Benthic Macroinvertebrate Assemblages 

and Their Relations with Environmental 

Variables in the Sacramento and 

San Joaquin River Drainages, California, 

1993-1997

oo

NATIONAL WATER-QUALITY ASSESSMENT PROGRAM

Water-Resources Investigations Report 00-4125

U.S. Department of the Interior 

U.S. Geological Survey

Benthic Macroinvertebrate Assemblages and 

Their Relations with Environmental Variables in 

the Sacramento and San Joaquin River 

Drainages, California, 1993-1997

ByLarry R. Brown and Jason T. May 1

U.S. GEOLOGICAL SURVEY

Water-Resources Investigations Report 00-4125

National Water-Quality Assessment Program

ONi i

O 

CO 

CN

California State University Sacramento Foundation, Placer Hall, 6000 J Street, Sacramento, 

California 95619

Sacramento, California 

2000
U.S. DEPARTMENT OF THE INTERIOR 

BRUCE BABBITT, Secretary

U.S. GEOLOGICAL SURVEY 

Charles G. Groat, Director

The use of firm, trade, and brand names in this report is for identification purposes only and does 

not constitute endorsement by the U.S. Geological Survey.

For additional information write to:

District Chief

U.S. Geological Survey

Water Resources Division

Placer Hall

6000 J Street

Sacramento, California 95819-6129

Copies of this report can be purchased 

from:

U.S. Geological Survey 

Branch of Information Services 

Box 25286 

Denver, CO 80225-0286
FOREWORD

The mission of the U.S. Geological Survey 

(USGS) is to assess the quantity and quality of the 

earth resources of the Nation and to provide information that will assist resource managers and policymakers at Federal, State, and local levels in making sound 

decisions. Assessment of water-quality conditions and 

trends is an important part of this overall mission.

One of the greatest challenges faced by waterresources scientists is acquiring reliable information 

that will guide the use and protection of the Nation's 

water resources. That challenge is being addressed by 

Federal, State, interstate, and local water-resource 

agencies and by many academic institutions. These 

organizations are collecting water-quality data for a 

host of purposes that include: compliance with permits 

and water-supply standards; development of remediation plans for specific contamination problems; operational decisions on industrial, wastewater, or watersupply facilities; and research on factors that affect 

water quality. An additional need for water-quality 

information is to provide a basis on which regionaland national-level policy decisions can be based. Wise 

decisions must be based on sound information. As a 

society we need to know whether certain types of 

water-quality problems are isolated or ubiquitous, 

whether there are significant differences in conditions 

among regions, whether the conditions are changing 

over time, and why these conditions change from 

place to place and over time. The information can be 

used to help determine the efficacy of existing waterquality policies and to help analysts determine the 

need for and likely consequences of new policies.

To address these needs, the U.S. Congress appropriated funds in 1986 for the USGS to begin a pilot program in seven project areas to develop and refine the 

National Water-Quality Assessment (NAWQA) Program. In 1991, the USGS began full implementation of 

the program. The NAWQA Program builds upon an 

existing base of water-quality studies of the USGS, as 

well as those of other Federal, State, and local agencies. 

The objectives of the NAWQA Program are to:

 Describe current water-quality conditions 

for a large part of the Nation's freshwater 

streams, rivers, and aquifers.

 Describe how water quality is changing 

over time.

 Improve understanding of the primary 

natural and human factors that affect 

water-quality conditions.

This information will help support the development 

and evaluation of management, regulatory, and monitoring decisions by other Federal, State, and local 

agencies to protect, use, and enhance water resources.

The goals of the NAWQA Program are being 

achieved through ongoing and proposed investigations 

of 60 of the Nation's most important river basins and 

aquifer systems, which are referred to as study units. 

These study units are distributed throughout the 

Nation and cover a diversity of hydrogeologic settings. 

More than two-thirds of the Nation's freshwater use 

occurs within the 60 study units and more than twothirds of the people served by public water-supply systems live within their boundaries.

National synthesis of data analysis, based on 

aggregation of comparable information obtained from 

the study units, is a major component of the program. 

This effort focuses on selected water-quality topics 

using nationally consistent information. Comparative 

studies will explain differences and similarities in 

observed water-quality conditions among study areas 

and will identify changes and trends and their causes. 

The first topics addressed by the national synthesis are 

pesticides, nutrients, volatile organic compounds, and 

aquatic biology. Discussions on these and other waterquality topics will be published in periodic summaries 

of the quality of the Nation's ground and surface water 

as the information becomes available.

This report is an element of the comprehensive 

body of information developed as part of the NAWQA 

Program. The program depends heavily on the advice, 

cooperation, and information from many Federal, 

State, interstate, Tribal, and local agencies and the 

public. The assistance and suggestions of all are 

greatly appreciated.

fh.

Robert M. Hirsch 

Chief Hydrologist

CONTENTS

Abstract..........................................................................................--.............---.-^ 1

Introduction ..............................................................................................................................................................^ 1

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

Description of the Study Area ..................................................................................................................................... 2

Methods ..............................................................................................................................................................^ 4

Sampling Design.......................................................................................................................................................... 4

Collection of Data........................................................................................................................................................ 6

Macroinvertebrate Data..................................................................................................................................... 6

Habitat and Water Quality Data......................................................................................................................... 6

Data Analysis......................................................................................................................................................^ 7

Principal Components Analysis of Environmental Variables................................................................................................ 8

Riffle Samples............................................ 8

Snag Samples...-.-..-.-.-..--.....-.----.-......-.-.-..........-..-.......--.- ..........--..-...---.......--.....-^ 8

TWINSPAN Groupings.........................................................,............^^ 11

Sample Groups............................................................................................................................................................ 11

Riffle Samples............................................................. 11

Snag Samples-------.-----..----.- ---.-...--..----..--.-----..-----------.-...-...-..-...-..------..-- 12

Taxa Groups........................................................................... 12

Riffle Samples.......................................................... 12

Snag Samples-----.-.--.--...---..-----..----..------.-....---.---..-.----....---.-----.--..-.-.-............ 12

Comparisons of Biotic and Environmental Variables Among Sample Groups ..................................................................... 13

Riffle Samples.......................................................... 13

Snag Samples................................................................................................................................................ 16

Macroinvertebrate Assemblages.................................................................................................................................. 16

Associations with Environmental Variables ................................................................................................................ 16

Riffle Samples................... ...................................................................................... ................................... 16

Snag Samples................................................................................................................................. 20

Annual and Spatial Variability......................................................-......................................-...............-....... ....... 22

Implications for Bioassessments ............................................................... .............. .... ................ ...... ...................... 23

Summary.................................................................................................................................................... 23

References --.---------. - ...-.-.-. ...-........ .....-......... ...-...----............----......-.-..---....-....-......-......-...-.. 23

FIGURES

1. Locations of sampling sites and ecoregions in the Sacramento and San Joaquin river drainages, California......... 3

2. Classification of sampling sites into TWINSPAN sample groups for both riffle and snag samples in the

Sacramento and San Joaquin river drainages, California. .. .... .............................. ........ ...... 4

3. Scores on the first two canonical correspondence analysis axes for riffle samples and riffle taxa, SacramentoSan Joaquin river drainages, California.............................................. .. .... ............ .. 18

4. Scores on the first two canonical correspondence analysis axes for snag samples and snag taxa scores................ 21

Contents
TABLES

1. TWINSPAN taxa groups and occurrence of taxa in samples in TWINSPAN sample groups for riffle and

snag samples ........................................................................................................................................................... 9

2. Loadings of environmental variables on the first two principal components (PC) derived from principal

components analyses of environmental data from all samples, only riffle samples, and only snag samples......... 11

3. Mean or geometric mean (for transformed variables) values of biological variables for sample types and

TWINSPAN sample groups.................................................................................................................................... 15

5. Results of canonical correspondence analyses relating benthic macroinvertebrate density to environmental

variables for riffle and snag samples from the Sacramento and San Joaquin river drainages, California.............. 17

CONVERSION FACTORS, VERTICAL DATUM, ACRONYMS and 

ABBREVIATIONS, and CHEMICAL ELEMENTS

Conversion Factors

Multiply By To obtain

cm (centimeter) 0.3937 inch

km (kilometer) 0.6214 mile

km2 (square kilometer) 0.3861 square mile

m (meter) 3.281 foot

m2 (square meter) 1.196 square yard

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

mg (milligram) 0.00003527 ounce avoirdupois

mg/L (milligram per liter) 8.345 pound per million gallon (U.S.)

mL (milliliter) 0.06103 cubic inch

mm (millimeter) 0.03937 inch

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

Temperature is given in degrees Celsius (°C), which can be converted to degrees 

Fahrenheit (°F) by the following equation:

°F=1.8(°C)+32.

Vertical Datum

Sea level: In this paper, "sea level" refers to the National Geodetic Vertical Datum of 1929 a geodetic datum derived from a 

general adjustment of the first-order level nets of the United States and Canada, formerly called Sea Level Datum of 1929.

Abbreviations and Acronyms

uS/cm, microsiemens per centimeter at 25 degrees Celsius

ANOVA, one-way analysis of variance

CCA, canonical correspondence analysis

EPT, Ephemeroptera, Plecoptera, and Trichoptera

PC, principal components

PCA, principal components analysis

TWINSPAN, two-way indicator species analysis

NAWQA, National Water-Quality Assessment (Program)

USGS, U.S. Geological Survey

VI Contents
Benthic Macroinvertebrate Assemblages and Their Relations 

with Environmental Variables in the Sacramento and San 

Joaquin River Drainages, California, 1993-1997

/tyLarry R. Brown and Jason I May 

ABSTRACT

Data were collected in the San Joaquin and 

Sacramento river drainages to evaluate associations between macroinvertebrate assemblages and 

environmental variables as part of the National 

Water-Quality Assessment Program of the U.S. 

Geological Survey. Samples were collected at 53 

sites from 1993 to 1995 in the San Joaquin River 

drainage and in 1996 and 1997 in the Sacramento 

River drainage. Macroinvertebrates were collected 

from riffles or from large woody debris (snags) 

when riffles were absent. Macroinvertebrate taxa 

were aggregated to the family (or higher) level of 

taxonomic organization, resulting in 81 taxa for 

analyses. Only the 50 most common taxa were 

used for two-way indicator species analysis 

(TWINSPAN) and canonical correspondence 

analysis. TWINSPAN analysis defined four 

groups of riffle samples and four groups of snag 

samples based on macroinvertebrate assemblages. 

Analysis of variance identified differences in environmental and biotic characteristics of the groups. 

These results combined with the results of canonical correspondence analysis indicated that patterns 

in riffle sample assemblage structure were highly 

correlated with a gradient in physical and chemical 

conditions associated with elevation. The results 

also suggested that flow regulation associated with 

large storage reservoirs has negative effects on the 

total number of taxa and density of macroinvertebrates below foothill dams. Analysis of the snag 

samples showed that, although elevation remained 

a significant variable, mean dominant substrate

size, gradient, specific conductance, water temperature, percentage of the basin in agricultural land 

use, and percentage of the basin in combined agricultural and urban land uses were more important 

factors in explaining assemblage structure. Macroinvertebrate assemblages on snags may be useful 

in family level bioassessments of environmental 

conditions in valley floor habitats. In the Sierra 

Nevada and its foothills, the strong influence of 

elevation made it difficult to attribute differences 

in macroinvertebrate assemblage structure among 

sites to specific environmental conditions. Additional work is needed in the foothills and Sierra 

Nevada to better define macroinvertebrate assemblages and their relations to environmental 

variables.

INTRODUCTION

The use of benthic macroinvertebrate assemblages for bioassessments of water-quality conditions 

is a commonly used technique (Lenat, 1988; Ohio 

Environmental Protection Agency, 1987a,b,c; Plafkin 

and others, 1989; Fore and others, 1996). Development of bioassessment techniques and implementation 

of biocriteria has been an ongoing effort in California 

since 1993. In 1996, standardized procedures for using 

benthic macroinvertebrates in assessing water quality 

conditions (California Stream Bioassessment Procedure) were introduced by the California Department of 

Fish and Game (Harrington, 1996). Current efforts 

have focused on developing biocritera on a watershed 

basis and in wadeable streams where riffles are 

available for sampling. Development of methods for

Introduction 1
nonwadeable streams or streams without riffle habitat 

is exploratory at this time.

Published information on the taxonomy, distribution, and responses to environmental variables of macroinvertebrates in the Sacramento and San Joaquin 

river drainages is limited. Hawkins and others (1997) 

sampled higher elevation streams in the Sierra Nevada, 

but did not sample lower elevation streams. Leland 

and Fend (1998) studied macroinvertebrate communities in the lower San Joaquin River and some tributaries using artificial substrates, but did not include the 

Sacramento River system or higher elevations in the 

San Joaquin River system. Bottorf and Knight (1989) 

sampled all elevations in the Cosumnes River system, 

but limited their analyses to stoneflies (Plecoptera). 

Two literature reviews failed to identify any additional 

published studies at the geographic scale of drainage 

or larger (Brown, 1996; Erman, 1997).

The National Water-Quality Assessment 

(NAWQA) Program of the U.S. Geological Survey 

(USGS) includes collections of fishes, benthic macroinvertebrates, and benthic algae as part of the assessment of water quality conditions of the nation's 

surface waters. The three NAWQA study areas in California are in the San Joaquin, Sacramento, and Santa 

Ana river systems. Data collection has been completed 

in the San Joaquin (1993-1995) and Sacramento 

(1996-1998) river study areas and is ongoing in the 

Santa Ana River (1999-2001) study area. Analysis of 

the data from the San Joaquin and Sacramento river 

drainages provides an excellent opportunity to assess 

the relations of benthic macroinvertebrate communities to water quality and habitat conditions in a large 

river system of critical importance as a water supply to 

central and southern California.

Purpose and Scope

The purpose of this report is to assess the practicality of developing regional biocriteria for the combined Sacramento-San Joaquin river system by 

determining whether samples can be categorized on 

the basis of benthic macroinvertebrate assemblage 

structure, and to evaluate the relations of the sample 

categories to a variety of environmental variables. The 

use of macroinvertebrate assemblages on snags 

(woody debris) for bioassessments in lower elevation 

streams without riffle habitat also was evaluated. 

Water quality of such streams is a major concern to

water managers, but the development of bioassessment techniques in California has been limited to 

wadeable streams with riffle habitat.

Description of the Study Area

The Sacramento and San Joaquin rivers drain a 

combined area of about 137,000 km2 (fig. 1) (Domagalski and others, 1998; Gronberg and others, 1998). 

The climate in the Sacramento and San Joaquin valleys varies from semiarid in the north to arid in the 

south. Winters are mild and summers are hot. Mean 

annual precipitation on the valley floor varies from 

about 36 to 63 cm in the Sacramento Valley and from 

about 13 to 30 cm in the San Joaquin Valley. Precipitation declines from a high in the northern Sacramento 

Valley to a low in the southern San Joaquin Valley.

The range of elevation in the combined Sacramento-San Joaquin river drainage is considerable. The 

Sierra Nevada reaches elevations exceeding 4,000 m 

in contrast to the lowest parts of the valley floor, which 

are near sea level. Most of the precipitation in the 

drainage falls in the Sierra Nevada as snow, with more 

than 200 cm/yr falling in some areas.

The study area includes a total of 10 ecoregions 

(fig. 1) (Omernik, 1987). The Sacramento and San 

Joaquin river drainages are both dominated by the 

Central California Valley, Southern and Central California chaparral and woodlands, and Sierra Nevada 

ecoregions. All but two sites in this study were within 

these three ecoregions. The Sacramento River drainage includes small parts of the Klamath Mountains, 

which contains one site (fig. 1), Snake River High 

Desert, Eastern Cascades Slopes and Foothills, Northern Basin and Range, and Coast Ranges ecoregions. 

The San Joaquin River drainage includes small parts 

of the Southern Basin and Range ecoregion and the 

Southern California Mountains ecoregion, which contains one site (fig. 1).

The natural flow regime of Central Valley streams 

has been significantly modified by water development 

activities (Domagalski and others, 1998; Gronberg and 

others, 1998). All of the large rivers, and many of the 

smaller streams, have been dammed for flood control 

and storage of runoff. Most of the large storage reservoirs are located in the Sierra Nevada foothills. The 

stored water is transported through natural channels or 

constructed canals for a variety of purposes, including 

irrigation of agricultural land, fulfillment of

2 Bentic Macroinvertebrate Assemblages and Their Relations with Environmental Variables in Sacramento, San Joaquin River Drainages, Calif.
environmental requirements, and municipal and industrial uses for downstream communities (Domagalski 

and others, 1998; Gronberg and others, 1998). Water is 

routinely transported out of the drainage to southern

California. Water- quality concerns include agricultural return flows, urban runoff, mine drainage, and 

others that result from human activities (Domagalski 

and others, 1998; Gronberg and others, 1998).

121 122°

42'

EXPLANATION 

Ecological Sites

 Riffle sample

Snag sample 

Ecoregions

Sierra Nevada 

Klamath Mountains 

Cascades

Eastern Cascades Slopes and Foothills 

Snake River High Desert 

Nothern Basin and Range 

Southern Basin and Range 

Southern California Mountains 

Central California Valley 

Southern and Central California 

Chaparral and Woodlands

Sacramento 

Valley

SacramentoSan Joaquin 

Delta

25 50 MILES

0 25 50 KILOMETERS 

Figure 1. Locations of sampling sites and ecoregions in the Sacramento and San Joaquin river drainages, California.

Introduction 3
METHODS

Sampling Design

Twenty-three sites were sampled in the Sacramento River system and 30 sites were sampled in the

San Joaquin River system (fig. 2). The primary focus 

of sampling activities was to document water-quality 

conditions at lower elevations where human disturbances are prevalent. The secondary purpose was to 

document gradients in macroinvertebrate assemblages 

and environmental conditions from the valley floor to

0 25 50 KILOMETERS

EXPLANATION 

TWINSPAN Site Groups

A Mountain 

g Foothill 

<D Transition 

<f> Valley floor

Figure 2. Classification of sampling sites into TWINSPAN sample groups for both riffle (A) and snag (B) samples in the 

Sacramento and San Joaquin river drainages, California. Sampling sites with more than one code were sampled in more 

than one year and samples from different years were placed in the groups indicated.

4 Bentic Macroinvertebrate Assemblages and Their Relations with Environmental Variables in Sacramento, San Joaquin River Drainages, Calif.
higher elevations in the Sierra Nevada. All sites were 

sampled at least once during low-flow conditions during the late summer or early autumn.

Data from multiyear sampling of selected sites 

provide a measure of annual variability in macroinvertebrate assemblages. All sites could not be sampled in 

all years and multiple-reach sampling was not done at

all sites because of economic and logistic constraints. 

In the Sacramento River drainage, 10 sites were sampled during both 1996 and 1997. In the San Joaquin 

River drainage, two sites were sampled in 1993 and 

1994, one site was sampled in 1994 and 1995, and 

four sites were sampled during all 3 years. In addition, 

three adjacent stream reaches were sampled at each of

122

42'

EXPLANATION 

TWINSPAN Sample Group

San Joaquin 

^ Tributary 

 Drain 1 

A Drain 2

0 25 50 KILOMETERS

Figure 2. Continued

Methods
two sites in the Sacramento River system (fig. 2A, 

McCloud River site and second-most downstream site 

on Deer Creek) and at each of three sites in the San 

Joaquin River system (fig. 2B, most downstream site 

on Merced River and second-most downstream site on 

the Tuolumne and Stanislaus rivers) to provide a measure of reach-scale variability. In addition to macroinvertebrate sampling, a variety of water quality and 

habitat variables was measured at each site.

Sampling was done within selected stream 

reaches (Meador and others, 1993). At sites where two 

or more types of geomorphic channel units (riffles, 

runs, and pools) were present, reach length was 

defined as the length of stream, including at least two 

repetitions of each type of geomorphic channel unit 

present at the site. At sites without two or more types 

of geomorphic channel unit, reach length was defined 

as 20 times the mean channel width. Reach lengths in 

this study varied from 150 m at small wadeable 

streams to 1,200 m at large rivers. Within each stream 

reach, macroinvertebrates were collected from a habitat expected to have a high diversity of taxa (Cuffney 

and others, 1993). Riffles were the preferred sampling 

habitat. Large woody debris (snags) was the preferred 

sampling habitat when riffles were absent.

Collection of Data

Macroinvertebrate Data

Sampling was done using a large kick net with a 

rectangular 0.5-m-wide by 0.25-m-tall opening fitted 

with a 425-^im mesh net and removable sample bottle. 

At sites where riffles were present, a sample was collected at each of five locations within the riffle habitats 

available. Samples were collected by placing the opening of the net firmly on the substrate and collecting the 

organisms within a 0.5 m by 0.5 m (0.25 m2) area in 

front of the net. Rocks (large gravel and larger) were 

scrubbed with a vegetable brush or by hand, and then 

examined for closely adhering organisms. Any organisms present were removed by hand or with forceps. 

The remaining smaller substrate particles were disturbed to a depth of 10 cm using a metal rod or by 

kicking for 30 seconds. Organisms from all five locations were composited into a single sample.

Snag sampling was done with the same kick net 

used for riffle sampling. Snags were sampled at five 

locations within the sampling reach. The snags were

visually examined, and only those that had clearly 

been in the stream for an extended period and were 

well colonized by aquatic biota were selected; however, there was no objective way to assess the colonization period for each snag sampled. The net was held 

downstream of the snag selected. When feasible, snags 

were sampled in place by brushing organisms into the 

net; otherwise, the snags were carefully removed using 

a pruning saw or pruning shears and the organisms 

brushed into a bucket. Loose bark was removed, and 

any concealed organisms were brushed into the net or 

bucket. Snags were then carefully examined for boring 

organisms, and any organisms present were removed 

with forceps. Aquatic vegetation that had become 

entangled around the snag was considered part of the 

habitat and also was examined for organisms. The 

length and diameter of the sampled area were measured and a sample area was calculated. Depending on 

the size of the snags available, one or more snags were 

sampled at each of the five locations within the reach. 

Organisms from all five locations were composited 

into a single sample.

Composited samples were sieved through a 425- 

|j,m mesh screen. Large debris was removed by hand. 

If the volume of the remaining sample was 750 mL or 

less, the entire sample was preserved in 10-percent 

formalin. If the volume of the remaining sample was 

greater than 750 mL, the sample was split into equalsized components prior to adding the preservative (see 

Cuffney and others [1993] for additional details). 

Large or rare taxa that might be missed in a random 

split were extracted from the sample by hand and 

included with the split to be analyzed to ensure that all 

taxa present at a site were included.

Samples were shipped to the Biological Quality 

Assurance Unit of the USGS National Water Quality 

Laboratory, Arvada, Colo., for identification of organisms. Organisms were identified to the lowest possible 

taxon. Outside experts in various taxonomic groups 

were consulted for difficult organisms. San Joaquin 

data were based on complete counts of the sample or 

subsample analyzed. Sacramento data were based on 

counts of 500 organisms from the sample or subsample. To ensure comparability of samples, taxonomic 

data were aggregated to family level or higher.

Habitat and Water Quality Data

Habitat variables were measured at each of six 

transects within each sampling reach (Meador and

6 Bentic Macroinvertebrate Assemblages and Their Relations with Environmental Variables in Sacramento, San Joaquin River Drainages, Calif.
others, 1993). At sites with distinct geomorphic channel units (riffle, run, or pool), transects were placed to 

reflect the availability of each habitat; otherwise, 

transects were placed at equally spaced intervals. 

Stream width (wetted channel) was measured with a 

fiberglass tape or rangefinder. Open canopy (number 

of degrees of sky above the transect not obscured by 

objects) was measured at midstream with a clinometer. 

Percent canopy was measured with a spherical densiometer.

Depth, velocity, and substrate were measured at a 

minimum of three points at each transect, including 

points at about one-quarter, one-half, and three-quarters of the stream width. Depth was measured with a 

wading rod. Velocity was measured with a MarshMcBirney electronic flow meter. Substrate was measured as the dominant substrate at each transect point 

and was classified as (1) organic detritus, (2) silt, (3) 

mud, (4) sand (0.02-2 mm), (5) gravel (2-64 mm), (6) 

cobble (64-256 mm), (7) boulder, or (8) bedrock or 

hardpan (solid rock or clay forming a continuous surface). Additional measurements were made as needed 

to account for morphological features, such as channel 

bars and islands.

Stream gradient, stream sinuosity, and elevation 

were determined from USGS 1:24,000 topographic 

maps. Stream sinuosity was calculated as river distance divided by the straightline distance between the 

upstream and downstream ends of a segment of stream 

(minimum length of 2 km) containing the sample site. 

Basin area and percentages of agricultural and urban 

land use within a basin were determined using geographic information system databases.

Water quality measurements taken at each site 

included specific conductance, pH, and alkalinity. 

Specific conductance and pH were measured with 

electronic meters. Alkalinity was determined by titration. Water temperature and dissolved oxygen were 

measured directly in the river with electronic meters. 

Discharge measurements were daily mean values for 

gaged sites and instantaneous measurements at 

ungaged sites.

Data Analysis

A total of 85 macroinvertebrate samples was 

included in the analysis. Taxa were aggregated at the 

family level or higher taxonomic levels as appropriate. 

For the multivariate analyses described below,

macroinvertebrate data were analyzed as the natural 

logarithm of relative abundance. Only taxa present in 

5 percent or more of the 85 samples were included in 

two-way indicator species analysis (TWINSPAN) and 

canonical correspondence analysis (CCA). Taxa that 

were not sampled efficiently by our methods were 

excluded from all analyses. These taxa included crayfish, semiaquatic hemipterans (except Naucoridae), 

and clams.

Water quality and habitat variables were examined for normality with normal probability plots. Values were logjo(x+l) transformed to improve normality 

when appropriate. Statistical analyses were done on all 

samples, riffle samples only, and snag samples only.

Relations among the habitat and water quality 

variables were examined using principal components 

analysis (PCA). Only principal components (PC) with 

eigenvalues greater than one were retained for interpretation. Loadings were arbitrarily designated as high 

for absolute values greater than 0.70, moderate for 

absolute values from 0.5 to 0.69, and low for absolute 

values less than 0.5.

TWINSPAN (Hill, 1979) was used to determine 

groupings of samples on the basis of macroinvertebrate assemblages. TWINSPAN is a divisive classification technique that produces an ordered matrix of 

samples and species. The analysis was limited to two 

sequential divisions that could potentially produce 

four groups. The four TWINSPAN sample groups produced by the second division were used for comparison of environmental variables using one-way analysis 

of variance (ANOVA). Differences were considered 

statistically significant at p < 0.05. The Tukey method 

(Wilkinson and Coward, 1998) was used for pairwise 

comparisons when the ANOVA was statistically significant. Comparisons of basic biological metrics 

between sample types (riffle and snag) and among 

TWINSPAN sample groups also were done. Sample 

types were compared using a t-test. Sample groups 

were compared using ANOVA, similar to the environmental variables. The metrics analyzed include total 

number of taxa, total density, total number of EPT 

(Ephemeroptera, Plecoptera, and Trichoptera) taxa, 

EPT taxa density, and dominance (percentage of total 

density comprised by the most abundant taxon). Metrics were examined for normality with normal probability plots. Values were ln(x+l) transformed to 

improve normality when appropriate. Metric analysis 

was based on all taxa collected.

Methods
Associations of benthic macroinvertebrate assemblages with environmental variables were explored 

using CCA (terBraak, 1986, 1987; Jongman and others, 1995). The forward selection mode of CCA was 

used. This method tests the statistical significance of 

each environmental variable using a Monte Carlo simulation before adding it to the final model. All variables significant at p < 0.05 were included in the final 

model.

Spatial and annual variabilities were assessed by 

calculating Jaccard and Bray-Curtis similarities 

(Wilkinson and others, 1998) among samples collected at each reach for each multiple-reach site and 

among samples from each year for each site sampled 

in more than 1 year. Jaccard similarities are calculated 

on the basis of the presence or absence of taxa, making 

it a somewhat qualitative measure of assemblage similarity. Bray-Curtis similarities are calculated on the 

basis of percentage abundances of taxa, giving a more 

quantitative measure of similarity compared to Jaccard 

similarities. Separate analyses were done for riffle and 

snag samples.

A total of 81 taxa were collected during the study. 

The majority of the taxa (67) were insects. Of the 81 

taxa collected, 31 were excluded from multivariate 

analyses. The 50 taxa retained for multivariate analyses included 41 insect families; 3 amphipod families water mites (order Acari), snails (order 

Limnophila), and leeches (class Hirudinea); nematodes (class Nematoda); oligochaetes (class Oligochaeta); and flatworms (Class Turbellaria) (table 1).

PRINCIPAL COMPONENTS ANALYSIS OF 

ENVIRONMENTAL VARIABLES

Examination of the factor loadings of the original 

variables on the first two PCs of the three data sets 

revealed the major environmental gradients potentially 

affecting benthic macroinvertebrates (table 2). Principal components analysis of the environmental data 

from all samples resulted in four PCs with eigenvalues 

greater than 1, which explained 75 percent of the variance in the data. The first two PCs explained 39 and 19 

percent of the variance, respectively. The first principal component represents a gradient in elevation and 

correlated variables, including gradient, basin area, 

open canopy, land use, discharge, and mean dominant 

substrate. None of the water quality variables had high 

loadings on PCI. No variable loaded highly on PC2,

but the moderate loadings of six variables indicate that 

this component represents a stream-size and waterquality gradient.

Riffle Samples

Analysis of data from the riffle sites resulted in 

six PCs with eigenvalues greater than 1, which 

explained 86 percent of the variance in the environmental data. The first two PCs explained 30 and 21 

percent of the variance, respectively.

Similar to the analysis of all samples, the first 

principal component of the riffle sample analysis represents a gradient in elevation and correlated variables, 

including gradient, basin area, and open canopy (table 

2). Mean velocity and mean width also had high loadings on PCI for the riffle samples. None of the water 

quality variables had high loadings on PCI. Alkalinity 

and specific conductance loaded highly on PC2 and 

described a gradient in water quality independent of 

the gradient in elevation described by PCI.

Snag Samples

Analysis of the data from the snag samples 

resulted in five PCs with eigenvalues greater than 1, 

which explained 79 percent of the variance in the snag 

sample environmental data. The first two PCs 

explained 33 and 21 percent of the variance, respectively.

Results for the snag samples were very different 

from the results of the analysis of all the samples or 

the riffle samples (table 2). The first PC represents a 

stream-size gradient, relatively independent of elevation. The stream-size gradient included a moderate 

association with combined agricultural and urban land 

use in the basin. The second PC represents a gradient 

in water quality associated with agricultural land use.

Overall, the results of the three analyses suggest 

that environmental gradients on the valley floor, where 

the snag samples were collected, were very different 

than the environmental gradients associated with the 

riffle samples. Also, the strong elevational gradient 

evident in the riffle samples seems to dominate the 

combined analysis. Thus, separate analyses of riffle 

and snag samples are probably most appropriate for 

assessing the relations of benthic macroinvertebrate 

assemblages with environmental variables in these 

very different environmental settings.

8 Bentic Macroinvertebrate Assemblages and Their Relations with Environmental Variables in Sacramento, San Joaquin River Drainages, Calif.
Table 1. TWINSPAN taxa groups and occurrence of taxa in samples in TWINSPAN sample groups for riffle and snag samples, Sacramento-San 

[Taxa are indented in the order class, order, and family. Taxa groups refer to the TWINSPAN taxa groups for riffle (R) and snag (S) samples. The numbers (1-4) in

sions of the riffle and snag samples. Taxa code refers to codes used in figures 2B and 35. TWINSPAN, two-way indicator species analysis; , taxon was not prese

Taxa groups

a'

 5'

EL

0

o

 o

o

CD

i

S.

VI

m

3

a

CD

|

m

Taxon

Arachnoidea

Acari

Gastropoda

Limnophila

Hirudinae

Insecta

Coleoptera

Elmidae

Psephenidae

Ptilodactylidae

Diptera

Athericidae

Blephariceridae

Ceratopogonidae

Chironomidae

Empididae

Simuliidae

Tipulidae

Ephemeroptera

Ameletidae

Baetidae

Caenidae

Ephemerellidae

Heptageniidae

Leptohyphidae

Leptophlebiidae

Hemiptera

Naucoridae

Lepidoptera

Pyralidae

Megaloptera

Corydalidae

R

2

4

2

2

1

3

2

2

2

2

1

1

1

3

4

2

2

4

1

4

4

1

S

1

4

4

3

4

4

3

1

1

2

1

2

4

1

2

1

1

1

Taxa 

code

ACARI

GASTRO

HIRU

Cl

C2

C3

Dl

D2

D3

D4

D5

D6

D7

El

E2

E3

E4

E5

E6

E7

HI

LI

Ml

Valley 

(N = 13)

12

7

0

7

0

0

0

1

1

12

5

7

2

0

13

0

10

10

13

2

1

8

2

Riffle Sample Groups

Transition 

(N = 7)

7

1

0

7

6

2

5

3

4

7

6

5

4

0

7

1

7

7

6

0

2

6

1

Foothills 

(N = 19)

18

2

0

18

8

6

4

11

9

19

14

15

17

4

19

0

19

19

1

9

0

7

10

Mountain 

(N = 6)

6

1

0

6

0

0

1

2

2

6

2

6

5

3

6

0

6

6

0

5

0

0

5

San 

Joaquin 

(N = 7)

4

1

0

0

0

0

0

0

1

7

5

4

2

0

2

1

0

2

2

0

0

0

0

T
Table 1. TWINSPAN taxa groups and occurrence of taxa in samples in TWINSPAN sample groups for riffle and snag samples, Sacramento-San Joa

California Continued

Bentic Macroinverteb

S

CD

>

n

oT

ia

CD

v>

01

3

s.

30 

CD

Ol

5'

a

s

?

rn

1.

i

CD

i

of

2. 

o>o5a"

01 

n

2

CD

0 

V)

Ol

a

o

01

.0

c

a' 

3

CD

0

01

Taxa groups

Taxon

Odonata

Calopterygidae

Coenagrionidae

Gomphidae

Libellulidae

Plecoptera

Capniidae

Chloroperlidae

Nemouridae

Perlidae

Perlodidae

Pteronarcyidae

Trichoptera

Brachycentridae

Glossosomatidae

Helicopsychidae

Hydropsychidae

Hydroptilidae

Lepidostomatidae

Leptoceridae

Limnephilidae

Philipotomatidae

Rhyacophilidae

Uenoidea

Malacostraca

Amphipoda

Corophiidae

Crangonyctidae

Talitridae

Nematoda

Oligochaeta

Turbellaria

R

4

3

4

4

1

1

1

1

1

3

1

3

2

3

4

1

4

1

1

1

1

4

4

2

4

4

S

2

4

1

1

1

2

1

1

4

4

2

4

4

Taxa 

code

01

O2

03

04

PI

P2

P3

P4

P5

P6

Tl

T2

T3

T4

T5

T6

T7

T8

T9

T10

Til

Al

A2

A3

NEMA

OLIGO

TURB

Valley 

(N = 13)

4

5

1

3

0

0

0

4

2

2

1

8

1

13

6

1

5

0

1

0

0

0

3

1

3

13

8

Riffle Sample Groups

Transition 

(N = 7)

2

2

4

2

0

0

0

5

5

7

6

6

5

7

6

0

7

0

3

5

0

0

0

0

5

7

2

Foothills 

(N = 19)

1

3

3

3

3

14

10

19

19

10

9

14

4

19

12

3

2

6

14

17

1

0

0

0

8

17

5

Mountain 

(N = 6)

0

0

0

0

1

3

6

6

5

0

3

5

0

5

3

4

0

1

1

6

3

0

0

0

3

7

0

San 

Joaquin 

(N = 7)

0

2

0

0

0

0

0

0

0

0

0

0

0

7

1

0

1

0

0

0

0

7

0

1

3

7

0

Sn

Tr

(N 
Table 2. Loadings of environmental variables on the first two principal components (PC) derived from principal components analyses of 

environmental data from all samples, only riffle samples, and only snag samples, Sacramento-San Joaquin river drainages, California

[Boldfaced values, absolute value of loading was greater than 0.70 and was considered high, mg CaCO3/L, milligrams of calcium carbonate per liter; 

mg/L, milligram per liter; uS/cm, microsiemens per centimeter; km2, square kilometer; m3/s, cubic meter per second; m/s, meter per second; , absolute 

value of loading was less than 0.30; NA, not included in analysis]

All Samples

Variable

Water quality

Alkalinity (mg CaCOS/L) 1

Dissolved oxygen (mg/L)

Oxygen saturation (percent)

pH

Specific conductance (uS/cm) 1

Habitat variables

Agricultural land use (percent) 1

Agricultural and urban land use (percent) 1

Basin area (km2) 1

Discharge (rrvVs) 1

Elevation (m) 1

Gradient (percent)

Mean depth (m)

Mean dominant substrate

Mean velocity (m/s)

Mean width (m) 1

Open canopy (degrees)

Percent canopy (percent)

Sinuosity 1

Water temperature (°C)

PC1

0.44

-0.31

0.53

0.85

0.80

0.77

0.72

-0.90

-0.77

0.47

-0.72

0.47

0.63

0.77

-0.57

0.47

0.59

PC2

-0.68

0.54

-0.40

-0.65

-0.42

0.48

0.51

0.40

0.37

0.50

0.65

0.34

-0.34

-0.49

Riffle Samples

PC1

NA

0.65

0.83

0.61

-0.79

-0.73

0.44

-0.38

0.70

0.76

0.87

-0.63

0.42

PC2

-0.88

0.65

-0.89

NA

-0.32

0.43

0.31

0.57

-0.51

-0.62

Snag Samples

PC1

-0.37

0.58

0.36

. 

-0.64

0.91

0.85

-0.55

-0.69

0.56

0.37

0.59

0.89

0.74

-0.53

0.51

-0.35

PC2

0.87

0.70

0.87

0.79

0.55

-0.31

-0.37

0.40

-0.48

0.56

'Variable was Iog 10(x+l) transformed for analysis.

TWINSPAN GROUPINGS

TWINSPAN analysis of all samples largely separated the riffle samples from the snag samples. The 

first TWINSPAN division resulted in one group composed entirely of riffle samples. The second group, 

resulting from the first TWINSPAN division, included 

12 riffle samples and all of the snag samples. Riffle 

samples included in this second group were all samples from low elevation sites. Because the TWINSPAN analysis of the combined samples largely 

separated riffle and snag samples, the remainder of 

this report presents the results of the separate analyses, 

with a few exceptions. The results of the PCA analyses 

are consistent with this decision because they suggest 

that the macroinvertebrate assemblages of the riffle 

and snag samples are responding to a different suite of 

environmental variables.

Sample Groups

Riffle Samples

The first two TWINSPAN divisions of the riffle 

samples resulted in four groups that represent elevational strata (fig. 2A). The valley floor group includes 

samples from the lowest elevations sampled. Most 

samples are from larger streams below major storage 

reservoirs. The sample from the most downstream site 

on Big Chico Creek is an exception because of the relatively small size of the creek. The transition group 

includes samples from sites located at the transition 

from foothill to valley-floor habitat, on Deer Creek and 

Big Chico Creek, both unregulated streams. The foothill group includes samples from sites located at a 

wide range of elevations in the Sierra Nevada foothills 

and mountains (286-1,268 m). The mountain group 

includes samples from the sites at higher elevations 

(682-1,426 m), including sites that overlap with the

TWINSPAN Groupings 11
foothill group. Samples for different years or reaches 

were split between the foothill and mountain groups 

for the most upstream site on the Merced River and the 

McCloud River site.

Snag Samples

The first two TWINSPAN divisions of the snag 

samples resulted in four groups (fig. 2E) that represent 

different habitat types. The tributary group includes 

samples from sites on the tributary rivers and samples 

from the Sacramento River in 1997 and the most 

downstream site on the San Joaquin River in 1994. 

The San Joaquin group includes samples from the 

mainstem San Joaquin River and Salt Slough, except 

for the sample from the most downstream San Joaquin 

River site in 1994. The San Joaquin group also 

includes the sample from the Sacramento River in 

1996. Drain group 1 includes samples from sites on 

agricultural drains and natural creeks affected by agricultural return flows, urban runoff, or water diversions. 

Two exceptions, because of the larger size of the 

streams, are the 1994 sample from the second-most 

downstream site on the Tuolumne River and the 1997 

sample from the Feather River. Drain group 2 includes 

the 1996 sample from Arcade Creek and the sample 

from Orestimba Creek.

Taxa Groups

Riffle Samples

The riffle samples included 48 of the 50 common 

taxa analyzed (table 1). Leeches (Hirudinae) and 

corophiid amphipods were absent. The first two 

TWINSPAN divisions of the riffle samples resulted in 

four groups of taxa (table 1). The first group (riffle 

group 1 in table 1) comprised 17 taxa, including 2 

dipteran families, 2 ephemeropteran families, 1 megalopteran family, 5 plecopteran families, 6 trichopteran 

families, and 1 coleopteran family. These taxa generally were most abundant in mountain and foothill samples and were generally absent from the valley 

samples. All but two of these taxa are considered intolerant of environmental degradation on the basis of tolerance values developed for benthic 

macroinvertebrates (Bob Wisseman, Aquatic Biology 

Associates, written commun., 1996). One 

ephemeropteran family (Ameletidae), three plecopteran families (Capniidae, Chloroperlidae, and

Nemouridae) and two trichopteran families 

(Lepidostomidae and Uenoidae) were found only in 

foothill and mountain samples.

The second group (riffle group 2 in table 1) comprised 11 taxa, including the water mites (order Acari), 

nematodes, 2 coleopteran families, 4 dipteran families, 

2 ephemeropteran families, and 1 trichopteran family. 

These taxa were broadly distributed among the samples, but tended to be less abundant or absent from valley samples. Eight of these taxa are considered 

moderately tolerant of environmental degradation, and 

the remaining three taxa are considered intolerant 

(Bob Wisseman, Aquatic Biology Associates, written 

commun., 1996).

The third group (riffle group 3 in table 1) comprised 6 taxa, including 1 dipteran family, 1 

ephemeropteran family, 1 plecopteran family, 2 trichopteran families, and 1 odonate family. These taxa 

tended to be most abundant or occurred most frequently in samples from the foothill and transition 

groups. There is no clear pattern in tolerance.

The fourth group (riffle group 4 in table 1) comprised 14 taxa, including the gastropods, oligochaetes, 

turbellarians, 2 ephemeropteran families, the only 

hemipteran family, the only lepidopteran family, 3 

odonate families, 2 trichopteran families, and the only 

2 amphipod families. These taxa were most abundant 

or occurred most frequently in samples from valley or 

transition group sites. All but one of the taxa are considered moderately tolerant or tolerant of environmental degradation (Bob Wisseman, Aquatic Biology 

Associates, written commun., 1996).

Snag Samples

Only 31 of the 50 common taxa occurred in snag 

samples (table 1). Megalopterans and plecopterans 

were completely absent and only 4 of 11 trichopteran 

families were present. The first group (snag group 1 in 

table 1) resulting from the first two TWINSPAN divisions of the snag samples comprised 13 taxa, including 3 ephemeropteran families; 3 trichopteran 

families; 2 dipteran families; one each of hemipteran, 

lepidopteran, odonate, and amphipod families; and the 

water mites. These taxa occurred most frequently in 

San Joaquin or tributary group samples, with few 

occurrences in drain samples. Seven of these taxa' are 

considered moderately tolerant of environmental degradation and the remaining four are considered intolerant (Bob Wisseman, Aquatic Biology Associates, 

written commun., 1996).

12 Bentic Macroinvertebrate Assemblages and Their Relations with Environmental Variables in Sacramento. San Joaquin River Drainages. Calif.
The second group (snag group 2 in table 1) comprised 6 taxa, including the nematodes; 2 

ephemeropteran families; and one each of the 

dipteran, odonate, and trichopteran families. These 

taxa were most abundant or frequent in tributary samples but also occurred in some samples from all of the 

other site groups. Five of these taxa are considered 

moderately tolerant of environmental degradation 

(Bob Wisseman, Aquatic Biology Associates, written 

commun., 1996).

The third group (snag group 3 in table 1) comprised only two broadly distributed taxa. Chironomids 

were found in all but one sample and were abundant in 

some samples from all sample groups. The elmids 

(Coleoptera) occurred sporadically in samples from all 

site groups, except the San Joaquin group. Both of 

these taxa are considered moderately tolerant of environmental degradation (Bob Wisseman, Aquatic Biology Associates, written commun., 1996).

The fourth group (snag group 4 in table 1) comprised 10 taxa, including the leeches, gastropods, oligochaetes, turbellarians, 1 coleopteran family, 1 

dipteran family, 1 ephemeropteran family, 1 odonate 

family, and 2 amphipod families. This group included 

taxa that occurred sporadically, but most frequently 

and most abundantly in samples from the two drain 

groups. These taxa are considered tolerant or moderately tolerant of environmental degradation (Bob Wisseman, Aquatic Biology Associates, written commun., 

1996).

Overall, the riffle taxa groups were dominated by 

intolerant and moderately tolerant taxa, and the snag 

taxa groups were dominated by moderately tolerant 

and tolerant taxa. These results suggest that the snag 

samples represent macroinvertebrate assemblages 

responding to environmental conditions harsher than 

those associated with the riffle samples.

COMPARISONS OF BIOTIC AND ENVIRONMENTAL VARIABLES AMONG SAMPLE GROUPS

In addition to the differences in environmental 

gradients between riffle and snag samples revealed by 

PCA, there were statistically significant differences 

between riffle and snag samples for several biological 

variables (table 3). Snag samples had fewer taxa than 

riffle samples, but total densities of organisms were 

not statistically different. The number of EPT taxa and 

the EPT density were statistically different with snag

samples having fewer EPT taxa and lower densities of 

EPT taxa. Snag samples also tended to be more dominated by a single taxon with mean dominance of snag 

samples averaging over 50 percent.

Riffle Samples

The valley group had fewer taxa and fewer EPT 

taxa than the other groups (table 3). The highest number of taxa occurred in the transition and foothill 

groups. Total density was highly variable with wide 

ranges in values for all groups. The transition group 

had the highest mean total density but was not statistically different from the mountain group. EPT density 

was significantly higher in the transition sample group 

than in any other of the groups. The valley group had 

the highest dominance value but was significantly different only from the foothill group, which had the 

lowest value.

The dominant taxa in the valley group samples 

were baetids (6 samples), hydropsychids (3 samples), 

chironomids (2 samples), and pyralids (1 sample). The 

dominant taxa in the transition group samples were 

chironomids (3 samples), oligochaetes (1 sample), 

hydropsychids (1 sample), acari (1 sample), and 

hydroptilids (1 sample). The dominant taxa in the 

foothill group samples were baetids (6 samples), 

hydropsychids (3 samples), chironomids (2 samples), 

elmids (2 samples), simuliids (1 sample), heptageniids 

(1 sample), brachycentrids (1 sample), and acari (1 

sample). Mountain samples were dominated by either 

chironomids (4 samples) or heptageniids (2 samples). 

The dominant taxa are all moderately tolerant of environmental degradation, except for the intolerant 

brachycentrid trichopterans and the tolerant oligochaetes (Bob Wisseman, Aquatic Biology Associates, 

written commun., 1996).

There were statistically significant differences in 

environmental conditions among riffle sample groups 

for 8 of the 18 variables compared (table 4). In six 

cases, the valley group and mountain group had the 

most extreme values and were significantly different 

from each other. The foothill and transition groups 

were generally intermediate and grouped with either 

the valley group or the mountain group. In the remaining two cases, the mountain or valley group represented one extreme and the transition group the other 

extreme.

Comparisons of Biotic and Environmental Variables Among Sample Groups 13
Table 3. Mean or geometric mean (for transformed variables) values of biological variables for sample types and TWINSPAN sample groups, Sacram

California. Differences among means were tested with a t-test for sample types and one-way analysis of variance within TWINSPAN sample groups

[TWINSPAN, two-way indicator species analysis. Densities are organisms per square meter. EPT, families in the orders Ephemeroptera, Plecoptera, and Trichoptera. 

density represented by the most abundant taxa. Similar superscripts (A-C) indicate means that were not significantly different (t-test, or Tukey method after analysis 

0)

o 

3_

i

3 Sample types

> Riffles

| Snags

5T Riffle sample groups

* Valley

a. Transition 

Z. Foothill

{£ Mountain

x. Snag sample groups

» San Joaquin 

5. Tributary

=j Drain group 1

| Drain group 2

Sample Total number of taxa 

Size

45

40

13

7 

19

6

7 

24

7

2

Mean

25 A

15 B

19 A

30 B 

27 B,C

25 c

12 A 

17 B

14 A

11 A

Range

15-34

7-22

15-24

27-34 

23-33

21-28

9-17 

13-22

11-18

7-15

Total density 1 

1x1,000)

Mean

6.3

4.5

5.5 A

23.7 B 

4.4 A

5.6 A'B

4.7 

4.6

4.2

3.7

Range

1.3-98.2

0.4-^5.3

1.6-90.7

4.8-98.2 

1.3-32.6

2.6-24.4

1.2-19.3 

0.4-45.3

1.3-12.1

0.7-20.8

Number of 

EPT taxa

Mean

11 A

4 B

7 A

13 B 

13 B

13 B

2 A

6 B

2 A

2 A

Range

5-16

0-8

5-10

11-16 

8-16

7-16

1-5 

4-8

0-5

1-3

EPT density 1 

(xl.OOO)

Mean

3.1 A

0.7 B

2.9 A

10.5 B

2.4 A

2.1 A

1.3 A 

1.2 A

0.1 B

0.4 A3

Ran

0.6-^

0-2

0.6-1

1.8-4

0.8-1

0.7-

0.3-

0.1-2

0-

0.2-

CD

~ 1Data were ln(x+l) transformed for analysis.

i

55°

cb~

V)

a"

V)

te 

n

D> 

CD

i

vt
Table 4. Mean or geometric mean (for transformed variables) values of environmental variables for TWINSPAN sample groups and the results of o

comparisons of group means, Sacramento-San Joaquin river drainages, California

[Similar superscripts (A-C) indicate means values that were not significantly different (Tukey method, p < 0.05). TWINSPAN, two-way indicator species analysis; m

bonate per liter; mg/L, milligram per liter; uS/cm, microsiemens per centimeter; km2, square kilometer; m3/s, cubic meter per second; m/s, meter per second. , da

Riffle Sample Groups

0

o

 o

a> 

1

M

O^

00

S o'

0)

0.

m

<

3

3

O

|

^

Variable

Water quality

Alkalinity (mg CaCOS/L) 1

Dissolved oxygen (mg/L)

Oxygen saturation (percent)

PH

Specific conductance (^.S/cm) 1

Habitat variables

Agricultural land use (percent) 1

Agricultural and urban land use (percent) 1

Basin area (km2) 1

Discharge (ir^/s) 1

Elevation (m) 1

Gradient (percent)

Mean depth (m)

Mean dominant substrate

Mean velocity (m/s)

Mean width (m) 1

Open canopy (degrees)

Percent canopy

Sinuosity1

Water temperature (°C)

Valley 

(N = 13)

40

9.1

99

7.5A

102

3.6A

2,228A

3.6

35A

0.160*

0.87

5.1A

0.42

32.6A'2

132A

24

1.21

19.3A'B

Transition 

(N = 7)

65

9.0

103

8.2 B

143

0.2B

402B

1.7

109B

0.741 A 'B

1.01

4.9 A

0.22

16.3B

117A,B

22

1.22

21.4A

Foothills 

(N = 19)

30

9.3

102

S.O^3

73

0.2B

565B

2.2

630C

2.0088

0.84

5.9B

0.27

20.0^

SO8'0

25

1.24

15.4B'C

Mountain 

(N = 6)

24

9.7

98

77A,B

61

0.1 B

298B

1.3

1,034C

2.1768

0.83

57A,B

0.18

15.9B

51C

50

1.21

10.6C

San Joaquin 

(N = 7)

124A

7.8

88

7.9

831 A

28.9A

30.3A

8,689A

21.2A

10

0.019A

1.51

3.7A

0.48A

46.8A

158A

2A,2

1.71 A

21.0

Snag Sam

Tributary 

(N = 24)

39B

8.6

94

7.5

114B

8.4B

10.4B

4,216A'B

12.8A

12

0.036A

1.10

3.8A

0.40*

37.8A

127A

17A,B

1.63A

20.7

Variable was logjo(x+l) transformed for analysis.

2Although the one-way analysis of variance was significant (p < 0.05), none of the pairwise tests were significant at p < 0.05. Pairwise tests signi

o

5
Snag Samples

The snag sample groups showed fewer differences in biological variables than the riffle samples 

(table 3). The tributary group had more taxa than the 

San Joaquin group and drain groups; however, total 

density did not vary among groups. The tributary 

group had the highest number of EPT taxa, but the differences in EPT density were not as definitive. EPT 

density of drain group 1 was significantly lower than 

the San Joaquin and tributary groups. Mean dominance exceeded 50 percent for all groups.

The tributary group samples were dominated by 

chironomids (15 samples); hydropsychids (5 samples); 

and oligochaetes, baetids, simuliids, and lepidostomatids (1 sample each). The dominant taxa in the San 

Joaquin group samples were oligochaetes (2 samples), 

hydropsychids (2 samples), corophiid ampipods (2 

samples), and chironomids (1 sample). The dominant 

taxa in drain group 1 samples were chironomids (4 

samples), oligochaetes (2 samples), and caenids (1 

sample). The dominant taxa in the two drain group 2 

samples were chironomids (1 sample) and gastropods 

(1 sample). The dominant taxa are all moderately tolerant of environmental degradation, except for the 

intolerant lepidostomatid trichopterans and the tolerant gastropods and oligochaetes (Bob Wisseman, 

Aquatic Biology Associates, written commun., 1996).

The snag sample groups tended to have broadly 

overlapping means for most environmental variables 

with no obvious common pattern even though 13 of 19 

comparisons were significant (table 4). There were a 

few obvious differences. Tributary samples had the 

lowest values of alkalinity and specific conductance 

and also the lowest percentages of human land use. 

For most comparisons, the two drain groups were similar, except for basin area, gradient, and mean width.

MACROINVERTEBRATE ASSEMBLAGES

Associations with Environmental Variables

Riffle samples

The forward selection procedure in CCA resulted 

in retention of seven variables in the CCA model for 

the riffle samples (table 5). The first axis of the riffle 

analysis was dominated by the association of elevation

with macroinvertebrate assemblages. The remaining 

axes were less dominated by any one variable but 

appeared to stress the correlations of variables reflective of stream size, including basin area, discharge, 

and open canopy with macroinvertebrate assemblages. 

In general, the environmental gradients identified as 

important to organisms in the CCA were similar to the 

environmental gradients identified by PCA of the 

physical variables alone (tables 2 and 5). However, 

some variables with only low to moderate loadings on 

one of the first two PCs had significant explanatory 

value in CCA. These variables included agricultural 

and urban land use, discharge, dissolved oxygen, and 

pH.

The CCA plot of the riffle sample scores indicates 

relatively good separation of the valley group and transition group from the other groups and each other, but 

a great deal of overlap between the foothill and mountain groups (fig. 3/4). The good separation of the valley 

sample group from the other three groups appears to 

represent a response of the benthic macroinvertebrate 

assemblage to the strong elevation and land-use gradient. High percentages of snails, flatworms, libellulid 

and coenagrionid odonates, leptohyphid 

ephemeroptera, and amphipods, particularly in the 

family Crangonyctidae, characterized the valley samples (fig. 3B). These taxa are considered tolerant or 

moderately tolerant of environmental degradation.

The elevation land-use gradient also was important for separating the transition sample group from 

the foothill and mountain sample groups, but stream 

discharge, dissolved oxygen, pH, and open canopy 

also were important. The transition sample group is 

well separated from the foothill group, except for three 

foothill samples, and is well separated from the mountain samples. The separation of the mountain and transition groups is reflected by the associated taxa (fig. 

35). The mountain samples are characterized by megalopterans and a variety of EPT taxa. Most of these 

taxa are considered intolerant of environmental degradation (Bob Wisseman, Aquatic Biology Associates, 

written commun., 1996). Lepidopterans, leptocerid trichopterans, caenid ephemeroptera, gomphid odonates, 

and naucorid hemipterans characterized the transition 

group samples. These taxa are considered moderately 

tolerant to environmental degradation (Bob Wisseman, 

Aquatic Biology Associates, written commun., 1996). 

The foothill sample group was so diffuse that it was 

not characterized by any particular group of taxa.

16 Bentic Macroinvertebrate Assemblages and Their Relations with Environmental Variables in Sacramento. San Joaquin River Drainages, Calif.
The extensive overlap of foothill and mountain 

sample groups argues against using the TWINSPAN 

groupings. The CCA plot (fig. 3A) suggests that the 

samples in the upper left quadrant of the plot form a 

more legitimate mountain group especially because it 

puts all of the McCloud River samples and the two 

samples from the most upstream site on the Merced 

River together. The importance of gradients in elevation and correlated environmental variables has been 

noted in other studies, and the classification of sites 

into montane and nonmontane groups is a common 

result (Carter and others, 1996; Cuffney and others, 

1997; Whittier and others, 1998). Defining subgroups 

within these categories appears to be more difficult 

and may be dependent on geographic scale arid sampling intensity. Two studies of the moderately sized 

Yakima River drainage (15,540 km2) in Washington 

successfully defined subgroups within larger montane 

groups (Carter and others, 1996; Cufrhey and others,

1997). In addition, Cuffney and others (1997) were 

able to distinguish among different sites in a group of 

lower elevation small stream sites and among different 

sites in a group of large river sites on the basis of the 

effects of agricultural activities on algae, macroinvertebrate, and fish communities. In contrast, Whittier 

and others (1998) were unable to distinguish among 

groups of montane sites from five different ecoregions. 

The overlapping results for the foothill and mountain groups of the riffle samples could be due to several factors. TWINSPAN and CCA are very different 

types of analyses. The most basic difference is that 

TWINSPAN is based on a conversion of continuous 

data into categories whereas CCA is based on direct 

analyses of continuous data. This suggests that CCA is 

more sensitive to small differences in the data, and the 

groups suggested by that technique should be accepted 

especially because the CCA sample scores group in a 

more intuitively appealing manner. However, further

Table 5. Results of canonical correspondence analyses relating benthic macroinvertebrate density to environmental variables for riffle and 

snag samples from the Sacramento and San Joaquin river drainages, California

[Boldfaced coefficients had t-values greater than 2.1, indicating a significant contribution to the axis]

Environmental Variable Eigenvalue

Canonical Coefficient

Axis 1 Axis 2 Axis 3 Axis 4

Riffle samples

Agricultural and urban land use

Basin area

Discharge

Dissolved oxygen

Elevation

Open canopy

pH

Percentage of species variance explained

Percentage of species environment relation explained

0.03

0.04

0.05

0.03

0.19

0.05

0.07

-0.15

0.23

-032

-0.11

-1.03

-0.01

0.16

18.4

46.3

0.38

0.39

-0.01

0.32

-0.18

-0.68

-0.69

6.7

16.8

-0.22

-0.67

0.70

-0.15

0.25

1.02

-0.36

4.9

12.3

0.41

-0.65

-0.39

-0.43

0.40

0.55

-0.53

3.4

8.6

Snag samples

Agricultural land use

Agricultural and urban land use

Elevation

Gradient

Mean dominant substrate

Specific conductance

Water temperature

Percentage of species variance explained

Percentage of species environment relation explained

0.08

0.09

0.06

0.14

0.08

0.15

0.06

-0.54

0.75

-0.06

0.08

-0.29

0.37

0.03

10.4

26.7

0.62

-0.35

0.06

-0.22

0.20

0.73

-0.22

8.0

20.4

1.25

-0.66

-0.13

1.49

0.72

-0.12

0.16

7.9

20.2

-0.41

0.87

0.79

-0.72

0.22

0.14

-1.00

5.3

13.8

Macroinvertebrae Assemblages 17
3 -

2 -

" 4

< 1 -

CO

o

Riffle Samples

A Mountain 

L ® Foothill 

Transition 

Valley floor

-2 -1.5 -1 -0.5 0 0.5 1 1.5

1.5

< 0.5

o 

o

-0.5

T11

i ' ' ' ' T 

AMP2 B

PI

ELEV

 H1

' T3 . C2

-1.5 -1 -0.5 0 0.5 

CCA Axis 1

1.5

Figure 3. Scores on the first two canonical correspondence analysis axes for riffle samples (A) 

and riffle taxa (B), Sacramento-San Joaquin river drainages, California. See table 1 for taxa 

codes. Level-2 TWINSPAN groups are enclosed by lines. For both plots, the arrows represent 

the correlation of physical variables with the axes (AGUR = agricultural + urban land use, BA = 

basin area, DISCH = discharge, 00 = dissolved oxygen, ELEV = elevation, and OC = open 

canopy). Arrows parallel to an axis indicate a high correlation and perpendicular to an axis 

indicate a low correlation. TWINSPAN, two-way indicator species analysis.

18 Bentic Macroinvertebrate Assemblages and Their Relations with Environmental Variables in Sacramento, San Joaquin River Drainages, Calif.
study is needed to identify the sources of variation 

causing the different results.

Two sources may be particularly important. First, 

the foothill and mountain sample sites may have had 

very different temperature regimes associated with the 

steep elevation gradient and different channel morphologies. In addition, the relatively prolonged period 

of sample collection of a month or more in any particular year could result in samples collected at different 

times in the seasonal progression of the macroinvertebrate community. Hawkins and others (1997) found 

that stream temperature and sampling date were the 

most important factors in explaining insect assemblage structure in samples from many of the same geographic areas within the same range in elevation that 

were sampled at foothill and mountain sites in this 

study.

Second, the family level of identification may be 

insufficient to understand the response of the macroinvertebrate assemblage to the environment in the Sierra 

Nevada, especially on a regional level. Erman (1997) 

compiled various species lists for the Sierra Nevada 

and found records for 122 species of Plecoptera, of 

which 32 were endemic to the Sierra Nevada, and 199 

species of Trichoptera, including 37 endemic species. 

Diversity in particular drainages also can be high. Bottorff and Knight (1989) documented 69 species of Plecoptera in 36 genera in the Cosumnes River drainage, 

one of the smaller Sierra Nevada rivers. Bottorff and 

Knight (1989) also noted the highest species richness 

at elevations between about 500 and 1,500 m, which 

encompasses most of the mountain and foothill sites in 

this study. Thus, the highest elevation sites in this 

study actually may have been at a transition zone 

between areas of higher and lower species richness. A 

greater monitoring effort at the species level is needed 

in the Sierra Nevada to fully describe the diversity and 

long-term trends in the macroinvertebrate fauna 

(Erman, 1997).

The sites in the transition group represent areas of 

transition between foothill and valley habitat. The 

number of total taxa and number of EPT taxa were 

comparable to the foothill and mountain groups and 

greater than the valley group (table 3). Total macroinvertebrate density in the transition group was greater 

than for any other, although it was not significantly 

different from the mountain sites because of high variability (table 3). EPT density in the transition samples 

was the highest of any of the groups (table 3). The valley sites had the lowest taxa richness, primarily

because of the loss of EPT taxa. The absence of Plecoptera from valley floor habitats has been noted previously (Bottorff, 1989). Transition group sites 

occurred only on relatively small, unregulated streams 

in the Sacramento River drainage (fig. 2A). This type 

of habitat either has been submerged under reservoirs 

or occurs downstream of large dams that alter the 

hydrologic regime for most of the medium to largesized streams of the Central Valley.

The absence of transition zone sites in the regulated reaches of streams with large storage reservoirs 

is important for two reasons. First, the data suggest 

that the reservoirs have negatively affected biodiversity and assemblage structure of aquatic macroinvertebrates in Central Valley stream systems. 

Unfortunately, the historical species-level data needed 

to assess the importance of such effects do not exist 

for Central Valley streams (Brown, 1996; Erman, 

1997). The effects of dams, diversions, and flow regulation on benthic macroinvertebrates can be significant 

and complex (Brittain and Saltveit, 1989; Ward and 

Stanford, 1995). Second, reductions in the diversity 

and productivity of the benthic macroinvertebrate 

assemblages in regulated stream reaches may be an 

important consideration in management of anadromous salmonids in the Central Valley. Regulated 

stream reaches represent the only remaining habitat 

for anadromous salmonids in many Central Valley 

streams (Yoshiyama and others, 1996, 1998). Adult 

and larval aquatic macroinvertebrates are the major 

food resource for juvenile anadromous salmonids in 

freshwater habitats (Groot and Margolis, 1991). A loss 

of production of food for young chinook salmon 

(Oncorhynchus tchawytscha) and steelhead (Oncorhynchus mykiss) could be a contributing factor to 

their declines in the Central Valley. These declines 

would represent an indirect effect of dams on these 

fish species in addition to the direct effects of flow regulation, water diversion, temperature regime alterations, loss of upstream spawning habitat, and 

degradation of existing spawning habitat. Additional 

studies addressing food habits of juvenile salmonids 

and biomass of benthic macroinvertebrates, as well as 

density, are needed to assess this hypothesis more 

fully. If food production for fish has been reduced by 

human activities, then restoration of such production 

might be an important factor to consider as part of 

ongoing stream restoration activities in the Central 

Valley.

Macroinvertebrae Assemblages 19
Snag Samples

The forward selection procedure in CCA resulted 

in retention of seven variables in the CCA model for 

the snag samples (table 5). The first two axes of the 

model stressed the association of macroinvertebrate 

assemblages with land use and associated water quality conditions as represented by specific conductance. 

The third and fourth axes were more complex. Agricultural land use was important on the first three axes, 

highlighting the important association of this activity 

on the valley floor with macroinvertebrate assemblages. As for the riffle samples, the environmental 

gradients identified as important to macroinvertebrates 

on snags in the CCA were similar to the environmental 

gradients identified by PCA of the environmental variables alone (tables 2 and 5). Similar to the riffle samples, some variables with only low to moderate 

loadings on one of the first two PCs, including agricultural and urban land use, elevatipn, gradient, mean 

dominant substrate, and water temperature, had significant explanatory value in CCA.

The snag sample groups (fig. 4A) were better separated than the riffle groups (fig. 3A) in the CCA plot. 

The San Joaquin group was isolated from the other 

snag sample groups. The tributary sample group was 

isolated near and to the left of the origin. The two 

drain groups overlapped and formed a diffuse group to 

the right of the origin. Agricultural land use and specific conductance were the most important variables 

separating the San Joaquin and tributary groups. Sites 

in the tributary group were characterized by low concentrations of total dissolved solids (as measured by 

specific- conductance) and low levels of human land 

use (table 4). Gradient and combined agricultural and 

urban land use were the most important factors in separating out the drain sites.

The San Joaquin group separated from the tributary group along the gradients of agricultural land use 

and specific conductance (fig. 4A). The separation was 

largely due to high percentage abundances of 

corophiid amphipods associated with high values of 

agricultural land use and specific conductance (fig. 

45). The tributary group was characterized by a variety of ephemeropterans, trichopterans, odonates, and 

the naucorid hemipterans. The taxa present are considered intolerant or moderately tolerant of degraded 

environmental conditions (Bob Wisseman, Aquatic

Biology Associates, written commun., 1996). Leland 

and Fend (1998) also noted the major difference 

between San Joaquin River and tributary sites and 

identified the dominant amphipod as Corophium spinicornae, an estuarine amphipod common in the Sacramento-San Joaquin Delta (Hazel and Kelley, 1966). 

Leland and Fend (1998) identified the major environmental gradient as total dissolved solids, which is 

closely correlated to specific conductance. The classification of the samples from the most downstream site 

on the San Joaquin River in 1994 is also consistent 

with Leland and Fend's (1998) results. They noted that 

summertime water quality actually improves from 

upstream to downstream because of dilution of agricultural return flows by high quality water from the 

tributary rivers. Thus, total dissolved solids concentrations at the most downstream San Joaquin River site 

most resembled the tributary sites, and the macroinvertebrate community reflected that difference. Examination of the raw data for the 1994 San Joaquin 

sample revealed low densities of corophiid amphipods 

and hydropsychid caddisflies, the two dominant taxa 

in samples in the San Joaquin group, and the presence 

of taxa more abundant in tributary group samples. The 

inclusion of the Sacramento River 1996 sample in the 

San Joaquin group was based on the occurrence of 

corophiid amphipods at low density.

Corophium spinicornae was absent from the 1997 

Sacramento River sample. C. spinicornae is most 

abundant in the Sacramento-San Joaquin Delta (Hazel. 

and Kelley 1966), and the area we sampled may be 

near its upstream distribution limit. This species shows 

large fluctuations in abundance in response to environmental conditions even in the Sacramento-San 

Joaquin Delta, where it is most abundant (Hymanson 

and others, 1994). It seems likely that the absence (or 

extreme rarity) of the taxon was indicative of environmental conditions, perhaps related to a large flood in 

January 1997.

The two drain groups were separated from the 

other groups primarily on the basis of gradient, mean 

dominant substrate, and combined agricultural and 

urban land use. The drain groups were characterized 

by crangonyctid amphipods, ceratopogonid dipterans, 

leeches, snails, flatworms, coenagrionid odonates, and 

elmid coleopterans. These taxa are considered tolerant 

or moderately tolerant of environmental degradation 

(Bob Wisseman, Aquatic Biology Associates, written

20 Bentic Macroinvertebrate Assemblages and Their Relations with Environmental Variables in Sacramento, San Joaquin River Drainages, Calif.
5

4

3 

2 

1 

0 -

-1 -

-2 -

-3 -

-4

© \SanJoaquin 

group

Snag Samples

o San Joaquin group 

0 Tributary group

Drain group 1 

^ Drain group 2

MDS

Tributary 

group

-2

-0.5 0.5 1 

CCA Axis 1

1.5 2.5

Figure 4. Scores on the first two canonical correspondence analysis axes for snag samples (A) 

and snag taxa scores (B). See table 1 for taxa codes. Level-2 TWINSPAN groups are encircled. 

For both plots, the arrows represent the correlation of physical variables with the axes (AG = 

agricultural land use, AGUR = agricultural + urban land use, ELEV = elevation, GRAD = gradient, 

MDS = mean dominant substrate, SPC = specific conductance, and WT = water temperature). 

Arrows parallel to an axis indicate a high correlation and perpendicular to an axis indicate a 

low correlation. TWINSPAN, two-way indicator species analysis.

Macroinvertebrae Assemblages 21
commun., 1996). The two sites in drain group 2 (fig. 

44) were separated on the basis of high percentage 

abundances of gastropods and baetid mayflies compared with the other samples; however, these differences were relatively minor compared to the 

separation of the drain groups from the San Joaquin 

and tributary groups. The differences in gradient 

among groups were caused mainly by Orestimba 

Creek and Arcade Creek (fig. 2#). These creeks are 

natural streams with relatively high gradients (0.16 

and 0.17 percent, respectively) compared with the 

other snag sites (<0.06 percent), but carry primarily 

agricultural return flows and urban runoff, respectively. The finer substrate at drain sites is likely due to 

sedimentation of silt and mud from agricultural and 

urban erosion. The substrate at San Joaquin and tributary sites was dominated by sand.

In general, the sites in the drain groups are stressful to aquatic organisms in ways not captured by the 

environmental variables included in the analysis. Discharge in these waterways can be highly variable on 

even hourly periods, depending on agricultural and 

urban water sources. In addition, both the larger drains 

and the smaller creeks can carry high levels of dissolved pesticides, at times (Domagalski, 1996; Panshin and others, 1998) reaching levels toxic to 

Ceriodaphnia dubia in bioassays (Valeric Connor, 

Central Valley Regional Water Quality Control Board, 

written commun., 1999).

The two unusual samples in the group are located 

to the far left of the others in figure 4A (points labeled 

FR and TR2). In 1997, the snags at the Feather River 

site (FR in fig. 44) were covered with a thick layer of 

fine sediment during sampling, probably deposited 

during the January 1997 flood when large quantities of 

sediment were transported into the stream. Most EPT 

taxa present in 1996 were absent in 1997. This 

resulted in a macroinvertebrate assemblage dominated 

by chironomids and oligochaetes, similar to that found 

in the drain groups. The Tuolumne River site near 

Modesto (TR2 in fig. 4A) was dominated by talitrid 

amphipods and oligochaetes in 1994. This assemblage 

was unusual compared to all the other sites, but most 

resembled samples in the drain groups.

Annual and Spatial Variability

Similarity among reaches was higher than similarity among years for all comparisons, but the differences were not statistically significant (t-tests, all 

p > 0.05). Jaccard similarities were (mean ± 1 standard 

deviation) 0.73 ± 0.08 (n = 6) for multiple-reach riffle 

comparisons, 0.66 ± 0.10 (n = 11) for multiple-year 

riffle comparisons, 0.65 ± 0.10 (n = 9) for multiplereach snag comparisons, and 0.57 ± 0.11 (n = 14) for 

multiple-year snag comparisons. Bray-Curtis similarities were 0.54 ± 0.16 (n = 6) for multiple-reach riffle 

comparisons, 0.49 ± 0.15 (n = 11) for multiple-year 

riffle comparisons, 0.55 ± 0.17 (n = 9) for multiplereach snag comparisons, and 0.47 ± 0.22 (n = 14) for 

multiple-year snag comparisons. Bray-Curtis similarities always had higher standard deviations compared 

with Jaccard similarities, indicating greater variability. 

These results indicate that presence and absence of 

taxa were more similar and less variable than percentage abundances of taxa.

The variability in reach similarity was not associated with any changes in TWINSPAN sample group 

membership for any of the three reaches sampled at 

any of the snag multiple-reach sites. All of the samples 

from snag multiple-reach sites were in the tributary 

sample group and included 1995 samples from the 

most downstream site on the Merced River and the 

second-most downstream sites on the Tuolumne and 

Merced rivers. This was not the case for riffle samples. 

All three reaches sampled in 1996 at the second-most 

downstream site on Deer Creek were in the transition 

group, but reaches sampled at the McCloud River in 

1996 were split between the mountain (2 reaches) and 

foothill (1 reach) sample groups.

The multiple-reach samples suggest that our 

results are robust with regard to reach-scale variability 

at a site. The multiple-reach snag sample results are 

consistent with results from artificial substrate samples 

from the lower San Joaquin river system. Based on 

results from replicate substrates, within-reach variability was low (Leland and Fend, 1998). Leland and Fend 

(1998) found annual variability to be greater than 

within-reach variability, but our results showed no statistical difference between annual and reach variability. This difference between studies is likely due to 

differences in sampling. Leland and Fend (1998) sampled all of their sites in 2 consecutive years (1985 and 

1986), one much wetter than the other, resulting in 

large annual differences. Our comparisons included a 

mixture of comparisons from similar and different 

water years, resulting in a lower mean annual 

variability.

22 Bentic Macroinvertebrate Assemblages and Their Relations with Environmental Variables in Sacramento, San Joaquin River Drainages, Calif.
IMPLICATIONS FOR BIOASSESSMENTS

Our results have several implications for development of regional bioassessments in the combined Sacramento-San Joaquin river drainage. The concepts of 

ecoregions and watersheds are complementary, and 

both levels of organization must be considered when 

designing and interpreting bioassessments (Omernik 

and Bailey, 1997). Clearly, the sites in the Central Valley ecoregion are different from the foothills and 

mountains, although the differences between the latter 

two ecoregions remain unclear. As suggested earlier, 

differences between these ecoregions may become 

clearer at lower levels of taxonomic resolution. If so, 

these ecoregions probably should be subdivided to 

account for zonation by elevation or other factors. 

From a bioassessment perspective, the ecoregion must 

be suitably homogenous so that the response of the 

macroinvertebrate assemblage to human activities can 

be distinguished from the response to natural variation. This appears to be the case for Central Valley 

snag samples, but not for foothill and mountain riffle 

samples. As our understanding of the California macroinvertebrate fauna improves, it seems likely that the 

concept of watershed may be needed to account for 

patterns of endemism and differences in seasonal 

development of macroinvertebrate assemblages in 

response to differing temperature regimes associated 

with canyon morphologies or other factors. The concept of watershed is obviously critical in understanding the effects of human and natural processes on the 

biota of any particular stream.

There has also been recent discussion of the 

degree of taxonomic resolution necessary to assess 

variation in benthic macroinvertebrate assemblage 

structure. Bowman and Bailey (1997) reviewed eight 

data sets from the literature and concluded that results 

at the genus level of identification remained consistent 

when aggregated to higher levels (up to and including 

Class). One caveat was that there was a significant 

negative correlation between the level of consistency 

and the diversity of the community, as defined by the 

lowest level of taxonomy used. Similarly, Bournad and 

others (1996) concluded that the family level was sufficient to detect environmental disturbances in the 

Rhone River, France, but indicated that the species 

level of identification would be necessary to elucidate 

finer scale processes associated with the effects of tributary streams. Our data suggest that, for Central Valley 

snag samples, the family level is sufficient for

evaluating the effects of the environment on macroinvertebrate assemblages, but for the Sierra Nevada and 

foothill riffle samples, genus or species level data may 

be needed.

SUMMARY

Except for foothill and mountain riffle samples, 

the macroinvertebrate assemblages of the combined 

Sacramento-San Joaquin River drainage could be 

grouped using multivariate statistical techniques (figs. 

2, 3A, 44). There were differences in biological (table 

3) and environmental (table 4) characteristics of the 

sample groups suggesting that the differences in 

benthic macroinvertebrate assemblages were related to 

environmental conditions. The CCA analyses emphasized these differences and highlighted the correlation 

of benthic macroinvertebrate assemblages with environmental gradients (table 5, figs. 3 and 4). For the riffle samples, elevation was the most important factor 

(table 5). For the snag samples, land use, specific conductance, and mean dominant substrate were important (table 5). Results from the riffle samples indicate 

that stream regulation may be associated with declines 

in the number of taxa and density of macroinvertebrates in the transition area between the valley floor 

and Sierra Nevada foothills. Our results suggest that 

natural environmental conditions in the Central Valley 

ecoregion are sufficiently homogenous for detection of 

the effects of human land use on macroinvertebrate 

assemblages. Additional work, probably at lower levels of taxonomy, is needed in the foothill and Sierra 

Nevada ecoregions.

REFERENCES

Bottorff, R.L., and Knight, A.W., 1989, Stonefly (Plecoptera) 

feeding modes: Variation along a California river continuum, in Abell, D.L., ed., Proceedings of the California riparian systems conference: Protection, 

management, and restoration for the 1990s: Berkeley, 

Calif., U.S. Forest Service, Pacific Southwest Forest 

and Range Experiment Station, General Technical 

Report PWS series, no. 110, p. 235-241.

Bournaud, M., Cellot, B., Richoux, P., and Berrahou, A., 

1996, Macroinvertebrate community structure and 

environmental characteristics along a large river: congruity of patterns for identification to species or family: 

Journal of the North American Benthological Society, 

v. 15, p. 232-253.

References 23
Bowman, M.F., and Bailey, R.C., 1997, Does taxonomic resolution affect the multivariate description of the structure of freshwater benthic macroinvertebrate 

communities?: Canadian Journal of Fisheries and 

Aquatic Sciences, v. 54, p. 1802-1807.

Brittain, I.E., and Saltveit, S.J., 1989, A review of the effect 

of river regulation on mayflies (Ephemeroptera): Regulated rivers: Research and Management, v. 3, p. 191- 

204.

Brown, L.R., 1996, Aquatic biology of the San JoaquinTulare Basins, California: Analysis of available data 

through 1992: U.S. Geological Survey Water-supply 

Paper 2471,89 p.

Carter, J.L., Fend, S.V., and Kennelly, S.S., 1996, The relationships among three habitat scales and stream benthic 

macroinvertebrate community structure: Freshwater 

Biology, v. 35, p. 109-124.

Cuffney, T.F., Meador, M.R., Porter, S.D., and Gurtz, M.E., 

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6 U.S. GOVERNMENT PRINTING OFFICE: 2000 589-383 / 15016 Region No. 10
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Sacramento and San Joaquin River Drainages, California, 1993-1997 USGS WRIR 00-4125