. Taxa codes were only assigned to species occurring in more than one sample. —, no code assigned; “?” denotes unidentified species]

28 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Scientific Name Taxa code Salt Slough Merced River Orestimba CreeK Tuolumne River San Joaquin River June September June September June September June September June September

Gomphonema kobayasii Kociolek & 

Kingston

— 0 0 0 0 3,854 0 0 0 0 0

Gomphonema mexicanum Grun. in 

V. H.

— 0 0 0 0 0 0 14,387 0 0 0

Gomphonema parvulius (Lange-Bertalot et Reichardt) Lange-Bertalot 

et Reichardt

19 0 0 0 0 7,709 0 0 79,752 0 0

Gomphonema parvulum (Kütz.) 

Kütz.

20 452 21,287 0 14,373 7,709 16,706 0 19,938 0 0

Gyrosigma spencerii (Quek.) Griff. 

& Henfr.

— 0 0 0 0 0 55,686 0 0 0 0

Hippodonta capitata (Ehrenberg) 

Lange-Bertalot, Metzeltin et Witkowski

21 452 21,287 5,812 28,746 0 0 14,387 39,876 85,037 365,158

Luticola mutica (Kutz.) Mann — 0 0 0 0 3,854 0 0 0 0 0Luticola nivalis (Ehrenberg) Mann 22 0 0 0 0 19,272 33,412 0 0 0 0Mayamaea atomus (Kützing) LangeBertalot 23 0 0 9,687 0 3,854 0 14,387 39,876 0 0Melosira varians Ag. 24 226 10,644 9,687 14,373 0 0 0 39,876 63,778 15,876Navicula arvensis Hustedt — 0 0 0 0 0 11,137 0 0 0 0Navicula cryptotenella L.B. in 

Kramm. & L.-B.

25 905 53,219 0 0 543,471 100,235 57,547 0 0 79,382

Navicula exigua var. capitata Patr. — 0 0 0 28,746 0 0 0 0 0 0Navicula festiva Krass. — 0 0 0 0 0 0 14,387 0 0 0Navicula gregaria Donk. 26 3,392 10,644 3,875 57,491 73,234 334,117 172,641 19,938 21,259 63,506Navicula minima Grunow 27 0 0 25,185 100,610 11,563 5,569 374,055 39,876 35,432 0Navicula notha Wallace 28 0 0 0 0 69,379 361,960 0 0 0 0Navicula praeterita Hustedt — 0 10,644 0 0 0 0 0 0 0 0Navicula radiosa Kützing 29 2,262 42,575 0 14,373 80,943 211,607 14,387 39,876 99,210 142,888Navicula recens Lange-Bert. 30 8,820 10,644 0 0 389,295 501,175 86,320 0 240,939 523,923Navicula rostellata Kützing 31 0 0 79,430 0 0 0 0 99,690 0 0Navicula sanctaecrucis Østrup 32 0 0 0 28,746 0 0 158,254 0 0 476,293

Table 6. Periphyton taxa from r [Periphyton taxa units are density in cells/cm2. Taxa codes were only assigned to species occurring in more than one sample. —, no code assigned; “?” denotes unidentified species]

Tables 29
Scientific Name Taxa code Salt Slough Merced River Orestimba CreeK Tuolumne River San Joaquin River June September June September June September June September June September

Navicula schroeteri var. escambia 

Patr.

33 0 21,287 0 0 154,176 16,706 0 0 70,864 0

Navicula subminuscula Mang. 34 452 0 29,060 71,864 15,418 5,569 86,320 139,566 14,173 15,876Navicula tripunctata (O. F. Müll.) 

Bory

35 0 0 0 0 0 38,980 0 0 21,259 0

Navicula trivialis Lange-Bertalot

— 0 0 0 0 0 0 0 0 63,778 0

Navicula viridulacalcis (Hustedt) 

Lange-Bertalot

36 0 63,862 42,621 114,983 0 100,235 14,387 0 49,605 0

Neidium ampliatum (Ehr.) Kramm.

— 0 0 1,937 0 0 0 0 0 0 0

Nitzschia amphibia Grunow 37 3,845 95,794 11,624 100,610 80,943 83,529 100,707 179,441 42,519 174,641Nitzschia clausii Hantz.

— 0 0 0 0 0 0 0 0 0 111,135

Nitzschia dissipata (Kützing) 

Grunow

38 905 21,287 9,687 0 15,418 194,902 0 0 0 63,506

Nitzschia flexa Schum. 39 0 0 0 0 7,709 11,137 0 0 0 0Nitzschia fonticola Grunow 40 12,891 627,981 1,937 28,746 15,418 50,118 115,094 179,441 85,037 31,753Nitzschia inconspicua Grunow 41 1,357 53,219 0 0 558,889 0 0 0 21,259 0Nitzschia lanceolata W. Sm.

— 0 0 0 0 0 0 0 0 7,086 0

Nitzschia linearis (Ag. ex W. Sm.) 

W. Sm.

— 0 0 0 0 0 0 0 0 28,346 0

Nitzschia nana Grun. in V. H.

— 0 0 0 0 57,816 0 0 0 0 0

Nitzschia palea (Kützing) Smith 42 63,549 3,608,229 46,495 301,830 84,797 1,007,919 676,176 199,379 956,669 3,175,289Nitzschia reversa W. Sm. 43 9,272 659,912 1,937 0 0 27,843 0 0 28,346 0Nitzschia sigma (Kütz.) W. Sm. 44 0 0 0 0 0 22,274 0 0 14,173 0Nitzschia sinuata var. tabellaria 

(Grun.) Grun. in V.H.

— 0 0 0 0 0 0 14,387 0 0 0

Pinnularia intermedia (Lagerst.) Cl.

— 2,488 0 0 0 0 0 0 0 0 0

Placoneis clementis (Grun) Cox 46 226 0 15,498 143,728 0 0 86,320 119,628 0 79,382Placoneis elginensis (Greg.) Cox

— 0 0 0 0 0 0 14,387 0 0 0

Plagiotropis lepidoptera var. proboscidea (Cl.) Reim.

— 0 0 0 0 0 0 0 0 0 15,876

Planothidium apiculatum (Patrick) 

Lange-Bertalot

47 0 0 5,812 0 0 0 0 19,938 0 15,876

Table 6. Periphyton taxa from r [Periphyton taxa units are density in cells/cm2. Taxa codes were only assigned to species occurring in more than one sample. —, no code assigned; “?” denotes unidentified species]

30 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Scientific Name Taxa code Salt Slough Merced River Orestimba CreeK Tuolumne River San Joaquin River June September June September June September June September June September

Planothidium biporomum (Hohn et 

Hellerman) Lange-Bertalot

— 0 0 3,875 0 0 0 0 0 0 0

Planothidium delicatulum (Kützing) 

Round et Bukhtiyarova

— 0 0 0 0 0 0 0 0 7,086 0

Planothidium lanceolatum (Brébisson ex Kützing) Lange-Bertalot 48 452 10,644 30,997 0 0 0 86,320 199,379 7,086 0Planothidium rostratum (Østrup) 

Lange-Bertalot

49 0 0 0 158,101 0 0 187,027 19,938 0 0

Psammothidium bioretii (Germ.) 

Bukht. et Round

— 0 0 0 28,746 0 0 0 0 0 0

Pseudostaurosira brevistriata (Grun. 

in V.H.) Williams & Round

50 226 0 3,875 0 0 0 0 0 21,259 0

Reimeria sinuata (Greg.) Kociolek & 

Stoermer

— 0 0 1,937 0 0 0 0 0 0 0

Rhoicosphenia abbreviata (Agardh) 

Lange-Bertalot

51 0 0 0 0 0 0 0 19,938 0 47,629

Rhopalodia operculata (C. Ag.) 

Häkens.

— 0 0 0 0 0 0 0 19,938 0 0

Sellaphora bacillum (Ehr.) Mann 53 0 0 5,812 28,746 0 0 0 0 7,086 0Sellaphora pupula (Kütz.) Meresckowsky 54 1,131 10,644 27,122 43,118 3,854 0 1,424,285 179,441 262,198 428,664Sellaphora rectangularis (Greg.) 

Lange-Bertalot & Metzeltin

— 0 0 0 0 0 0 14,387 0 0 0

Sellaphora seminulum (Grun.) Mann 55 0 0 11,624 14,373 0 5,569 28,773 39,876 28,346 0Staurosira construens var. venter 

(Ehr.) Hamilton

56 3,845 244,806 583,131 7,042,690 7,709 11,137 3,740,547 8,593,254 942,497 1,698,780

Staurosirella pinnata (Ehrenberg) 

Williams et Round

57 226 0 25,185 0 0 0 589,855 1,076,649 134,642 79,382

Surirella brebissonii Kramm. & 

Lange-Bert.

— 0 10,644 0 0 0 0 0 0 0 0

Synedra ulna (Nitz.) Ehr. 58 905 21,287 0 28,746 0 0 28,773 59,814 0 0Tabellaria flocculosa (Roth) Kütz. — 0 10,644 0 0 0 0 0 0 0 0Thalassiosira weissflogii (Grun.) 

Fryxell & Hasle

59 0 0 0 0 0 0 0 0 14,173 63,506

Table 6. Periphyton taxa from r [Periphyton taxa units are density in cells/cm2. Taxa codes were only assigned to species occurring in more than one sample. —, no code assigned; “?” denotes unidentified species]

Tables 31
Scientific Name Taxa code Salt Slough Merced River Orestimba CreeK Tuolumne River San Joaquin River June September June September June September June September June September

Tryblionella apiculata Greg. 60 678 53,219 0 0 0 0 0 0 28,346 15,876Tryblionella calida (Grun.) Mann 61 0 0 0 0 0 5,569 0 0 14,173 0Cyanophyta (Blue-green algae)

—

Microcystis aeruginosa Kützing

— 0 0 0 0 0 0 0 0 0 31,859

Oscillatoria sp. 45 0 0 0 56,643 0 0 27,759 0 13,351 0

Table 6. Periphyton taxa from r [Periphyton taxa units are density in cells/cm2. Taxa codes were only assigned to species occurring in more than one sample. —, no code assigned; “?” denotes unidentified species]

32 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Taxon

Frequency 

of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Total taxa per sampling 

site

19 24 49 49 33 24 54 51 40 54

Platyhelminthes

Turbellaria 3 0 0 0 0 1 1 0 1 0 0

Nemertea

Enopla

Hoplonemertea

Tetrastemmatidae

Prostoma sp. 5 0 0 0 1 1 1 1 1 0 0

Nematoda 3 0 0 0 0 1 1 0 0 0 1

Bryozoa

Phylactolaemata

Urnatella gracilis

 Leidy

3 0 0 0 0 1 0 1 0 0 1

Mollusca

Gastropoda

Basommatophora

Ancylidae

Ferrissia sp. 3 0 0 1 0 1 0 0 1 0 0

Lymnaeidae 2 0 0 0 0 0 1 0 0 0 1

Pseudosuccinea 

columella (Say)

2 0 0 1 0 0 0 0 1 0 0

Fossaria sp. 1 0 0 0 1 0 0 0 0 0 0

Physidae

Physella sp. 9 1 1 1 1 1 1 0 1 1 1

Planorbidae

Menetus sp. 3 0 0 1 0 0 0 0 1 0 1

Bivalvia

Veneroida

Corbiculidae

Corbicula sp. 9 0 1 1 1 1 1 1 1 1 1

Annelida

Oligochaeta

Megadrile 3 0 0 0 1 1 1 0 0 0 0

Lumbriculida

Lumbriculidae 1 0 0 0 0 1 0 0 0 0 0

Tubificida

Naididae 10 1 1 1 1 1 1 1 1 1 1

Table 7. Macroinvertebrate taxa collected from each of five sites in June and September 2001 in the San Joaquin River Basin, 

California.

[Frequency of occurrence refers to the number of samples in which a taxon was found.]

Tables 33
Taxon

Frequency 

of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Tubificidae 4 1 0 0 0 1 1 0 0 0 1

Enchytraeida

Enchytraeidae 2 0 0 0 0 1 1 0 0 0 0

Polychaeta 1 0 0 0 0 0 1 0 0 0 0

Sabellida

Sabellidae 2 0 0 0 0 1 1 0 0 0 0

Arthropoda

Arachnida

Acari 8 0 0 1 1 1 1 1 1 1 1

Malacostraca

Isopoda 1 0 0 0 0 0 0 0 0 1 0

Decapoda

Cambaridae 1 0 0 0 1 0 0 0 0 0 0

Amphipoda 1 0 0 0 0 0 0 0 0 0 1

Corophiidae

Corophium sp. 4 1 1 0 0 0 0 0 0 1 1

Gammaridae

Gammarus sp. 2 1 0 0 0 0 1 0 0 0 0

Hyalellidae

Hyalella azteca 

(Saussure)

5 1 0 1 1 1 0 0 0 1 0

Insecta

Collembola 1 0 0 0 0 0 0 0 1 0 0

Ephemeroptera

Baetidae 7 0 0 1 1 1 0 1 1 1 1

Baetis sp. 1 0 0 0 0 0 0 0 0 0 1

Baetis tricaudatus Dodds

1 0 0 0 0 0 0 0 0 0 1

Callibaetis sp. 5 1 1 1 1 0 0 1 0 0 0

Camelobaetidius

sp.

3 0 0 1 0 0 0 1 1 0 0

Centroptilum/

Procloeon sp.

4 0 0 0 0 0 0 1 1 1 1

Fallceon quilleri 

(Dodds)

7 0 1 1 1 0 0 1 1 1 1

Heterocloeon sp. 2 0 0 0 1 0 0 1 0 0 0

Caenidae

Caenis sp. 2 0 0 0 1 0 0 0 1 0 0

Ephemerellidae

Ephemerella sp. 1 0 0 1 0 0 0 0 0 0 0

Heptageniidae 3 0 0 1 0 0 0 0 1 0 1

Table 7. Macroinvertebrate taxa collected from each of five sites in June and September 2001 in the San Joaquin River Basin, 

California.—Continued

[Frequency of occurrence refers to the number of samples in which a taxon was found.]

34 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Taxon

Frequency 

of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Heptagenia sp. 2 0 0 0 0 0 0 0 0 1 1

Leptohyphidae

Tricorythodes sp. 3 0 0 1 0 0 0 1 1 0 0

Odonata

Zygoptera

Calopterygidae

Hetaerina sp. 3 0 0 1 1 0 0 1 0 0 0

Hetaerina 

americana 

(Fabricius)

1 0 0 1 0 0 0 0 0 0 0

Coenagrionidae 6 1 1 1 1 0 0 1 1 0 0

Argia sp. 2 0 0 0 0 0 0 1 0 0 1

Argia emma 

Kennedy

1 0 0 0 0 0 0 0 1 0 0

Coenagrion/

Enallagma 

sp.

3 0 1 0 1 0 0 1 0 0 0

Anisoptera

Aeshnidae

Anax sp. 1 0 0 0 0 0 0 1 0 0 0

Gomphidae 1 0 0 0 1 0 0 0 0 0 0

Hemiptera

Corixidae 1 0 0 0 0 0 1 0 0 0 0

Palmacorixa sp. 1 1 0 0 0 0 0 0 0 0 0

Trichocorixa sp. 7 1 1 1 1 0 0 1 0 1 1

Corisella sp. 2 0 0 1 0 0 0 1 0 0 0

Gelastocoridae

Gelastocoris 

oculatus 

(Fabricius)

2 0 0 0 0 0 0 0 1 1 0

Gerridae 2 0 0 0 1 0 0 0 1 0 0

Naucoridae

Ambrysus sp. 1 0 0 0 0 0 0 0 0 1 0

Saldidae

Saldula sp. 1 0 0 0 0 0 0 1 0 0 0

Veliidae

Rhagovelia sp. 3 1 1 1 0 0 0 0 0 0 0

Rhagovelia distincta 

Champion

2 0 1 1 0 0 0 0 0 0 0

Trichoptera

Hydroptilidae 3 0 0 0 1 0 0 1 0 1 0

Table 7. Macroinvertebrate taxa collected from each of five sites in June and September 2001 in the San Joaquin River Basin, 

California.—Continued

[Frequency of occurrence refers to the number of samples in which a taxon was found.]

Tables 35
Taxon

Frequency 

of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Hydroptila sp. 7 0 0 1 1 1 0 1 1 1 1

Hydropsychidae 6 0 0 1 1 0 0 1 1 1 1

Hydropsyche sp. 8 1 1 1 1 0 0 1 1 1 1

Hydropsyche 

californica 

Banks

8 1 1 1 1 0 0 1 1 1 1

Leptoceridae

Nectopsyche sp. 2 0 0 1 0 0 0 0 1 0 0

Nectopsyche 

gracilis (Banks)

2 0 0 0 1 0 0 1 0 0 0

Lepidoptera 2 0 0 0 1 1 0 0 0 0 0

Pyralidae

Petrophila sp. 3 0 0 0 0 0 0 0 1 1 1

Coleoptera

Dytiscidae

Oreodytes sp. 1 0 0 0 0 0 0 0 0 0 1

Laccophilus sp. 2 0 0 0 0 0 0 0 1 0 1

Elmidae

Microcylloepus

sp.

1 0 0 0 1 0 0 0 0 0 0

Hydraenidae

Ochthebius sp. 1 0 0 0 0 1 0 0 0 0 0

Hydrophilidae 3 0 0 1 1 0 0 0 0 0 1

Enochrus sp. 1 0 0 0 0 0 0 0 0 0 1

Tropisternus sp. 1 0 1 0 0 0 0 0 0 0 0

Diptera

Nematocera 1 0 0 0 0 1 0 0 0 0 0

Ceratopogonidae 1 0 0 0 0 1 0 0 0 0 0

Dasyheleinae

Dasyhelea sp. 2 0 0 0 0 1 0 0 0 0 1

Chironomidae 7 0 0 1 1 1 0 1 1 1 1

Chironominae 5 0 0 1 1 0 0 1 1 0 1

Chironomini 

(tribe)

5 0 1 1 0 0 1 1 0 0 1

Apedilum

sp.

1 0 0 0 0 0 0 0 0 0 1

Chironomus

sp.

3 1 0 0 0 0 0 1 1 0 0

Cryptochironomus 

sp.

4 0 0 0 1 0 0 1 1 1 0

Table 7. Macroinvertebrate taxa collected from each of five sites in June and September 2001 in the San Joaquin River Basin, 

California.—Continued

[Frequency of occurrence refers to the number of samples in which a taxon was found.]

36 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Taxon

Frequency 

of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Dicrotendipes sp.

9 1 1 1 1 0 1 1 1 1 1

Endotribelos 

hesperium 

(Sublette)

1 0 1 0 0 0 0 0 0 0 0

Glyptotendipes sp.

2 0 0 1 0 0 0 0 0 0 1

Goeldichironomus 

sp.

1 0 1 0 0 0 0 0 0 0 0

Nilothauma

sp.

2 0 0 0 1 0 0 1 0 0 0

Parachironomus

sp.

1 0 0 0 0 0 0 0 0 0 1

Paracladopelma sp.

1 0 0 0 0 0 0 1 0 0 0

Paralauterborniella 

nigrohalterale

(Malloch)

2 0 0 1 0 0 0 0 1 0 0

Polypedilum

sp.

5 0 0 1 1 0 0 1 1 1 0

Robackia sp. 1 0 0 0 0 0 0 0 1 0 0

Stenochironomus

sp.

4 0 0 1 1 0 0 0 1 1 0

Tanytarsini 4 0 0 1 0 0 0 1 0 1 1

Cladotanytarsus sp.

5 0 0 0 1 0 0 1 1 1 1

Micropsectra/Tanytarsus sp.

6 0 0 1 1 0 0 1 1 1 1

Paratanytarsus sp.

1 1 0 0 0 0 0 0 0 0 0

Rheotanytarsus sp.

6 0 0 1 1 0 0 1 1 1 1

Tanytarsus

sp.

6 0 0 1 1 0 0 1 1 1 1

Orthocladiinae 6 0 0 1 1 1 0 0 1 1 1

Psectrocladius sp.

1 0 0 0 0 0 0 1 0 0 0

Pseudosmittia

sp.

1 0 0 0 0 1 0 0 0 0 0

Table 7. Macroinvertebrate taxa collected from each of five sites in June and September 2001 in the San Joaquin River Basin, 

California.—Continued

[Frequency of occurrence refers to the number of samples in which a taxon was found.]

Tables 37
Taxon

Frequency 

of

occurrence

Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River

June September June September June September June September June September

Cricotopus/

Orthocladius sp.

8 0 1 1 1 1 1 1 0 1 1

Cricotopus sp. 10 1 1 1 1 1 1 1 1 1 1

Cricotopus 

bicinctus 

group

10 1 1 1 1 1 1 1 1 1 1

Nanocladius

sp.

4 0 1 0 0 1 0 1 0 0 1

Parakiefferiella sp.

4 0 0 0 1 0 0 0 1 1 1

Rheocricotopus sp.

2 0 0 0 0 1 0 0 0 1 0

Synorthocladius sp.

1 0 0 1 0 0 0 0 0 0 0

Thienemanniella sp.

3 0 0 1 0 0 0 1 1 0 0

Tanypodinae

Pentaneurini 1 0 0 1 0 0 0 0 0 0 0

Ablabesmyia

sp.

4 0 0 1 1 0 0 1 1 0 0

Thienemannimyia

group sp. 

(Coffman 

and Ferrington)

4 0 1 0 0 0 1 1 0 0 1

Tanypodini

Tanypus sp. 3 1 1 0 0 0 0 0 0 0 1

Psychodidae

Psychoda sp. 1 0 0 0 0 0 1 0 0 0 0

Simuliidae 5 0 0 0 1 0 0 1 1 1 1

Simulium sp. 4 0 0 0 0 0 0 1 1 1 1

Tipulidae 1 0 0 0 1 0 0 0 0 0 0

Antocha sp. 1 0 0 0 0 0 0 0 0 1 0

Limonia sp. 1 0 0 0 0 0 0 0 1 0 0

Brachycera 3 0 0 0 0 1 1 1 0 0 0

Tabanidae

Tabanus sp. 1 0 0 0 0 0 1 0 0 0 0

Empididae 1 0 0 0 0 0 0 1 0 0 0

Hemerodromia

sp.

5 0 0 1 0 1 0 1 0 1 1

Neoplasta sp. 2 0 0 0 0 0 0 1 1 0 0

Dolichopodidae 3 0 0 0 1 1 0 0 0 0 1

Table 7. Macroinvertebrate taxa collected from each of five sites in June and September 2001 in the San Joaquin River Basin, 

California.—Continued

[Frequency of occurrence refers to the number of samples in which a taxon was found.]

38 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Taxon Taxa code Frequency of occurrence Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River June September June September June September June September June September

Total taxa per sampling site 15 10 19 27 21 12 22 22 18 24Platyhelminthes

Turbellaria 1 3 0 0 0 0 18 25 0 62 0 0

Nemertea

Enopla

Hoplonemertea

Tetrastemmatidae

Prostoma sp. 2 4 0 0 0 139 54 148 0 132 0 0

Nematoda 3 4 0 135 0 0 1,089 1,582 0 0 0 285Bryozoa

Phylactolaemata

Urnatella gracilis Leidy 4 5 126 135 0 0 18 0 509 0 0 143

Mollusca

Gastropoda

Basommatophora

Ancylidae

Ferrissia sp. 5 2 0 0 48 0 18 0 0 0 0 0

Physidae

Physella sp. 6 2 0 0 0 69 127 0 0 0 0 0

Bivalvia

Veneroida

Corbiculidae

Corbicula sp. 7 7 126 135 0 69 36 41 0 132 0 577

Annelida

Oligochaeta

Megadrile — 1 0 0 0 10 0 0 0 0 0 0Lumbriculida

Table 8. Macroinvertebrate [Taxa codes were only assigned to taxa found in two or more samples. Frequency of occurrence refers to the number of samples in which a taxon was found. Macroinvertebrate taxa units are in organisms/m2; —, no code assigned.]

Tables 39
Taxon Taxa code Frequency of occurrence Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River June September June September June September June September June September

Lumbriculidae

— 1 0 0 0 0 42 0 0 0 0 0

Tubificida

Naididae 8 10 4,319 2,399 371 3,330 563 1,533 24,997 1,171 18,206 7,327Tubificidae 9 2 0 0 0 0 109 227 0 0 0 0

Enchytraeida 10 3 126 0 0 0 944 25 0 0 0 0

Polychaeta

Sabellida

Sabellidae

— 1 0 0 0 0 0 239 0 0 0 0

Arthropoda

Arachnida

Acari 11 8 0 0 3,155 4,301 381 25 13,771 7,952 2,342 2,730

Malacostraca

Amphipoda

Corophiidae

Corophium sp. 12 2 5,977 270 0 0 0 0 0 0 0 0

Gammaridae

Gammarus sp.

— 1 378 0 0 0 0 0 0 0 0 0

Hyalellidae

Hyalella azteca (Saussure) 13 3 0 0 0 69 18 0 0 0 258 0

Insecta

Ephemeroptera

Baetidae 14 7 0 0 141 347 18 0 3,060 784 781 713Caenidae

Caenis sp.

— 1 0 0 0 69 0 0 0 0 0 0

Heptageniidae 15 2 0 0 0 0 0 0 0 62 0 285

Heptagenia sp.

Leptohyphidae

Tricorythodes sp.

— 1 0 0 0 0 0 0 1,018 0 0 0

Odonata

Table 8. Macroinvertebrate taxa from [Taxa codes were only assigned to taxa found in two or more samples. Frequency of occurrence refers to the number of samples in which a taxon was found. Macroinvertebrate taxa units are in organisms/m2; —, no code assigned.]

40 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Taxon Taxa code Frequency of occurrence Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River June September June September June September June September June September

Zygoptera

Calopterygidae

Hetaerina sp. 16 3 0 0 12 69 0 0 1,018 0 0 0

Coenagrionidae 17 5 0 0 48 139 0 0 1,533 62 0 7

Trichoptera

Hydroptilidae

Hydroptila sp. 18 7 126 0 326 833 18 0 2,042 652 1,303 0

Hydropsychidae

Hydropsyche sp. 19 8 11,961 26,839 1,398 3,553 0 0 7,675 5,881 15,626 13,806

Lepidoptera

Pyralidae

Petrophila sp. 20 2 0 0 0 0 0 0 0 62 0 143

Coleoptera

Elmidae

Microcylloepus sp. — 1 0 0 0 69 0 0 0 0 0 0

Hydrophilidae — 1 0 0 0 69 0 0 0 0 0 0

Diptera

Nematocera

Ceratopogonidae 21 3 126 0 0 0 73 0 0 0 0 143Chironomidae

Chironominae

Chironomini (tribe)

Cryptochironomus sp. — 1 0 0 0 69 0 0 0 0 0 0Dicrotendipes sp. 22 8 889 667 141 2,775 0 0 1,533 388 1,303 2,010Endotribelos hesperium 

(Sublette) — 1 126 0 0 0 0 0 0 0 0 0

Glyptotendipes sp. — 1 0 0 0 0 0 0 0 0 0 862Goeldichironomus sp. — 1 0 270 0 0 0 0 0 0 0 0Nilothauma sp. 23 2 0 0 0 69 0 0 509 0 0 0

Table 8. Macroinvertebrate taxa from [Taxa codes were only assigned to taxa found in two or more samples. Frequency of occurrence refers to the number of samples in which a taxon was found. Macroinvertebrate taxa units are in organisms/m2; —, no code assigned.]

Tables 41
Taxon Taxa code Frequency of occurrence Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River June September June September June September June September June September

Parachironomus sp.

— 1 0 0 0 0 0 0 0 0 0 428

Paracladopelma sp.

— 1 0 0 0 0 0 0 509 0 0 0

Polypedilum sp. 24 3 0 0 512 1,734 0 0 0 0 258 0Stenochironomus sp. 25 4 0 0 93 208 0 0 0 264 258 0

Tanytarsini

Cladotanytarsus sp. 26 4 0 0 0 486 0 0 0 62 258 143Paratanytarsus sp.

— 1 511 0 0 0 0 0 0 0 0 0

Rheotanytarsus sp. 27 6 0 0 927 1,804 0 0 6,634 264 1,819 1,290Tanytarsus sp. 28 6 0 0 3,807 2,359 0 0 96,923 3,972 8,839 8,332

Orthocladiinae

Pseudosmittia sp.

— 1 0 0 0 0 18 0 0 0 0 0

Cricotopus sp. 29 10 4,199 6,807 560 1,873 2,015 346 7,658 590 9,626 3,015Nanocladius sp. 30 5 889 397 0 0 18 0 509 0 0 143Parakiefferiella sp. 31 4 0 0 0 416 0 0 0 194 523 285Rheocricotopus sp.

— 1 0 0 0 0 0 0 0 0 258 0

Synorthocladius sp.

— 1 0 0 48 0 0 0 0 0 0 0

Thienemanniella sp. 32 3 0 0 649 0 0 0 4,083 264 0 0

Tanypodinae

Pentaneurini

Ablabesmyia sp. 33 4 0 0 93 69 0 0 509 62 0 0Thienemannimyia group 

sp. (Coffman and Ferrington) 34 5 0 0 234 69 0 0 509 62 0 428

Psychodidae

Psychoda sp.

— 1 0 0 0 0 0 12 0 0 0 0

Simuliidae 36 3 0 0 0 0 0 0 1,533 0 258 285Tipulidae

Limoniinae 37 2 6 0 0 0 0 0 0 0 258 0

Brachycera

— 1 0 0 0 0 0 214 0 0 0 0

Empididae

Table 8. Macroinvertebrate taxa from [Taxa codes were only assigned to taxa found in two or more samples. Frequency of occurrence refers to the number of samples in which a taxon was found. Macroinvertebrate taxa units are in organisms/m2; —, no code assigned.]

42 Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, June and September, 2001
Taxon Taxa code Frequency of occurrence Salt Slough Merced River Orestimba Creek Tuolumne River San Joaquin River June September June September June September June September June September

Hemerodromia sp. 38 5 0 0 234 0 54 0 509 0 258 720Neoplasta sp. 35 2 0 0 0 0 0 0 2,551 62 0 0

Dolichopodidae 39 2 0 0 0 0 18 0 0 0 0 143

Table 8. Macroinvertebrate taxa from [Taxa codes were only assigned to taxa found in two or more samples. Frequency of occurrence refers to the number of samples in which a taxon was found. Macroinvertebrate taxa units are in organisms/m2; —, no code assigned.]

Tables 43