U.S. DEPARTMENT OF THE INTERIOR

U.S. GEOLOGICAL SURVEY

Water Quality of Selected Effluent-Dependent

Stream Reaches in Southern Arizona as Indicated 

by Concentrations of Periphytic Chlorophyll a

and Aquatic-Invertebrate Communities

National Water-Quality Assessment Program

Central Arizona Basins Study Unit

By Joseph B. Gebler

Tucson, Arizona

1998

Water-Resources Investigations Report 98—4199
For additional information write to:

District Chief

U.S. Geological Survey

Water Resources Division

520 N. Park Avenue, Suite 221

Tucson, AZ 85719–5035

Copies of this report can be purchased from:

U.S. Geological Survey

Information Services

Box 25286

Federal Center

Denver, CO 80225–0046

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.

Information about U.S. Geological Survey programs in Arizona is available online at http://az.water.usgs.gov.

U.S. DEPARTMENT OF THE INTERIOR

BRUCE BABBOTT, Secretary

U.S. GEOLOGICAL SURVEY

Charles G. Groat, Director

FIRST PAGE TITLE-BLOCK PHOTOGRAPH: 

Treated sewage effluent is discharged from the wastewater-treatment plant into the Salt River at 91st Avenue

near Phoenix.
Contents i

CONTENTS

Page

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

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

Study sites ................................................................................................................................................... 2

Field methods.............................................................................................................................................. 4

Data analysis ............................................................................................................................................... 5

Periphytic chlorophyll a.............................................................................................................................. 5

Aquatic-Invertebrate communities.............................................................................................................. 5

Water-quality indicators....................................................................................................................................... 6

Concentrations of chlorophyll a.................................................................................................................. 6

Aquatic-invertebrate communities.............................................................................................................. 6

Similarities and differences among effluent-dependent streams and natural streams ......................................... 10

Summary .............................................................................................................................................................. 10

References cited ................................................................................................................................................... 11
ii Contents

FIGURES

Page

1. Map showing location of Central Arizona Basins study area .............................................................. 2

2. Map showing Central Arizona Basins study area and effluent-dependent stream and 

comparison-stream reaches .................................................................................................................. 3

3. Graph showing concentrations of periphytic chlorophyll a for effluent-dependent stream 

and comparison-stream reaches............................................................................................................ 7

4. Graphs showing results of total taxa-richness (TTR) and EPT taxa-richness computations 

for aquatic-invertebrate communities from riffle samples from effluent-dependent stream 

and comparison-stream reaches............................................................................................................ 7

5. Graphs showing results of computations of percent dominant taxa and 

Family Biotic Index for aquatic-invertebrate communities from effluent-dependent 

stream and comparison-stream reaches ................................................................................................ 8

6. Charts showing taxonomic composition, in percent, and total abundances of aquatic 

invertebrates from effluent-dependent stream and comparison-stream reaches .................................. 9

TABLES

1. Selected characteristics for effluent-dependent stream and comparison-stream reaches .................... 4
Abstract 1

Abstract

Concentrations of chlorophyll a and indices computed for aquatic-invertebrate communities in two 

effluent-dependent stream reaches on the Santa Cruz River and one on the Salt River were compared to 

those in noneffluent-dependent streams to examine potential differences in water quality. Periphytic 

chlorophyll a from riffle habitats and aquatic-invertebrate communities from riffle and multiple habitats 

were used for the comparison. Concentrations of chlorophyll a from effluent-dependent streams were 

elevated compared with concentrations in noneffluent-dependent streams. Aquatic-invertebrate 

communities from effluent-dependent streams were characterized by an abundant, yet taxonomically 

depauperate fauna of tolerant organisms; whereas, noneffluent-dependent streams supported a diverse 

assemblage of aquatic invertebrates including taxa considered sensitive to water-quality degradation. 

These results indicate that water quality of effluent-dependent streams is poor compared with water 

quality of noneffluent-dependent streams. Patterns of taxonomic composition of aquatic-invertebrate 

communities and abundances of aquatic invertebrates from effluent-dependent streams are the same as 

patterns discussed in the scientific literature.

By JOSEPH B. GEBLER

Water-Resources Investigations Report 98—4199

Water Quality of Selected Effluent-Dependent

Stream Reaches in Southern Arizona as Indicated

by Concentrations of Periphytic Chlorophyll a

and Aquatic-Invertebrate Communities 

National Water-Quality Assessment Program

Central Arizona Basins Study Unit

INTRODUCTION 

Effluent-dependent streams in Arizona consist 

primarily of discharge of treated wastewater. Although 

the effects of sewage effluent on aquatic biota have 

been studied for about 100 years (Cairns and Pratt, 

1993), interest in the biota of effluent-dependent 

streams in the western United States has been renewed 

recently as regulators and managers consider modifying 

existing water-quality criteria or developing new 

criteria that may be more appropriate for arid and 

semiarid areas (Baumgartner and Smith, 1993). Few 

studies, however, have been done on aquatic biota in 

effluent-dependent streams in arid and semiarid areas.

From 1995 to 1997, as part of the National WAterQuality Assessment (NAWQA) program of the U.S. 

Geological Survey (USGS), aquatic biota were 

sampled from selected effluent-dependent and 

noneffluent-dependent (natural) stream reaches 

(hereafter referred to as comparison sites) in the 

Central Arizona Basins (CAZB) study area (fig. 1). 

The purpose of the NAWQA program is to describe the 

status of and trends in the Nation’s ground-water and 

surface-water resources and to identify human and 

natural factors that affect water quality (Gilliom and 

others, 1995). Surveys of aquatic biota are an integral 

part of the NAWQA program as the only direct 

measure of biological integrity (Gurtz, 1994) and thus 

an indication of water quality.
2 Water Quality of Selected Effluent-Dependent Stream Reaches as Indicated by Concentrations of Periphytic Chlorophyll a and Aquatic-Invertebrates

This report describes concentrations of periphytic 

chlorophyll a and aquatic-invertebrate communities of 

two effluent-dependent stream reaches on the Santa 

Cruz River and one on the Salt River (fig. 2). These 

biological characteristics are compared with biological 

characteristics of the comparison sites on the San Pedro 

and Salt Rivers and are used as indicators of water 

quality. In addition, patterns of biological 

characteristics of effluent-dependent streams are 

compared to patterns described in scientific literature 

on organic loading.

Most previous studies on biological effects of 

sewage effluent have been in wet climates, particularly 

eastern North America, the United Kingdom, and 

northern Europe, where receiving streams generally 

have sufficient surface water to dilute effluent and 

lessen harmful effects. In these studies, algal growth 

generally was enhanced downstream from sewage 

discharges because of the addition of plant nutrients, 

primarily nitrogen and phosphorus (Hynes, 1960; 

Hellawell, 1986). In addition, sensitive taxa, such as 

aquatic worms (the order Oligochaeta) and midges (the 

insect family Chironomidae), dominate aquaticinvertebrate communities in the presence of low 

concentrations of dissolved oxygen, toxicants (such as 

ammonia), and sedimentation by suspended solids 

(Hynes, 1960; Hellawell, 1986). Streams receiving 

effluent in arid areas differ from receiving streams in 

wetter areas because they typically have little or no 

natural flow, and the flow often ends before reaching 

other streams because of infiltration and evaporation. 

Information is limited on how biological communities 

that develop in these systems after effluent is 

discharged into the channels compare with biological 

communities in other areas.

Study Sites

As part of the CAZB NAWQA study, aquatic biota 

were sampled from two effluent-dependent stream 

reaches on the Santa Cruz River (Santa Cruz River at 

Tubac and Santa Cruz River at Cortaro), and one on 

the Salt River at the wastewater-treatment plant 

(WWTP) at 91st Avenue near Phoenix (fig. 2). Surface 

water in the channel of all three reaches is almost 

exclusively sewage effluent except during floodflows, 

which are typically of short duration. Results from 

effluent-dependent reaches were compared to those 

form the comparison sites that were selected on the 

basis of their similarity to the effluent reaches 

(table 1).

The comparison sites are not necessarily classified as 

regional sites (Hughes and others, 1986) but serve a 

similar function in that they are not affected to any 

great extent by treated-sewage effluent.

The NAWQA sampling reach at Tubac is about 

24 km downstream from the Nogales International 

Wastewater-Treatment Plant (NIWWTP), which 

supplies most of the water for this stream segment. 

Ground water, however, probably contributes some 

flow in the segment (Lawson, 1995). Wennmacher 

(1996) studied algal communities of the segment 

created by the NIWWTP and reported low species 

diversity and high ratios of pollution-tolerant species 

to natural-water species, which she concluded 

indicated poor water quality. Lawson(1995) studied 

macroinvertebrate communities from the same segment 

and concluded that the community was severely 

impaired immediately downstream from the NIWWTP. 

Lawson (1995) also observed that the communities 

recovered partially near the end of the segment, about 

26 km from the NIWWTP, but did not recover to 

control-site conditions.

The NAWQA sampling reach at Cortaro is about 

1.6 and 11.3 km downstream from two wastewatertreatment plants near Tucson. Minimal contributions of 

ground water are possible within the segment (Ken 

Galyean, hydrologist, USGS, oral commun., 1997). 

Two studies by Harding Lawson Associates (1986, 

1997) included sampling of aquatic-invertebrate 

communities from six locations in the segment. 

A maximum abundance of 17 individuals per square 

meter in six families was reported (Harding Lawson 

Associates, 1986). Harding Lawson Associates (1997) 

reported similar low taxonomic richness but did not 

report abundance data. 

Yuma Colorado

River

River

Colorado

River

Ri ver

Colorado Ri ver

Phoenix

Flagstaff

Gila

Lit

Ri v er

Ri v er

Gila

Verde

San 

Cruz

Santa 

Pedro

River

ARIZONA

MEXICO

A R I Z O N A

Tucson

Salt Rive r

tle

Figure 1. Location of Central Arizona Basins 

study area.
Introduction 3

ARIZONA

MEXICO

Base from U.S. Geological Survey

digital data, 1:100,000, 1972

Albers Equal-Area Conic projection

Standard parallels 29°30', 45°30',

central meridian 111°30'

0

0 25 50 75 KILOMETERS

25 50 75 MILES

Nogales 

International 

WastewaterTreatment Plant 

INTERMITTENT OR 

 EPHEMERAL STREAM

CENTRAL ARIZONA BASINS 

 STUDY AREA BOUNDARY

PERENNIAL STREAM

35°

34°

33°

32°

113°

112°

111°

110°

GILA

PIMA

PINAL

YAVAPAI

NAVAJO

GREENLEE

GRAHAM

COCONINO

P ni to

Pinal Coon Cr

C r C r

Granite Cr

Sycamore Cr

GILA

PIMA

PINAL

SANTA

CRUZ

YAVAPAI

MARICOPA

NAVAJO APACHE

GREENLEE

GRAHAM

COCHISE

COCONINO

Big

Chino

Wash

Sedona

Cottonwood

Sierra

Vista

Gila

Bend

PHOENIX

Eloy

Globe

Payson McNary

Flagstaff

Winkelman Stanfield

TUCSON

Prescott

EXPLANATION Tubac

EFFLUENT-DEPENDENT SITE

COMPARISON SITE

Cortaro

Nogales

Salt River 

 near Roosevelt

San Pedro River

Santa Cruz River at Charleston

 at Tubac

 Wastewater-treatment plant 

 at 91st Avenue

Santa Cruz River 

 at Cortaro

Apache

Lake

C r C r

Cr

Hassayam

pa River

New

R

Verde

Rive r

Oak Cr

Dry B eaver Cr

West Clear Cr

Cave

Cr

Syc amo re Cr

Tonto Cr

C herry Creek

Cibeque Cr

Canyon Creek

Car r izo

Cr

River Whit e

Black

River

Bonito

Gila River

Santa

Cruz

Altar Wash

Waterman Wash Santa Rosa Wash

San

Pedro

River

River

Santa Cruz Wash

Salt

River

Theodore

 Roosevelt

 Lake

Lake

Pleasant

Painted

Rock

Reservoir

(Intermittent)

San

Carlos

Reservoir

East VerdeR

Coon Cr

Ba bocomari R

Beaver Cr

Wet B eaver Cr

Bitter Cr

French 

Gulch

Jackrabbit

Wash

M ni eral C r

D r i pping Spr

Donnelly Wash

Rillito Cr

Pantan o W

Cienega Cr

Tangle Cr

Miami Wash

Brawley Wash

El Tiro Wash

River

David son W.

Fria Agua

Que e n Creek

Figure 2. Central Arizona Basins study area and effluent-dependent stream and comparison-stream reaches.
4 Water Quality of Selected Effluent-Dependent Stream Reaches as Indicated by Concentrations of Periphytic Chlorophyll a and Aquatic-Invertebrates

Each effluent-dependent reach of the Santa Cruz

River was compared to a reach on the San Pedro River 

at Charleston. The water quality of the Sand Pedro 

River at Charleston has been affected occasionally by 

sewage effluent (Arizona Department of Environmental Quality, 1996) and mine-tailings spills from 

Mexico (King and others, 1992). Flow in perennial 

sections of the river, however, is sustained by groundwater inflow from the regional aquifer (Jackson and 

others, 1987) rather than treated-sewage effluent. 

Recover of aquatic life following mine spills appears to 

occur quickly; recovery of aquatic organisms was 

recorded 4 months after a major spill in 1979 (Jackson 

and others, 1987). Although the San Pedro River is not 

pristine, the reach at Charleston is the best available 

site for comparison with sites on the Santa Cruz River 

because it is similar in channel size and has noneffluent 

perennial flow.

The sampling reach on the Salt River is about 

0.2 km downstream from the WWTP at 91st Avenue 

near Phoenix, which creates this effluent-dependent 

stream segment. Effluent from the WWTP at 23rd 

Avenue may contribute subsurface flow to the sampling 

reach at 91st Avenue. CH2MHill and others (1997) 

reported 12 taxa of macroinvertebrates collected from 

six sites within the segment. Only two taxa (chironomids and oligochaetes, totaling 247 individuals per 

square meter) were reported from their sampling site 

immediately downstream from the outfall. CH2MHill 

and others (1997) noted that these taxa were 

representative of high organic loads and variable 

oxygen content.

A sampling reach on the Salt River near Roosevelt 

was selected for comparison with the sampling reach at 

the WWTP at 91st Avenue because of similarities in 

channel size and particularly specific conductance of 

the water. Potential sources of water-quality impairment of the Salt River near Roosevelt include grazing 

and forestry practices within the basin and inflow from 

Pinal Creek, which contains manganese (Brown and 

Eychaner, 1996). Pinal Creek is immediately upstream 

from the sampling reach on the Salt River; however, the 

volume of flow from Pinal Creek is minimal in relation 

to the volume of flow from the Salt River (Brown and 

Eychaner, 1996). In addition, manganese toxicity is 

low compared with toxicity of other metals and 

metalloids (Kaiser, 1980). Alteration of benthic habitat 

by precipitation of metallic oxides could affect algal 

and aquatic-invertebrate communities (Lewis and 

Burraychak, 1979).

Field Methods

Quantitative samples of attache algae were 

collected from riffles at all sampling sites using 

nationally standardized NAWQA methods (Porter and 

others, 1993). Twenty-five samples of epilithic algae 

Table 1. Selected characteristics for effluent-dependent stream and comparison-stream reaches

[Downstream distance is approximate. Dominant substrate is sand. NA, not applicable; WWTP, wastewater-treatment plant; km, kilometer; m, meter; 

m/s, meters per second; υS/cm at 25°C, microsiemens per centimeter at 25 degrees Celsius]

Stream name Date of sample

Downstream 

distance 

from 

effluent 

source 

(km)

Width at time of sampling 

(m)

Depth at time of sampling 

(m)

Velocity at time of sampling 

(m/s)

Specific 

conductance 

(uS.cm at 

25°C)

Number 

of 

samples Mean Range

Number 

of 

samples Mean Range

Number 

of 

samples Mean Range

San Pedro at 

Charleston

Dec. 6–8, 1995 NA 6 8.6 2.7–15.6 17 0.20 0.07–.54 17 0.34 0.05–.67 490

Santa Cruz at 

Tubac

Jan. 17–19, 1996 24 6 12.6 7.2–18.8 19 .23 .08–.30 19 .62 .07–1.13 660

Santa Cruz at 

Cortaro

Jan. 22–24, 1996 1.6 and 

1.3

6 13.8 8.3–23.1 18 .33 .16–.69 18 .87 .47–1.28 990

Salt River near 

Roosevelt

Dec. 12–14, 1995 NA 6 47.2 22.2–66.7 20 .70 .10–1.15 20 .54 .03–1.82 3,680

WWTP at 91st 

Avenue

Nov. 28–30, 1995 .2 5 20.1 16.4–27.1 15 .62 .20–1.30 15 .88 0–1.35 1,510
Introduction 5

were collected from rocks that were selected from 

riffles within the sampling reach. These individual 

samples were composited to obtain a single sample for 

each reach that represented a total sampled area of 

75 cm 2. A portion of known volume from each 

composite sample was submitted to the USGS National 

WAter-Quality Laboratory (NWQL) for analysis of 

chlorophyll a.

Aquatic invertebrates were sampled using 

nationally standardized NAWQA methods (Cuffney 

and others, 1993). Two types of samples were 

collected—a semiquantitative sample was collected 

from riffle habitats and a qualitative sample was 

collected from all habitat types in the reach.

Riffles, which generally support a taxonomically 

rich invertebrate fauna (Hynes, 1970), are targeted for 

sampling by the NAWQA program. Five benthic 

samples were collected from riffles distributed 

throughout each reach using a modified Surber1

sampler with a 425-micrometer mesh net. Large rocks 

were scrubbed to remove organisms, and the bottom 

was disturbed to a depth of about 10 cm for 30 seconds. 

Individual samples were combined to yield a single 

composite sample for each reach; total area sampled 

was about 1.25 m2. Samples were processed in the field 

to remove mineral material and were sent to the 

Biological Unit of the USGS NWQL for taxonomic 

determination.

A 210-micrometer mesh, D-frame sweep net was 

used for qualitative multihabitat sampling (Cuffney and 

others, 1993). The goal of this sampling was to obtain 

as complete a list as possible of invertebrate taxa from 

all habitat types, which included macrophytes, woody 

debris, depositional zones, and riffles within the reach. 

This qualitative technique results in a list of taxa in the 

sampled reach but is not intended to provide abundance 

data for specific organisms.

Geomorphological features were used to select 

sampling reaches. At least one habitat cycle was 

included in each reach. Habitat cycles included two 

riffles and all intervening habitat types, such as pools, 

runs, and (or) glides. Criteria for reach definition are 

detailed by Cuffney and others (1993) and Porter and 

others (1993).

Data Analysis

Data in this report are presented in two separate 

sets. One set presents data for the two effluentdependent reaches of the Santa Cruz River and the 

comparison site, San Pedro River at Charleston. The 

second set presents data for the effluent-dependent 

reach at 91st Avenue and the comparison site, Salt 

River at Charleston. The second set presents data for 

the effluent-dependent reach at 91st Avenue and the 

comparison site, Salt River near Roosevelt. After initial 

within-set comparisons, the effluent-dependent and 

comparison sites were examined to determine if there 

were similarities among the stream types and if the 

similarities corresponded with results of other studies.

Periphytic Chlorophyll a

Samples of algae submitted to the NWQL were 

analyzed for concentrations of chlorophyll a. The 

concentrations, in milligrams per square meter, are a 

measurement of algal standing crop. Concentrations of 

chlorophyll a from effluent-dependent reaches were 

compared with concentrations from their respective 

comparison sites.

Aquatic-Invertebrate Communities

Aquatic-invertebrate samples were submitted to the 

Biological Unit of the USGS NWQL for taxonomic 

determinations. Abundance data for aquatic invertebrates were normalized to number of individuals per 

square meter. In order to avoid overestimating measure 

of taxonomic richness and to maintain comparability 

among sites, the lowest taxonomic level common to all 

samples was used in data analyses. Family-level data 

resulted for the insecta orders Odonata, Ephemeroptera, Plecoptera, Trichoptera, Diptera, Megaloptera, 

Coleoptera, and Hemiptera. Lepidoptera was summed 

to order. Aquatic worms were resolved to class 

(Oligochaeta), and water mites were identified to 

subcohort (Hydrachnidia). Specimens that were 

identified to levels higher than these were not included 

in the analyses. The semiaquatic groups, Colembola 

and Staphylinidae (Merritt and Cummins, 1996), also 

were not included in analyses because they may not 

reflect water quality.

1Any use of trade, product, or firm names in this publication is for 

descriptive purposes only and does not constitute endorsement by the U.S. 

Government.
6 Water Quality of Selected Effluent-Dependent Stream Reaches as Indicated by Concentrations of Periphytic Chlorophyll a and Aquatic-Invertebrates

Four biological indices were used to evaluate

semiquantitative aquatic-invertebrate data from 

riffles—total taxa richness (TTR); taxonomic richness 

of insects in the orders Ephemeroptera, Plecoptera, and 

Trichoptera (EPT taxa richness); the percentage 

contribution of the two most dominant taxa (PDT-2); 

and the Family Biotic Index (FBI; Hilsenhoff, 1988). 

The first two indices are simply the number of taxa or 

taxonomic groups present; whereas, the latter two 

indices are used to indicate community balance 

(Barbour and others, 1992). The FBI also is a biotic 

index that uses empirically derived tolerance values of 

taxa to organic contamination. Total diversity within a 

sampling reach was determined by combining data 

from multihabitat samples with data from riffle 

samples. These data were evaluated using only TTR 

and EPT.

TTR is the number of taxa found within samples 

collected from a reach, regardless of abundances, and 

generally is high in streams with good water quality 

and low in streams with poor water quality. EPT taxa 

richness is the number of taxa from the orders 

Ephemeroptera, Plecoptera, and Trichoptera, which 

generally are regarded as intolerant to water-quality 

impairment (Lenat, 1988). Consequently, EPT values 

also are high in streams with good water quality and 

low in streams with poor water quality. Although EPT 

is a subset of TTR, by enumerating only clean water 

taxa, it extracts and highlights information within TTR.

Communities numerically dominated by few taxa 

often indicate environmental stress (Klemm and

others, 1990). The percentage of the two most 

dominant taxa (PDT-2) from each sample was used for 

this assessment.

A modification of the FBI (Hilsenhoff, 1988) also 

was used to examine semiquantitative-invertebrate 

data. Hilsenhoff’s (1988) index was developed 

specifically to evaluate organic loading from sewage. 

Following protocols by Plafkin and others (1989), 

tolerance values from Bode (1988) were used to 

supplement Hilsenhoff’s (1988) tolerance values. 

Pollution-tolerance values of the U.S. Environmental 

Protection Agency (Donald J. Klemm and Philip A. 

Lewis, research aquatic biologists, U.S. Environmental 

Protection agency, oral commun., 1997) were used for 

Hydrachnidia (equivalent to Hydracarina), Nematoda, 

Nematea, and Culicidae. Average tolerance values were 

computed from Hilsenhoff (1988) for chironomids 

(mean = 7) and from Bode (1988) for oligochaetes 

(mean = 8). Bivalva, Naucoridae, Nepidae, and 

Corixidae were excluded from FBI computations as 

tolerance values were not available. These four groups 

were rare in samples. The FBI ranges from 0 to 10, and 

higher scores indicate poorer water quality.

WATER-QUALITY INDICATORS

Concentrations of Chlorophyll a

Concentrations of periphytic chlorophyll a at 

effluent-dependent sites were one to two orders of 

magnitude greater than at the respective comparison 

sites (fig. 3). Samples from effluent-dependent reaches 

of the Santa Cruz River contained concentrations of 

chlorophyll a that were an order of magnitude greater 

than concentrations in samples from the San pedro 

River at Charleston. The estimated concentration of 

chlorophyll a in the sample from the WWTP at 91st 

Avenue was two orders of magnitude greater than the 

sample from the Salt River near Roosevelt. These 

findings are consistent with those from other studies in 

which increased concentrations of plant nutrients, 

primarily nitrogen and phosphorus, resulted in 

increased algal standing crop below sewage-inflow 

points (Hynes, 1960; Hellawell, 1986), and indicate 

that water quality of the effluent-dependent sites is 

poor compared with water quality at the comparison 

sites.

Aquatic-Invertebrate Communities

Reduced values of TTR and EPT for all three 

effluent-dependent sampling reaches relative to their 

respective comparison sites (fig. 4) indicate that water 

quality of the effluent-dependent reaches is poor. 

Ten EPT taxa were collected from the San Pedro River; 

whereas, none were collected from the Santa Cruz 

River at Cortaro, and only two EPT taxa were collected 

from the Santa Cruz River at Tubac. Intermediate TTR 

values for the Tubac site could indicate some degree of 

improvement in the invertebrate community as water 

quality improves with increased distance from the 

outfall; however, the improvement is slight as shown by 

the low EPT values and high values of PDT-2 and FBI. 

Generally, a few moderately tolerant groups of 

dipterans, odonates, and coleopterans account for the 

increased TTR at the Tubac site compared with TTR at 

the Cortaro site. Field measurements of temperature 

and specific conductance within a 1,000-meter section 

of the Santa Cruz River, which included the site at 

Tubac, indicated a localized area of possible groundwater inflow. Consequently, the increase in TTR may 

be a result of localized streamflow dilution in the reach 

at Tubac. In this case, the increased TTR would 

indicate a reach-specific rather than general 

phenomenon. 
Water-Quality Indicators 7

0

100

200

300

400

500

600

WASTEWATERTREATMENT PLANT 

AT 91ST AVENUE

NEAR PHOENIX

SALT RIVER

NEAR 

ROOSEVELT

SANTA CRUZ

 RIVER

 AT CORTARO

SANTA CRUZ

 RIVER

AT TUBAC

SAN PEDRO 

RIVER AT

 CHARLESTON

CONCENTRATIONS OF PERIPHYTIC CHLOROPHYLL a,

IN MILLIGRAMS PER SQUARE METER

Comparison site

Effluent-dependent site

45 4.8

590

(estimated)

300

490

Figure 3. Concentrations of periphytic chlorophyll a for effluent-dependent stream and comparison-stream reaches. (Value for 

wastewater-treatment plant at 91st Avenue was estimated because of a spillage of 20–30 percent of the aliquot before 

analysis.)

TOTAL TAXA RICHNESS (TTR) EPT TAXA RICHNESS (EPT)

0

2

4

6

8

10

12

0

5

10

15

20

25

30

35

40

RIFFLE AND MULTIPLE-HABITAT 

 SAMPLES COMBINED

RIFFLE SAMPLE ONLY EFFLUENT-DEPENDENT SAMPLE

EXPLANATION

WASTEWATERTREATMENT PLANT 

AT 91ST AVENUE 

NEAR PHOENIX

SALT RIVER

NEAR 

ROOSEVELT

SANTA CRUZ

 RIVER

 AT CORTARO

SANTA CRUZ

 RIVER

AT TUBAC

SAN PEDRO 

RIVER AT

 CHARLESTON

WASTEWATERTREATMENT PLANT 

AT 91ST AVENUE

NEAR PHOENIX

SALT RIVER

NEAR 

ROOSEVELT

SANTA CRUZ

 RIVER

 AT CORTARO

SANTA CRUZ

 RIVER

AT TUBAC

SAN PEDRO 

RIVER AT

 CHARLESTON

28

23

32

27

9

2

1

10

12/12

0/0 0/0

6

9

16

7/7

38 

Figure 4. Results of total taxa-richness (TTR) and EPT taxa-richness computations for aquatic-invertebrate communities from riffle samples 

from effluent-dependent stream and comparison-stream reaches.
8 Water Quality of Selected Effluent-Dependent Stream Reaches as Indicated by Concentrations of Periphytic Chlorophyll a and Aquatic-Invertebrates

The two dominant taxa in the San Pedro River at 

Charleston were a capniid stonefly and a baetid mayfly 

(orders Plecoptera and Ephemeroptera, respectively), 

which accounted for about 40 percent of the sample 

(figs. 5 and 6). These taxa generally are considered to 

be intolerant of water-quality impairment. Oligochaetes and chironomids, which are tolerant to organic 

loading, were abundant and dominated both sites on the 

Santa Cruz River. These two groups accounted for 

nearly 100 and 93 percent of aquatic invertebrates at 

the Cortaro and Tubac sites, respectively. The finding 

that oligochaetes and chironomids were extremely 

abundant and dominated the community structure of 

these effluent-dependent reaches is identical to the 

pattern reported in the scientific literature for severely 

degraded zones of streams that are subjected to organic 

loading (Hynes, 1960; Hellawell, 1986). This finding 

indicates that poor water quality favors these tolerant 

types and precludes more sensitive taxa from inhabiting the effluent-dependent reaches of the Santa Cruz 

River. Additionally, FBI values were higher for the 

effluent-dependent sites than for comparison sites 

(fig. 5), which also indicates poor water quality.

Similar results were obtained from the comparison 

of aquatic-invertebrate communities at the WWTP at 

91st Avenue and Salt River near Roosevelt. Thirty-two 

taxa, including 2 EPT taxa, were found at the Salt River 

near Roosevelt site, compared with only 9 total and 

0 EPT taxa at the 91st Avenue site (fig. 4). Abundant 

tolerant taxa (chironomids and oligochaetes), which 

indicate severely degraded zones of effluent-affected 

streams in other areas accounted for nearly 99 percent 

of the community at 91st Avenue; whereas, the two 

dominant taxa at the site near Roosevelt were the 

intolerant baetid mayflies and hydropsychid caddisfles 

(orders Ephmeroptera and Trichoptera, respectively). 

These two taxa accounted for almost 50 percent of the 

community (figs. 5 and 6). High values of PDT-2 and 

the FBI at the 91st Avenue site compared to lower 

values at Salt River near Roosevelt (fig. 5) indicate 

poor water quality at the 91st Avenue site. 

PERCENT DOMINANT TAXA (PDT-2) FAMILY BIOTIC INDEX (FBI)

0

20

40

60

80

100

0

1

2

3

4

5

6

7

8

COMPARISON SITE EFFLUENT-DEPENDENT SITE 

EXPLANATION

WASTEWATERTREATMENT PLANT 

AT 91ST AVENUE 

NEAR PHOENIX

SALT RIVER

NEAR 

ROOSEVELT

SANTA CRUZ

 RIVER

 AT CORTARO

SANTA CRUZ

 RIVER

AT TUBAC

SAN PEDRO 

RIVER AT

 CHARLESTON

WASTEWATERTREATMENT PLANT 

AT 91ST AVENUE

NEAR PHOENIX

SALT RIVER

NEAR 

ROOSEVELT

SANTA CRUZ

 RIVER

 AT CORTARO

SANTA CRUZ

 RIVER

AT TUBAC

SAN PEDRO 

RIVER AT

 CHARLESTON

39.7 

49.4

93

99.3

4.10

7.52

7.73 98.7

4.27

7.29

Figure 5. Results of computations of percent dominant taxa and Family Biotic Index for aquatic-invertebrate communities from effluentdependent stream and comparison-stream reaches.
Water-Quality Indicators 9

SANTA CRUZ RIVER AT CORTARO

Total abundance 5,688 per square meter

Oligochaeta

60.4

Oligochaeta

72.4

Chironomidae

32.6

Chironomidae

26.9 

Other

7

SANTA CRUZ RIVER AT TUBAC

Total abundance 7,090 per square meter

Chironomidae

15.6

Capniidae

22.9

Hydropsychidae

6.4

Leptohyphidae

6.3

Simulidae

5.3

SAN PEDRO RIVER AT CHARLESTON 

Total abundance 4,138 per square meter

Baetidae

 16.8

Other

19.6

Oligochaeta

24.8

Chironomidae

73.9

Other

1.3

WASTEWATER-TREATMENT PLANT AT 91ST AVENUE

Total abundance 6,079 per square meter

Other

12.7

Baetidae

28.5

Capniidae

4

Hydropsychidae

20.9

Leptohyphidae

5.8

Simulidae Philopotamidae

13.7

4.1

SALT RIVER NEAR ROOSEVELT

Total abundance 18,741 per square meter

Oligochaeta

7.1

-

Chironomidae

10.3

EXPLANATION

COMPARISON SITE

EFFLUENT-DEPENDENT SITE

Other

0.7

Figure 6. Taxonomic composition, in percent, and total abundances of aquatic invertebrates from effluent-dependent stream 

and comparison-stream reaches.
10 Water Quality of Selected Effluent-Dependent Stream Reaches as Indicated by Concentrations of Periphytic Chlorophyll a and Aquatic-Invertebrates

SIMILARITIES AND DIFFERENCES AMONG 

EFFLUENT-DEPENDENT STREAMS AND NATURAL 

STREAMS

High concentrations of chlorophyll a and lack of 

sensitive taxa, low taxonomic richness, and high

abundances of tolerant taxa of aquatic invertebrates at 

the sampling sites close to wastewater-treatment plant 

outfalls (Cortaro and 91st Avenue) are consistent with 

patterns reported in scientific literature on effects of 

sewage effluent on aquatic biota. Increased taxa 

richness of aquatic invertebrates at the sampling station 

farther downstream in an effluent-dependent stream 

(Tubac) corresponds to the general pattern reported in 

the scientific literature of increasing taxa richness that 

results from improving water quality with increasing 

downstream distance from the source of organic 

loading. Such recovery at Tubac, however, is minimal 

as indicated by (1) the dominance of tolerant taxa in the 

community and 92) the low abundance and low 

taxonomic richness of sensitive taxa. Dilution of 

effluent by localized ground-water inflow may account 

for this pattern, and if so, the conclusion that 

invertebrate communities exhibit any degree of 

recovery with increasing distance from the source of 

effluent would be false in this case.

Aquatic-invertebrate taxa that are sensitive to 

water-quality degradation dominated the community 

structure of the comparison sites at San Pedro River at 

Charleston and Salt River near Roosevelt. TTR and 

EPT taxa richness were high in these streams. Total 

diversity of aquatic-invertebrate groups in the 

comparison sites was similar to the diversity found in

other desert streams without sewage-effluent inflows. 

For example, about 30 families of aquatic invertebrates 

were collected from the San Pedro River at Charleston 

and from the Salt River near Roosevelt in this study. 

Bruns and Minckley (1980) found more than 

45 families of aquatic invertebrates in Arivaipa Creek 

in ARizona. Gray (1981) found more than 45 families in 

Sycamore Creek Arizona; whereas, Lewis and 

Burraychak (1979) found more than 35 families in

Pinto Creek, Arizona, which was affected by coppermining operations.

SUMMARY

As part of the NAWQA program of the USGS, 

aquatic biota were sampled at two effluent-dependent 

reaches on the Santa Cruz River and one on the Salt 

River and at comparison sites on the San Pedro and Salt 

Rivers. Nationally standardized methods were used to 

collect periphyton samples from riffles for analysis of 

chlorophyll a and to collect aquatic invertebrates from 

riffle and multiple habitats for community assessments. 

Aquatic-invertebrate data were evaluated using TTR, 

EPT taxonomic richness, percent contribution of the 

two most dominant taxa, and a modified FBI.

Analyses of concentrations of chlorophyll a and 

aquatic-invertebrate communities indicated that water 

quality in three effluent-dependent streams was poor 

compared with water quality in two comparison sites. 

Concentrations of periphytic chlorophyll a in the 

effluent-dependent stream reaches were greater than in 

the comparison sites. This finding correspond to 

increases of algal standing crop downstream from 

sewage-effluent sources documented in other studies.

Aquatic-invertebrate taxa in the effluent-dependent 

streams were the same as taxa that inhabit severely 

degraded zones of streams reported in many similar 

studies during the last 100 years throughout the world. 

Oligochaetes and chironomids, which are tolerant of 

organic loading and are indicators of water-quality 

degradation, dominated communities of the effluentdependent stream reaches. These organisms were in 

great abundances, which indicates that these streams 

are capable of supporting aquatic life but are precluded 

form supporting sensitive taxa because of limitations 

imposed by water quality.

The results of this study show that the pattern of 

biological responses in selected effluent-dependent 

streams in southern Arizona is identical to that reported 

for effluent-dependent streams in other parts of the 

world. One potential difference is that intolerant taxa 

may not be able to colonize downstream areas of 

effluent-dependent streams because water quality is not 

sufficiently improved by dilution from inflows of 

natural water.
References Cited 11

REFERENCES CITED 

Arizona Department of Environmental Quality, 1996, 

Arizona Water-quality assessment, 1996: Arizona 

Department of Environmental Quality Report EQR 

96—33, 218 p.

Barbour, M.T., Plafkin, J.L., Bradley, B.P., Graves C.G., 

and Wisseman, R.W., 1992, Evaluation of EPA’s rapid 

bioassessment benthic metrics—Metric redundancy and 

variability among reference stream sites: Great Britain, 

Pergamon Press, Environmental Toxicology and 

Chemistry, v. 11, no. 4, p. 437–449.

Baumgartner, D.J., and Smith, E.L., 1993, Rationale for a 

program of research to develop water-quality criteria 

for effluent-dependent ephemeral streams and riparian 

habitats in the arid west: Tucson, Arizona, University 

of Arizona, Environmental Research Laboratory 

Report 93–1, 53 p., reprinted 1997.

Bode, R.W., 1988, Quality assurance workplan for biological 

stream monitoring in New York State: Albany, 

New York State Department of Environmental 

Conservation report, v.p.

Brown, J.G., and Eychaner, J.H., 1996, Distribution of 

chemical constituents in surface water, Pinal Creek 

Basin, Arizona, in Brown, J.G., and Favor, Barbara, 

eds., Hydrology and Geochemistry of Aquifer and 

Stream Contamination Related to Acidic Water in Pinal 

Creek Basin near Globe, ARizona: U.S. Geological 

Survey Water-Supply Paper 2466, p. 61–79.

Bruns, D.A., and Minckley, W.L., 1980, Distribution and 

abundance of benthic invertebrates in a Sonoran Desert 

stream: London, England, Academic Press, Inc., 

Journal of Arid Environments, v. 3, p. 117–131.

Cairns, J., Jr., and Pratt, J.R., 1993, A history of biological 

monitoring using benthic invertebrates, in Rosenberg, 

D.M., and Resh, V.H., eds., Freshwater biomonitoring 

and Benthic Invertebrates: New York, Chapman and 

Hall, p. 10–27.

CH2MHill, 1997, Salt-Gila baseline ecological 

characterization: Phoenix, Arizona CH2MHill in 

association with Logan, Simpson, and Dye; and 

EcoPlan Associates, Inc., Report 131457.01.

Cuffney, T.F., Gurtz, M.E., and Meador, M.R., 1993, 

Methods for collecting benthic invertebrate samples 

as part of the National Water-Quality Assessment 

program: U.S. Geological Survey Open-File 

Report 93—406, 66 p.

Gilliom, R.J., Alley, W.M., and Gurtz, M.E., 1995, Design of 

the National Water-Quality Assessment program—

Occurrence and distribution of water-quality 

conditions: U.S. Geological Survey Circular 1112, 33 p.

Gray, L.J. 1981, Species composition and life histories of 

aquatic insects in a lowland Sonoran Dessert stream: 

The American Midland Naturalist, v. 106, no. 2, 

p. 229–242.

Gurtz, M.E., 1994, Design of biological components of the 

National Water-Quality Assessment (NAWQA) 

program, in Loeb, S.L., and Spacie, Anne, eds., 

Biological Monitoring of Aquatic Systems: Boca 

Raton, Florida, Lewis Publishers, p. 323–354.

Harding Lawson Associates, 1986, Site-specific waterquality criteria study for the Santa Cruz River, Pima 

County, Arizona: Harding Lawson Associates, 

HLA Job No. 17, 144,010.01, 116 p.

____1997, Field sampling and analysis report—Site survey 

of the Santa Cruz River, Pima County, Arizona: 

Harding Lawson Associates, HLA Project No. 36581–

003, 14 p.

Helawell, J.M., 1986, Biological indicators of freshwater 

pollution and environmental management: London, 

England, Elsevier Applied Science Publishers, Ltd., 

546 p.

Hilsenhoff, W.L., 1988, Rapid field assessment of organic 

pollution with a family-level biotic index: Journal of the 

North American Benthological Society, v. 7, no. 1, 

p. 65–68.

Hughes, R.M., Larsen, D.P., and Omernik, J.M., 1986, 

Regional reference sites—A method for assessing 

stream potentials: New York, Springer-Verlag, Inc., 

Environmental Management, v. 10, no. 5, p. 629–635.

Hynes, H.B.N., 1960, The biology of polluted waters: 

Liverpool, England, Liverpool University Press, 202 p.

____1970, The ecology of running waters: Toronto, Ontario, 

University of Toronto Press, 555 p.

Jackson, W., Martinez, T., Cuplin, P., Minckley, W.L., 

Shelby, B., Summers, P., McGlothlin, D., and 

Van Haveren, B., 1987, Assessment of water conditions 

and management opportunities in support of riparian 

values—BLM San Pedro River Properties, Arizona: 

Denver, Colorado, Bureau of Land Management, 

Project Completion Report BLM/YA/PT-88/004+7200, 

180 p.

Kaiser, K.L.E., 1980, Correlation and prediction of metal 

toxicity to aquatic biota: Canadian Journal of Fisheries 

and Aquatic Sciences, v. 37, no. 2, February 1980, 

p. 211–218.

King, K.A., Baker, D.L., and Kepner, W.G., 1992, 

Organochlorine and trace-element concentrations in the 

San Pedro River Basin, Arizona: Phoenix, Arizona, 

U.S. Fish and Wildlife Service unnumbered report, 

17 p.
12 Water Quality of Selected Effluent-Dependent Stream Reaches as Indicated by Concentrations of Periphytic Chlorophyll a and Aquatic-Invertebrates

Klemm, D.J., Lewis, P.A., Fulk, F., and Lazorchak, J.M., 

1990, Macroinvertebrate field and laboratory methods 

for evaluating the biological integrity of surface waters: 

Washington, D.C., U.S. Environmental Protection 

Agency Report EPA/600/4–90/030, 256 p.

Lawson, Lin, 1995, Upper Santa Cruz River intensive 

survey—A volunteer-driven study of the water quality 

and biology of an effluent-dominated desert grassland 

stream in southeast Arizona: Phoenix, Arizona 

Department of Environmental Quality Open-File 

Report 95—5, 68 p.

Lenat, D.R., 1988, Water-quality assessment of streams 

using a qualitative collection method for benthic 

macroinvertebrates: Journal of the North American 

Benthological Society, v. 7, no. 3, p. 222–233.

Lewis, M.A., and Burraychak, R., 1979, Impact of copper 

mining on a desert intermittent stream in central 

Arizona—A summary: Journal of the Arizona-Nevada 

Academy of Science, v. 14, February 1979, p. 22–29.

Merritt, R.W. and Cummins, K.W., 1996, An introduction to 

the aquatic insects of North America, 3rd ed.: Dubuque, 

Iowa, Kendall/Hunt Publishing Company, 862 p.

Plafkin, J.L., Barbour, M.T., Porter, K.D., Gross, S.K., and 

Hughes, R.M., 1989, Rapid bioassessment protocols for 

use in streams and rivers, benthic macroinvertebrates 

and fish: Washington, D.C., U.S. Environmental 

Protection Agency Report EPA/444/4–89/001, v.p.

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

1993, Methods for collecting algal samples as part of 

the National wAter-Quality assessment program: U.S. 

Geological Survey Open-File Report 93–409, 39 p.

Wenmacher, C.L., 1996, The Santa Cruz River—A use 

attainability analysis: Tempe, Arizona State University, 

master’s thesis, 124 p. 
Biological communities and water quality were sampled

along the effluent-dependent reach of the Santa Cruz

River at Tubac.

 The effluent-dependent Santa Cruz River near 

 Cortaro.

Top photograph: 

Biological communities and water quality were sampled along the effluent-dependent reach of the Santa Cruz River at Tubac.

Bottom photograph: 

The effluent-dependent Santa Cruz River near Cortaro.
Natural (noneffluent streamflow in the San Pedro River at Charleston, comparison site.