U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2012–1019

Prepared in cooperation with the Pennsylvania Fish and Boat Commission and 

the Pennsylvania Department of Environmental Protection

Streamflow and Water-Quality Monitoring in Response to 

Young-of-Year Smallmouth Bass (Micropterus dolomieu) 

Mortality in the Susquehanna River and Major Tributaries, 

with Comparisons to the Delaware and Allegheny Rivers, 

Pennsylvania, 2008–10

Streamflow and Water-Quality Monitoring 

in Response to Young-of-Year Smallmouth 

Bass (Micropterus dolomieu) Mortality 

in the Susquehanna River and Major 

Tributaries, with Comparisons to 

the Delaware and Allegheny Rivers, 

Pennsylvania, 2008–10

By Jeffrey J. Chaplin and J. Kent Crawford

Prepared in cooperation with the 

Pennsylvania Fish and Boat Commission and 

the Pennsylvania Department of Environmental Protection

Open-File Report 2012–1019

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

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

For more information on the USGS—the Federal source for science about the Earth, its natural and living 

resources, natural hazards, and the environment, visit http://www.usgs.gov or call 1–888–ASK–USGS.

For an overview of USGS information products, including maps, imagery, and publications, 

visit http://www.usgs.gov/pubprod

To order this and other USGS information products, visit http://store.usgs.gov

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

U.S. Government.

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

reproduce any copyrighted materials contained within this report.

Suggested citation:

Chaplin, J.J., and Crawford, J.K., 2012, Streamflow and water-quality monitoring in response to young-of-year smallmouth bass (micropterus dolomieu) mortality in the Susquehanna River and major tributaries, with comparisons to the 

Delaware and Allegheny Rivers, Pennsylvania, 2008–10: U.S. Geological Survey Open-File Report 2012–1019, 39 p.
iii

Contents

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

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

Purpose and Scope ..............................................................................................................................3

History of Mortality in Young-of-Year Smallmouth Bass, 2005–07................................................7

Study Design...................................................................................................................................................7

Methods...........................................................................................................................................................7

Quality Assurance...............................................................................................................................11

Quality Control.....................................................................................................................................11

Streamflow and Water Quality in the Susquehanna River Basin in 2008, 2009, and 2010 ...............11

Comparison of Streamflow and Water Quality in 2008, 2009, and 2010 with Available 

Historical Data .......................................................................................................................18

Differences in Dissolved Oxygen and Water Temperature among the Susquehanna, 

Delaware, and Allegheny Rivers, 2008–10 .................................................................................22

Summary and Conclusions.........................................................................................................................22

Acknowledgments.......................................................................................................................................24

References Cited .........................................................................................................................................25

Appendix 1. Summary Statistics for Water-Quality Data Collected in the Susquehanna 

River Basin.......................................................................................................................................28

Appendix 2. Summary Statistics for Water-Quality Data Collected in the Delaware and 

Allegheny River Basins..................................................................................................................34
iv

Figures

1. Photograph showing young-of-year smallmouth bass (Micropterus dolomieu) 

with a skin lesion swimming in the Susquehanna River near Mahantango, Pa................2

2. Graphs showing example of typical diurnal fluctuations and associated daily values 

for water temperature, dissolved oxygen, pH, and specific conductance measured 

in the Susquehanna River at Harrisburg, Pa. (station C8), June 28–30, 2010 .....................4

3. Map showing location of selected continuous water-quality and streamgages 

in the Delaware, Susquehanna, and Ohio River Basins, Pa., 2008–10.................................5

4. Timeline showing selected tasks undertaken by agencies studying young-of-year 

smallmouth bass mortalities in the Susquehanna River Basin, Pa......................................6

5. Maps showing geographic distribution of disease incidence in young-of-year 

smallmouth bass, Pennsylvania, 2005–07.................................................................................8

6. Graphs showing streamflow in the Susquehanna River at Harrisburg, Pa. (station C8), 

during water years 2005, 2006, 2007, 2008, 2009, and 2010 compared to the range of 

streamflows for the entire period of record (1890–2010).......................................................9

7. Graph showing median daily streamflow in the Susquehanna River at Harrisburg, Pa. 

(station C8), during the critical period (May through July) and the number of stations 

with diseased young-of-year (YOY) smallmouth bass, Pennsylvania, 2005–10................12

8. Maps showing geographic distribution of disease incidence in young-of-year 

smallmouth bass, Pennsylvania, 2008–10...............................................................................13

9. Graphs showing dissolved oxygen (A–C), water temperature (D–F), pH (G–I), 

and specific conductance (J–L) in the Susquehanna River at Harrisburg, Pa. 

(station C8), 2008–10...................................................................................................................14

10. Graphs showing dissolved oxygen (A–C), water temperature (D–F), pH (G–I), 

and specific conductance (J–L) in the Juniata River at Newport, Pa. (station C5), 

2008–10 .........................................................................................................................................15

11. Graphs showing dissolved oxygen (A and B), water temperature (C and D), 

pH (E and F), and specific conductance (G and H) in the Susquehanna River 

at Clemson Island, Pa. (station C4), 2008–09 ..........................................................................16

12. Graphs showing dissolved oxygen (A and B), water temperature (C and D), 

pH (E and F), and specific conductance (G and H) in the Juniata River near 

Howe Township Park, Pa. (station C6), 2008 and 2010..........................................................17

13. Graphs showing streamflow in the Susquehanna River at Harrisburg, Pa. 

(station C8), during water years 1974, 1975, 1976, 1977, 1978, and 1979 compared 

to the range of streamflows for the entire period of record (1890–2010)..........................19

14. Graphs showing daily mean streamflow, daily maximum water temperature, 

and daily minimum dissolved oxygen for May through July of water years 

1974–79 and 2008–10 in the Susquehanna River at Harrisburg, Pa. (station C8). ............20

15. Graphs showing water-quality characteristics and streamflow for the Susquehanna 

River at Harrisburg, Pa. (station C8); Delaware River at Trenton, N.J. (station C1); 

and Allegheny River at Acmetonia, Pa. (station C10), 2008–10 ...........................................23

Tables

1. Stations used for collection of streamflow and continuous water-quality data, 

Pennsylvania, 2008–10 ...............................................................................................................10

2. Statistical results from comparison of 2008, 2009, and 2010 water-quality data to 

historical (1974–79) data for the Susquehanna River at Harrisburg, Pa. (station C8). ....21
v

Conversion Factors and Datums

SI to Inch/Pound

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

Area

square kilometer (km2) 0.3861 square mile (mi2)

Volume

liter (L) 0.2642 gallon (gal)

cubic meter (m3) 264.2 gallon (gal) 

Flow rate

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

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

cubic meter per second (m3/s) 22.83 million gallons per day (Mgal/d) 

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

°F=(1.8×°C)+32

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

°C=(°F-32)/1.8

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

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

unless otherwise noted.

Altitude, as used in this report, refers to distance above the vertical datum.

*Transmissivity: The standard unit for transmissivity is cubic foot per day per square foot times 

foot of aquifer thickness [(ft3

/d)/ft2]ft. In this report, the mathematically reduced form, foot 

squared per day (ft2/d), is used for convenience.

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius 

(μS/cm at 25°C).

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

or micrograms per liter (μg/L).

A water year is the period extending from October 1 through September 30. It is designated by 

the calendar year in which it ends.
vi

(This page intentionally left blank.)
Abstract

Since 2005, spring hatched young-of-year (YOY) smallmouth bass in Pennsylvania reaches of the Susquehanna River 

have experienced above-normal mortality when summertime 

streamflows are near or lower than normal. Stress factors 

include, but are not limited to, low dissolved oxygen and 

elevated water temperatures during times critical for survival 

and development (critical period is May 1 through July 31). 

At this time (2010), widespread disease and mortality are 

believed to be more prevalent for YOY smallmouth bass in the 

Susquehanna River Basin than in the Delaware or Allegheny 

River Basins.

The U.S. Geological Survey began a study in 2008 to 

investigate water temperature and dissolved oxygen as possible stressors to the YOY smallmouth bass. Monitoring began 

in 2008 and continued in 2009 and 2010 in selected reaches. 

Continuous (30-minute intervals) measurements of dissolved 

oxygen, water temperature, pH, and specific conductance 

were made during all or parts of the study at stations including, but not limited to, the Delaware River at Trenton, N.J. 

(station C1), Susquehanna River at Clemson Island (station 

C4), Juniata River at Newport, Pa. (station C5), Juniata River 

at Howe Township Park (station C6), Susquehanna River at 

Harrisburg, Pa. (station C8), and Allegheny River at Acmetonia, Pa. (station C10). At stations C1, C5, and C8, streamflow 

data also were collected. Streamflow data were not collected 

at stations C4, C6, and C10; therefore, data from nearby 

streamgages on the Susquehanna River at Sunbury, Pa. (station N8), the Juniata River at Newport, Pa (station C5), and 

the Allegheny River at Natrona, Pa. (station C9), were used to 

represent flow conditions at these stations.

Streamflow during the critical period of each year influenced dissolved-oxygen concentrations and water temperature, 

and was associated with the incidence of disease in YOY 

smallmouth bass. During the critical period of 2009, station 

C8 had a median daily streamflow of 26,300 cubic feet per 

second (ft3/s), approximately two times higher than for the 

critical periods in 2008 and 2010. Diseased YOY smallmouth 

bass were captured at only 3 sites in 2009 but 19 sites in 2008 

and 28 sites in 2010.

During relatively low streamflow in the critical periods 

of 2008 and 2010, dissolved-oxygen concentrations also were 

lower (more stressful to aquatic life) than in 2009. During the 

critical period, median daily minimum dissolved-oxygen concentrations in main-channel habitat of the Susquehanna River 

at station C8 were lower in 2008 and 2010 by 1.2 milligrams 

per liter (mg/L) and 1.5 mg/L, respectively, in comparison to 

the median daily minimum concentrations in 2009. Despite 

the year-to-year differences in dissolved oxygen, results of a 

comparison of data for station C8 from each year of the study 

period with historical data from 1974–79 indicate daily minimum dissolved-oxygen concentrations in all 3 years of the 

study were significantly lower than those from the historical 

dataset (p-values less than 0.05). Although lower streamflows 

for critical periods of 2008–10 may help explain statistical 

differences in dissolved oxygen between the two time periods, 

other factors such as long-term streamwater warming trends 

also may play a role.

Median daily minimum dissolved-oxygen concentration in the microhabitat of the Susquehanna River at Clemson 

Island (station C4) was 1.6 mg/L lower in 2008 than 2009. No 

data were collected at station C4 in 2010. For the microhabitat 

of the Juniata River near Howe Township Park (station C6), 

median daily minimum dissolved-oxygen concentrations were 

about 0.6 mg/L lower in 2008 than in 2010. At station C6, no 

data were collected in 2009.

Nighttime concentrations of dissolved oxygen in microhabitats at stations C4 and C6 were at times lower than the 

5.0-mg/L criterion established by the U.S. Environmental 

Protection Agency for early life stages of warm-water fish. 

The most frequent occurrence of dissolved oxygen less than 

5.0 mg/L was at station C4 (31 of 92 days in the critical 

period of 2008). The longest duration that dissolved oxygen 

was lower than 5.0 mg/L was 8.5 hours (station C4; 23:30 on 

June 10, 2008, to 08:00 on June 11, 2008).

Median daily maximum water temperatures in the main 

channel of the Susquehanna River at station C8 were 4.0 

degrees Celsius (°C) higher in 2008 and 4.3°C warmer in 2010 

Streamflow and Water-Quality Monitoring in Response to 

Young-of-Year Smallmouth Bass (Micropterus dolomieu) 

Mortality in the Susquehanna River and Major Tributaries, 

with Comparisons to the Delaware and Allegheny Rivers, 

Pennsylvania, 2008–10
2 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10

than in 2009 during the critical periods. At station C8, the 

water temperatures during the critical periods of all 3 years 

were significantly warmer (p-values <0.05) than during the 

critical periods of 1974–79. Year-to-year water-temperature 

differences in the main-channel habitat of the Juniata River 

at station C5 were slightly less than year-to-year differences 

in the Susquehanna River at station C8. During the critical 

periods, the water temperature at station C5 was 3.5°C warmer 

in 2008 and 3.3°C warmer in 2010 than in 2009. These results 

are consistent with warming trends documented in other 

streams of the northeastern United States with much more 

robust water-temperature datasets.

For the critical period of each year, dissolved oxygen 

in the Susquehanna River at station C8 typically was 1.5 to 

3.0 mg/L lower than in the Delaware River at station C1 and 

the Allegheny River at station C10. Median daily maximum 

water temperatures during the critical period of each year 

ranged from 1.6 to 2.7°C warmer at station C8 than at stations 

C1 and C10.

Introduction

The smallmouth bass (Micropterus dolomieu) is native to 

the Great Lakes and Ohio River watersheds but was introduced throughout the United States in the second half of the 

19th century (Pennsylvania Fish and Boat Commission, 2009). 

Today, major drainages to the Chesapeake Bay, including the 

Potomac and Shenandoah Rivers in Maryland, West Virginia, 

and Virginia and the Susquehanna River in New York, Pennsylvania, and Maryland, are widely recognized as high-quality 

smallmouth-bass fisheries with historically strong recruitment. Great public concern over the viability of smallmouth 

bass and other fish species living in these rivers began in the 

summer of 2002, when extensive die-offs of primarily adult 

fish (including smallmouth bass) were documented in the West 

Virginia part of the South Branch Potomac River (Garman and 

Orth, 2007). From 2004 to 2006, additional fish kills occurred 

in the Shenandoah River Basin in Virginia, with 80 percent 

mortality of adult smallmouth bass and redbreast sunfish along 

100 miles of the South Fork Shenandoah River in 2005 (Ripley and others, 2008).

In reaches of the Susquehanna River within Pennsylvania, dead and moribund (nearly dead) young-of-year (YOY) 

smallmouth bass (those hatched in the spring of a given calendar year) were found in quantities greater than background 

levels in the summer of 2005. Since 2005, mortality has been 

widespread in years with near-normal or low streamflow. The 

dead and dying YOY smallmouth bass have had internal and 

external bacterial infections (Pennsylvania Fish and Boat 

Commission, 2005; Vicki Blazer, U.S. Geological Survey, 

written commun., 2010). The external infections are characterized by white skin lesions (fig. 1).

Environmental stressors that may predispose fish to 

colonization by bacteria and other pathogens include, but are 

not limited to, low dissolved-oxygen, elevated ammonia, and 

elevated nitrite concentrations, and warm water temperatures 

Figure 1. Young-of-year smallmouth bass (Micropterus dolomieu) with a skin lesion swimming in the Susquehanna 

River near Mahantango, Pa. Photograph by Joseph Cukjati, U.S. Geological Survey, July 12, 2010.

Skin lesion

Young-of-year smallmouth bass

(approximately 2 inches long)
Introduction 3

(Durborow and others, 1998). Low dissolved oxygen and (or) 

elevated water temperatures, along with other environmental 

stressors, have the potential to cause a physiological stress 

response, resulting in altered circulating concentrations of the 

hormone cortisol (Ripley and others, 2008). Immunosuppression from increased cortisol concentrations can cause reductions in circulating immune cell numbers and bactericidal 

activity coinciding with an inflammatory response (Maule 

and Schreck, 1990; Wang and others, 2005). Reconnaissance water-quality sampling by Pennsylvania Fish and Boat 

Commission (PFBC) biologists in 2007 indicated nighttime 

concentrations of dissolved oxygen in the Susquehanna River 

near Sunbury, Pa., were sometimes less than 5.0 milligrams 

per liter (mg/L), which is the recommended national criterion 

for protecting early life stages of warm-water fish (U.S. Environmental Protection Agency, 1986). As a result, the U.S. Geological Survey (USGS) began investigating dissolved oxygen 

and water temperature as possible stressors. The solubility of 

oxygen in equilibrium with water and air is inversely related 

to water temperature and atmospheric pressure; however, in 

summertime and early fall, equilibrium conditions rarely are 

achieved because of photosynthesis and respiration. During the day, the rate of oxygen production by photosynthesis 

exceeds the rate at which oxygen exsolves into the atmosphere. As a result, the water becomes supersaturated with 

oxygen despite relatively high daytime water temperatures. In 

contrast, cooler nighttime water temperature generally results 

in lower dissolved-oxygen concentrations because respiration 

consumes oxygen in the water faster than it dissolves into the 

water column.

In 2008, low dissolved-oxygen concentrations (less than 

5.0 mg/L) were measured primarily in habitat characterized 

by relatively shallow, slow-moving water in nearshore areas 

(Chaplin and others, 2009). These areas are inhabited by 

YOY smallmouth bass for the first few months of life and are 

referred to as “YOY smallmouth bass microhabitats” in this 

report. In most Pennsylvania rivers, summertime dissolvedoxygen concentrations and water temperatures typically follow 

a diurnal pattern characterized by daily minima in the early 

morning hours (between 0300 and 0700) and daily maxima 

in late afternoon (between 1400 and 1800) (fig. 2). In 2008, 

concentrations of dissolved oxygen less than 5.0 mg/L were 

documented during the expected timeframe (nighttime to early 

morning hours; Chaplin and others, 2009) in the Susquehanna 

River between Sunbury, Pa., and Harrisburg, Pa., and in the 

Juniata River downstream from Newport, Pa. (fig. 3). 

Since continuous monitoring of dissolved oxygen, water 

temperature, and other characteristics was initiated in 2008, 

the PFBC, USGS, and Pennsylvania Department of Environmental Protection (PADEP) have collaborated on a variety of 

other investigations in the Susquehanna River, Juniata River, 

and selected tributaries (fig. 4). These investigations have 

included annual population surveys of YOY smallmouth bass 

by PFBC; health assessments of YOY and adult smallmouth 

bass by USGS, PFBC, and PADEP; assessment of bacterial 

and viral infection in YOY and adult smallmouth by USGS; 

and measurement of contaminants in water using passive 

samplers by USGS and PFBC. Although many results are still 

pending, these research efforts have revealed that the causes of 

a declining smallmouth bass population and disease in YOY 

are complicated and cannot be explained by one environmental stressor or pathogen.

Despite the complicated nature of disease in YOY 

smallmouth bass, some associations with streamflow and 

water-quality characteristics are apparent. Streamflow and 

disease records indicate the incidence of disease was widespread in summers with near-normal or low streamflow and 

relatively high water temperature (Chaplin and others, 2009). 

When water temperature is relatively warm, dissolved-oxygen 

concentrations can be depressed, leading to a stressed aquatic 

environment that does not directly cause disease in YOY 

smallmouth bass, but can modify the role of pathogens, contaminants, or other factors more directly linked to a cause. 

Continuous data for streamflow, dissolved oxygen, and 

water temperature, along with other characteristics including 

pH and specific conductance, provide an important context 

for interpreting the role of pathogens, contaminants, or other 

causes of disease. Recognizing the need for additional study 

beyond 2008, the USGS, in cooperation with PFBC and 

PADEP, continued to monitor streamflow and water-quality 

characteristics in 2009 and 2010 in selected reaches of the 

Susquehanna River and major tributaries. This study focused 

on water-quality characteristics in 2009 and 2010, which were 

then compared with water-quality characteristics in 2008, 

which are documented by Chaplin and others (2009).

Purpose and Scope

This report presents results and analysis of water-quality 

data collected from sondes measuring dissolved oxygen, 

water temperature, pH, and specific conductance continuously (30-minute intervals) from May 1 through July 31 of 

2008, 2009, and 2010 (study period). It also provides streamflow data for all or parts of the study period at the following 

stations: the Susquehanna River at Harrisburg, Pa. (station 

C8); Juniata River at Newport, Pa. (station C5); Susquehanna 

River at Sunbury, Pa. (station N8); Delaware River at Trenton, 

N.J. (station C1); and the Allegheny River at Natrona, Pa. 

(station C9).

Water-quality data for main-channel habitat in the 

Susquehanna River, Juniata River, Delaware River, and 

Allegheny River from 2009 and 2010 are compared with data 

from 2008. Water-quality data initially collected in 2008 at 

microhabitats in the Susquehanna River at Clemson Island 

(station C4) and the Juniata River near Howe Township Park 

(station C6) are compared with data available for these stations during the same periods of 2009 (station C4 only) and 

2010 (station C6 only). For the Susquehanna River at station 

C8, statistical tests were used to compare historical (1974–79) 

streamflow and water-quality characteristics with data collected throughout the study period.
4 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10

Figure 2. Example of typical diurnal fluctuations and associated daily values for water temperature, dissolved oxygen, pH, and 

specific conductance measured in the Susquehanna River at Harrisburg, Pa. (station C8), June 28–30, 2010.

28 29 30

0H 4H 8H 12H 16H 20H 0H 4H 8H 12H 16H 20H 0H 4H 8H 12H 16H 20H 0H

June 2010

4

5

6

7

8

9

10

Water temperature,

in degrees Celsius

Dissolved-oxygen 

concentration,

in milligrams per liter

22

23

24

26

27

28

29

30

31

25

7.2

7.4

7.6

7.8

8.0

8.2

8.4

8.6

8.8

pH, in standard untis

Specific conductance, in 

microsiemens per centimeter

at 25 degrees Celsius

264

268

272

276

280

284

Daily mean

Daily median

Daily maximum

Daily minimum

EXPLANATION
Figure 3. Location of selected continuous water-quality and streamgages in the Delaware, Susquehanna, and Ohio River Basins, Pa., 2008–10. (Selemunicipalities are shown to orient the reader.)

r w

Lehigh

River

Schuylk il l

River Raystown Lake

Juniata River

West

Branch Susq u e hanna River

Susquehanna

River

Allegheny

River

Ohio Riv e r

Water features from U.S. Geological Survey N

Dataset (NHD). Basin boundaries from U.S. Geolo

Watershed Boundary Dataset coded by Hydrolog

Base modified from U.S. Geological Survey 1:24,000-scale digital files

00

50 KILOM

40°

41°

42°

80°

79° 78° 77° 76° 

C10

Pittsburgh

Williamsport

C4

C3 C5

C6

C7

Danville

Sunbury

Mahantango

Harrisburg

Newport Clemson Island

C8

Wilkes-Barre

Acmetonia

EXPLANATION

Major riverBasin boundaryCounty boundaryState boundary

Delaware River Basin

Ohio River BasinGenesee River BasinLake Erie BasinSusquehanna River BasinPotomac River BasinChesapeake Bay Basin

Selected municipalitiesSampling station with streamflowSampling station without streamflowStreamgage without sampling

C9

Natrona

N8

Howe Township Park
6 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10

Figure 4. Selected tasks undertaken by agencies studying young-of-year smallmouth bass mortalities in the Susquehanna River 

Basin, Pa.

2005

J F M A M J J A S O N D

2006

J F M A M J J A S O N D

2007

J F M A M J J A S O N D

2008

J F M A M J J A S O N D

2009

J F M A M J J A S O N D

2010

J F M A M J J A S O N D

External lesions on young-of-year

smallmouth bass at 17 stations

PFBC dissolved-oxygen reconnaissance identifies low 

 (less than 5.0 mg/L) dissolved oxygen in main-channel 

 settings near Sunbury, Pa.

U.S. Geological Survey nutrient synoptic survey

PFBC young-of-year smallmouth bass surveys

PFBC young-of-year smallmouth bass surveys

PFBC young-of-year smallmouth bass surveys

PFBC young-of-year smallmouth bass surveys

PFBC young-of-year smallmouth bass surveys

PFBC young-of-year smallmouth bass surveys

Pre-spawn adult smallmouth bass health assessment

First 2010 young-of-year smallmouth bass health assessment

Pre-spawn adult smallmouth bass health assessment

Second 2010 young-of-year smallmouth bass health assessment

First 2009 young-of-year smallmouth bass health assessment

Second 2009 young-of-year smallmouth bass health assessment

Passive samplers deployed for contaminants of emerging concern

Continuous water-quality monitoring

External lesions on young-of-year

smallmouth bass at only 5 stations

External lesions on young-of-year

smallmouth bass at 32 stations

External lesions on young-of-year

smallmouth bass at 20 stations

External lesions on young-of-year

smallmouth bass at only 3 stations

External lesions on young-of-year

smallmouth bass at 29 stations

including some smaller tributaries to 

the Susquehanna River

Tasks

Occurrence of lesions

on young-of-year

smallmouth bass

Continuous water-quality monitoring during critical period {

{

{

Continuous water-quality monitoring during critical period

Continuous water-quality monitoring during critical period

EXPLANATION

Young-of-year smallmouth

 bass health assessment

Pennsylvania Fish and Boat

 Commission (PFBC) young-of-

 year smallmouth bass survey

Other surveys and

 assessments

Fish health assessments included:

(1) Morphometric characteristics like length,

 weight, condition factor, age, sex

(2) Gross lesion documentation

(3) Examination for evidence of disease

 (lesions/abnormalities) in major organs

 including gills, liver, spleen, anterior kidney,

 posterior kidney, and gonad

(4) Culture for bacteria and viruses

(5) Analysis for vitellogenin (egg yolk precursor

 protein) in male and female fish

[Tasks were completed in the month or months 

they appear next to; critical period defined as 

May 1 through July 31]
Methods 7

History of Mortality in Young-of-Year 

Smallmouth Bass, 2005–07

PFBC has conducted annual surveys of YOY smallmouth 

bass throughout Pennsylvania since the 1980s. Dead and dying 

YOY smallmouth bass were first documented in Pennsylvania 

in July 2005, when surveys by PFBC found YOY with skin 

lesions in the Susquehanna River, West Branch Susquehanna 

River, and Juniata River. The lesions were not found on adult 

fish as in the Shenandoah and Potomac Rivers. No fish kills 

and no lesions on YOY smallmouth bass were documented 

between 2005 and 2007 or reported by fishermen in other large 

rivers of Pennsylvania, such as the Delaware or Allegheny 

(fig. 5). The lesions and associated mortalities were initially 

thought to be caused solely from infection by Flavobacterium 

columnare (Pennsylvania Fish and Boat Commission, 2005; 

Chaplin and others, 2009); however, additional bacteria, 

including Aeromonas spp., are now known to also infect the 

fish (Vicki Blazer, U.S. Geological Survey, written commun., 

2010). In addition to skin lesions, infection by bacteria is often 

accompanied by gill necrosis and fin rot, all occurring in varying degrees of severity (Decostere and others, 1999). These 

conditions were widely reported by PFBC biologists and 

anglers in July 2005. Fish with these symptoms are described 

as diseased throughout this report; however, it is beyond the 

scope of this study to differentiate among the various pathogens and diseases responsible for the symptoms.

After discovering diseased YOY smallmouth bass in 

2005, PFBC biologists continued to document the presence 

or absence of disease during subsequent annual summertime 

population surveys at sampling sites across Pennsylvania 

(fig. 5). In 2006, which had relatively high spring and summer streamflows (fig. 6), few diseased YOY smallmouth bass 

were observed in the reaches studied, including reaches where 

diseased fish had first been discovered in 2005. After the 

2006 sampling season, it was unknown whether the disease 

in 2005 was a one-time event or could be an ongoing problem likely to recur. It also was unknown whether relatively 

high streamflows in 2006 (compared to 2005) prevented the 

disease occurrence.

In 2007, summertime streamflows were similar to 

streamflows in 2005. Diseased fish were again observed in the 

Susquehanna River Basin but were absent during sampling 

of the Delaware and Allegheny River Basins. In the summer 

of 2007, results from water-quality testing by PFBC biologists indicated nighttime concentrations of dissolved oxygen 

were sometimes stressful (less than 5.0 mg/L). These findings 

provided the impetus for beginning a water-quality monitoring 

program in 2008.

Study Design

The study was designed to compare water-quality characteristics at seven stations from May 1 to July 31, defined 

here as the critical period for the survival and development of 

YOY smallmouth bass, in 2008, 2009, and 2010. Sondes were 

first deployed during the critical period in 2008 to continuously measure dissolved oxygen, water temperature, pH, and 

specific conductance in main-channel habitats and microhabitats (Chaplin and others, 2009). The 2008 effort represented 

the beginning of long-term monitoring needed to understand 

water-quality characteristics associated with disease in YOY 

smallmouth bass. Similar monitoring was conducted in 2009 

and 2010. Data from two sondes already operating in the Delaware River at station C1 and the Allegheny River at station 

C10 were used in all 3 years for comparison to Susquehanna 

River data to provide insight about why diseased fish were 

more prevalent in the Susquehanna River than in the Delaware 

or Allegheny River.

In 2008, four sondes were deployed in pairs to evaluate 

differences between main-channel habitats and YOY smallmouth bass microhabitats of the Susquehanna River in the 

vicinity of Clemson Island and the Juniata River near Howe 

Township Park (table 1; fig. 3). These paired sondes are differentiated as “main-channel” (Susquehanna River below 

Clemson Island at station C3 and Juniata River near Howe 

Township Park at station C7) and “microhabitat” (Susquehanna River at station C4 and Juniata River at station C6) 

throughout this report. Two additional sondes were collocated 

with streamgages at stations C8 and C5 to represent mainchannel habitats of the Susquehanna River at Harrisburg, 

Pa., and Juniata River at Newport, Pa., respectively. In 2009, 

sondes were redeployed at all the same stations as in 2008 

except stations C6 and C7 in the Juniata River near Howe 

Township Park. Stations C6 and C7 were eliminated in favor 

of monitoring microhabitat and main-channel habitat in the 

Susquehanna River near Clemson Island (stations C3 and C4). 

In 2010, sondes were deployed in main-channel habitats at 

stations C8 and C5 only.

Methods

Sondes were serviced every 1 to 2 weeks following 

guidelines established by Wagner and others (2006). For 

servicing, freshly calibrated field water-quality meters were 

positioned with the deployed sonde to collect side-by-side 

measurements of water temperature, dissolved oxygen, pH, 

and specific conductance. The deployed sonde was removed, 

cleaned, and returned to the water. A second set of side-byside readings was then recorded to determine whether any 

corrections were necessary as a result of fouling of probes. 

Following the checks against the field water-quality meter, 

the deployed sonde was again removed from the water, and 

data stored in it were downloaded to a field data logger. The 

calibration of each probe was then checked against calibration standards to determine the drift correction. If the probe 

exceeded the calibration criteria from Wagner and others 

(2006), the sondes were recalibrated. The stored data from 
8 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10

Figure 5. Geographic distribution of disease incidence in young-of-year smallmouth bass, Pennsylvania, 2005–07. (Data presented 

on maps for years 2005–07 differ slightly from those presented on similar maps in Chaplin and others (2009) because of new 

information provided through written and oral communications from Geoffrey Smith, Pennsylvania Fish and Boat Commission, 2010)

r w

Lehigh

River

Schuyl k i l l River

Raystown

Lake

Juniata Rive r

West Branch Susq u ehanna River

Susquehanna River

Allegheny

River

Ohio Ri v e r

Delaware

R i ver

r w

Lehigh

River

Schuyl k i l l River

Raystown

Lake

Juniata Rive r

West Branch Susq u ehanna River

Susquehanna River

Allegheny

River

Ohio Ri v e r

Delaware

R i ver

r w

Lehigh

River

Schuyl k i l l River

Raystown

Lake

Juniata Rive r

West Branch Susq u ehanna River

Susquehanna River

Allegheny

River

Ohio Ri v e r

Delaware

R i ver

Major river

Basin boundary

County boundary

State boundary

Delaware River Basin

Ohio River Basin

Genesee River Basin

Lake Erie Basin

Susquehanna River Basin

Potomac River Basin

Chesapeake Bay Basin

No diseased young-of-year

smallmouth bass captured

Diseased fish captured

Sampled, but no young-of-year

smallmouth bass captured

EXPLANATION

Young-of-year smallmouth bass

captured, but disease unassessed

0

0

50 MILES

50 KILOMETERS

40°

41°

42°

80°

79° 78° 77° 76° 2005 75°

40°

41°

42°

80°

79° 78° 77° 76° 2006 75°

40°

41°

42°

80°

79° 78° 77° 76° 2007 75°

Water features from U.S. Geological Survey National Hydrography

Dataset (NHD). Basin boundaries from U.S. Geological Survey Digital

Watershed Boundary Dataset coded by Hydrologic Unit Codes (HUC)

Base modified from U.S. Geological Survey 

1:24,000-scale digital files
Methods 9

Figure 6. Streamflow in the Susquehanna River at Harrisburg, Pa. (station C8), during water years 2005, 2006, 2007, 2008, 2009, and 2010 

compared to the range of streamflows for the entire period of record (1890–2010).

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

EXPLANATION 

Median daily mean flow for period October 1890 to September 2010

Daily mean flow for indicated water year 

Minimum daily mean flow for period October 1890 to September 2010

Maximum daily mean flow for period October 1890 to September 2010

Critical time period for recruitment and

survival of young-of-year smallmouth bass

Water Year 2005 Water Year 2006

Water Year 2007 Water Year 2008

Water Year 2009 Water Year 2010
Table 1. Stations used for collection of streamflow and continuous water-quality data, Pennsylvania, 2008–10. [Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83) unless otherwise noted; QW, water quality; mi2, square miles; Twp., Township--, not available] Station number Map identifier Station description Drainage area (mi2) Period of QW record, calendar year 2008 Period of QW record, calendar year 2009 Period of QW record, calendar year 2010 

01463500 C1 Delaware River at Trenton, N.J. 6,780 01-01 to 12-27 01-02 to 12-31 01-01 to 07-31 40

101554000 N8 Susquehanna River at Sunbury, Pa. 18,300 SF only SF only SF only 240

01555710 C3 Susquehanna River below Clemson Island, Pa. (Main Channel) 19,673 05-16 to 09-25 05-06 to 10-01 -- 4001555725 C4 Susquehanna River at Clemson Island, Pa. (Microhabitat) 19,674 05-16 to 09-25 05-06 to 10-01 -- 4001567000 C5 Juniata River at Newport, Pa. (Main Channel) 3,354 05-08 to 10-15 04-24 to 10-02 05-07 to 07-31 24001567150 C6 Juniata River near Howe Twp. Park (Microhabitat) 3,379 05-23 to 09-29 -- 05-05 to 07-31 4001567151 C7 Juniata River near Howe Twp. Park (Main Channel) 3,379 06-04 to 10-15 -- -- 4001570500 C8 Susquehanna River at Harrisburg, Pa. (Main Channel) 24,100 05-15 to 10-10 04-24 to 10-02 05-08 to 07-31 24003049500 C9 Allegheny River at Natrona, Pa. 11,410 SF only SF only SF only 24003049640 C10 Allegheny River at Lock and Dam 3 at Acmetonia, Pa. 11,592 01-01 to 12-30 01-01 to 12-30 01-01 to 07-31 240

1Map identifier is “N8” to maintain consistency with the naming convention in Chaplin and others (2009). 2Horizontal coordinate information is referenced to the North American Datum of 1927 (NAD 27).
Streamflow and Water Quality in the Susquehanna River Basin in 2008, 2009, and 2010 11

the deployed sondes were corrected for any fouling or drift, 

following recommendations of Wagner and others (2006). The 

adjustments were made using the USGS computer program 

Automated Data Processing System (ADAPS) (U.S. Geological Survey, 2003). After all adjustments were made for each 

water-quality characteristic, the records were peer-reviewed, 

rated, and approved, following methods described in Wagner 

and others (2006).

ADAPS also was used to store the water-quality data 

collected every 30 minutes and to compute daily values for 

each of the characteristics. Examples of daily values include 

the daily minimum, daily median, daily maximum, and daily 

mean of water temperature, dissolved oxygen, pH, and specific 

conductance (fig. 2). These daily values are used throughout 

this report to summarize the data and for statistical comparisons at station C8. For statistical comparisons, historical daily 

values during 1974–79 (historical dataset) are compared with 

(1) data for individual datasets collected in 2008, 2009, and 

2010 and (2) median daily values that result from combining the 3 years of data. A two-sided Wilcoxon signed-rank 

test (Helsel and Hirsch, 2002) was used to test for significant 

differences at station C8 in streamflow, dissolved oxygen, and 

water temperature between data collected during the study 

period and the historical dataset. The pH data were excluded 

from the tests because there were too few daily values. The 

null hypothesis for the statistical tests is that there is no difference between data collected during the study period and the 

historical dataset. For this study, a significant difference exists 

(the null hypothesis is rejected) if the p-value (probability that 

a difference occurs by chance) is less than 0.05.

For the statistical comparisons, only data that were available for common days in the historical dataset and the study 

period (May through July of 2008, 2009, and 2010) were 

used. For example, if the daily mean water temperature was 

available for May 10 of 1974, 1975, 1976, 1977, 1978, 1979, 

and 2008, then this value was included in the comparison. If 

the value for May 10 was missing in any of those years, then 

the value was excluded from the analyses. Because some daily 

values for water temperature and other characteristics are 

missing in any given year, especially for the historical dataset, the number of observations used in the analyses ranges 

from 19 (dissolved oxygen) to 92 (streamflow). In general, 

the power of the statistical tests increases with the number 

of observations.

Quality Assurance

Protocols for calibrating, deploying, and servicing the 

continuous-monitoring water-quality meters were derived 

from the manufacturer’s instruction manual (Yellow Springs 

Instruments, 1999; Wilde and others, 1998; Wagner and others, 2006). Log books for recording calibration, performance, 

and service information were prepared for each field instrument. Information in these log books was updated during 

each service visit for each instrument. Log-book records 

were used to document calibration accuracies and to track the 

performance of each instrument over the course of the project. Comprehensive field data sheets were used to record field 

observations and to ensure that all necessary field observations 

were completed.

Quality Control

Several quality-control measures were adhered to during 

the project. Prior to the sampling season, thermistors for field 

instruments were checked for accuracy against a National Institute for Standards and Technology (NIST) certified thermometer. Instruments for other field measurements (pH, specific 

conductance, and dissolved oxygen) were calibrated on the day 

of sampling. Only certified standards and buffers were used 

for calibrations. Buffers and standards were discarded if the 

expiration date had passed. One-point dissolved-oxygen calibrations were made using the air-saturation approach (Yellow 

Springs Instruments, 1999). Readings were adjusted for atmospheric pressure using a Thommen® pocket barometer that 

had been adjusted to National Weather Service readings and 

adjusted for the elevation at Harrisburg, Pa. A zero dissolved 

oxygen solution of sodium sulfite and cobalt chloride, freshly 

prepared on the days it was needed, was used to check that the 

dissolved-oxygen meters were accurate at the low end of the 

range of expected dissolved-oxygen concentrations. Any meter 

that did not return a dissolved-oxygen reading of 0.3 mg/L or 

less in a zero dissolved oxygen solution was not used.

Streamflow and Water Quality in the 

Susquehanna River Basin in 2008, 2009, 

and 2010

In this section, streamflow and water-quality characteristics measured at selected stations in the Susquehanna River in 

2009 and 2010 are compared with results from 2008 (Chaplin 

and others, 2009) but selected data prior to 2008 are used to 

provide additional context. Since 2005, when streamflow and 

disease prevalence data first became available, near-normal 

or lower streamflows during the critical period [with medians 

from 9,600 ft3/s (2007) to 14,300 ft3/s (2010)] have been associated with relatively high incidence of disease (fig. 7). Critical 

periods with higher median streamflows, like those in 2006 

(26,100 ft3/s) and 2009 (26,300 ft3/s), have been associated 

with lower incidence of disease.

During the study period, diseased YOY smallmouth bass 

in the Susquehanna River Basin were captured by PFBC at 

19 stations in 2008 (median streamflow of 13,100 ft3/s) and 

28 stations in 2010 but only 3 stations in 2009 (figs. 7 and 8). 

For the critical period of 2006, which was characterized by a 

median streamflow similar to that of the critical period of 2009, 

only five stations had diseased YOY smallmouth bass.
12 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10

Annual YOY smallmouth bass collections were expanded 

by PFBC in 2010 to include 10 additional tributaries to the 

Susquehanna River within Pennsylvania. Bacterial infections 

resulting in lesions were documented in 7 of the 10 previously unassessed tributaries. These were the first records of the 

disease condition in smaller, warm-water streams within the 

Susquehanna River Basin.

During relatively low streamflow in 2008 and 2010, 

water-quality characteristics were appreciably different from 

those in 2009, when fewer diseased YOY were observed 

(fig. 8). In main-channel habitats at stations C8 and C5, 

dissolved-oxygen concentrations during the critical period 

presented more stressful conditions for YOY in 2008 and 

2010 than in 2009. During the critical periods of 2008 and 

2010, median daily minimum dissolved-oxygen concentrations in the Susquehanna River at station C8 were 1.2 mg/L 

and 1.5 mg/L, respectively, lower than in 2009 (fig. 9A, B, 

and C; tables 1–1, 1–2, and 1–3). Differences in median daily 

minimum dissolved-oxygen concentrations were similar at station C5, with concentrations in 2008 and 2010 being 1.5 mg/L, 

1.1 mg/L lower than in 2009 (fig. 10A, B, and C; tables 1–1, 

1–2, and 1–3).

YOY smallmouth bass microhabitats generally have 

lower dissolved-oxygen concentrations than nearby mainchannel habitats (Chaplin and others, 2009). In this report, 

few comparisons can be made for microhabitats because 

water-quality data were not collected over all 3 years of the 

study period. Nonetheless, data that are available indicate the 

microhabitat setting in the Susquehanna River at station C4 

had daily minimum dissolved-oxygen concentrations that were 

about 1.6 mg/L lower during the critical period of 2008 than 

in the same timeframe in 2009 (fig. 11A and B). No data were 

collected at station C4 in 2010. For the Juniata River at station 

C6, dissolved-oxygen concentrations were about 0.6 mg/L 

lower in 2008 than in 2010; (fig. 12A and B). No comparison 

with 2009 can be made at station C6 because no water-quality 

data were collected in 2009.

In microhabitat of the Susquehanna River at station C4, 

daily minimum dissolved-oxygen concentrations in 2008 were 

lower than 5.0 mg/L for periods lasting up to 8.5 hours on 

31 days during the critical period (fig. 11A). In contrast, dissolved oxygen at station C4 was at or lower than the 5.0-mg/L 

criterion on only 2 days during the critical period in 2009 

(fig. 11B). For the microhabitat at station C6, dissolved oxygen was less than 5.0 mg/L on 20 days in 2008 for periods up 

to 7 hours and on 11 days in 2010 for periods up to 8.0 hours 

(fig. 12A and B, respectively).

Relatively low flows during the critical periods of 2008 

and 2010 were associated with warmer, more stressful water 

temperatures to YOY smallmouth bass than were observed in 

2009. Overall, river conditions in 2009 were relatively cool 

and apparently not conducive to disease occurrence. Diseased 

YOY smallmouth bass that were discovered by PFBC biologists in 2009 were living primarily within the areas of warmwater discharges (Geoffrey Smith, Pennsylvania Fish and Boat 

Commission, oral commun., 2009). Median daily maximum 

water temperatures in 2008 and 2010 in the main-channel 

habitat of the Susquehanna River at station C8 were 4.0 and 

4.3°C warmer than in 2009 (fig. 9D, E, and F). Water temperatures in the main-channel habitat of the Juniata River at 

station C5 were 3.5°C warmer in 2008 than in 2009 and 3.3°C 

warmer in 2010 than 2009 (fig. 10D, E, and F).

Although most research relating to pH stress has focused 

on acidic conditions rather than near-neutral or alkaline conditions, Scott and others (2005) determined that perch (Perca 

fluviatilis), a warm-water fish that coexists with smallmouth 

bass in inland lakes, can experience interruption of ammonia 

excretion in lakes with persistently high pH (up to 9.9). The 

pH in the study area rarely exceeded 9.0, and pH greater than 

9.0 lasted for only short periods of time (hours). Therefore, 

the pH of streamwater in the study area is not expected to be 

stressful to YOY smallmouth bass.

The pH in main-channel habitat of the Susquehanna 

River at station C8 was similar throughout the study period, 

ranging from 7.3 to 9.2 in 2008, 7.2 to 9.1 in 2009, and 7.2 to 

9.1 in 2010 (tables 1–1, 1–2, and 1–3). Median daily maximum pH for the critical period of each year ranged from 8.1 

in 2008 to 8.5 in 2009 (fig. 9G, H, and I). The pH of mainchannel habitat in the Juniata River at station C5 ranged from 

7.3 to 9.2 in 2008, 6.8 to 9.0 in 2009, and 7.2 to 9.1 in 2010 

(tables 1–1, 1–2, and 1–3). At this station, median daily maximum pH for the critical period of each year ranged from 8.3 in 

2009 to 8.5 in 2008 and 2010 (fig. 10G, H, and I).

Figure 7. Median daily streamflow in the Susquehanna River 

at Harrisburg, Pa. (station C8), during the critical period (May 

through July) and the number of stations with diseased young-ofyear (YOY) smallmouth bass, Pennsylvania, 2005–10.

2005 2006 2007 2008 2009 2010

0

5

10

15

20

25

30

35

Streamflow, in thousand of cubic feet per second

Median streamflow during the critical period 

(May through July)

Number of sampling stations where diseased 

young-of-year smallmouth bass were captured

0

5

10

15

20

25

30

35

Number of sampling stations 

EXPLANATION
Streamflow and Water Quality in the Susquehanna River Basin in 2008, 2009, and 2010 13

Figure 8. Geographic distribution of disease incidence in young-of-year smallmouth bass, Pennsylvania, 2008–10. (Data presented on 

the map for 2008 differ slightly from those presented on similar maps in Chaplin and others (2009) because of new information provided 

through written and oral communications from Geoffrey Smith, Pennsylvania Fish and Boat Commission, 2010)

r w

Lehigh

River

Schuyl k i l l River

Raystown

Lake

Juniata Rive r

West Branch Susq u ehanna River

Susquehanna River

Allegheny

River

Ohio Ri v e r

Delaware

R i ver

r w

Lehigh

River

Schuyl k i l l River

Raystown

Lake

Juniata Rive r

West Branch Susq u ehanna River

Susquehanna River

Allegheny

River

Ohio Ri v e r

Delaware

R i ver

r w

Lehigh

River

Schuyl k i l l River

Raystown

Lake

Juniata Rive r

West Branch Susq u ehanna River

Susquehanna River

Allegheny

River

Ohio Ri v e r

Delaware

R i ver

Major river

Basin boundary

County boundary

State boundary

Delaware River Basin

Ohio River Basin

Genesee River Basin

Lake Erie Basin

Susquehanna River Basin

Potomac River Basin

Chesapeake Bay Basin

No diseased young-of-year

smallmouth bass captured

Diseased fish captured

Sampled, but no young-of-year

smallmouth bass captured

EXPLANATION

Young-of-year smallmouth bass

captured but disease unassessed

0

0

50 MILES

50 KILOMETERS

40°

41°

42°

80°

79° 78° 77° 76° 2008 75°

40°

41°

42°

80°

79° 78° 77° 76° 2009 75°

40°

41°

42°

80°

79° 78° 77° 76° 2010 75°

Water features from U.S. Geological Survey National Hydrography

Dataset (NHD). Basin boundaries from U.S. Geological Survey Digital

Watershed Boundary Dataset coded by Hydrologic Unit Codes (HUC)

Base modified from U.S. Geological Survey 

1:24,000-scale digital files
Figure 9. Dissolved oxygen (

A

–

C), water temperature (

D–

F), pH (

G–I), and specific conductance (

J–L) in the Susquehanna River at Harrisburg, Pa. (s

[ft3/s, cubic feet per second]

5.8

27.8

243

7.3

23.5

8.5

206

6.1

27.5

8.1

299

1012162024283234

6789

10

May June July

100200300400

May June July May Jun

468

101214

0.1110100

Daily mean streamflow, 

in thousands of ft3/s 

0.1110100

Daily mean streamflow, 

in thousands of ft3/s 

0.1110100

Daily mean streamflow, 

in thousands of ft3/s 

0.1110100

Daily mean streamflow, 

in thousands of ft3/s 

0.1110100

Daily mean streamflow, 

in thousands of ft3/s 

0.1110100

Daily mean streamflow, 

in thousands of ft3/s 

0.1110100

Daily mean streamflow, 

in thousands of ft3/s 

0.1110100

Daily mean streamflow, 

in thousands of ft3/s 

A

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

1012162024283234

6789

10

100200300400

468

101214

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

1012162024283234

6789

10

100200300400

468

101214

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

D

E

G

H 

B

J

K 

EXPLANATION

2008 2009 20

Daily mean streamflowMinimum dissolved-oxygen concentration, maximum water temperature, maximum pH, or mean specific conductance

Daily valueMedian value (May 1 through July 31)

National criterion, early life stages (U.S. Environmental Protection Agency, 1986)
Figure 10. Dissolved oxygen (

A

–

C), water temperature (

D–

F), pH (

G–I), and specific conductance (

J–L) in the Juniata River at Newport, Pa. (station C

[ft3/s, cubic feet per second]

228

205

8.5 8.3 8.5

251

25.9

22.4

7.7

6.6

25.7

6.2

456789

1011

0.1110

101520253035

789

10

100150200250300

456789

1011

101520253035

789

10

100150200250300

456789

1011

101520253035

789

10

100150200250300

100300

0.11101003000.11101003000.1110100300

0.11101003000.11101003000.11101003000.1110100300

May June July May June July May Jun

Daily mean streamflow, 

in thousands of ft3

/s 

Daily mean streamflow, 

in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3

/s 

Daily mean streamflow, 

in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3/s 

A

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

D

E

G

H 

B

J

K 

EXPLANATION

2008 2009 201

Daily mean streamflowMinimum dissolved-oxygen concentration, maximum water temperature, maximum pH, or mean specific conductance

Daily valueMedian value (May 1 through July 31)

National criterion, early life stages (U.S. Environmental Protection Agency, 1986)
16 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10

Figure 11. Dissolved oxygen (A and B), water temperature (C and D), pH (E and F), and specific conductance (G and H) in 

the Susquehanna River at Clemson Island, Pa. (station C4), 2008–09. [ft3/s, cubic feet per second; streamflow at station C4 

is represented by flows measured at a streamgage on the Susquehanna River at Sunbury, Pa. (station N8), approximately 

30 miles upstream]

7.0

24.2

8.5

218

5.4

28.5

8.4

308

3

6

4

5

9

8

7

10

11

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

10

15

20

25

30

35

7

8

9

10

100

200

300

400

3

6

4

5

9

8

7

10

11

10

15

20

25

30

35

7

8

9

10

100

200

300

400

May June July May June July

Daily mean streamflow, 

in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s 

A

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

C D

E F

B

G H

EXPLANATION

2008 2009

Daily mean streamflow

Minimum dissolved-oxygen concentration, 

maximum water temperature, maximum pH, 

or mean specific conductance

Daily value

Median value (May 1 through July 31)

National criterion, early life stages (U.S. 

Environmental Protection Agency, 1986)
Streamflow and Water Quality in the Susquehanna River Basin in 2008, 2009, and 2010 17

Figure 12. Dissolved oxygen (A and B), water temperature (C and D), pH (E and F), and specific conductance (G and H) 

in the Juniata River near Howe Township Park, Pa. (station C6), 2008 and 2010. [ft3/s, cubic feet per second; streamflow 

at station C6 is represented by flows measured at a streamgage on the Juniata River at Newport, Pa. (station C5), 

approximately 1 mile upstream]

6.1

26.9 26.1

8.5

8.4

259

305

5.5

2

4

6

8

10

7

8

9

10

11

150

200

250

300

350

2

4

6

8

10

7

8

9

10

11

150

200

250

300

350

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

0.1

1

10

100

1,000

10

15

20

25

30

35

10

15

20

25

30

35

May June July May June July

Daily mean streamflow, 

in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s Daily mean streamflow, in thousands of ft3/s 

A

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

C D

E F

B

G H

EXPLANATION

2008 2010

Daily mean streamflow

Minimum dissolved-oxygen concentration, 

maximum water temperature, maximum pH, 

or mean specific conductance

Daily value

Median value (May 1 through July 31)

National criterion, early life stages (U.S. 

Environmental Protection Agency, 1986)
18 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10

The pH of microhabitat in the Susquehanna River at station C4 ranged from 7.1 to 9.3 in 2008 and 7.2 to 9.1 in 2009 

(tables 1–1 and 1–2). The median daily maximum pHs for the 

critical periods of 2008 and 2009 were 8.4 and 8.5, respectively (fig. 11E and F). In the Juniata River microhabitat at 

station C6, pH was very similar to the values observed in the 

Susquehanna River, ranging from 7.3 to 9.2 in 2008 and 6.9 to 

9.2 in 2010 (tables 1–1 and 1–3). The median daily maximums 

for the critical periods of 2008 and 2009 were 8.5 and 8.4, 

respectively (fig. 12E and F).

Specific conductance is a gross measure of the capacity of dissolved ions in water to conduct an electrical current 

(Wilde and others, 1998). Although linking specific conductance directly to fish health is difficult, it is related to the 

dissolved-solids concentration (Hem, 1985, p. 67) and can be 

used as a qualitative measure to distinguish between waters 

with high and low concentrations of dissolved solids. Ions 

dissolved in the water that may contribute to specific conductance include dissolved nutrients, sulfate, chloride and other 

salts, and metals. Nutrient and metal concentrations are known 

to fluctuate in concentration during the day (Scholefield and 

others, 2005; Nimick and others, 2005) in response to changes 

like those observed in this study for water temperature, pH, 

and dissolved oxygen.

Daily mean specific conductance varied as a function of 

streamflow and location. In the Susquehanna River at Harrisburg (station C8; fig. 9J, K, and L) and Juniata River at Newport (station C5; fig. 10J, K, and L), specific conductance was 

highest in the critical period of 2008 (medians of 299 μS/cm 

and 251 μS/cm, respectively), when streamflow was relatively 

low and dissolved solids were concentrated. Specific conductance was lowest at stations C8 and C5 during the critical period of 2009 (medians of 206 μS/cm and 205 μS/cm, 

respectively) when streamflow was high because because 

dissolved-solids concentrations in runoff were relatively low.

Comparison of Streamflow and Water 

Quality in 2008, 2009, and 2010 with Available 

Historical Data

Continuous streamflow and water quality data collected 

by the USGS in the 1970s were compared to data collected 

by USGS in 2008 at station C8 using a two-sided Wilcoxon 

signed-rank test 8. The comparisons indicate some statistically 

significant differences (p-values <0.05) between the historical dataset (1974–79) and the study period (2008–10) for 

streamflow, dissolved oxygen, and water temperature. However, streamflows and associated water-quality characteristics 

at station C8 were highly variable from year to year (figs. 6 

and 13), and the datasets used for the comparisons are small. 

Methods for continuous water-quality data collection have 

improved greatly since the 1970s, allowing for fewer missing daily values and greater confidence in the data collected 

during 2008–10. Continued streamflow and water-quality 

data collection beyond 2010 is necessary to allow for a more 

thorough analysis of trends.

Daily streamflows during the critical period of 2008 

did not differ from those of the historical dataset (p-value = 

0.0952); however, streamflows in the critical period of 2009 

were significantly higher than those for the historical dataset 

(p-value = 0.0002), and streamflows in 2010 were significantly 

lower (p-value <0.0001). Variability of streamflow during the 

critical period of 2008 (quantified by a standard deviation of 

17,000 ft3/s) was higher than in 2009 (standard deviation of 

12,700 ft3/s) and 2010 (standard deviation of 10,800 ft3/s). 

This could explain why the Wilcoxon signed-rank test did not 

indicate any significant difference between streamflows during 

the critical period of 2008 and the historical dataset.

Comparison of the historical dataset with the combined 

2008–10 dataset (fig. 14) indicates that daily mean streamflows at station C8 were significantly lower in the study period 

(p-value <0.0001; table 2). Although lower streamflows for the 

combined 2008–10 dataset may help explain statistical differences in dissolved oxygen and water temperature between the 

two time periods, other factors such as long-term streamwater 

warming trends (Kaushal and others, 2010) also may play 

a role.

Daily minimum dissolved-oxygen concentrations at station C8 for all 3 years of the study were significantly lower 

than those for the historical dataset (p-values of 0.0001or less), 

even though streamflow was at times no different than (2008), 

higher than (2009), or lower than (2010) streamflow for the 

historical dataset (table 2). The differences in dissolved-oxygen concentrations were greatest in 2008 and 2010, the 2 years 

with critical periods characterized by relatively low streamflow 

and high water temperature. Comparisons using the 19 days 

that are common to the 2008, 2009, 2010, and historical datasets at station C8 indicate median daily minimum dissolvedoxygen concentrations were 1.4 mg/L lower in 2008 than in 

the historical dataset, 0.5 mg/L lower in 2009 than in the historical dataset, and 2.2 mg/L lower in 2010 than in the historical dataset. For the combined study-period dataset at station 

C8, daily minimum dissolved oxygen was 1.4 mg/L lower than 

in the historical dataset. These lower dissolved-oxygen concentrations were associated with warmer water temperatures.

 Daily maximum water temperatures at station C8 were 

significantly warmer (p-values <0.05) during the critical 

periods of 2008, 2009, and 2010 than during the historical 

period (table 2). Results of a comparison of combined data 

for the critical periods of 2008–10 with the historical dataset 

also indicate daily maximum water temperatures were significantly warmer in the study period. The median daily maximum water temperature was 2.3°C warmer for the combined 

2008–10 dataset than for the same days during 1974–79. 

These results are consistent with warming trends documented 

in seven streams in the northeastern United States, including 

the Potomac River, which drains to the Chesapeake Bay and 

has a robust water temperature dataset extending back to 1922 

(Kaushal and others, 2010).
Streamflow and Water Quality in the Susquehanna River Basin in 2008, 2009, and 2010 19

Figure 13. Streamflow in the Susquehanna River at Harrisburg, Pa. (station C8), during water years 1974, 1975, 1976, 1977, 1978, 

and 1979 compared to the range of streamflows for the entire period of record (1890–2010). (A water year extends from October 1–

September 30 and is designated by the calendar year in which it ends.)

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

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

1

2

5

10

20

50

100

200

500

1,000

1,500

Streamflow, in thousands of cubic feet per second

EXPLANATION 

Median daily mean flow for period October 1890 to September 2010

Daily mean flow for indicated water year 

Minimum daily mean flow for period October 1890 to September 2010

Maximum daily mean flow for period October 1890 to September 2010

Critical time period for recruitment and

survival of young-of-year smallmouth bass

Water Year 1974 Water Year 1975

Water Year 1976 Water Year 1977

Water Year 1978 Water Year 1979
20 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10

Figure 14. Daily mean streamflow, daily maximum water temperature, and daily minimum dissolved oxygen for May through 

July of water years 1974–79 and 2008–10 in the Susquehanna River at Harrisburg, Pa. (station C8). (A water year extends from 

October 1–September 30 and is designated by the calendar year in which it ends.)

5

10

20

50

100

200

300

10

12

16

20

24

28

32

36

3

6

9

12

Daily mean streamflow, in thousands 

of cubic feet per second

Daily maximum water temperature, 

in degrees Celsius

Daily minimum dissolved oxygen, 

in milligrams per liter

May

1 5 10 15 20 25 30 1 5 10 15 20 25 30 1 5 10 15 20 25 30

June July

May

1 5 10 15 20 25 30 1 5 10 15 20 25 30 1 5 10 15 20 25 30

June July

May

1 5 10 15 20 25 30 1 5 10 15 20 25 30 1 5 10 15 20 25 30

June July

EXPLANATION

Median value for common days for which data are available 

during the study period, May through July of 2008, 2009, and 2010

Daily value for the given flow or water-quality characteristic 

during the study period, May through July of 2008, 2009, and 2010

Daily value for the given flow or water-quality characteristic 

during the historical period, May through July 1974–79

Median value for common days for which data are available 

during the historical period, May through July 1974–79
Table 2. Statistical results from comparison of 2008, 2009, and 2010 water-quality data to historical (1974–79) data for the Susquehanna River at Harr[N, number of samples; °C, degrees Celsius; mg/L, milligrams per liter; ft3/s, cubic feet per second; <, less than; >, greater than; ns, no significant difference (p-value is greater 

Parameter

Susquehanna River at Harrisburg, 

2008, compared to 

Susquehanna River at Harrisburg, 

historical1

Susquehanna River at Harrisburg, 

2009, compared to 

Susquehanna River at Harrisburg, 

historical1

Susquehanna River at Harrisburg, 

2010, compared to 

Susquehanna River at Harrisburg, 

historical1

Susq

me

Susq

p-value2 Direction of significance3 N p-value2 Direction of significance3 N p-value2 Direction of significance3 N p-va

Mean streamflow (ft3/s) 0.0952 ns 92 0.0002 > 92 <0.0001 < 92 <0.0Minimum dissolved oxygen (mg/L) 0.0001 < 19 <0.0001 < 19 0.0001 < 19 <0.0Maximum dissolved oxygen (mg/L) <0.0001 < 20 0.3759 ns 19 0.4688 ns 19 0.8Dissolved-oxygen range (mg/L) 0.0006 > 20 0.0031 > 19 0.0001 > 19 <0.0Mean dissolved oxygen (mg/L) <0.0001 < 20 0.2935 ns 19 <0.0001 < 19 <0.0Minimum water temperature (°C) 0.0132 > 39 0.0066 < 37 <0.0001 > 37 0.0Maximum water temperature (°C) 0.0021 > 39 0.0232 > 37 <0.0001 > 37 <0.0Water temperature range (°C) 0.0083 > 39 0.9940 ns 37 0.0001 > 37 0.0Mean water temperature (°C) 0.0056 > 39 0.0158 < 37 <0.0001 > 37 <0.0

1Results of two-sided Wilcoxon signed-rank test. For historical data, the medians of daily values computed from May 1 to July 31, 1974–79, are used. Only days that had da

in this analysis. As a result, some characteristics could not be tested because there were too few data (N<19). 

2For this study, a statistically significant difference exists if the p-value is less than 0.05. 3 Indicates whether the value of the parameter in the given year(s) is significantly greater than or less than the historical data value.
22 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10

Differences in Dissolved Oxygen 

and Water Temperature among 

the Susquehanna, Delaware, and 

Allegheny Rivers, 2008–10

At this time (2010), bacterial infections and associated 

lesions are believed to be most prevalent in the Susquehanna 

River Basin. In this section, differences in water quality 

characteristics among the basins are explored as a possible 

explanation for the higher incidence of disease in the Susquehanna River basin. Water-temperature, dissolved-oxygen, and 

pH data collected in the Susquehanna River at station C8 are 

compared with corresponding data from the Delaware River at 

Trenton, N.J. (station C1), and the Allegheny River at Acmetonia, Pa. (station C10).

Regardless of year-to-year variability in streamflow, daily 

minimum dissolved oxygen at station C8 was consistently 

lower than at stations C1 and C10, especially in June and July 

of each year (fig. 15). Median daily minimum dissolved-oxygen concentrations during the critical period at station C8 were 

6.1 mg/L in 2008, 7.3 mg/L in 2009, and 5.8 mg/L in 2010 

(tables 1–1, 1–2, and 1–3) compared to 7.8, 8.7, and 7.8 mg/L, 

respectively, at station C1 (tables 2–1, 2–2, and 2–3). Station 

C10 had median daily minimum dissolved-oxygen concentrations that were greater than those at station C8 but lower than 

those at station C1; median daily minimum values at station 

C10 were 7.1 mg/L in 2008, 7.6 mg/L in 2009, and 7.1 mg/L 

in 2010. Dissolved oxygen did not fall below the U.S. Environmental Protection Agency (1986) criterion of 5.0 mg/L 

at station C1 or C10 during the study period. In contrast, 

dissolved oxygen at station C8 was at or below 5.0 mg/L on 

5 days in 2008, no days in 2009, and 14 days in 2010.

Results of a comparison of water temperatures during 

the critical period of each year indicate that streamwater of 

the Susquehanna River at station C8 was usually warmer than 

that of the Allegheny River at station C10 and the Delaware 

River at station C1. Median daily maximum temperatures 

at station C8 were 2.0°C warmer than at station C1 in 2008, 

2.7°C warmer in 2009, and 1.6°C warmer in 2010. Likewise, 

streamwater at station C8 was warmer than that at station C10 

by 3.1°C in 2008, 1.2°C in 2009, and 3.4°C in 2010.

Summary and Conclusions

Since 2005, spring hatched young-of-year (YOY) smallmouth bass living in Pennsylvania reaches of the Susquehanna 

River have experienced widespread disease and above-normal 

mortality when summertime streamflows are near normal or 

lower. At this time (2010), widespread disease and mortality 

are believed to be more prevalent in the Susquehanna River 

Basin than in the Delaware or Allegheny River Basin. The 

symptoms of disease include skin lesions, gill necrosis, and fin 

rot, all occurring in varying degrees of severity. Reconnaissance water-quality monitoring by the Pennsylvania Fish and 

Boat Commission (PFBC) in the spring and summer of 2007 

measured low dissolved-oxygen concentrations (<5.0 mg/L) 

in the Susquehanna River near Sunbury, Pa. In response to 

the mortalities and initial findings by PFBC, the U.S. Geological Survey (USGS) began a study in 2008 to investigate 

dissolved oxygen and water temperature as possible stressors 

to YOY smallmouth bass in affected reaches of the Susquehanna River. In cooperation with PFBC and the Pennsylvania 

Department of Environmental Protection, monitoring initiated 

in 2008 was continued in 2009 and 2010 in selected reaches 

of the river. Streamflow data from USGS streamgages and 

data collected from continuous (30-minute intervals) waterquality sondes measuring dissolved oxygen, water temperature, pH, and specific conductance were analyzed. The focus 

was on data for May 1 through July 31 of 2008, 2009, and 

2010, the critical period for YOY smallmouth bass survival 

and development.

Near-normal or lower streamflows, like those during the 

critical periods of 2008 and 2010, were associated with lower 

dissolved-oxygen concentrations, warmer water temperatures, 

and increased incidence of disease compared to higher flows 

like those during the critical period of 2009. Median daily 

streamflows during the critical periods of 2008 and 2010 were 

approximately one-half the streamflow for the same period in 

2009—13,100 ft3/s and 14,300 ft3/s in 2008 and 2010, respectively, compared to 26,300 ft3

/s in 2009. These streamflows 

were associated with the capture of diseased YOY smallmouth 

bass at 19 and 28 sites in 2008 and 2010, respectively, but 

only 3 sites in 2009.

Datasets for this study are relatively small and trends that 

have been documented in other tributaries to the Chesapeake 

Bay, such as streamwater warming, are not well established 

for the Susquehanna River. Nonetheless, the effect of warming 

streamwater in the Susquehanna River could be superimposed 

on the influence of yearly streamflow fluctuation. If warming 

is occurring in the Susquehanna River, the same magnitude 

of streamflow today may result in water-quality characteristics that are more stressful than they would have been 

decades ago.

During conditions of relatively low streamflow in the 

critical periods of 2008 and 2010, dissolved-oxygen concentrations were lower (more stressful to aquatic life) than in 

2009. During the critical periods of 2008 and 2010, median 

daily minimum dissolved-oxygen concentrations in mainchannel habitat of the Susquehanna River at Harrisburg 

(station C8) were 1.2 mg/L and 1.5 mg/L lower, respectively, 

than in 2009. Despite the year-to-year differences, comparison 

of water-quality data for each year of the study period with 

historical data available for station C8 from 1974–79 indicates 

daily minimum dissolved-oxygen concentrations were significantly lower in all 3 years of the study (p-values <0.05). This 

was the case even though streamflow was at times no different 

than (2008), significantly higher than (2009), or significantly 

lower than (2010) streamflow in the historical dataset.
Figure 15. Water-quality characteristics and streamflow for the Susquehanna River at Harrisburg, Pa. (station C8); Delaware River at Trenton, N.J. (River at Acmetonia, Pa. (station C10), 2008–10. [ft3/s, cubic feet per second; streamflow at station C10 is represented by flows measured at a streamgaat Natrona, Pa. (station C9), approximately 10 miles upstream] May June July May June July May Ju

Daily mean streamflow, 

in thousands of ft3

/s 

Daily mean streamflow, 

in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3

/s 

Daily mean streamflow, 

in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3/s 

Daily mean streamflow, 

in thousands of ft3/s 

A

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

Daily minimum dissolvedoxygen concentration, 

in milligrams per liter

Daily maximum pH, 

in standard units

Daily mean specific conductance, 

in microsiemens per centimeter 

at 25 degrees Celsius

Daily maximum water

temperature, 

in degrees Celsius

D

E

F

G

H I

B

J

K L

EXPLANATION

2008 2009 20

Minimum dissolved-oxygen concentration, maximum water temperature, maximum pH, or mean specific conductance

Delaware River at Trenton, N.J. (station C1)Susquehanna River at Harrisburg, Pa. (station C8)Allegheny River at Acmetonia, Pa. (station C10)Delaware River at Trenton, N.J. (station C1)Susquehanna River at Harrisburg, Pa. (station C8)Allegheny River at Natrona, Pa. (station C9)

Daily mean streamflow

23456789

1011

02468

1012

3101001,000

3101001,000

3101001,000

3101001,000

3101001,000

3101001,000

3101001,000

3101001,000

0

10203034

456789

10

6789

10

0

100200300400475

02468

1012

0

10203034

456789

10

0

100200300400475

0

10203034

0

100200300400475
24 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10

Along with lower dissolved-oxygen concentrations, 

warmer, more stressful water temperatures also were observed 

in 2008 and 2010 compared to 2009. Median daily maximum 

water temperatures in the main channel of the Susquehanna 

River at station C8 were 4.0°C warmer in 2008 and 4.3°C 

warmer in 2010 than in 2009 during the critical periods. 

In main-channel habitat of the Juniata River at station C5, 

critical-period water temperatures were 3.5°C warmer in 

2008 and 3.3°C warmer in 2010 than in 2009. Comparison of 

water temperatures at station C8 with those in the historical 

dataset from 1974–79 indicates all three study-period years 

had significantly warmer critical-period water temperatures 

(p-values <0.05).

During the critical period of each year, YOY smallmouth 

bass microhabitats, characterized by shallow, slow-moving 

water in nearshore areas, had lower dissolved-oxygen concentrations than nearby main-channel habitats. Few year-to-year 

comparisons can be made for microhabitats because waterquality data were not collected over all 3 years of the study 

period. Data that are available indicate that the median daily 

minimum dissolved-oxygen concentration at the microhabitat 

in the Susquehanna River at Clemson Island (station C4) was 

1.6 mg/L lower during the critical period of 2008 than in the 

same timeframe in 2009. No data were collected at station C4 

in 2010. Water-quality data are available for the microhabitat 

in the Juniata River at Howe Township Park (station C6) in 

2008 and 2010 only. Median daily minimum dissolved-oxygen concentrations were about 0.6 mg/L lower in 2008 than 

in 2010.

In 2008 at station C4 and in 2010 at station C6, concentrations of dissolved oxygen sometimes were lower than the 

5.0-mg/L criterion established by the U.S. Environmental 

Protection Agency for early life stages of warm-water fish. 

Daily minimum dissolved-oxygen concentrations during the 

study period were lower than 5.0 mg/L for as many as 31 of 

92 days during the critical period (station C4 in 2008). The 

longest duration for which dissolved oxygen was lower than 

5.0 mg/L was 8.5 hours (station C4; 23:30 on June 10, 2008, 

to 08:00 on June 11, 2008).

For the critical period of each year, dissolved oxygen 

was consistently lower and water temperatures were consistently warmer in the Susquehanna River at station C8 than 

in the Delaware River at station C1 and the Allegheny River 

at station C10, especially in June and July of each year. The 

median daily minimum dissolved-oxygen concentration during the critical period at station C8 was 6.1 mg/L in 2008, 7.3 

mg/L in 2009, and 5.8 mg/L in 2010, whereas concentrations 

were 7.8, 8.7, and 7.8 mg/L, respectively, in the Delaware 

River at station C1. Daily minimum dissolved-oxygen concentrations in the Allegheny River at station C10 were greater 

than concentrations in the Susquehanna River at station C8, 

but lower than those in the Delaware River at station C1; 

median daily minimum values at station C10 were 7.1°C in 

2008, 7.6°C in 2009, and 7.1°C in 2010. Water temperatures 

at station C8 within the critical period of each year typically were warmer than in the Delaware River at station C1; 

median daily maximum temperatures at station C8 were 2.0°C 

warmer than at station C1 in 2008, 2.7°C warmer in 2009, and 

1.6°C warmer in 2010. Comparison of median daily maximum 

water temperatures within the critical period of each year 

indicates the Susquehanna River at station C8 typically was 

warmer than the Allegheny River at station C10 by 3.1°C in 

2008, 1.2°C in 2009, and 3.4°C in 2010.

In conclusion, the data collected during this study indicate 

the following: (1) Microhabitats where YOY smallmouth bass 

live have lower dissolved oxygen, contributing to more stressful conditions to aquatic life, than are observed in the mainchannel habitats, even during critical periods with relatively 

high streamflow (such as 2009). (2) Dissolved-oxygen concentrations and water temperatures are associated with streamflow, 

with lower dissolved oxygen and higher water temperatures in 

years with relatively low flow such as 2008 and 2010. (3) Dissolved oxygen was significantly lower and water temperature 

was significantly higher during 2008–10 compared to historical 

conditions during 1974–79. (4) Under higher flow conditions 

like those experienced in 2009, increased dissolved oxygen and 

cooler water temperatures were observed in all three major rivers; however, the Susquehanna River still had lower dissolvedoxygen concentrations and warmer water temperatures than 

the Delaware or Allegheny River. (5) Specific conductance and 

pH in the Susquehanna River are within the range of fluctuations observed in the Delaware and Allegheny Rivers and are 

not expected to be major stressors linked to the occurrence of 

disease in YOY smallmouth bass.

Acknowledgments

The cooperation, guidance, and support from Pennsylvania Fish and Boat Commission (PFBC) and Pennsylvania 

Department of Environmental Protection (PADEP) for study 

efforts in 2008 are gratefully acknowledged. For continuation 

of the study in 2009 and 2010, John Arway and Geoff Smith 

served as the study directors for the PFBC and contributed scientific expertise, ideas, and coordination skills to help make the 

project successful. Michael Burton of the Pennsylvania Bass 

Federation and Geoff Smith contributed time, equipment, and 

expertise as boat operators for the project. Robert Lorantas of 

the PFBC is acknowledged for contributions of annual survey 

data for YOY smallmouth bass across Pennsylvania.

Many individuals in the PADEP are recognized for their 

contributions, including Richard Shertzer, Robert Schott, 

Joseph Hepp, and Michael (Joshua) Lookenbill. Staff from 

the Susquehanna River Basin Commission, including David 

Heicher and Andrew Gavin, also are recognized for their contributions to this study. Linda Zarr, Joanne Irvin, David Smith, 

Randall Conger, and Joseph Cukjati of the U.S. Geological 

survey assisted with the data collection, compilation, management, and graphics-presentation tasks. USGS reviewers Robin 

Brightbill and Kimberly Shaffer, along with Rodney Kime of 

PADEP and Geoffrey Smith of PFBC, offered valuable suggestions for improving the report.
References Cited 25

References Cited 

Chaplin, J.J., Crawford, J.K., and Brightbill, R.A., 2009, Water 

quality monitoring in response to young-of-the-year smallmouth bass (Micropterus dolomieu) mortality in the Susquehanna River and major tributaries, Pennsylvania: 2008: U.S. 

Geological Survey Open-File Report 2009–1216, 59 p.

Decostere, A., Haesebrouck, F., Turnbull, J.F., and Charlier, 

G., 1999, Influence of water quality and temperature on 

adhesion of high and low virulence Flavobacterium columnare strains to isolated gill arches: Journal of Fish Diseases, 

v. 22, p. 1–11.

Durborow, R.M., Thune, R.L., Hawke, J.P., and Camus, A.C., 

1998, Columnaris disease—A bacterial infection caused by 

Flavobacterium columnare: Southern Regional Aquaculture 

Center, no. 479, 4 p.

Garman, Greg, and Orth, Donald, 2007, Fish kills in the 

Shenandoah River basin—Preliminary report of the Shenandoah River basin Science Team: Virginia Department of 

Environmental Quality, Va., 16 p.

Helsel, D.R., and Hirsch, R.M., 2002, Statistical methods 

in water resources: U.S. Geological Survey Techniques 

of Water-Resources Investigations, book 4, chap. A3, 

p. 118–124 and 142–147.

Hem, J.D., 1985, Study and interpretation of the chemical 

characteristics of natural water (3d ed.): U.S. Geological 

Survey Water-Supply Paper 2254, 263 p.

Kaushal, S.S., Likens, G.E., Jaworski, N.A., Pace, M.L., 

Sides, A.M., Seekell, D., Belt, K.T., Secor, D.H., and Wingate, R.L., 2010, Rising stream and river temperatures in the 

United States: Frontiers in Ecology and the Environment, 

v. 8, p. 461-466.

Maule, A.G., and Schreck, C.B., 1990, Changes in number 

of leukocytes in immune organs of juvenile coho salmon 

(Oncorhynchus kisutch) after acute stress or cortisol treatment: Journal of Aquatic Animal Health, v. 2, p. 298–304.

Nimick, D.A., Cleasby, T.E., and McCleskey, R.B., 2005, 

Seasonality of diel cycles of dissolved metal concentrations 

in a Rocky Mountain stream: Environmental Geology, v. 47, 

p. 603–614.

Pennsylvania Fish and Boat Commission, 2005, As research 

continues into causes and effects of smallmouth bass dieoff, young of the year analysis provides encouraging news, 

accessed July 10, 2009, at http://www.fish.state.pa.us/newsreleases/2005/smb_yoy.htm.

Pennsylvania Fish and Boat Commission, 2009, Pennsylvania 

fishes, accessed January 11, 2011, at http://www.fish.state.

pa.us/pafish/fishhtms/chapindx.htm.

Ripley, J., Iwanowicz, L., Blazer, V., and Foran, C., 2008, 

Utilization of protein expression profiles as indicators of 

environmental impairment of smallmouth bass (Micropterus 

dolomieui) from the Shenandoah River, Virginia, USA: 

Environmental Toxicology and Chemistry, v. 27, no. 8, 

p. 1756–1767.

Scholefield, David, Goff, T.L., Braven, Jim, Ebdon, Les, Long, 

Terry, and Butler, Mark, 2005, Concerted diurnal patterns 

in riverine nutrient concentrations and physical conditions: 

Science of the Total Environment, v. 344, p. 201–210.

Scott, D.M., Lucas, M.C., and Wilson, R.W., 2005, The effect 

of high pH on ion balance, nitrogen excretion, and behavior 

in freshwater fish from an eutrophic lake—A laboratory and 

field study: Aquatic Toxicology, v. 73, p. 31–43.

U.S. Environmental Protection Agency, 1986, Ambient 

water quality criteria for dissolved oxygen: Washington, 

D.C., U.S. Environmental Protection Agency, Office of 

Water Regulations and Standards, Criteria and Standards 

Division, EPA 440/5-86-003, April 1986, 46 p., accessed 

May 3, 2011, at http://nepis.epa.gov/Exe/ZyPURL.

cgi?Dockey=00001MSS.txt.

U.S. Geological Survey, 2003, User’s manual for the National 

Water Information System of the U.S. Geological Survey 

automated data processing system (ADAPS): U.S. Geological Survey Open-File Report 03–123, version 4.3, 407 p.

Wagner, R.J., Boulger, R.W., Jr., Oblinger, C.J., and Smith, 

B.A., 2006, Guidelines and standard procedures for continuous water quality monitors—Station operation, record 

computation, and data reporting: U.S. Geological Survey 

Techniques and Methods I-D3, 51 p. plus attachments.

Wang, W.B., Li, A.H., Cai, T.Z., and Wang, J.G., 2005, Effects 

of intraperitoneal injection of cortisol on nonspecific 

immune functions of Ctenopharyngodon idella: Journal of 

Fish Biology, v. 67, p.779–793.

Wilde, R.D., Radtke, D.B., Gibs, J., and Iwatsubo, R.T., 

1998, National field manual for the collection of water 

quality data: U.S. Geological Survey Techniques of WaterResources Investigations, book 9, variously paged.

Yellow Springs Instruments, 1999, Environmental monitoring 

systems operations manual: Yellow Springs, Ohio, 264 p.
26 Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10
Appendixes 1–2
Table 1–1. Summary statistics for water-quality data collected at selected sampling stations in the Susquehanna River Basin, Pennsylvania, May 1 t—Continued [C3, Susquehanna River below Clemson Island (Main Channel); C4, Susquehanna River at Clemson Island (Microhabitat); C5, Juniata River at Newport; C6, Juniata River near habitat); C7, Juniata River near Howe Township Park (Main Channel); C8, Susquehanna River at Harrisburg; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, mdaily values; P25, 25th percentile; P75, 75th percentile] Statistic Daily minimum temperature (°C) Daily mean temperature (°C) Daily maximum temperature (°C) Dai

Station Station Station 

C3 C4 C5 C6 C7 C8 C3 C4 C5 C6 C7 C8 C3 C4 C5 C6 C7 C8 C3 C4 

n 76 76 81 65 57 77 76 76 80 65 57 77 76 76 83 65 57 77 76 76 Minimum 10.9 11.0 10.9 13.5 19.5 11.8 11.8 11.8 11.5 14.5 21.0 12.2 12.4 12.4 12.0 15.6 22.4 12.8 1.0 1.P25 20.7 20.4 18.3 22.6 23.6 21.7 22.5 22.4 18.8 24.1 25.0 23.0 25.0 24.9 19.4 25.5 26.6 23.9 3.4 3.3 Median 24.1 23.7 22.6 24.0 24.8 25.2 26.1 25.8 24.3 25.5 26.4 26.3 28.4 28.5 25.9 26.9 27.8 27.5 4.3 4.P75 25.5 24.9 24.0 25.8 26.0 26.4 27.6 27.4 26.0 27.3 27.6 28.0 30.5 30.8 27.6 28.8 29.3 29.6 5.5 6.2 Maximum 27.7 27.0 26.4 27.5 27.8 29.2 29.9 29.7 28.7 29.5 29.6 30.3 32.8 33.5 31.2 31.5 31.8 31.7 6.8 7.9 Mean 22.5 22.1 20.6 23.4 24.6 23.4 24.4 24.2 22.1 24.9 26.1 24.6 26.7 26.8 23.4 26.4 27.7 26.0 4.2 4.7 Standard deviation 4.5 4.2 4.7 3.1 1.9 4.7 4.8 4.7 5.1 3.3 2.0 4.9 5.3 5.5 5.7 3.4 2.2 5 1.4 1.9 

Statistic Daily minimum dissolved oxygen (mg/L) Daily mean dissolved oxygen (mg/L) Daily maximum dissolved oxygen (mg/L) Daily d

Station Station Station 

C3 C4 C5 C6 C7 C8 C3 C4 C5 C6 C7 C8 C3 C4 C5 C6 C7 C8 C3 C4 

n 76 76 74 65 57 73 76 76 74 65 57 73 76 76 74 65 58 73 76 76 Minimum 5.3 3.3 4.1 4.1 4.6 4.8 7.5 5.8 6.6 6.0 6.6 6.1 9.5 8.2 8.2 8.2 9.1 7.3 0.6 0.6 P25 6.0 4.9 5.7 5.0 5.5 5.9 8.0 7.0 8.1 7.2 8.2 6.9 10.3 9.1 10.3 9.3 10.5 8.2 3.3 3.3 Median 6.4 5.4 6.2 5.5 6.0 6.1 8.4 7.3 8.5 7.8 8.6 7.4 10.6 9.5 11.1 10.1 11.5 8.6 4.1 4.4 P75 7.3 5.9 7.7 6.1 6.4 6.6 8.9 7.8 9.4 8.3 9.0 8.1 11.0 10.5 12.2 10.7 12.5 9.4 4.9 5.0 Maximum 10.3 10.2 10.0 9.8 7.9 10.0 11.1 10.5 10.3 10.1 10.3 10.2 15.2 12.5 13.3 11.8 13.6 10.7 7.7 6.4 Mean 6.8 5.7 6.7 5.8 6.1 6.5 8.6 7.6 8.7 7.9 8.6 7.6 10.7 9.7 11.2 9.9 11.5 8.8 3.9 4.0 Standard deviation 1.4 1.6 1.5 1.3 0.8 1.2 0.9 1.1 0.9 0.9 0.7 0.9 0.8 0.9 1.1 0.9 1.2 1 1.5 1.5 

Appendix 1. Summary Statistics for Water-Quality Data Collected in the Susquehanna R
Table 1–1. Summary statistics for water-quality data collected at selected sampling stations in the Susquehanna River Basin, Pennsylvania, May 1 t—Continued[C3, Susquehanna River below Clemson Island (Main Channel); C4, Susquehanna River at Clemson Island (Microhabitat); C5, Juniata River at Newport; C6, Juniata River near habitat); C7, Juniata River near Howe Township Park (Main Channel); C8, Susquehanna River at Harrisburg; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, mdaily values; P25, 25th percentile; P75, 75th percentile]

Statistic

Daily minimum pH (standard units) Daily median pH (standard units) Daily maximum pH (standard units) Daily 

Station Station Station 

C3 C4 C5 C6 C7 C8 C3 C4 C5 C6 C7 C8 C3 C4 C5 C6 C7 C8 C3 C4 

n 76 76 79 65 57 76 76 76 79 65 57 76 76 76 79 65 57 76 76 76 Minimum 7.4 7.1 7.3 7.3 7.6 7.3 7.5 7.3 7.5 7.6 7.9 7.5 7.6 7.4 7.8 8.0 8.4 7.6 0.2 0.P25 7.7 7.3 7.5 7.7 7.8 7.5 8.2 7.6 7.8 8.0 8.2 7.6 8.6 8.1 8.2 8.4 8.6 7.8 0.8 0.7 Median 7.8 7.4 7.6 7.8 7.9 7.5 8.3 7.8 8.0 8.2 8.4 7.8 8.8 8.4 8.5 8.5 8.7 8.1 0.9 0.9 P75 7.8 7.5 7.7 8.0 8.1 7.6 8.5 7.9 8.1 8.4 8.6 8.0 8.9 8.6 8.7 8.7 8.8 8.4 1.1 1.Maximum 8.9 8.5 8.3 8.6 8.3 8.7 9.2 9.0 8.5 9.0 8.7 8.9 9.4 9.3 9.2 9.2 9.0 9.2 1.5 1.6 Mean 7.8 7.4 7.6 7.9 7.9 7.6 8.3 7.8 8.0 8.2 8.4 7.9 8.7 8.3 8.4 8.6 8.7 8.2 0.9 0.9 Standard deviation 0.3 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.3 0.2 0.3 0.4 0.4 0.3 0.3 0.2 0.4 0.3 0.4 

Statistic

Daily minimum specific conductance (μS/cm) Daily mean specific conductance (μS/cm) Daily maximum specific conductance (μS/cm) Daily spec

Station Station Station 

C3 C4 C5 C6 C7 C8 C3 C4 C5 C6 C7 C8 C3 C4 C5 C6 C7 C8 C3 C4 

n 76 76 81 65 57 77 76 76 80 65 57 77 76 76 81 65 57 77 76 76 Minimum 127 129 106 191 162 142 129 131 146 198 187 144 130 133 157 202 214 146 2 3 P25 224 225 179 265 241 194 229 237 197 281 263 199 240 248 199 298 276 205 11 10 Median 294 296 241 300 272 273 313 308 251 305 294 279 319 318 256 311 304 285 16 17 P75 317 319 256 307 298 293 326 327 265 313 306 298 336 334 272 320 314 303 24 23 Maximum 358 366 288 333 330 349 364 368 300 345 344 352 368 369 305 355 354 356 61 69 Mean 267 268 219 284 262 248 276 278 231 293 280 254 286 287 238 300 293 260 19 20 Standard deviation 67 66 46 35 46 59 69 67 44 33 37 60 68 67 45 34 31 61 12 13 
Table 1–2. Summary statistics for water-quality data collected at selected stations in the Susquehanna River Basin, Pennsylvania, May 1 through Ju[C3, Susquehanna River below Clemson Island (Main Channel); C4, Susquehanna River at Clemson Island (Microhabitat); C5, Juniata River at Newport; C8, Susquehanna RiveCelsius; μS/cm, microsiemens per centimeter; mg/L, milligrams per liter; n, number of daily values; P25, 25th percentile; P75, 75th percentile] Statistic Daily minimum temperature (°C) Daily mean temperature (°C) Daily maximum temperature (°C) Dai

Station Station Station 

C3 C4 C5 C8 C3 C4 C5 C8 C3 C4 C5 C8 C3 

n 86 86 91 87 86 86 91 87 86 86 91 87 86 Minimum 15.2 15.1 11.1 11.7 16.2 16.2 11.6 12.8 16.9 16.8 13.0 14.2 0.6 P25 18.0 17.8 15.8 17.9 19.2 19.2 16.9 18.6 20.5 20.3 17.8 19.7 2.2 Median 21.9 21.6 20.0 21.6 23.4 23.2 21.2 22.5 24.5 24.2 22.4 23.5 2.8 P75 23.1 22.7 21.4 23.6 24.6 24.3 23.1 24.8 26.2 26.1 24.4 26.0 3.3 Maximum 25.3 24.4 24.1 26.2 26.5 26.1 25.3 26.8 29.1 28.6 27.3 28.1 4.8 Mean 20.6 20.4 18.7 20.6 21.9 21.8 20.0 21.7 23.4 23.3 21.3 22.8 2.8 Standard deviation 2.9 2.7 3.4 3.5 3.0 2.9 3.6 3.6 3.3 3.2 3.9 3.7 1.0 

Statistic Daily minimum dissolved oxygen (mg/L) Daily mean dissolved oxygen (mg/L) Daily maximum dissolved oxygen (mg/L) Daily di

Station Station Station 

C3 C4 C5 C8 C3 C4 C5 C8 C3 C4 C5 C8 C3 

n 86 86 92 87 86 86 92 87 86 86 92 87 86 Minimum 6.3 4.5 5.7 5.7 7.7 6.3 7.4 6.9 7.9 7.7 8.4 7.4 0.3 P25 7.1 6.1 6.9 6.6 8.6 7.7 8.5 7.9 10.2 9.1 9.9 9.0 2.0 Median 7.7 7.0 7.7 7.3 9.3 8.3 9.2 8.5 11.0 10.2 10.6 9.9 2.9 P75 8.8 8.2 8.6 8.5 10.0 9.2 9.7 9.4 11.6 10.7 11.9 10.4 4.1 Maximum 9.5 9.4 9.7 10.1 10.8 10.2 10.4 10.5 13.2 12.6 13.8 11.3 5.7 Mean 7.9 7.0 7.7 7.5 9.3 8.4 9.1 8.6 10.9 10.0 10.8 9.7 3.0 Standard deviation 0.9 1.2 1.1 1.1 0.8 0.9 0.7 0.9 1.2 1.1 1.3 0.9 1.4 
Table 1–2. Summary statistics for water-quality data collected at selected stations in the Susquehanna River Basin, Pennsylvania, May 1 through Ju[C3, Susquehanna River below Clemson Island (Main Channel); C4, Susquehanna River at Clemson Island (Microhabitat); C5, Juniata River at Newport; C8, Susquehanna RiveCelsius; μS/cm, microsiemens per centimeter; mg/L, milligrams per liter; n, number of daily values; P25, 25th percentile; P75, 75th percentile]

Statistic

Daily minimum pH (standard units) Daily median pH (standard units) Daily maximum pH (standard units) Daily 

Station Station Station 

C3 C4 C5 C8 C3 C4 C5 C8 C3 C4 C5 C8 C3 

n 86 86 92 87 86 86 92 87 86 86 92 87 86 Minimum 7.3 7.2 6.8 7.2 7.4 7.4 6.9 7.4 7.5 7.5 7.2 7.5 0.1 P25 7.6 7.4 7.5 7.4 8.1 7.7 7.6 7.7 8.5 8.2 8.0 8.1 0.8 Median 7.8 7.6 7.6 7.6 8.3 7.9 7.8 8.0 8.8 8.5 8.3 8.5 0.9 P75 7.9 7.7 7.7 7.7 8.6 8.2 8.1 8.3 9.0 8.7 8.7 8.8 1.1 Maximum 8.6 8.0 8.1 8.3 9.1 8.8 8.7 8.8 9.4 9.1 9.0 9.1 1.5 Mean 7.8 7.5 7.6 7.6 8.3 8.0 7.9 8.0 8.8 8.4 8.3 8.4 0.9 Standard deviation 0.3 0.2 0.2 0.2 0.4 0.3 0.4 0.4 0.4 0.4 0.5 0.4 0.3 

Statistic

Daily minimum specific conductance (μS/cm) Daily mean specific conductance (μS/cm) Daily maximum specific conductance (μS/cm) Daily spec

Station Station Station 

C3 C4 C5 C8 C3 C4 C5 C8 C3 C4 C5 C8 C3 

n 86 86 92 87 86 86 92 87 86 86 92 87 86 Minimum 146 165 120 149 157 170 131 162 165 173 143 165 3 P25 184 192 171 182 192 204 177 185 201 216 183 190 8 Median 202 208 196 195 209 218 205 198 215 233 213 208 14 P75 227 235 230 221 235 248 245 226 244 254 252 233 21 Maximum 277 274 276 259 285 282 279 266 297 289 293 277 46 Mean 207 214 198 200 215 224 210 206 222 234 217 213 15 Standard deviation 32 30 37 28 33 29 38 29 34 29 39 29 9 
Table 1–3. Summary statistics for water-quality data collected at selected sampling stations in the Susquehanna River Basin, Pennsylvania, May 1 t—Continued [C5, Juniata River at Newport ; C6, Juniata River near Howe Township Park (Microhabitat); C8, Susquehanna River at Harrisburg; °C, degrees Celsius; μS/cm, microsiemens pper liter; n, number of daily values; P25, 25th percentile; P75, 75th percentile] Statistic Daily minimum temperature (°C) Daily mean temperature (°C) Daily maximum temperature (°C) Dai

Station Station Station 

C5 C6 C8 C5 C6 C8 C5 C6 C8 C5 

n 86 88 84 86 88 84 86 88 84 86 Minimum 11.3 12.0 12.4 11.5 12.3 13.0 11.9 12.5 13.5 0.6 P25 18.7 18.9 21.6 20.0 20.1 23.3 21.6 21.5 25.0 2.1 Median 22.7 23.4 25.3 24.2 24.5 26.5 25.7 26.1 27.8 2.8 P75 25.4 26.1 27.3 27.1 27.8 28.9 28.9 29.3 30.4 4.0 Maximum 27.9 28.7 29.7 30.1 30.8 31.4 32.5 33.2 33.4 6.0 Mean 21.8 22.3 23.7 23.3 23.7 25.1 24.7 25.0 26.5 3.0 Standard deviation 4.4 4.6 4.8 4.8 4.9 4.9 5.1 5.1 5.1 1.3 

Statistic Daily minimum dissolved oxygen (mg/L) Daily mean dissolved oxygen (mg/L) Daily maximum dissolved oxygen (mg/L) Daily di

Station Station Station 

C5 C6 C8 C5 C6 C8 C5 C6 C8 C5 

n 87 88 85 87 88 85 87 88 85 87 Minimum 4.1 3.5 4.1 6.3 5.7 5.8 7.1 7.4 6.9 0.1 P25 5.6 5.4 5.2 7.8 7.5 7.0 9.5 9.0 8.8 1.9 Median 6.6 6.1 5.8 8.4 8.1 7.6 10.5 10.0 9.4 3.2 P75 7.9 7.3 7.1 8.8 8.9 8.2 11.5 10.9 10.1 5.5 Maximum 10.0 10.0 10.0 10.9 10.6 10.7 12.5 13.2 11.3 7.5 Mean 6.7 6.4 6.4 8.4 8.2 7.8 10.4 10.0 9.4 3.6 
Table 1–3. Summary statistics for water-quality data collected at selected sampling stations in the Susquehanna River Basin, Pennsylvania, May 1 t—Continued[C5, Juniata River at Newport ; C6, Juniata River near Howe Township Park (Microhabitat); C8, Susquehanna River at Harrisburg; °C, degrees Celsius; μS/cm, microsiemens pper liter; n, number of daily values; P25, 25th percentile; P75, 75th percentile]Standard deviation 1.4 1.6 1.6 0.9 1.1 1.1 1.2 1.4 0.9 2.0 

Statistic

Daily Minimum pH (standard units) Daily Median pH (standard units) Daily Maximum pH (standard units) Daily 

Station Station Station 

C5 C6 C8 C5 C6 C8 C5 C6 C8 C5 

n 87 88 85 87 88 85 87 88 85 87 Minimum 7.2 6.9 7.2 7.3 7.2 7.4 7.5 7.4 7.6 0.1 P25 7.6 7.5 7.4 7.8 7.8 7.6 8.2 8.1 8.0 0.6 Median 7.7 7.8 7.5 8.0 8.0 7.8 8.5 8.4 8.3 0.9 P75 7.8 8.0 7.6 8.4 8.4 8.1 8.8 8.7 8.6 1.0 Maximum 8.1 8.5 7.7 8.8 8.9 8.4 9.1 9.2 9.1 1.3 Mean 7.7 7.8 7.5 8.1 8.1 7.8 8.5 8.4 8.3 0.8 Standard deviation 0.2 0.3 0.1 0.3 0.4 0.3 0.4 0.4 0.4 0.3 

Statistic

Daily minimum specific conductance (μS/cm) Daily mean specific conductance (μS/cm) Daily maximum specific conductance (μS/cm) Daily spec

Station Station Station 

C5 C6 C8 C5 C6 C8 C5 C6 C8 C5 

n 87 88 85 87 88 85 87 88 85 87 Minimum 138 121 131 154 175 138 157 191 141 3 P25 189 211 192 196 221 196 202 231 199 8 Median 221 248 237 228 259 243 237 271 251 10 P75 260 287 287 270 296 298 277 307 300 14 Maximum 288 318 340 294 325 349 302 342 358 152 Mean 221 248 237 230 259 244 238 270 250 16 Standard deviation 40 43 59 39 41 59 39 41 59 23 
Table 2–1. Summary statistics for water-quality data collected at selected sampling stations in the Delaware and Allegheny River Basins, May 1 thro—Continued [C1, Delaware River at Trenton, N.J.; C10, Allegheny River at Lock and Dam 3 at Acmetonia, Pa.; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams values; P25, 25th percentile; P75, 75th percentile] Statistic Daily minimum temperature (°C) Daily mean temperature (°C) Daily maximum temperature (°C) Dai

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 87 92 87 92 87 92 87 Minimum 12.8 12.0 13.9 12.3 14.3 12.6 0.6 P25 18.0 15.0 18.8 15.2 19.9 15.6 1.6 Median 23.4 23.5 24.5 23.9 25.5 24.4 2.0 P75 25.5 24.9 26.7 25.4 27.9 26.4 2.5 Maximum 28.1 27.1 29.2 27.7 30.5 29.5 3.4 Mean 21.8 20.8 22.8 21.2 23.8 22.0 2.0 Standard deviation 4.7 5.1 4.8 5.2 5.0 5.5 0.7 

Statistic Daily minimum dissolved oxygen (mg/L) Daily mean dissolved oxygen (mg/L) Daily maximum dissolved oxygen (mg/L) Daily di

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 87 85 87 85 87 85 87 Minimum 5.7 5.6 6.6 6.4 7.0 6.8 0.5 P25 7.4 6.6 8.9 7.0 9.9 7.3 1.3 Median 7.8 7.1 9.3 7.3 10.7 7.7 2.4 P75 8.8 9.0 9.7 9.1 11.2 9.3 3.4 Maximum 10.0 9.6 11.0 9.7 12.7 9.8 5.1 Mean 8.0 7.6 9.2 7.9 10.4 8.1 2.4 Standard deviation 1.1 1.2 1.0 1.1 1.3 1.0 1.3 Appendix 2. Summary Statistics for Water-Quality Data Collected in the Delaware and Basins
Table 2–1. Summary statistics for water-quality data collected at selected sampling stations in the Delaware and Allegheny River Basins, May 1 thro—Continued[C1, Delaware River at Trenton, N.J.; C10, Allegheny River at Lock and Dam 3 at Acmetonia, Pa.; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams values; P25, 25th percentile; P75, 75th percentile]

Statistic

Daily minimum pH (standard units) Daily median pH (standard units) Daily maximum pH (standard units) Daily 

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 87 91 87 91 87 91 87 Minimum 7.1 6.6 7.2 6.7 7.2 6.7 0.1 P25 7.8 6.7 8.0 6.8 8.3 6.8 0.5 Median 8.0 6.9 8.4 7.0 8.8 7.0 0.7 P75 8.2 7.3 8.8 7.4 9.1 7.4 0.8 Maximum 8.8 7.5 9.2 7.6 9.4 7.7 1.1 Mean 8.0 7.0 8.4 7.1 8.7 7.1 0.6 Standard deviation 0.4 0.3 0.5 0.3 0.6 0.3 0.3 

Statistic

Daily minimum specific conductance (μS/cm) Daily mean specific conductance (μS/cm) Daily maximum specific conductance (μS/cm) Daily spec

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 87 92 87 92 87 92 87 Minimum 105 214 110 220 118 224 2 P25 198 241 204 248 209 255 5 Median 217 264 222 271 227 283 7 P75 234 296 239 301 245 306 11 Maximum 254 361 261 367 266 375 123 Mean 212 269 218 276 223 283 11 Standard deviation 32 35 30 36 29 38 14 
Table 2–2. Summary statistics for water-quality data collected at selected sampling stations in the Delaware and Allegheny River Basins, May 1 thr—Continued [C1, Delaware River at Trenton, N.J.; C10, Allegheny River at Lock and Dam 3 at Acmetonia, Pa.; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams values; P25, 25th percentile; P75, 75th percentile] Statistic Daily minimum temperature (°C) Daily mean temperature (°C) Daily maximum temperature (°C) Dai

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 91 92 91 92 91 92 91 Minimum 14.6 14.5 14.9 14.8 15.6 14.9 0.3 P25 17.4 18.0 17.9 18.3 18.5 18.6 1.0 Median 19.4 21.4 20.0 21.7 20.8 22.3 1.4 P75 21.8 23.1 22.5 23.4 23.2 23.9 1.7 Maximum 25.0 24.1 25.8 24.7 27.0 25.9 2.9 Mean 19.6 20.4 20.2 20.7 21.0 21.3 1.4 Standard deviation 2.8 3.0 2.9 3.1 3.0 3.3 0.5 

Statistic Daily minimum dissolved oxygen (mg/L) Daily mean dissolved oxygen (mg/L) Daily maximum dissolved oxygen (mg/L) Daily di

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 91 84 91 84 91 84 91 Minimum 6.8 6.4 7.4 6.9 7.8 7.1 0.1 P25 8.4 7.2 8.8 7.3 9.2 7.5 0.5 Median 8.7 7.6 9.2 7.8 9.6 8.0 0.7 P75 9.0 8.8 9.5 9.0 10.1 9.2 1.7 Maximum 9.6 9.4 10.2 9.5 12.8 9.6 4.8 Mean 8.6 7.9 9.2 8.1 9.8 8.2 1.2 Standard deviation 0.6 0.9 0.6 0.8 0.9 0.8 1.1 
Table 2–2. Summary statistics for water-quality data collected at selected sampling stations in the Delaware and Allegheny River Basins, May 1 thr—Continued[C1, Delaware River at Trenton, N.J.; C10, Allegheny River at Lock and Dam 3 at Acmetonia, Pa.; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams values; P25, 25th percentile; P75, 75th percentile]

Statistic

Daily minimum pH (standard units) Daily median pH (standard units) Daily maximum pH (standard units) Daily 

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 91 92 91 92 91 92 91 Minimum 7.1 7.0 7.3 7.1 7.4 7.1 0.1 P25 7.5 7.2 7.6 7.3 7.7 7.3 0.2 Median 7.6 7.3 7.7 7.3 7.8 7.4 0.3 P75 7.7 7.3 8.0 7.4 8.4 7.4 0.5 Maximum 8.8 7.5 9.1 7.5 9.3 7.6 1.3 Mean 7.7 7.3 7.8 7.3 8.0 7.4 0.4 Standard deviation 0.4 0.1 0.4 0.1 0.5 0.1 0.2 

Statistic

Daily minimum specific conductance (μS/cm) Daily mean specific conductance (μS/cm) Daily maximum specific conductance (μS/cm) Daily spec

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 91 92 91 92 91 92 91 Minimum 120 194 122 197 123 199 3 P25 152 239 162 246 168 252 6 Median 175 249 185 255 190 264 9 P75 202 264 207 268 215 276 13 Maximum 224 298 231 306 248 312 82 Mean 176 249 182 256 189 264 13 Standard deviation 31 22 30 23 31 24 13 
Table 2–3. Summary statistics for water-quality data collected at selected sampling stations on the Delaware and Allegheny River Basins, May 1 thr—Continued [C1, Delaware River at Trenton, N.J.; C10, Allegheny River at Lock and Dam 3 at Acmetonia, Pa.; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams values; P25, 25th percentile; P75, 75th percentile] Statistic Daily minimum temperature (°C) Daily mean temperature (°C) Daily maximum temperature (°C) Dai

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 80 92 80 92 80 92 80 Minimum 12.3 12.4 13.4 12.7 14.0 13.0 0.4 P25 19.5 17.8 20.3 18.0 21.3 18.3 1.7 Median 23.9 23.5 25.1 23.9 26.2 24.4 2.2 P75 26.4 27.2 27.6 27.5 28.9 27.9 2.6 Maximum 28.7 28.5 29.7 28.7 30.9 29.5 3.8 Mean 22.8 22.2 23.8 22.6 24.9 23.1 2.1 Standard deviation 4.6 5.1 4.7 5.1 4.9 5.1 0.7 

Statistic Daily minimum dissolved oxygen (mg/L) Daily mean dissolved oxygen (mg/L) Daily maximum dissolved oxygen (mg/L) Daily di

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 80 92 80 92 80 92 80 Minimum 6.3 5.0 7.1 5.5 7.7 6.0 0.5 P25 7.2 6.2 8.6 6.7 9.6 7.1 1.4 Median 7.8 7.1 9.3 7.2 10.4 7.6 2.1 P75 8.7 8.9 9.9 9.0 11.4 9.1 3.0 Maximum 10.6 10.5 11.7 10.6 15.7 10.7 7.9 Mean 8.0 7.4 9.3 7.7 10.7 8.0 2.7 Standard deviation 1.0 1.5 1.0 1.3 1.8 1.2 1.9 
Table 2–3. Summary statistics for water-quality data collected at selected sampling stations on the Delaware and Allegheny River Basins, May 1 thr—Continued[C1, Delaware River at Trenton, N.J.; C10, Allegheny River at Lock and Dam 3 at Acmetonia, Pa.; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams values; P25, 25th percentile; P75, 75th percentile]

Statistic

Daily minimum pH (standard units) Daily median pH (standard units) Daily maximum pH (standard units) Daily 

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 80 92 80 92 80 92 80 Minimum 7.3 7.0 7.5 7.2 7.7 7.2 0.1 P25 7.6 7.2 7.7 7.2 7.9 7.3 0.4 Median 7.7 7.2 8.0 7.3 8.4 7.4 0.6 P75 8.0 7.3 8.6 7.4 8.9 7.4 0.8 Maximum 8.5 7.5 9.1 7.5 9.4 7.6 1.2 Mean 7.8 7.3 8.1 7.3 8.4 7.4 0.6 Standard deviation 0.3 0.1 0.5 0.1 0.5 0.1 0.3 

Statistic

Daily minimum specific conductance (μS/cm) Daily mean specific conductance (μS/cm) Daily maximum specific conductance (μS/cm) Daily spec

Station Station Station 

C1 C10 C1 C10 C1 C10 C1 

n 80 92 80 92 80 92 80 Minimum 165 170 170 173 181 176 3 P25 212 234 217 237 222 246 6 Median 234 254 241 261 243 265 8 P75 245 335 250 340 254 346 11 Maximum 272 435 276 465 277 482 45 Mean 230 281 235 289 239 296 10 Standard deviation 23 69 23 71 23 73 6 

For additional information:

Director

U.S. Geological Survey

215 Limekiln Road

New Cumberland, PA 17070

http://pa.water.usgs.gov/

Document prepared by the West Trenton Publishing Service Center
Chaplin and Crawford—Streamflow and Water-Quality Monitoring in Response to Young-of-Year Bass Mortality, Pennsylvania, 2008–10—Open-File Report 2012–1019