U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2007–5229

Prepared in cooperation with the Indiana Department of Environmental Management, 

Division of Water, Assessment Branch

Relations of Principal Components Analysis Site Scores to 

Algal-Biomass, Habitat, Basin-Characteristics, Nutrient, and 

Biological-Community Data in the Whitewater River and 

East Fork White River Basins, Indiana, 2002

Relations of Principal Components 

Analysis Site Scores to Algal-Biomass, 

Habitat, Basin-Characteristics, Nutrient, 

and Biological-Community Data in the 

Whitewater River and East Fork White 

River Basin, Indiana, 2002

By Brian J. Caskey, Jeffrey W. Frey, and B. Scott Lowe

Prepared in cooperation with the Indiana Department of Environmental 

Management, Division of Water, Assessment Branch

Scientific Investigations Report 2007–5229

U.S. Department of the Interior

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

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2007

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

reproduce any copyrighted materials contained within this report.

Suggested citation:

Caskey, B.J., Frey, J.W., and Lowe, B. S., 2007, Relations of Principal Component Analysis site scores algal-biomass, 

habitat, basin-characteristics, nutrient, and biological community data in the Whitewater River and East Fork White 

River Basin, Indiana, 2002: U.S. Geological Survey Scientific Investigations Report 2007–5229, 31 p.
iii

Contents

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

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

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

Description of the Whitewater River Basin......................................................................................4

Description of the East Fork White River Basin...............................................................................4

Study Methods ...............................................................................................................................................4

Site Selection and Sampling Strategies ..........................................................................................4

Algal-Biomass, Habitat, Nutrient, and Biological-Community Data-Collection and 

Processing Methods ..............................................................................................................9

Data Analysis.......................................................................................................................................10

Basin-Characteristics Data ..........................................................................................................10

Nutrient Data...................................................................................................................................10

Principal Components Analysis ...................................................................................................10

Comparison With U.S. Environmental Protection Agency Data ............................................11

Relations of the Principal Components Analysis Site Scores to Algal-Biomass, Habitat, 

Basin-Characteristics, Nutrient, and Biological-Community Data ........................................11

Drainage Area and Land-Use Analysis....................................................................................................14

Comparison of the Data to Ecoregion Nutrient Criteria ........................................................................15

Conclusions...................................................................................................................................................26

Acknowledgments.......................................................................................................................................26

Reference......................................................................................................................................................27

Appendix 1.....................................................................................................................................................30

Figures

1. Map showing location of the 76 algal-biomass sampling sites in the 

Whitewater River and East Fork White River Basins, Indiana, May through 

September, 2002............................................................................................................................3

 2. Graphs showing the percentages of drainage area and agricultural, forest, 

and urban land use in the Whitewater River and East Fork White River Basins, 

Indiana, 2002................................................................................................................................14

Tables

1. Location and basin characteristics of the 76 algal-biomass sampling sites in the 

Whitewater River and East Fork White River Basins, Indiana, May through 

September, 2002............................................................................................................................5

2. Significant Spearman’s rho relations of the yearly periphyton Principal Components 

Analysis axis 1 site scores (PC1) to algal-biomass, habitat, basin-characteristics, 

and nutrient parameters and fish- and invertebrate-community attributes and metric 

scores, 2002. ................................................................................................................................12
iv

3. Significant Spearman’s rho relations of the yearly seston Principal Components 

Analysis axis 1 site scores (PC1) to algal-biomass, habitat, basin-characteristics, 

and nutrient parameters and fish- and invertebrate-community attributes and metric 

scores, 2002. .................................................................................................................................13

4. Basin characteristics of the 76 algal-biomass sampling sites in the Whitewater 

River and East Fork White River Basins, Indiana, May through September 2002. ..........16

5. Total Kjeldahl nitrogen as N values collected in 2002 from the Indiana 

Department of Environmental Management/U.S. Geological Survey study 

and the published U.S. Environmental Protection Agency values for Aggregate 

Nutrient Ecoregions VI and IX and Level III Ecoregions 55 and 71. ...................................20

6. Nitrite plus nitrate as N values collected in 2002 from the Indiana Department of 

Environmental Management/U.S. Geological Survey study and the published 

U.S. Environmental Protection Agency values for Aggregate Nutrient Ecoregions 

VI and IX and Level III Ecoregions 55 and 71. ........................................................................21

7. Total nitrogen as N values collected in 2002 from the Indiana Department of 

Environmental Management/U.S. Geological Survey study and the published 

U.S. Environmental Protection Agency values for Aggregate Nutrient Ecoregions 

VI and IX and Level III Ecoregions 55 and 71. ........................................................................22

8. Total phosphorus as P values collected in 2002 from the Indiana Department of 

Environmental Management/U.S. Geological Survey study and the published 

U.S. Environmental Protection Agency values for Aggregate Nutrient Ecoregions 

VI and IX and Level III Ecoregions 55 and 71. ........................................................................23

9. Mean periphyton chlorophyll a values collected in 2002 from the Indiana 

Department of Environmental Management/U.S. Geological Survey study and the 

published U.S. Environmental Protection Agency values for Aggregate Nutrient 

Ecoregions VI and IX and Level III Ecoregions 55 and 71....................................................24

10. Mean seston chlorophyll a values collected in 2002 from the Indiana Department 

of Environmental Management/U.S. Geological Survey study and the published 

U.S. Environmental Protection Agency values for Aggregate Nutrient Ecoregions 

VI and IX and Level III Ecoregions 55 and 71. ........................................................................25
v

Multiply By To obtain

centimeter (cm) 0.3937 inch (in.)

square kilometer (km2) 0.3861 square mile (mi2)

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

liter (L) 0.2642 gallon (gal)

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

°F=(1.8×°C)+32

Horizontal coordinate information used in the map is referenced to the North American Datum 

of 1927 (NAD 27). Sampling-site coordinate information used a Global Positioning System (GPS) 

referenced to North American Datum of 1983 (NAD 83), which then was converted to NAD 27.

Concentrations of chemical and algal-biomass constituents in water are given either in 

milligrams per liter (mg/L) or micrograms per liter (μg/L). Concentrations of periphyton algal 

biomass are given in milligrams per meter squared (mg/m2).

Conversion Factors and Datum
vi

Abbreviations 

Abbreviations and acronyms used in this report:

PC1 Principal components analysis first axis site score

EPT Ephemeroptera, Plecoptera, and Trichoptera

USEPA U.S. Environmental Protection Agency

N nitrogen

P phosphorus

CWA Clean Water Act

IBI Index of Biotic Integrity

TN total nitrogen

TP total phosphorus

CHLa chlorophyll a

TKN total Kjeldahl nitrogen

IDEM Indiana Department of Environmental Management

USGS U.S. Geological Survey

WMP Watershed Monitoring Program

PCA Principal components analysis

AFDM ash-free dry mass

POC particulate organic carbon

IN Indiana

NAWQA National Water-Quality Assessment Program

NWQL National Water Quality Laboratory

QHEI Qualitative Habitat Evaluation Index

NLCD National Land Cover Dataset

r

s

 Spearman’s rho statistic
Relations of Principal Components Analysis Site Scores 

to Algal-Biomass, Habitat, Basin-Characteristics, Nutrient, 

and Biological-Community Data in the Whitewater River 

and East Fork White River Basins, Indiana, 2002

By Brian J. Caskey, Jeffrey W. Frey and B. Scott Lowe

To understand how the choice of sampling sites might 

have affected the results, an analysis of the drainage area 

and land use was done. The sites selected in the Whitewater 

River Basin were generally small drainage basins; compared 

to Whitewater River Basin sites, the sites selected in the East 

Fork White River Basin were generally larger drainage basins. 

Although both basins were dominated by agricultural land use 

the Whitewater River Basin sites had more land in agriculture 

than the East Fork White River Basin sites.

The values for nutrients (nitrate, total Kjeldahl nitrogen, 

total nitrogen, and total phosphorus) and chlorophyll a (periphyton and seston) were compared to published U.S. Environmental Protection Agency (USEPA) values for Aggregate 

Nutrient Ecoregions VI and IX and USEPA Level III Ecoregions 55 and 71. Several nutrient values were greater than 

the 25th percentile of published USEPA values. Chlorophyll a

(periphyton and seston) values were either greater than the 

25th percentile of published USEPA values or they extended 

data ranges in the Aggregate Nutrient and Level III Ecoregions. If the values for the 25th percentile as proposes by the 

USEPA were adopted as nutrient water-quality criteria, many 

samples in the Whitewater River and East Fork White River 

Basins would have exceeded the criteria.

Introduction

Excessive inputs of nutrients into streams have humanhealth, economic, and ecological consequences. Excess 

amounts of nutrients—nitrogen (N) and phosphorus (P)—have 

been shown to be a source of eutrophication in aquatic ecosystems, which sometimes has been linked to fish kills, shifts in 

species composition, taste and odor in drinking-water supplies, and blooms of harmful algae in freshwater and estuaries 

(Munn and Hamilton, 2003; U.S. Environmental Protection 

Agency, 2000 a,b).

The Clean Water Act (CWA) established a national goal 

of achieving water quality that provides for the protection and 

Abstract

Data were gathered from May through September 2002 

at 76 randomly selected sites in the Whitewater River and East 

Fork White River Basins, Indiana, for algal biomass, habitat, 

nutrients, and biological communities (fish and invertebrates). 

Basin characteristics (land use and drainage area) and biological-community attributes and metric scores were determined 

for the basin of each sampling site. Yearly Principal Components Analysis site scores were calculated for algal biomass 

(periphyton and seston). The yearly Principal Components 

Analysis site scores for the first axis (PC1) were related using 

Spearman’s rho to the seasonal algal-biomass, basin-characteristics, habitat, seasonal nutrient, and biological-community 

attribute and metric score data. 

The periphyton PC1 site score was not significantly 

related to the nine habitat or 12 nutrient variables examined. 

One land-use variable, drainage area, was negatively related to 

the periphyton PC1. Of the 43 fish-community attributes and 

metrics examined, the periphyton PC1 was negatively related 

to one attribute (large-river percent) and one metric score (carnivore percent metric score). It was positively related to three 

fish-community attributes (headwater percent, pioneer percent, 

and simple lithophil percent). The periphyton PC1 was not 

statistically related to any of the 21 invertebrate-community 

attributes or metric scores examined.

Of the 12 nutrient variables examined two were negatively related to the seston PC1 site score in two seasons: total 

Kjeldahl nitrogen (July and September), and TP (May and 

September). There were no statistically significant relations 

between the seston PC1 and the five basin-characteristics or 

nine habitat variables examined. Of the 43 fish-community 

attributes and metrics examined, the seston PC1 was positively 

related to one attribute (headwater percent) and negatively 

related to one metric score (large-river percent metric score) . 

Of the 21 invertebrate-community attributes and metrics examined, the seston PC1 was negatively related to one metric score 

(number of individuals metric score).
2 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002

propagation of aquatic organisms and wildlife, and recreation 

in and on the water. In 1996, the U.S. Environmental Protection Agency’s (USEPA) National Water Quality Inventory 

identified excess amounts of nutrients as the second leading 

cause of impairment in rivers and streams across the United 

States (the first cause was siltation) (U.S. Environmental 

Protection Agency, 1997a). The excess amounts of nutrients 

that have been documented in many rivers and streams have 

resulted in streams that do not meet the goal of the CWA in 

Indiana and the nation.

USEPA drinking-water criteria (maximum contaminant 

levels) are 10 mg/L for nitrate as N and 1 mg/L nitrite as N 

(U.S. Environmental Protection Agency, 2005). In addition, 

aquatic-life criteria established to protect aquatic organisms 

have been set for ammonia as N (the ammonia as N aquaticlife criteria varies with pH, temperature, and life-stage) 

(U.S. Environmental Protection Agency, 2005). These criteria 

do not address the effects on the biological communities 

resulting from increased nutrients in rivers and streams. Typically, nutrient concentrations must be extremely high to be 

toxic to biological communities; such concentrations rarely 

are found in the environment (Ohio Environmental Protection 

Agency, 1999). For example, nitrate as N concentrations below 

90 mg/L would not have direct effects on warmwater fish. 

Exceptions are concentrations of ammonia after accidental discharges from wastewater-treatment facilities, combined-sewer 

overflows, or confined-animal feedlots (Ohio Environmental 

Protection Agency, 1999). Previous analysis of the effects of 

nutrients on biological communities in Ohio found few relations between nutrients and fish and invertebrate-community 

data (Miltner and Rankin, 1998). Only total phosphorus was 

significantly correlated with any of the fish or invertebrate 

attributes or metrics (fish Index of Biotic Integrity [IBI] scores 

in headwater streams). 

Many streams have been placed by the USEPA on the 

CWA Section 303(d) list of impaired water bodies because of 

excess amounts of nutrients. In 2000, the USEPA proposed 

nutrient water-quality criteria for causal variables—total 

nitrogen (TN) and total phosphorus (TP)—and for response 

variables—periphyton and seston chlorophyll a (CHLa) and 

turbidity. Criteria also have been proposed for nitrate and total 

Kjeldahl nitrogen (TKN) because TN is the sum of nitrate 

and TKN. These proposed nutrient water-quality criteria are 

based on Aggregate Nutrient Ecoregions, areas with similar 

geographic features (topography, soils, geology, land use, and 

biogeography) (U.S. Environmental Protection Agency, 2000 

a,b). USEPA reviewed selected data and set the proposed 

nutrient water-quality criteria for nitrate, TKN, TN, TP, CHLa 

(periphyton and seston), and turbidity at the 25th-percentile 

value of all data for each variable.

USEPA mandated that by 2004 states either accept the 

proposed nutrient water-quality criteria or provide their own 

set of criteria that are more appropriate to the waters within 

each state (U.S. Environmental Protection Agency, 2000 

a,b). An extension was given to Indiana and other states that 

adopted plans describing the data needs and the process to 

develop nutrient water-quality criteria. Beginning in 2001, the 

Indiana Department of Environmental Management (IDEM) 

and the U.S. Geological Survey (USGS) are cooperating on 

several studies that will assist the State of Indiana in developing nutrient water-quality criteria as mandated by the USEPA. 

The multivariate approach used in this report should allow the 

results to be used in similar ecoregions in Illinois and Ohio.

Purpose and Scope

Data in this report were collected as part of an ongoing 

cooperative effort between IDEM and the USGS in which 

similar studies have been conducted as part of the IDEM 

probabilistic Watershed Monitoring Program (WMP) in the 

West Fork White River Basin (2001), Upper Wabash River 

Basin (2003), Lower Wabash River and Kankakee River 

Basins (2004), and Ohio River and Great Lakes Basins (2005) 

(Indiana Department of Environmental Management, 2001). In 

all of these yearly WMP studies, IDEM collected habitat and 

biological-community data and the nutrient data from 2001 

through 2003; to augment the IDEM WMP studies and better 

understand nutrient enrichment in streams, the USGS collected 

algal biomass during all years of the study and also collected 

the nutrient data in 2004 and 2005. The long-term goal of 

these studies is to provide data and analysis to aid IDEM in the 

development of nutrient water-quality criteria. An objective of 

this report was to develop a preliminary understanding of how 

algal biomass relates to biological community and environmental variables in the Whitewater River and East Fork White 

River Basins in 2002. In this report, the environmental variables included nutrients, habitat, and basin characteristics. An 

additional purpose of this report was to compile a list of the 

most statistically significant relations between algal biomass, 

nutrients, and biological metrics that may be helpful in future 

investigations. 

Two approaches were used for the preliminary analysis 

of the data sets. The first approach included ordination and 

regression analyses of the algal biomass, nutrient, and environmental data. The second approach compared the CHLa

and nutrient values collected by IDEM and USGS personnel 

to USEPA published values. The purpose of this preliminary 

analysis was to investigate all potential relations and identify 

those relations that were the strongest and warrant further 

investigation. 

This report discusses the relations of yearly Principal 

Components Analysis (PCA) site axis scores, which represent algal biomass (periphyton and seston) to habitat, basincharacteristics, nutrient, and biological-community (fish 

and invertebrates) attributes and metric scores (appendix 1; 

Dufour, 2002). Data were collected at 76 randomly selected 

sites in 2002; 38 sites in the Whitewater River Basin and 38 

sites in the East Fork White River Basin in 2002 (fig. 1). A 

discussion of the basin characteristics of the 76 sites describes 

how drainage area and land use affect the analysis. This report 

also compares nutrient values (nitrite plus nitrate as N, TKN 
Introduction 3

85°

Whit ewater R

East Fo rk

Wh itewater R

Whitewater R INDIANA

OHIO

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Columbus

East

Sugar Creek

Graham Creek

Clifty Creek

White

River Fork

Richmond

Greensburg

Seymour

West Fork

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Base from U. S. Geological Survey digital data,

scales ranging from 1:24,000 to 1:100,000, 1999

Albers Equal Area projection

Standard parallels 29° 30' and 45° 30', central meridian -86°

North American Datum, 1927

INDIANA OHIO

EAST FORK WHITE RIVER 

DRAINAGE BASIN

WHITEWATER RIVER

DRAINAGE BASIN

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 EXPLANATION

U.S. ENVIRONMENTAL PROTECTION AGENCY AGGREGATE NUTRIENT ECOREGION VI,

 LEVEL III ECOREGION 55

U.S. ENVIRONMENTAL PROTECTION AGENCY AGGREGATE NUTRIENT ECOREGION IX,

 LEVEL III ECOREGION 71

U.S. ENVIRONMENTAL PROTECTION AGENCY AGGREGATE NUTRIENT ECOREGION IX,

 LEVEL III ECOREGION 72

MAJOR STREAM

DRAINAGE-BASIN BOUNDARY

WHITEWATER RIVER SAMPLING SITES WITH SITE IDENTIFIER

EAST FORK WHITE RIVER SAMPLING SITES WITH SITE IDENTIFIER

U.S. GEOLOGICAL SURVEY STREAMFLOW-GAGING STATION

523

412

U

U

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WHITEWATER RIVER AT BROOKVILLE, IN

WHITE RIVER AT SHOALS, IN

Figure 1. Map showing location of the 76 algal-biomass sampling sites in the Whitewater River and East Fork White River Basins, 

Indiana, May through September, 2002.
4 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002

as N, TN as N, TP as P) and CHLa (periphyton and seston) 

collected by IDEM and USGS for the Whitewater River and 

East Fork White River Basins to values published by the 

USEPA for Aggregate Nutrient Ecoregion VI—Corn Belt and 

Northern Great Plains, for Aggregate Nutrient Ecoregion IX—

Southeastern Temperate Forested Plains and Hills, for Level 

III Ecoregion 55—Eastern Corn Belt Plains, and for Level III 

Ecoregion 71—Interior Plateau. Aggregate Nutrient Ecoregions consist of one or more Level III Ecoregions 

(U.S. Environmental Protection Agency, 2000 a,b).

In the text, the Aggregate Nutrient Ecoregions are 

referred to as Ecoregion VI or IX; Level III Ecoregions are 

referred to as Ecoregion 55 or 71. The nutrients are described 

as concentrations of nitrate, TKN, TN, and TP. For this report 

periphyton CHLa, ash-free dry mass (AFDM), seston CHLa, 

and particulate organic carbon (POC) are measures of algal 

biomass.

Description of the Whitewater River Basin

The Whitewater River Basin (fig. 1) drains more than 

3,170 km2 of southeastern Indiana and southwestern Ohio 

before draining into the Ohio River (Debrewer and others, 

2000). The annual mean streamflow in the 2002 water year 

at the USGS streamflow-gaging station, Whitewater River at 

Brookville, IN (03276500) (fig. 1), was 66.6 m3/s (Stewart and 

others, 2003). Streamflow in the 2002 water year was above 

average; the annual mean long-term streamflow (1916–2002) 

was 37.2 m3/s at Brookville (Stewart and others, 2003). 

The climate in the Whitewater River Basin is characterized as temperate continental with warm, occasionally hot 

summers and cold winters. The mean annual temperature 

within the Whitewater River Basin is 10.6°C, and average 

monthly temperatures range from -3.3°C in January to 22.8°C 

in July (Indiana Department of Natural Resources, 1988). 

Average annual precipitation is about 101.6 cm; however, 

annual totals range from 73.7 cm in very dry years to 127 cm 

in very wet years (Indiana Department of Natural Resources, 

1988). 

The dominant land use is row-crop agriculture (93 

percent), primarily corn and soybean (Debrewer and others, 

2000). Less than 4 percent of the basin is forest and urban. 

Typical of many streams in the state, streams in the Whitewater River Basin streams have low gradients and velocities. 

The largest urban area is Richmond, which has a population of 

about 37,900 (U.S. Census Bureau, 2000) (fig. 1).

Description of the East Fork White River Basin

The East Fork White River Basin (fig. 1) drains more 

than 14,880 km2 of central and southern Indiana and flows 

into the main branch of the White River (Hogatt, 1975). In 

water year 2002, the annual mean streamflow at the USGS 

streamflow-gaging station East Fork White River at Shoals, IN 

(03373500)(fig. 1), was 291.7 m3/s (Stewart and others, 2003). 

Streamflow in the 2002 water year was above average; the 

annual mean long-term streamflow (1904-2002) was 

158.3 m3/s at Shoals (Stewart and others, 2003). 

The climate in the East Fork White River Basin is characterized as humid continental with well-defined winter and 

summer seasons. The mean monthly temperature at Columbus, 

IN ranged from -2.8°C in January to 23.8°C in July (Schnoebelen and others, 1999). The mean annual precipitation ranged 

from 96.5 cm in the northern part of the basin to 111.8 cm in 

the southern part (Schnoebelen and others, 1999). 

The dominant land use is row-crop agriculture (69 percent), primarily corn and soybeans (Baker and Frey, 1997). 

Twenty-five percent of the basin area is forest and 5 percent 

is urban (Baker and Frey, 1997). Typical of many streams in 

the state, streams in the East Fork White River Basin have low 

gradients and velocities. The largest urban areas are Columbus (population about 32,500), Greensburg (population about 

9,300), and Seymour (population about 15,600) (U.S. Census 

Bureau, 2000) (fig. 1). 

Study Methods

This study used field and analytical methods from the 

IDEM and the USGS. The following sections describe the site 

selection and sampling strategies; field and laboratory methods 

used in collecting, processing, and analyzing algal-biomass, 

habitat, basin-characteristics, nutrients, and biological-community data; and data analysis used in this report.

Site Selection and Sampling Strategies 

Sampling sites were selected randomly by the USEPA as 

part of the IDEM probabilistic Watershed Monitoring Program 

(WMP)(Indiana Department of Environmental Management, 

1999, 2001). Each selected sampling site (table 1) represents 

a specific stream order; therefore, statistically valid extrapolations can be made from the randomly sampled streams to the 

entire class of streams in a particular basin. The IDEM WMP 

works on a 5-year rotating basin schedule, focusing on 1-2 

selected basins each year, with a complete assessment of the 

state at the end of each 5-year cycle. In 2002, the focus was 

the Whitewater River and East Fork White River Basins. After 

the sampling sites were selected and prior to collection of field 

data, IDEM personnel completed a visual assessment of the 

potential sampling sites and determined the area to be sampled 

at each site. At each of the USEPA randomly selected sites, 

the latitude and longitude was used as the middle point of the 

reach, with half of the reach upstream and half downstream of 

the middle point.

During periods of stable flow from May through September 2002, a total of 76 sites (fig. 1, table 1) in the Whitewater River and the East Fork White River Basins (38 sites in 

each basin) were sampled three times for algal biomass and 

nutrients. The samples were collected three times to measure 
Study Methods 

5

Table 1. Location and basin characteristics of the 76 algal-biomass sampling sites in the Whitewater River and East Fork White River Basins, Indiana, May through September, 2002.—Continued[IDEM, Indiana Department of Environmental Management; USGS, U.S. Geological Survey; ID, identification number; USEPA, U.S. Environmental Protection Agency; FT, feet; US, upstream; R, River; RD, Road; CR, County Road; SR, State Route; DS, downstream; CK, Creek; FK, Fork; DCH, Ditch; NR, near; AV, Avenue; ST, Street; N, North; S, South; E, East; W, West; IN, Indiana; OH, Ohio; trib, tributary; USHWY, U.S. Highway; RMI, River mile]

Short IDEM site number1 USGS station ID USGS station name

USEPA 

Aggregate 

Nutrient 

Ecoregion2

Level III 

Ecoregion3

Latitude

(degrees)

Longitude

(degrees)

Whitewater River Basin

401 395620085090801 WHITEWATER R 400 FT DS HOOVER RD NR HAGERSTOWN, IN VI 55 39.93886 -85.15209402 394041084562001 RICHLAND CK 3800 FT US CR 100W NR CLIFTON, IN VI 55 39.67814 -84.93903403 393827085001401 E FK WHITEWATER R 2700 FT US SR 44 NR LIBERTY, IN VI 55 39.64075 -85.00390404 392010085163801 SALT CK 1500 FT DS ENOCHSBURG RD AT ENOCHSBURG, IN VI 55 39.33613 -85.27721407 393249085113501 N BR GARRISON CK 200 FT DS CR 650S AT ALPINE, IN IX 71 39.54706 -85.19307408 395649084545201 FOUNTAIN CK AT WHITEWATER RD AT FOUNTAIN CITY, IN VI 55 39.94703 -84.91431409 395350085054001 MORGAN CK 2000 FT DS SR 38 NR GREENS FK, IN VI 55 39.89713 -85.09450410 392254084554401 BIG CEDAR CK 9400 FT US USHWY52 NR CEDAR GROVE, IN IX 71 39.38171 -84.92901411 393609085155801 FALL CK 1000 FT DS CR 425W NR COLUMBIA, IN VI 55 39.60240 -85.21611412 392251085074801 PIPE CK 900 FT US PUMPHOUSE RD NR OAK FOREST, IN IX 71 39.38089 -85.12989413 395148085074801 MARTINDALE CK 3900 FT US I-70 NR JACKSONBURG, IN VI 55 39.86319 -85.12989415 393514084580001 UNNAMED TRIB 1800 FT DS CR 175W NR ROSEBURG, IN VI 55 39.58728 -84.96669416 395158084535701 W FK WHITEWATER R 2000 FT DS I-70 NR RICHMOND, IN VI 55 39.86605 -84.89922417 394735084561001 LICK CK 2200 FT US ABINGTON PIKE NR RICHMOND, IN VI 55 39.79307 -84.93633419 393439085092401 WHITEWATER R 1200 FT US CR 480S AT NULLTOWN, IN VI 55 39.57748 -85.15678420 392645085071101 WHITEWATER R 8200 FT DS USHWY 52 AT METAMORA, IN IX 71 39.44582 -85.11985421 395344085064201 OSER CK 2700 FT DS SR 38 NR HAGERSTOWN, IN VI 55 39.89553 -85.11174422 392616085042301 WHITEWATER R 4 MI DS USHWY 52 AT YELLOW BANK, IN IX 71 39.43783 -85.07293423 393913084491301 LITTLE FOUR MI CK 2 MI US SR 44 NR FAIRHAVEN, OH VI 55 39.65362 -84.82024
6 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002 Table 1. Location and basin characteristics of the 76 algal-biomass sampling sites in the Whitewater River and East Fork White River Basins, Indiana, May through September, 2002.—Continued [IDEM, Indiana Department of Environmental Management; USGS, U.S. Geological Survey; ID, identification number; USEPA, U.S. Environmental Protection Agency; FT, feet; US, upstream; R, River; RD, Road; CR, County Road; SR, State Route; DS, downstream; CK, Creek; FK, Fork; DCH, Ditch; NR, near; AV, Avenue; ST, Street; N, North; S, South; E, East; W, West; IN, Indiana; OH, Ohio; trib, tributary; USHWY, U.S. Highway; RMI, River mile] Short IDEM site number1 USGS station ID USGS station name USEPA Aggregate Nutrient Ecoregion2 Level III Ecoregion3 Latitude (degrees) Longitude (degrees) 425 394904085002401 CROWN CK 400 FT DS MCMINN RD AT CENTERVILLE, IN VI 55 39.81765 -85.00669 427 394318085073301 WHITEWATER R 7200 FT US CR 440N AT BEESONS, IN VI 55 39.72157 -85.12593 428 395902084530801 FOUNTAIN CK 2800 FT US SEANEY RD NR BETHEL, IN VI 55 39.98391 -84.88557 429 394649085023001 NOLANDS FK 2600 FT DS MCCONAHA RD NR PINHOOK, IN VI 55 39.78034 -85.04153 430 392142085152501 SALT CK 2300 FT US CR 250W NR HAMBURG, IN VI 55 39.36165 -85.25686 431 393259084502801 INDIAN CK 900 FT DS SAND RUN RD NR CONTRERAS, OH VI 55 39.54973 -84.84098 432 395301084511501 M FK E FK WW R 2500 FT US SR 227 NR MIDDLEBORO, IN VI 55 39.88351 -84.85426 433 394527084541701 ELKHORN CK 5000 FT US USHWY 27 NR LOCUST GROVE, IN VI 55 39.75750 -84.90459 434 394545084540201 ELKHORN CK 6600 FT US USHWY 27 NR LOCUST GROVE, IN VI 55 39.76244 -84.90065 435 393450085061401 WILSON CK 700 FT DS SR 1 NR EVERTON, IN VI 55 39.58044 -85.10384 436 392755085181001 BULL FK 2 MI US STIPPS HILL RD NR BUENA VISTA, IN VI 55 39.46538 -85.30271 437 394550085073301 WHITEWATER R 2 ML DS E MILTON RD NR MILTON, IN VI 55 39.76390 -85.12593 438 392638085063101 WHITEWATER R 2 MI DS USHWY 52 NR METAMORA, IN IX 71 39.44398 -85.10865 439 392809085103801 WHITEWATER R 2 MI DS LAUREL RD NR LAUREL, IN IX 71 39.46913 -85.17668 440 395821084572801 MORGAN CK 2600 FT US MEYERS RD NR WILLIAMSBURG, IN VI 55 39.97276 -84.95754 441 395348085023701 GREENS FK 1200 FT US SR 38 AT GREENS FK, IN VI 55 39.89619 -85.04318

442 392610084531501 E FK BIG CEDAR CK 2 MI US SR 252 NR PALESTINE, IN VI 55 39.43597 -84.88743443 394147085064301 WHITEWATER R 2900 FT DS CR 440N AT WATERLOO, IN VI 55 39.69634 -85.11201445 394540085031701 CENTERAL RUN 7100 FT US CHAPEL RD NR PINHOOK, IN VI 55 39.76121 -85.05469
Study Methods 

7

Table 1. Location and basin characteristics of the 76 algal-biomass sampling sites in the Whitewater River and East Fork White River Basins, Indiana, May through September, 2002.—Continued[IDEM, Indiana Department of Environmental Management; USGS, U.S. Geological Survey; ID, identification number; USEPA, U.S. Environmental Protection Agency; FT, feet; US, upstream; R, River; RD, Road; CR, County Road; SR, State Route; DS, downstream; CK, Creek; FK, Fork; DCH, Ditch; NR, near; AV, Avenue; ST, Street; N, North; S, South; E, East; W, West; IN, Indiana; OH, Ohio; trib, tributary; USHWY, U.S. Highway; RMI, River mile]

Short IDEM site number1 USGS station ID USGS station name

USEPA 

Aggregate 

Nutrient 

Ecoregion2

Level III 

Ecoregion3

Latitude

(degrees)

Longitude

(degrees)

East Fork White River Basin

501 395651085222501 BIG BLUE R 2000 FT N NORTH RD AT NEW CASTLE,IN VI 55 39.94761 -85.37384502 390637085350201 SAND CK 1450 FT N CR 850N NR BREWERSVILLE, IN VI 55 39.11014 -85.58388503 392348085315501 CLIFTY CK 840 FT N CR 400N NR ADAMS, IN VI 55 39.39670 -85.53197504 384632086094201 E FK WHITE R 1 RMI US MUSCATATUCK R NR MEDORA, IN VI 55 38.77558 -86.16173505 392221085483701 FLATROCK R 300 FT DS CR 150W NR FLATROCK, IN VI 55 39.37244 -85.81015506 385657086275601 LITTLE SALT CK 400 FT DS CR 650N NR COVEYVILLE, IN IX 71 38.94904 -86.46553508 384054086530301 BOGGS CK 1600 FT DS CR 15 NR LOOGOOTEE, IN IX 71 38.68172 -86.88416509 394628085321301 BIG BLUE R 1400 FT W CR 450W NR KNIGHTSTOWN, IN VI 55 39.77432 -85.53700510 391917085520901 FLATROCK R 900 FT N CR 800N AT ST LOUIS CROSSING, IN VI 55 39.32146 -85.86906511 385539085431501 VERNON FK MUSC R 2700 FT E CR 400 S NR HAYDEN, IN VI 55 38.92737 -85.72081512 384810086284601 E FK WHITE R I MI N CR 500 S NR YOCKEY, IN IX 71 38.80266 -86.47955513 395149085263701 BIG BLUE R 1200 FT N CR 500S NR GREENSBORO, IN VI 55 39.86362 -85.44368515 385836086062401 LITTLE SALT CK 2700 FT S SR 258 AT FREETOWN, IN IX 71 38.97669 -86.10655516 383934086463201 BEAVER CK 900 FT S CR 44 AT IRONTON, IN IX 71 38.65946 -86.77551518 390659085383801 WYALOOSING CK 200 FT S 900N NR SARDINIA, IN VI 55 39.11632 -85.64397519 390745085273801 SUGAR CK 1000 FT W CR 1000N NR ZENAS, IN VI 55 39.12909 -85.46048521 392751085291801 LITTLE FLATROCK R 2700 FT W SR 3 NR MILROY, IN VI 55 39.46429 -85.48840522 385730086102801 S FK SALT CK 1200 FT N SR 58 NR KURTZ, IN IX 71 38.95841 -86.17455523 384717085320901 BIG CK I MI W CR 700W AT VOLGA, IN VI 55 38.78793 -85.53588
8 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002 Table 1. Location and basin characteristics of the 76 algal-biomass sampling sites in the Whitewater River and East Fork White River Basins, Indiana, May through September, 2002.—Continued [IDEM, Indiana Department of Environmental Management; USGS, U.S. Geological Survey; ID, identification number; USEPA, U.S. Environmental Protection Agency; FT, feet; US, upstream; R, River; RD, Road; CR, County Road; SR, State Route; DS, downstream; CK, Creek; FK, Fork; DCH, Ditch; NR, near; AV, Avenue; ST, Street; N, North; S, South; E, East; W, West; IN, Indiana; OH, Ohio; trib, tributary; USHWY, U.S. Highway; RMI, River mile] Short IDEM site number1 USGS station ID USGS station name USEPA Aggregate Nutrient Ecoregion2 Level III Ecoregion3 Latitude (degrees) Longitude (degrees) 524 383107086502501 E FK WHITE R 4000 FT W CR 400E NR THALES, IN IX 71 38.51858 -86.84026 525 392508085545301 BIG BLUE R 2700 FT E CR 750W NR MT AUBURN, IN VI 55 39.41886 -85.91475 526 384832086340901 E FK WHITE R 1300 FT W CR 450W NR COXTON, IN IX 71 38.80884 -86.56921 527 384838085383401 BIG CK 900 FT E SR 3 NR DEPUTY, IN VI 55 38.81067 -85.64281 528 382939087060901 BEAR CK 200 FT N CR 400N NR OTWELL, IN IX 72 38.49412 -87.10251 530 384635086041401 MUSCATATUCK R 2600 FT N MT EDEN RD NR MILLPORT,IN VI 55 38.77645 -86.07056 531 390939086202001 N FK SALT CK 2250 FT US SR 46 AT BELMONT, IN IX 71 39.16073 -86.33886 532 384433086434501 E FK WHITE R 100 FT N WILLIAMS RD NR HURON, IN IX 71 38.74239 -86.72917 533 393950085544601 SUGAR CK 1500 FT DS CR 1000N NR PLEASANT VIEW, IN VI 55 39.66397 -85.91280 534 390028085365701 VERNON FK MUSC R 1150 FT US WWTF AT N VERNON, IN VI 55 39.00767 -85.61584 535 391848085333801 FALL FK 650 FT N SR 3 AT EWINGTON, IN VI 55 39.31332 -85.56055 536 384525086014401 MUSCATATUCK R 1200 FT E MT EDEN RD NR MILPORT, IN VI 55 38.75708 -86.02883 537 393249085294401 FLATROCK R 500 FT DS CR 450S NR MILROY, IN VI 55 39.54688 -85.49546 539 385607085325901 GRAHAM CK 300 FT S CR 350E AT WALNUT RIDGE, IN VI 55 38.93529 -85.54985 542 392105085592401 BIG BLUE R 2400 FT W SR 31 AT EDINBURGH, IN VI 55 39.35142 -85.99013 543 384858085525501 VERNON FK MUSC R 1800 FT E CR 800E NR RETREAT, IN VI 55 38.81615 -85.88198

544 383726086202701 LOST R 100 FT N CR 450N NR ORLEANS, IN IX 71 38.62390 -86.34069545 392544085585801 SUGAR CK 2600 FT E CR 350S AT AMITY, IN VI 55 39.42880 -85.98279551 395221085483001 SUGAR CK 500 FT N CR 600N NR MAXWELL, IN VI 55 39.87275 -85.80836

1The full IDEM site number has a prefix of INRB, for example INRB401.2U.S. Environmental Protection Agency, 2000a,b.3U.S. Environmental Protection Agency, 1997b
Study Methods 9

seasonal changes in the algal biomass and nutrients. Round 

one sampling was done in May and June (spring); round two 

sampling was done in July and August (summer); and round 

three sampling was done in September (fall). In this report, 

round one sampling will be referred to as May or spring, round 

two as July or summer, and round three as September or fall. 

The algal-biomass and nutrient samples were collected on the 

same day at about the same time. Sampling at two sites in late 

spring was delayed until early July because of high water. The 

biological community (fish and invertebrate) and habitat were 

sampled one time by IDEM personnel, June through October 

2002.

Algal-Biomass, Habitat, Nutrient, and BiologicalCommunity Data-Collection and Processing 

Methods 

Algal-biomass samples were collected and processed for 

periphyton and seston, as described in USGS protocols, with 

several modifications. The National Water-Quality Assessment 

(NAWQA) Program algal protocols for periphyton (Moulton 

and others, 2002) are a reach-based sampling methodology in 

which five periphyton subsamples were collected from five 

different locations within the sampling reach. At each location, the stream depth, velocity, shading, and substrate were 

recorded. The subsamples were composited and marked as a 

single sample. At each site, periphyton samples were collected 

using the same substrate type—epilithic (rocks), epidendric 

(sticks), or epipsammic (sand)—during the sampling period. 

One modification to this study from the NAWQA protocols 

was that ten periphyton subsamples were collected from the 

same substrate as close to the center of the reach as possible. 

Then five subsamples were selected that best represented the 

average algal cover at the sampled reach and these subsamples 

were composited into a single sample (Charles and others, 

2000). 

Seston samples were collected in the center of the sampling reach along a line that extended from the left edge to the 

right edge of the streambank (transect). The wetted channel 

width and water depths (one-quarter, one-half, and three-quarters points) along the chosen transect were recorded. The seston samples were collected with a 3-L bottle and a 0.476-cm 

nozzle; either a grab sample or a multiple vertical method was 

used (Shelton, 1994). 

Algal-biomass samples were collected, homogenized, and 

filtered onto glass-fiber filters in the field by USGS personnel. 

All filters collected by the USGS were placed on dry ice and 

transported to the USGS Indiana Water Science Center laboratory for analysis. The CHLa and AFDM filters were analyzed 

at the USGS Indiana Water Science Center laboratory; all the 

POC filters were analyzed at the USGS National Water Quality Laboratory (NWQL) in Lakewood, Colorado. 

Concentrations of CHLa were determined, following 

USEPA method 445, with a Turner Designs TD-700 fluorometer outfitted for CHLa analysis (Arar and Collins, 1997). 

There were two exceptions to method 445; filters were ground 

in Nalgene centrifuge tubes instead of glass to counter the 

problem of tube breakage, and samples were centrifuged at 

1,500 revolutions per minute (approximately 320 g) for 

15 minutes. At the modified centrifuge rate, the filter residue and acetone solution separated well. If samples did not 

separate well, they were placed in the centrifuge a second time 

or care was taken not to decant the solute. For consistency, all 

samples were allowed to steep for 2.5 hours. Concentrations of 

AFDM were determined, following USGS method B-3520-85 

(Britton and Greeson, 1988) with two exceptions: the samples 

were filtered in the field, and the filters were not baked and 

weighed in the crucibles before use. 

Quality-assurance methods for algal biomass samples 

included triplicate filters from the same sample to measure 

variability and a blank filter collected at each sampling reach 

to measure bias. Additionally, a fifth filter was collected at 

each site and 10 percent of these fifth CHLa filters were analyzed at the NWQL to measure laboratory variability.

Habitat assessments were collected one time from June 

through October 2002 at each site by IDEM personnel following standard IDEM methods (Indiana Department of Environmental Management, 1992, 2002). Habitat assessments 

were made at the same time fish communities were sampled. 

Habitat assessments include in-stream and riparian measurements that are incorporated into the Qualitative Habitat Evaluation Index (QHEI). A list of these habitat metrics are listed in 

appendix 1 (Dufour, 2002).

Nutrient samples (ammonia, nitrate, TKN, TN, and TP) 

were collected by IDEM personnel following approved IDEM 

methods (Beckman, 2000). Nutrient quality-assurance methods followed approved IDEM methods (Bowren and Ghiasuddin, 1999). The nutrient samples were preserved by IDEM 

personnel, placed on wet ice, and taken to an independent 

laboratory (Test America, Indianapolis) for analysis.

Biological-community (fish and invertebrates) samples 

were collected one time, June through October 2002, at each 

site by IDEM personnel following standard IDEM methods 

(Indiana Department of Environmental Management, 1992, 

2002; Barbour and others, 1999). IDEM personnel calculated 

the biological-community attributes and metric scores for 

this study. Attributes are the raw data and metric scores are 

rankings of the data from poor (a score of one), fair to good (a 

score of three), and excellent (a score of 5). The metric scores 

are ranked using a large data set that includes unimpaired 

reference sites to impaired sites. Each attribute has a corresponding metric score (Dufour, 2002). A list of the fish and 

invertebrate attributes and metrics are listed in appendix 1.

Data sets for sampling dates, laboratory-analysis dates, 

and algal-biomass (periphyton and seston) are available at: 

http://in.water.usgs.gov/NAWQAWHMI/neet.php
10 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002

Data Analysis

In large environmental datasets, natural variability often 

masks the relations among variables. An objective of this 

report was to develop a preliminary understanding of how 

algal biomass relates to biological community and environmental variables in the Whitewater River and East Fork 

White River Basins in 2002. In this report, the environmental 

variables included nutrients, habitat, and basin characteristics. Two approaches were used for the preliminary analysis 

of the data sets. The first approach included ordination and 

regression analyses of the algal biomass, nutrient, and environmental data. The second approach compared the CHLa 

and nutrient values collected by IDEM and USGS personnel 

to USEPA published values. These approaches provided an 

exploratory analysis to identify which biological and environmental variables were significantly related to algal biomass. 

These approaches also were used as a data censoring tool and 

allowed researchers to determine the relations of interest to 

use as a starting point in future studies.

The ordination approach consisted of determining yearly 

site scores for the periphyton and seston data using PCA. 

In each PCA two measures of algal biomass for periphyton 

(CHLa and AFDM) and seston (CHLa and POC) were used. 

The site scores are considered yearly because all of the seasonal algal biomass data are included in the PCA site score 

determination. The regression approach related the periphyton 

and seston PCA site scores from the first axis to five basin 

characteristics, nine habitat, 12 nutrient variables, and 43 

fish and 21 invertebrate attribute and metric scores. All data 

were normalized to a z-score prior to use in the data analyses, 

allowing for comparison of variables that were recorded in 

different units.

Basin-Characteristics Data

The basin characteristics used in this analysis were drainage area and land use (percentage of agriculture, forest, other, 

and urban) and these were determined by the USGS for this 

study. Drainage area was derived from the basin boundaries. 

Basin boundaries for each site were generated following the 

method outlined by Ries, III, and others (2004). This method 

combines the National Elevation Dataset, Digital Elevation 

Model data, and the National Hydrography Dataset, which is a 

comprehensive set of digital surface-water features. The basin 

boundaries were used to extract land-use information from 

the National Land Cover Dataset (NLCD) (U.S. Geological 

Survey, 2000). This conversion allowed the land-use data to be 

compared among and between basins. Each sampling site was 

assessed to determine in which Aggregate Nutrient Ecoregion 

(U.S. Environmental Protection Agency, 2000 a,b) and Level 

III Ecoregion (U.S. Environmental Protection Agency, 1997b) 

it was located.

Nutrient Data

The nutrients used in this analysis were dissolved ammonia as N, dissolved nitrate plus nitrite as N, total Kjeldahl 

nitrogen as N, total nitrogen as N, and total phosphorus as 

P. Because concentrations of nitrate typically are two orders 

of magnitude greater than nitrite and because nitrite usually does not exceed 0.5 mg/L in surface water (National 

Research Council, 1978), concentrations of nitrite plus nitrate 

are referred to as nitrate in this report. Concentrations of total 

nitrogen were calculated as the sum of nitrate and TKN. More 

than ninety percent of the ammonia data were censored below 

the reporting levels. Because most of the ammonia concentrations were below the reporting level, it was not included in 

the analysis. About eleven percent of the TP concentrations 

and two percent of the nitrate concentrations were below the 

reporting levels of 0.03 mg/L and 0.01 mg/L, respectively. For 

nitrate and TP concentrations, one-half of the reporting level 

was used in the analysis. For nutrient analyses, the scope of 

this report is narrowed to nitrate, TKN, TN, and TP. Nutrient 

data was analyzed separately for the spring (May), summer 

(July) and the fall (September) samples; the seasonal nutrient 

and the seasonal algal-biomass data were then compared to the 

PC1 sites scores using Spearman’s rho to determine the most 

significant seasonal relations.

Principal Components Analysis

Principal Components Analysis, an ordination technique, was used to calculate individual yearly algal-biomass 

site scores for the periphyton and seston samples. PCA site 

scores (Gauch, 1982; Jongman and others, 1995; McCune 

and Grace, 2002) are theoretical variables that minimize the 

total residual sum of squares after fitting straight lines to the 

algal-biomass data. Mean CHLa (periphyton and seston) and 

AFDM values were calculated from the three filters for each 

sample. Mean algal-biomass (periphyton and seston) and other 

data were normalized prior to running the ordination analysis. 

To calculate the yearly periphyton PCA site scores, the mean 

periphyton CHLa and mean AFDM data from the May, July, 

and the September samplings were used; for the yearly seston 

PCA site scores the mean seston CHLa and POC data from the 

May, July, and the September samplings were used.

In this report, a positive site score indicates an increase in 

algal-biomass along the axis and a negative site score indicates 

a decrease in algal-biomass along the axis. Only the principal 

components (PC) site scores from the first axis (PC1) are presented in this preliminary analysis, because the PC1 axis best 

explains the algal-biomass data (McCune and Grace, 2002). 

In theory, the PC1 site scores should be related to the variables that were used in the calculations, and the variable with 

the highest loading accounts for the majority of the variation, 

which should also have the highest correlation coefficient. 

As a validation step, the yearly periphyton and yearly seston 

PC1 site scores were related to the algal biomass-values, using 

Spearman’s rho. The purpose of this preliminary analysis was 
Relations of the Principal Components Analysis Site Scores to Data 11

to investigate all potential relations and identify those relations that were the strongest and warrant further investigation. In this report, for a relation to be considered statistically 

significant using PCA, the Spearman’s rho statistic (rS) was 

required to be greater than the absolute value of 0.45 and have 

at least a 95 percent significance level based on the sample 

size. Although an rS of 0.45 is considered significant, it has a 

possibility of introducing a Type I error.

Several procedures – such as the Bonferroni correction – 

are available for adjusting the significance level when performing a large number (or “family”) of tests simultaneously 

(Van Sickle, 2003). This adjustment reduces the chances of a 

Type I error (the relation is declared present when the relation is not present) at a specific alpha level. Although useful 

in reducing Type I error, this technique increases the chance 

of producing a Type II error (no relation declared when a 

relation is present). In this study, the goal was to investigate 

all potential relations and identify which relations were the 

strongest. Because this was a preliminary analysis and there 

were a limited number of significant relations, no corrections 

were applied. 

The yearly PC1 site scores spatially represent the 

(periphyton and seston) algal-biomass and were related, 

using Primer V.6.1.5 (Primer-E Ltd, 2006), to the habitat, 

basin-characteristics (drainage area and land use), seasonal 

nutrient (spring (May), summer (July), and fall (September) 

nitrate, TKN, TN, and TP), seasonal algal biomass (spring 

(May), summer (July), and fall (September) CHLa, AFDM, 

and POC), and biological-community (fish and invertebrates) 

attributes and metric score data collected in 2002. Spearman’s 

rank order (rho) correlations are the preferred method when 

determining relations among environmental data because (1) 

the initial sample size was greater than 30 for most variables 

and (2) environmental data typically are not normally distributed. Although the data from this study were normalized prior 

to analysis, all variables were not normally distributed, requiring a non-parametric statistic. PC site scores were related in 

a correlation matrix to determine the strongest relations. The 

variables with the strongest relations could help in the development of nutrient criteria. 

Comparison With U.S. Environmental Protection 

Agency Data 

The USEPA proposed criteria in 2000 for nitrate, TKN, 

TN, TP, CHLa (periphyton and seston), and turbidity at the 

25th-percentile value of all data for each variable for each 

Aggregate Nutrient and Level III Ecoregions. Consequently, 

the second analytical approach was to determine how the 

data collected by IDEM and USGS for CHLa and nutrients 

compared to USEPA published values (U.S. Environmental 

Protection Agency, 2000 a,b). For the USEPA method, the 

median value for each variable for each stream was calculated. Then, percentiles were determined for each of the 

four seasons in each ecoregion and the 25th-percentile of the 

combined four seasons was used as the proposed criteria. In 

this report, median nutrient (nitrate, TKN, TN, and TP) and 

CHLa values were calculated for all streams sampled within 

the same Aggregate Nutrient and Level III Ecoregions. However, seasonal statistics were not calculated because IDEM and 

USGS did not collect winter samples and spring samples were 

limited—USEPA considers May as part of spring—which left 

a small number of samples in the USEPA “spring” season. 

In this report, the median values for all the streams within a 

specific ecoregion were used to calculate descriptive statistics 

(ranges—minimum and maximum—and percentiles—10th, 

25th, 50th, 75th, and 90th). For CHLa (periphyton and seston), a 

mean of the three filters collected at each site was calculated 

and then a median of the means for all streams within each 

ecoregion was used to calculate the descriptive statistics. The 

descriptive statistics then were compared to published USEPA 

values for Ecoregions VI, IX, 55, and 71 (U.S. Environmental 

Protection Agency, 2000 a,b).

Relations of the Principal Components 

Analysis Site Scores to Algal-Biomass, 

Habitat, Basin-Characteristics, 

Nutrient, and Biological-Community 

Data

PCA was used to calculate PC1 site scores from the 

algal-biomass (periphyton and seston) data for each site (all 

seasons). In the preliminary analysis of the 2002 IDEM/

USGS data, the periphyton PC1 site score was constrained 

by AFDM (September); the PC2 site score was constrained 

by CHLa (May). The combination of PC1 (43.3 percent) and 

PC2 (21.9 percent) site scores accounted for 65.2 percent of 

the total variation in the data set. The seston PC1 site score 

was constrained by the POC (July); the PC2 site score was 

constrained by the POC (May). The combination of PC1 

(52.4 percent) and PC2 (23.7 percent) site scores accounted 

for 76.1 percent of the variation in the data set. Because the 

PC1 site score accounted for a large amount of the total variation in both of the algal-biomass data sets, only PC1 (periphyton and seston) site score were related to the seasonal algalbiomass, habitat, basin-characteristics (drainage area and land 

use), seasonal nutrient, and biological-community (fish and 

invertebrates) attributes and metric score data.

The periphyton PC1 site score (table 2) was negatively 

related to one algal-biomass variable in three seasons: mean 

AFDM (May, July, and September). Although this result does 

not offer inferences about the relations of the periphyton PC1 

site score to the environmental or biological-community (fish 

and invertebrate attributes and metric scores) data, these relations demonstrate that the periphyton PC1 site score represents 

an algal-biomass gradient that is largely defined by AFDM. 
12 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002

One basin-characteristic variable, drainage area, was 

negatively related to the periphyton PC1 site score. This relation suggests that as the drainage area (a surrogate for stream 

order) decreases, the amount of periphyton CHLa and AFDM 

increase. This relation supports the River Continuum Concept 

(Vannote and others, 1980) that periphyton is more important 

than seston for primary production in small and medium-sized 

streams than in large streams.

The periphyton PC1 site score, which was most influenced by September AFDM (table 2), had no statistically 

significant relations between the periphyton PC1 and the nine 

habitat or 12 nutrient variables examined. The lack of relations 

between nutrients and periphyton algal biomass is surprising. Biggs (2000) listed several studies that found significant 

relations between periphyton chlorophyll and nutrients. In 

similar studies conducted in 2001 in the West Fork White 

River Basin (Frey and others, 2007) and in 2003 in the Upper 

Wabash River Basin (Leer and others, 2007), no significant 

relations were found between the nutrients and the periphyton 

algal biomass. Algal biomass can be influenced by several 

natural factors that could account for this lack of relations. 

Scouring of algal growth by increased streamflow can cause 

algal growth to restart in the stream (Biggs and others, 1999) 

and annual and seasonal differences in storm events can allow 

for “wet” and “dry” years with high levels of algal biomass 

corresponding to high and low nutrients, depending upon the 

season. Other factors include shading from canopy cover and 

turbidity (Wehr, 2003) and grazing by snails, invertebrates, 

and fish (Lamberti and others, 1987).

Of the 21 fish-community attributes and metric scores 

examined, the periphyton PC1 site score was negatively 

related to one attribute (large-river percent) and one metric 

score (carnivore percent metric score). The periphyton PC1 

site score was positively related to three attributes (headwater 

percent, pioneer percent, and simple lithophil percent). These 

findings suggest that as periphyton algal biomass increases, 

fish-community composition shifts from one dominated by 

carnivores and other niche-specific specialists to a community 

dominated by generalist-feeding and pioneer species. The 

central stoneroller (Campostoma anomalum), an algivore that 

is included in the pioneer species metric is commonly found 

in the nutrient and algal-rich streams in Indiana. It may be 

useful to create some nutrient-related metrics such as percentage central stoneroller, instead of grouping them into pioneer 

species that could mask possible relations. Petersen and 

Femmer (2002) found the percentage of central stonerollers 

was important to explain benthic chlorophyll levels in Ozark 

streams. 

Of the 21 invertebrate-community attributes and metric 

scores examined, there were no statistically significant relations with the periphyton PC1 site score. The lack of significant findings with invertebrate communities may be the result 

of three possible factors: (1) sample size, (2) sample method, 

and (3) resolution of invertebrate data. In multivariate studies, 

Table 2. Significant Spearman’s rho relations of the yearly periphyton Principal Components Analysis axis 1 site scores (PC1) to algalbiomass, habitat, basin-characteristics, and nutrient parameters and fish- and invertebrate-community attributes and metric scores, 

2002.

[rs, Spearman’s rho statistic (probability <0.05); n, number of samples; ns, no statistically significant relations]

Category Parameter and attribute/metric r

s

Parameter

Periphyton algal biomass (n=50) Mean ash-free dry mass, May-June -0.7289

Mean ash-free dry mass, July-August - .6469

Mean ash-free dry mass, September - .8203

Habitat (n=41) ns ns

Basin characteristics (n=52) Drainage area - .5191

Nutrients (n=41) ns ns

Attribute/metric

Fish (n=51) Carnivore percent metric score - .4942

Headwater percent .5258

Large-river percent - .5697

Pioneer percent .4890

Simple lithophil percent .5519

Invertebrates (n=34) ns ns
Relations of the Principal Components Analysis Site Scores to Data 13

sample size has been shown to affect the inferences that can 

be drawn from a data set; this may be why no relations were 

noted between the PC1 (periphyton and seston) site scores 

and the invertebrate-community attributes and metric scores. 

In this study, invertebrates were collected only at sites with 

riffles; only 45 sites had invertebrate data, compared to 73 and 

76 sites for fish-community and algal-biomass data, respectively. Another possible reason for the lack of invertebratecommunity attributes and metric score relations could be the 

result of the collection methods. The invertebrate-community 

samples were collected from a specific habitat type (riffle) 

within the sampling reach; this targeted-habitat approach 

represents only the habitat sampled. If a multihabitat approach 

had been used for the collection of the invertebrate communities it may have revealed a community more representative 

of the entire sampling reach; this multihabitat approach may 

have increased the number of significant relations between the 

PC1 sites scores and the invertebrate-community attributes and 

metrics. Finally, the lack of invertebrate-community attribute/

metric score relations also could be the result of invertebrateidentification resolution. IDEM identifies invertebrates to 

family level; therefore, it is possible that if identification were 

to the lower taxonomic level, a statistically significant relation between PC1 (periphyton and seston) site scores and 

invertebrate-community attributes and metric scores could be 

documented.

The seston PC1 site score (table 3) was negatively related 

to two algal-biomass variables in three seasons: mean seston 

CHLa (May, July, and September), and POC (May, July, and 

September). Although this result does not offer inferences 

about the relations of the seston PC1 site score to the environmental or biological-community (fish and invertebrate 

attributes and metric scores) data, these relations demonstrate 

that the periphyton PC1 site score represents an algal-biomass 

gradient that is largely defined by seston CHLa and POC. 

The seston PC1 site score, which was most influenced 

by July POC (table 3), had no statistically significant relations 

with the basin-characteristics or habitat variables. The lack 

of a significant relation between the seston PC1 and drainage 

area was surprising. Vannote demonstrated in the River Continuum Concept, that as drainage area (surrogate for stream 

order) increases, the amount of primary production from 

seston CHLa and POC should increase (Vannote and others, 

1980). On the basis of the River Continuum Concept, it was 

expected that seston CHLa would become more significant in 

this study compared to a similar study conducted by IDEM 

Table 3. Significant Spearman’s rho relations of the yearly seston Principal Components Analysis axis 1 site scores (PC1) to algalbiomass, habitat, basin-characteristics, and nutrient parameters and fish- and invertebrate-community attributes and metric scores, 

2002.

[rs, Spearman’s rho statistic (probability <0.05); n, number of samples; ns, no statistically significant relations;N, nitrogen; P, Phosphorus]

Category Parameter and attribute/metric r

s

Parameter

Seston algal biomass (n=50) Mean seston chlorophyll a, May-June -0.4502

Mean seston chlorophyll a, July-August - .6886

Mean seston chlorophyll a, September - .6816

Particulate organic carbon, May-June - .4883

Particulate organic carbon, July-August - .7538

Particulate organic carbon, September - .7132

Habitat (n=51) ns ns

Basin characteristics (n=50) ns ns

Nutrients (n=39) Total Kjeldahl nitrogen-N, July-August - .5525

Total Kjeldahl nitrogen-N, September - .7010

Total phosphorus-P, May-June - .5814

Total phosphorus-P, September - .4846

Attribute/metric

Fish (n=50) Headwater percent .5897

Large-river percent metric score - .5204

Invertebrates (n=33) Number of individuals metric score - .5024
14 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002

and USGS in 2001. Basins with large drainage areas (boat 

sites) were sampled in 2002 and not in 2001 (Frey and others, 

2007). 

Of the 12 nutrient variables examined two were negatively related to the seston PC1 site score in two seasons: TKN 

(July and September), and TP (May and September). More 

significant relations were found in summer and fall samples 

than in spring samples which suggest that the time to see the 

strongest relations between nutrients and algal biomass may 

be in the late summer and fall. Nutrient concentrations may 

be uniformly high in these basins during the spring and early 

summer because of fertilizer application and subsequent runoff 

into streams. Also, higher algal growth tends to occur during 

periods of stable flow and warmer weather typically associated 

with summer and fall. Previous studies (Van Nieuwenhuyse 

and Jones, 1996; Soballe and Kimmel, 1987) found significant 

relations between seston CHLa and TP. However, seston algae 

(whether euplankters or dislodged periphyton) in streams and 

rivers can account for appreciable total nutrient concentrations 

in water samples because algal cells contain both phosphorus 

and organic nitrogen (Stephen D. Porter, Texas State University, written commun., August 8, 2007).

Of the 43 fish-community attributes and metric scores 

examined, the seston PC1 site score was positively related to 

one attribute (headwater percent) and negatively related to 

one metric score (large-river percent metric score). Of the 21 

invertebrate-community attributes and metric scores examined, 

the seston PC1 site score was negatively related to one metric 

score (number of individuals metric score). This suggests that 

the impacts of nutrients may be reflected better by the fish 

than by invertebrates. In this study and in the 2001 West Fork 

White River Basin study, there were more significant relations 

between algal biomass and fish communities (9) than between 

invertebrates and algal biomass (Frey and others, 2007).

Drainage Area and Land-Use Analysis

Basin characteristics such as drainage area and land use 

can affect the relations between nutrients, algal-biomass, and 

biological-community data. To understand how the sampling 

sites used in this analysis might have affected the results, an 

analysis of the drainage area and land use was done.

The sites selected in the Whitewater River Basin were 

generally small drainage basins; compared to Whitewater 

River Basin sites, the sites selected in the East Fork White 

River Basin were generally larger drainage basins (fig. 2A). Of 

the 38 sites sampled in the Whitewater River Basin, about 55 

percent of the sites were headwater streams (less than 50 km2); 

about 10 percent of the 38 sites sampled in East Fork White 

River Basin were headwater streams (fig. 2A). About 13 percent of sites sampled in the Whitewater River Basin were large 

streams (greater then 1,000 km2), and almost 29 percent of 

the sites sampled in East Fork White River Basin were large 

streams (fig. 2A). The drainage basins of the Whitewater River 

20

40

60

80

100

0-25 26-50 51-75 76-100

PERCENTAGE OF BASIN, AGRICULTURE

PERCENTAGE OF SITES WITHIN BASIN

0

20

40

60

80

100

0-50 51-1000 > 1,000

DRAINAGE AREA (SQUARE KILOMETERS)

PERCENTAGE OF SITES WITHIN BASIN

Headwater

Wadeable Boat

100

0-25 26-50 51-75 76-100

PERCENTAGE OF BASIN, FOREST 

PERCENTAGE OF SITES WITHIN BASIN

20

40

60

80

100

0-25 26-50 51-75 76-100

PERCENTAGE OF BASIN, URBAN

PERCENTAGE OF SITES WITHIN BASIN

A.

0

B.

0

20

40

60

80

C.

0

D.

Figure 2. Graphs showing the percentages of drainage area and 

agricultural, forest, and urban land use in the Whitewater River 

and East Fork White River Basins, Indiana, 2002.
Drainage Area and Land-Use Analysis, Comparison of the Data to Ecoregion Nutrient Criteria 15

Basin sites ranged from 3.3 km2 to 2,134 km2, and the drainage basins of the East Fork White River Basin sites ranged 

from 9.3 km2 to 14,362 km2 (table 4). 

The large range of basin drainage areas that was 

sampled could account for or influence the significant relations documented by the PC1 (periphyton and seston) and 

the environmental and biological-community data. Previous 

studies suggest that drainage-basin size (stream order) could 

mask relations of environmental variables to biological communities. Stream size was significant in explaining relations 

between algal-community assemblages (Carpenter and Waite, 

2000) and fish-community assemblages (Caskey, 2003) and 

environmental variables. Different fish and algal communities 

were found in small streams than in large streams. Additionally, stronger relations were found between nutrients and fishand invertebrate-community attributes and metric scores when 

data was analyzed by basin size (Frey and Caskey, 2007). 

Miltner and Rankin (1998) found the only significant relations between nutrients (TP and total inorganic nitrogen) and 

biological communities (fish) were in headwater streams. For 

this report, to keep the sample size large, analysis was done on 

all sites combined. This preliminary data analysis, however, 

indicates statistically significant relations between PC1 (periphyton) and drainage area (table 2). 

Although both basins were dominated by agricultural 

land use the Whitewater River Basin sites had more land in 

agriculture than the East Fork White River Basin sites; about 

90 percent of the sites in the Whitewater River Basin and 

about 50 percent of the sites in the East Fork White River 

Basin had basins that consisted of more than 

75 percent agricultural land use (fig. 2B). Land use ranged 

from 51.5 to 98.2 percent agricultural, and in the East Fork 

White River Basin sites ranged from 14.5 to 98.4 percent 

(table 4). In a study of Midwest agriculturally dominated landscapes, Wang and others (1997) noted when land use within 

a drainage basin consists of less than 50 percent agriculture, 

biological-community relations are complex and difficult to 

identify. As the percentage of agricultural land use increases to 

more than 50 percent, however, a significant negative relation 

can be seen with Index of Biological Integrity (IBI) scores. 

Because most basins in this study had more than 80 percent 

agricultural land use, especially in the Whitewater River 

Basin, an agricultural land-use gradient was not found. This 

lack of a gradient potentially could mask relations between the 

PC1 (periphyton and seston) and the environmental variables 

and biological-community (fish and invertebrates) attributes 

and metric scores.

Almost 95 percent of the sites in the Whitewater River 

Basin and about 55 percent of the sites in the East Fork White 

River Basin had basins that consisted of less than 25 percent 

forest land use (fig. 2C). The forested land use of the Whitewater River Basin sites ranged from 1.8 to 48.4 percent, and 

the forested land use of the East Fork White River Basin sites 

ranged from 0.2 to 83.6 percent (table 4). Studies have shown 

that forested landscapes are less likely to have elevated nutrients, in part, because an established riparian zone acts as a buffer and filters surface-water runoff (Jordan and others, 1993).

All of the sites in the Whitewater River Basin and in the 

East Fork White River Basin had basins that consisted of 

less than 25 percent urban land use (fig. 2D). The urban 

land use of the Whitewater River Basin sites ranged from 

0 to 22.1 percent, and the urban land use of the East Fork 

White River Basin sites ranged from 0 to 8.6 percent (table 4). 

Studies from across the U.S. have shown that agricultural and 

urban landscapes can have elevated levels of nutrients (Mueller and Helsel, 1996). If nutrient concentrations were elevated 

at all the sites and a nutrient gradient was not detected, it 

potentially could mask relations between the PC1 (periphyton 

and seston), the environmental variables, and biological-community (fish and invertebrates) attributes and metric scores.

Comparison of the Data to Ecoregion 

Nutrient Criteria

The values for nutrients (nitrate, TKN, TN, and TP) and 

CHLa (periphyton and seston) were compared to published 

USEPA values for the respective ecoregions (U.S. Environmental Protection Agency, 2000 a,b). A comparison of the 

values from the IDEM/USGS and USEPA data sets was done 

to (1) determine whether USEPA data that were used to set 

the nutrient water-quality criteria and the IDEM/USGS data 

had similar ranges of values and (2) determine if the streams 

in Indiana would exceed the proposed USEPA 25th-percentile 

nutrient water-quality criteria for the ecoregions. Of the 76 

sites sampled, 57 sites on 38 streams were in Ecoregion VI; 

19 sites on 13 streams were in Ecoregion IX (fig. 1, table 1). 

All of the 57 sites on 38 streams in Ecoregion VI were also in 

Ecoregion 55. Of the 19 sites on 13 streams in Ecoregion IX, 

18 sites on 12 streams were in Ecoregion 71. The one remaining stream sampled in Ecoregion IX was in USEPA Level III 

Ecoregion 72. Because only one stream was in Ecoregion 72, 

no comparison was made with published USEPA values.

The IDEM/USGS values for TKN fell within the range of 

the published values for Ecoregions VI, IX, 55, and 71 (table 

5). The IDEM/USGS 25th-percentile TKN values were greater 

than published values for Ecoregion IX, 55, and 71. If the proposed USEPA TKN water-quality criteria for Ecoregions VI 

and IX were enacted, 46.3 percent of the individual samples 

collected in Ecoregion VI and 89.1 percent of the samples in 

Ecoregion IX would have exceeded those criteria.

The IDEM/USGS values for nitrate fell within or were 

close to the range of the published values for Ecoregions VI, 

IX, 55, and 71 (table 6). The IDEM/USGS 25th-percentile 

nitrate values were greater than or equal to the published 

values for Ecoregions VI, IX, and 55. If the proposed USEPA 

nitrate water-quality criteria for Ecoregions VI and IX were 

enacted, 63.4 percent of the individual samples collected in 

Ecoregion VI and 88.0 percent of the samples in Ecoregion IX 

would have exceeded those criteria.
16 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002 Table 4. Basin characteristics of the 76 algal-biomass sampling sites in the Whitewater River and East Fork White River Basins, Indiana, May through September 2002.— Continued [IDEM, Indiana Department of Environmental Management; USGS, U.S. Geological Survey; ID, identification number; USEPA, U.S. Environmental Protection Agency; FT, feet; US, upstream; R, River; RD, Road; CR, County Road; SR, State Route; DS, downstream; CK, Creek; FK, Fork; DCH, Ditch; NR, near; AV, Avenue; ST, Street; N, North; S, South; E, East; W, West; IN, Indiana; OH, Ohio; trib, tributary; USHWY, U.S. Highway; RMI, River mile] Short IDEM site number1 USGS station name Drainage area (km2

)

Landuse (percentage)2

Ag Forest Urban Other

Whitewater River Basin

401 WHITEWATER R 400 FT DS HOOVER RD NR HAGERSTOWN, IN 64.2 86.9 12.5 0.2 0.4402 RICHLAND CK 3800 FT US CR 100W NR CLIFTON, IN 17.8 98.2 1.8 0 .1403 E FK WHITEWATER R 2700 FT US SR 44 NR LIBERTY, IN 607 78.2 15.2 5.5 1.1404 SALT CK 1500 FT DS ENOCHSBURG RD AT ENOCHSBURG, IN 71.5 79.8 19.5 .5 .2407 N BR GARRISON CK 200 FT DS CR 650S AT ALPINE, IN 29.2 51.5 48.4 .1 .1408 FOUNTAIN CK AT WHITEWATER RD AT FOUNTAIN CITY, IN 17.6 92.6 7.1 0 .3409 MORGAN CK 2000 FT DS SR 38 NR GREENS FK, IN 38.6 95.3 4.6 0 .1410 BIG CEDAR CK 9400 FT US USHWY52 NR CEDAR GROVE, IN 57.7 86.9 12.7 0 .3411 FALL CK 1000 FT DS CR 425W NR COLUMBIA, IN 8.4 88.3 11.7 0 0412 PIPE CK 900 FT US PUMPHOUSE RD NR OAK FOREST, IN 93.2 66.8 31.5 1.0 .8413 MARTINDALE CK 3900 FT US I-70 NR JACKSONBURG, IN 139 92.4 6.7 .2 .7415 UNNAMED TRIB 1800 FT DS CR 175W NR ROSEBURG, IN 4.0 94.4 5.3 0 .3416 W FK WHITEWATER R 2000 FT DS I-70 NR RICHMOND, IN 46.7 90.2 7.0 2.2 .6417 LICK CK 2200 FT US ABINGTON PIKE NR RICHMOND, IN 40.4 68.2 8.9 22.1 .8419 WHITEWATER R 1200 FT US CR 480S AT NULLTOWN, IN 1,352 88.0 9.3 1.7 1.0420 WHITEWATER R 8200 FT DS USHWY 52 AT METAMORA, IN 1,944 79.2 18.5 1.4 .9421 OSER CK 2700 FT DS SR 38 NR HAGERSTOWN, IN 4.5 95.9 3.0 .2 .9422 WHITEWATER R 4 MI DS USHWY 52 AT YELLOW BANK, IN 2,134 77.5 20.3 1.3 .9423 LITTLE FOUR MI CK 2 MI US SR 44 NR FAIRHAVEN, OH 49.0 96.4 3.1 .3 .3425 CROWN CK 400 FT DS MCMINN RD AT CENTERVILLE, IN 6.9 81.7 4.1 14.2 .1427 WHITEWATER R 7200 FT US CR 440N AT BEESONS, IN 798 89.7 8.2 1.1 1.0428 FOUNTAIN CK 2800 FT US SEANEY RD NR BETHEL, IN 5.3 89.3 10.3 0 .3
Comparison of the Data to Ecoregion Nutrient Criteria 17

Table 4. Basin characteristics of the 76 algal-biomass sampling sites in the Whitewater River and East Fork White River Basins, Indiana, May through September 2002.—Continued[IDEM, Indiana Department of Environmental Management; USGS, U.S. Geological Survey; ID, identification number; USEPA, U.S. Environmental Protection Agency; FT, feet; US, upstream; R, River; RD, Road; CR, County Road; SR, State Route; DS, downstream; CK, Creek; FK, Fork; DCH, Ditch; NR, near; AV, Avenue; ST, Street; N, North; S, South; E, East; W, West; IN, Indiana; OH, Ohio; trib, tributary; USHWY, U.S. Highway; RMI, River mile]

Short IDEM 

site number1 USGS station name Drainage area (km2) Landuse (percentage)2 Ag Forest Urban Other

429 NOLANDS FK 2600 FT DS MCCONAHA RD NR PINHOOK, IN 187 90.6 7.0 1.6 .8430 SALT CK 2300 FT US CR 250W NR HAMBURG, IN 102 73.6 23.8 1.5 1.1431 INDIAN CK 900 FT DS SAND RUN RD NR CONTRERAS, OH 45.4 96.7 2.5 .4 .4432 M FK E FK WW R 2500 FT US SR 227 NR MIDDLEBORO, IN 107 91.4 7.6 .3 .7433 ELKHORN CK 5000 FT US USHWY 27 NR LOCUST GROVE, IN 50.8 87.0 11.1 .3 1.6434 ELKHORN CK 6600 FT US USHWY 27 NR LOCUST GROVE, IN 50.4 87.3 10.9 .3 1.5435 WILSON CK 700 FT DS SR 1 NR EVERTON, IN 3.3 82.7 15.2 2.1 .1436 BULL FK 2 MI US STIPPS HILL RD NR BUENA VISTA, IN 7.1 97.5 2.5 0 0437 WHITEWATER R 2 ML DS E MILTON RD NR MILTON, IN 520 89.1 8.6 1.3 1.0438 WHITEWATER R 2 MI DS USHWY 52 NR METAMORA, IN 1,949 79.1 18.7 1.4 1.0439 WHITEWATER R 2 MI DS LAUREL RD NR LAUREL, IN 1,557 83.6 13.9 1.5 1.0440 MORGAN CK 2600 FT US MEYERS RD NR WILLIAMSBURG, IN 4.2 95.7 4.1 0 .2441 GREENS FK 1200 FT US SR 38 AT GREENS FK, IN 172 92.8 5.7 .7 .8442 E FK BIG CEDAR CK 2 MI US SR 252 NR PALESTINE, IN 13.6 94.4 5.1 0 .5443 WHITEWATER R 2900 FT DS CR 440N AT WATERLOO, IN 805 89.7 8.2 1.1 1.1445 CENTERAL RUN 7100 FT US CHAPEL RD NR PINHOOK, IN 7.4 96.4 3.4 0 .2

Minimum 3.3 51.5 1.8 0 0

Mean 345.0 86.7 11.0 1.7 .6

Median 50.6 89.2 8.4 .3 .6

Maximum 2,134 98.2 48.4 22.1 1.6

Standard deviation 613.5 9.9 9.1 4.2 .4
18 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002 Table 4. Basin characteristics of the 76 algal-biomass sampling sites in the Whitewater River and East Fork White River Basins, Indiana, May through September 2002.— Continued [IDEM, Indiana Department of Environmental Management; USGS, U.S. Geological Survey; ID, identification number; USEPA, U.S. Environmental Protection Agency; FT, feet; US, upstream; R, River; RD, Road; CR, County Road; SR, State Route; DS, downstream; CK, Creek; FK, Fork; DCH, Ditch; NR, near; AV, Avenue; ST, Street; N, North; S, South; E, East; W, West; IN, Indiana; OH, Ohio; trib, tributary; USHWY, U.S. Highway; RMI, River mile] Short IDEM site number1 USGS station name Drainage area (km2

)

Landuse (percentage)2

Ag Forest Urban Other

East Fork White River Basin

501 BIG BLUE R 2000 FT N NORTH RD AT NEW CASTLE,IN 113 85.7 9.7 1.6 3.0502 SAND CK 1450 FT N CR 850N NR BREWERSVILLE, IN 34 81.0 16.0 2.5 .5503 CLIFTY CK 840 FT N CR 400N NR ADAMS, IN 145 96.0 3.4 .1 .4504 E FK WHITE R 1 RMI US MUSCATATUCK R NR MEDORA, IN 6,662 85.3 10.5 2.8 1.3505 FLATROCK R 300 FT DS CR 150W NR FLATROCK, IN 1,037 93.4 4.6 1.1 1.0506 LITTLE SALT CK 400 FT DS CR 650N NR COVEYVILLE, IN 113 21.7 77.9 .3 .1508 BOGGS CK 1600 FT DS CR 15 NR LOOGOOTEE, IN 224 33.2 57.1 .6 9.2509 BIG BLUE R 1400 FT W CR 450W NR KNIGHTSTOWN, IN 414 84.6 8.9 4.9 1.5510 FLATROCK R 900 FT N CR 800N AT ST LOUIS CROSSING, IN 1,280 93.4 4.2 1.4 1.0511 VERNON FK MUSC R 2700 FT E CR 400 S NR HAYDEN, IN 595 61.0 36.5 1.3 1.2512 E FK WHITE R I MI N CR 500 S NR YOCKEY, IN 10,355 76.2 19.5 2.3 2.0513 BIG BLUE R 1200 FT N CR 500S NR GREENSBORO, IN 176 78.3 10.5 8.6 2.6515 LITTLE SALT CK 2700 FT S SR 258 AT FREETOWN, IN 28.8 39.1 58.9 .2 1.7516 BEAVER CK 900 FT S CR 44 AT IRONTON, IN 179 22.4 76.6 .2 .8518 WYALOOSING CK 200 FT S 900N NR SARDINIA, IN 62.1 89.1 9.9 .6 .4519 SUGAR CK 1000 FT W CR 1000N NR ZENAS, IN 18.4 66.5 33.2 0 .3521 LITTLE FLATROCK R 2700 FT W SR 3 NR MILROY, IN 120 96.5 2.5 .6 .4522 S FK SALT CK 1200 FT N SR 58 NR KURTZ, IN 75.8 40.8 58.0 .5 .8523 BIG CK I MI W CR 700W AT VOLGA, IN 215 43.8 44.3 1.2 10.7524 E FK WHITE R 4000 FT W CR 400E NR THALES, IN 14,362 65.8 29.9 2.2 2.1525 BIG BLUE R 2700 FT E CR 750W NR MT AUBURN, IN 1,480 89.6 6.1 3.0 1.3526 E FK WHITE R 1300 FT W CR 450W NR COXTON, IN 12,196 69.3 26.0 2.5 2.2
Comparison of the Data to Ecoregion Nutrient Criteria 19

Table 4. Basin characteristics of the 76 algal-biomass sampling sites in the Whitewater River and East Fork White River Basins, Indiana, May through September 2002.—Continued[IDEM, Indiana Department of Environmental Management; USGS, U.S. Geological Survey; ID, identification number; USEPA, U.S. Environmental Protection Agency; FT, feet; US, upstream; R, River; RD, Road; CR, County Road; SR, State Route; DS, downstream; CK, Creek; FK, Fork; DCH, Ditch; NR, near; AV, Avenue; ST, Street; N, North; S, South; E, East; W, West; IN, Indiana; OH, Ohio; trib, tributary; USHWY, U.S. Highway; RMI, River mile]

Short IDEM 

site number1 USGS station name Drainage area (km2) Landuse (percentage)2 Ag Forest Urban Other

527 BIG CK 900 FT E SR 3 NR DEPUTY, IN 415 54.2 37.6 1.4 6.8528 BEAR CK 200 FT N CR 400N NR OTWELL, IN 12.1 93.7 6.3 0 0530 MUSCATATUCK R 2600 FT N MT EDEN RD NR MILLPORT, IN 2,898 60.4 34.5 1.5 3.5531 N FK SALT CK 2250 FT US SR 46 AT BELMONT, IN 278 14.5 83.6 .5 1.3532 E FK WHITE R 100 FT N WILLIAMS RD NR HURON, IN 12,311 69.1 26.2 2.5 2.2533 SUGAR CK 1500 FT DS CR 1000N NR PLEASANT VIEW, IN 327 92.5 4.4 2.2 .8534 VERNON FK MUSC R 1150 FT US WWTF AT N VERNON, IN 284 70.5 28.0 .7 .8535 FALL FK 650 FT N SR 3 AT EWINGTON, IN 9.3 98.4 .2 1.3 .1536 MUSCATATUCK R 1200 FT E MT EDEN RD NR MILPORT, IN 2,799 61.4 33.4 1.6 3.6537 FLATROCK R 500 FT DS CR 450S NR MILROY, IN 505 93.9 3.5 1.6 1.0539 GRAHAM CK 300 FT S CR 350E AT WALNUT RIDGE, IN 195 48.2 44.7 .3 6.8542 BIG BLUE R 2400 FT W SR 31 AT EDINBURGH, IN 1,520 89.5 6.2 2.9 1.4543 VERNON FK MUSC R 1800 FT E CR 800E NR RETREAT, IN 993 63.9 32.2 1.9 2.0544 LOST R 100 FT N CR 450N NR ORLEANS, IN 86.8 91.7 7.7 .1 .4545 SUGAR CK 2600 FT E CR 350S AT AMITY, IN 891 91.3 4.0 4.0 .7551 SUGAR CK 500 FT N CR 600N NR MAXWELL, IN 147 94.1 4.4 .6 .9

Minimum 9.3 14.5 .2 0 0

Mean 1,943.8 71.1 25.3 1.6 2.0

Median 305.8 77.3 17.7 1.4 1.2

Maximum 14,362 98.4 83.6 8.6 10.7

Standard deviation 3,825.5 23.8 23.4 1.6 2.4

1The full IDEM site number has a prefix of INRB, for example INRB02-401.2Land use percentages were determined by the USGS using the National Land Cover Dataset (U.S. Geological Survey, 2000).
20 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002

Table 5. Total Kjeldahl nitrogen as N values collected in 2002 from the Indiana Department of Environmental Management/U.S. 

Geological Survey study and the published U.S. Environmental Protection Agency values for Aggregate Nutrient Ecoregions VI and IX 

and Level III Ecoregions 55 and 71.

[All data except number of streams are total Kjeldahl nitrogen as nitrogen values in milligrams per liter; N, nitrogen; IDEM, Indiana Department of Environmental Management; USGS, U.S. Geological Survey; USEPA, U.S. Environmental Protection Agency; shading indicates value exceeds published U.S. Environmental Protection Agency value for Aggregate Nutrient Ecoregions VI and IX, all seasons; bold text indicates value exceeds published U.S. Environmental Protection Agency value for Level III Ecoregions 55 and 71 reference conditions, all seasons; nc, not calculated in U.S. Environmental Protection Agency Nutrient 

Criteria documents]

Statistic

IDEM/

USGS 

values

USEPA values, 

all seasons1

IDEM/

USGS 

values

USEPA values, 

all seasons

IDEM/

USGS 

values

USEPA values, 

all seasons

Aggregate 

Nutrient

Ecoregion VI2

Level III 

Ecoregion 552

Aggregate 

Nutrient

Ecoregion IX3

Level III 

Ecoregion 713

Number of streams 38 628 198 13 1,609 12 65

Minimum value .240 .025 .050 .265 .000 .265 .050

10th percentile .300 nc nc .350 nc .350 nc

25th percentile .430 .591 .400 .490 .300 .465 .284

50th percentile .578 nc nc .710 nc .683 nc

75th percentile .650 nc nc .790 nc .820 nc

90th percentile .820 nc nc .880 nc .880 nc

Maximum value 1.05 4.50 3.50 1.01 4.83 1.01 2.05

1

Values are the median of all seasons for all samples collected from a single stream.

2

U.S. Environmental Protection Agency, 2000a.

3

U.S. Environmental Protection Agency, 2000b.
Comparison of the Data to Ecoregion Nutrient Criteria 21

Table 6. Nitrite plus nitrate as N values collected in 2002 from the Indiana Department of Environmental Management/

U.S. Geological Survey study and the published U.S. Environmental Protection Agency values for Aggregate Nutrient Ecoregions VI and 

IX and Level III Ecoregions 55 and 71.

[All data except number of streams are nitrite plus nitrate as nitrogen values in milligrams per liter; N, nitrogen; IDEM, Indiana Department of Environmental 

Management; USGS, U.S. Geological Survey; USEPA, U.S. Environmental Protection Agency; shading indicates value exceeds or equals published U.S. Environmental Protection Agency value for Aggregate Nutrient Ecoregions VI and IX, all seasons; all seasons; nc, not calculated in U.S. Environmental Protection 

Agency Nutrient Criteria documents]

Statistic

IDEM/

USGS 

values

USEPA 

values, 

all seasons1

IDEM/

USGS 

values

USEPA values, 

all seasons

IDEM/

USGS 

values

USEPA values, 

all seasons

Aggregate 

Nutrient

Ecoregion VI2

Level III 

Ecoregion 552

Aggregate 

Nutrient

Ecoregion IX3

Level III 

Ecoregion 713

Number of streams 38 717 219 13 1,671 12 109

Minimum value .125 .010 .025 .060 .000 .060 .008

10th percentile .380 nc nc .072 nc .072 nc

25th percentile 1.60 .633 1.60 .395 .125 .274 .345

50th percentile 3.00 nc nc .915 nc .778 nc

75th percentile 4.20 nc nc 2.50 nc 2.03 nc

90th percentile 6.40 nc nc 4.10 nc 2.97 nc

Maximum value 7.85 10.7 8.13 5.00 9.78 5.00 5.37 

1

Values are the median of all seasons for all samples collected from a single stream.

2

U.S. Environmental Protection Agency, 2000a.

3

U.S. Environmental Protection Agency, 2000b.
22 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002

Table 7. Total nitrogen as N values collected in 2002 from the Indiana Department of Environmental Management/

U.S. Geological Survey study and the published U.S. Environmental Protection Agency values for Aggregate Nutrient Ecoregions VI and 

IX and Level III Ecoregions 55 and 71.

[All data except number of streams are total nitrogen as nitrogen values in milligrams per liter; N, nitrogen; IDEM, Indiana Department of Environmental Management; USGS, U.S. Geological Survey; USEPA, U.S. Environmental Protection Agency; shading indicates a new minimum value or exceeds the published 

U.S. Environmental Protection Agency value for Aggregate Nutrient Ecoregions VI and IX, all seasons; bold text indicates a new minimum value or exceeds the 

published U.S. Environmental Protection Agency value for Level III Ecoregions 55 and 71 reference conditions, all seasons; nc, not calculated in U.S. Environmental Protection Agency Nutrient Criteria documents]

Statistic

IDEM/

USGS 

values

USEPA 

values, 

all seasons1

IDEM/

USGS 

values

USEPA values, 

all seasons

IDEM/

USGS 

values

USEPA values, 

all seasons

Aggregate 

Nutrient

Ecoregion VI2

Level III 

Ecoregion 552

Aggregate 

Nutrient

Ecoregion IX3

Level III 

Ecoregion 713

Number of streams 38 77 2 13 274 12 10

Minimum value .560 .885 3.63 .758 .240 .758 .625

10th percentile 1.37 nc nc .950 nc .950 nc

25th percentile 2.19 2.18 3.63 1.04 .692 1.02 .800

50th percentile 3.58 nc nc 1.45 nc 1.44 nc

75th percentile 4.69 nc nc 2.97 nc 2.44 nc

90th percentile 7.04 nc nc 4.75 nc 3.46 nc

Maximum value 8.23 10.1 3.78 5.51 12.4 5.51 4.35 

1

Values are the median of all seasons for all samples collected from a single stream.

2

U.S. Environmental Protection Agency, 2000a.

3

U.S. Environmental Protection Agency, 2000b.

The IDEM/USGS values for TN fell within or were close 

to the range of the published values for Ecoregions VI, IX, 55, 

and 71 (table 7). The IDEM/USGS 25th-percentile TN values 

were greater than published values for Ecoregions VI, IX and 

71. New minimum concentrations were measured for Ecoregions VI and 55 and new maximum concentrations were measured for Ecoregions 55 and 71. If the proposed USEPA TN 

water-quality criteria for Ecoregions VI and IX were enacted, 

70.5 percent of the individual samples collected in Ecoregion 

VI and 91.3 percent of the samples in Ecoregion IX would 

have exceeded those criteria.

The IDEM/USGS values for TP fell within the range of 

the published values for Ecoregions VI, IX, 55, and 71 (table 

8). The IDEM/USGS 25th-percentile TP values were less than 

values for Ecoregions VI, IX, 55, and 71. The IDEM/USGS 

maximum concentrations were about 10 times lower than for 

Ecoregions VI, IX, 55, and 71. If the proposed USEPA TP 

water-quality criteria for Ecoregions VI and IX were enacted, 

46.0 percent of the individual samples collected in Ecoregion 

VI and 72.5 percent of the samples in Ecoregion IX would 

have exceeded those criteria.

The IDEM/USGS values for mean periphyton CHLa 

provided a new range for Ecoregions VI, 55, and 71 (table 

9). The IDEM/USGS 25th-percentile mean periphyton CHLa 

value was greater than the published value for Ecoregion IX. 

The IDEM/USGS maximum concentration was about two 

times higher than that for Ecoregion IX. No criteria were set 

for Ecoregions VI, 55, or 71. If the proposed USEPA mean 

periphyton CHLa water-quality criterion for Ecoregion IX 

were enacted, 72.5 percent of the individual samples collected 

in Ecoregion IX would have exceeded that criterion.

The IDEM/USGS values for mean seston CHLa fell 

within or were close to the range of the published values 

for Ecoregions VI, IX, and 71 and provided a new range for 

Ecoregion 55 (table 10). The IDEM/USGS 25th-percentile 

mean seston CHLa values were less than published values for 
Comparison of the Data to Ecoregion Nutrient Criteria 23

Table 8. Total phosphorus as P values collected in 2002 from the Indiana Department of Environmental Management/

U.S. Geological Survey study and the published U.S. Environmental Protection Agency values for Aggregate Nutrient Ecoregions VI and 

IX and Level III Ecoregions 55 and 71.

[All data except number of streams are total phosphorus as phosphorus values in milligrams per liter; P, phosphorus; IDEM, Indiana Department of 

Environmental Management; USGS, U.S. Geological Survey; USEPA, U.S. Environmental Protection Agency; nc, not calculated in U.S. Environmental 

Protection Agency Nutrient Criteria documents]

Statistic

IDEM/

USGS 

values

USEPA 

values, 

all seasons1

IDEM/

USGS 

values

USEPA values, 

all seasons

IDEM/

USGS 

values

USEPA values, 

all seasons

Aggregate 

Nutrient

Ecoregion VI2

Level III 

Ecoregion 552

Aggregate 

Nutrient

Ecoregion IX3

Level III 

Ecoregion 713

Number of streams 38 815 225 13 2,104 12 117

Minimum value .015 .005 .010 .015 .000 .015 .003

10th percentile .032 nc nc .015 nc .015 nc

25th percentile .043 .076 .063 .033 .037 .029 .030

50th percentile .063 nc nc .055 nc .057 nc

75th percentile .084 nc nc .062 nc .068 nc

90th percentile .150 nc nc .105 nc .105 nc

Maximum value .210 2.23 1.82 .130 2.40 .130 1.28 

1

Values are the median of all seasons for all samples collected from a single stream.

2

U.S. Environmental Protection Agency, 2000a.

3

U.S. Environmental Protection Agency, 2000b.

Ecoregions VI, IX, and 71. A new minimum concentration for 

Ecoregion IX and a new maximum concentration for Ecoregion 71 were established. No criteria were set for Ecoregion 

55. If the proposed USEPA mean seston water-quality criteria 

for Ecoregions VI and IX were enacted, 56.9 percent of the 

individual samples collected in Ecoregion VI and 70.6 percent 

of the samples in Ecoregion IX would have exceeded those 

criteria.
24 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002

Table 9. Mean periphyton chlorophyll a values collected in 2002 from the Indiana Department of Environmental Management/U.S. 

Geological Survey study and the published U.S. Environmental Protection Agency values for Aggregate Nutrient Ecoregions VI and IX 

and Level III Ecoregions 55 and 71.

[All data except number of streams are mean periphyton chlorophyll a values in milligrams per square meter; IDEM, Indiana Department of Environmental 

Management; USGS, U.S. Geological Survey; USEPA, U.S. Environmental Protection Agency; shading indicates value exceeds published U.S. Environmental 

Protection Agency value for Level II Ecoregions VI and IX, all seasons; nd, no data collected or published in U.S. Environmental Protection Agency Nutrient 

Criteria documents; nc, not calculated in U.S. Environmental Protection Agency Nutrient Criteria documents] 

Statistic

IDEM/

USGS 

values

USEPA values, 

all seasons1

IDEM/

USGS 

values

USEPA values, 

all seasons

IDEM/

USGS 

values

USEPA values, 

all seasons

Aggregate 

Nutrient

Ecoregion VI2

Level III 

Ecoregion 552

Aggregate 

Nutrient

Ecoregion IX3

Level III 

Ecoregion 713

Number of streams 38 nd nd 13 6 12 nd

Minimum value 2.89 nd nd 11.6 11.0 11.6 nd

10th percentile 12.3 nd nd 17.6 nc 17.6 nd

25th percentile 35.1 nd nd 26.4 20.4 29.1 nd

50th percentile 55.5 nd nd 47.4 nc 47.8 nd

75th percentile 70.9 nd nd 80.6 nc 80.9 nd

90th percentile 97.7 nd nd 81.4 nc 81.4 nd

Maximum value 288 nd nd 113 62.0 113 nd

1

Values are the median of all seasons for all samples collected from a single stream.

2

U.S. Environmental Protection Agency, 2000a.

3

U.S. Environmental Protection Agency, 2000b.
Comparison of the Data to Ecoregion Nutrient Criteria 25

Table 10. Mean seston chlorophyll a values collected in 2002 from the Indiana Department of Environmental Management/U.S. 

Geological Survey study and the published U.S. Environmental Protection Agency values for Aggregate Nutrient Ecoregions VI and IX 

and Level III Ecoregions 55 and 71.

[All data except number of streams are mean seston chlorophyll a values in micrograms per liter; IDEM, Indiana Department of Environmental Management; 

USGS, U.S. Geological Survey; USEPA, U.S. Environmental Protection Agency; bold text indicates a new minimum value or exceeds the published U.S. Environmental Protection Agency value for Level III Ecoregions 55 and 71 reference conditions, all seasons; nd, no data collected or published in U.S. Environmental Protection Agency Nutrient Criteria documents; nc, not calculated in U.S. Environmental Protection Agency Nutrient Criteria documents] 

Statistic

IDEM/

USGS 

values

USEPA values, 

all seasons1

IDEM/

USGS 

values

USEPA values, 

all seasons

IDEM/

USGS 

values

USEPA values, 

all seasons

Aggregate 

Nutrient

Ecoregion VI2

Level III 

Ecoregion 552

Aggregate 

Nutrient

Ecoregion IX3

Level III 

Ecoregion 713

Number of streams 38 63 nd 13 71 12 9

Minimum value .993 .250 nd .807 .225 .807 2.60

10th percentile 1.30 nd nd .910 nd .910 nd

25th percentile 2.10 2.70 nd 2.02 2.25 2.00 3.85

50th percentile 2.95 nc nd 3.48 nc 3.91 nc

75th percentile 4.22 nc nd 7.28 nc 7.45 nc

90th percentile 6.07 nc nd 8.20 nc 8.20 nc

Maximum value 20.8 47.6 nd 19.4 36.7 19.4 15.4 

1

Values are the median of all seasons for all samples collected from a single stream.

2

U.S. Environmental Protection Agency, 2000a.

3

U.S. Environmental Protection Agency, 2000b.
26 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002

Conclusions

Excessive inputs of nutrients into streams have humanhealth, economic, and ecological consequences. In 2000, the 

USEPA proposed nutrient water-quality criteria to protect 

streams from excess nutrients. This report is one of several 

reports done as a cooperative effort between IDEM and the 

USGS to collect new data to assist IDEM in determination 

of nutrient criteria. Data were gathered at 38 sites in both the 

Whitewater River and East Fork White River Basins, Indiana 

from May through September 2002, on algal biomass, habitat, 

nutrients, and biological communities (fish and invertebrates). Basin characteristics (land use and drainage area) 

and biological-community attributes and metric scores were 

determined for the basin of each sampling site. The yearly 

Principal Components Analysis site scores were calculated for 

algal biomass (periphyton and seston). The yearly Principal 

Components Analysis site scores for the first axis (PC1) were 

related using Spearman’s rho to the algal-biomass, habitat, 

basin-characteristics, nutrient, biological-community attribute 

and metric score data.

On the basis of this initial analysis in the Whitewater 

River and East Fork White River Basins, periphyton PC1 does 

not relate to nutrient variables; no significant relations were 

found between nutrients and periphyton PC1 in similar studies conducted in 2001 in the West Fork White River and in 

2003 in the Upper Wabash River Basin. Significant relations 

between nitrogen variables and seston algal biomass were 

found in late summer (July) and fall (September) but not in the 

spring. Significant relations between seston algal biomass and 

TP were found throughout the growing season. Based on the 

preliminary analysis in this report, fish-community attributes 

and metric scores may reflect the effects of algal biomass 

better than invertebrate-community attributes and metric 

scores. There were significant relations between periphyton 

and seston algal biomass and fish-community attributes and 

metrics. As periphyton algal biomass increases, fish-community composition shifts from one dominated by carnivores and 

other niche-specific specialists to one dominated by generalistfeeding and pioneer species.

There was one significant relation between periphyton 

or seston algal biomass and invertebrate communities. This 

lack of relations may be the result of three possible factors: (1) 

sample size, (2) sample method, and (3) resolution of invertebrate data. Additionally, previous studies and results from 

this analysis suggest that drainage-basin size and land use are 

factors affecting the relations between algal biomass, nutrients, 

and biological communities. 

The values for nutrients (nitrate, TKN, TN, and TP) and 

CHLa (periphyton and seston) were compared to published 

USEPA values for the respective ecoregions. CHLa (periphyton and seston) values either were greater than 25th-percentile 

published USEPA values or extended data ranges in Aggregate 

Nutrient and Level III Ecoregions. If the values for the 25th 

percentile proposed by the USEPA were adopted as nutrient 

water-quality criteria, the percentage of samples in the Whitewater River and East Fork White River Basins that would have 

exceeded these criteria ranged from 46.0 percent in Ecoregion 

VI for TP to 91.3 percent in Ecoregion IX for TN.

Acknowledgments

The authors thank Indiana Department of Environmental Management and U.S. Geological Survey personnel for 

collecting and processing the data. We thank Patricia H. Long 

and Donald R. Leer of the USGS for editorial support and 

Dennis Clark (IDEM) and Stephen D. Porter (USGS) for their 

technical reviews of the manuscript. Projects of this type are 

a team effort and could not have been completed without the 

efforts of the IDEM and USGS personnel, which are sincerely 

appreciated.
Conclusions, Acknowledgments, and References 27

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30 Relations of PCA Site Scores in the Whitewater River and East Fork White River Basins, Indiana, 2002

Appendix 1. Metrics used by Indiana Department of Environmental Management for habitat, fish, and invertebrates (Dufour, 2002).

Metrics1 Definition

Habitat 

SubstrateScore A metric to evaluate substrate type, origin, silt cover, and embeddedness.

InstreamCoverScore Instream cover types and the amount (availability) of instream cover.

ChannelMorphologyScore Quality of the stream channel related to the creation and stability of instream habitat (channel 

sinuosity, channel development, channelization, stability, and modifications).

RiparianZoneandBankErosionScore Quality of the riparian buffer zone and flood-plain vegetation, looking at riparian width, 

predominant surrounding land uses, and bank-erosion status.

PoolGlideQualityScore Quality of pool/glide taking into account maximum pool depth, morphology, and velocity.

RiffleRunQualityScore Quality of riffle/run, taking into account riffle/run depth, substrate, and embeddedness.

GradientScore A measure of the influence of gradient and stream size on the biological community and available 

habitat.

Fish2

SpeciesCount Number of species, excluding hybrid species (exclude gizzard shad if in the Wabash River 

mainstem and drainage area is greater than 5,180 square kilometers).

DMS_SpeciesCount Number of darter, madtom, and sculpin species, excluding hybrid species.

Darter_SpeciesCount Number of darter species, excluding hybrid species.

Headwater_Percent Percent of headwater individuals.

LargeRiver_Percent Percent of large river individuals (exclude gizzard shad if in the Wabash River mainstem and 

drainage area greater than 5,180 square kilometers).

Sunfish_SpeciesCount Number of sunfish species, excluding hybrid species.

Centrarchid_SpeciesCount Number of centrarchidae species, excluding hybrid species. 

Minnow_SpeciesCount Number of minnow species, excluding hybrid species.

Sucker_SpeciesCount Number of sucker species, excluding hybrid species. 

RoundBodySucker_SpeciesCount Number of round-body sucker species, excluding hybrid species.

Salmonid_SpeciesCount Number of salmonid species, excluding hybrid species.

Sensitive_SpeciesCount Number of sensitive species, excluding hybrid species.

Tolerant_Percent Percent of tolerant individuals (exclude gizzard shad if in the Wabash River mainstem and drainage 

area greater than 5,180 square kilometers).

Omnivore_Percent Percent of omnivore individuals (exclude gizzard shad if in the Wabash River mainstem and 

drainage area greater than 5,180 square kilometers).

Insectivore_Percent Percent of insectivore or invertivore individuals (exclude gizzard shad if in the Wabash River 

mainstem and drainage area greater than 5,180 square kilometers).

Pioneer_Percent Percent of pioneer individuals.

Carnivore_Percent Percent of carnivore or piscivore individuals (exclude gizzard shad if in the Wabash River mainstem and drainage area greater than 5,180 square kilometers).

CatchPerUnitEffort Catch per unit effort (CPUE) or total number of individuals.

CPUElessShads Catch per Unit Effort (CPUE), excluding the number of gizzard shad individuals if in the Wabash 

River mainstem and drainage area greater than 5,180 square kilometers).

SimpleLithophil_Percent Percent of simple lithophilic species (exclude gizzard shad if in the Wabash River mainstem and 

drainage area greater than 5,180 square kilometers).

DELT_Percent

Percent of individuals with deformities, eroded fins, lesions, and tumors (DELT), including 

multiple DELTs (exclude gizzard shad if in the Wabash River mainstem and drainage area 

greater than 5,180 square kilometers).
Appendix 1 31

Invertebrates

Family Level HBI Summation of the tolerance value times the number of individuals for a specific family divided by 

the total count of individuals for families with a tolerance value.

Number of Taxa Number of families identified in the subsample.

Number of Individuals Total number of individuals for all families identified in the subsample.

Percent Dominant Taxa Highest number of individuals for a given family divided by the total number of individuals in the 

subsample.

EPT Index Total number of families represented in the orders Ephemeroptera, Plecoptera, and Trichoptera.

EPT Count Total number of individuals for orders Ephemeroptera, Plecoptera, and Trichoptera.

EPT Count to Total Number of Individuals Total number of individuals for orders Ephemeroptera, Plecoptera, and Trichoptera divided by the 

total number of individuals in the subsample.

EPT Count to Chironomid Count Total number of individuals for orders Ephemeroptera, Plecoptera, and Trichoptera divided by the 

total number of chironomidae.

Chironomid Count Total number of chironomids in the subsample.

Total Number of Individuals to Number of 

Squares Sorted

Total number of individuals in the subsample divided by the number of squares needed to reach the 

total number of individuals.

1

Each of the fish- and invertebrate community metrics also has a corresponding attribute with the same name but consists of the raw data. 

2

 Specific fish species associated with each metric can be found in Dufour, 2002. 

Caskey, Frey, and Lowe—Relations of Principal Components Analysis Site Scores to Algal-Biomass, Habitat, Basin-Characteristics, Nutrient, and BiologicalCommunity in the Whitewater River and East Fork White River Basins, Indiana, 2002—Scientific Investigations Report 2007–5229

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