U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2009-1216

In cooperation with the Pennsylvania Fish and Boat Commission, 

Pennsylvania Department of Environmental Protection, and PPL Corporation

Water-Quality Monitoring in Response to Young-of-theYear Smallmouth Bass (Micropterus dolomieu) Mortality 

in the Susquehanna River and Major Tributaries, 

Pennsylvania: 2008
Cover:

Dead young-of-the-year smallmouth bass collected from the Susquehanna River at Shady Nook boat launch near Selinsgrove, Pa. Photographed by J. Chaplin, U.S. Geological Survey, July 2008.
Water-Quality Monitoring in Response 

to Young-of-the-Year Smallmouth Bass 

(Micropterus dolomieu) Mortality in the 

Susquehanna River and Major Tributaries, 

Pennsylvania: 2008

By Jeffrey J. Chaplin, J. Kent Crawford, and Robin A. Brightbill

In cooperation with the Pennsylvania Fish and Boat Commission, Pennsylvania 

Department of Environmental Protection, and PPL Corporation

Open-File Report 2009-1216

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2009

Revised: April, 2011

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reproduce any copyrighted materials contained within this report.

Suggested citation:

Chaplin, J.J., Crawford, J.K., and Brightbill, R.A., 2009, Water-quality monitoring in response to young-ofthe-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.
iii

Contents

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

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

Purpose and Scope ..............................................................................................................................6

Description of Study Reaches ............................................................................................................6

Dissolved-Oxygen Criteria and Standards for Protection of Aquatic Life...................................7

Monitoring Strategy.......................................................................................................................................8

Study Design..........................................................................................................................................8

Monitoring Stations..............................................................................................................................9

Susquehanna River at Shady Nook Boat Launch ..................................................................9

Susquehanna River in the Vicinity of Clemson Island ...........................................................9

Juniata River at Newport, Pennsylvania .................................................................................9

Juniata River in the Vicinity of Howe Township Park ..........................................................14

Susquehanna River at Harrisburg, Pennsylvania.................................................................14

Delaware River at Trenton, New Jersey................................................................................14

Allegheny River at Lock and Dam 3 at Acmetonia, Pennsylvania .....................................14

Methods................................................................................................................................................14

Continuous Water-Quality Monitoring....................................................................................14

Nutrient Sampling......................................................................................................................15

Biochemical Oxygen Demand Sampling................................................................................15

Quality Assurance...............................................................................................................................15

Quality Control.....................................................................................................................................17

Blank Samples............................................................................................................................17

Duplicate Samples.....................................................................................................................17

Reference Samples ...................................................................................................................18

Monitoring Results and Implications, Susquehanna River...................................................................18

Comparison of Water Quality Observed in Young-of-the-Year Smallmouth Bass

Microhabitats and Main-Channel Habitats ......................................................................18

Dissolved Oxygen.......................................................................................................................18

Water Temperature ...................................................................................................................26

pH .................................................................................................................................................28

Specific Conductance...............................................................................................................28

Influence of Warm-Water Discharge at Shady Nook...................................................................28

Spatial Variability of Nutrients in Selected Reaches in the Susquehanna River Basin..........30

Nitrogen in Water ......................................................................................................................30

Phosphorus in Water.................................................................................................................32

Biochemical Oxygen Demand in Water.................................................................................32

Nutrients in Streambed Sediments.........................................................................................32

Implications of Nutrients in the Susquehanna River...........................................................34

Water Quality in 2008 Compared with Available Historical Data................................................35

Correlation between Streamflow and Disease Incidence...........................................................36

Water-Quality Differences among the Susquehanna, Delaware, and Allegheny Rivers ................40

Summary and Conclusions.........................................................................................................................46
iv

Acknowledgments.......................................................................................................................................48

References Cited..........................................................................................................................................48

Appendix 1. Quality Control.....................................................................................................................53

Appendix 2. Selected Statistics for Dissolved-Oxygen Concentrations .........................................54

Appendix 3. Nutrient Concentrations in Water and Streambed Sediment.....................................55

Figures

1. Map showing location of selected continuous water-quality monitoring stations in

the Delaware, Susquehanna, and Ohio River Basins, Pennsylvania, 2008.........................3

2. Photographs showing moribund (A) and dead (B) young-of-the-year smallmouth

bass with skin lesions caused by Flavobacterium columnare bacteria..............................4

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

smallmouth bass, Pennsylvania, 2005–07.................................................................................5

4. Graph showing solubility of oxygen in water at temperatures ranging from 5 to 40

degrees Celsius and atmospheric pressure of 755 millimeters of mercury........................7

5. Orthophotos and channel cross sections in the vicinity of selected

continuous-monitoring stations in free-flowing reaches of the A) Delaware,

B) Susquehanna, and C and D) Juniata Rivers, Pennsylvania............................................12

6. Orthophotos and channel cross sections in the vicinity of selected

continuous-monitoring stations in impounded reaches of the A) Susquehanna, and

B) Allegheny Rivers, Pennsylvania ..........................................................................................13

7. Map showing locations of stations selected for the nutrient synoptic survey in the

Susquehanna River Basin, Pennsylvania, June 11 and 12, 2008 ........................................16

8-13.—Graphs showing: 

8. Water quality in young-of-the-year smallmouth-bass microhabitat and

main-channel habitats of the Susquehanna River in the vicinity of Clemson

Island, Pennsylvania, 2008 ...............................................................................................20

9. Water quality in young-of-the-year smallmouth-bass microhabitat and

main-channel habitats of the Juniata River in the vicinity of Howe Township

Park, Pennsylvania, 2008 ..................................................................................................21

10. Seven-day mean dissolved-oxygen concentrations in A) the Susquehanna

River in the vicinity of Clemson Island and B) the Juniata River in the vicinity of 

Howe Township Park, Pennsylvania, 2008.....................................................................26

11. Daily range in water temperature, dissolved-oxygen concentration, and pH in

the Susquehanna River in the vicinity of Clemson Island, Pennsylvania, 2008.......27

12. Daily range in water temperature, dissolved-oxygen concentration, and pH in

the Juniata River in the vicinity of Howe Township Park, Pennsylvania, 2008........29

13. Comparison of mean daily water temperatures downstream of a warm-water

discharge with mean daily water temperature at Clemson Island,

Pennsylvania, July–September 2008..............................................................................30

14-15.—Maps showing:

14. Relative comparison of nitrate nitrogen concentrations in water from selected 

reaches of the Susquehanna River and major tributaries, Pennsylvania,

June 11 and 12, 2008..........................................................................................................31
v

15. Relative comparison of orthophosphate phosphorus concentrations in water

of selected reaches of the Susquehanna River and major tributaries, June 11

and 12, 2008.........................................................................................................................33

16. Graphs showing relation between A) streamflows in the Susquehanna River

at Harrisburg, Pennsylvania (station C8), and B) water temperature measured

approximately 6 miles upstream at Rockville, Pennsylvania, 2005–08 ..............................37

17. Maps showing geographic distribution of disease incidence in 2008 compared to

2005–07, Pennsylvania ...............................................................................................................38

18-20.—Graphs showing: 

18. Relation between 2008 streamflow and historical streamflow at selected

streamgages in Pennsylvania and New Jersey ...........................................................39

19. Comparison of water quality in the Susquehanna River at Harrisburg,

Pennsylvania, Delaware River at Trenton, New Jersey, and Allegheny River at

Acmetonia, Pennsylvania, 2008.......................................................................................41

20. Seven-day mean dissolved-oxygen concentration and streamflow conditions in the 

Susquehanna River at Harrisburg, Pennsylvania, Delaware River at Trenton, 

New Jersey, and Allegheny River at Acmetonia, Pennsylvania, 2008............................45

Tables

1. Summary statistics for historical streamflow at selected streamgages in study

reaches of the Susquehanna River Basin, Pennsylvania......................................................6

2. National criteria for ambient dissolved-oxygen concentrations for protection of

warm-water fishes .......................................................................................................................7

3. Pennsylvania standards for dissolved-oxygen concentration in waters designated

as warm-water fisheries .............................................................................................................8

4. Stations for collection of streamflow, continuous water-quality data, and nutrient 

synoptic samples, Pennsylvania, 2008 ....................................................................................10

5. Statistical comparison of water quality in young-of-the-year smallmouth-bass

microhabitats and main-channel habitats in the Susquehanna and Juniata Rivers,

Pennsylvania, 2008 .....................................................................................................................19

6. Summary statistics for water-quality data collected at selected stations in the

Susquehanna River Basin, Pennsylvania, May 1 through July 31, 2008............................22

7. Statistical comparison of 2008 and historical (1974–79) water-quality data from the

Susquehanna River, Pennsylvania...........................................................................................35

8. Summary statistics for water-quality data collected in the Delaware River at

Trenton, New Jersey, Susquehanna River at Harrisburg, Pennsylvania, and the

Allegheny River at Acmetonia, Pennsylvania, 2008 ..............................................................42

9. Statistical comparison of water quality in the Susquehanna River at Harrisburg,

Pennsylvania, to water quality in the Delaware River at Trenton, New Jersey, and

the Allegheny River at Acmetonia, Pennsylvania, 2008 .......................................................44
vi

Conversion Factors, Abbreviations, and Datums

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

square mile (mi2) 259.0 hectare (ha)

square mile (mi2) 2.590 square kilometer (km2) 

Volume

gallon (gal) 3.785 liter (L) 

gallon (gal) 0.003785 cubic meter (m3) 

gallon (gal) 3.785 cubic decimeter (dm3) 

Flow rate

foot per second (ft/s) 0.3048 meter per second (m/s)

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

million gallons per day (Mgal/d) 0.04381 cubic meter per second (m3/s)

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).

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

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

25°C).

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

or micrograms per liter (μg/L).

Concentrations of chemical constituents in streambed sediment are given in grams per kilogram 

(g/kg)
Abstract

Mortalities of young-of-the-year (YOY) smallmouth bass 

(Micropterus dolomieu) recently have occurred in the Susquehanna River due to Flavobacterium columnare, a bacterium 

that typically infects stressed fish. Stress factors include but 

are not limited to elevated water temperature and low dissolved oxygen during times critical for survival and development of smallmouth bass (May 1 through July 31). The 

infections were first discovered in the Susquehanna River and 

major tributaries in the summer months of 2005 but also were 

prevalent in 2007.

 The U.S. Geological Survey, Pennsylvania Fish and Boat 

Commission, Pennsylvania Department of Environmental 

Protection, and PPL Corporation worked together to monitor dissolved oxygen, water temperature, pH, and specific 

conductance on a continuous basis at seven locations from 

May through mid October 2008. In addition, nutrient concentrations, which may affect dissolved-oxygen concentrations, 

were measured once in water and streambed sediment at 25 

locations.

Data from water-quality meters (sondes) deployed as 

pairs showed daily minimum dissolved-oxygen concentration 

at YOY smallmouth-bass microhabitats in the Susquehanna 

River at Clemson Island and the Juniata River at Howe Township Park were significantly lower (p-value < 0.0001) than 

nearby main-channel habitats. The average daily minimum 

dissolved-oxygen concentration during the critical period 

(May 1–July 31) was 1.1 mg/L lower in the Susquehanna 

River microhabitat and 0.3 mg/L lower in the Juniata River. 

Daily minimum dissolved-oxygen concentrations were lower 

than the applicable national criterion (5.0 mg/L) in microhabitat in the Susquehanna River at Clemson Island on 31 days 

(of 92 days in the critical period) compared to no days in the 

corresponding main-channel habitat. In the Juniata River, daily 

minimum dissolved-oxygen concentration in the microhabitat 

was lower than 5.0 mg/L on 20 days compared to only 5 days 

in the main-channel habitat. The maximum time periods that 

dissolved oxygen was less than 5.0 mg/L in microhabitats of 

the Susquehanna and Juniata Rivers were 8.5 and 5.5 hours, 

respectively. Dissolved-oxygen concentrations lower than the 

national criterion generally occurred during nighttime and 

early-morning hours between midnight and 0800. The lowest 

instantaneous dissolved-oxygen concentrations measured in 

microhabitats during the critical period were 3.3 mg/L for the 

Susquehanna River at Clemson Island (June 11, 2008) and 

4.1 mg/L for the Juniata River at Howe Township Park (July 

22, 2008).

Comparison of 2008 data to available continuous-monitoring data from 1974 to 1979 in the Susquehanna River at 

Harrisburg, Pa., indicates the critical period of 2008 had an 

average daily mean dissolved-oxygen concentration that was 

1.1 mg/L lower (p-value < 0.0001) than in the 1970s and an 

average daily mean water temperature that was 0.8°C warmer 

(p-value = 0.0056). Streamflow was not significantly different 

(p-value = 0.0952) between the two time periods indicating 

that it is not a likely explanation for the differences in water 

quality.

During the critical period in 2008, dissolved-oxygen 

concentrations were lower in the Susquehanna River at Harrisburg, Pa., than in the Delaware River at Trenton, N.J., or 

Allegheny River at Acmetonia near Pittsburgh, Pa. Daily 

minimum dissolved-oxygen concentrations were below the 

national criterion of 5.0 mg/L on 6 days during the critical 

period in the Susquehanna River at Harrisburg compared to 

no days in the Delaware River at Trenton and the Allegheny 

River at Acmetonia. Average daily mean water temperature in 

the Susquehanna River at Harrisburg was 1.8°C warmer than 

in the Delaware River at Trenton and 3.4°C warmer than in the 

Allegheny River at Acmetonia. These results indicate that any 

stress induced by dissolved oxygen or other environmental 

conditions is likely to be magnified by elevated temperature in 

the Susquehanna River at Harrisburg compared to the Delaware River at Trenton or the Allegheny River at Acmetonia.

Water-Quality Monitoring in Response to Young-of-theYear Smallmouth Bass (Micropterus dolomieu) Mortality 

in the Susquehanna River and Major Tributaries,

Pennsylvania: 2008

By Jeffrey J. Chaplin, J. Kent Crawford, and Robin A. Brightbill
2 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

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). During 2004–06, additional fish kills occurred 

in the Shenandoah River Basin in Virginia, with 80 percent 

mortality of adult smallmouth bass and redbreast sunfish along 

100 mi of the South Fork Shenandoah River in 2005 (Ripley 

and others, 2008).

The first documented problems in Pennsylvania were in 

July 2005, when surveys by the Pennsylvania Fish and Boat 

Commission (PFBC) found an unusually high number of 

smallmouth bass in the Susquehanna River (fig. 1) with skin 

lesions (fig. 2). The lesions were not found on adult fish as in 

the Shenandoah and Potomac Rivers but instead were limited 

to young-of-the-year (YOY) smallmouth bass (those hatched 

in the spring of a given calendar year) in the mainstem of the 

Susquehanna River, West Branch Susquehanna River, and 

Juniata River (hereinafter termed “affected reaches”). In addition, no lesions on YOY smallmouth bass were documented 

by PFBC biologists or reported by fishermen in other large 

rivers of Pennsylvania like the Delaware or Allegheny (fig. 3). 

Pathology examinations in 2005 determined the mortalities 

in affected reaches of the Susquehanna River Basin were 

caused by Flavobacterium columnare, a common soil and 

water bacterium that causes a secondary infection in stressed 

fish (Pennsylvania Fish and Boat Commission, 2005). Infection by F. columnare is characterized by gill necrosis, grey to 

white lesions or spots on the body, skin erosion, and fin rot, all 

occurring in varying degrees of severity (Decostere and others, 

1999). Other opportunistic bacteria including Enterobacter sp. 

and Aeromonas salmonicida and parasite infections were 

implicated in die-offs of adult fish in the Shenandoah and 

Potomac Rivers (Blazer and others, 2006) but not in the 

Susquehanna River.

After discovering the F. columnare infections in affected 

reaches of the Susquehanna River Basin in 2005, PFBC 

biologists continued to document the presence or absence 

of disease in YOY smallmouth bass at sampling sites across 

Pennsylvania during annual summertime surveys (fig. 3). In 

2006, no YOY smallmouth bass captured during the annual 

surveys were infected by F. columnare at any sampling site, 

including those in affected reaches where diseased fish had 

first been discovered in 2005. After the 2006 sampling season, 

it was unknown if the disease in 2005 was a one-time event or 

if it could be an ongoing problem likely to reoccur. It was also 

unknown if relatively high streamflows in 2006 compared to 

2005 prevented the disease occurrence. In 2007, summertime 

streamflows were similar to streamflows in 2005, and the disease returned at most sampling stations in the affected reaches 

but was once again absent from the Delaware or Allegheny 

River Basins (fig. 3).

During the 2005–07 time period, reconnaissance sampling efforts by PFBC biologists indicated nighttime concentrations of dissolved oxygen in the Susquehanna River near 

Sunbury, Pa., were below the recommended national criterion 

for protecting earlylife stages of warm-water fish (5.0 mg/L; 

U.S. Environmental Protection Agency, 1986). Low dissolved 

oxygen and elevated water temperatures can elicit a physiological stress response (Ripley and others, 2008) that may 

predispose YOY smallmouth bass and other fish to infection 

by F. columnare (Durborow and others, 1998). Outbreaks 

of infection by F. columnare generally occur when fish are 

stressed and water temperatures are greater than 16°C. On the 

basis of PFBC findings and literature evidence, sub-optimal 

dissolved oxygen and relatively warm temperatures in habitats 

of the YOY smallmouth bass were suspected to have played 

a role in predisposing the fish to the bacterial infections. In 

most Pennsylvania rivers, summertime dissolved-oxygen 

concentration, water temperature, and pH follow a sinusoidal 

pattern characterized by daily minima in the early morning 

hours (between 0300 and 0700) and daily maxima in late 

afternoon (between 1400 and 1800). As the sun rises, photosynthesis by periphyton, phytoplankton, and other aquatic 

macrophytes begins to produce oxygen and consume dissolved 

carbon dioxide. As oxygen is produced and carbon dioxide is 

consumed, dissolved-oxygen concentration and pH increase. 

During nighttime hours, photosynthetic activity stops, but 

community respiration by aquatic plants and animals (fish and 

invertebrates) continues and consumes oxygen from the water 

so nighttime dissolved-oxygen concentrations typically are at 

their lowest and most stressful levels. Available historical measurements of dissolved oxygen by the U.S. Geological Survey 

(USGS), the Pennsylvania Department of Environmental Protection (PADEP), and others generally were made during the 

day and, therefore, represent times when concentrations are 

least stressful because dissolved oxygen is at or approaching 

daily maxima. Continuous measurement of dissolved oxygen 

(30-minute intervals, for example) is the best way to assess 

whether nighttime concentrations are in stressful ranges that 

could contribute to smallmouth bass disease and mortality.

Despite the availability of continuous water-quality data 

at some locations in the Susquehanna River, substantial data 

gaps exist. Recognizing the need for additional information, 

the USGS in cooperation with the PFBC, the PADEP, and 

PPL Corporation (PPL), conducted a study from May through 

October 2008 to assess water quality in selected reaches of the 

Susquehanna River and major tributaries where mortalities of 

smallmouth bass were documented. The results of the study 

are presented in this report. The data and interpretations within 

this report document conditions in 2008 and could be used as 

a foundation for development of a long-term network of data 

collection and interpretation.
Introduction 3Figure 1. Location of selected continuous water-quality monitoring stations in the Delaware, Susquehanna, and Ohio River Basins, Pennsylvania, 2008.

L e h i g h

R i v e r

S c h u y l k i l l R i v e r Raystown Lake

Jun ai

ta

Rive r

S u s q uehanna

River

Susquehanna

River

Al el

gheny

River

no M

al ehahno

i R ev r

O h

oi

R i v e r

Delaw a r e

River

W e s t

Branch

Sus q u e h a n

na

River

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).

C10

Pittsburgh

Williamsport

C2

C4

C3

C5

C6

C7

C1

Philadelphia

40°

41°

42°

80°

79° 78° 77° 76°

C9

Danville

Lewistown

Highspire

Basin boundaryMajor riverCounty boundaryState boundary

Sampling station and identifier without streamflowSampling station and identifier with streamflowSelected municipality

EXPLANATION

Streamgage and identifier without sampling 

Area containingstudy reaches

0

0

50 MILES

50 KILOMETERS

10 20 30 40

10 20 30 40

Selinsgrove

Sunbury

Mansfield

Renovo

Tioga Junction

Harrisburg

Rockville

C8

Lake Erie BasinOhio River BasinGenesee River BasinPotomac River BasinSusquehanna River BasinChesapeake Bay BasinDelaware River Basin
4 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Figure 2. Moribund (A) and dead (B) young-of-the-year 

smallmouth bass (Micropterus dolomieu) with skin lesions caused 

by Flavobacterium columnare bacteria. (The fish are approximately 

2 inches long. Photograph A by Jeffrey Chaplin, U.S. Geological 

Survey, July 14, 2008; Photograph B by Pennsylvania Fish and Boat 

Commission).

A

B

Lesion

Lesions
Introduction 5

Figure 3. Geographic distribution of disease incidence in young-of-the-year smallmouth bass, Pennsylvania, 2005–07.

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).

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

Diseased fish captured

No diseased fish captured

EXPLANATION

Sampled, but no fish captured

0

0

50 MILES

50 KILOMETERS

r w

Lehigh

River

Schuyl k i l l River

Raystown

Lake

Juniata Rive r

West Branch Susq u ehanna River

Susquehanna River

Susquehanna River

Allegheny

River

Mononhahela River

Ohio Ri v e r

Delaware

R i ver

40°

41°

42°

80°

79° 78° 77° 76°

Area containing

study reaches

r w

Lehigh

River

Schuyl k i l l River

Raystown

Lake

Juniata Rive r

West Branch Susq u ehanna River

Susquehanna River

Susquehanna River

Allegheny

River

Mononhahela River

Ohio Ri v e r

Delaware

R i ver

40°

41°

42°

80°

79° 78° 77° 76°

Area containing

study reaches

r w

Lehigh

River

Schuyl k i l l River

Raystown

Lake

Juniata Rive r

West Branch Susq u ehanna River

Susquehanna River

Susquehanna River

Allegheny

River

Mononhahela River

Ohio Ri v e r

Delaware

R i ver

40°

41°

42°

80°

79° 78° 77° 76°

Area containing

study reaches

2005

2006

2007
6 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Purpose and Scope

This report presents results and analysis of water-quality 

data collected from seven continuous (30-minute interval) 

water-quality meters (sondes) measuring dissolved oxygen, 

temperature, pH, and specific conductance. It also provides 

streamflow data from the Delaware, Susquehanna, Juniata, and 

Allegheny Rivers for the 2008 water year1. Water quality of 

main-channel habitat and YOY smallmouth-bass microhabitat 

on the Susquehanna and Juniata Rivers is compared using data 

from four sondes that were deployed as pairs. For the purpose 

of this report, microhabitat is defined as habitat where YOY 

smallmouth bass spend the first 2–3 months of their lives and 

is characterized by backwater and shoreline areas with relatively low velocities and depths compared to the main channel.

Two additional sondes were collocated with streamgages 

at Harrisburg and Newport, Pa. Historical streamflow and 

water-quality conditions in the Susquehanna River at Harrisburg, Pa., are compared with water-quality and streamflow 

data collected in 2008 at Harrisburg, Pa. The seventh sonde 

was deployed in July 2008 in the Susquehanna River near 

Selinsgrove, Pa., a location where bacterial infections were 

discovered during the 2008 annual surveys for YOY smallmouth bass by PFBC fisheries biologists (Robert Lorantas, 

Pennsylvania Fish and Boat Commission, written commun., 

2008). The report also examines water-quality differences 

between the Susquehanna River where YOY smallmouth-bass 

mortalities have occurred and the Delaware and Allegheny 

Rivers where no mortalities have been documented. The 

purpose of this comparison is to determine if water-quality 

conditions in the Susquehanna River are more stressful than in 

the Delaware or Allegheny Rivers.

Finally, concentrations of nitrogen and phosphorus in 

water and streambed-sediment samples along with biochemical oxygen demand (BOD) in water collected at 25 locations 

in the Susquehanna River and tributaries between Williamsport and Highspire, Pa., on June 11 and 12, 2008, are 

presented. Nutrient concentrations in the Susquehanna River 

1

Water year is defined as the year beginning on October 1 and ending 

September 30.

Basin are compared with concentrations reported to promote 

growth of algae and other aquatic vegetation.

Description of Study Reaches

The Susquehanna River flows generally southward for 

about 447 mi from its headwaters near Cooperstown, N.Y., to 

the Chesapeake Bay in Maryland. The river drains 20,962 mi2

of Pennsylvania (fig. 1) including parts of the Appalachian 

Plateau Physiographic Province in northern and west-central 

Pennsylvania and the Ridge and Valley and Piedmont Physiographic Provinces in central and south-central Pennsylvania (Pennsylvania Department of Conservation and Natural 

Resources, 2000). The West Branch Susquehanna River enters 

the mainstem between Danville and Sunbury, Pa. Streamflow 

records from 1951 through 1980 indicate that the mainstem 

upstream of the West Branch contributes about 40 percent 

of the streamflow measured at Conowingo, Md., before the 

Susquehanna River flows into the Chesapeake Bay, and the 

West Branch contributes about 28 percent. The Juniata River 

contributes about 11 percent of the streamflow in the Susquehanna River at Conowingo, Md., and is the largest tributary 

downstream of the West Branch. Historical streamflows for 

selected stations are summarized in table 1.

The study reaches that were selected to represent the 

affected reaches in the basin include the Susquehanna River 

roughly between Danville and Highspire, Pa., the West Branch 

Susquehanna River from Williamsport to the mouth, and the 

Juniata River from Lewistown, Pa., to the mouth (fig. 1). 

Established continuous water-quality stations in the Delaware 

and Allegheny River Basins were used for comparison with 

stations on the study reaches. The study reaches are underlain 

predominantly by shale and sandstone (Cuff and others, 1989); 

some upstream reaches and tributary streams flow through 

areas underlain by strata containing anthracite and bituminous 

coal. Bedrock is close to the land surface and is a common 

substrate for the Susquehanna River streambed. Because bedrock is resistant to the erosional forces of flowing water, the 

free-flowing reaches of the Susquehanna River tend to be wide 

and shallow compared to most other rivers.

Table 1. Summary statistics for historical streamflow at selected streamgages in study reaches of the Susquehanna River Basin, 

Pennsylvania.

[mi2, square miles; ft3/s, cubic feet per second; WY, water year beginning on October 1 and ending September 30]

Streamgage Period of record

Drainage

area

(mi2)

Annual mean

streamflow

(ft3/s)1

Highest annual

mean streamflow 

(ft3/s)1

Lowest annual

mean streamflow 

(ft3/s)1

Susquehanna River at Danville Mar. 1899 to Present 11,220 17,680 24,670 in WY 1978 6,948 in WY 1965

West Branch Susquehanna River at Lewisburg Oct. 1939 to Present 6,847 10,600 17,760 in WY 2004 6,158 in WY 1965

Susquehanna River at Sunbury Oct. 1937 to Present 18,300 27,131 43,380 in WY 2004 13,420 in WY 1965

Juniata River at Newport Apr. 1899 to Present 3,354 4,505 7,470 in WY 2004 2,241 in WY 2002

1

For period of record ending September 30, 2007.
Introduction 7

Dissolved-Oxygen Criteria and Standards for 

Protection of Aquatic Life

The solubility of oxygen in equilibrium with water and 

air is inversely correlated with water temperature (fig. 4) but 

positively correlated with atmospheric pressure. As a result, 

dissolved-oxygen concentrations are greater for conditions 

characterized by cold water and high atmospheric pressure than for warm water and low atmospheric pressure. 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 that oxygen exsolves into the atmosphere. As 

a result, the water becomes supersaturated with oxygen despite 

relatively high daytime water temperatures. By contrast, 

cooler nighttime water temperature generally are accompanied 

by lower dissolved-oxygen concentrations because respiration 

consumes oxygen in the water faster than it dissolves into the 

water column.

Water that is undersaturated will entrain oxygen from the 

atmosphere, a process referred to as reaeration. Turbulence 

enhances reaeration. Therefore, the rate of reaeration is slower 

in slow-moving microhabitats compared to the more turbulent 

and faster-moving water in the main channel of a river. Thus, 

different dissolved-oxygen concentrations would be expected 

in YOY smallmouth-bass microhabitats compared to mainchannel habitats because of the effects of reaeration alone.

Because of continued oxygen consumption by respiration and the cessation of photosynthesis at night, low oxygen levels can result in and have been shown to cause lethal 

and sub-lethal physiological and behavioral effects in many 

organisms, especially fish (Welker and others, 2007; Canadian 

Council of Ministers of the Environment, 1999; U.S. Environmental Protection Agency, 1986; Spoor, 1984; Siefert and 

others, 1974). Earlylife stages are more sensitive to exposure 

to low dissolved-oxygen concentrations than adult fish (U.S. 

Environmental Protection Agency, 1986), and these sensitivities commonly are magnified at higher temperatures (Spoor, 

1984). For example, smallmouth-bass larvae, which are highly 

sensitive to oxygen deficiency between the second and tenth 

days after hatching, were exposed to a sustained dissolvedoxygen concentration of 4.0 mg/L and temperatures of 20°C 

and 25°C in an experiment described in Spoor (1984). The 

normally sluggish larvae exhibited increased behavioral 

response at 25°C compared to 20°C, including swimming to 

the surface.

Because the response to low dissolved-oxygen concentrations varies with life stage, the U.S. Environmental Protection 

Agency (EPA) has recommended national dissolved-oxygen 

criteria for protecting earlylife stages and other life stages 

for non-salmonid warm-water species, including smallmouth 

bass (table 2). Criteria for dissolved-oxygen concentrations 

established in 1986 were based on available results primarily from laboratory tests conducted at temperatures near the 

mid-range of a species temperature tolerance. Thus, recommended criteria that are based on these laboratory tests may be 

under-protective at higher temperatures and over-protective at 

lower temperatures (U.S. Environmental Protection Agency, 

1986). For the purpose of this report, stressful conditions are 

considered to exist when the dissolved-oxygen concentration 

is at or below the applicable criteria recommended by the U.S. 

Environmental Protection Agency (1986).

Although EPA has recommended criteria for dissolved 

oxygen, PADEP has adopted standards that are applicable on 

a statewide basis (Pennsylvania Department of Environmental 

Protection, 2009a). These PADEP standards are somewhat less 

protective (lower) than the national criteria (table 3).

0

5

10

15

20

25

30

35

40

45

6 7 8 9 10 11 12 13

DISSOLVED-OXYGEN CONCENTRATION, IN MILLIGRAMS PER LITER

WATER TEMPERATURE,

IN DEGREES CELSIUS

Figure 4. Solubility of oxygen in water at temperatures ranging 

from 5 to 40 degrees Celsius and atmospheric pressure of 

755 millimeters of mercury. [Data for graph compiled from Wilde 

and others (1998)]

Table 2. National criteria for ambient dissolved-oxygen 

concentrations for protection of warm-water fishes.

[Criteria recommended by U.S. Environmental Protection Agency, 1986; 

NA, not applicable; 30-day mean, mean of daily means measured over a 

30-day period; 7-day mean; mean of daily means measured over a 7-day 

period; 7-day mean minimum, mean of daily minimum values measured 

over a 7-day period; Instantaneous minimum, minimum value measured on 

any given day]

Statistic

Warm-water criteria,

in milligrams per liter

Earlylife stages1 Other life stages

30-day mean NA 5.5

7-day mean 6.0 NA

7-day mean minimum NA 4.0

Instantaneous minimum 5.0 3.0

1

Includes all embryonic and larval stages and all juvenile forms to 

30 days following hatching.
8 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Monitoring Strategy

Spawning behavior of smallmouth bass, data from YOY 

smallmouth-bass surveys, and reconnaissance efforts by PFBC 

biologists indicating low dissolved-oxygen concentrations 

were all used to develop the monitoring strategy for this study. 

Further, the low flows and warm temperatures when the bacterial infections were observed in 2005 and 2007, compared 

to the higher flows and cooler temperatures when bacterial 

infections were not observed in 2006, suggested an underlying 

environmental cause for the problem.

Adult and YOY smallmouth-bass surveys by PFBC biologists indicate that YOY smallmouth bass in affected reaches 

of the Susquehanna River were being infected by F. columnare

usually in July, but adult smallmouth bass and other species 

of fish that died during fish kills in the Potomac River mostly 

were not infected with F. columnare (Pennsylvania Fish and 

Boat Commission, 2005). Because YOY smallmouth bass 

were primarily affected in the Susquehanna River, spawning 

behavior and nest-site selection were evaluated to develop a 

strategy for where and over what time period to monitor water 

quality.

In the Susquehanna River Basin, smallmouth bass 

typically spawn from late April to early June, when water 

temperature reaches approximately 15°C. Males sweep out a 

nest site in gravel or sand-sized substrate with their caudal fin 

and court females to deposit eggs in the nest, a process that 

can take hours to weeks. Nests typically are constructed in 

microhabitats characterized by relatively low velocities and 

depths of at least 0.8 ft (Dauwalter and Fisher, 2007). After the 

eggs are deposited and fertilized, males guard the nest while 

the embryos develop and provide sole parental care of the 

offspring (Ridgway and others, 1989). Depending on water 

temperature, the eggs hatch in 2 to 9 days and the young fish 

are ready to leave the nest (commonly referred to as swim up) 

and disperse in 5 to 6 days. The newly hatched fish are susceptible to predation and cannot withstand velocities common to 

main-channel habitats. As a result, the first 2 to 3 months after 

swim up (roughly May through July) are spent in the same 

microhabitat where they were born. During this time, YOY 

smallmouth bass require greater dissolved-oxygen concentrations for proper development and survival (U.S. Environmental Protection Agency, 1986). For the purpose of this report, 

the timeframe of May 1 through July 31 will be referred to as 

the critical period.

Because YOY smallmouth bass live in different habitats 

than adult fish, they may be exposed to different dissolvedoxygen concentrations and temperatures. This may be caused 

by varying exposure to sunlight and abundance of plant life, 

different reaeration rates, or different levels of sedimentoxygen demand. Microhabitats where YOY smallmouth bass 

live and main-channel habitats where adults primarily live 

were compared by deploying paired sondes with one in YOY 

smallmouth-bass microhabitat and another in nearby fastermoving waters of the main part of the channel. These paired 

sondes are differentiated as “microhabitat” and “main-channel” throughout this report. If low dissolved-oxygen concentrations and (or) high temperatures exist, they may stress and 

predispose YOY smallmouth bass to infection by the bacteria. 

Because YOY smallmouth bass in the Susquehanna River 

Basin were infected by F. columnare but fish in the Delaware 

and the Allegheny River Basins were not, sondes deployed in 

main-channel habitats of the Delaware and Allegheny Rivers 

were used for comparison with conditions in main-channel 

habitat of the Susquehanna River.

Study Design

F. columnare is widely recognized by the aquaculture 

industry and others as a dangerous pathogen to catfish, tilapia, 

and other fish reared in crowded conditions (Durborow and 

others, 1998; Suomalainen and others, 2005), but the bacteria 

typically does not infect unstressed smallmouth bass in riverine systems (Noga, 1988). Capture rates of YOY smallmouth 

bass by PFBC biologists from 1987 to 2008 (Robert Lorantas, 

Pennsylvania Fish and Boat Commission, written commun., 

2009) indicate crowding is not likely to stress or otherwise 

predispose these fish to infection (John Arway, Pennsylvania 

Fish and Boat Commission, oral commun., 2009). However, 

other environmental stressors that may predispose fish to colonization by F. columnare include low dissolved oxygen, elevated ammonia, elevated nitrite, and warm water temperatures 

(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 is a well-characterized effect of increased cortisol concentrations, causing reductions in circulating immune cell numbers and bactericidal activity coinciding with an inflammatory 

response (Maule and Schreck, 1990; Wang and others, 2005). 

The working hypothesis for this study is that dissolved-oxygen 

concentrations and water temperatures in study reaches of the 

Susquehanna River are at times stressful to YOY smallmouth 

bass. Stress induced by low dissolved-oxygen concentrations, 

high water temperatures, and other environmental factors may 

immunosuppress YOY smallmouth bass and thereby predispose them to infection by F. columnare.

Table 3. Pennsylvania standards for dissolved-oxygen 

concentration in waters designated as warm-water fisheries.

[Minimum daily mean, minimum arithmetic average of samples collected 

during a continuous 24-hour period]

Statistic

Warm-water standards

for all life stages,

in milligrams per liter

Minimum daily mean 5.0

Instantaneous minimum 4.0
Monitoring Strategy 9

The study was designed to document environmental conditions during the critical period for YOY smallmouth bass to 

determine whether stressful water-quality conditions occurred 

in microhabitats and main-channel habitats in 2008. Furthermore, the study attempted to document whether environmental 

conditions were different in smallmouth-bass microhabitats 

compared to main-channel locations. If so, this could be a 

factor explaining why YOY fish are affected whereas adults 

are not. Stations recording water-quality constituents on a 

continuous basis (referred to hereinafter as “continuousmonitoring stations”) and stations where nutrient samples 

were collected (referred to hereinafter as “nutrient synoptic 

stations”) (table 4) were located in reaches where mortalities of smallmouth bass were documented in 2005 and 2007 

(fig. 3). Finally, because diseased YOY smallmouth bass were 

observed in the Susquehanna River but not in the Delaware 

or Allegheny Rivers, comparisons of water-quality conditions 

among these rivers were planned as part of the study design.

Monitoring Stations

Cross-section geometry and flow characteristics vary 

greatly among the sites where the monitoring stations (including the continuous-monitoring stations and the nutrient 

synoptic stations) are located. For example, the width-tomean-depth ratio in riffle cross sections in the Susquehanna 

River at Clemson Island (fig. 5B) is 1,853 ft/ft compared to 

392 ft/ft for the Delaware River at Trenton (fig. 5A). Because 

the Susquehanna River at this site has a large width relative to 

its depth, the surface area exposed to sunlight is large, which 

results in relatively quick warming and cooling in comparison 

to the narrower Delaware River at Trenton. The river cross 

sections containing each sonde are described in more detail 

below, including the cross sections at stations in the Delaware 

and Allegheny Rivers. For the purpose of comparison among 

cross sections, river depths shown in figs. 5 and 6 are normalized to streamflow conditions on June 23, 2008, at 1600 hrs, a 

time of base flow.

Susquehanna River at Shady Nook Boat Launch

Although no channel cross-section data from streamflow 

measurements or other surveys were available at this cross 

section, the channel here is morphologically similar to most 

other affected reaches of the Susquehanna River. The cross 

section is characterized by pool habitat split into two primary 

channels by a large island in the middle. Total river width, 

including the island, is about 3,000 ft at base-flow conditions. 

The larger of the two primary channels is about 1,100 ft wide 

and is on the right side of the island. Throughout this report, 

the terms “right bank,” “left bank,” “right side,” and “left 

side” are determined while looking downstream and are used 

to identify the sampling locations and channel features.

On July 14, 2008, annual YOY smallmouth-bass surveys 

by PFBC biologists found F. columnare infections near the 

Shady Nook boat launch (near Selinsgrove, Pa.). In response 

to this finding, a sonde was deployed on July 16, 2008, at 

station C2 (Susquehanna River at Shady Nook Boat Launch) 

about 15 ft from the right bank of the right channel in flowing 

water of moderate velocity. There was no backwater effect 

from channel bars or other upstream features that divert or 

alter streamflow; however, abundant rooted aquatic plants 

were growing in the right channel in the vicinity of the sonde. 

A coal-fired power plant about 1.27 mi upstream from this 

station withdraws river water for cooling and discharges the 

heated effluent into the channel.

Susquehanna River in the Vicinity of Clemson 

Island

The Susquehanna River at Clemson Island includes riffle 

and pool habitat. The width of the channel at the cross section 

in figure 5B is more than six times wider than comparable 

habitat monitored in the Juniata River, but the depth is only 

slightly greater (figs. 5B and D). The width during base-flow 

conditions is about 3,630 ft, and maximum depth estimated for 

base-flow conditions on June 23, 2008, was 4.5 ft. This cross 

section has three channels, but the right channel carries the 

majority of streamflow. The microhabitat sonde was deployed 

at station C4 on May 16, 2008 (Susquehanna River at Clemson 

Island [Microhabitat]), in a backwater eddy off the east shore 

of Clemson Island where water was less than 2 ft deep during 

summer base flow. The main-channel sonde was deployed at 

station C3 (Susquehanna River below Clemson Island [Main 

Channel]) about 850 ft downstream of the microhabitat sonde 

and 25 ft streamward of the west shore of a small linear island 

downstream from Clemson Island (fig. 5B). Water depth at the 

main-channel sonde was comparable to depths in the microhabitat, but the water velocity was appreciably greater.

Juniata River at Newport, Pennsylvania

The channel cross section of the Juniata River at Newport, Pa., was characterized from width and depth data collected during a bridge measurement made from the S.R. 34 

Bridge in November 2007. The channel at this cross section 

is predominantly pool habitat and has a width of about 550 ft 

under base-flow conditions (fig. 5C). The maximum depth 

estimated for base-flow conditions on June 23, 2008, was 

6.8 ft. The sonde was deployed on May 8, 2008, at station C5 

(Juniata River at Newport, Pa.) in main-channel habitat about 

20 ft from the right bank. The water was about 2.5 ft deep during normal base-flow conditions. Velocity data from the measurement in November 2007 indicate velocities in the vicinity 

of the sonde are greater than the average velocity in the cross 

section (1.39 to 1.79 ft/s in the vicinity of the sonde, compared 

to an average of 1.33 ft/s for the cross section).
10 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania Table 4. Stations for collection of streamflow, continuous water-quality data, and nutrient synoptic samples, Pennsylvania, 2008.—Continued [mi2, square miles] Station number Map identifier Station description Drainage area (mi2

)

Latitude Longitude

Continuous Data Stations

01463500 C1 Delaware River at Trenton, N.J. 6,780 40° 13′ 18.0′′ 74° 46′ 41.0′′01554010 C2 Susquehanna River at Shady Nook Boat Launch 18,432 40° 49′ 21.5′′ 76° 50′ 21.9′′

101555710 C3 Susquehanna River below Clemson Island (Main Channel) 19,673 40° 27′ 42.1′′ 76° 56′ 56.1′′

01555725 C4 Susquehanna River at Clemson Island (Microhabitat) 19,674 40° 27′ 47.8′′ 76° 56′ 46.3′′

101567000 C5 Juniata River at Newport, Pa. 3,354 240° 28′ 42.0′′ 277° 07′ 46.0′′

01567150 C6 Juniata River near Howe Township Park (Microhabitat) 3,379 40° 29′ 29.2′′ 77° 05′ 52.5′′01567151 C7 Juniata River near Howe Township Park (Main Channel) 3,379 40° 29′ 28.2′′ 77° 05′ 50.8′′

101570500 C8 Susquehanna River at Harrisburg, Pa. 24,100 240° 15′ 17.0′′ 276° 53′ 11.0′′

03049500 C9 Allegheny River at Natrona, Pa. 11,410 240° 32′ 10.0′′ 279° 43′ 07.0′′

03049640 C10 Allegheny River at Lock and Dam 3 at Acmetonia, Pa. 11,592 240° 32′ 10.0′′ 279° 48′ 54.0′′

Nutrient Synoptic Stations3

01540500 N1 Susquehanna River at Danville, Pa. 11,220 240° 57′ 29.0′′ 276° 37′ 10.0′′01550400 N2 West Branch Susquehanna River at Duboistown, Pa. 5,384 41° 13′ 33.0′′ 77° 02′ 37.0′′01553012 N3 West Branch Susquehanna River at Muncy, Pa. 6,457 41° 12′ 18.0′′ 76° 48′ 09.0′′01553018 N4 West Branch Susquehanna River at Montgomery, Pa. 6,471 41° 09′ 57.0′′ 76° 52′ 11.0′′01553025 N5 West Branch Susquehanna River at Allenwood, Pa. 6,496 41° 06′ 29.0′′ 76° 53′ 24.0′′

01553115 N6 West Branch Susquehanna River at Watsontown, Pa. 6,580 241° 04′ 53.0′′ 276° 51′ 50.0′′

01553500 N7 West Branch Susquehanna River at Lewisburg, Pa. 6,847 240° 58′ 03.0′′ 276° 52′ 36.0′′01554000 N8 Susquehanna River at Sunbury, Pa. 18,300 240° 50′ 04.0′′ 276° 49′ 37.0′′01554590 N9 Susquehanna River near Fishers Island at Selinsgrove, Pa. 18,434 40° 47′ 57.0′′ 76° 50′ 50.0′′

015552108 N10 Susquehanna River at Hoover Island 19,007 40° 44′ 35.0′′ 76° 50′ 55.0′′

01555270 N11 Susquehanna River at Dalmatia, Pa. 19,198 40° 39′ 30.0′′ 76° 54′ 35.0′′01555565 N12 Susquehanna River at Liverpool, Pa. 19,471 40° 34′ 15.0′′ 76° 58′ 02.0′′01555645 N13 Susquehanna River at Montgomery Ferry, Pa. 19,623 40° 30′ 26.0′′ 76° 58′ 16.0′′

101555710 C3 Susquehanna River below Clemson Island (Main Channel) 19,673 40° 27′ 42.1′′ 76° 56′ 56.1′′

01564895 N14 Juniata River at Lewistown, Pa. 2,519 240° 35′ 40.0′′ 277° 34′ 58.0′′01565810 N15 Juniata River at Mifflintown, Pa. 2,840 240° 34′ 12.0′′ 277° 24′ 00.0′′01565812 N16 Juniata River at Port Royal, Pa. 2,848 40° 32′ 06.0′′ 77° 22′ 54.0′′01566290 N17 Juniata River at Thompsontown, Pa. 3,155 40° 33′ 12.0′′ 77° 14′ 15.0′′
Monitoring Strategy 11

Table 4. Stations for collection of streamflow, continuous water-quality data, and nutrient synoptic samples, Pennsylvania, 2008.—Continued[mi2, square miles]

Station

number

Map

identifier Station description

Drainage

area

(mi2)

Latitude Longitude

01566350 N18 Juniata River at Millerstown, Pa. 3,177 40° 32′ 05.0′′ 77° 09′ 28.0′′

101567000 C5 Juniata River at Newport, Pa. 3,354 240° 28′ 42.0′′ 277° 07′ 46.0′′

01567340 N19 Juniata River at Amity Hall, Pa. 3,405 40° 25′ 39.0′′ 77° 00′ 52.0′′01567330 N20 Susquehanna River near Duncannon, Pa. 19,728 40° 23′ 59.0′′ 77° 00′ 26.0′′01569100 N21 Susquehanna River at Marysville, Pa. 23,511 40° 20′ 26.0′′ 76° 54′ 58.0′′

101570500 C8 Susquehanna River at Harrisburg, Pa. 24,100 240° 15′ 17.0′′ 276° 53′ 11.0′′

01571515 N22 Susquehanna River at Highspire, Pa. 24,337 40° 12′ 16.0′′ 76° 48′ 09.0′′

1Station used for collection of continuous water-quality data and nutrient data.2Horizontal coordinate information is referenced to the North American Datum of 1927.3Two samples were collected at each station between June 11–12, 2008; one 100 feet from the left bank and the other 100 feet from the right bank. Latitudes and longitudes reported in this table represent the 

center of the river.
12 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Figure 5. Orthophotos and channel cross sections in the vicinity of selected continuous-monitoring stations in free-flowing 

reaches of the A) Delaware, B) Susquehanna, and C and D) Juniata Rivers, Pennsylvania.

[Orthophotos from Pennsylvania Spatial Data Access (2009), and New Jersey Office of Information Technology (2009)]

C4

C3

Clemson

Island

DISTANCE, IN THOUSANDS OF FEET

0

2

4

6

8

0 0.4 0.8 1.2 1.6 2.0 2.4 2.8 3.2 3.6

0

2

4

6

8

DEPTH, IN FEET DEPTH, IN FEET 

DEPTH, IN FEET DEPTH, IN FEET 

DISTANCE, IN THOUSANDS OF FEET

C1

Left

Right

Left

Right

Left

Right Left

Right

Left

Right

Left

Right

Left Right Left Right

Trenton, New Jersey

Newport, 

Pennsylvania

C5

Left

Right

0

2

4

6

8

DISTANCE, IN THOUSANDS OF FEET

Left Right Left Right 0

2

4

6

8

DISTANCE, IN THOUSANDS OF FEET

Left

Right

C6

C7

Howe Township Park

Sampling station with streamgage

Sampling station without streamgage

EXPLANATION

Cross-section location

0 1,500

0 500 1,000 METERS

3,000 FEET

SCALE FOR ORTHOPHOTOS

Morrisville, Pennsylvania

S.R. 34

Bridge

Calhoun

Street

Bridge

A Delaware River at Trenton, New Jersey B Susquehanna River at Clemson Island

C Juniata River at Newport, Pennsylvania D Juniata River at Howe Township Park

A Delaware River at Trenton, New Jersey B Susquehanna River at Clemson Island

C Juniata River at Newport, Pennsylvania D Juniata River at Howe Township Park

FLOW

FLOW

FLOW

FLOW

FLOW

0 0.4 0.8 1.2 1.6 2.0 2.4 2.8 3.2 3.6

0 0.4 0.8 1.2 1.6 2.0 2.4 2.8 3.2 3.6 0 0.4 0.8 1.2 1.6 2.0 2.4 2.8 3.2 3.6
Monitoring Strategy 13

Figure 6. Orthophotos and channel cross sections in the vicinity of selected continuous-monitoring stations in impounded reaches of the 

A) Susquehanna, and B) Allegheny Rivers, Pennsylvania.

[Orthophotos from Pennsylvania Spatial Data Access (2009)]

0

4

8

12

16

20

24

28

0 0.4 0.8 1.2 1.6 2.0 2.4 2.8 3.2 3.6

DEPTH, IN FEET

DISTANCE, IN THOUSANDS OF FEET

Left Right 0

4

8

12

16

20

24

28

0 0.4 0.8 1.2 1.6 2.0 2.4 2.8 3.2 3.6

DEPTH, IN FEET

DISTANCE, IN THOUSANDS OF FEET

Left Right

C10

Right

Left

C8

Left

Right

City Island

Sampling station with streamgage

Sampling station without streamgage

EXPLANATION

Cross-section location

0 1,500

0 500 1,000 METERS

3,000 FEET

SCALE FOR ORTHOPHOTOS

AA Susquehanna River at Harrisburg, Pennsylvania Susquehanna River at Harrisburg, Pennsylvania BB Allegheny River at Lock and Dam 3 at Acmetonia Allegheny River at Lock and Dam 3 at Acmetonia

FLOW

FLOW

FLOW
14 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Juniata River in the Vicinity of Howe Township 

Park

The channel cross section at Howe Township is predominantly riffle habitat and is approximately 580 ft wide during 

base-flow conditions (fig. 5D). The maximum depth estimated 

for base-flow conditions on June 23, 2008, was 3.5 ft. The 

deepest part of the channel was within the YOY smallmouthbass microhabitat near the left bank.

A sonde was deployed in the microhabitat on May 23, 

2008, at station C6 (Juniata River near Howe Township Park 

[Microhabitat]) about 75 ft upstream of the cross section 

shown in fig. 5D and approximately 25 ft from the left bank. 

The microhabitat extends out for about 100 ft from the left 

bank and is protected by a gravel bar deposited just upstream. 

Water here is slow-moving compared to the riffle habitat in the 

rest of the cross section. Most of the area in the microhabitat is 

approximately 2 ft deep during base-flow conditions. Another 

sonde was deployed nearby in the main-channel habitat on 

June 4, 2008, at station C7 (Juniata River near Howe Township Park [Main Channel]). This sonde was approximately 

190 ft from the left bank in a riffle characterized by relatively 

fast-moving water.

Susquehanna River at Harrisburg, Pennsylvania

The channel cross section of the Susquehanna River at 

Harrisburg, Pa., is within an impoundment 3,200 ft upstream 

of an 8-ft high, 3,000 ft wide dam that is notched out for 

about 33 ft on the left side. The cross section shown in fig. 6A 

represents the channel approximately 800 ft upstream from the 

sonde at station C8 (Susquehanna River at Harrisburg, Pa.). 

The width of the channel at this cross section is about 3,500 ft 

under normal base-flow conditions. Maximum depth estimated 

for base-flow conditions on June 23, 2008, was 9.2 ft. The 

channel on the left side of City Island is deeper and carries the 

majority of streamflow. The sonde was deployed on May 15, 

2008, in a location characteristic of main-channel habitat, 

about 15 ft from the east shore of City Island in water that is 

about 3 ft deep during base-flow conditions.

Delaware River at Trenton, New Jersey

The channel of the Delaware River at Trenton (fig. 5A) 

was characterized from depth and width data collected during 

a base-flow measurement in June 2008 from the upstream side 

of the Calhoun Street bridge. Data collected during this measurement indicate the channel is approximately 1,200 ft wide 

and had an estimated maximum depth on June 23, 2008, of 

7.0 ft. Velocities within this cross section varied from 0.56 to 

2.41 ft/s; the average was 1.33 ft/s. Relatively shallow points 

shown in fig. 5A are the result of sandbar features upstream 

of bridge piers. The sandbar features are not present in the 

cross section at station C1 where the sonde was deployed. The 

sonde was in a riffle about 1,780 ft upstream and about 365 ft 

from the right bank (Pennsylvania side of the river).

Allegheny River at Lock and Dam 3 at Acmetonia, 

Pennsylvania

The cross section at station C10 (Allegheny River at 

Acmetonia, Pa.) is heavily influenced by the C.W. Bill Young 

Lock and Dam (fig. 6B), which consists of a single lock chamber of the left side of the river and a concrete weir wall across 

the width of the river (U.S. Army Corps of Engineers, 2004). 

Under base-flow conditions, the dam backs water up to a maximum depth of approximately 28 ft (fig. 6B) in the vicinity of 

the sonde deployed at station C10. The sonde was deployed at 

a depth of approximately 5 ft during base-flow conditions.

Methods

Continuous Water-Quality Monitoring

All sondes deployed at each sampling station measured 

dissolved-oxygen concentration (in milligrams per liter), pH 

(in standard units), water temperature (in degrees Celsius), and 

specific conductance (in microsiemens per centimeter) every 

30 minutes. Sondes at USGS stations at Harrisburg on the 

Susquehanna River and at Newport on the Juniata River were 

connected to existing instrumentation so near real-time data 

could be transmitted to the Internet and used to monitor waterquality conditions throughout the summer.

 For this study, dissolved-oxygen measurements were 

most important. Therefore, newer and more reliable luminescent technology was used to determine the dissolved-oxygen 

concentration. All sondes except for one utilized this new technology. One sonde, deployed at the Shady Nook station, was 

equipped with a probe using older amperometric technology 

for dissolved oxygen. Each sonde was equipped with internal 

memory capable of storing the water-quality measurements. 

Set-up and calibration of the sondes followed manufacturer 

guidelines (Yellow Springs Instruments, 1999). In addition, a 

zero dissolved-oxygen solution (prepared on the day needed) 

was used to check the dissolved-oxygen performance of the 

sonde. Calibration values for independent field water-quality 

meters, which were used to check the measurements from 

the deployed sondes, were recorded in a logbook dedicated 

to that water-quality meter. Calibration values for the sondes 

deployed at each station were recorded on field data sheets for 

that station.

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 then cleaned 

and returned to the water and a second set of side-by-side 
Monitoring Strategy 15

readings was recorded. These readings were used to adjust the 

measurements stored in the memory of the deployed sonde. 

Adjustments to the record were made following recommendations of Wagner and others (2006) using the USGS computer 

program Automated Data Processing System (ADAPS) (U.S. 

Geological Survey, 2003). Following the checks against the 

field water-quality meter, the deployed sondes were retrieved 

and the data downloaded to a field data logger.

Most of the sondes worked well throughout the project. 

However, the one sonde deployed in the Susquehanna River 

at Shady Nook Boat Launch (station C2), which utilized the 

older amperometric technology, had spotty performance, and 

some data were lost.

Statistical differences between microhabitat and mainchannel stations were determined using the two-sided Wilcoxon signed-rank test (Helsel and Hirsch, 2002, p.142–147). 

The same test was also used to determine differences between 

data collected in 2008 and historical data from the 1970s. The 

Wilcoxon rank-sum test (Helsel and Hirsch, 2002, p. 118–124) 

was used for comparisons between the Susquehanna River and 

Delaware River and the Susquehanna River and Allegheny 

River. The null hypothesis for all tests was that there is no 

difference between median values of compared sites. For this 

report, the null hypothesis was rejected if the p-value was less 

than 0.05 (a less than 5 percent probability that a difference 

occurs by chance).

Nutrient Sampling

One of the largest oxygen-demanding in-stream processes is respiration from algae and rooted aquatic plants. 

Nutrients stimulate plant growth and, therefore, may be one 

of the factors that influence dissolved-oxygen concentrations. 

To evaluate spatial differences in nutrient concentrations, a 

one-time synoptic survey of 25 sampling locations (including 

3 stations where sondes were deployed) in the Susquehanna 

River and tributaries was conducted on June 11 and 12, 2008 

(fig. 7). Nutrient data collected as part of the Pennsylvania 

Black Fly Suppression Program indicate that for the mainstem 

of the Susquehanna River downstream from the confluence 

of the West Branch Susquehanna River, water chemistry is 

different for the west and east sides of the river (D. Rebuck, 

Pennsylvania Department of Environmental Protection, written commun., 2007). These data prompted a sampling strategy 

incorporating samples from both sides of the river.

Two separate depth-integrated samples, one 100 ft from 

the left bank and one 100 ft from the right bank at each of the 

25 sampling locations (50 samples total), were collected using 

a DH-81 sampler following methods adapted from Wilde 

and others (1998). Samples were collected in pre-cleaned 

3-L teflon bottles. Four subsamples were taken from the 3-L 

sample bottle. A 125-mL subsample collected for analysis 

of filtered ammonia nitrogen was filtered in the field using a 

flask-mounted suction device fitted with a 0.45 micron poresize polyamid filter and fixed with sulfuric acid to a pH of less 

than 2. A second 125-mL subsample collected for analysis 

of phosphorus and ammonia plus organic nitrogen was fixed 

with sulfuric acid without filtering. A third 125-mL sample 

collected for analysis of orthophosphate, nitrite nitrogen, 

and nitrate nitrogen was filtered without having any fixative 

added. A 500-mL subsample for total nitrogen was collected 

without filtration or fixation. All samples were chilled immediately. Laboratory analyses were performed by the PADEP 

laboratory.

In addition, samples for streambed sediment at right-bank 

and left-bank stations were collected for nutrient analyses. The 

samples were collected by inserting a teflon cylinder into the 

streambed sediment to a depth of 2 cm and then sliding a teflon wafer underneath the tube to hold the streambed sediment 

in place inside the tube. Five such streambed-sediment tubes 

were collected at each sampling station, combined in a stainless-steel bowl, and thoroughly mixed. A subsample of this 

mixture was then transferred into a 500 mL high-density polypropylene wide-mouth jar that was sealed and chilled. Laboratory analyses for ammonia plus organic nitrogen, ammonia, 

and phosphorus in the streambed sediment were conducted 

by the PADEP laboratory. Laboratory methods used for the 

analyses of streambed sediment are as follows: ammonia 

nitrogen in bottom material–EPA method 350.1; ammonia 

plus organic nitrogen in bottom material–EPA method 351.2; 

total phosphorus in bottom material–EPA method 365.1 (U.S. 

Environmental Protection Agency, 1993).

Biochemical Oxygen Demand Sampling

Along with the nutrient samples, a 500-mL subsample 

of the 3-L sample was poured into a pre-cleaned high-density 

polyethylene bottle at each station for analysis of BOD. BOD 

is a measure of the amount of organic pollution in water 

(Hem, 1985, p. 158). BOD is measured in milligrams per 

liter of oxygen and is typically used to determine the oxygen 

requirements of wastewaters (Alley, 2000, p. 3.19). As organic 

matter is decomposed or oxidized, the oxygen needed for the 

decomposition must come from the water. The purpose of 

these samples was to determine if there are oxygen-demanding materials present in the water that might cause oxygen 

deficits that are not related to community respiration. These 

BOD samples were not filtered and received no fixative, but 

they were chilled immediately. Samples were analyzed in the 

PADEP laboratory.

Quality Assurance

Protocols for calibrating, deploying, and servicing the 

continuous-monitoring sondes were derived from the manufacturer’s instruction manual (Yellow Springs Instruments, 

1999) and from Wilde and others (1998) and 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 
16 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Figure 7. Locations of stations selected for the nutrient synoptic survey in the Susquehanna River Basin, 

Pennsylvania, June 11 and 12, 2008.

Water features from U.S. Geological Survey National Hydrography Dataset (NHD)

EXPLANATION

We s t

Br a n c h Su s q u ehanna River

Juniata

R i v e r

Su s q u

e hanna

River

Williamsport

Danville Lewisburg

Lewistown

Port Royal

Millerstown

Newport

Thompsontown

Halifax

Harrisburg

Highspire

Base from U.S. Geological Survey 1:24,000 digital data

0

0 15 MILES

15 KILOMETERS

76°33' 76°36'

40°09'30''

40°15'30''

Major river

County boundary

Sampling station and identifier

Selected municipality

N1

Pennsylvania

Area containing study reaches

N1

N2 N3

N4

N5

N6

N7

N8

N9

N10 

N11

N12

N13

N14

N15

N16 N17

N18

N19

N20

N21

N22

C3

C8

C5

Bu ff a l o Cr e e k

Conodoguinet

Cre e k
Monitoring Strategy 17

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

Numerous quality-control measures were routinely 

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, prepared fresh 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 would not 

return a dissolved-oxygen reading of 0.3 mg/L or less in a zero 

dissolved-oxygen solution was not used.

Quality-control measures for the nutrient synoptic survey 

included submitting blank samples, duplicate samples, and 

reference samples for analysis of nutrients and BOD. A summary of all quality-control samples submitted for the project is 

presented in appendix 1.

Blank Samples

For the stream-water samples in the nutrient synoptic 

survey, six field blank samples (12 percent of all water nutrient samples collected) were submitted to the PADEP laboratory for nutrient analyses. The data-quality objective for the 

project was to determine if any constituents were measured 

at a concentration larger than the method detection limit in a 

blank sample. None of the constituents analyzed in the blank 

samples were measured at a concentration greater than the 

detection limit. The sample collected from the West Branch 

Susquehanna River at Duboistown, Pa., had a concentration 

of dissolved ammonia of 0.02 mg/L, which is the detection 

limit for this constituent. This concentration is comparable 

to most environmental samples collected during the study. 

All other results were lower than the detection limits. These 

results indicate that sampling procedures, sample containers, 

lab protocols, and cleaning procedures were not contributing 

contamination to the samples collected for the project. Blank 

samples were not submitted for bottom material.

Duplicate Samples

Field duplicate samples were used to identify the precision (reproducibility) of analytical results. Field duplicate 

samples were collected and processed immediately following 

each associated primary environmental sample (a sequential replicate), using identical procedures. For the duplicate 

samples, a relative percent difference (RPD) was calculated 

between the two samples according to the following equation:

RPD = (d/x) × 100, (1)

where d is the difference in concentration between the primary 

environmental sample and the field duplicate sample, and x 

is the average concentration of the primary environmental 

sample and the field duplicate sample. The data-quality objective for the project was that all duplicate samples would have 

RPD values of 20 percent or less. An acceptance value of 20 

percent for the RPD is commonly used for water-quality studies (for example, Allegheny County Sanitary Authority, 2008; 

Lombard and Kirchmer, 2004) and is the value supported by 

EPA in a Quality Assurance Plan that is a model for others to 

use (U.S. Environmental Protection Agency, 2009; Eagle Valley Environmental Program, 2005).

For the stream-water samples in the nutrient synoptic survey, four duplicate-sample pairs (8 percent of all water nutrient samples collected) were submitted for analysis. Except 

for ammonia, the RPD for every nutrient species analyzed 

in each duplicate-sample pair was less than 20 percent. The 

RPD for filtered ammonia from the West Branch Susquehanna 

River at Duboistown, Pa., was 40 percent. For this sample, the 

concentration of ammonia in the environmental sample was 

0.02 mg/L and the concentration in the replicate sample was 

0.03 mg/L. These low measured concentrations resulted in a 

large RPD, even though the actual difference was quite small. 

These results suggest that the precision in collecting and analyzing water samples for nutrients was within the data-quality 

objective, and data for the nutrient concentrations can be used 

with confidence.

For the streambed-sediment samples in the nutrient 

synoptic survey, five duplicate-sample pairs (10 percent of all 

streambed-sediment nutrient samples collected) were collected 

sequentially and submitted for analysis. Except for ammonia 

plus organic nitrogen in two samples, the RPD for every nutrient species analyzed in each duplicate-sample pair was less 

than 20 percent. The RPD for ammonia plus organic nitrogen 

from the Susquehanna River at Montgomery Ferry, Pa., and 

left bank was 93 percent. The RPD for ammonia plus organic 

nitrogen from the Susquehanna River near Duncannon, Pa., 

right bank was 33 percent. These results suggest that the precision in collecting and analyzing streambed-sediment samples 

for nutrients was usually within data-quality objectives and, 

with the exception of ammonia plus organic nitrogen, data for 

the nutrient concentrations can be used with confidence.
18 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Reference Samples

Standard reference samples are used to monitor the overall performance of a laboratory. Reference samples are made 

up in large quantities in a laboratory and sent to many labs for 

analysis. Results from all the labs are compiled, and a most 

probable value is calculated for each analyte in the sample. 

For this study, one standard reference sample for nutrients was 

obtained from the USGS Branch of Quality Assurance and 

submitted to the PADEP laboratory for analysis. The performance of the PADEP lab was evaluated against the most probable value using the same RPD calculation used to evaluate 

duplicate samples. The data-quality objective for the project 

was that analyses for all constituents in reference samples 

would have RPD values of 20 percent or less. This objective was met for all nutrients measured where an RPD could 

be calculated. For ammonia plus organic nitrogen, an RPD 

could not be calculated. The most probable value for ammonia 

plus organic nitrogen in the standard reference sample was 

0.675 mg/L. The PADEP lab returned a value of < 1.0 mg/L.

Monitoring Results and Implications, 

Susquehanna River

The acute effects of low dissolved-oxygen concentration (to 1.0 mg/L) on behavior and survival of a variety of 

fish are well characterized (Siefert and others, 1974; Spoor, 

1984), but for this project, the interest is in assessing primarily dissolved-oxygen concentrations and water temperatures 

that may be stressful in YOY smallmouth-bass microhabitat. 

In addition to stress, lower velocity microhabitats may also be 

more conducive to proliferation and growth of opportunistic 

bacteria like F. columnare, further increasing the probability of 

infection. The link between environmental stressors and bacterial infection, although not directly tested as part of this study, 

is that stress compromises the immune system (Ripley and 

others, 2008) and thereby predisposes the young to infection. 

The national criteria for dissolved-oxygen concentrations were 

developed primarily using behavioral response (increased 

swimming activity or swimming to the surface, for example) 

to indicate stressful concentrations of dissolved oxygen. Studies used to arrive at these criteria indicate progressively more 

abnormal behavior as dissolved-oxygen concentrations are 

decreased and temperatures are increased. In some cases, the 

behavioral response is death, indicating lethally stressful conditions. In other cases, the behavioral response is temporary, 

and the fish resume normal activity when dissolved-oxygen 

concentrations are increased to more normal levels (Spoor, 

1984; Siefert and others, 1974). Because most experimental 

tests have not exposed fish to daily sinusoidal cycles consistent with variability observed in this study, the effect of varying dissolved-oxygen concentration on fish is poorly understood (U.S. Environmental Protection Agency, 1986). Fish 

may be stressed by low dissolved oxygen for a period of hours 

at night and then recover with increasing dissolved oxygen. 

Little is known about recurring stress over a period of days or 

weeks in YOY smallmouth-bass microhabitats.

Comparison of Water Quality Observed 

in Young-of-the-Year Smallmouth-Bass 

Microhabitats and Main-Channel Habitats

In this section, water quality in microhabitats of the 

Susquehanna River at Clemson Island (station C4) and the 

Juniata River at Howe Township Park (station C6) is compared with water quality of corresponding nearby mainchannel habitats (stations C3 in the Susquehanna River below 

Clemson Island and C7 in the Juniata River at Howe Township 

Park) preferred by larger, older fish. For most comparisons, 

dissolved-oxygen concentration, pH, and water temperature 

were significantly different (p-values less than 0.05) in the 

microhabitats compared to the main-channel habitats (table 5).

Dissolved Oxygen

Daily minimum dissolved-oxygen concentrations in YOY 

smallmouth-bass microhabitats in the Susquehanna River at 

station C4 and the Juniata River at C6 generally were lower 

than nearby main-channel habitats (figs. 8C and 9C). The 

average daily minimum dissolved-oxygen concentrations at 

C4 and C6 were 1.1 and 0.3 mg/L lower, respectively, than 

in the corresponding main-channel habitat during the critical 

period (table 6). The lowest dissolved-oxygen concentrations 

in the microhabitats during the critical period were 3.3 mg/L at 

station C4 (June 11, 2008) and 4.1 mg/L at station C6 (July 22, 

2008) (table 6). The lowest instantaneous dissolved-oxygen 

concentrations in the main-channel habitats were 5.3 mg/L 

(Susquehanna River at station C3; July 31, 2008) and 4.6 mg/L 

(Juniata River at station C7; July 21 and 22, 2008).

The 7-day mean dissolved-oxygen concentrations 

at paired stations in the Susquehanna and Juniata Rivers 

remained above the 6.0 mg/L national criterion for protecting earlylife stages of warm-water fish (fig. 10A and B, 

appendix 2), but daily minimum dissolved-oxygen concentrations in both microhabitats and in the Juniata River 

main-channel habitat sometimes were lower than national 

dissolved-oxygen limits for protecting earlylife stages of 

warm-water fish (5.0 mg/L) (figs. 8C and 9C). Microhabitats 

had daily minimum dissolved-oxygen concentrations that were 

lower than the national criterion of 5.0 mg/L more often than 

the corresponding main-channel habitats. During the critical 

period, daily minimum dissolved-oxygen concentrations were 

less than 5.0 mg/L in microhabitat in the Susquehanna River 

at Clemson Island on 31 days (out of 92 days in the critical 

period) compared to no days in the corresponding main-channel habitat. The maximum time that dissolved oxygen was 

less than 5.0 mg/L lasted 8.5 hours. In the Juniata River, daily 

minimum dissolved-oxygen concentration in the microhabitat 

was less than 5.0 mg/L on 20 days compared to only 5 days 
Monitoring Results and Implications, Susquehanna River 19

Table 5. Statistical comparison of water quality in young-of-the-year smallmouth-bass microhabitats and main-channel habitats in 

the Susquehanna and Juniata Rivers, Pennsylvania, 2008.

[MH, Microhabitat; MC, Main Channel; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams per liter; <, less than]

Constituent1

p-value3

Susquehanna River, Clemson MH

compared to

Susquehanna River, Clemson MC2

Juniata River, Howe Township MH

compared to

Juniata River, Howe Township MC2

Minimum water temperature (°C) < 0.0001 < 0.0001

Maximum water temperature (°C) .0395 < .0001

Water temperature range (°C) < .0001 .3517

Mean water temperature (°C) < .0001 < .0001

Minimum specific conductance (μS/cm) .0246 < .0001

Maximum specific conductance (μS/cm) .0823 < .0001

Specific conductance range (μS/cm) .9773 .0008

Mean specific conductance (μS/cm) .0044 < .0001

Minimum pH (standard units) < .0001 .0010

Maximum pH (standard units) < .0001 < .0001

pH range (standard units) .8218 .0002

Median pH (standard units) < .0001 < .0001

Minimum dissolved oxygen (mg/L) < .0001 < .0001

Maximum dissolved oxygen (mg/L) < .0001 < .0001

Dissolved oxygen range (mg/L) .0354 < .0001

Mean dissolved oxygen (mg/L) < .0001 < .0001

7-day mean minimum dissolved oxygen (mg/L) < .0001 < .0001

7-day mean dissolved oxygen (mg/L) < .0001 < .0001

1

Summary statistics (minimum, maximum, mean, range, 7-day mean minimum, and 7-day mean) are based on daily values.

2

Results of two-sided Wilcoxon signed-rank test.

3

For this study, a statistically significant difference exists if the p-value is less than 0.05.
20 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Figure 8. Water quality in young-of-the-year smallmouth-bass microhabitat and main-channel habitats of the Susquehanna River in 

the vicinity of Clemson Island, Pennsylvania, 2008.

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

10

12

14

16

18

20

22

24

26

28

30

32

34

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

10

12

14

16

18

20

22

24

26

28

30

32

34

DAILY MINIMUM TEMPERATURE, IN DEGREES CELSIUS

DAILY MAXIMUM TEMPERATURE, IN DEGREES CELSIUS

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

2

4

6

8

10

12

14

16

18

20

2008

May

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

2

4

6

8

10

12

14

16

18

20

DAILY MINIMUM DISSOLVED-OXYGEN

CONCENTRATION, IN MILLIGRAMS PER LITER

DAILY MAXIMUM DISSOLVED-OXYGEN

CONCENTRATION, IN MILLIGRAMS PER LITER

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

7

7.5

8

8.5

9

9.5

10

2008

2 1 28

June

7 1 4 2 1 28

July

7 1 4 21 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

7

7.5

8

8.5

9

9.5

10

DAILY MINIMUM PH, IN STANDARD UNITS

DAILY MAXIMUM PH, IN STANDARD UNITS

A B

C D

E F

Microhabitat (Station C4)

Main Channel (Station C3)

Microhabitat (Station C4)

Main Channel (Station C3)

Microhabitat (Station C4)

Main Channel (Station C3)

Microhabitat (Station C4)

Main Channel (Station C3)

Microhabitat (Station C4)

Main Channel (Station C3)

Microhabitat (Station C4)

Main Channel (Station C3)

National Criterion, earlylife stages

(U.S. Environmental Protection Agency) 

Pennsylvania Standard, all stages of life

National Criterion, earlylife stages

(U.S. Environmental Protection Agency) 

Pennsylvania Standard, all stages of life

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record
Monitoring Results and Implications, Susquehanna River 21

Figure 9. Water quality in young-of-the-year smallmouth-bass microhabitat and main-channel habitats of the Juniata River in the 

vicinity of Howe Township Park, Pennsylvania, 2008.

2008

May

2 1 28

June

7 1 4 21 28

July

7 14 2 1 28

August

7 14 2 1 28

September

7 14 2 1 28

10

12

14

16

18

20

22

24

26

28

30

32

34

2008

May

2 1 28

June

7 1 4 21 28

July

7 14 2 1 28

August

7 1 4 2 1 28

September

7 14 2 1 28

2

4

6

8

10

12

14

16

18

20

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 14 2 1 28

August

7 14 2 1 28

September

7 14 2 1 28

7

7.5

8

8.5

9

9.5

10

2008

May

21 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

10

12

14

16

18

20

22

24

26

28

30

32

34

2008

May

21 28

June

7 1 4 2 1 28

July

7 1 4 21 28

August

7 1 4 21 28

September

7 1 4 2 1 28

2

4

6

8

10

12

14

16

18

20

2008

May

21 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

7

7.5

8

8.5

9

9.5

10

A B

C D

E F

DAILY MINIMUM TEMPERATURE, IN DEGREES CELSIUS

DAILY MAXIMUM TEMPERATURE, IN DEGREES CELSIUS

DAILY MINIMUM DISSOLVED-OXYGEN

CONCENTRATION, IN MILLIGRAMS PER LITER

DAILY MAXIMUM DISSOLVED-OXYGEN

CONCENTRATION, IN MILLIGRAMS PER LITER

DAILY MINIMUM PH, IN STANDARD UNITS

DAILY MAXIMUM PH, IN STANDARD UNITS

Microhabitat (Station C6)

Main Channel (Station C7)

Microhabitat (Station C6)

Main Channel (Station C7)

Microhabitat (Station C6)

Main Channel (Station C7)

Microhabitat (Station C6)

Main Channel (Station C7)

Microhabitat (Station C6)

Main Channel (Station C7)

National Criterion, earlylife stages

(U.S. Environmental Protection Agency) 

Pennsylvania Standard, all stages of life

National Criterion, earlylife stages

(U.S. Environmental Protection Agency) 

Pennsylvania Standard, all stages of life

Microhabitat (Station C6)

Main Channel (Station C7)

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record
22 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Table 6. Summary statistics for water-quality data collected at selected stations in the Susquehanna River Basin, Pennsylvania, 

May 1 through July 31, 2008.—Continued

[C2, Susquehanna River at Shady Nook Boat Launch; C3, Susquehanna River below Clemson Island (Main Channel); C4, Susquehanna River at Clemson 

Island (Microhabitat); C5, Juniata River at Newport; C6, Juniata River near Howe Township Park (Microhabitat); C7, Juniata River near Howe Township 

Park (Main Channel); shading provided for comparison of young-of-the-year microhabitats and main-channel habitats; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams per liter; n, number of daily values; P25, 25th percentile; P75, 75th percentile; —, not computed]

Statistic

Daily minimum temperature

(°C)

Daily mean temperature

(°C)

Station Station

C2 C3 C4 C5 C6 C7 C2 C3 C4 C5 C6 C7

n 15 76 76 81 65 57 15 76 76 80 65 57

Minimum 27.1 10.9 11.0 10.9 13.5 19.5 28.3 11.8 11.8 11.5 14.5 21.0

P25 28.2 20.7 20.4 18.3 22.6 23.6 29.5 22.5 22.4 18.8 24.1 25.0

Median 29.2 24.1 23.7 22.6 24.0 24.8 30.6 26.1 25.8 24.3 25.5 26.4

P75 30.4 25.5 24.9 24.0 25.8 26.0 31.6 27.6 27.4 26.0 27.3 27.6

Maximum 31.0 27.7 27.0 26.4 27.5 27.8 32.2 29.9 29.7 28.7 29.5 29.6

Mean 29.2 22.5 22.1 20.6 23.4 24.6 30.5 24.4 24.2 22.1 24.9 26.1

Standard deviation 1.3 4.5 4.2 4.7 3.1 1.9 1.3 4.8 4.7 5.1 3.3 2.0

Statistic

Daily maximum temperature

(°C)

Daily temperature range

(°C)

Station Station

C2 C3 C4 C5 C6 C7 C2 C3 C4 C5 C6 C7

n 16 76 76 83 65 57 15 76 76 80 65 57

Minimum 29.5 12.4 12.4 12.0 15.6 22.4 2.0 1.0 1.1 .8 .9 1.6

P25 30.6 25.0 24.9 19.4 25.5 26.6 2.5 3.4 3.3 2.3 2.3 2.5

Median 32.1 28.4 28.5 25.9 26.9 27.8 2.7 4.3 4.8 3.1 3.0 3.2

P75 33.4 30.5 30.8 27.6 28.8 29.3 3.0 5.5 6.2 3.9 3.4 3.6

Maximum 33.9 32.8 33.5 31.2 31.5 31.8 3.5 6.8 7.9 5.9 6.3 5.2

Mean 32.0 26.7 26.8 23.4 26.4 27.7 2.7 4.2 4.7 3.1 3.0 3.1

Standard deviation 1.5 5.3 5.5 5.7 3.4 2.2 .4 1.4 1.9 1.2 .9 .8
Monitoring Results and Implications, Susquehanna River 23

Table 6. Summary statistics for water-quality data collected at selected stations in the Susquehanna River Basin, Pennsylvania, 

May 1 through July 31, 2008.—Continued

[C2, Susquehanna River at Shady Nook Boat Launch; C3, Susquehanna River below Clemson Island (Main Channel); C4, Susquehanna River at Clemson 

Island (Microhabitat); C5, Juniata River at Newport; C6, Juniata River near Howe Township Park (Microhabitat); C7, Juniata River near Howe Township 

Park (Main Channel); shading provided for comparison of young-of-the-year microhabitats and main-channel habitats; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams per liter; n, number of daily values; P25, 25th percentile; P75, 75th percentile; —, not computed]

Statistic

Daily minimum dissolved oxygen

(mg/L)

Daily mean dissolved oxygen

(mg/L)

Station Station

 C2 C3 C4 C5 C6 C7 C2 C3 C4 C5 C6 C7

n — 76 76 74 65 57 — 76 76 74 65 57

Minimum — 5.3 3.3 4.1 4.1 4.6 — 7.5 5.8 6.6 6.0 6.6

P25 — 6.0 4.9 5.7 5.0 5.5 — 8.0 7.0 8.1 7.2 8.2

Median — 6.4 5.4 6.2 5.5 6.0 — 8.4 7.3 8.5 7.8 8.6

P75 — 7.3 5.9 7.7 6.1 6.4 — 8.9 7.8 9.4 8.3 9.0

Maximum — 10.3 10.2 10.0 9.8 7.9 — 11.1 10.5 10.3 10.1 10.3

Mean — 6.8 5.7 6.7 5.8 6.1 — 8.6 7.6 8.7 7.9 8.6

Standard deviation — 1.4 1.6 1.5 1.3 .8 — .9 1.1 .9 .9 .7

Statistic

Daily maximum dissolved oxygen

(mg/L)

Daily dissolved oxygen range

(mg/L)

Station Station

 C2 C3 C4 C5 C6 C7 C2 C3 C4 C5 C6 C7

n — 76 76 74 65 58 — 76 76 74 65 57

Minimum — 9.5 8.2 8.2 8.2 9.1 — .6 .6 .3 .6 2.0

P25 — 10.3 9.1 10.3 9.3 10.5 — 3.3 3.3 3.1 3.4 4.5

Median — 10.6 9.5 11.1 10.1 11.5 — 4.1 4.4 4.9 4.3 5.4

P75 — 11.0 10.5 12.2 10.7 12.5 — 4.9 5.0 5.9 4.8 6.3

Maximum — 15.2 12.5 13.3 11.8 13.6 — 7.7 6.4 8.6 7.3 8.9

Mean — 10.7 9.7 11.2 9.9 11.5 — 3.9 4.0 4.5 4.1 5.4

Standard deviation — .8 .9 1.1 .9 1.2 — 1.5 1.5 2.2 1.4 1.4
24 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Table 6. Summary statistics for water-quality data collected at selected stations in the Susquehanna River Basin, Pennsylvania, 

May 1 through July 31, 2008.—Continued

[C2, Susquehanna River at Shady Nook Boat Launch; C3, Susquehanna River below Clemson Island (Main Channel); C4, Susquehanna River at Clemson 

Island (Microhabitat); C5, Juniata River at Newport; C6, Juniata River near Howe Township Park (Microhabitat); C7, Juniata River near Howe Township 

Park (Main Channel); shading provided for comparison of young-of-the-year microhabitats and main-channel habitats; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams per liter; n, number of daily values; P25, 25th percentile; P75, 75th percentile; —, not computed]

Statistic

Daily minimum pH

(standard units)

Daily median pH

(standard units)

Station Station

 C2 C3 C4 C5 C6 C7 C2 C3 C4 C5 C6 C7

n 15 76 76 79 65 57 15 76 76 79 65 57

Minimum 7.2 7.4 7.1 7.3 7.3 7.6 7.4 7.5 7.3 7.5 7.6 7.9

P25 7.3 7.7 7.3 7.5 7.7 7.8 7.5 8.2 7.6 7.8 8.0 8.2

Median 7.3 7.8 7.4 7.6 7.8 7.9 7.6 8.3 7.8 8.0 8.2 8.4

P75 7.4 7.8 7.5 7.7 8.0 8.1 7.6 8.5 7.9 8.1 8.4 8.6

Maximum 7.5 8.9 8.5 8.3 8.6 8.3 7.8 9.2 9.0 8.5 9.0 8.7

Mean 7.3 7.8 7.4 7.6 7.9 7.9 7.6 8.3 7.8 8.0 8.2 8.4

Standard deviation .1 .3 .2 .2 .2 .2 .1 .4 .3 .2 .3 .2

Statistic

Daily maximum pH

(standard units)

Daily pH range

(standard units)

Station Station

 C2 C3 C4 C5 C6 C7 C2 C3 C4 C5 C6 C7

n 15 76 76 79 65 57 15 76 76 79 65 57

Minimum 7.5 7.6 7.4 7.8 8.0 8.4 .1 .2 .1 .1 .2 .2

P25 7.9 8.6 8.1 8.2 8.4 8.6 .6 .8 .7 .6 .6 .7

Median 8.2 8.8 8.4 8.5 8.5 8.7 .8 .9 .9 .9 .7 .8

P75 8.3 8.9 8.6 8.7 8.7 8.8 .9 1.1 1.1 1.0 .8 .9

Maximum 8.3 9.4 9.3 9.2 9.2 9.0 1.0 1.5 1.6 1.3 1.4 1.1

Mean 8.1 8.7 8.3 8.4 8.6 8.7 .7 .9 .9 .8 .7 .8

Standard deviation .3 .4 .4 .3 .3 .2 .3 .3 .4 .3 .2 .1
Monitoring Results and Implications, Susquehanna River 25

Table 6. Summary statistics for water-quality data collected at selected stations in the Susquehanna River Basin, Pennsylvania, 

May 1 through July 31, 2008.—Continued

[C2, Susquehanna River at Shady Nook Boat Launch; C3, Susquehanna River below Clemson Island (Main Channel); C4, Susquehanna River at Clemson 

Island (Microhabitat); C5, Juniata River at Newport; C6, Juniata River near Howe Township Park (Microhabitat); C7, Juniata River near Howe Township 

Park (Main Channel); shading provided for comparison of young-of-the-year microhabitats and main-channel habitats; °C, degrees Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams per liter; n, number of daily values; P25, 25th percentile; P75, 75th percentile; —, not computed]

Statistic

Daily minimum specific conductance

(μS/cm)

Daily mean specific conductance

(μS/cm)

Station Station

 C2 C3 C4 C5 C6 C7 C2 C3 C4 C5 C6 C7

n 15 76 76 81 65 57 15 76 76 80 65 57

Minimum 181 127 129 106 191 162 194 129 131 146 198 187

P25 233 224 225 179 265 241 256 229 237 197 281 263

Median 269 294 296 241 300 272 277 313 308 251 305 294

P75 288 317 319 256 307 298 301 326 327 265 313 306

Maximum 310 358 366 288 333 330 321 364 368 300 345 344

Mean 258 267 268 219 284 262 273 276 278 231 293 280

Standard deviation 41 67 66 46 35 46 38 69 67 44 33 37

Statistic

Daily maximum specific conductance

(μS/cm)

Daily specific conductance range

(μS/cm)

Station Station

 C2 C3 C4 C5 C6 C7 C2 C3 C4 C5 C6 C7

n 15 76 76 81 65 57 15 76 76 80 65 57

Minimum 215 130 133 157 202 214 10 2 3 2 3 3

P25 274 240 248 199 298 276 20 11 10 7 7 12

Median 289 319 318 256 311 304 29 16 17 13 12 16

P75 310 336 334 272 320 314 35 24 23 18 18 50

Maximum 344 368 369 305 355 354 74 61 69 169 125 96

Mean 289 286 287 238 300 293 31 19 20 19 17 31

Standard deviation 36 68 67 45 34 31 16 12 13 26 20 26
26 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

in the main-channel habitat. Dissolved-oxygen concentrations 

were below 5.0 mg/L longer in the microhabitat than in the 

main-channel habitat (the maximum time that dissolved oxygen was less than 5.0 mg/L in the microhabitat was 5.5 hours)

These data support the contention that YOY smallmouth 

bass in the study reaches are more likely to experience stress 

from sub-optimal dissolved-oxygen concentrations than older 

fish not living in or frequenting backwater and river-margin 

areas. Factors that may cause the lower dissolved-oxygen 

concentrations in microhabitats include lower reaeration rates 

relative to the main channel and respiration by aquatic biota. 

Respiration may consume oxygen more quickly in microhabitats than in the main channel because depths generally are 

lower, resulting in less volume of water compared to the main 

channel. Also, mixing with water from the main channel that 

potentially has more dissolved oxygen is slow because velocities are lower than those in the main channel.

Water Temperature

Rates of activity and physiological processes in smallmouth bass and other fish are influenced primarily by water 

temperature (Schreer and Cooke, 2002). The upper and 

lower thermal tolerances of different fish vary greatly and 

are flexible because fish may acclimate seasonally to different extremes (Barans and Tubb, 1973; Beitinger and 

others, 2000). The ability of smallmouth bass to acclimate 

to increasing temperature makes it difficult to determine a 

specific water-temperature threshold where stress may occur. 

While assigning a specific value that elicits a physiological or 

behavioral stress response is untenable, it is well established 

that increasing water temperature may contribute directly 

or indirectly to stress in YOY smallmouth bass by 1) lower 

solubility of dissolved oxygen (fig. 4), 2) direct stress resulting 

from an inability to acclimate to warming water temperatures, 

3) greater populations of F. columnare and other pathogens, 

4) magnified physiological and behavioral response to other 

stressors (Spoor, 1984), and 5) higher probability of impaired 

gill function because of enhanced adhesion of F. columnare to 

gill tissue (Decostere and others, 1999).

The implications of water temperature in microhabitats 

compared to the main channel are varied. Microhabitats did 

not always have warmer water temperatures than the main 

channel and are, therefore, not necessarily lower in dissolved 

oxygen or otherwise more stressful solely because of water 

temperature. Site-specific variables like exposure to sunlight 

and upstream inputs may have factored greatly in determining 

differences between water temperature of microhabitats and 

main-channel habitats.

The microhabitat in the Susquehanna River at station 

C4 was on the east side of Clemson Island (fig. 5), providing 

for exposure to sunlight for most of the day. This resulted in 

minimum, median, and maximum daily water temperatures 

that were comparable to the main-channel station at C3, which 

received similar exposure to sun. For example, mean daily 

water temperatures had medians of 25.8°C at station C4 and 

26.1°C at station C3, and maximum daily water temperatures had medians of 28.5°C at C4 compared to 28.4°C at C3 

(table 6). Median daily water-temperature range was 0.6°C 

greater (p-value < 0.0001; table 5) in the microhabitat compared to the main channel (fig. 11).

The microhabitat in the Juniata River at station C6 was 

shaded for most of each day by a canopy of trees, and mixing 

with faster-moving water in the main channel was poor under 

low to moderate streamflow conditions. These two factors 

allowed the microhabitat to maintain cooler temperatures compared to the main channel (p-value < 0.0001; table 5). Daily 

maximum water temperature in the microhabitat at station 

C6 had a median of 26.9°C compared to 27.8°C in the main 

channel at station C7 (table 6). Maximum instantaneous water 

temperature in the main-channel habitat was 31.8°C (July 19, 

2008) compared to 31.5°C in the microhabitat. Daily watertemperature range (fig. 12) was statistically equivalent in both 

settings (p-value = 0.3517; table 5).

5

6

7

8

9

10

11

NATIONAL CRITERION FOR 7-DAY MEAN DISSOLVED-OXYGEN

CONCENTRATION, EARLYLIFE STAGES

(U.S. Environmental Protection Agency)

5

6

7

8

9

10

11

7-DAY MEAN DISSOLVED-OXYGEN

CONCENTRATION, IN MILLIGRAMS PER LITER

7-DAY MEAN DISSOLVED-OXYGEN

CONCENTRATION, IN MILLIGRAMS PER LITER

A Susquehanna River, Clemson Island

B Juniata River, Howe Township Park

Microhabitat, Station C4

Main channel, Station C3

Microhabitat, Station C6

Main channel, Station C7

NATIONAL CRITERION FOR 7-DAY MEAN DISSOLVED-OXYGEN

CONCENTRATION, EARLYLIFE STAGES

(U.S. Environmental Protection Agency)

Gap indicates

missing record

Gap indicates

missing record

21 28 7 14 21 28 7 14 21 28 7 14 21 28 7 14 21 28

MAY JUNE JULY AUGUST SEPTEMBER

2008

21 28 7 14 21 28 7 14 21 28 7 14 21 28 7 14 21 28

MAY JUNE JULY AUGUST SEPTEMBER

2008

Figure 10. Seven-day mean dissolved-oxygen concentrations 

in A) the Susquehanna River in the vicinity of Clemson Island 

and B) the Juniata River in the vicinity of Howe Township Park, 

Pennsylvania, 2008.

[Value displayed on any day is the last day of the 7-day period.]
Monitoring Results and Implications, Susquehanna River 27

Figure 11. Daily range in water temperature, dissolved-oxygen concentration, and pH in the Susquehanna River in the vicinity 

of Clemson Island, Pennsylvania, 2008.

0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

DAILY PH RANGE, IN STANDARD UNITS

C

21 28 7 14 21 28 7 14 21 28 7 14 21 28 7 14 21 28

May June July August September

2008

Microhabitat (Station C4)

Main channel (Station C3)

Gap indicates

missing record

0

2

4

6

8

DAILY DISSOLVED-OXYGEN CONCENTRATION

RANGE, IN MILLIGRAMS PER LITER

B

21 28 7 14 21 28 7 14 21 28 7 14 21 28 7 14 21 28

May June July August September

2008

Microhabitat (Station C4)

Main channel (Station C3)

Gap indicates

missing record

0

2

4

6

8

10

12

14

16

18

DAILY WATER TEMPERATURE RANGE,

IN DEGREES CELSIUS

A

21 28 7 14 21 28 7 14 21 28 7 14 21 28 7 14 21 28

May June July August September

2008

Microhabitat (Station C4)

Main channel (Station C3)

Gap indicates

missing record
28 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

pH

During the critical period of May 1 through July 31, 

pH was near-neutral or alkaline at all stations in microhabitats and main-channel habitats (table 6). Daily pH minima, 

maxima, and medians in the microhabitats were up to 0.5 pH 

units lower (figs. 8E, 8F, 9E, and 9F) than the corresponding 

main-channel habitats (p-values < 0.0001 to 0.0010; table 5) 

but daily ranges were comparable (median daily range was 

0.7 to 0.9 pH units in microhabitat and main-channel habitats; 

table 6). The median daily median pH in the Susquehanna 

River microhabitat at station C4 was 7.8 compared to 8.3 

in the main channel at station C3. The median daily median 

pH value in the Juniata microhabitat at station C6 was 8.2 

compared to 8.4 in the main channel. Somewhat longer 

exposure to sunlight and the resulting increased productivity 

may explain why pH values are greater in the main-channel 

habitats relative to the microhabitats.

Despite significant statistical differences between pH 

of microhabitats and main-channel habitats (table 5), the 

biological significance is unclear. Most studies of pH effects 

on smallmouth bass have focused on survival (Hill and others, 1988) and foraging behavior (Hill, 1989) in acidic (pH 

less than 6.0) environments. Smallmouth bass young (3 to 

36 days post swim up) are sensitive to acidic pH and experience appreciable declines in survival rates at pH 5.7 compared 

to pH 7.4 (Hill and others, 1988). Potential stress during the 

critical period that may result from acute exposure to alkaline 

pH values (up to pH 9.4; fig. 8F) and large daily fluctuations 

(up to 1.6 pH units; table 6) as observed in the microhabitats 

and the main-channel habitats of the Susquehanna and Juniata 

Rivers is not well characterized.

A search of the scientific literature produced no studies focusing on the effects of alkaline environments on YOY 

smallmouth bass; however, Scott and others (2005) investigated the effect of high pH (up to pH 10.54) on ion balance, 

ammonia excretion, and behavior of perch (Perca fluviatilis), 

a warm-water fish that commonly coexists with smallmouth 

bass in lake habitats. Perch inhabiting alkaline lake waters 

(pH of 9.9) had three times more plasma ammonia compared 

to fish from neutral waters, indicating the fish were stressed 

because of a disruption of the ability to excrete ammonia 

(waste) (Scott and others, 2005). Despite apparently stressful pH levels, radio-tracking results indicated that adult perch 

and pike (Esox lucius) did not seek refuge in nearby water of 

neutral pH. Scott and others (2005) concluded that the benefits 

of withstanding the alkaline pH conditions were greater (better 

foraging, less predation) than the benefit of moving into more 

pH-neutral water.

The relevancy and implications of these findings on YOY 

smallmouth bass in the study reaches are unclear. Smallmouth bass typically inhabit waters with pH levels of 5.7 to 

9.0, although the optimal pH range is 7.9 to 8.1 (Edwards 

and others, 1983). In this study, YOY smallmouth bass were 

exposed to pH that changed by as much as 1.6 units in a day 

(table 6) but rarely were exposed to alkaline pH that exceeded 

9.0 during the critical period (figs. 8E, 8F, 9E, and 9F). Values 

of 9.0 or greater were only sustained for periods of less than 

12 hours. It seems unlikely that pH is a major stressor to YOY 

smallmouth bass in the study reaches, but perhaps when combined with temperatures that are relatively high and dissolvedoxygen concentrations that are below national criteria, alkaline 

pH and (or) large daily fluctuations in pH may contribute to 

overall stress.

Specific Conductance

Specific conductance is a measure of the capacity of 

dissolved ions in water to conduct an electrical current (Wilde 

and others, 1998). 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 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. This daily cycling may 

be responsible for some of the inconsistent data observed in 

specific conductance.

During the critical period, average daily mean specific 

conductance was similar in microhabitats and main-channel 

habitats near Clemson Island (287 μS/cm compared to 

286 μS/cm) but was greater in microhabitat at Howe Township 

Park compared to the main channel (300 μS/cm compared to 

293 μS/cm). Minimum daily mean specific conductance in 

the microhabitat and main-channel habitat at Clemson Island 

were 131 μS/cm (May 20 and 21, 2008) and 129 μS/cm (May 

20 and 21, 2008) compared to maximum values of 368 μS/cm 

(July 16, 2008) and 364 μS/cm (July 16, 2008), respectively. 

Specific conductance values at Howe Township Park were not 

as low (mean daily minima in the microhabitat and main-channel habitat were 198 μS/cm (May 24, 2008) and 187 μS/cm 

(June 24, 2008), respectively) or as high (maxima were 

345 μS/cm (July 10, 2008) in microhabitat and 344 μS/cm 

(July 10, 2008) in main-channel habitat) as those for the 

Susquehanna River at Clemson Island.

Influence of Warm-Water Discharge at Shady 

Nook

Stream water at station C2 had an average daily maximum temperature of 32°C but daily maximums were only 

determined for 16 days (table 6) near the end of the critical 

period (July 16–31). During this time period, daily mean water 

temperature was 2–3°C warmer at station C2 than at station 

C3 below Clemson Island (fig. 13) indicating any stress resulting from other factors is likely to be magnified by the warmwater discharge. The sonde deployed as station C2 was about 

15 ft from the right bank and was directly within the influence 
Monitoring Results and Implications, Susquehanna River 29

Figure 12. Daily range in water temperature, dissolved-oxygen concentration, and pH in the Juniata River in the vicinity of 

Howe Township Park, Pennsylvania, 2008.

2008

May

21 28

June

7 14 21 28

July

7 14 21 28

August

7 14 21 28

September

7 14 21 28

0

2

4

6

8

10

12

2008

May

21 28

June

7 14 21 28

July

7 14 21 28

August

7 14 21 28

September

7 14 21 28

0

0.5

1

1.5

2

DAILY DISSOLVED-OXYGEN CONCENTRATION 

RANGE, IN MILLIGRAMS PER LITER

DAILY PH RANGE,

IN STANDARD UNITS

B

C

Microhabitat (Station C6)

Main channel (Station C7)

Microhabitat (Station C6)

Main channel (Station C7)

Gap indicates

missing record

Gap indicates

missing record

2008

May

21 28

June

7 14 21 28

July

7 14 21 28

August

7 14 21 28

September

7 14 21 28

0

1

2

3

4

5

6

7

DAILY WATER TEMPERATURE

RANGE, IN DEGREES CELSIUS

A

Microhabitat (Station C6)

Main channel (Station C7)

Gap indicates

missing record
30 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

of the warm-water discharge. It was not determined how far 

from the right bank the warm-water discharge affects the river 

temperature.

The warm-water discharge influencing water temperature at station C2 is about 30 mi upstream of Clemson Island. 

Because of heat dissipation between stations C2 and C3, 

groundwater inputs, and mixing with cooler water in the main 

channel of the Susquehanna River and tributaries entering on 

the right bank, it is unlikely that the warm-water discharge 

at station C2 has an effect on water temperature as far downstream as Clemson Island.

Spatial Variability of Nutrients in Selected 

Reaches in the Susquehanna River Basin

Nutrients are relatively not toxic to aquatic life, except 

at concentrations much larger than are commonly observed in 

the Susquehanna River and its tributaries. However, nutrients 

in streams contribute to plant growth, both rooted aquatic 

plants and periphyton. Excessive nutrient concentrations can 

lead to excessive plant growth. Over a 24-hour period, plants 

go through a daily cycle of photosynthesis and respiration 

that causes fluctuations in dissolved oxygen. If plant growth 

is excessive, the daily fluctuations in dissolved oxygen can 

become stressful or even lethal to fish. Therefore, an understanding of nutrient concentrations in the Susquehanna River 

study reaches may contribute to understanding stressful conditions that lead to the observed bacterial infections.

A one-time survey was conducted on June 11 and 12, 

2008, for nutrients in water and streambed sediments. During the 2-day period, samples were collected from the right 

bank and left bank at 25 stations on the West Branch Susquehanna River, Juniata River, and mainstem Susquehanna River 

(fig. 7). In water samples, concentrations were determined 

for ammonia plus organic nitrogen, ammonia nitrogen, nitrite 

nitrogen, nitrate nitrogen, total nitrogen, orthophosphate 

phosphorus, and total phosphorus. Orthophosphate phosphorus 

and filtered nitrate nitrogen are considered to be the nutrient 

species most readily available for plant growth (Vollenweider, 

1968). Therefore, the discussion of nutrient concentrations in 

water will focus on orthophosphate phosphorus and nitrate 

nitrogen. For streambed-sediment samples, concentrations 

of ammonia plus organic nitrogen, total ammonia nitrogen, 

and total phosphorus were measured. The nutrient data from 

the entire survey for both water and streambed sediments are 

presented in appendix 3 in tables 3-1, 3-2, and 3-3.

Nitrogen in Water

Nutrient concentrations in the study reaches varied 

widely among the sampling locations. Considering all sampling stations, the highest concentration of nitrate nitrogen 

measured in water during the survey was in the sample 

collected from the right bank of the mainstem Susquehanna 

River at Harrisburg (fig. 14; appendix 3, table 3-3). This 

sampling station is about 1.7 mi downstream from the mouth 

of the Conodoguinet Creek. The Conodoguinet Creek receives 

inputs from five wastewater-treatment plants each having a 

designed flow of 1.0 Mgal/d or larger (Pennsylvania Department of Environmental Protection, 2009b). It is likely that the 

concentration of nitrate nitrogen in this sample was strongly 

influenced by water from the Conodoguinet Creek. The 

second highest concentration of nitrate nitrogen (2.08 mg/L) 

was in the sample collected from the left bank of the mainstem Susquehanna River at Highspire (station N22) (fig. 14; 

appendix 3, table 3-3). Samples from this location are believed 

to be influenced by effluent from the Harrisburg wastewatertreatment facility.

For the West Branch Susquehanna River, concentrations 

of nitrate nitrogen were similar for right-bank and left-bank 

samples, except for the sample from Lewisburg, which was 

twice as high as the next highest sample. Other concentrations 

of nitrate nitrogen in the West Branch fell within a narrow 

range from 0.41 to 0.74 mg/L (fig. 14; appendix 3, table 3-1).

For the Juniata River, concentrations of nitrate nitrogen 

were approximately twice as high as in the West Branch. 

Concentrations of nitrate nitrogen varied little from station to 

station. The highest concentration in the Juniata River samples 

was 1.42 mg/L, and the lowest concentration was 1.06 mg/L. 

Differences between left-bank and right-bank samples were 

minor (fig. 14; appendix 3, table 3-2).

For the mainstem of the Susquehanna River, concentrations of nitrate nitrogen were less than 1.0 mg/L for all stations 

except the two previously mentioned at Harrisburg (station 

C8, right bank) and at Highspire (station N22, left bank) where 

higher concentrations were suspected of being influenced by 

wastewater inputs. Concentrations in the mainstem were similar to concentrations in the West Branch but were only about 

half as large as concentrations in the Juniata River. Higher 

concentrations in the mainstem were expected in the left-bank 

WATER TEMPERATURE, IN DEGREES CELSIUS

15 18 21 24 27 30 3 6 9 12 15 18 21 24 27 30 3 6 9 12 15 18 21 24

JULY AUGUST SEPTEMBER

Gap indicates

missing record

Shady Nook

Clemson main channel

34

32

30

28

26

24

22

20

2008

Figure 13. Comparison of mean daily water temperatures 

downstream of a warm-water discharge with mean daily water 

temperature at Clemson Island, Pennsylvania, July–September 

2008.
Monitoring Results and Implications, Susquehanna River 31

Figure 14. Relative comparison of nitrate nitrogen concentrations in water from selected reaches of the 

Susquehanna River and major tributaries, Pennsylvania, June 11 and 12, 2008.

Water features from U.S. Geological Survey National Hydrography Dataset (NHD)

EXPLANATION

We s t

Br a n c h Su s q u ehanna River

Juniata

R i v e r

Su s q u

e hanna

River

Williamsport

Danville Lewisburg

Lewistown

Port Royal

Millerstown

Newport

Thompsontown

Halifax

Harrisburg

Highspire

Base from U.S. Geological Survey 1:24,000 digital data

0

0 15 MILES

15 KILOMETERS

76°33' 76°36'

40°09'30''

40°15'30''

Major river

County boundary

Sampling station identifier

Selected municipality

N1

Pennsylvania

Area containing study reaches

Left-bank sample (bar height equal to 1.0 mg/L)

Right-bank sample (bar height equal to 1.0 mg/L)

Direction of streamflow FLOW

N1

N2 N3

N4

N5

N6

N7

N8

N9

N10 

N11

N12

N13

N14 N15

N16 N17

N18

N19

N20

N21

N22

C3

C8

C5

Bu ff a l o Cr e e k

Conodoguinet

Cre e k

FLOW FLOW

FLOW

FLOW

FLOW

FLOW
32 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

samples, based on data from the Pennsylvania Black Fly 

Suppression Program (D. Rebuck, Pennsylvania Department 

of Environmental Protection, oral commun., December 10, 

2007); however, the data from this study indicate the opposite. 

Concentrations of nitrate nitrogen were higher for right-bank 

samples than left-bank samples at 9 of the 12 sampling stations (fig. 14).

Concentrations of ammonia nitrogen in water were very 

low at all stations and varied from less than detection limits 

to 0.06 mg/L. Low ammonia concentrations in stream water 

are typical because ammonia is quickly oxidized to nitrite 

and then to nitrate when oxygen is present. Concentrations of 

ammonia plus organic nitrogen in water were below detection 

limits at every sampling station.

Concentrations of total nitrogen ranged from 0.7 mg/L 

(West Branch Susquehanna River at Duboistown (station N2) 

and Susquehanna River near Fishers Island (station N9)) to 

3.77 mg/L (mainstem Susquehanna River at Harrisburg (station C8, right bank)). The downstream-most station at Highspire (station N22) on the left bank had a concentration of total 

nitrogen of 2.08 mg/L. Other than at Harrisburg, the highest 

concentrations of total nitrogen were in the Juniata River and 

ranged from 1.46 to 1.86 mg/L (appendix 3, tables 3-1, 3-2, 

3-3).

Phosphorus in Water

The highest concentration of filtered orthophosphate 

phosphorus measured during the 2-day survey was 0.035 mg/L 

in the sample from the right bank of the West Branch Susquehanna River at Lewisburg (fig. 15; appendix 3, table 3-1). This 

sample was collected about 1,000 ft downstream from the 

mouth of Buffalo Creek. It is likely that the 100-ft distance 

from shore for this sample did not avoid collecting primarily 

Buffalo Creek water. Buffalo Creek receives effluent from several wastewater-treatment facilities, including a 3.75 Mgal/d 

designed-flow plant (Kelly Township Municipal Authority) 

that empties into Buffalo Creek near the mouth (T. Randis, 

Pennsylvania Department of Environmental Protection, oral 

commun., July 13, 2009). Therefore, water from Buffalo 

Creek may be expected to have higher nutrient concentrations 

than water from the West Branch Susquehanna River. The second highest concentration of filtered orthophosphate phosphorus measured during the 2-day survey was 0.028 mg/L in the 

sample from the left bank of the mainstem Susquehanna River 

at Highspire. This station is approximately 3.8 mi downstream 

from the wastewater-treatment plant effluent from the City 

of Harrisburg. This treatment facility has a designed flow of 

37.7 Mgal/d (Pennsylvania Department of Environmental Protection, 2009b) and is the largest wastewater-treatment facility 

that discharges directly to the Susquehanna River. Effluent 

from this facility likely influenced phosphorus concentrations 

in samples collected at the Highspire sampling station.

For the West Branch Susquehanna River, concentrations 

of orthophosphate phosphorus were less than 0.01 mg/L for 

all sampling stations except for the right-bank sample from 

Lewisburg (station N7). Concentrations of total phosphorus 

were less than 0.020 mg/L except for the right-bank sample at 

Lewisburg (0.060 mg/L) and the right-bank sample at Duboistown (station N2) (0.034 mg/L). Concentrations were similar 

for right bank and left bank samples, except for the samples 

from Lewisburg and Duboistown.

In general, concentrations of phosphorus are higher in the 

Juniata River than in the West Branch Susquehanna River or 

in the mainstem Susquehanna River. Concentrations of orthophosphate phosphorus were larger than the detection level 

of 0.01 mg/L at all sampling stations. Concentrations ranged 

from 0.013 to 0.027 mg/L. Differences between left-bank 

and right-bank samples were small. Concentrations of total 

phosphorus ranged from 0.03 to 0.048 mg/L for the Juniata 

River sampling stations. As with orthophosphate, differences 

between left-bank and right-bank samples were small.

Biochemical Oxygen Demand in Water

Concentrations of BOD in untreated wastewaters typically range between 150 and 450 mg/L (Salvato, 1992, p. 479). 

Treated wastewaters commonly have BOD concentrations of 

20 mg/L or less. Moderately polluted rivers might have BOD 

concentrations of 2–8 mg/L (Sawyer and others, 2003). Concentrations of BOD were low throughout the study reaches. 

The highest concentration was measured in the sample from 

the Susquehanna River at Danville (left bank), where the concentration was 3.7 mg/L. The next highest concentration was 

3.4 mg/L in the sample from the Susquehanna River at Hoover 

Island, Pa. (left bank). Of the 50 samples collected during the 

survey, 38 had BOD concentrations less than 2.0 mg/L. These 

data indicate that dissolved-oxygen concentrations below the 

national criterion of 5.0 mg/L were not likely to have been 

caused by oxygen-demanding materials in the water.

Nutrients in Streambed Sediments

Nutrient concentrations in streambed sediments were 

even more variable than nutrients in water. This may be a 

reflection of the nature of the sediments available for sampling rather than the nutrient regime of the sampling location. 

Nutrients (particularly phosphorus) tend to sorb to fine-grained 

particles. Therefore, a sampling location having finer-grained 

sediment deposits may have higher nutrient concentrations 

than a location having more coarse sediment deposits. The 

sampling protocol for the nutrient synoptic survey called for 

collecting fine-grained sediment samples, but the grain size of 

the samples actually collected varied substantially from station 

to station.

For the survey, the highest concentration of total phosphorus in streambed sediments was 1.43 g/kg measured in 

the sample from the left bank of the Susquehanna River at 

Liverpool (station N12). The second highest concentration of 

total phosphorus was 1.04 g/kg in the sample from the right 

bank of the Susquehanna River at Harrisburg (station C8). 
Monitoring Results and Implications, Susquehanna River 33

Figure 15. Relative comparison of orthophosphate phosphorus concentrations in water of selected reaches of the 

Susquehanna River and major tributaries, June 11 and 12, 2008.

Water features from U.S. Geological Survey National Hydrography Dataset (NHD)

EXPLANATION

We s t

Br a n c h Su s q u ehanna River

Juniata

R i v e r

Su s q u

e hanna

River

Williamsport

Danville Lewisburg

Lewistown

Port Royal

Millerstown

Newport

Thompsontown

Halifax

Harrisburg

Highspire

Base from U.S. Geological Survey 1:24,000 digital data

0

0 15 MILES

15 KILOMETERS

76°33' 76°36'

40°09'30''

40°15'30''

Major river

County boundary

Sampling station identifier

Selected municipality

N1

Pennsylvania

Area containing study reaches

N1

N2 N3

N4

N5

N6

N7

N8

N9

N10 

N11

N12

N13

N14 N15

N16 N17

N18

N19

N20

N21

N22

C3

C8

C5

Bu ff a l o Cr e e k

Conodoguinet

Cre e k

FLOW FLOW

FLOW

FLOW

FLOW

FLOW

Left-bank sample (bar height equal to 0.01 mg/L)

Right-bank sample (bar height equal to 0.01 mg/L)

<

<

<

<

< Indicates concentration is less than 0.01 mg/L.

Direction of streamflow

< <

< <

< <

< <

< <

< <

< <

< <

< <

< <

< <

< <

< <

< <

FLOW
34 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

As previously stated, this sampling station was likely influenced by inputs from the Conodoguinet Creek (appendix 3, 

tables 3-1, 3-2, 3-3).

The highest concentration of ammonia plus organic nitrogen, 4.0 g/kg, was measured in sediments from the left-bank 

sample from the Susquehanna River at Dalmatia (station N11). 

The second highest, 3.6 g/kg, was in the right-bank sample 

from the Juniata River at Amity Hall (station N19) (appendix 3, tables 3-1, 3-2, 3-3). No large wastewater effluents are 

immediately upstream from either of these sampling stations.

Implications of Nutrients in the Susquehanna 

River

As indicated previously, excessive nutrients in water can 

spur excessive plant growth leading to dramatic daily swings 

in dissolved-oxygen concentrations. Previous studies have 

primarily assessed concentrations of total nitrogen and (or) 

total phosphorus that are capable of producing nuisance plant 

growths. The emphasis here is on the word “total.” Some 

studies have looked at algal growth to draw their conclusions 

(Biggs, 2000; Dodds and others, 2002; Stevenson and others, 

2006) and some have looked at the trophic state of the system 

(Whitmore, 1989; Dodds and others, 1998; Potapova and 

Charles, 2007; Ponader and others, 2007). Discussions center 

on whether to set limits using total nitrogen and total phosphorus or their soluble components. Concentrations of total 

phosphorus attributed to causing excessive growths of algae 

are between 0.021 and 0.9 mg/L (Dodds and others, 1997; 

Chetelat and others, 1999; Lohman and others, 1992). Some 

studies indicate that concentrations of total nitrogen between 

0.25 and 0.65 mg/L (Dodds and others, 1997; Lohman and 

others, 1992) are enough to cause nuisance growths of algae 

in streams. Sheeder and Evans (2004) calculated concentration thresholds for impaired versus non-impaired watersheds 

in Pennsylvania. Their analysis established somewhat higher 

threshold concentrations than other researchers with the 

threshold for total phosphorus at 0.07 mg/L and for total 

nitrogen at 2.01 mg/L. Dodds and Welch (2000) recommend 

that in order to avoid chronic toxicity by ammonia to fish and 

invertebrates, no more than 0.02 mg/L of ammonia should be 

present. To date, no consensus limits for phosphorus and nitrogen species in streams and rivers have been reached.

The states have been charged with developing defensible 

nutrient criteria by EPA. EPA has published recommendations for establishing nutrient criteria by ecoregion. States 

may adopt the EPA recommended criteria or develop their 

own. The EPA recommendations are for total nitrogen and 

total phosphorus. The Susquehanna River Basin is located 

primarily in nutrient ecoregion XI, the Central and Eastern 

Forested Uplands, but with portions of the basin in nutrient ecoregions VIII and XI (Commission for Environmental 

Cooperation, 1997). The area for the current study is almost all 

in ecoregion XI. For ecoregion XI, the concentration of total 

phosphorus recommended by EPA is 0.01 mg/L and the concentration of total nitrogen is 0.31 mg/L (U.S. Environmental 

Protection Agency, 2002). All stations sampled during the June 

2008 survey had concentrations of total phosphorus larger than 

the EPA recommendation to control nuisance algal growth and 

to promote clean water for ecoregion XI. Similarly, all stations 

exceeded the recommendation for total nitrogen.

The Commonwealth of Pennsylvania has not yet established water-quality standards for nutrients. However, as of 

July 2008, 5 states have adopted numeric nutrient standards 

for one or more constituents for all of their rivers/streams, 

9 states have adopted numeric nutrient standards for one or 

more constituents for part of their rivers/streams, and 36 states 

have not adopted numeric nutrient standards (U.S. Environmental Protection Agency, 2008). For states that border 

Pennsylvania, New Jersey has adopted a limit of 0.1 mg/L 

total phosphorus in streams (Cohen and others, 2009). None 

of the Susquehanna River stations had a concentration of total 

phosphorus that exceeded this limit. New York has narrative criteria for nutrients. Delaware has “target” criteria of 

0.05 mg/L for total phosphorus and 1.0 mg/L for total nitrogen. Two Susquehanna River Basin stations had concentrations of total phosphorus that exceeded the Delaware target 

concentration. Applying the Delaware criteria, 22 of the 50 

Susquehanna River Basin sampling stations exceeded the 

target for total nitrogen including all 14 stations on the Juniata 

River. Maryland, Ohio, and West Virginia have not adopted 

nutrient criteria for streams.

Concentrations of total phosphorus measured in the 

study reaches were all in the range considered to be indicative 

of excessive algal growth. Concentrations of total nitrogen 

measured in the study reaches routinely exceed the recommendations for controlling nuisance algal growth as recommended 

by previous studies. The highest nutrient concentrations were 

measured at stations immediately downstream from wastewater-treatment plants. It should be emphasized that the nutrient 

survey was conducted during a low-flow period. Nutrient contributions from nonpoint sources would be expected to be at 

a minimum under these conditions. In general, for all nutrient 

species, concentrations in the Juniata River were higher than 

in the West Branch Susquehanna River or in the mainstem 

Susquehanna River.
Monitoring Results and Implications, Susquehanna River 35

Water Quality in 2008 Compared with Available 

Historical Data

YOY smallmouth-bass mortalities were first recognized 

in 2005 and continued in 2007 and 2008. Comparison of 

continuous-monitoring data collected in the Susquehanna 

River at Harrisburg (station C8) in 2008 with historical data 

available from the 1970s may indicate if and how temperature 

and dissolved-oxygen concentrations have changed over time. 

Further, if growth of periphyton and rooted aquatic plants 

is contributing to daily oxygen swings, perhaps present-day 

nutrient concentrations are higher than historic concentrations 

and are causing that increased growth.

For the Susquehanna River at Harrisburg, Pa., a station that characterizes water quality of the main channel, 

continuous water-quality data collected by USGS from 

1974 to 1979 were compared to water-quality data collected 

by USGS in 2008. Statistical analyses using the two-sided 

Wilcoxon signed-rank test indicate daily values for minimum 

temperature, maximum temperature, temperature range, and 

mean temperature were all significantly different in the 1970s 

than in 2008 (table 7). The average daily mean water temperature was 0.8°C warmer (p-value = 0.0056) in 2008 than in the 

historical record and the average daily mean dissolved-oxygen 

concentrations was 1.1 mg/L lower (p-value = < 0.0001). 

These results are consistent with a study that suggests water 

temperatures in streams in other parts of the world are 

warming (Webb and Noblis, 2007). Daily mean streamflow 

was not significantly different between the two time periods 

(p-value = 0.0952) indicating that it is not a likely explanation 

for the differences in water quality.

Long-term data indicate that nutrient concentrations are 

lower presently (2009) than 20 or 30 years ago. This stands to 

reason because of the large investment that has been made in 

improving wastewater treatment and the emphasis placed on 

implementing nonpoint-source best-management practices. A 

Susquehanna River Basin Commission (SRBC) assessment of 

trends using flow-adjusted concentrations covering the period 

Table 7. Statistical comparison of 2008 and historical (1974–79) water-quality data from the Susquehanna River, Pennsylvania.

[°C, Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams per liter; ft3/s, cubic feet per second; <, less than; —, too few data to test (N < 20)]

Parameter

Susquehanna River at Harrisburg, historical

compared to

Susquehanna River at Harrisburg, 20081

p-value2 N

Minimum water temperature (°C) 0.0132 39

Maximum water temperature (°C) .0021 39

Water temperature range (°C) .0083 39

Mean water temperature (°C) .0056 39

Minimum specific conductance (μS/cm) < .0001 39

Maximum specific conductance (μS/cm) < .0001 39

Specific conductance range (μS/cm) .3145 39

Mean specific conductance (μS/cm) < .0001 39

Minimum pH (standard units) —

Maximum pH (standard units) —

pH range (standard units) —

Median pH (standard units) —

Minimum dissolved oxygen (mg/L) .0001 20

Maximum dissolved oxygen (mg/L) < .0001 20

Dissolved oxygen range (mg/L) .0006 20

Mean dissolved oxygen (mg/L) < .0001 20

7-day mean minimum dissolved oxygen (mg/L) —

7-day mean dissolved oxygen (mg/L) —

Mean streamflow (ft3/s) .0952 92

1

Results of two-sided Wilcoxon signed-rank test. For historical data, the median of daily mean values computed from May 1–July 31, 1974–79 is used. 

Only days that had data in all 7 years were included in this analysis. As a result, some parameters could not be tested because there were too few data 

(N < 20).

2

For this study, a statistically significant difference exists if the p-value is less than 0.05.
36 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

1985 through 2007 (McGonigal, 2008) indicates downward 

trends in concentrations of most nutrient species at most monitoring stations.

However, analyses of a subset of data from 1998 to 2004 

indicates increases in dissolved orthophosphate phosphorus concentrations (for the purpose of this report, dissolved 

orthophosphate phosphorus will be considered equivalent to 

dissolved inorganic phosphorus (DIP)). McGonigal (2008) 

states “[over the past several years there has been] a dramatic 

increase in dissolved phosphorus and more specifically in 

dissolved orthophosphate phosphorus. This was apparent during the time period from 1998 to 2004, at all mainstem sites 

and Newport.” For example, the annual mean concentration 

for DIP in 2007 for the Susquehanna River at Danville was 

0.047 mg/L, which is almost three times the long-term mean 

of 0.018 mg/L for that station (McGonigal, 2008).

Nutrient trends in the Susquehanna River Basin also 

are analyzed periodically (roughly every 3–5 years) for the 

Chesapeake Bay Program. Analysis of nutrient data from 1985 

through 2004 (Langland and others, 2006) indicates downward 

trends (0 to 50 percent decrease) in flow-adjusted concentrations of total phosphorus and total nitrogen at all Susquehanna 

River Basin stations. A recently released summary report 

updates the trends analyses to include data through 2008 for 

the Chesapeake Bay tributaries (Langland and others, 2009). 

This update reaffirms the downward trends in flow-adjusted 

concentrations of total nitrogen (significant downward trends 

at all eight stations) and total phosphorus (significant downward trends at seven of eight stations) in the Susquehanna 

River Basin. However, trends for DIP were significantly 

upward for five of six stations in the Susquehanna River Basin 

where DIP was evaluated. These results confirm the observations of recent upward trends in DIP observed by McGonigal 

(2008).

Periphyton production is known to increase as nutrient concentrations increase (Biggs, 2000; Dodds and others, 2002). The increases in DIP documented by McGonigal 

(2008) and Langland and others (2009) may have promoted 

increased periphyton growth over the last few years. If so, 

then perhaps increased periphyton growth is contributing to 

stressful levels of dissolved oxygen that could explain why 

YOY smallmouth bass have only recently been affected by 

F. columnare infections. In summary, it appears that DIP concentrations have increased during the past half decade but the 

data are not available to evaluate whether these increases lead 

to F. columnare infections in smallmouth bass.

Correlation between Streamflow and Disease 

Incidence

Because dissolved oxygen and water temperature are suspected to play a role in incidence of F. columnare infection, it 

would be logical to compare water-quality conditions in 2008 

with previous years when the disease did (2005 and 2007) and 

did not (2006) occur. Unfortunately, continuous monitoring of 

dissolved oxygen in reaches affected by F. columnare infection did not begin until 2008 but streamflow data are available 

for a much longer period of record. Although streamflow is 

not a surrogate for dissolved-oxygen concentration or water 

temperature, some generalizations about the correlation 

between streamflow and water quality can be made. Relatively 

high streamflows during summer months, such as those in 

2006 (fig. 16A), usually result from runoff that is cooler than 

the ambient river temperature. Water temperature data collected by SRBC (Andrew Gavin, Susquehanna River Basin 

Commission, written commun., 2009) in the Susquehanna 

River approximately 6 mi upstream from station C8 (fig. 6A) 

at Rockville, Pa., indicate conditions frequently were cooler 

in May and June 2006 than in the same time period in 2007 

(fig. 16B). Stormflows with peaks on June 6 and June 29, 

2006, are correlated with an initial decrease in temperature 

as flow increased, followed by a gradual recovery in water 

temperature as stormflows receded. As the river water cooled 

through mixing with the stormwater runoff, dissolved oxygen likely would have increased owing to greater dissolution 

of oxygen in cool water compared to warm water (fig. 4). In 

addition, relatively high streamflows commonly increase turbidity, which diminishes penetration of sunlight into the river 

water. Photosynthesis and respiration by periphyton, algae, 

and other aquatic vegetation is suppressed with decreasing 

sunlight causing the amplitude of daily sinusoidal dissolvedoxygen fluctuations to be smaller. For these reasons, relatively 

high-streamflow conditions and cooler water temperatures in 

2006 would promote greater dissolved-oxygen concentrations.

Whether or not water-quality conditions are less stressful 

to YOY smallmouth bass during relatively high-streamflow 

summers, streamflow and disease-incidence data indicate that 

higher streamflows may moderate or eliminate the incidence 

of F. columnare infection in YOY smallmouth bass. No 

F. columnare infections were documented in 2006, a year with 

relatively high spring and summertime streamflows, but YOY 

smallmouth-bass mortalities were widespread in years 2005, 

2007, and 2008 (fig. 17) when flows during the critical period 

were lower. Summertime months of 2008 had conditions 

similar to 2005 and 2007, with streamflows that generally are 

closer to historical median flows than minimum flows for the 

period of record (fig. 18B and C). Thus, the occurrence of 

the disease does not seem to be limited to exceptionally low 

streamflow summers. Moderate or near-normal summertime 

streamflows and associated water-quality conditions seem 

to be conducive to widespread occurrence of F. columnare

infection.
Monitoring Results and Implications, Susquehanna River 37

Figure 16. Relation between A) streamflows in the Susquehanna River at Harrisburg, Pennsylvania (station C8), and 

B) water temperature measured approximately 6 miles upstream at Rockville, Pennsylvania, 2005–08.

[Water temperature data provided by Susquehanna River Basin Commission] STREAMFLOW, IN THOUSANDS OF CUBIC FEET PER SECOND

5

10

20

50

100

200

400

4

WATER TEMPERATURE, IN DEGREES CELSIUS

10

12

14

16

18

20

22

24

26

28

30

32

May

4 8 12 16 20 24 28

June

4 8 12 16 20 24 28

July

4 8 12 16 20 24 28

Stormflow peak

on June 6, 2006

Stormflow peak A on June 29, 2006

B

2006

2005

2007

2006

2005

2007

2008

Gap indicates

missing record
38 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Figure 17. Geographic distribution of disease incidence in 2008 compared to 2005–07, Pennsylvania.

Basin boundaryMajor riverCounty boundaryState boundary

Delaware River Basin

Lake Erie BasinOhio River BasinGenesee River Basin

Susquehanna River Basin

Potomac River Basin

Chesapeake Bay Basin

No diseased fish capturedDiseased fish captured

EXPLANATION

Sampled, but no fish captured

00

50 MILES

50 KILOMETERS

Lehigh

River

Schuyl k i l l River Raystown Lake

Jun ai at Rive r

West Branch Susq u ehanna River

Susquehanna River

Susquehanna River

Al el gheny

River

ono M

al ehahn i R ev r

Oh oi Ri v e r

Delaware

R i ver

40°

41°

42°

80°

79° 78° 77° 76°

Area containingstudy reaches

Lehigh

River

Schuyl k i l l River Raystown Lake

Jun ai at Rive r

West Branch Susq u ehanna River

Susquehanna River

Susquehanna River

Al el gheny

River

ono M

al ehahn i R ev r

Oh oi Ri v e r

Delaware

R i ver

40°

41°

42°

80°

79° 78° 77° 76°

Area containingstudy reaches

Lehigh

River

Schuyl k i l l River Raystown Lake

Jun ai at Rive r

West Branch Susq u ehanna River

Susquehanna River

Susquehanna River

Al el gheny

River

ono M

al ehahn i R ev r

Oh oi Ri v e r

Delaware

R i ver

40°

41°

42°

80°

79° 78° 77° 76°

Area containingstudy reaches

Lehigh

River

Schuyl k i l l River Raystown Lake

Jun ai at Rive r

West Branch Susq u ehanna River

Susquehanna River

Susquehanna River

Al el gheny

River

ono M

al ehahn i R ev r

Oh oi Ri v e r

Delaware

R i ver

40°

41°

42°

80°

79° 78° 77° 76°

Area containingstudy reaches

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).

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2005 2006

2007 2008
Monitoring Results and Implications, Susquehanna River 39Figure 18. Relation between 2008 streamflow and historical streamflow at selected streamgages in Pennsylvania and New Jersey.

A Delaware River at Trenton, N.J.

B Juniata River at Newport, Pa.

521

502010

500200100

1,5001,000

521

502010

300200100

C Susquehanna River at Harrisburg, Pa. 300

200100

0.5

521

502010

D Allegheny River at Natrona, Pa.

STREAMFLOW, IN THOUSANDS OF CUBIC FEET PER SECOND 0.5 0.2 0.1

521

502010

200100

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep

14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep

14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep

14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep

14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28 14 28

STREAMFLOW, IN THOUSANDS OF CUBIC FEET PER SECOND STREAMFLOW, IN THOUSANDS OF CUBIC FEET PER SECOND

STREAMFLOW, IN THOUSANDS OF CUBIC FEET PER SECOND

Period of record: Feb. 1913 to Mar. 2009 Period of record: Apr. 1899 to Mar. 2009

Period of record: Oct. 1938 to Mar. 2009 Period of record: Oct. 1890 to Mar. 2009

EXPLANATION 

Maximum daily mean flow for period of recordMedian daily mean flow for period of recordMinimum daily mean flow for period of recordDaily mean flow in 2008

Defines critical time period for recruitment and survival of young-of-the-year smallmouth bass
40 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Water-Quality Differences among 

the Susquehanna, Delaware, and 

Allegheny Rivers

In Pennsylvania, infection of YOY smallmouth bass by 

F. columnare has been documented through annual surveys by 

PFBC biologists in the mainstem of the Susquehanna River 

and major tributaries including the Juniata River and the West 

Branch Susquehanna River. Collections of fish for development of an index of biotic integrity in Pennsylvania streams 

indicate YOY smallmouth bass in smaller tributaries to the 

Susquehanna River may also be afflicted (Douglas Fischer, 

Pennsylvania Fish and Boat Commission, written commun., 

2009). At this time (2009), no incidents of bacterial infection 

have been reported in the Delaware River Basin to the east or 

the Allegheny River Basin to the west (fig. 17). The objective of this section is to compare water temperature, dissolved 

oxygen, and pH collected in the Susquehanna River at Harrisburg (station C8) with corresponding data from the Delaware 

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

at Acmetonia, Pa. (station C10). In addition, a discussion of 

the possible role of emerging contaminants (contaminants not 

commonly monitored, but recently detected in the environment) is provided.

If dissolved-oxygen concentrations and water temperatures are indicative of more stressful conditions in the Susquehanna River compared to the Delaware or Allegheny Rivers, 

this may be viewed as evidence that they play a role in predisposing YOY smallmouth bass to infection by F. columnare. 

However, there are many other pathogens (viral and bacterial) 

and water-quality stressors like pharmaceutical and pesticide 

contaminants that were not investigated in this study but may 

be larger factors in fish diseases in the Susquehanna River 

compared to the Delaware or Allegheny Rivers. In addition, 

there are differences in management of water quantity among 

the three rivers, including how stored water is released from 

reservoirs, that may influence water quality and factor into the 

incidence of infection by F. columnare.

Daily range in dissolved-oxygen concentration was 

similar in the Susquehanna River at Harrisburg (station C8) 

and the Delaware River at Trenton (station C1) (mean daily 

ranges of 2.3 and 2.4 mg/L) but appreciably lower in the 

Allegheny River at Acmetonia (station C10) (mean daily range 

of only 0.5 mg/L, table 8). This indicates the sinusoidal daily 

fluctuations in the Allegheny River were suppressed compared 

to the Susquehanna and Delaware Rivers. As a result, daily 

mean dissolved-oxygen concentrations in the Allegheny River 

were only slightly greater than in the Susquehanna River 

(average daily means were 7.9 mg/L compared to 7.6 mg/L; 

p-value = 0.0624, table 9) even though daily minimum 

dissolved-oxygen concentrations were consistently lower in 

the Susquehanna River than in the Allegheny River (fig. 19C).

Daily minimum dissolved-oxygen concentrations were 

lower than the national criterion for protecting earlylife stages 

of warm-water fish (5.0 mg/L) on 6 days during the critical 

period in the Susquehanna River at Harrisburg (station C8) 

but did not drop below this criterion in the Delaware River 

at Trenton or the Allegheny River at Acmetonia. Seven-day 

mean dissolved-oxygen concentrations did not fall below the 

national criterion at any of the three stations (fig. 20) but were 

appreciably lower in the Susquehanna River at station C8 and 

Allegheny River at station C10 (average values of 7.5 mg/L at 

station C8 and 7.9 mg/L at station C10; appendix 2) compared to the Delaware River at station C1 (average value of 

9.1 mg/L).

During the critical period, average daily mean water 

temperature in the Susquehanna River at station C8 was 

1.8°C warmer than in the Delaware River at station C1 and 

3.4°C warmer than in the Allegheny River at station C10 

(table 8). Daily minimum water temperature was similar 

(p-value = 0.0709) between stations C8 and C1 (fig. 19A) but 

the average was 2.6°C warmer at station C8 than at station 

C10 (p-value = 0.0102). These results indicate that stress 

induced by sub-optimal dissolved-oxygen conditions is likely 

to be magnified by elevated temperature in the Susquehanna 

River at station C8 compared to the Delaware River at station 

C1 or the Allegheny River at station C10.

The pH of the Susquehanna River at station C8 during 

the critical period typically was less than the Delaware River 

at station C1 (median daily median was 0.6 pH units lower) 

but greater than the Allegheny River at station C10 (median 

daily median was 0.8 pH units greater) (table 8) and was well 

within the tolerance limits for smallmouth bass (Cooper and 

Wagner, 1973). Although the daily maximum, minimum, and 

median pH values in the Susquehanna River station C8 are 

all statistically different compared to stations on the Allegheny and Delaware Rivers (p-values < 0.0001), the biological 

significance of these differences has not been tested. Other 

research indicates that sustained alkaline pH can disrupt ion 

balance and ammonia excretion in perch, but despite this stress 

these fish are not inclined to move to more neutral water (Scott 

and others, 2005). YOY smallmouth bass in the Delaware 

River were exposed to the highest pH during the critical period 

(maximum pH = 9.4; table 8) and commonly experienced pH 

that exceeded 9.0 (fig. 19E and F) yet F. columnare infections 

are prevalent in the lower pH waters of the Susquehanna River 

but have not been documented in the Delaware River. If the 

infections were brought on by stress from alkaline pH alone 

the Delaware River would be expected to have greater incidence of infection than the Susquehanna River. Other potential 

stressors such as concentration of carbon dioxide have not 

been studied but may be important.

Speculation about the role of emerging contaminants in 

aquatic systems is growing. Some emerging contaminants can 

act as endocrine disruptors (chemicals having the potential to 

affect hormonal processes, such as reproduction or immune 

responses [Glassmeyer, 2007]). This disruption can affect 

the immune system of fish, making them more susceptible 

to disease and bacterial infections (Robertson and others, 

2009). An ongoing joint effort between the USGS and PADEP 
Water-Quality Differences among the Susquehanna, Delaware, and Allegheny Rivers 41

Figure 19. Comparison of water quality in the Susquehanna River at Harrisburg, Pennsylvania, Delaware River at Trenton, New Jersey, 

and Allegheny River at Acmetonia, Pennsylvania, 2008.

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

10

12

14

16

18

20

22

24

26

28

30

32

34

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

4

6

8

10

12

14

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

6

6.5

7

7.5

8

8.5

9

9.5

10

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

10

12

14

16

18

20

22

24

26

28

30

32

34

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

4

6

8

10

12

14

2008

May

2 1 28

June

7 1 4 2 1 28

July

7 1 4 2 1 28

August

7 1 4 2 1 28

September

7 1 4 2 1 28

6

6.5

7

7.5

8

8.5

9

9.5

10

DAILY MINIMUM TEMPERATURE,

IN DEGREES CELSIUS

DAILY MAXIMUM TEMPERATURE,

IN DEGREES CELSIUS

DAILY MINIMUM DISSOLVED-OXYGEN

CONCENTRATION, IN MILLIGRAMS PER LITER

DAILY MAXIMUM DISSOLVED-OXYGEN

CONCENTRATION, IN MILLIGRAMS PER LITER

DAILY MINIMUM PH,

IN STANDARD UNITS

DAILY MAXIMUM PH,

IN STANDARD UNITS

EXPLANATION

Station C1 (Delaware River at Trenton, N.J.)

Station C8 (Susquehanna River at Harrisburg, Pa.)

Station C10 (Allegheny River at Acmetonia, Pa.)

A B

C D

E F

NATIONAL CRITERION, EARLYLIFE STAGES (U.S. Environmental Protection Agency) NATIONAL CRITERION, EARLYLIFE STAGES (U.S. Environmental Protection Agency)

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record

Gap indicates

missing record
42 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania Table 8. Summary statistics for water-quality data collected in the Delaware River at Trenton, New Jersey, Susquehanna River at Harrisburg, Pennsylvania, and the Allegheny River at Acmetonia, Pennsylvania, 2008.—Continued [C1, Delaware River at Trenton, N.J.; C8, Susquehanna River at Harrisburg, Pa.; C10, Allegheny River at Lock and Dam 3 at Acmetonia, Pa.; °C, degrees Celsius; mg/L, milligrams per liter; μS/cm, microsie- mens per centimeter; n, number of daily values; P25, 25th percentile; P75, 75th percentile] Statistic Daily minimum temperature (°C) Daily mean temperature (°C) Daily maximum temperature (°C) Daily temperature range (°C) Station Station Station Station C1 C8 C10 C1 C8 C10 C1 C8 C10 C1 C8 C10

n 87 77 92 87 77 92 87 77 92 87 77 92Minimum 12.8 11.8 12.0 13.9 12.2 12.3 14.3 12.8 12.6 .6 .6 .1P25 18.0 21.7 15.0 18.8 23.0 15.2 19.9 23.9 15.6 1.6 2.1 .7Median 23.4 25.2 23.5 24.5 26.3 23.9 25.5 27.5 24.4 2.0 2.7 1.0P75 25.5 26.4 24.9 26.7 28.0 25.4 27.9 29.6 26.4 2.5 3.2 1.5Maximum 28.1 29.2 27.1 29.2 30.3 27.7 30.5 31.7 29.5 3.4 4.1 3.3Mean 21.8 23.4 20.8 22.8 24.6 21.2 23.8 26.0 22.0 2.0 2.6 1.1Standard deviation 4.7 4.7 5.1 4.8 4.9 5.2 5.0 5.0 5.5 .7 .8 .6

Statistic

Daily minimum dissolved oxygen 

(mg/L)

Daily mean dissolved oxygen

(mg/L)

Daily maximum dissolved oxygen 

(mg/L)

Daily dissolved oxygen range

(mg/L)

Station Station Station Station

C1 C8 C10 C1 C8 C10 C1 C8 C10 C1 C8 C10

n 87 73 85 87 73 85 87 73 85 87 73 85Minimum 5.7 4.8 5.6 6.6 6.1 6.4 7.0 7.3 6.8 .5 .3 .1P25 7.4 5.9 6.6 8.9 6.9 7.0 9.9 8.2 7.3 1.3 2.0 .3Median 7.8 6.1 7.1 9.3 7.4 7.3 10.7 8.6 7.7 2.4 2.3 .4P75 8.8 6.6 9.0 9.7 8.1 9.1 11.2 9.4 9.3 3.4 2.7 .6Maximum 10.0 10.0 9.6 11.0 10.2 9.7 12.7 10.7 9.8 5.1 3.9 2.1Mean 8.0 6.5 7.6 9.2 7.6 7.9 10.4 8.8 8.1 2.4 2.3 .5Standard deviation 1.1 1.2 1.2 1.0 .9 1.1 1.3 .8 1.0 1.3 .8 .4
Water-Quality Differences among the Susquehanna, Delaware, and Allegheny Rivers 43

Table 8. Summary statistics for water-quality data collected in the Delaware River at Trenton, New Jersey, Susquehanna River at Harrisburg, Pennsylvania, and the Allegheny River at Acmetonia, Pennsylvania, 2008.—Continued[C1, Delaware River at Trenton, N.J.; C8, Susquehanna River at Harrisburg, Pa.; C10, Allegheny River at Lock and Dam 3 at Acmetonia, Pa.; °C, degrees Celsius; mg/L, milligrams per liter; μS/cm, microsiemens per centimeter; 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 pH Range

(standard units)

Station Station Station Station

C1 C8 C10 C1 C8 C10 C1 C8 C10 C1 C8 C10

n 87 76 91 87 76 91 87 76 91 87 76 91Minimum 7.1 7.3 6.6 7.2 7.5 6.7 7.2 7.6 6.7 .1 .1 .0P25 7.8 7.5 6.7 8.0 7.6 6.8 8.3 7.8 6.8 .5 .4 .1Median 8.0 7.5 6.9 8.4 7.8 7.0 8.8 8.1 7.0 .7 .6 .1P75 8.2 7.6 7.3 8.8 8.0 7.4 9.1 8.4 7.4 .8 .8 .2Maximum 8.8 8.7 7.5 9.2 8.9 7.6 9.4 9.2 7.7 1.1 1.3 .4Mean 8.0 7.6 7.0 8.4 7.9 7.1 8.7 8.2 7.1 .6 .6 .1Standard deviation .4 .2 .3 .5 .3 .3 .6 .4 .3 .3 .3 .1

Statistic

Daily minimum specific conductance 

(μS/cm)

Daily mean specific conductance

(μS/cm)

Daily maximum specific conductance

(μS/cm)

Daily specific conductance range

(μS/cm)

Station Station Station Station

C1 C8 C10 C1 C8 C10 C1 C8 C10 C1 C8 C10

n 87 77 92 87 77 92 87 77 92 87 77 92Minimum 105 142 214 110 144 220 118 146 224 2 1 2P25 198 194 241 204 199 248 209 205 255 5 7 8Median 217 273 264 222 279 271 227 285 283 7 10 11P75 234 293 296 239 298 301 245 303 306 11 15 16Maximum 254 349 361 261 352 367 266 356 375 123 47 64Mean 212 248 269 218 254 276 223 260 283 11 12 14Standard deviation 32 59 35 30 60 36 29 61 38 14 8 11
44 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Table 9. Statistical comparison of water quality in the Susquehanna River at Harrisburg, Pennsylvania, to water quality in the 

Delaware River at Trenton, New Jersey, and the Allegheny River at Acmetonia, Pennsylvania, 2008.

[°C, Celsius; μS/cm, microsiemens per centimeter; mg/L, milligrams per liter; <, less than]

Constituent

p-value1

Susquehanna River at Harrisburg

compared to

Delaware River at Trenton2

Susquehanna River at Harrisburg

compared to

Allegheny River at Acmetonia2

Minimum water temperature (°C) 0.0709 0.0102

Maximum water temperature (°C) .0104 < .0001

Water temperature range (°C) < .0001 < .0001

Mean water temperature (°C) .0276 .0001

Minimum specific conductance (μS/cm) < .0001 .0504

Maximum specific conductance (μS/cm) < .0001 .0304

Specific conductance range (μS/cm) .0493 .3196

Mean specific conductance (μS/cm) < .0001 .0408

Minimum pH (standard units) < .0001 < .0001

Maximum pH (standard units) < .0001 < .0001

pH range (standard units) .0360 < .0001

Median pH (standard units) < .0001 < .0001

Minimum dissolved oxygen (mg/L) < .0001 < .0001

Maximum dissolved oxygen (mg/L) < .0001 < .0001

Dissolved oxygen range (mg/L) .0406 < .0001

Mean dissolved oxygen (mg/L) < .0001 .0624

7-day mean minimum dissolved oxygen (mg/L) < .0001 < .0001

7-day mean dissolved oxygen (mg/L) < .0001 .0631

1

For this study, a statistically significant difference exists if the p-value is less than 0.05.

2

Results of two-sided Wilcoxon rank-sum test.
Water-Quality Differences among the Susquehanna, Delaware, and Allegheny Rivers 45

Figure 20. Seven-day mean dissolved-oxygen concentration and streamflow conditions in the Susquehanna River at Harrisburg, 

Pennsylvania, Delaware River at Trenton, New Jersey, and Allegheny River at Acmetonia, Pennsylvania, 2008. [Steamflow data are 

not available for the Allegheny River at Acmetonia, Pennsylvania. Therefore, hydrologic conditions for this station are represented by 

streamflow measured at Natrona, Pennsylvania (Station C9), which is located approximately 9.75 mi upstream.]

EXPLANATION

2008

May

21 28

June

7 14 21 28

July

7 14 21 28

August

7 14 21 28

September

7 14 21 28 4

5

6

7

8

9

10

11

0

10

20

30

40

50

60

70

80

90

100

7-DAY MEAN DISSOLVED-OXYGEN CONCENTRATION,

IN MILLIGRAMS PER LITER

STREAMFLOW, IN THOUSANDS OF CUBIC FEET PER SECOND

7-Day Mean Dissolved-Oxygen Concentration in the Delaware River at Trenton, N.J. (Station C1)

7-Day Mean Dissolved-Oxygen Concentration in the Susquehanna River at Harrisburg, Pa. (Station C8)

7-Day Mean Dissolved-Oxygen Concentration in the Allegheny River at Acmetonia, Pa. (Station C10)

Streamflow in the Delaware River at Trenton, N.J. (Station C1)

Streamflow in the Susquehanna River at Harrisburg, Pa. (Station C8)

Streamflow in the Allegheny River at Natrona, Pa. (Station C9)

NATIONAL CRITERION FOR 7-DAY MEAN DISSOLVED-OXYGEN CONCENTRATION

(U.S. Environmental Protection Agency)

Gap indicates

missing record
46 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

measured antibiotics, pharmaceutical compounds, hormones, 

and wastewater compounds at two locations in the Susquehanna River in 2007. These locations are the Susquehanna 

River at Danville, Pa., and the Susquehanna River at Wolverton, Pa. (approximately 4.7 mi upstream from the confluence 

with the West Branch Susquehanna River). These sampling 

stations were selected to be upstream and downstream of the 

municipal wastewater discharge from Danville, Pa. Similar 

sampling was conducted at limited locations in the Delaware 

River Basin and the Ohio River Basin. Coincident with the 

water-quality sampling, smallmouth bass were captured and 

examined for incidence of intersex, the presence of oocytes 

(immature ova or egg cells) within the testes of male fishes. 

The intersex condition was common in smallmouth bass from 

the Susquehanna River but not in smallmouth bass from the 

Delaware or Ohio River Basins (Blazer and others, 2009). It 

is not clear whether the incidence of intersex in smallmouth 

bass and the F. columnare infections are related. Further, it is 

not clear whether the very low concentrations (typically less 

than 1 μg/L) of emerging contaminants measured in samples 

from the Susquehanna River contribute to the prevalence of 

intersex. Additional studies would be needed to more clearly 

define any associations. The USGS, in cooperation with PFBC 

and PADEP, is conducting a pilot study in 2009 to investigate 

the issue.

Summary and Conclusions

In the summer of 2005, Pennsylvania Fish and Boat 

Commission fisheries biologists discovered an unusually 

high number of the young-of-the-year (YOY) smallmouth 

bass (Micropterus dolomieu) in the mainstem of the Susquehanna River, West Branch Susquehanna River, and Juniata 

River (affected reaches) infected by Flavobacterium columnare, a ubiquitous bacterium common in soil and water. No 

YOY smallmouth bass captured during 2005 surveys in the 

Delaware or Allegheny River Basins were infected. In the 

summer months of 2006, which had relatively high streamflows compared to 2005, no F. columnare infections were 

observed in Pennsylvania streams, but the disease returned 

to affected reaches of the Susquehanna River Basin in 2007 

when streamflow was measured at lower levels. After the 

disease and subsequent mortalities were discovered, reconnaissance efforts by Pennsylvania Fish and Boat Commission 

biologists documented concentrations of dissolved oxygen in 

the Susquehanna River that were stressful (below 5.0 mg/L, 

the national criterion for protecting earlylife stages of warmwater fish). Adequate concentrations of dissolved oxygen are 

especially important for proper development and survival of 

YOY smallmouth bass because the young bass require more 

dissolved oxygen than more mature fish. After hatching, the 

young spend the critical period (defined for this study as 

May 1 through July 31) in the same habitat where they were 

born.

In response to the YOY smallmouth bass mortalities, the 

U.S. Geological Survey, in cooperation with the Pennsylvania Fish and Boat Commission, Pennsylvania Department of 

Environmental Protection, and PPL Corporation, conducted 

a study from May through October 2008 to assess dissolved 

oxygen, temperature, pH, and specific conductance in reaches 

of the Susquehanna River and major tributaries that represent 

affected reaches within the basin. Water-quality data were collected between May and October 2008 by continuous (30-minute interval) water-quality meters (sondes). Four sondes were 

deployed as pairs to evaluate differences between mainchannel habitats and YOY smallmouth-bass microhabitats 

(habitat of YOY smallmouth bass) on the Susquehanna River 

and Juniata River. Two additional sondes were collocated with 

streamgages at Harrisburg and Newport, Pa. Historical waterquality and streamflow data at Harrisburg allowed for comparison with 2008 conditions. Discrete samples for nitrogen 

and phosphorus in water and streambed sediment were also 

collected on June 11 and 12, 2008, to determine concentrations at 25 locations in the Susquehanna River and tributaries 

between Williamsport and Highspire, Pa.

Daily minimum dissolved-oxygen concentration at 

microhabitats in the Susquehanna River at Clemson Island 

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

(station C6) generally were lower than nearby main-channel 

habitats indicating YOY smallmouth bass are exposed to more 

stressful conditions than adult fish occupying habitat outside 

of microhabitat areas. Average daily minimum dissolvedoxygen concentrations at C4 and C6 were significantly lower 

(1.1 and 0.3 mg/L, respectively) than in the corresponding 

main-channel habitat during the critical period. The lowest 

dissolved-oxygen concentrations in the microhabitats during 

the critical period were 3.3 mg/L at station C4 (June 11, 2008) 

and 4.1 mg/L at station C6 (July 22, 2008).

The 7-day mean dissolved-oxygen concentrations at all 

stations remained above the 6.0 mg/L national criterion for 

protecting earlylife stages of warm-water fish, but daily minimum dissolved-oxygen concentrations in both microhabitats 

and in the Juniata River main-channel habitat sometimes were 

lower than the national criterion (5.0 mg/L) during nighttime 

and early-morning hours (midnight to 0800). For example, 

during the critical period, daily minimum dissolved-oxygen 

concentrations in the Susquehanna River at station C4 were 

lower than 5.0 mg/L on 31 out of 92 days compared to no 

days in the main-channel habitat at station C3. In the Juniata 

River, daily minimum dissolved-oxygen concentration in the 

microhabitat at station C6 was lower than 5.0 mg/L on 20 days 

compared to only 5 days in the main channel. The maximum 

time periods that dissolved oxygen was less than 5.0 mg/L in 

microhabitats of the Susquehanna and Juniata Rivers were 8.5 

and 5.5 hours, respectively. These data support the contention that YOY smallmouth bass in the study reaches are more 

likely to experience stress from sub-optimal dissolved-oxygen 

concentrations than older fish not living in or frequenting 

microhabitat.
Summary and Conclusions 47

Microhabitats did not uniformly have warmer water 

temperatures and are, therefore, not necessarily more stressful 

than main-channel habitats solely because of water temperature. Site-specific variables like exposure to sunlight may 

have factored greatly in the measured differences between 

microhabitats in the Susquehanna and Juniata Rivers. The 

microhabitat in the Susquehanna River at station C4 had 

minimum, median, and maximum daily water temperatures 

comparable to the main channel at station C3, which received 

similar exposure to sun. Mean daily water temperatures had 

medians of 25.8°C at station C4 and 26.1°C at station C3 and 

maximum daily water temperatures had medians of 28.5°C at 

C4 compared to 28.4°C at C3. By contrast, the microhabitat in 

the Juniata River at station C6 had significantly cooler water 

temperatures compared to the main channel owing to shade 

from a canopy of trees. Daily maximum water temperature in 

the microhabitat at station C6 had a median of 26.9°C compared to 27.8°C in the main-channel habitat.

During the critical period, pH for microhabitat and mainchannel stations in the Susquehanna River at Clemson Island 

and Juniata River at Howe Township Park ranged from 7.2 

to 9.4 and had a daily change of as much as 1.6 units. YOY 

smallmouth bass are sensitive to acidic pH and experience 

appreciable declines in survival rates at pH 5.7 and below, but 

the primary concern for this study was exposure to alkaline 

(greater than 9.0) pH. For stations in microhabitats of the 

Susquehanna and Juniata Rivers, daily pH minima, maxima, 

and medians generally were up to 0.5 pH units lower than in 

the main-channel habitats. Despite significant statistical differences between pH of the microhabitats and main-channel 

habitats, the biological significance is unclear. YOY smallmouth bass rarely were exposed to pH that exceeded 9.0 during the critical period, and values this high were sustained for 

periods of less than 12 hours. It therefore seems unlikely that 

pH is a major stressor to YOY smallmouth bass in the study 

reaches, but perhaps when combined with temperatures that 

are relatively high and dissolved-oxygen concentrations that 

are below national criteria, alkaline pH and (or) large daily 

fluctuations in pH may contribute to overall stress.

Susquehanna River streamflow conditions during the 

critical period of 2008 were similar to those in 2005 and 2007 

when the disease previously occurred. As in 2005 and 2007, 

mortality of YOY smallmouth bass throughout the affected 

reaches was prevalent. Streamflow during the critical period 

of 2008 (or 2005 and 2007) was not extremely low when 

compared to historical streamflows. Instead, streamflow was 

comparable to or slightly lower than historical medians. Thus, 

the occurrence of the disease does not seem to be limited to 

exceptionally low streamflow summers. Moderate or nearnormal summertime streamflows and associated water-quality 

conditions seem to be conducive to widespread occurrence of 

F. columnare infection.

Dissolved-oxygen data indicate stressful conditions 

existed more often at stations in the Susquehanna River than in 

the Delaware or Allegheny Rivers. Daily minimum dissolvedoxygen concentrations were lower than the national criterion 

for protecting earlylife stages of warm-water fish (5.0 mg/L) 

on 6 days during the critical period in the Susquehanna River 

at Harrisburg (station C8) but did not drop below this criterion 

in the Delaware River at Trenton or the Allegheny River at 

Acmetonia. The 7-day mean dissolved-oxygen concentrations 

did not fall below the national criterion at any of the three 

stations, but the 7-day mean dissolved-oxygen concentration 

was appreciably lower in the Susquehanna River at station C8 

and in the Allegheny River at station C10 than in the Delaware River at Trenton. On average, 7-day mean dissolvedoxygen concentrations during the critical period were 7.5 

mg/L at station C8 and 7.9 mg/L at station C10 compared to 

9.1 mg/L at station C1 in the Delaware River. More stressful 

conditions (lower dissolved oxygen accompanied by higher 

water temperature) in the Susquehanna River compared to the 

Delaware or Allegheny Rivers may be viewed as evidence 

that environmental factors such as dissolved oxygen and water 

temperature play a role in predisposing YOY smallmouth bass 

to colonization by F. columnare. However, many other waterquality factors (pharmaceutical and pesticide contaminants, for 

example) and pathogens (viral and bacterial) were not investigated in this study and may contribute to fish diseases in the 

Susquehanna River more than in the Delaware or Allegheny 

Rivers.

The average daily mean water temperature in the Susquehanna River at station C8 was 1.8°C warmer than in the 

Delaware River at station C1 and 3.4°C warmer than in the 

Allegheny River at station C10. These results indicate that 

stress induced by sub-optimal dissolved-oxygen conditions is 

likely to be magnified by elevated temperature in the Susquehanna River station C8 compared to the Delaware River at 

station C1 or the Allegheny River at station C10.

Concentrations of total phosphorus and total nitrogen 

measured in water from the Susquehanna River and its tributaries were routinely within the range considered to be conducive to excessive algal growth, based on previous studies. 

The highest nutrient concentrations were measured at stations 

immediately downstream from wastewater-treatment plants. In 

general, for all nutrient species, concentrations in the Juniata 

River were higher than in the West Branch Susquehanna River 

or in the mainstem Susquehanna River. Concentrations of 

nutrients in streambed-sediment samples were variable suggesting these concentrations may have been more dependent 

on the sediment grain size rather than on the nutrient regime 

of the sampling location. As a result, the streambed-sediment 

analyses were inconclusive.

Statistical analyses using the two-sided Wilcoxon 

signed-rank test indicate minimum temperature, maximum 

temperature, temperature range, and mean temperature were 

all significantly different during the critical period in 2008 

compared to a historical dataset from 1974 to 1979. The average daily mean water temperature was 0.8°C warmer in 2008 

compared to the available historical data. Dissolved-oxygen 

concentrations were significantly lower in 2008 compared to 

the available historical data. Streamflow was not significantly 

different between the two time periods indicating that it is not 
48 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

a likely explanation for the differences in water temperature or 

dissolved oxygen.

 In summary, the data collected during this study indicate 

1) microhabitats where YOY smallmouth bass live were more 

stressful, based on measured water-quality conditions, than 

nearby main-channel habitats; 2) dissolved-oxygen concentrations and water temperatures in the Susquehanna River were 

more stressful in 2008 than in the 1970s; 3) moderate or nearnormal and lower summertime streamflows and associated 

water-quality conditions seem to be conducive to widespread 

occurrence of F. columnare infection; and 4) dissolved-oxygen 

concentrations and water temperatures during this study were 

more stressful for YOY smallmouth bass in the Susquehanna 

River than in the Delaware or Allegheny Rivers. Although the 

YOY smallmouth bass mortalities cannot be linked to any one 

water-quality factor or environmental condition on the basis of 

this study, the results from this study and ongoing investigations of other pathogens (viral and bacterial) and water-quality 

stressors (like pharmaceutical and pesticide contaminants) 

could be used as a foundation for a long-term network of data 

collection and interpretation.

Acknowledgments

The cooperation, guidance, and support of the PFBC 

are gratefully acknowledged. John Arway served as the study 

director for the PFBC during the study and contributed his 

scientific expertise, ideas, and coordination skills to help 

make the project successful. John Frederick of the PFBC 

contributed his time and skill as a boat operator to the project. 

Robert Lorantas, Kris Kuhn, Leroy Young, and Karl Stephan 

of the PFBC are also acknowledged for their contributions 

to this study. Numerous individuals in the PADEP are recognized for their contributions, including: Richard Shertzer, 

Robert Schott, Joseph Hepp, Martin Friday, Kristen Bardell, 

Jay Gerber, and Michael Lookenbill. Staff from the SRBC, 

including David Heicher, Jennifer Hoffman, Andrew Gavin, 

and Susan Obleski, also are recognized for their contributions 

to this study. Linda Zarr, Joanne Irvin, and David Smith of 

the USGS assisted with the data compilation, data management, and graphics-presentation tasks. Mark Beaver (USGS) 

offered insight on sonde placement and deployment. David 

O’Brien (USGS) provided boat operation support. Kim Otto 

of the USGS provided valuable support and guidance in report 

preparation. USGS reviewers John Clune, Douglas Chambers, Robert Hainly, and Kevin Breen along with John Arway 

of PFBC, Joseph Hepp of PADEP, and Nancy Evans of PPL 

Corporation offered valuable suggestions for improving the 

report. Finally, we acknowledge Anthony Trease of the USGS 

for being the primary data-collection technician and Michael 

Burton of the Pennsylvania Bass Federation for volunteering 

his time, equipment, and boating expertise. To all who helped 

in any way, the authors thank you.

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Appendix 1. Quality Control 53

Appendix 1. Quality Control

Summary of results for quality-control samples and results for nutrients in water and streambed sediment, 2008.

Medium Type of

quality-control sample

Number of

samples submitted

Number of constituents

exceeding

data-quality objective

Water Field blank sample 6 0 out of 42 analyzed

Duplicate sample 4 1 out of 28 analyzed

Reference water sample 1 1 out of 7 analyzed

Bottom sediment Duplicate sample 5 2 out of 15 analyzed
54 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania

Appendix 2. Selected Statistics for Dissolved-Oxygen Concentrations

Values for 7-day mean minimum and 7-day mean dissolved-oxygen concentrations at selected stations in Pennsylvania and New 

Jersey, May 1 through July 31, 2008.

[C1, Delaware River at Trenton, N.J.; C2, Susquehanna River at Shady Nook Boat Launch; C3, Susquehanna River below Clemson Island (Main Channel); 

C4, Susquehanna River at Clemson Island (Microhabitat); C5, Juniata River at Newport, Pa.; C6, Juniata River near Howe Township Park (Microhabitat); C7, 

Juniata River near Howe Township Park (Main Channel); C8, Susquehanna River at Harrisburg, Pa.; C10, Allegheny River at Lock and Dam 3 at Acmetonia, 

Pa.; mg/L, milligrams per liter; n, number of 7-day mean minimum or 7-day mean values; P25, 25th percentile; P75, 75th percentile; —, not computed]

Statistic

7-Day mean minimum dissolved oxygen

(mg/L)

Station

C1 C2 C3 C4 C5 C6 C7 C8 C10

n 69 — 70 70 56 53 51 67 73

Minimum 6.0 — 5.4 3.8 4.8 4.6 5.1 5.0 6.0

P25 7.4 — 6.0 4.9 5.8 5.2 5.7 5.9 6.5

Median 7.8 — 6.3 5.3 6.0 5.4 6.0 6.0 7.0

P75 8.6 — 6.9 5.6 6.4 5.6 6.2 6.3 9.0

Maximum 9.7 — 10.0 9.7 9.7 6.6 7.0 9.6 9.4

Mean 7.9 — 6.7 5.6 6.3 5.4 6.0 6.3 7.6

Standard deviation 1.0 — 1.2 1.3 1.0 .5 .5 1.0 1.2

Statistic

7-Day mean dissolved oxygen

(mg/L)

Station

C1 C2 C3 C4 C5 C6 C7 C8 C10

n 69 — 70 70 56 53 51 67 73

Minimum 6.8 — 7.8 6.2 7.8 6.9 7.8 6.6 6.6

P25 9.0 — 8.1 7.0 8.1 7.4 8.3 7.1 7.0

Median 9.3 — 8.2 7.3 8.3 7.6 8.6 7.2 7.3

P75 9.7 — 8.7 7.6 8.9 7.8 8.8 7.8 9.2

Maximum 10.7 — 10.5 10.1 10.0 8.8 9.8 9.8 9.5

Mean 9.1 — 8.5 7.5 8.5 7.6 8.6 7.5 7.9

Standard deviation .9 — .7 .9 .6 .4 .5 .7 1.1
Appendix 3. Nutrient Concentrations in Water and Streambed Sediment 55

Appendix 3. Nutrient Concentrations in Water and Streambed Sediment

Water features from U.S. Geological Survey National Hydrography Dataset (NHD)

EXPLANATION

We s t

Br a n c h Su s q u ehanna River

Juniata

R i v e r

Su s q u

e hanna

River

Williamsport

Danville Lewisburg

Lewistown

Port Royal

Millerstown

Newport

Thompsontown

Halifax

Harrisburg

Highspire

Base from U.S. Geological Survey 1:24,000 digital data

0

0 15 MILES

15 KILOMETERS

76°33' 76°36'

40°09'30''

40°15'30''

Major river

County boundary

Sampling station and identifier

Selected municipality

N1

Pennsylvania

Area containing study reaches

N1

N2 N3

N4

N5

N6

N7

N8

N9

N10 

N11

N12

N13

N14

N15

N16 N17

N18

N19

N20

N21

N22

C3

C8

C5

Bu ff a l o Cr e e k

Conodoguinet

Cre e k

Figure 3-1. Locations of stations selected for the nutrient synoptic survey in the Susquehanna River Basin, 

Pennsylvania, June 11 and 12, 2008.
56 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania Table 3-1. Concentrations of nitrogen and phosphorus species from water and streambed-sediment samples collected from the West Branch Susquehanna River, June 11 and 12, 2008. [mg/L, milligrams per liter; g/kg, grams per kilogram; <, less than] Station name Map identi- fier Water Streambed sediment Ammonia plus organic nitrogen as nitrogen (mg/L) Ammonia as nitrogen (mg/L) Nitrate as nitrogen (mg/L) Nitrite as nitrogen (mg/L) Total nitrogen (mg/L) Ortho- phosphate as phosphate (mg/L) Phosphorus as phosphorus (mg/L) Ammonia plus organic nitrogen as nitrogen (g/kg) Total ammonia as nitrogen (g/kg) Total phosphorus as phosphorus (g/kg) West Branch Susquehanna River at Duboistown, Pa. (right bank) N2 < 1 0.03 0.45 < 0.01 0.75 < 0.01 0.034 1.161 0.01 0.5 Duboistown, Pa. (left bank) N2 < 1 < .02 .41 < .01 .7 < .01 .011 1.798 .02 .54 Muncy, Pa. (right bank) N3 < 1 < .05 .59 < .01 .78 < .01 .014 .606 .01 .25 Muncy, Pa. (left bank) N3 < 1 < .05 .75 < .01 .99 < .01 .018 .302 .01 .1 Montgomery, Pa. (right bank) N4 < 1 .02 .51 < .01 .72 < .01 .011 .28 .01 .2 Montgomery, Pa. (left bank) N4 < 1 .02 .5 < .01 .71 < .01 .013 1.207 .01 .4 Allenwood, Pa. (right bank) N5 < 1 < .05 .56 .01 .81 < .01 .015 .509 10 .24 Allenwood, Pa. (left bank) N5 < 1 < .05 .5 < .01 .74 < .01 .016 .767 .01 .33 Watsontown, Pa. (right bank) N6 < 1 < .05 .56 < .01 .8 < .01 .021 .996 .01 .34 Watsontown, Pa. (left bank) N6 < 1 < .05 .53 < .01 .77 < .01 .015 .231 0 .15 Lewisburg, Pa. (right bank) N7 < 1 .03 1.54 .02 1.85 .035 .061 .665 .01 .24 Lewisburg, Pa. (left bank) N7 < 1 .02 .74 < .01 .98 < .01 .016 .364 .01 .21
Appendix 2. Selected Statistics for Dissolved-Oxygen Concentrations 57

Table 3-2. Concentrations of nitrogen and phosphorus species from water and streambed-sediment samples collected from the Juniata River, June 11 and 12, 2008.[mg/L, milligrams per liter; g/kg, grams per kilogram; <, less than]

Station name

Map 

identifier

Water Streambed sediment

Ammonia 

plus

organic 

nitrogen

as nitrogen 

(mg/L)

Ammonia 

as nitrogen 

(mg/L)

Nitrate

as nitrogen 

(mg/L)

Nitrite

as nitrogen 

(mg/L)

Total

nitrogen 

(mg/L)

Orthophosphate

as

phosphate 

(mg/L)

Phosphorus 

as

phosphorus 

(mg/L)

Ammonia

plus

organic 

nitrogen

as nitrogen 

(g/kg)

Total

ammonia

as nitrogen 

(g/kg)

Total

phosphorus 

as

phosphorus 

(g/kg)

Juniata River at

Lewistown, Pa. (right bank) N14 < 1 < 0.1 1.23 < 0.04 1.56 0.022 0.037 1.583 0.02 0.4Lewistown, Pa. (left bank) N14 < 1 .11 1.22 < .04 1.59 .026 .044 1.983 .04 .91Mifflintown, Pa. (right bank) N15 < 1 < .1 1.42 < .04 1.72 .023 .043 .43 .01 .35Mifflintown, Pa. (left bank) N15 < 1 .11 1.41 < .04 1.72 .027 .044 2.639 .05 .83Port Royal, Pa. (right bank) N16 < 1 < .05 1.25 .02 1.7 .019 .042 2.747 .05 .95Port Royal, Pa. (left bank) N16 < 1 < .05 1.32 .02 1.8 .019 .048 2.294 .01 .26Thompsontown, Pa. (right bank) N17 < 1 .05 1.19 .01 1.67 .017 .04 .606 .01 .26Thompsontown, Pa. (left bank) N17 < 1 .05 1.32 .02 1.79 .017 .041 .844 .01 .28Millerstown, Pa. (right bank) N18 < 1 < .05 1.15 .01 1.6 .017 .03 2.14 .03 .6Millerstown, Pa. (left bank) N18 < 1 < .05 1.38 .02 1.84 .021 .043 1.491 .02 .47Newport, Pa. (right bank) C5 < 1 < .05 1.12 .01 1.54 .014 .039 1.043 .03 .25Newport, Pa. (left bank) C5 < 1 < .05 1.28 .02 1.78 .02 .042 1.69 .04 .54Amity Hall, Pa. (right bank) N19 < 1 < .05 1.06 .02 1.46 .013 .033 3.63 .08 .99Amity Hall, Pa. (left bank) N19 < 1 < .05 1.2 .02 1.62 .017 .041 2.676 .06 .69
58 Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania Table 3-3. Concentrations of nitrogen and phosphorus species from water and streambed-sediment samples collected from the mainstem Susquehanna River, June 11 and 12, 2008.—Continued [mg/L, milligrams per liter; g/kg, grams per kilogram; <, less than; na, no sample collected] Station name Map identi- fier Water Streambed sediment Ammonia plus organic nitrogen as nitrogen (mg/L) Ammonia as nitrogen (mg/L) Nitrate as nitrogen (mg/L) Nitrite as nitrogen (mg/L) Total nitrogen (mg/L) Ortho- phosphate as phosphate (mg/L) Phosphorus as phosphorus (mg/L) Ammonia plus organic nitrogen as nitrogen (g/kg) Total ammonia as nitrogen (g/kg) Total phosphorus as phosphorus (g/kg) Right bank—Susquehanna River at Danville, Pa. N1 < 1 0.02 0.29 < 0.04 0.84 < 0.01 0.05 1.101 0.02 0.36 at Sunbury, Pa. N8 < 1 < .05 .18 < .01 .78 < .01 .018 1.702 .01 .52 near Fishers Island at Selinsgrove, Pa. N9 < 1 < .05 .48 < .01 .7 < .01 .017 1.114 .01 .44 at Hoover Island N10 < 1 < .05 .48 < .01 .79 < .01 .017 1.122 .01 .37 at Dalmatia, Pa. N11 < 1 < .1 .92 < .04 1.18 .013 .039 2.02 .02 .46 at Liverpool, Pa. N12 < 1 < .1 .72 < .04 .99 < .01 .024 1.027 .01 .33 at Montgomery Ferry, Pa. N13 < 1 < .1 .6 < .04 .88 < .01 .02 1.271 .02 .29 at Clemson Island C4 < 1 < .02 .65 < .04 .88 < .01 .024 1.244 .01 .27 near Duncannon, Pa. N20 < 1 < .1 .6 < .04 .86 < .01 .019 1.543 .01 .28 at Marysville, Pa. N21 < 1 < .1 .97 < .04 1.29 < .01 .027 2.964 .07 .84 at Harrisburg, Pa. C8 < 1 < .1 3.54 < .04 3.77 .016 .03 3.004 .05 1.04 at Highspire, Pa. N22 < 1 .06 .27 .01 .91 < .01 .041 1.733 .02 .56
Appendix 2. Selected Statistics for Dissolved-Oxygen Concentrations 59

Table 3-3. Concentrations of nitrogen and phosphorus species from water and streambed-sediment samples collected from the mainstem Susquehanna River,June 11 and 12, 2008.—Continued[mg/L, milligrams per liter; g/kg, grams per kilogram; <, less than; na, no sample collected]

Station name

Map 

identifier

Water Streambed sediment

Ammonia 

plus

organic 

nitrogen

as nitrogen 

(mg/L)

Ammonia 

as nitrogen 

(mg/L)

Nitrate

as nitrogen 

(mg/L)

Nitrite

as nitrogen 

(mg/L)

Total

nitrogen 

(mg/L)

Orthophosphate

as

phosphate 

(mg/L)

Phosphorus 

as

phosphorus 

(mg/L)

Ammonia

plus

organic 

nitrogen

as nitrogen 

(g/kg)

Total

ammonia

as nitrogen 

(g/kg)

Total

phosphorus 

as

phosphorus 

(g/kg)

Left bank—Susquehanna River

at Danville, Pa. N1 < 1 < 0.02 0.37 < 0.04 0.9 < 0.01 0.037 0.878 0.02 0.35at Sunbury, Pa. N8 < 1 < .05 .18 < .01 .78 < .01 .033 2.223 .01 .55near Fishers Island at Selinsgrove, Pa. N9 < 1 < .1 .29 < .04 .76 < .01 .025 1.201 .01 .53at Hoover Island N10 < 1 < .05 .31 < .01 .82 < .01 .035 1.862 .02 .69at Dalmatia, Pa. N11 < 1 < .05 .42 < .01 .88 < .01 .029 3.955 .04 .94at Liverpool, Pa. N12 < 1 < .05 .5 < .01 .98 < .01 .028 3.16 .04 1.43at Montgomery Ferry, Pa. N13 < 1 < .05 .66 < .01 1.14 < .01 .051 .413 .01 .17at Clemson Island C4 < 1 < .05 .45 < .01 1.02 < .01 .038 2.312 .04 .65near Duncannon, Pa. N20 < 1 .03 .55 < .01 1.01 < .01 .04 2.134 .03 .73at Marysville, Pa. N21 < 1 .03 .23 < .01 .72 < .01 .027 1.184 .03 .37at Harrisburg, Pa. C8 < 1 .04 .21 < .01 .74 < .01 .032 na na naat Highspire, Pa. N22 < 1 .1 2.08 < .04 2.37 .028 .047 2.473 .04 .73

Chaplin and others—Water-Quality Monitoring in Response to Young-of-the-Year Smallmouth Bass Mortality, Pennsylvania—OFR 2009-1216