Chemical Quality of Base Flow in 

18 Selected Streams in the Upper 

Susquehanna River Basin, New York

U.S. Department of the Interior

U.S. Geological Survey

Water-Resources Investigations Report 03-4100

In cooperation with New York State Department of Environmental Conservation
This page has been left blank intentionally.
i Contents

Chemical Quality of Base Flow in 18 Selected Streams 

in the Upper Susquehanna River Basin, New York

By Kari K. Hetcher, Todd S. Miller, and Steven C. Komor

U.S. GEOLOGICAL SURVEY 

Water-Resources Investigations Report 03-4100

In cooperation with

NEW YORK STATE DEPARTMENT OF ENVIRONMENTAL CONSERVATION

Ithaca, New York

2004
ii Contents

U.S. DEPARTMENT OF THE INTERIOR

GAIL NORTON, Secretary

U.S. GEOLOGICAL SURVEY

Charles G. Groat, Director

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

is for descriptive purposes only and does not imply

endorsement by the U.S. Government

For additional information Copies of this report can be

write to: purchased from:

Subdistrict Chief U.S. Geological Survey

U.S. Geological Survey Branch of Information Services

30 Brown Road Box 25286

Ithaca, NY 14850 Denver, CO 80225

Web: http://ny.usgs.gov Web: http://www.usgs.gov
Contents III

CONTENTS

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

I. Introduction 

A. Base-Flow Concerns and Study Objectives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

B. Study-Area Characteristics and Quality-Control Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

II. Base-Flow-Separation Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

III. Hydrogeology 

A. Air-Temperature and Precipitation Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

B. Precipitation, Runoff, Evapotranspiration, and Recharge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 

C. Bedrock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

D. Surficial Material . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

IV. Water Quality 

A. Sampling-Site Locations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

B. Inorganic Constituents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

C. Effect of Carbonate Bedrock on Base-Flow Quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

D. Nitrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

E. Nitrate - Seasonal Patterns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

F. Nitrate - Spatial Patterns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

G. Pesticides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

H. Detected Herbicides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

I. Two Streams with Anomalous Salt and Herbicide Concentrations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

V. Age Dating of Well Water to Detect Induced Infiltration 

A. Dating Technique . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

B. Results and Interpretation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Summary and Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

References Cited . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Figures

1. Location of 18 surface-water sampling sites and 4 production wells, and principal geographic features of 

the upper Susquehanna River Basin between Millers Mills and Conklin, New York. . . . . . . . . . . . . . . . . . . . . . . . . . 3

2. Annual mean base flow as percentage of total annual streamflow for the period 1941-93 at four streamflow-gaging 

stations in study area. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

3. A. Mean monthly air temperature and precipitation at Cooperstown and Bainbridge weather stations in upper 

Susquehanna River Basin, N.Y., 1960-90. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

B. Annual mean precipitation and runoff in the upper Susquehanna River Basin, N.Y., 1951-80 . . . . . . . . . . . . . . . . . 11

C. Bedrock geology of the upper Susquehanna River Basin, N.Y. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

D. Surficial geology of the upper Susquehanna River Basin, N.Y. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

4. A. Land use in the upper Susquehanna River basin, N.Y. and land-use categories in the 18 subbasins sampled 

in 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

B. Concentrations of inorganic constituents in base-flow samples collected in January and June 2001 in the upper 

Susquehanna River Basin, N.Y. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

C. Mean concentrations of calcium and alkalinity, and mean specific conductance, for water samples collected

during base-flow conditions in Areas A and B of the upper Susquehanna River Basin, N.Y., January and 

June 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

D. Agricultural field in the upper Susquehanna River Basin, N.Y. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

E. Nitrate concentration and discharge of five streams within the upper Susquehanna River Basin, N.Y., on 

selected base-flow sampling dates, 2001, by land-use and bedrock category . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
IV Contents

F. Median nitrate concentrations in base-flow samples from the 18 stream sites in the upper Susquehanna River 

Basin, N.Y., January and June 2001, by land-use category. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

G. Locations of the 12 sites in the upper Susquehanna River Basin, N.Y., where water samples were analyzed for 

pesticides, November 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

H. Concentrations of the six herbicides detected (atrazine, deethylatrazine, alachlor ESA, metolachlor, and its two 

metabolites) in relation to land use at the 12 sites sampled under base-flow conditions in the upper Susquehanna 

River Basin, N.Y., November 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

I. Concentrations of sodium, chloride, iron, manganese, and four herbicides detected in base-flow samples from 

sites 14 and 16 in relation to those at all other sites and in relation to Federal water-quality standards . . . . . . . . . . . 33

5. Locations of wells near Susquehanna River that were used for chlorofluorocarbon (CFC) analysis . . . . . . . . . . . . . . . 35

Tables

1. Site information, land use, and stream discharge at 18 surface-water sampling sites within the upper Susquehanna 

River Basin study area, N.Y., January and June 2001. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2. Mean, median, maximum, and minimum values for solutes, pH, and specific conductance of base-flow samples 

from upper Susquehanna River Basin study area, N.Y., January and June 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

3. Median concentrations of calcium and alkalinity and specific conductance values in base-flow samples from Area 

A (underlain by carbonate bedrock) and Area B (underlain by noncarbonate bedrock), January and June 2001 . . . . . 20

4. Six biological transformation processes of the nitrogen cycle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

5. Mean, median, maximum, and minimum concentrations of nitrate in base-flow samples from upper Susquehanna 

River Basin study area, N.Y., by land-use and bedrock category, January and June 2001 . . . . . . . . . . . . . . . . . . . . . . . 27

6. Pesticides for which base-flow samples collected from 12 sites in upper Susquehanna River Basin in November 

2001 were analyzed. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

7. Sites and concentrations at which herbicides were detected in November 2001 base-flow samples from upper 

Susquehanna River Basin, and Federal or State concentration limit (USEPA, 2000). . . . . . . . . . . . . . . . . . . . . . . . . . . 31

8. Data on the four production wells sampled for chlorofluorocarbons (CFCs) to estimate potential for induced 

infiltration of water from Susquehanna River in study area, February 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

9. Concentrations of CFCs in water samples from four production wells on the Susquehanna River in February 2001 

and the calculated model ages of the water (time of recharge) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Contents V

CONVERSION FACTORS AND VERTICAL DATUM

Multiply By To Obtain

Length

inch (in.) 2.54 centimeter

foot (ft) 0.3048 meter

mile (mi) 1.609 kilometer

Area

square mile (mi2) 2.59 square kilometer

Flow

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

inch per year (in/yr) 25.4 millimeter per year 

Mass

pound, avoirdupois (lb) 0.4536 kilogram (kg)

Temperature

degrees Fahrenheit ( ̊F)  ̊C = 5/9 ( ̊F-32) degrees Celsius 

Specific Conductance

microsiemens per centimeter at 25 ̊ Celsius (μS/cm)

Equivalent Concentration Terms

milligrams per liter (mg/L) = parts per million

micrograms per liter (μg/L) = parts per billion

Horizontal coordinate information is referenced to the North American Datum of 1927 (NAD 27).
VI Contents
Abstract 1

Chemical Quality of Base Flow in 18 Selected 

Streams in the Upper Susquehanna River 

Basin, New York

By Kari K. Hetcher, Todd S. Miller, and Steven C. Komor

ABSTRACT

The base-flow and runoff components of 

total streamflow at four selected sites in the upper 

Susquehanna River Basin in New York were 

calculated through hydrograph-separation 

techniques from long-term (1941-93) discharge 

records. Base flow was found to constitute more 

than 60 percent of the total annual flow of each 

stream. Base-flow samples were then collected at 

18 stream sites several times during 2001 to 

define the chemical quality of base flow. The 

concentrations of selected common ions, 

nutrients, and pesticides were plotted in relation 

to the amount of agricultural land and carbonate 

bedrock in the drainage basin upstream of each 

site. Sites were selected at locations distant from 

and unaffected by development and urban areas. 

Twelve of the sites were again sampled in 

November 2001 for pesticide analysis. 

The predominant cations detected in the 

samples were calcium, magnesium, and sodium; 

the major anions were chloride, sulfate, and 

bicarbonate. The predominant nutrient was 

nitrate. Higher nitrate concentrations in the winter 

samples than in the summer samples are attributed 

to the seasonal decrease in plant growth and 

microbial activity in the streams during the 

winter, which allows nitrate to persist in the 

stream water. Lower nitrate concentrations in the 

summer samples probably result from nitrogen 

uptake by vegetation and microbial activity in the 

streams. 

Base-flow samples from the agricultural, 

carbonate-rich northern part of the study area had 

higher concentrations of most inorganic chemical 

constituents than those from the forested, 

noncarbonate (shale, siltstone, and sandstone) 

central and southern parts. The highest nitrate 

concentrations were in samples from subbasins 

dominated by agricultural land, and the lowest 

were in subbasins dominated by forest. The 

concentrations in samples from subbasins with 

forested as well as agricultural land were 

intermediate. 

Six pesticides were detected in samples 

from 10 of the 12 sites. All were herbicides. The 

highest concentrations of pesticides, and the most 

frequent pesticide detections, were in samples 

from agricultural subbasins and large main-stem 

subbasins with mixed land use and mixed bedrock 

geology. A correlation was indicated between 

land use and concentrations of atrazine and 

deethylatrazine. The concentrations of all six 

compounds were at least an order of magnitude 

lower than New York State and Federal waterquality standards.

Ground water from four production wells in the 

villages of Afton, Sidney, Unadilla, and Otego was 

analyzed for chlorofluorocarbons (CFCs) to 

indicate the approximate age of the water in these 

wells and the potential for induced infiltration of 

river water. The water at two of these wells is 

probably between 26 and 50 years old; the ages of 

water at the other two wells could not be reliably 

estimated because of CFC contamination from a 

nonatmospheric source. The two wells for which 

CFC analysis gave relable results (Afton and 

Otego) probably do not induce infiltration of river 

water into the aquifer. 
2 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

I. INTRODUCTION

A. Base-flow concerns and study objectives 

Concentrations of nutrients, sediment, and other constituents in the Susquehanna River and 

Chesapeake Bay have been increasing for several decades. At least 60 percent of the annual 

discharge at four stream sites in the upper Susquehanna River Basin consists of base flow.

The chemical quality of base flow in streams in the northernmost part of the Susquehanna River Basin 

has not been extensively documented. This study was designed to calculate the base-flow contribution 

to total annual flow and document the chemical quality of base flow at selected sites.

The Susquehanna River Basin drains most of 

south-central New York and half of Pennsylvania and 

eventually flows into Chesapeake Bay, the nation’s 

largest estuary (fig. 1). Concentrations of nutrients, 

sediment, and other constituents in Chesapeake Bay 

have increased over the past 50 years as a result of 

deforestation, growth of urban areas, poor land 

management, and water-treatment plant effluent within 

its basin (Sprague, 2001; U.S. Environmental 

Protection Agency, 1988; Bell and others, 1996; Belval 

and others, 1995; Belval and Sprague, 1999). 

Concerns about water quality of Chesapeake 

Bay and its principal tributary, the Susquehanna River, 

have led to hydrologic investigations by several 

Federal, State, and local organizations, including the 

New York State Department of Environmental 

Conservation (NYSDEC), the Upper Susquehanna 

Coalition, the Susquehanna River Basin Commission, 

and the U.S. Geological Survey (USGS). Most of the 

assessments that were done in New York, which 

contains the uppermost part of the basin, addressed 

surface-water quality (Ku and others, 1975), surfacewater and ground-water quantity, or the interaction 

between surface water and ground water (MacNish 

and Randall, 1982; Randall, 1986; Randall and others, 

1988; Yager, 1986; Yager, 1993), but none investigated 

the chemical quality of base flow (the ground-water 

component of streamflow). Base flow is defined as the 

component of streamflow that remains when little or 

no precipitation or snowmelt has occurred for at least 5 

days and a hydrograph of the stream is steady or 

slowly declining. Most of the flow in the stream during 

base-flow conditions is derived from ground water; 

therefore, a base-flow sample is an approximation of 

the chemical quality of the ground water discharging 

to that stream.

In 2001, the USGS, in cooperation with the 

NYSDEC, began a 1-year study to (1) calculate the 

contribution of base flow to annual flow at four sites in 

the upper Susquehanna River Basin, (2) measure the 

concentrations of common ions and nutrients in base 

flow at 18 selected stream sites within the upper 

Susquehanna River Basin during the winter and 

summer of 2001, and (3) document whether the 

drainage basin above each site was mostly agricultural, 

mostly forested, or a mixture, and whether it was 

underlain by carbonate (limestone) bedrock, 

noncarbonate bedrock, or a mixture, for comparison 

with the analytical results. Sampling was done at 12 of 

the sites in November 2001 to document the 

concentrations of pesticides in base flow and their 

relation to the presence or absence of agricultural land 

within their drainage areas. 

This report (1) explains the base-flow separation 

analysis, (2) briefly summarizes the hydrogeologic 

conditions within the study area, (3) presents and 

interprets the results of the common-ion and nutrient 

analyses in relation to agricultural land use and 

bedrock geology, and the results of the pesticide 

analyses and their relation to agricultural land, and (4) 

estimates the age of ground water at 4 production wells 

on the Susquehanna River and the potential for 

induced infiltration of river water at these sites. This 

data can be used by water managers throughout the 

upper Susquehanna River Basin to compare the 

concentrations of chemical constituents in base flow to 

those in production wells, or in future studies to 

compare base-flow water quality to the water quality 

of stormflow.

Acknowledgments

The authors thank the landowners for permitting 

access to streams along their property, for allowing the 

installation of monitoring equipment, and for 

information on the history of their land. Thanks also 

are extended to the USGS colleagues who helped 

collect samples, interpret results, and prepare the 

graphics for this report. 
3

76o 75o

42o

43o

75o

42o

76o

43o

NEW YORK

PENNSYLVANIA

WEST

VIRGINIA

VIRGINIA

MARYLAND

DELAWARE Atlantic Ocean

+

73o45o

42o

80o

42o

80o

36o30' +

76o

36o30'

Location Map

Chesapeake Bay

Chesapeake Bay

Drainage Area

Susquehanna River Basin

Upper Susquehanna 

River Basin

study area

NJ

Susquehanna

River

76o

0

0

10 20 MILES

10 20 KILOMETERS

EXPLANATION

Base-flow sample site -- where samples were

collected for nutrient, inorganic chemical, and

pesticide analysis, names are given in table 1 

Municipal well -- from which water samples

were collected for chlorofluorocarbon (CFC)

analysis, April 2001

City or Village

Weather Station

7

Base from U.S. Census TIGER/line Files,1990, Albers equal-area conic projection 1:100,000 scale;

Streams are 1:2,000,000 scale

Susquehanna 

River

Susquehanna

River

Unadilla River

Wharton Creek

Otego Creek

Oaks Creek

Cherry Schenevus Creek

Charlotte Creek

Ouleout Creek

Creek

Valley

Butternut Creek

NEW YORK

PENNSYLVANIA

1

2

3

4

5

6

7 8

9

10

11

12 13

14

15

16

17

18

30-mile reach in which CFCs

were analyzed at 4 sites

Cooperstown

Index

Rockdale

Bainbridge

Conklin

Middlefield

Unadilla

Afton

Millers Mills

Otego

Oneonta

Windsor

DELAWARE

MADISON

CHENANGO

BROOME

HERKIMER

MONTGOMERY SCHOHARIE

ULSTER

SULLIVAN

OTSEGO

CORTLAND

FULTON

ONEIDA

Figure 1. Location of 18 surface-water sampling sites and 4 production wells, and principal geographic features 

of the upper Susquehanna River Basin between Millers Mills and Conklin, New York. (Site names are given in 

table 1.)

Introduction
4 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

I. INTRODUCTION (CONTINUED) 

B. Study-area characteristics and quality-control procedures

Base-flow samples were collected at 18 sites representing three 

land-use categories and three bedrock categories.

The sampling sites represent drainage areas dominated by forested, agricultural, or 

mixed land use underlain by carbonate bedrock, noncarbonate bedrock, or both. 

Base-flow samples were analyzed for common inorganic constituents, nutrients, and 

pesticides. Standard analytical and quality-control procedures were followed. 

The upper Susquehanna River Basin 

encompasses 2,235-mi2 in the northernmost part of the 

Susquehanna River Basin (fig. 1). The northern part of 

the study area is characterized by low relief and 

contains mostly agricultural land and wetlands, 

whereas the central and southern parts are 

characterized by moderate to high relief and a mixture 

of forested and agricultural land. The study area is 

predominantly rural; it contains one major city 

(Oneonta) and many scattered villages in the valleys. It 

consists mostly of undeveloped, forested land (71 

percent) and agricultural land (26 percent); 2 percent 

of the area consists of water, commercial, 

transportation, or other land uses, and the few urban or 

residential areas represent only about 1 percent of the 

area. Most of the developed areas are within the 

Susquehanna and Unadilla River valleys. Total 

population of the study area in 2000 was about 

112,000 (U.S. Bureau of Census, 2000). Communitywater-supply systems provide water to more than 

53,000 people in the study area (New York State 

Department of Health, 1982). Most of the watersupply systems primarily use ground water; the rest 

use surface water from reservoirs and lakes. 

The concentrations of certain chemical 

constituents in base flow can be related to land use, 

bedrock geology, and carbonate content of the surficial 

material. Base-flow samples were collected at 18 sites 

in January and June 2001; 9 sites also were sampled 

during August or September 2001. Twelve of the sites 

were resampled in November 2001 for pesticide 

analysis. Sampling sites were selected according to the 

predominant land use within their drainage 

basins—some represent mostly agricultural land, some 

mainly forested land, and others a mixture of both. 

Locations directly affected by contamination from 

urban runoff and point sources such as sewage outfalls 

were excluded. A description of all sites is given in 

table 1; their locations are shown in figure 1.

Water samples were collected and processed by 

methods described in Wilde and others (1998) and 

were analyzed for selected nutrients and inorganic 

constituents by the USGS at the National Water 

Quality Laboratory (NWQL) in Denver, Colo. 

Samples collected for pesticide analyses were 

collected and processed by the methods of Shelton 

(1994) and Sandstrom and others (2001) and were 

analyzed at the NWQL and the Kansas Organic 

Geochemistry Research Laboratory (OGRL) for 113 

pesticides and pesticide degradates through methods 

described by Zaugg and others (1995), Meyer and 

others (1993), and Ferrer and others (1997). The 

analytical method devised by Zaugg and others (1995), 

developed in cooperation with the U.S. Environmental 

Protection Agency, detects some of the most 

commonly used pesticides in the United States. 

Quality-assurance samples were collected to 

assess the accuracy and reproducibility of the 

analytical data. Blank and replicate samples were 

collected for at least 10 percent of the samples. Blank 

samples used either inorganic-grade blank water or 

pesticide-grade blank water provided by the USGS 

Water-Quality Services Unit in Ocala, Fla; no blank 

samples contained any constituents in concentrations 

above the detection limits of the analytical methods 

used. The replicate samples showed no statistically 

significant differences in concentrations of any of the 

constituents detected.

A pilot study was conducted within a 30-mile 

reach of the Susquehanna River valley (fig. 1) in 

February 2001 to calculate the age of ground water at 

four production wells that tap sand and gravel aquifers 

beneath the flood plain and to assess the likelihood that 

these wells are inducing infiltration of river water into 

the aquifer. Concentrations of chlorofluorocarbons 

(CFCs) in the samples were measured to estimate the 

age of the well water and to assess the likelihood of 

induced infiltration.
5

Table 1. Site information, land use, and stream discharge at 18 surface-water sampling sites within the 

upper Susquehanna River Basin study area, N.Y., January and June 2001.

[mi2

, square miles; agr, agricultural; Vt, valley tributary; Ut, upland headwater tributary; Vm, main-stem valley stream; 

carb, carbonate; noncarb, noncarbonate. Site locations are shown in fig. 1.]

1

 Station identifier is downstream-order station number assigned by U.S. Geological Survey.

2

 Drainage area upstream from sampling point. Data from U.S. Geological Survey (1997).

3 Land-use classification based on land-use percentages and field reconnaissance (site 14). Four of the six mixed-land-use sites (6, 10, 12, and 18) 

have drainage areas greater than 100 mi2

. They contain more forested land than agricultural land but also contain urban land, transportation 

corridors, and commercial land. These sites are on large streams that receive drainage from forested and agricultural subbasins and therefore are 

classified as mixed-land-use sites.

4 Sites 14 and 16 originate on the valley floor, not the upland, and most of their drainage areas are underlain by stratified glacial drift. The actual 

drainage area in such terrane is a function of the water-table configuration (not delineated in this study) and may not coincide with the topographic 

drainage divide on which the drainage-area value here is based.

5

 Discharge, in cubic feet per second (cfs), was measured at the time of sampling during base-flow conditions. 

Site

no. Station name

USGS 

station 

 number1

Lat./

long.

Drainage 

area

(mi2)

2

Land use

Type

of stream4

Bedrock 4

Stream 

discharge5 Category3

Percent of basin

Forest Agr Jan. June

1 Unadilla River at 

Millers Mills

01500832 425527/

0750508

2.2 agr 37.7 60.4 Vt carb 0.58 0.63

2 North Winfield Creek at 

West Winfield

01500850 425303/

0751120

16.0 agr 37.3 58.8 Vt carb 11.5 25.9

3 Cambell Brook at 

Lloydsville

01500859 424955/

0751317

3.5 forest 73.6 26.3 Ut carb 2.55 6.64

4 Shadow Brook at

East Springfield

01496330 424952/

0744906

7.0 agr 31.1 65.9 Vt carb 1.80 1.74

5 Dundee Brook tributary

at Brainard Corners

01501092 424728/

0750652

0.47 agr 46.4 53.6 Ut carb 0.40 0.19

6 Oaks Creek at Index 01496500 423956/

0745736

102.0 mixed 49.8 40.9 Vm carb 108 92.4

7 Butternut Creek at Morris 01502000 423243/

0751422

60.0 mixed 69.6 28.6 Vm noncarb 40.1 27.7

8 Schenevus Creek tributary 

southwest of Chaseville

01497818 423153/

0745139

0.75 forest 96.8 0.2 Ut noncarb 0.34 0.37

9 Upland tributary east of 

Portlandville

01497309 423147/

0745708

0.22 forest 99.8 0.2 Ut noncarb 0.11 0.08

10 Unadilla River at 

Rockdale

01502500 422240/

0752423

520.0 mixed 63.7 34.1 Vm noncarb 357 566

11 Unadilla Springs at 

Unadilla

0150050210 421957/

0751903

0.32 forest 77.6 22.1 Ut noncarb 0.02 0.02

12 Susquehanna River at 

Unadilla

01500500 421917/

0751901

982.0 mixed 69.6 26.1 Vm noncarb 518 557

13 Smokey Kill west of

Sidney Center

01500628 421806/

0751644

0.30 mixed 50.2 49.8 Ut noncarb 0.14 0.07

14 Route 41 stream south of 

Afton

01502702 421256/

0753132

1.1 agr 74.0 23.7 Vt noncarb 0.38 0.04

15 Route 7 stream south of 

Afton

01502703 421253/

0753200

0.66 forest 91.0 9.0 Ut noncarb 0.23 0.06

16 Unnamed stream at Plains 

Road east of Nineveh

01502707 421153/

0753534

0.51 forest 86.1 7.6 Vt noncarb 0.29 0.48

17 Hotchkiss Creek near 

Windsor

0150273301 420452/

0753654

0.72 forest 99.5 0.4 Ut noncarb 0.18 0.05

18 Susquehanna River at 

Conklin

01503000 420207/

0754812

2,232.0 mixed 70.6 26.0 Vm noncarb 1190 1550

Introduction
6 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

II. BASE-FLOW-SEPARATION ANALYSIS 

The base-flow component of streamflow was calculated as a percentage of 

total annual streamflow through hydrograph-separation techniques. 

Base flow at four stream sites in the study area that had continuous long-term discharge records 

(1941-93) was found to constitute more than 60 percent of total annual flow of each stream. 

Streamflow consists of a mixture of base flow 

(ground water that has discharged to the stream) and 

stormflow except under base-flow conditions, when 

most stormflow is absent. A stream is considered to be 

under base-flow conditions when little or no 

precipitation or snowmelt has occurred in the drainage 

area for at least 5 days or if the streamflow hydrograph 

shows that discharge is steady or slowly declining. 

Most flow in a stream during base-flow conditions 

consists of ground water that has discharged to the 

stream; therefore, a water sample collected during base 

flow is an approximation of the chemical quality of the 

ground water discharging to that stream. 

Base-flow (and ground-water) chemistry differs 

from stormflow chemistry in that base flow has been in 

contact with the subsurface material long enough to 

leach soluble minerals from it; thus, the concentrations 

of most inorganic chemical constituents in base flow 

tend to be higher than those in stormflow (Ku and 

others, 1975). The chemistry of base flow is also 

important because base flow in a stream is an 

aggregate of the ground-water quality over the whole 

basin above the sampling point, in contrast to a water 

sample from a single well, which may recieve water 

from a smaller area.

The HYSEP hydrograph-separation program 

(Sloto and Crouse, 1996) quantifies the base-flow and 

stormflow components of total streamflow and was 

used to calculate base flow as a percentage of mean 

total annual flow at four sites in the study area that had 

continuous discharge data for 1941-93 (fig. 2A). These 

sites were selected because they met the conditions 

recommended for use of HYSEP: (1) the stream is not 

regulated by a dam or flood-control reservoir, which 

would cause an apparent decrease in stormflow and an 

apparent increase in base flow after a storm, and (2) 

streamflow records span a period sufficient (at least 30 

years) to represent long-term average conditions and 

thereby increase the accuracy of the estimates. All data 

were retrieved from the USGS National Water 

Information System (NWIS). 

Results of the analysis indicate that base flow 

constitutes more than 60 percent of total annual 

discharge of each of the four streams (fig. 2B). The 

stream with the highest percentage of base flow 

(82 percent) was Oaks Creek at Index, possibly 

because (1) the carbonate bedrock in the northern part 

of this subbasin may allow more precipitation to 

infiltrate into the aquifer than in areas to the south, 

providing less stormflow in the stream and more 

ground-water discharge to the stream as base flow, and 

(2) the low relief in the northern part of the study area 

could allow more precipitation to infiltrate, and less to 

enter the stream as stormflow, than in the high-relief 

areas to the south. 
7

B. Base flow as percentage of total streamflow

1

2

3

4

5

6

7 9 8

10

11

12 13

14 15

16

17

18

Susquehanna

River

Susquehanna

River

Oaks Cree

k

Unadilla

River

0

0

10 MILES

10 KILOMETERS

+

75o43o

+ 76o

42o

A. Subbasin locations

Unadilla River above Rockdale (Site 10)

Oaks Creek above Index (Site 6)

Susquehanna River above Unadilla (Site 12)

Susquehanna River above Conklin (Site 18)

Base-flow sampling sites – site

names are listed in table 1

EXPLANATION

SUBBASINS

9

Components of total streamflow

Base flow, as percentage of total streamflow

EXPLANATION

Runoff, as percentage of total streamflow

Cities and Villages

Base-flow percentage calculation sites

Cooperstown

Index

Oneonta

Rockdale

Unadilla

Bainbridge

Afton

Windsor

Conklin

Millers Mills

Unadilla River at Rockdale

38% 62%

Site 10

Oaks Creek at Index

82%

18%

Site 6

Susquehanna River at Unadilla

32% 68%

Site 12

Susquehanna River at Conklin

39% 61%

Site 18

Base from U.S. Census TIGER/line Files ,1990,

Albers equal-area conic projection 1:100,000 scale;

Streams are 1:2,000,000 scale

Figure 2. Annual mean base flow as percentage of total annual streamflow for the period 1941-93 at four streamflow-gaging 

stations in study area. (Locations are shown in map above.)

Base-Flow-Separation Analysis
8 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

III. HYDROGEOLOGY 

A. Air-temperature and precipitation data

Air temperature and precipitation patterns are similar throughout most of the study area.

Precipitation and air-temperature records from two monitoring sites indicate that mean 

air temperatures and precipitation volumes are similar throughout the study area. Mean 

monthly temperatures range from about 20 ̊ F to 70 ̊ F. Precipitation typically ranges from 

2.4 in. in January and February to 4.1 in. in June, and averages 3.3 in. per month.

Air-temperature and precipitation data from two 

weather stations in the study area (Cooperstown and 

Bainbridge, fig. 1) were obtained from the Northeast 

Regional Climate Center CLIMOD system (http://metwww.cit.cornell.edu/nrcc_web_climod.html); 

[accessed April 2001]. The long-term (1961-90) mean 

air temperature for Cooperstown was 45.0  ̊F and for 

Bainbridge was 45.3  ̊F (fig. 3A). Air Temperatures 

during the growing season (May through September) 

averaged 62.1  ̊F at Cooperstown and 62.8  ̊F at 

Bainbridge; air temperatures for October through April 

averaged 32.8  ̊F at both locations. Mean monthly 

temperatures ranged from about 20 ̊ F to 70 ̊ F.

Mean annual precipitation at Cooperstown 

during 1961-90 was 39.1 in., and at Bainbridge was 

40.1 in. (fig. 3A). Monthly mean precipitation at 

Cooperstown was 3.26 in. and at Bainbridge was 

3.34 in.; Monthly means are slightly lower during the 

winter and early spring (December through March) 

than at other times. Nearly half of the precipitation 

during 1961-90 occurred during the growing season 

(May-September). Precipitation typically ranges from 

2.4 in. in January and February to 4.1 in. in June, and 

averages 3.3 in. per month.

Parts of the study area that are distant from 

Cooperstown and Bainbridge may have slightly 

different temperature and precipitation rates, 

depending on elevation, topography, and average cloud 

cover. 
9

PRECIPITATION, IN INCHES

Mean monthly precipitation (1961-90)

Mean for Cooperstown

Mean for Bainbridge

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep

4.5

4.0

3.5

3.0

2.5

2.0

1.5

1.0

0.5

0.0

Cooperstown

Bainbridge

0

AIR TEMPERATURE,

IN DEGREES FAHRENHEIT

Mean monthly air temperatures (1961-90)

Mean for Cooperstown 

and Bainbridge

80

70

60

50

40

30

20

10

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep

Cooperstown

Bainbridge

Figure 3A. Mean monthly air temperature and precipitation at Cooperstown and Bainbridge weather stations in 

upper Susquehanna River Basin, N.Y., 1960-90. (Data from Northeast Regional Climate Center CLIMOD system, 

2001.) (Locations are shown in fig. 1.) 

Hydrogeology
10 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

III. HYDROGEOLOGY (CONTINUED) 

B. Precipitation, runoff, evapotranspiration, and recharge 

Recharge depends on precipitation and on the rates of evapotranspiration and infiltration. 

Some of the runoff that infiltrates into the soil is returned to the atmosphere through 

evapotranspiration (ET); the rest infiltrates to the water table. Published mean

 precipitation, runoff, and ET values are as follows: precipitation, 

38-46 in/yr; runoff, 19-27 in/yr; and evapotranspiration, 19 in/yr.

Once precipitation has saturated the thin soils 

and till in the uplands of the study area, it flows 

quickly overland into streams. Some surface runoff 

seeps into openings in the soil such as frost cracks, 

desiccation cracks, root tubes, burrows, etc., then 

makes its way to streams and rivers in the drainage 

area. Some shallow ground water is lost to the 

atmosphere through evaporation or through uptake by 

plant roots and transpiration of the moisture from plant 

leaves before it reaches a stream or river. This process 

(evapotranspiration) increases during summer months 

when temperatures increase and more plants and crops 

are growing, and decreases the amount of shallow 

ground water that recharges streams.

The amount and distribution of precipitation, 

runoff, and evapotranspiration (ET) in the 

Susquehanna River Basin in New York were calculated 

in a previous study by Randall (1996), who estimated 

precipitation to range from 38 to 46 in/yr (fig. 3B)

from an analysis of 1951-80 precipitation records from 

stations managed by the U.S. National Oceanic and 

Atmospheric Association and summarized by Lyford 

and Cohen (1988). Randall (1996) also partitioned 

precipitation at each station into runoff and ET so that 

the ET values would vary smoothly across the region 

and would decrease with increasing altitude and 

latitude. Runoff in the study area (fig. 3B) was 

considered to represent all precipitation that did not 

return to the atmosphere as ET and was estimated from 

streamflow records for 1951-80 to range from 19 to 

27 in/yr (Randall, 1996). Runoff increases with 

increasing precipitation and, in this case, includes the 

component of precipitation that recharges the ground 

water. 

The valley-fill aquifers that supply water to the 

local residents are recharged by (1) precipitation that 

falls directly on the coarse-grained, permeable surficial 

material, (2) infiltration of streamflow in reaches that 

cross the aquifer (losing reaches), (3) unchanneled 

runoff from upland hillsides that seeps into the coarse 

valley-fill deposits along the edges of the main-stem 

river valleys, and (4) induced infiltration of river water 

in response to pumping (Randall and others, 1988; 

MacNish and Randall, 1982). Main-stem river 

channels within the study area are commonly floored 

by sand and gravel deposits that provide direct 

hydraulic connection to underlying unconfined 

aquifers (fig.3D; MacNish and Randall, 1982). 

Aquifers in the study area discharge water to streams 

and rivers, springs, and pumping wells. 

Whether a stream or river reach gains or loses 

water through the streambed depends on whether the 

water level is higher or lower than the surrounding 

water table. Water seeps from a streambed or riverbed 

into the underlying aquifer where the stream water is 

higher than the water table, and moves from the 

aquifer into the streambed or riverbed where the water 

table is higher than the stream surface. Most mainstem rivers gain ground water throughout their course, 

whereas upland tributaries typically gain water in the 

uplands but lose some or all their flow where they 

cross alluvial fans as they enter main-stem river valleys 

(Ku and others, 1975; Morrissey and others, 1988).

Some valley reaches do not entirely consist of 

permeable material but also contain thick deposits of 

lacustrine fine sand, silt, or clay. These materials do 

not readily transmit water to underlying aquifers but, 

rather, confine them (Randall, 2001). These confined 

aquifers can receive recharge along the edges of the 

valleys where course-grained permeable glacial 

deposits are in contact with the confined units 

(MacNish and Randall, 1982). Water discharged to a 

stream from a deep, confined aquifer may be older 

than water from shallow, unconfined sand and gravel 

aquifers and, therefore, may have higher 

concentrations of inorganic chemical constituents. The 

complexity of the ground-water flow paths in the upper 

Susquehanna River Basin was not investigated in this 

study.
11

24

22

20

22 24

24

20

22

24

26

+

75o

43o

+

76o

42o

0

0

10 MILES

10 KILOMETERS

20 Annual mean runoff, in inches

EXPLANATION

Cooperstown

Index

Oneonta

Bainbridge

Afton

Windsor

Unadilla

Rockdale

Conklin

Weather Station

Weather Station

+

75o

43o

+

76o

42o

42

40

40

38

42

42

44

40

38

40

42

42

44

46

EXPLANATION

Annual mean precipitation, in inches 40

Millers Mills

Millers Mills

Cooperstown

Index

Oneonta

Bainbridge

Afton

Windsor

Unadilla

Rockdale

Conklin

PRECIPITATION

RUNOFF

Base from U.S. Census TIGER/line Files,1990,

Albers equal-area conic projection 1:100,000 scale;

Streams are 1:2,000,000 scale

Figure 3B. Annual mean precipitation and runoff in the upper Susquehanna River Basin, N.Y., 1951-80. 

(Modified from Randall, 1996, plates 1 and 2). 

Hydrogeology

Cities and Villages

Cities and Villages
12 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

III. HYDROGEOLOGY (CONTINUED)

C. Bedrock 

The northern part of the study area is underlain by carbonate bedrock; the central and southern 

parts are underlain by younger noncarbonate sandstone, siltstone, and noncalcareous shale.

The bedrock in the northernmost part of the study area consists of Upper Silurian and Lower Devonian 

carbonates (limestone, dolostone), and calcareous shales, whereas bedrock in the central and southern 

parts consists of later (Middle and Upper Devonian) sandstone, siltstone, and noncalcareous shale. 

The eastern part of North America during the 

late Ordovician period (460 to 435 million years ago) 

and Devonian period (409-363 million years ago) was 

undergoing mountain-building events (orogenies) that 

occurred when part of the North American plate, 

including the area that is now southeastern Canada and 

New England, collided with an island arc (Taconic 

Orogeny) and a microcontinent called the Avalon 

terrane (Acadian Orogeny) (Isachsen and others, 1991; 

Dott and Prothero, 1994). These collisions caused 

uplift of mountains to the east of New York and 

downwarping of much of the region west of the 

mountains. This downwarping resulted in the 

formation of a hinterland basin (Hancock, 1994) in the 

area that is now central and western New York. A wide, 

shallow inland sea occupied the basin during the 

Upper Silurian and Lower Devonian periods, and thick 

layers of carbonate minerals (the precursors of 

limestone and dolostone) were deposited upon the sea 

floor through the precipitation of calcium and 

magnesium. Later, erosion of the mountains to the east 

resulted in the deposition of sediment along the edges 

of this sea. Later uplift to the east resulted in renewed 

deposition of mud and sand above the carbonate 

layers; these deposits subsequently became 

consolidated by the weight of still later sediments to 

form the Upper Devonian sandstones, shales, and 

siltstones that are now exposed in the central and 

southern parts of the study area. 

Later stresses from subsequent tectonic events 

caused the bedrock units to dip gently southward and 

southwestward; thus, the older (deep) carbonate layers 

are exposed in the northern part of the study area, and 

the overlying younger (noncarbonate) layers become 

exposed progressively southward.

The northern part of the study area is 

characterized by low relief, with gently rolling hills, 

numerous bedrock outcrops, and localized karst 

topography (fig. 3C). The central and southern parts 

are characterized by steep-sided valleys, uplands 

incised by many small headwater streams, and several 

broad valleys whose floors range from 600 to 800 feet 

below the upland summits.
13

Figure 3C. Bedrock geology of the upper Susquehanna River Basin, N.Y. (Modified from New York State Geological Survey, 

Map and Chart Series No. 15, Fisher and others, 1970.) 

Unadilla River at Millers Mills

North Winfield Creek at West Winfield

Cambell Brook at Lloydsville

Shadow Brook at East Springfield

Dundee Brook tributary at Brainard Corners

Oaks Creek at Index

Butternut Creek at Morris

Schenevus Creek tributary southwest of

Chaseville

Upland tributary east of Portlandville

Unadilla River at Rockdale

Unadilla Springs at Unadilla

Susquehanna River at Unadilla

Smokey Kill west of Sidney Center

Route 41 stream south of Afton

Route 7 stream south of Afton

Unnamed stream at Plains Road east

of Nineveh

Hotchkiss Creek near Windsor

Susquehanna River at Conklin

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

SITE NAMES

Base-flow sampling site and number

EXPLANATION

Water

Cobleskill Limestone (limestone)

Gardeau Formation, Upper Walton Formation 

(shale, sandstone, conglomerate)

Cashagua Shale, Lower Walton Formation 

(shale, sandstone, conglomerate)

West River Shale, Unadilla Formation 

(shale, sandstone, siltstone, conglomerate)

Moscow Formation (shale, sandstone)

Panther Moutain Formation

(shale, siltstone, sandstone)

Marcellus Formation (shale, sandstone, limestone)

Onondaga Limestone (limestone)

Helderberg Group (limestone, dolostone)

New Milford Formation (shale)

PALEOZOIC

Upper 

Silurian

Lower

Devonian

Middle

Devonian

Upper

Devonian

Era Period

Beers Hill Shale

18

Base from U.S. Census TIGER/line Files,1990,

Albers equal-area conic projection, 1:100,000 scale

42o +

76o

+

75o43o

Rockdale

Oneonta

Index Cooperstown

Afton

Bainbridge

Unadilla

Windsor

Conklin

0

0

10 MILES

10 KILOMETERS

1

2

3

4

5

6

7

8 9

10

11

12

13

14 15

16

17

18

Miller Mills

Hydrogeology
14 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

III. HYDROGEOLOGY (CONTINUED)

D. Surficial material

Glaciers modified the topography and deposited glacial sediments throughout the study area.

Glaciers eroded the bedrock surface of the entire study area and deposited till in the uplands 

and glaciofluvial and glaciolacustrine sediments in the major valleys. Thick layers of till 

mantle south-facing upland hillsides in the central and southern parts of the study area. 

Continental glaciers covered most of New York 

at least twice during the Pleistocene Epoch (between 1 

million and 13,000 years ago) as they advanced and 

retreated in response to changes in climate. The 

glaciers deeply incised and widened the major valleys; 

then, during deglaciation, left large amounts of 

glaciofluvial material (sand and gravel deposited 

beneath, in front of, or alongside a glacier by 

meltwater streams) and glaciolacustrine deposits (clay, 

silt, and fine sand that settled within proglacial lakes) 

within the valleys (fig. 3D). 

Glacially derived landforms within the valleys 

throughout the study area include kames, eskers, 

outwash valley terraces, kettles, and morainal valley 

plugs and ridges. Recent alluvium covers most of the 

flood plains of the larger streams and rivers. The 

glaciofluvial deposits form the most productive 

aquifers within the study area; the fine-grained 

glaciolacustrine deposits are relatively impermeable 

and form confining units that yield little water to wells 

but may confine deeper aquifers locally.

The most recent glacier scraped the tops and 

northern sides of most hills down to bedrock. As it 

flowed over the bedrock hilltops, generally southward, 

it deposited a mantle of till (a poorly sorted mixture of 

clay, silt, sand, and cobbles that can be more than 100 

ft thick locally) along the southern sides of the hills 

(Coates, 1966). Subtle differences in the glacier’s 

direction of flow probably resulted in the deposition of 

some till on the west and east-facing slopes as well. 

The glacial processes and glacial deposits within the 

study area are described in detail by Randall (2001), 

Fleisher (1977, 1986a, 1986b), and MacNish and 

Randall (1982). 

Upland streams within the study area commonly 

begin on thick till or on bedrock slopes, then flow 

through small upland valleys to a main-stem river 

valley, where they lose velocity and deposit alluvial 

material as fans at the valley edge. The main-stem river 

valley floors are characterized by a few hummocky 

moraines, many gently sloping terraces capped by 

gravel, and flood plains of modern streams. Silt and 

clay deposits are widespread at depth beneath the 

valley floors. 
15

Figure 3D. Surficial geology of the upper Susquehanna River Basin, N.Y. (Pennsylvania portion was formatted 

differently than New York portion; alluvial and stratified drift deposits are shown undifferentiated). (Modified from 

New York State Geological Survey, Map and Chart Series No. 40, Cadwell and others, 1991.)

Number and location of sampling sites 

Alluvial deposits

Fan gravel

Water

Kame sand and gravel

Kame moraine

Lacustrine fine sand

Lacustrine silt and clay

Outwash sand and gravel

Swamp deposits

Bedrock

Till

Till moraine

0

0

10 MILES

10 KILOMETERS

EXPLANATION

18

Base from U.S. Census TIGER/line Files,1990,

Albers equal-area conic projection 1:100,000 scale

Unadilla River at Millers Mills

North Winfield Creek at West Winfield

Cambell Brook at Lloydsville

Shadow Brook at East Springfield

Dundee Brook tributary at Brainard Corners

Oaks Creek at Index

Butternut Creek at Morris

Schenevus Creek tributary southwest of Chaseville

Upland tributary east of Portlandville

Unadilla River at Rockdale

Unadilla Springs at Unadilla

Susquehanna River at Unadilla

Smokey Kill west of Sidney Center

Route 41 stream south of Afton

Route 7 stream south of Afton

Unnamed stream at Plains Road east of Nineveh

Hotchkiss Creek near Windsor

Susquehanna River at Conklin

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

SITE NAMES

Pennsylvania

+

75o

43o

+

76o

42o

1

2

3

5 4

6

7

8 9

10

11

12 13

14 15 16

17 18 Conklin

Windsor

Afton

Bainbridge

Unadilla

Rockdale

Oneonta

Cooperstown

Index

New York

Hydrogeology
16 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

IV. WATER QUALITY

A. Sampling-site locations 

Base-flow samples were collected at least twice from each of 18 stream sites in 

2001 for nutrients and inorganic-constituent analysis; 12 of these 

sites were resampled in November for pesticide analysis.

Sampling sites represented three land-use categories (agricultural, forested, or mixed) and were 

established in areas unaffected by local wastewater discharge and urban runoff; they also were 

classified in terms of their geographic location within the upper Susquehanna River Basin. 

Base-flow samples were collected at each of 18 

stream sites during January and again in June 2001 for 

analysis for nutrients, and common inorganic 

constituents (cations and anions) to characterize the 

chemistry of base flow representing each type of land 

use. Additional samples were collected at 12 of these 

sites during November 2001 for pesticide analysis. 

Results are presented in the sections that follow.

Base flow is an approximaiton of the chemical 

quality of ground water, but the concentrations of 

some constituents can be altered in the stream through 

contact with air and stream biota. For example, 

increased temperatures in the spring and summer cause 

an increase in microbial activity and algal growth in 

the streams, which can decrease dissolved oxygen 

concentrations, utilize the nitrogen in the water, and 

might decrease nitrate concentrations through 

denitrification if denitrifying bacteria are present. 

Therefore, base-flow quality under non-snowmelt 

conditions in winter, when temperatures, microbial 

activity, and algal growth are minimal, provides a good 

approximation of the average chemical quality of 

shallow ground water within the drainage area. 

Of the 18 sites sampled, five represented 

subbasins dominated by agriculture, seven represented 

subbasins dominated by forests, and six represented 

subbasins with a mixture of forest and agricultural 

land. Six were in the northern part of the study area 

that is mostly underlain by carbonate bedrock 

(limestone, dolostone, and calcareous shale), and 12 

were in the central and southern parts that are 

underlain by noncarbonate bedrock (sandstone, 

siltstone, and shale). Site data are summarized in 

table 1; land use within each subbasin is depicted in 

figure 4A.

Site selection was facilitated through a GIS 

(Geographic Information System) analysis of spatial 

data sets of topography. The subbasins were classified 

according to predominant land use (at least 50 percent 

of subbasin area) and bedrock type, as listed below: 

• mostly agricultural land underlain by carbonate 

bedrock, 

• mostly agricultural land underlain by noncarbonate 

shale, siltstone, and sandstone, 

• mostly forested land underlain by carbonate 

bedrock, 

• mostly forested land underlain by noncarbonate 

shale, siltstone, and sandstone, and 

• mixed land use (nearly equal amounts of forested 

and agricultural land use), underlain by carbonate 

bedrock and noncarbonate shale, siltstone, and 

sandstone. 

The “mixed” subbasins tend to be along the 

main stem of the Susquehanna and Unadilla Rivers, 

and those that encompass more than 100 mi2 contain 

tributaries that drain two or more of the above land-use 

and bedrock categories. The drainage areas above the 

sampling sites ranged from 0.22 mi2 (site 9) to 2,232 

mi2 (site 18, table 1.) 

Most of the sampling locations were upstream 

from the nearest village and sewage outfalls to 

minimize the local effects of wastewater and urban 

runoff. The sampling sites also were designated as one 

of three types according to relative location (See table 

1), as listed below: 

• upland headwater tributaries (streams that originate 

in the uplands), 

• valley tributaries (streams that originate within the 

valley instead of in the uplands), or 

• main-stem valley streams. 

These three types were designated to determine 

if small streams that originate in the main valley have 

water quality similar to those that originate in the 

uplands or to the large, main-stem valley streams.
17

Figure 4A. Land use in the upper Susquehanna River basin, N.Y. (Modified from U.S. Geological Survey, 1997) and 

land-use categories in the 18 subbasins sampled in 2001. 

1

2

3 4

5

6

7

8

9

10 11

12

13

14 15 16

17

18

LAND USE

75o

+43o

Millers Mills

Cooperstown Index

Oneonta

Rockdale

Unadilla

Bainbridge

Afton

Windsor

Conklin

42o

76o

+

75o

+43o

42o

76o

+

Agricultural carbonate

Forested carbonate

Mixed

Agricultural noncarbonate

Forested noncarbonate

18 Location and number of sampling sites.

Base from U.S. Census TIGER/line Files,1990, Subbasin boundaries from fig. 2.

Albers equal area conic projection 1:100,000 scale

EXPLANATION

1

2

3

4

5

6

7 9 8

10

12

13

14 15

16

17

18

11

LAND-USE

CATEGORY AND

BEDROCK TYPE

Unadilla River at Millers Mills (2.2 mi2)

North Winfield Creek at West Winfield (16.0 mi2)

Cambell Brook at Lloydsville (3.5 mi2)

Shadow Brook at East Springfield (7.0 mi2)

Dundee Brook tributary at Brainard Corners

(0.47 mi2)

Oaks Creek at Index (102.0 mi2)

Butternut Creek at Morris (60.0 mi2)

Schenevus Creek tributary southwest of

Chaseville (0.75 mi2)

Upland tributary east of Portlandville (0.22 mi2)

Unadilla River at Rockdale (520.0 mi2)

Unadilla Springs at Unadilla (0.32 mi2)

Susquehanna River at Unadilla (982.0 mi2)

Smokey Kill west of Sidney Center

(0.30 mi2)

Route 41 stream south of Afton (1.1 mi2)

Route 7 stream south of Afton (0.66 mi2)

Unnamed stream at Plains Road

east of Nineveh (0.51 mi2)

Hotchkiss Creek near Windsor (0.72 mi2)

Susquehanna River at Conklin

(2,232.0 mi2)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

SITE NAMES

Forest or wetlands

Agricultural land

Urban land

Water

Location and number

of sampling sites.

18

EXPLANATION

0

0

10 MILES

10 KILOMETERS

Water Quality
18 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

IV. WATER QUALITY (CONTINUED)

B. Inorganic constituents 

Concentrations of common inorganic constituents in base flow reflect upstream land use and 

showed little change from winter to summer.

The predominant cations in base flow were calcium, sodium, and magnesium, and the predominant 

anions were chloride, sulfate, and bicarbonate. Concentrations in the January samples were 

similar to those in the June samples. The highest concentrations of most inorganic constituents 

were in samples from agricultural subbasins underlain by carbonate bedrock, and the lowest 

were in samples from forested subbasins underlain by noncarbonate bedrock. Concentrations 

in samples from subbasins with mixed land use were intermediate.

Base-flow samples were analyzed for pH, 

alkalinity, specific conductance, dissolved solids, and 

common inorganic chemical constituents (cations and 

anions). The predominant cations in the samples were 

calcium, magnesium, and sodium; the predominant 

anions were chloride, sulfate, and bicarbonate (table 

2). Concentrations of most constituents in the January 

2001 samples were similar to those in the June 2001 

samples (table 2). 

The highest concentrations of most inorganic 

constituents were in samples from agricultural 

subbasins underlain by carbonate bedrock, and the 

lowest were in samples from the forested subbasins 

with noncarbonate bedrock (fig. 4B). The 

concentrations in samples from the largest subbasins, 

which contain agricultural and forested land as well as 

a mixture of carbonate and noncarbonate bedrock, had 

intermediate concentrations of most constituents. An 

exception was the samples from two small streams that 

receive runoff from a major highway (sites 14 and 16); 

these samples contained anomalously high 

concentrations of sodium, chloride, and other 

constituents, as discussed in section IV-I. 

Figure 4B. Concentrations of inorganic constituents in base-flow samples collected in January and June 2001 in the 

upper Susquehanna River Basin, N.Y. (Land-use category and bedrock type shown in fig. 4A and table 1.) 

0

1

10

100

1000

Ca

Mg

Na

K

Cl

SO4

SiO2

pH

Alkalinity

CONCENTRATION IN

 MILLIGRAMS PER LITER

January 2001

Dissolved Solids

Specific Conductance

0

1

10

100

1000

June 2001

Agricultural, carbonate Mixed

Agricultural, noncarbonate

Forested, carbonate

Forested, noncarbonate

Ca

Mg

Na

K

Cl

SO4

SiO2

pH

Dissolved Solids

Specific

Alkalinity

Conductance

EXPLANATION

Land-use category and bedrock type
19

Table 2. Mean, median, maximum, and minimum values for solutes, pH, and specific conductance of base-flow

samples from upper Susquehanna River Basin study area, N.Y., January and June 2001. 

[Concentrations are in milligrams per liter; pH in units, specific conductance in microsiemens per centimeter. n = number of samples.]

Constituent

or physical 

property

Agricultural,

carbonate

(n = 4)

Agricultural, 

noncarbonate 

(n = 1)

Mixed land use 

and bedrock

(n = 6)

Forested, 

carbonate

(n = 1)

Forested, 

noncarbonate 

(n = 6)

January June January June January June January June January June

Calcium (Ca)

mean 74.6 64.5 15.2 26.1 27.8 30.1 29.9 45.8 6.0 10.9

median 87.2 65.8 25.3 28.8 4.3 7.3

maximum 95.5 94.1 51.1 53.1 13.7 30.0

minimum 28.3 32.1 9.2 8.2 2.9 5.0

Magnesium (Mg) 

mean 7.5 7.9 3.5 5.0 2.9 6.8 1.9 2.5 1.8 2.8

median 7.5 7.4 2.8 3.4 1.7 2.3

maximum 12.7 14.7 3.9 24.5 3.2 5.9

minimum 2.2 2.4 2.2 2.7 0.9 1.4

Sodium (Na)

mean 3.9 4.7 26.0 39.1 7.3 6.4 2.4 3.1 5.3 7.1

median 3.8 4.9 7.5 6.7 1.7 2.6

maximum 6.0 6.1 8.4 8.9 23.7 28.1

minimum 2.2 2.9 5.5 2.4 1.3 1.9

Potassium (K) 

mean 1.5 1.7 1.2 2.4 1.0 1.1 0.7 0.8 0.5 1.2

median 1.7 1.9 1.0 1.1 0.5 0.7

maximum 1.7 2.6 1.3 1.4 1.0 4.2

minimum 0.9 0.4 0.7 0.5 0.2 0.3

Chloride (Cl)

mean 7.2 7.9 48.1 77.2 12.9 11.5 3.3 3.9 8.7 12.7

median 7.0 8.2 13.0 12.9 1.4 2.4

maximum 9.9 10.9 15.1 16.4 45.2 59.5

minimum 4.8 4.5 10.6 1.6 0.9 1.0

Sulfate (SO4

2-)

mean 15.6 19.7 13.7 10.1 10.1 8.9 8.7 8.5 9.1 8.3

median 10.0 8.2 9.8 8.6 9.4 9.2

maximum 37.3 58.4 12.9 10.3 12.1 9.9

minimum 5.0 3.9 8.5 8.1 5.7 4.7

Silica (SiO2)

mean 4.1 4.0 7.1 2.0 4.2 3.9 4.0 4.8 5.9 6.4

median 4.2 4.7 4.4 4.1 5.8 6.7

maximum 4.5 5.6 4.9 4.9 7.0 7.5

minimum 3.5 1.1 3.1 2.8 4.5 4.0

Dissolved solids

mean 249.8 222.0 149.0 198.0 116.5 108.8 102.0 133.0 50.2 65.5

median 278.0 240.5 114.0 112.0 35.0 42.0

maximum 329.0 298.0 183.0 158.0 130.0 181.0

minimum 114.0 109.0 54.0 43.0 28.0 39.0

pH

mean 7.7 8.0 6.5 7.2 7.0 7.6 7.2 7.6 6.5 7.2

median 7.7 8.0 7.0 7.6 6.5 7.2

maximum 8.1 8.1 7.7 8.2 6.8 7.5

minimum 7.3 7.8 6.2 6.8 6.0 7.1

Specific conductance 

mean 400.3 392.3 266.0 396.0 215.5 210.5 185.0 239.0 83.8 126.0

median 495.0 424.5 208.5 212.0 56.0 80.0

maximum 576.0 519.0 332.0 335.0 247.0 368.0

minimum 35.0 201.0 115.0 79.8 34.0 67.3

Alkalinity (as CaCO3)

mean 216.3 162.5 26.0 54.0 67.5 70.7 73.0 90.0 10.8 28.9

median 237.0 164.5 61.0 68.0 8.5 21.9

maximum 246.0 240.0 132.0 136.0 20.0 73.0

minimum 145.0 81.0 19.0 23.0 5.0 11.0

Water Quality
20 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

IV. WATER QUALITY (CONTINUED)

C. Effect of carbonate bedrock on base-flow quality

Carbonate minerals in bedrock and unconsolidated deposits affect base-flow quality. 

The study area was divided into two water-quality domains on the basis of bedrock type—the northern 

part, underlain by carbonate rocks and blanketed by carbonate-rich surficial deposits, and the central 

and southern parts, underlain by noncarbonate bedrock and mainly noncarbonate surficial deposits. 

The presence of carbonate material in a subbasin 

increases the concentration of calcium (Ca) and the 

alkalinity and, therefore, the specific conductance and 

dissolved-solids concentrations of base flow. Carbonate 

minerals (calcium and magnesium carbonates) are 

more soluble than the silicate minerals that make up the 

remainder of the bedrock and glacial deposits; thus, the 

dissolved mineral content of water where carbonate 

minerals are abundant is typically much higher (and the 

water much “harder”). The northern part of the study 

area is underlain mostly by carbonate-rich bedrock of 

the Onondaga Formation (limestone), the Helderberg 

Group (limestones and dolostones), and the Marcellus 

Formation (calcareous shales, sandstone, and 

limestone) (fig. 3C); the central and southern parts are 

underlain by sandstone, siltstone, and shales that 

contain little carbonate. 

Glaciers eroded the carbonate rocks in the 

northern part of the study area and deposited them as 

carbonate-rich till throughout the uplands and for many 

miles southward into the noncarbonate-bedrock area. 

Meltwater during deglaciation transported carbonaterich fluvial sediments several tens of miles down major 

valleys. For example, sand and gravel terraces whose 

composition is at least 40 percent limestone clasts are 

found in the Unadilla River valley north of South 

Edmeston, the Susquehanna River valley north of 

Index, and Cherry Valley north of Middlefield (Ku and 

others, 1975). 

The study area was divided into two waterquality domains that reflect the presence or absence of 

carbonate material. The northern domain (Area A in 

fig. 4C) is underlain by carbonate bedrock, its uplands 

contain carbonate-rich till, or the glacial deposits in the 

major valleys are at least 10 percent carbonate pebbles. 

Area B to the south is underlain by noncarbonate shale, 

siltstone, and sandstone, the till in the uplands contains 

little carbonate material, and the glacial deposits in the 

major valleys are less than 10 percent carbonate 

pebbles (percentages from Ku and others, 1975). The 

median concentration of calcium, and the median 

alkalinity and specific conductance values of base flow 

in the major valleys of Area A were markedly higher 

than those in Area B. Upland sites in both areas had 

much lower concentrations of calcium and alkalinity, 

and lower specific conductance values than the valley 

sites, and the upland sites in Area A had higher 

concentrations of calcium and alkalinity, and higher 

specific conductance values, than upland sites in Area B

(table 3). 

Streams throughout Area B were similar in water 

quality and had fairly low concentrations of major 

cations and anions (table 2). Three sampling sites in 

Area B [sites 10, 12, and 18] have their headwaters in 

Area A and were along the main-stem of the Unadilla 

or Susquehanna Rivers, receive water from subbasins 

representing more than one land-use and bedrock 

category, and had drainage areas larger than 100 mi2

(fig. 4C). Median calcium and alkalinity concentrations 

and specific conductance values for these “mixed” sites 

are intermediate between those of the agricultural 

carbonate-bedrock sites and the forested noncarbonatebedrock sites (fig. 4C). 

Table 3. Median concentrations of calcium and alkalinity and specific conductance values in base-flow samples 

from Area A (underlain by carbonate bedrock) and Area B (underlain by noncarbonate bedrock), January and 

June 2001.

[Locations of Areas A and B are shown in fig. 4C. mg/L, milligrams per liter; μS/cm, microsiemens per centimeter.]

Area

Site 

description

No. of 

samples

Calcium

(mg/L)

Alkalinity as CaCO3 (mg/L)

Specific conductance

(μS/cm) 

A

(carbonate)

Upland sites 2 31 91 193

Valley sites 4 87 234 495

B

(noncarbonate)

Upland sites 6 5 14 66

Valley sites 6 26 61 233
21

Cooperstown

Index

Oneonta

Rockdale

Unadilla

Bainbridge

Afton

Windsor

Conklin

+

75o

43o

+

76o

42o

A

B

22, 47, 308

5, 15, 67

27, 63, 210

5, 8, 61 21, 40, 331

42, 92, 273

9, 23, 75

27, 66, 211 9, 21, 97

17, 38, 154 4, 10, 48

5, 11, 59

52, 134, 334

36, 87, 217 30, 113, 118

92, 240, 545

78, 217, 441

92, 241, 517

0

0

10 MILES

10 KILOMETERS

EXPLANATION

Upland forested subbasin site

First two values represent mean concentrations of calcium and 

alkalinity (as CaCO3), respectively, in milligrams per liter; third

value is mean specific conductance, in microsiemens per

centimeter at 25oC. Means are based on one sample collected

in January and one in June 2001.

NEW YORK

PENNSYLVANIA

Area underlain by carbonate bedrock (From fig. 3C)

Boundary between Area A (water strongly affected by

carbonate minerals) and Area B (water slightly affected by 

carbonate minerals)

A

B

Upland agricultural subbasin site 

Valley agricultural subbasin site 

Upland mixed subbasin site 

Middlefield

 South

Edmeston

SAMPLING SITES

Calcium Alkalinity Specific Conductance

Valley forested subbasin site

WATER QUALITY

36, 87, 217 

City or Village

Weather station

Unadilla River at Millers Mills

North Winfield Creek at West Winfield

Cambell Brook at Lloydsville

Shadow Brook at East Springfield

Dundee Brook tributary at Brainard Corners

Oaks Creek at Index

Butternut Creek at Morris

Schenevus Creek tributary southwest of Chaseville

Upland tributary east of Portlandville

Unadilla River at Rockdale

Unadilla Springs at Unadilla

Susquehanna River at Unadilla

Smokey Kill west of Sidney Center

Route 41 stream south of Afton

Route 7 stream south of Afton

Unnamed stream at Plains Road east of Nineveh

Hotchkiss Creek near Windsor

Susquehanna River at Conklin

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

SITE NAMES

Millers Mills

18

1

2

3

4

5

6

7

8

9

10 11

12 13

14

15

16

17

Valley mixed subbasin site 

Area underlain by noncarbonate bedrock

Base from U.S. Census TIGER/line Files,1990,

Albers equal-area conic projection 1:100,000 scale;

Streams are 1:100,000 scale

Figure 4C. Mean concentrations of calcium and alkalinity, and mean specific conductance, for water samples collected 

during base-flow conditions in Areas A and B of the upper Susquehanna River Basin, N.Y., January and June 2001.

Water Quality
22 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

IV. WATER QUALITY (CONTINUED)

D. Nitrogen

Nitrogen concentration in water can be an indicator of water quality.

Nitrogen is vital to the growth of vegetation, but too much nitrogen in streams, 

derived mainly from fertilizers and sewage, can cause excessive plant and algal 

growth that can clog waterways and deplete oxyen needed by other aquatic life. 

Nitrogen sustains the growth of plants. It is 

derived from precipitation, biological fixation of 

nitrogen, and the decomposition of organic matter, 

but rarely in amounts sufficient to replenish the 

nitrogen lost from the soils through the harvesting of 

crops and denitrification (conversion of nitrogen to 

unusable N2 gas by soil bacteria). Therefore, most 

crops require fertilizer. 

Excessive amounts of nitrogen within a water 

body stimulate the growth of algae and aquatic plants 

that can clog waterways and deplete oxygen needed by 

other aquatic life (fig. 4D). The chemical fertilizers 

and manure that are applied to agricultural land, and 

fertilizers used by homeowners and commercial lawncare companies, can be be washed into rivers and 

streams; effluent from point sources such as seweroverflow pipes also add substantial amounts of 

nitrogen to rivers. Excessive nitrate in drinking water 

is also a human health concern; as a result, the U.S. 

Environmental Protection Agency (USEPA) has 

established 10 mg/L (as N) as the maximum 

contaminant level of nitrate in drinking water (USEPA, 

2000). Recent initiatives by Federal, State, and local 

governments to provide water-treatment-facility 

upgrades have led to decreased nitrogen loadings to 

waterways, and measures such as crop rotation and 

erosion control have decreased the erosion of soil. 

Nevertheless, runoff from agricultural areas 

throughout the Susquehanna River Basin has been a 

major cause of eutrophication in Chesapeake Bay.

Nitrogen occurs in terrestrial and aquatic 

systems in several forms that are interconverted 

through what is known as the nitrogen cycle (table 4)

(Maidment, 1993). The predominant form of nitrogen 

in stream water is nitrate. The principal source of 

nitrate that enters terrestrial and aquatic systems is 

nitrification of ammonia, which entails two steps that 

are brought about primarily by aerobic bacteria. The 

first step oxidizes ammonia (NH4

+) to nitrite (NO2-

), 

and the second step oxidizes NO2

-

 to nitrate (NO3

-

). 

Nitrite generally does not accumulate during 

nitrification; rather, it is oxidized to NO3

- as quickly as 

it forms. The conversion of ammonia to nitrite requires 

oxygen; therefore, waters receiving large loadings of 

ammonia have a considerable demand for oxygen.

The principal nitrate sinks are denitrification to 

gaseous forms, and assimilation by plants. 

Denitrification is carried out by anaerobic bacteria that 

reduce nitrate to the gaseous forms (N2 and N2O) in 

oxygen-poor conditions, which are common in many 

aquatic systems. Assimilation entails the consumption 

of inorganic nitrogen by plants and algae to form 

organic nitrogen. Nitrogen fixation is the reduction of 

nitrogen gas (N2) to ammonia and organic nitrogen; 

plants that “fix” nitrogen are the source of virtually all 

nitrogen used by living organisms. Ammonification 

(mineralization) is the conversion of organic nitrogen 

to ammonia. Heterotrophic conversion is the 

conversion of organic nitrogen from one organic 

compound to another when organisms consume 

organic matter. 

The base-flow samples collected in January and 

June 2001 were analyzed for several nitrogen species; 

the predominant species in all samples was nitrate. 

(See sections IV-E, IV-F.)
23

Figure 4D. Agricultural field in the upper Susquehanna River Basin, N.Y.

Table 4. Six biological transformation processes of the nitrogen cycle.

[Modified from Atlas, 1998.] 

Process Description

1. Nitrogen fixation biological and industrial reduction of molecular nitrogen gas (N2) to ammonia (NH3) 

and organic nitrogen (ammonium; NH4

+)

2. Nitrification aerobic bacterial oxidation of ammonia (NH3) to nitrite (NO2

-

), then from nitrite to 

nitrate (NO3

-

)

3. Denitrification anaerobic bacterial reduction of nitrate to gaseous forms—nitric oxide (NO), nitrous 

oxide (N2O) and molecular nitrogen (N2)—under anoxic conditions

4. Assimilation inorganic forms of nitrogen (NO3

-

) are absorbed and incorporated (as food) by 

autotrophic algae and higher plants to form organic nitrogen

5. Heterotrophic conversion conversion of organic nitrogen from one organic compound to another when organisms 

consume organic matter

6. Ammonification decomposition of organic nitrogen to ammonia

Water Quality

Molecular nitrogen

Plants, animals, 

and decomposition

Ammonia 

and Ammonium

Nitrate 1

3

2

4,5

6
24 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

IV. WATER QUALITY (CONTINUED)

E. Nitrate - seasonal patterns 

Nitrate concentrations in base flow fluctuated seasonally in all subbasins.

Nitrate concentrations in streamflow are lowest in summer when the growth of aquatic plants 

results in consumption of nitrogen, and increased denitrification and miminal recharge inhibit 

the migration of nitrate to the stream. Nitrate concentrations are highest during winter, when 

nitrate moves into streams through increased recharge, and aquatic plant growth is minimal. 

Nitrate concentration in base flow fluctuates 

seasonally and is highest in winter (Bauters and 

Eckhardt, 1999; Lindsey and others, 1997). The 

summer decrease can be attributed to a combination of 

factors, including (1) microbial processes in anaerobic 

sediments along streambanks increase in summer, 

thereby decreasing the nitrate concentrations in base 

flow through denitrification (Lindsey and others, 

1997), (2) summer recharge of shallow ground water is 

lower than in the winter because most rainfall is lost to 

ET, which thereby inhibits the movement of nitrogen 

from the soil into the stream, and (3) nitrogen in the 

soil is taken up by plant roots and soil biota during the 

growing season. However, the strongest influence on 

nitrate concentrations in summer base flow can be 

attributed to algae and other aquatic plants that 

consume much of the nitrate that enters the stream, 

resulting in apparent decreases in nitrate 

concentrations.

During the fall and winter, (1) temperatures and 

biologic activity (plant and algae growth) in streams 

decrease, allowing more nitrate from ground-water 

recharge to persist in base flow, (2) decreasing 

temperatures inhibit the denitrification process along 

the stream, (3) less rainfall is lost to ET, resulting in 

more shallow ground-water recharge to the stream, and 

(4) plants within the subbasin consume less nitrogen. 

Therefore, cold-weather, non-growing-season baseflow samples are better indicators of nutrient 

concentrations in ground-water discharge than are 

samples collected during the summer. 

An exception was noted in the June 2000 

samples from two streams in agricultural subbasins 

(sites 2 and 14 in fig. 4E and table 1). These streams 

were sampled during base-flow conditions in January, 

June, and September of 2001; the stream at site 2 was 

also sampled in August 2001. The nitrate concentrations in the January and June samples from site 2 

had the highest nitrate concentrations of any site 

sampled during this study (2.27 mg/L and 2.40 mg/L, 

respectively). The relative proportions of nitrate in the 

January, August, and September base-flow samples at 

site 2 show the effects of increased biologic activity 

(and lower nitrate concentrations) in the streams that 

would be expected during warmer months and 

decreased biologic activity (and higher nitrate 

concentrations) in the streams during the colder 

months. However, the elevated June concentrations at 

both sites may be influenced by fertilizer and manure 

applications to agricultural fields near these streams 

before the samples were collected. 

Two sites in large, mixed land use subbasins 

(sites 10 and 18 in fig. 4E and table 1) had their 

greatest nitrate concentrations in the January samples, 

concentrations decreased in the June samples, and 

were lowest in the September samples. These sites did 

not show the early-summer nitrate peak seen at the 

agricultural sites in figure 4E, possibly because these 

sites represent mixed subbasins that are much larger 

than the agricultural subbasins and contain a smaller 

percentage of agricultural land, and (or) because much 

of their base flow is from thick glacial deposits that 

provide relatively long ground-water traveltimes that 

would obscure seasonal changes in base-flow 

chemistry.

Nitrate concentrations at site 9, a small upland 

stream that drains a forested basin (fig. 4E) differ 

markedly from those at the agricultural and main-stem 

sites—the nitrate concentrations in the January and 

June samples from this site were the lowest of all 

January and June samples in the study and also were 

lower than the August and September nitrate 

concentrations at this site. The most likely reason is 

that this forested subbasin receives no applications of 

manure or other fertilizers, and its soils are thin and 

could become quickly saturated by any late-summer 

and fall storms. This would allow any nitrate to be 

flushed through the hydrologic system quickly and 

would result in relatively low nitrate concentrations in 

base flow during winter.
25

Figure 4E. Nitrate concentration and discharge of five streams within the upper Susquehanna River Basin, N.Y., on 

selected base-flow sampling dates, 2001, by land-use and bedrock category. (Site locations are shown in fig. 1.) 

0.01

0.1

1

10

1

10000

Site 2. Small agricultural subbasin

underlain by carbonate bedrock.

Site 14. Small agricultural subbasin 

underlain by noncarbonate bedrock.

Site 10. Large main-stem valley site with 

mixed land use and bedrock geology. Site 18. Large main-stem valley site with 

mixed land use and bedrock geology.

NITRATE CONCENTRATION, 

IN MILLIGRAMS PER LITER, AS N

NITRATE CONCENTRATION, 

IN MILLIGRAMS PER LITER, AS N

NITRATE CONCENTRATION, 

IN MILLIGRAMS PER LITER, AS N

NITRATE CONCENTRATION, 

IN MILLIGRAMS PER LITER, AS N

DISCHARGE, IN

CUBIC FEET PER SECOND

DISCHARGE, IN

CUBIC FEET PER SECOND

DISCHARGE, IN

CUBIC FEET PER SECOND

DISCHARGE, IN

CUBIC FEET PER SECOND

Site 9. Small forested subbasin 

underlain by noncarbonate bedrock.

DISCHARGE, IN

CUBIC FEET PER SECOND

NITRATE CONCENTRATION, 

IN MILLIGRAMS PER LITER, AS N

1/22/01 6/28/01 8/16/01 9/24/01 1/24/01 6/28/01 9/24/01

1/23/01 6/29/01 9/25/01 1/23/01 6/29/01 9/25/01

1/25/01 6/28/01 8/16/01 9/24/01

1000

100

10

0.1

0.01

0.001

Nitrate

Discharge

0.01

0.1

1

10

1

10000

1000

100

10

0.1

0.01

0.001

Nitrate

Discharge

0.01

0.1

1

10

1

10000

1000

100

10

0.1

0.01

0.001

Nitrate

Discharge

Nitrate

Discharge

0.01

0.1

1

10

1

10000

1000

100

10

0.1

0.01

0.001

0.01

0.1

1

10

1

10000

1000

100

10

0.1

0.01

0.001

Nitrate

Discharge

Water Quality
26 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

IV. WATER QUALITY (CONTINUED)

F. Nitrate - spatial patterns

Spatial patterns of nitrate concentrations in base flow reflect land use.

Median base-flow nitrate concentrations were highest in samples from subbasins 

dominated by agriculture and lowest in samples from forested subbasins; 

mixed land-use watersheds had intermediate nitrate concentrations.

The nitrate concentrations in the January and 

June 2001 samples from all sites reflect the effects of 

the dominant land use within the subbasins on nitrate 

concentrations. In general, the highest median nitrate 

concentrations were in agricultural subbasins, the 

lowest were in forested subbasins, and those in mixed 

(agricultural and forested) subbasins were intermediate 

(fig. 4f, table 5). 

0.1

1.0

10.0

NITRATE CONCENTRATION,

IN MILLIGRAMS PER LITER, AS N

FORESTED SITES

(n=7)

MIXED SITES

(n=6)

AGRICULTURAL SITES

(n=5)

January June June January June January

0.5

5.0

Figure 4F. Median nitrate concentrations in base-flow samples from the 18 stream sites in the upper 

Susquehanna River Basin, N.Y., January and June 2001, by land-use category. (Site locations with 

land-use category shown in fig. 4A and table 1.)
27

Table 5. Mean, median, maximum, and minimum concentrations of nitrate in base-flow samples from upper 

Susquehanna River Basin study area, N.Y., by land-use and bedrock category, January and June 2001.

Statistic

Agricultural,

carbonate

(n = 4)

Agricultural, 

noncarbonate 

(n = 1)

Mixed land use 

and bedrock

(n = 6)

Forested, 

carbonate

(n = 1)

Forested, 

noncarbonate 

(n = 6)

January June January June January June January June January June

mean 1.46 1.62 .662 1.47 .713 .526 .344 .591 .302 .242

median 1.43 1.69 .775 .567 .175 .119

maximum 2.27 2.40 .996 .743 .674 .902

minimum .708 .692 .30 .183 .102 .938

Water Quality
28 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

IV. WATER QUALITY (CONTINUED)

G. Pesticides 

Six pesticide compounds were detected in base-flow samples. 

Samples from 10 of the 12 sites sampled for pesticides in November 2001 contained at least 

one pesticide. The concentrations of these pesticides were at least an order 

of magnitude below any New York State or Federal limit.

Information on the distribution and 

concentrations of pesticides in ground water and 

surface water in the study area is scant, but recent 

studies in other parts of New York have shown 

seasonal trends in pesticide concentrations in ground 

water and correlations between pesticide occurrence 

and land use (Eckhardt and others, 1999, 2001; 

Phillips and others, 1998, 1999a, 1999b). 

Base-flow samples were collected at 12 sites in 

November 2001 (fig. 4G) and analyzed for the 113 

pesticides or their degradates listed in table 6.

(Degradates are the degradation products of parent 

compounds.) The concentrations of all pesticides 

detected were at least an order of magnitude below any 

New York State or Federal limit. However, samples 

were collected in November, several months after the 

summer applications to fields, lawns, roads, and utility 

rights-of-way; this indicates that the compounds 

detected in base flow were derived from a sustained 

ground-water contribution and are probably not the 

result of direct runoff from land surface. 

NEW YORK

PENNSYLVANIA

0

0

10 20 MILES

10 20 KILOMETERS

Susquehanna 

River

Susquehanna

River

Unadilla River

Wharton Creek

Otego Creek

Oaks Creek

Cherry Schenevus Creek

Charlotte Creek

Ouleout Creek

Creek

Valley

76o

43o

75o

42o

1

2

4

6

9

Unadilla River at Millers Mills

North Winfield Creek at West Winfield

Shadow Brook at East Springfield

Oaks Creek at Index

Upland tributary east of Portlandville

Unadilla River at Rockdale

Susquehanna River at Unadilla

Smokey Kill west of Sidney Center

Route 41 stream south of Afton

Unnamed stream at Plains Road east of Nineveh

Hotchkiss Creek near Windsor

Susquehanna River at Conklin

1

2

4

6

9

10

12

13

14

16

17

18

SITE NAMES

2

+

+

Butternut Creek

10

12 13

14

16

18 17

EXPLANATION

Surface-water sites at which samples 

were collected for pesticide analysis

Base from U.S. Census TIGER/line Files ,1990,

Albers equal-area conic projection 1:100,000 scale;

streams are 1:2,000,000 scale

Figure 4G. Locations of the 12 sites in the upper Susquehanna River Basin, N.Y., where water samples were analyzed for 

pesticides, November 2001. (USGS station numbers are given in table 1.)
29

Table 6. Pesticides for which base-flow samples collected from 12 sites in upper Susquehanna River Basin 

in November 2001 were analyzed.

[Boldface type indicates compound detected in this study. Asterisk indicates degradation product.] 

Compounds for which samples were analyzed 

2,4-D Deisopropylatrazine * Metribuzin 

2,4-D methyl ester * Deethyldeisopropylatrazine * Molinate 

2,4-DB Diazinon Napropamide 

2,6-Diethylaniline * Dicamba Neburon 

2-Hydroxyatrazine * Dichlorprop Nicosulfuron 

3-(4-chlorophenyl)-1-methyl urea * Dieldrin Norflurazon 

3-Hydroxycarbofuran * Dimethenamid ESA * Oryzalin 

3-ketocarbofuran * Dimethenamid OA * Oxamyl 

Acetachlor ESA * Dinoseb Oxamyl oxime *

Acetachlor OA * Diphenamid p,p’-DDE *

Acifluorfen Diuron Parathion 

Alachlor ESA * Disulfoton Parathion-methyl 

Alachlor OA * EPTC Pebulate 

Alachlor Ethalfluralin Pendimethalin 

Aldicarb Ethopropos cis-Permethrin 

Aldicarb sulfone * Fenuron Phorate 

Aldicarb sulfoxide * Flufenacet OA * Picloram 

alpha-HCH Flufenacet ESA * Prometon 

Atrazine Flumetsulam Propachlor 

Bendiocarb Fluometuron Propanil 

Benfluralin Fonofos Propargite 

Benomyl Imazaquin Propham 

Bensulfuron-methyl Imazethapyr Propiconazole 

Bentazon Imidacloprid Propyzamide 

Bromacil Lindane Propoxur 

Bromoxynil Linuron Siduron 

Butylate MCPA Simazine 

Carbaryl MCPB Sulfometruron methyl 

Carbofuran Malathion Tebuthiuron 

Chloramben methyl ester * Metalaxyl Terbacil 

Chlorimuron-ethyl * Methiocarb Terbufos 

Chlorothalonil Methomyl Terbuthylazine 

Chlorpyrifos Methomyl oxime * Thiobencarb 

Clopyralid Methyl azinphos Tri-allate 

Cycloate Metsulfuron-methyl Tribenuron-methyl 

Dacthal Metolachlor Triclopyr 

Dacthal mono-acid * Metolachlor ESA * Trifluarlin 

Deethylatrazine * Metolachlor OA *

Water Quality
30 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

IV. WATER QUALITY (CONTINUED)

H. Detected herbicides

All six of the pesticide compounds detected were agricultural herbicides.

Two of the compounds (atrazine and deethylatrazine) were found in 

samples from every stream in which a pesticide was detected.

The six pesticide compounds that were detected 

were agricultural herbicides—a class of pesticides 

used to control broadleaf weeds and grasses in fields, 

lawns, utility right-of-ways, and other areas. These 

herbicides and their degradates are usually highly 

soluble and can move through the hydrologic system 

in surface runoff or ground water. Their toxicity to 

humans is relatively low compared to that of 

insecticides (Ware, 1983), which are used more 

extensively than pesticides in residential and urban 

areas (Templeton and others, 1998) and were not 

detected in this study. The measured concentrations 

did not exceed any New York State or Federal 

regulatory limits (table 7). 

Ten of the 12 streams that were sampled for 

pesticides contained at least one of these herbicides, and 

one of these streams (site 16, forested) contained all six 

compounds (fig. 4H). Two of the compounds (atrazine 

and deethylatrazine) were found in samples from all 10 

of the streams in which a pesticide was detected. 

Atrazine is one of the most commonly used 

pesticides in the nation (Koplin and others, 1998; 

Larson and others, 1999) and has been the pesticide 

detected most frequently in previous ground-water and 

surface-water studies in the United States as a result of 

its wide-spread use (Barbash and Resek, 1996). Its 

maximum concentration during this study was 0.073 

μg/L. Deethylatrazine is a degradate of atrazine and was 

detected at a maximum concentration of 0.024 μg/L. 

Metolachlor ESA, the ethanasulfonic acid 

degradate of metolachlor, was detected in samples 

from nine sites and had a maximum concentration of 

1.26 μg/L. Metolachlor was detected in samples from 

six sites, and metolachlor OA, the oxanilic acid 

degradate of metolachlor, was detected in samples 

from three sites; the maximum concentrations were 

0.417 μg/L and 1.19 μg/L, respectively. Alachlor ESA, 

a degradate of alachlor, was detected in samples from 

two sites; the maximum concentration was 0.08 μg/L. 

The pesticide analyses indicate a correlation 

between atrazine and deethylatrazine concentrations 

and land use. Samples from the four subbasins with the 

highest percentages of agricultural land (sites 1, 2, 4, 

and 14; table 1) had the highest concentrations of 

atrazine plus deethylatrazine (fig. 4H). Samples from 

two of the subbasins dominated by forested land with 

virtually no agricultural land (sites 9 and 17; table 1) 

contained no pesticides. The anomalously high 

pesticide detections at sites 14 and 16 are discussed in 

the next section (IV-I). 

Metolachlor did not show a strong correlation 

with land use; it was detected in samples from two 

agricultural sites, one forested site, and all three mainstem river sites sampled (fig. 4H). Metolachlor ESA 

and OA, where detected, were at higher concentrations 

than metolachlor. Similarly, alachlor was not detected, 

but its degradate, alachlor ESA, was detected in 

samples from two sites. Concentrations of parent 

compounds can exceed those of their degradates if the 

parent compounds are flushed into streams by 

precipitation soon after application (Eckhardt and 

others, 2001), but the summer of 2001 in the study area 

was dry, and the pesticide sampling was not until 

November. Thus, the lack of precipitation allowed the 

parent compounds time to break down into their 

degradation products within the soils, from which the 

degradation products were transported to ground water 

before the November sampling. 
31

0.001

0.01

0.1

1

Deethylatrazine

Atrazine

Alachlor ESA

9 17 18 12 10 13 6 1 2 4 16 14

 CONCENTRATION, INMICROGRAMS PER LITER

0.001

0.01

0.1

1

10

Metolachlor

Metolachlor ESA 

Metolachlor OA

9 17 18 12 10 13 6 1 2 4 16 14

 CONCENTRATION, INMICROGRAMS PER LITER

SITE NUMBER AND LAND-USE CATEGORY

Forested Mixed Agricultural

Forested Mixed Agricultural

Figure 4H. Concentrations of the six herbicides detected (atrazine, deethylatrazine, alachlor ESA, 

metolachlor, and its two metabolites) in relation to land use at the 12 sites sampled under base-flow 

conditions in the upper Susquehanna River Basin, N.Y., November 2001. (Site locations are shown 

in fig. 4G.)

Table 7. Sites and concentrations at which herbicides were detected in November 2001 base-flow samples 

from upper Susquehanna River Basin, and Federal or State concentration limit (USEPA, 2000).

[Site locations are shown in fig. 4G and listed in table 1. Dash indicates no limit has been established. μg/L, micrograms per liter.] 

 Maximum detected

Name Sites concentration (μg/L) Federal or State limit (μg/L) 

Alachlor ESA 12, 16 0.08 --

Atrazine 1, 2, 4, 6, 10, 12, 13, 14, 16, 18 0.073 3.0

Deethylatrazine 1, 2, 4, 6, 10, 12, 13, 14, 16, 18 0.024 --

Metolachlor 2, 10, 12, 14, 16, 18 0.417 50 

Metolachlor ESA 1, 2, 4, 6, 10, 12, 14, 16, 18 1.26 50

Metolachlor OA 10, 14, 16 1.19 50

Water Quality
32 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

IV. WATER QUALITY (CONTINUED)

I. Two streams with anomalous salt and herbicide concentrations

Two streams sampled during this study contained chemicals in concentrations 

indicative of deicing salt and herbicide applications within the subbasin.

Samples from two streams near Interstate 88 in the southern part of the study area had higher 

concentrations of iron, manganese, sodium chloride, and several pesticides than the other sites. 

Two small tributaries to the Susquehanna River 

in the south-central part of the study are—sites 14 

(agricultural) and 16 (forested)—that were sampled in 

January and June 2001 for nutrient and common 

inorganic constituent analyses (table 2) and in 

November 2001 for pesticide analysis (table 6) showed 

higher concentrations of sodium, chloride, manganese, 

iron, and the herbicides atrazine, metolachlor, 

metolachlor ESA, and metolachlor OA than all other 

sites sampled. 

The elevated sodium and chloride 

concentrations in these two streams are probably the 

result of road salting on Interstate 88 (I-88), a major 

four-lane divided highway that crosses the drainage 

area of each stream less than 0.5 mi upstream from the 

sampling sites. Construction of I-88 in the 1970s 

entailed the channelizing of many natural drainages 

and the routing of many channels through culverts 

beneath the highway. The new drainage patterns may 

increase the runoff of precipitation and might also 

channel highway runoff toward these streams.

Deicing salt (NaCl) is initially applied to I-88 at 

rates of 225 to 270 lb/mi per lane during snowstorms; 

if a second application is required, 115 to 270 lb/mi 

per lane is applied (New York State Department of 

Transportation, 1994). The high concentrations of 

sodium and chloride in the June base-flow samples 

from these streams, as well as the January samples, 

indicate that road salt is probably reaching these 

streams as dissolved sodium and chloride in ground 

water throughout the year. 

These two streams also had the highest 

concentrations of four herbicides (atrazine, 

metolachlor, and the two metolachlor degradates) of 

all streams sampled (fig. 4I), although the 

concentrations did not exceeded State or Federal 

limits. Pesticides are applied to transportation rightsof-way along I-88 to control the growth of broad-leaf 

weeds and grasses (Edward Capria, New York State 

Department of Transportation, Chenango County 

Division, oral commun., 2002). A utility corridor 

(powerline) runs just east of I-88 in the headwaters of 

these two sites; thus, the application of herbicides 

along this corridor, as well as along the highway, could 

be the principal source of these constituents in the two 

streams. Runoff from cornfields that surround the 

stream above site 14 also could be contributing some 

of the metolachlor and atrazine. 

Base-flow samples from sites 8, 14, and 16 

(locations shown in fig. 1) also had higher 

concentrations of iron and manganese than samples 

from the other sites (fig. 4I). These indicate anoxic, 

acidic conditions probably caused by the decay of 

organic matter that would dissolve iron and manganese 

minerals within the alluvial and glacial deposits, and 

once the water bearing these minerals discharges to the 

stream, the iron and and manganese would precipitate, 

either through redox reactions (higher redox potential 

within the stream water than within the alluvial 

material), or through iron-converting bacteria along 

the streambank, which live in the interface between 

anoxic conditions of the riparian soil and the 

oxygenated surface-water environment (Hem, 1992, p. 

83-89). 

The mean concentrations of sodium, chloride, 

iron, manganese, and the four herbicides at sites 14 

and 16 are plotted in relation to those at all other sites 

in figure 4I. The concentrations of these constituents at 

both sites are shown to exceed those at the other sites, 

and the manganese concentration at sites 14 and 16 

exceeded the U.S. Environmental Protection Agency’s 

SMCL (secondary maximum contaminant level) of 

50 μg/L, as did the iron concentration at sites 8 and 14 

(SMCL 300 μg/L) (U.S. Environmental Protection 

Agency, 2000). 
33

0.1

1.0

10

100

1000

CONCENTRATION, IN MILLIGRAMS PER LITER

Sodium

(Na)

Chloride

(Cl)

1.0

10

100

1000

CONCENTRATION, IN MICROGRAMS PER LITER

Iron

(Fe)

Manganese

(Mn)

0.001

0.01

0.1

1

10

CONCENTRATION, IN MICROGRAMS PER LITER

Atrazine

MetolachlorMetolcahlor

ESA

Metolachlor

OA

Site 2

Site 1

Site 4

Site 5

Site 6

Site 12

Site 18

Site 7

Site 10

Site 13

Site 11

Site 3

Site 17

Site 15

Site 9

Site 8

Site 16

Site 14

Secondary Maximum Contaminant Level 

(SMCL)1 

1 SMCL- secondary maximum contaminant level for Cl, Fe, and Mn 

(U.S. Environmental Protection Agency, 2000). For Na, the EPA has

recommended a drinking-water advisory limit of 30 to 60 mg/L;

however, this is not an enforceable SMCL (U.S. Environmental

Protection Agency, 2002).

Agricultural

Mixed

Forested

EXPLANATION

Anomalous Sites

Mean for January and June 2001 Mean for January and 

June 2001

November 2001

Figure 4I. Concentrations of sodium, chloride, iron, manganese, and four herbicides detected in base-flow samples 

from sites 14 and 16 in relation to those at all other sites and in relation to Federal water-quality standards. (Site 

locations are shown in fig. 1.)

Water Quality
34 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

V. AGE DATING OF WELL WATER TO DETECT INDUCED INFILTRATION 

A. Dating technique

Chlorofluorocarbons, known as CFCs, can be used to indicate the age of ground water 

and, thus, the potential for induced infiltration of river water to nearby wells.

Four municipalities in the study area have production wells near the Susquehanna River. 

CFC concentrations in water from these wells were used to calculate the age of the 

water and the potential for induced infiltration from the river.

The yield of a pumped well finished in a sand 

and gravel aquifer can be greatly increased through 

induced recharge from a nearby surface-water body, 

but most surface water contains microorganisms and 

other contaminants that can be hazardous to humans. 

Most of these contaminants can be filtered out by 

aquifer material before reaching the well, but the 

pumped water must be sampled routinely to ensure 

complete removal of contaminants. Therefore, a well’s 

potential for induced infiltration of river water is a 

concern to local water managers. 

A pilot study was conducted in a 30-mi reach of 

the study area (fig. 5) in February 2001 to calculate the 

age of ground water at four production wells in an 

effort to assess whether these wells are inducing 

infiltration of river water. The age of ground water, 

defined as the number of years from infiltration at the 

water table to discharge from a pumping well or 

natural spring, can be used for other purposes, 

including calculation of recharge rates, refinement of 

hydrologic models, assessment of the potential for 

contamination from local sources, and detection of 

river water that infiltrates into the aquifer. The 

chemical quality of ground water affected by 

infilitration of river water is intermediate between that 

of the river and that of the aquifer. 

Chlorofluorocarbons (CFCs) are synthetic 

industrial compounds that occur in the atmosphere and 

in precipitation. CFC concentrations in precipitation, 

and in ground water recently derived from 

precipitation, correspond to that in the 

contemporaneous atmosphere. Atmospheric CFC 

concentrations have been recorded since about 1945 

(Plummer and Busenberg, 2000); therefore, 

comparison of CFC concentrations in a water sample 

with the historical records of atmospheric CFC 

concentrations can indicate the year in which that 

water entered the water table (since about 1945). River 

water has an age of zero because it is in constant 

contact with the atmosphere. 

The accuracy of an estimated age depends in 

part on the degree to which transport through the 

aquifer affected the CFC concentrations; for example, 

chemical processes such as microbial degradation and 

sorption can decrease the concentrations (Plummer 

and Busenberg, 2000). For this reason, the estimated 

age of the water is normally referred to as “model age” 

or “apparent age.”

CFC concentrations in water samples from the 

four wells were used to indicate the water’s age and the 

presence of river water. Extremely young water (less 

than 1 year) would indicate induced recharge from the 

river, but this interpretation would need to be 

compared with other data, such as well logs, microbial 

and other chemical analyses of the water, and seasonal 

changes in water temperature at the wells (Winslow 

and others, 1965; Randall, 1977, 1981; and Miller, 

2000). The four wells tap glacial sand and gravel 

aquifers (table 8). Their distances from the river are as 

follows: Unadilla, 95 ft; Sidney, 110 ft; Otego, 65 ft; 

Afton, 450 ft. All samples were collected in February 

2001 and analyzed through standard techniques 

(Kendall and Caldwell, 1998; Plummer and 

Busenberg, 2000). Results are summarized in the 

following section. 
35

Figure 5. Locations of wells near Susquehanna River that were used for chlorofluorocarbon (CFC) analysis. 

(Site descriptions are given in table 8.) 

Susquehanna 

River

Susquehanna 

River

Unadilla River

Wharton Creek

Otego Creek

Oaks Creek

Cherry 

Schenevus Creek

Charlotte Creek

Ouleout Creek

Creek

Valley

Butternut Creek

0

0

5 MILES

5 KILOMETERS

Sidney

Unadilla

Otego

Afton

Church St. Well

75o30' 75o20' 75o10'

42o20'

42o25'

42o15'

0

10 MILES

10 KILOMETERS

0

Susquehanna

2-88

River

Well from which samples were 

collected for CFC analysis

Pennsylvania

New York

Sidney

Unadilla

Otego

Afton

Base from U.S. Census TIGER/line Files ,1990,

Albers equal-area conic projection, 1:100,000 scale;

streams are 1:2,000,000 scale

Table 8. Data on the four production wells sampled for chlorofluorocarbons (CFCs) to estimate potential for

induced infiltration of water from Susquehanna River in study area, February 2001. 

[Distance is in feet; well depths and screened intervals are in feet below land surface. Dashes indicate sample contamination. 

Well locations are shown in fig. 5.] 

* C, confined; U, unconfined 

Well 

Distance 

from 

river

Well 

depth 

Screened 

interval

Type of 

aquifer* Lithology 

Infiltration 

from

river

Village of Unadilla 

Church Street well

95 99 89-99 C 0-14 ft, clay; 14-49 ft, sand and gravel; 49-62 ft, 

clay and gravel; 94-98 ft, sand & gravel; 98-106 ft, 

till; 106-108 ft, bedrock.

--

Village of Sidney 

well 2-88

110 95 75-95 U 0-5 ft, fine sand; 5-54 ft, sand and gravel; 54-62 ft, 

fine to coarse sand; 62-95 ft, sand and gravel.

--

Village of Otego

well

65 78 63-78 C 0-3 ft, fill; 3-25 ft, clay; 25-50 ft, clay & gravel; 

50-63 ft, sand and clay; 63-66 ft, gravel; 66-68 ft, 

till; 68-80 ft, gravel, fine sand and clay.

No

Village of Afton 

well

450 133 123-133 C 0-10 ft, sand & gravel; 10-20 ft, sand; 20-30 ft, 

gravel; 30-98 ft, fine sand, silt and clay; 98-110 ft; 

sand & gravel; 110-119 ft, silty gravel; 119-134 ft, 

sand & gravel; 134-137 ft, sand with trace gravel; 

137-185 ft, unknown; 185 ft, bedrock.

No

Age Dating of Well Water to Detect Induced Infiltration
36 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

V. AGE DATING OF WELL WATER TO DETECT INDUCED INFILTRATION (CONTINUED) 

B. Results and Interpretation

Water from the Otego production well is probably 26 to 43 years old, and water from the Afton 

production well is probably 37 to 50 years old. The age of water from the other wells 

could not be ascertained because the samples contained CFCs from urban sources.

CFCs have three major forms—CFC-12 

(dichlorodifluoromethane), which was first used in 

1931 as an alternative to ammonia and sulfurdioxide in 

refrigeration and other industrial applications; CFC-11 

(trichlorofluoromethane), first used in 1936 for 

airconditioners and refrigeration, insulation, 

propellants in aerosol cans, and as solvents; and CFC113 (trichlorotrifluoro-methane), first used in the mid1950s for semiconductor chip manufacturing in vapor 

degreasing and cold immersion cleaning of electronic 

components (Plummer and Friedman, 1999). If all 

three CFC forms indicate a similar age, that value can 

be considered fairly reliable. The certainty is 

diminished if only two of the CFC forms are used or 

yield similar values. If only one form can be used, the 

value is not considered reliable. 

The feasibility of using CFCs as tracers of recent 

recharge and indicators of ground-water age was first 

recognized in the 1970s (Plummer and Busenberg, 

2000). Ground-water dating with CFC-11, CFC-12, 

and CFC-113 is possible because (1) their amounts in 

the atmosphere over the past 50 years have been 

reconstructed, (2) their solubilities in water are known, 

and (3) concentrations in air and young water are high 

enough that they can be measured. Age is detemined 

from CFCs by relating their measured concentrations 

in ground water back to known historical atmospheric 

concentrations and/or to calculated concentrations 

expected in water in equilibrium with air. Water 

samples for CFC analysis can be collected from 

domestic, irrigation, monitoring, and municipal wells, 

and from springs. A closed path is established between 

the well or pump to a valve system that is used to fill 

glass ampoules with water, creating a headspace with 

CFC-free, ultra-pure nitrogen gas. The samples are 

then transported to the U.S. Nuclear Regulatory 

Commission-licensed USGS laboratory for analysis of 

CFC content by gas chromatography to a detection 

limit of 0.3 parts per quadrillion.

CFC contamination of ground water—that is, 

the presence of CFCs from sources other than the 

atmosphere, can occur in developed areas from local 

sources such as septic-tank effluent, leaking 

sewerlines, industrial wastes, and induced recharge 

from rivers carrying sewage-treatment-plant effluent. 

Samples that contain CFCs from local sources yield 

ages that are too young—sometimes impossibly young 

if the concentrations exceed those set by air-water 

equilibrium. Samples from three of the four wells 

sampled were contaminated by one or more forms of 

CFCs from nonatmospheric sources (table 9). The 

Otego production-well samples showed CFC-113 

contamination, the Sidney samples showed CFC-12 

and CFC-113 contamination and possibly CFC-11 

contamination, and the Unadilla production well 

showed contamination by all three CFC forms. Only 

the Afton production well showed no CFC 

contamination. 

Water pumped by the Afton production well is 

from a confined aquifer and was indicated to range 

from 37 to 53 years old; it is probably about 50 years 

old because CFC-11 and CFC-12 indicated ages of 50 

and 53 years, respectively (table 9). This relatively old 

age indicates that pumping from this confined aquifer 

does not induce recharge from the Susquehanna River, 

450 ft away. The lack of induced infiltration would 

indicate that the confining unit, which consists of 68 ft 

of fine sand, silt, and clay (table 8) is continuous and 

extensive, and (or) that the confined aquifer is 

recharged by downward infiltration from the overlying 

unconfined aquifer far from the well and river. 

Water pumped from the Otego well was 

indicated to range from 26 to 43 years old (table 9), but 

the uncertainty is large because the age ranges 

indicated by the CFC-11 and CFC-12 analyses (43 and 

26 years, respectively) differ considerably. Age based 

on CFC-113 was not available in the Otego analysis 

because the samples showed contamination. The 

relatively old age of water at this well indicates that 

little or no infiltration of river water is induced by 

pumping, probably because the aquifer is confined by 

a clay layer 10 to 25 ft thick (table 8) that underlies the 

river and overlies the aquifer. 

No reliable age could be inferred from the CFC 

data for the Sidney and Unadilla wells because the 

samples reflect contamination, probably from local 

sources within the contributing area of these wells. 
37

Table 9. Concentrations of CFCs in water samples from four production wells on the Susquehanna River in February 

2001 and the calculated model ages of the water (time of recharge). 

[Values are in parts per trillion per volume (pptv). C, contaminated with CFCs from nonatmospheric sources. Well locations are 

shown in fig. 5.] 

Well 

location

Concentration in solution 

as indicated by 

Concentration in 

atmosphere, as 

indicated by

Model 

ground-water age Ground-water age and

CFC-11 CFC-12 CFC-113 CFC-11 CFC-12 CFC-113 CFC-11 CFC-12 CFC-113 date of recharge

Village of 

Afton 3.4 3.2 4.1 1.2 5.1 3.5 50.0 53.0 37.0 37 to 50 years. Late 1940’s to early 1960’s

Village of 

Otego 

19.8 135 0.0 7.2 214 0.0 43.0 26.0 C 26 to 43 years. Mid-1970’s with 

degradation of CFC-11 and(or) 

CFC-113, or possible CFC-12 

contamination of 1950’s water

Village of 

Sidney, 

well 2-88

519 2910 3520 188 4610 3020 19.0 C C Probably early 1980’s; contamination precludes reliable 

estimate

Village of 

Unadilla, 

Church St. 

979 1270 987 355 2010 848 C C C All samples contaminated. 

Age Dating of Well Water to Detect Induced Infiltration
38 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

SUMMARY AND CONCLUSIONS

Base flow is an approximation of the quality of 

shallow ground water and constitutes more than 

60 percent of total annual flow of streams within the 

upper Susquehanna River Basin. Nitrate, inorganic 

chemical constituents, and pesticide concentrations 

reflect land use and carbonate content of bedrock 

upstream of the 18 sampling sites.

Base flow from 18 streams in the upper 

Susquehanna River Basin from Millers Mills to 

Conklin, N.Y., was sampled and analyzed several 

times during 2001 for common ions, nutrients, and 

pesticides to characterize the quality of shallow 

ground water. The CFC concentrations of water from 

four production wells were measured to estimate the 

age and the potential for induced infiltration from the 

river.

The upper Susquehanna River Basin is mainly 

rural. It is about 26 percent agricultural land and about 

71 percent undeveloped, forested land and contains 

one city (Oneonta) and several small villages. The 

northernmost part is underlain by carbonate 

(limestone) bedrock; the rest is underlain by 

noncarbonate siltstone, sandstone, and noncalcareous 

shale. 

Base flow (the ground-water component of 

streamflow) of a stream is an approximation of the 

chemical quality of shallow ground water within the 

stream’s drainage area. Hydrograph-separation 

analyses of the 1941-93 discharge records of four 

streams with streamflow-gaging stations indicated that 

base flow constitutes more than 60 percent of total 

annual flow in streams of the study area. Hence, the 

chemical quality of baseflow is an important factor 

influencing the total stream flow that leaves the upper 

Susquehanna River Basin and eventually empties into 

Chesapeake Bay.

Base-flow samples were analyzed for pH, 

alkalinity, specific conductance, dissolved solids, and 

common inorganic cations and anions. The 

predominant cations in the samples were calcium, 

magnesium, and sodium; the predominant anions were 

chloride, sulfate, and bicarbonate. Base-flow quality 

was found to reflect land use and the presence or 

absence of carbonate bedrock and carbonate-rich 

glacial deposits in the subbasins. The 18 subbasins 

were categorized by predominant land use according 

to whether they were predominantly agricultural, 

forested, or a mixture of both, and whether they were 

dominated by carbonate or noncarbonate rocks.

Base-flow samples collected in January and 

June 2001 from agricultural subbasins underlain by 

carbonate bedrock contained higher concentrations of 

most inorganic constituents than base flow from the 

forested subbasins that lack carbonate material. The 

largest subbasins, which contain a mixture of 

agricultural and forested land as well as a mixture of 

carbonate and noncarbonate rock, had intermediate 

concentrations of most inorganic constituents.

Median nitrate (NO3

-

) concentrations were 

lowest in base-flow samples from forested subbasins 

and highest in samples from agricultural subbasins; 

concentrations in samples from sites from large 

subbasins with mixed land use were intermediate. 

Nitrate concentrations in the forested and mixed 

subbasins were lower in summer than in winter as a 

result of the increased biological activity, reduced 

recharge, and denitrification in the soil and streams 

during the growing season. The agricultural subbasins 

generally showed the opposite—higher nitrate 

concentrations in the early summer than in the 

winter—probably as a result of fertilizer and manure 

applications near these streams. 

Pesticides were detected in 10 of the 12 streams 

sampled in November 2001 for pesticide analysis. 

Only 6 of the 113 compounds for which samples were 

analyzed were detected; these were metolachlor and 

its two degradates (metolachlor OA and metolachlor 

ESA), atrazine and its degradate (deethylatrazine), 

and alachlor ESA. The highest concentrations of 

atrazine plus deethylatrazine were in samples from 

the four streams with the largest percentage of 

agricultural land in their drainage areas. No pesticides 

were detected in samples from the two streams that 

drain subbasins with nearly 100 percent forested land. 

Pesticide concentrations at main-stem river sites 

representing mixed land use generally were 

intermediate between those of the agricultural and the 

forested subbasins. No pesticides were detected at 

concentrations that exceeded New York State or 

Federal water-quality standards. 

Two small streams had unusually high 

concentrations of sodium, chloride, iron, manganese, 

and metolachlor and its two degradates. These two 

sites probably receive runoff from a nearby utility 

right-of-way to which herbicides are applied, as well 

as from Interstate 88, which crosses the headwaters of 

both streams and to which road salt is applied in the 
39

winter. The elevated iron and manganese 

concentrations in these streams may result from 

anoxic conditions in the source aquifers. Anoxic, 

acidic conditions caused by decaying organic matter 

would allow iron and manganese minerals within the 

unconsolidated deposits in the valley to dissolve 

readily. Once the water discharges into the stream, iron 

and manganese oxidize and precipitate.

Concentrations of chlorofluorocarbons (CFCs) 

in ground-water samples from two of four wells 

sampled in villages near the Susquehanna River 

indicate the age of the water in these wells and the 

likelihood that these wells are inducing some surface 

water from the river. Water in the Otego well is 

probably 26 to 43 years old; water in the Afton well is 

probably 37 to 50 years old. These apparent old ages 

indicate that neither well induces surface-water 

infiltration from the river, probably because both are 

confined by a layer of fine-grained material. No 

reliable age could be estimated from water samples 

from the production wells at Sidney and Unadilla 

because the samples contained CFCs from local 

sources.

The data presented in this report demonstrates 

the importance of understanding the water quality of 

base flow in the upper Susquehanna River Basin. Most 

chemical constituents for which analyses were done 

were below any State or Federal water-quality 

standards, though 2 streams had manganese 

concentrations above the USEPA SMCL and 2 had 

iron concentrations above the USEPA SMCL. This 

data can be used by water managers throughout the 

study area for comparisons of the concentrations of 

chemical constituents in production wells with the 

baseflow concentrations, or in possible future 

stormflow studies to compare base-flow to stormflow 

concentrations. 

Upland stream (site 9 in table 1) in upper 

Susquehanna River Basin, N.Y., 

during base-flow conditions, June 2001. 

Summary and Conclusions
40 Chemical Quality of Base Flow in 18 Selected Streams in the Upper Susquehanna River Basin, New York

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