U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2004-5008

Hydrogeology and Water Quality of the Pepacton 

Reservoir Watershed in Southeastern New York

Part 3. Responses of Stream Base-Flow Chemistry to Hydrogeologic Factors and 

Nonpoint-Sources of Contamination

In cooperation with

NEW YORK STATE DEPARTMENT OF ENVIRONMENTAL CONSERVATION
This page has been left blank intentionally. 
Hydrogeology and Water Quality of the Pepacton 

Reservoir Watershed in Southeastern New York

Part 3. Responses of Stream Base-Flow Chemistry 

to Hydrogeologic Factors and Nonpoint-Sources of 

Contamination 

By Paul M. Heisig and Patrick J. Phillips

In cooperation with New York State Department of Environmental Conservation

Scientific Investigations Report 2004-5008

U.S. Department of the Interior

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

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia: 2004

Version 1.1

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iii

Contents

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

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

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

Previous Investigations........................................................................................................................2

Description of Study Area ...................................................................................................................2

Hydrogeology................................................................................................................................4

Precipitation and Runoff.............................................................................................................4

Methods and Approach.......................................................................................................................4

Sampling-Site Selection .............................................................................................................5

Sampling and Analytical Procedures.......................................................................................5

Acknowledgments................................................................................................................................5

Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources 

of Contamination ..............................................................................................................................5

Major-Ion Water Type .........................................................................................................................7

Hydrogeologic and Human Controls on Water Type..............................................................7

Naturally Occurring Water Types ...........................................................................................10

Chloride- and Sodium-Affected Water Types .......................................................................11

Implications of Spatial and Temporal Water-Type Variation..............................................12

Selected Constituents Associated with Nonpoint Sources ........................................................12

Chloride and Sodium .................................................................................................................13

Nitrogen Species .......................................................................................................................15

Characterization of Nitrogen Sources ..........................................................................15

Atmospheric Deposition, Nitrogen Saturation, and Nitrogen Depletion........16

Septic-System Wastewater...................................................................................16

Manure and Commercial Fertilizers .....................................................................16

Biological Uptake and Transformation of Nitrogen in Streams ................................17

Dissolved Organic Nitrogen and Nitrate in Base Flow...............................................17

Organic Nitrogen .....................................................................................................17

Nitrate .......................................................................................................................19

Effects of Seasonal Changes on Nitrogen Concentrations ..............................21

Phosphorus ................................................................................................................................21

Mobility of Orthophosphate and Organic Phosphorus ..............................................22

Orthophosphate in Base Flow ........................................................................................22

Herbicides...................................................................................................................................24

Summary and Conclusions.........................................................................................................................27

References Cited .........................................................................................................................................28
iv

Figures

1. Hydrography, sampling network sites with associated drainage basins, and location of 

reference stream-gaging station within the Pepacton watershed, western Catskill 

Mountains, New York..............................................................................................................................3

2. Streamflow at the East Branch Delaware River at Roxbury, N.Y. stream-gaging station 

(01413088) and sampling dates of network surveys and additional index-site surveys .............7

3. A. Major-ion water types and selected chemical concentrations for samples from four 

base-flow surveys, December 2000 through October 2001, compared with B. streamflow 

at the reference stream-gaging station...............................................................................................8

4. A. Conceptual model of shallow ground-water evolution from base-flow water-type 

determinations, starting with dilute mixed-ion water types and proceeding through natural 

and human-induced changes. B. Generalized stream basin depicting the hydrogeologic 

framework with ground-water flowpaths and the distribution of major-ion water types in 

ground water that discharges to the stream.. ....................................................................................9

5. Bicarbonate (HCO3) concentration at the three index sites over time, with the major-ion 

water type, chloride concentration, and corresponding daily mean streamflow from the 

reference stream-gaging station keyed to each sample................................................................11

6. Base-flow concentrations of chloride and sodium as a function of annual road-saltapplication rate in each subbasin during the four network sample surveys, Pepacton 

Reservoir watershed, southeastern New York, December 2000 through October 2001 ...........14

7. Comparison of base-flow chloride concentration as a function of subbasin annual salt 

application rate among the four network sample surveys, Pepacton Reservoir watershed 

in southeastern New York, December 2000 through October 2001...............................................15

8. Nitrate concentration, organic nitrogen concentration, and stream-water temperature at 

the three index sites (ANGLH, MRSNH, and SEMNH) during base-flow conditions, and 

discharge of the East Branch Delaware River at the reference stream-gaging station at 

Roxbury, N.Y., December 2000 through November 2001 .................................................................18

9. Base-flow nitrate concentration as a function of annual manure-production rate in 

sampled subbasins of the Pepacton Reservoir watershed in southeastern New York 

during four sample surveys, December 2000 through October 2001 ............................................20

10. Concentrations of orthophosphate, iron, atrazine, metolachlor ESA, manganese, dissolved 

organic carbon, and sulfate at the three index sites, and discharge at the reference 

stream-gaging station (Roxbury, N.Y.), December 2000 through November 2001 ......................23

11. Orthophosphate concentrations as a function of annual manure-production rate in 

sampled subbasins of the Pepacton Reservoir watershed in southeastern New York 

during four sampling surveys, December 2000 through October 2001.........................................25

12. Total herbicide concentration (sum of atrazine, metolachlor, simazine, and associated 

degradates) in base flow as a function of basin area under cultivation. ...................................26

Tables

1. Physical and land-use characteristics of stream subbasins in which base-flow 

samples were collected in Pepacton Reservoir watershed in southeastern New York, 

2000-01 ........................................................................................................................................................6
v

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

square mile (mi2) 2.590 square kilometer (km2) 

Volume

million gallons (Mgal) 3,785 cubic meter (m3)

cubic foot (ft3) 0.02832 cubic meter (m3) 

Flow rate

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

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

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

 °F=(1.8×°C)+32

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

 °C=(°F-32)/1.8

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

(NAVD 88).

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

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

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

25 °C).

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

or micrograms per liter (μg/L).

Conversion Factors, Datum and Abbreviations
vi
Hydrogeology and Water Quality of the Pepacton 

Reservoir Watershed in Southeastern New York 

Part 3. Responses of Stream Base-Flow Chemistry to Hydrogeologic 

Factors and Nonpoint-Sources of Contamination 

By Paul M. Heisig and Patrick J. Phillips

base-flow water quality. Chloride and sodium, which are 

relatively conservative constituents, showed strong linear 

relations with annual estimates of road-salt application during 

all four sampling periods. Nonconservative constituents, 

such as the nutrients nitrate and orthophosphate, showed 

linear relations with manure production rate among farmed 

basins, but only at specific times of the year because of 

losses through biologic activity. Nitrate showed the strongest 

relation in winter because losses to biological activity were 

at a minimum. Orthophosphate showed the strongest relation 

in early summer, when hydrologic and chemical conditions 

appear to favor release from sediments. Atmospheric nitrogen 

deposition is an additional source of nitrogen that can be 

released from mature or stressed forested basins. 

Detections of herbicides (atrazine, metolachlor, simazine) 

and herbicide degradates (Metolachlor ESA, alachlor 

ESA, deethylatrazine) in base flow were closely correlated 

with subbasins in which corn was grown during the study. 

Atrazine was detected at the farmed index site only in early 

summer, after application and two rain storms. This detection 

corresponded to the peak orthophosphate concentration. In 

contrast, metolachlor ESA was detected in nearly all farmedindex-subbasin samples and peaked in late summer, when 

percent base-flow contributions from farmed valley-bottom 

areas were likely highest.

The implications of this study are that seasonal and 

more frequent base-flow surveys of water chemistry from 

small stream basins can help refine the understanding of local 

hydrogeologic systems and define the effects of nonpointsource contamination on base-flow water quality. The 

concentration of most nonpoint sources in valley-bottom or 

lower-hillside areas helped indicate the relative contributions 

of water from hillside and valley-bottom areas at different 

times of year. The positive correlations between the intensity 

of nonpoint-source activities and nonpoint-source constituents 

in base flow underscores the link between land use (nonpoint 

sources), ground-water quality, and surface-water quality. 

Abstract

Base-flow samples were collected seasonally from 20 

small streams in the 372-square-mile Pepacton Reservoir 

watershed to evaluate the effects of hydrogeologic factors 

and nonpoint sources of contamination on the chemical 

composition of ground-water discharge. The reservoir 

provides part of New York City’s water supply. The subbasins 

represented one of three general types of land use, each with at 

least 45 percent forested area (mostly on the hillsides): farmed 

(dairy) land, formerly farmed land with low-density residential 

development, or forested land with little or no development. 

The subbasin areas ranged from 0.38 to 10.23 square miles. 

All streams were sampled in December 2000 and in May, July, 

and October 2001. Three of the sites were designated as landuse-index sites and were sampled as many as five additional 

times during the study. No samples exceeded state or federal 

drinking-water standards for chloride, sodium, nitrate, 

orthophosphate, herbicides, or herbicide degradates. 

The chemical composition of base-flow samples was 

classified into major-ion water types, which were broadly 

defined as naturally occurring and road-salt-affected water 

types. About one-third of the base-flow samples were roadsalt-affected types. Natural water types were differentiated 

as dilute or evolved. Dilute waters have bicarbonate and 

sulfate as dominant anions and evolved waters have only 

bicarbonate as a dominant anion. Dilute water types indicate 

relatively short ground-water residence times or contact 

with unreactive aquifer material. Evolved waters have either 

longer ground-water residence time or contact with more 

reactive aquifer material than dilute ground waters. The 

larger subbasins with wider valley-bottom areas were more 

likely to have evolved water types than small subbasins with 

little floodplain development.

Positive correlations between selected constituents and 

the intensity of nonpoint sources emphasize the connection 

between land use, shallow ground-water quality, and stream 
Introduction

Nonpoint-source contamination of ground water and 

surface water is a particular concern within New York City’s 

upstate water-supply watersheds. Contaminant loading in 

these watersheds affects ground-water, which discharges to 

streams that flow to the reservoirs. Nutrient loading to New 

York City water-supply reservoirs can promote excessive algal 

growth that can impair reservoir water-quality. Definition of 

natural water chemistry and chemical responses to different 

types and degrees of nonpoint sources within watershed areas 

can provide useful information to water-resource managers.

Streamflow during dry periods (base flow) is sustained by 

ground-water discharge, either from springs or from seepage 

directly into stream channels. A base-flow sample from a 

stream draining a small basin thus provides a composite 

sample of shallow ground water discharge from the stream 

basin above the sampling point. Such samples provide an 

overview of the effects of nonpoint sources within a watershed 

subbasin; similar results based on only ground-water samples 

would require a much more expensive and extensive well 

network. Base-flow samples are desirable in that they also 

indicate the quality of water flowing to the local reservoir. 

The Pepacton Reservoir, in the western Catskill 

Mountains of southeastern New York (fig. 1) is a part of the 

East Branch Delaware River, impounded by the Downsville 

Dam. It is the largest reservoir within the Delaware watershed, 

whose four reservoirs provide about 50 percent of New York 

City’s water supply. Land use within the 372 mi2 Pepacton 

watershed is characterized by scattered hamlets and large areas 

of forested and formerly farmed lands, with smaller areas 

supporting agriculture (primarily dairy farms). Low-density 

residential development is most common within the formerly 

farmed areas. 

In 2000, the U.S. Geological Survey (USGS), in 

cooperation with the New York State Department of 

Environmental Conservation (NYSDEC), began two parallel 

studies covering hydrogeology and water quality within 

the Pepacton watershed. One 2-year study of the quality of 

ground-water discharge resulted in three reports: two covering 

small upland basins with different land uses (this report (part 

3) and Phillips and Heisig, 2004 (part 1)) and one covering 

streams in reaches of major valleys (Heisig, 2004 (part 4)). 

The concurrent study compiled and summarized the surficial 

geology and presented estimates of recharge for basins 

with stream-gaging stations within the Pepacton watershed 

(Reynolds, 2004 (part 2)). 

Purpose and Scope

This report documents the results of base-flow waterquality sampling from 20 small basins in the Pepacton 

watershed over a one-year period. Samples are classified 

according to major-ion water type and are interpreted as a 

response to local hydrogeology (ground-water flow paths) and 

(or) nonpoint source contamination of shallow ground water. 

The occurrence of selected nonpoint-source constituents 

(chloride and sodium, nitrate, orthophosphate, and herbicides) 

in base flow are compared to their rate of production or 

application within each subbasin.

The principal objectives of this investigation were to 

(1) collect and analyze the chemistry of base-flow samples 

from 20 streams in small (0.38- to 10.23-mi2)subbasins over 

a 1-year period, as a surrogate for shallow ground-water 

chemistry, (2) classify the samples according to major-ion 

type (dilute or evolved, and whether affected by road salt), (3) 

identify the probable sources of the constituents of concern, 

and (4) relate the occurrence and concentrations of those 

constituents (chloride and sodium, nitrate, orthophosphate, and 

herbicides) to their annual production or application rate in 

each subbasin. 

The study entailed (1) establishing streamflow-sampling 

sites in small subbasins, each representing one of three 

general land-use categories (forested, farmed, or formerly 

farmed), then designating one site in each category as an 

“index” site, (2) collecting base-flow samples for chemical 

analysis from all sites four times a year, and from the three 

index sites as often as nine times a year, and (3) correlating 

the application or production rates (or application area) of 

selected nonpoint-source contaminants (road salt, livestock 

manure, and herbicides) within each subbasin with the baseflow concentrations in the respective streams. The results 

of the study provide watershed managers with stream baseflow chemistry responses to different types and intensities 

of nonpoint sources within the Pepacton watershed. These 

responses can be used to assess whether water-quality goals 

for the watershed are being met. The results also approximate 

average shallow ground-water quality within the sampled 

areas of the watershed

Previous Investigations

Previous investigations that include parts of the Pepacton 

watershed have described the geologic framework, glacial 

deposits and deglaciation, and nitrogen species in stream 

water. The geologic framework has been discussed by Fluhr 

(1953) (Pepacton Reservoir area) and by Soren (1963) (all of 

Delaware County). Glacial geology and deglaciation in the 

western Catskill mountains was discussed by Kirkland (1973) 

and Ozvath (1985). A study of nitrogen species in stream 

water from forested Catskill watersheds (Lovett and others, 

2000) included five sites within the Pepacton watershed.

Description of Study Area

The Pepacton watershed covers 372 mi2 within the 

western Catskill Mountains of New York, mostly within 

Delaware County, but also in small sections of Greene and 

Ulster Counties (fig. 1). The Downsville Dam impounds 

the East Branch Delaware River (Pepacton Reservoir) at 

 Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
the downgradient end of the watershed. Maximum relief in 

the watershed is about 2,800 ft, with the highest elevations 

bordering the eastern and southeastern edges. The Pepacton 

watershed is rural, with scattered small villages and hamlets 

in the valleys. Upland areas are largely forested, but valley 

bottoms and lower hillsides are largely open fields. Land use 

within this watershed has undergone a major change in the 

last few decades. Agriculture (primarily dairy farming) was 

widespread in valley-bottom and hillside areas - only the 

steepest upland areas remained forested. Dairy farming has 

decreased sharply over the past thirty years, and presently 

(2002) is generally limited to the most favorable lands in the 

larger valleys, and in some upland basins with relatively low 

average slopes. Former dairy-farmed areas in upland basins 

Figure 1. Hydrography, sampling network sites with associated drainage basins, and location of reference stream-gaging station 

within the Pepacton watershed, western Catskill Mountains, New York.

0

0 5 KILOMETERS 

5 MILES 

DELAWARE 

COUNTY

GREENE

COUNTY

GREENE

COUNTY

ULSTER

COUNTY

ULSTER

COUNTY

DELAWARE 

COUNTY

75o 74o52'30" 45' 37'30" 30' 22'30"

42o

07'

30"

15'

42o

22'

30" NEW

YORK

ANAND Gladstone Hollow Brook near Andes 

ANCBH Campbell Hollow Brook 

ANGLH Gladstone Hollow Brook north of Andes 

ARTIL Mill Brook Tributary 

DNCTH Cat Hollow Brook 

DNPP2 Pepacton Reservoir West End Tributary 

FLLRK Little Red Kill 

FLRDK Red Kill 

MRBYB Bryants Brook 

MRSNH Sanford Hollow Brook 

MRWRH Winter Hollow Brook 

MRWVH Weaver Hollow Brook 

RXBTK Batavia Kill 

RXMGH Montgomery Hollow 

RXVGA Tributary to Batavia Kill 

SEHMB Mill Brook 

SEMNH Rider Hollow Brook east of Mapledale 

SERDH Rider Hollow Brook near Mapledale 

WKJSH Vly Creek above Halcott Center 

WKVLY Vly Creek near Halcott Center 

Base from U.S. Geological Survey digital data, 1:100,000, 1983 

p

p

pp

p

p

p

p

p

p

p

p

p

p

p

p

p

p

p

p

p

Drainage area of sampling site 

Index basin 

Sampling site 

Reference stream-gaging station 

(East Branch Delaware 

River at Roxbury, NY 

(01413088))

Watershed boundary 

County Boundary 

£ National Weather 

Service station 

Arkville

EXPLANATION 

Pepacton

Reservoir

Catskill

Mountains

ANGLH

SEHMB ARTIL

SEMNH

SERDH

WKVLY 

FLLRK

FLRDK

RXVGA WKJSH

RXBTK

RXMGH

MRWRH

MRSNH

MRWVH

MRBYB

DNCTH

DNPP2

ANCBH

ANAND

ANGLH

East Branch Delaware

River

East Branch Delaware River 

Dam at Downsville 

£

Introduction 3
are now either overgrown fields in various stages of forest 

regrowth, along with some hayfields, or areas of low-density 

residential development. Many of the dwellings are second 

homes of New York City and New Jersey residents.

Hydrogeology

The general hydrogeologic framework within the 

Pepacton watershed is nearly flat-lying clastic sedimentary 

rock of Devonian age (Fisher and others, 1970) overlain by 

discontinuous glacial deposits and minor recent alluvium. 

Most of the upland subbasins are well drained and contain few 

lakes or wetlands. 

Bedrock within this part of the Catskills includes cliffforming sandstone and conglomerate units alternating with 

softer shale and siltstone units that result in a stepped pattern 

that is visible on steep hillslopes. Ground-water flow in the 

bedrock is chiefly through fracture openings. The groundwater flow system in upper hillslope areas is primarily within 

bedrock (the water table is within the bedrock, although 

perched water-table conditions can occur in overlying glacial 

deposits) and is most active within the upper 150 ft of rock 

(Heisig, 1999). The water table is within glacial deposits as 

they become thicker down slope toward the valley bottom. 

Bedrock underlying the valley bottom is completely saturated.

The glacial deposits typically mantle all but the steepest 

hillslopes and hilltops. Till is most common on hillslopes and 

valley bottoms in small upland subbasins. Stratified deposits 

(ice-contact deposits, outwash, and recent alluvium) generally 

increase in valley bottoms in the downvalley direction. 

Till is the most widespread glacial deposit within the 

upland subbasins investigated in this study. It is an unsorted 

mixture of clay to boulder-sized materials, and deposits 

may reach thicknesses of nearly 100 ft (Fluhr, 1953). These 

deposits are typically thickest on the lower parts of southfacing hillslopes that were in the lee of advancing ice (Coates, 

1966), and in upland valleys (Soren, 1963). Till is thin or 

absent on hilltops and on steep hillsides, particularly in highrelief uplands along the extreme eastern and southeastern 

boundaries of the watershed. 

Ozvath (1985) reported on (1) textural differences 

among till deposits and (2) downvalley transitions from till to 

stratified deposits within small upland valleys of the western 

Catskill Mountains. Till on upper hillslopes is fine-grained 

(sandy silt to silty loam), compact, and lacks stratification. 

These deposits grade into looser colluvium on steep slopes. 

In contrast, till in the valley bottom and lower hillsides of 

upland valleys is typically coarser grained (loamy silt to silty 

sand) and less compact than that on the upper hillslopes, 

and commonly includes discontinuous lenses of stratified 

sediments. Ozvath (1985) interpreted the upper hillslope 

deposits as lodgement till (deposited by ice) and the lower 

hillslope and valley-bottom deposits as ablation till (deposited 

during melt-out of stagnant ice). Ablation till in the valleybottom areas gradually transitions to stratified sediments in the 

down-valley direction, as increasing drainage area gave rise to 

greater amounts of meltwater (and runoff) from stagnant ice.

Ground-water flow paths from bedrock in the hillslopes 

to glacial deposits and streams in the valley bottoms depend 

largely on the permeability of the glacial deposits. Deposits 

of low permeability (lodgement or ablation till) will likely 

shunt much of shallow ground-water flow from hillsides to 

land surface as spring discharges that flow to the valley stream 

(Burns and others, 1998; Heisig, 1999). Most hillside groundwater flow will remain in the subsurface as permeability 

increases in the valley bottom with the downvalley transition 

from ablation tills to more permeable stratified deposits. 

Ground water will discharge directly to the valley stream, 

rather than as springs on the lower hillsides. Differences in 

ground-water flow paths can affect ground-water chemistry, as 

explained further on. 

Precipitation and Runoff

High relief (2,800 ft) within the watershed results 

in a wide range in annual precipitation and runoff among 

subbasins. Mean annual precipitation (1951-80) ranges from 

about 40 in/yr in the center of the watershed to about 55 in/yr 

at the highest elevations in the southeast corner (Randall, 

1996). Runoff, the part of precipitation available for groundwater recharge and overland flow, can be as little as 22 in/yr 

in the center of the watershed and as much as 40 in/yr in the 

southeast corner (Randall, 1996). 

Precipitation measurements at the National Weather 

Service station at Arkville (fig. 1) indicate that 2001 was a 

relatively dry year; annual precipitation was about 5 in. below 

the long-term annual mean (K. Eggleston, Cornell University 

Northeast Regional Climate Center, written commun., 2002). 

Monthly precipitation for April, May, October, and November 

2001 was 22 to 65 percent lower than the 1948-2000 monthly 

means. These months are typically favorable for ground-water 

recharge. April recharge, however, was increased by a midmonth melting of a thick snowpack, especially in the higher 

elevations, that had persisted from March snowstorms. 

Methods and Approach

Use of base-flow samples as a surrogate for ground-water 

discharge required definition of ‘base-flow conditions’ as a 

guide for sampling the small streams (≤10 mi2 drainage area) 

used in this study. Base-flow conditions were defined by at 

least three consecutive preceding days with less than 0.25 in. 

total rain and no snowpack. Most late-winter and earlyspring sampling was omitted to avoid the meltwater from the 

snowpack because of extended periods with above-freezing 

daytime high temperatures. Base flow can be diluted by 

meltwater under natural conditions, or it can be concentrated 

by the addition of road-salt leachate. 

The East Branch Delaware River at Roxbury, NY 

stream-gaging station (01413088) was used as a reference site 

 Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
(fig.1) for assessment of base-flow conditions and seasonal 

changes in base-flow discharge because none of the network 

sites were gaged. The Roxbury station was chosen because 

its small drainage area (13.5 mi2) was closest in size to the 

network subbasins.

Sampling-Site Selection

Criteria for selection of sampling sites were based on 

physical characteristics of the upgradient drainage area. 

Subbasins were chosen to avoid lakes, wetlands, and pointsources of contaminants, such as wastewater-treatment plants 

and road-salt storage facilities. Discharges from any of these 

sources could alter the chemical composition of base flow 

so that it is not representative of ground-water discharge. 

The subbasins also were selected to collectively represent 

(1) the range in degree of till cover, bedrock exposure, and 

slope, and (2) three general types of land use—forested land 

with little or no residential development or roads, former 

farmland with low-density residential housing, and currently 

(2001) farmed land (primarily dairy farms). The farmed and 

formerly farmed land uses all had at least 45 percent forested 

area. ‘Formerly farmed’ refers to unforested land that was not 

used for row crops or as pasture for a dairy farm during the 

study. Information on subbasin characteristics (area, annual 

runoff, slope), nonpoint sources of contaminants (septicsystem density, annual road-salt-application rates, manure 

production), land use (percentage of subbasin occupied 

by forest and cornfields), and site-naming conventions are 

provided in table 1. 

Sampling and Analytical Procedures

Each of the 20 sites (table 1) was sampled four times—in 

December 2000 and in May, July, and October 2001). Three 

of these sites were used as land-use index sites — SEMNH 

(forested), ANGLH (dairy farmed), MRSNH (formerly 

farmed) — and were sampled as many as five times in 

addition to the four network surveys. The dates of network 

and index-site sampling are indicated on the streamflow 

hydrograph in figure 2. 

The narrow width and shallowness of most of the 

streams required grab samples, but equal-width-increment 

samples (Shelton, 1994) were collected during the December 

2000 sample survey at sites representing the two largest 

subbasins (WKVLY, RXBTK; fig. 1). Specific conductance, 

temperature, dissolved oxygen, and pH were measured in 

the field during sample collection. Dissolved oxygen and pH 

were not measured in about 15 percent of samples because 

of subfreezing temperatures and equipment failure. Stream 

discharge was measured at the time of sampling during the 

December 2000 and July 2001 surveys. 

Base-flow samples were analyzed for major ions, 

dissolved organic carbon (DOC), iron, manganese, selected 

trace elements, and nutrients (dissolved nitrogen species 

and dissolved orthophosphate) by the USGS National Water 

Quality Laboratory in Denver, Colo. Orthophosphate was 

included because an analytical technique with a low minimum 

reporting limit (MRL) of 0.007 mg/L was available.

All samples from the index sites, and a subset of 12 other 

sites in the December and July sample surveys were analyzed 

for dissolved agricultural pesticides and their degradates. 

The 12 sites included nine of the farmed subbasins and the 

remainder represented formerly farmed land or predominantly 

forested land. 

Two analytical procedures were used for the pesticide 

analyses—the SH2010 method (for 47 pesticides and selected 

degradates) at the USGS National Water Quality Laboratory 

(Zaugg and others, 1995), and the LCAA method (for three 

degradates of chloroacetanilide herbicides) at the USGS 

Kansas Organic Geochemistry Research Laboratory (Lee and 

others, 2001). A list of all pesticides and pesticide degradates 

for which samples were analyzed is given in Phillips and 

Heisig (2004). The detection limits of the SH2010 and LCAA 

methods range from 0.001 to nearly 0.01 μg/L. 

Replicate and field blank samples were collected for 13 

and 8 percent of the samples, respectively. Results of these 

analyses met project data-quality objectives. Results of the 

laboratory analyses are given in Butch and others (2002). 

Acknowledgments

Thanks are extended to the dairy farmers and other 

livestock owners, the highway superintendents, and the 

landowners for their cooperation, which was essential for 

completion of the study. Dairy and other livestock owners 

provided information on their herds. The Watershed 

Agricultural Council facilitated contact with dairy farmers. 

Highway superintendents from town, county, and state 

highway departments provided information on road-salt 

usage and application practices. John Thurgood and Dale 

Dewing of Cornell Cooperative Extension, Delaware County, 

provided information on farming practices and manure 

production. Thanks also are extended to the following USGS 

staff members: Kevin Reisig, Jason Martin, Daniel Edwards, 

Thomas Suleski, and Brett Phillips, who assisted in sample 

collection and stream-discharge measurements, and Hannah 

Ingleston, Krysta Button, and Julia Guastella, who processed 

and shipped samples to USGS laboratories.

Stream Base-Flow Chemistry - 

Responses to Hydrogeologic 

Factors and Nonpoint Sources 

of Contamination

Base-flow chemistry in small streams largely indicates 

the average chemistry of the discharging ground-water that 

Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination 
Table 1. Physical and land-use characteristics of stream subbasins in which base-flow samples were collected in 

Pepacton Reservoir watershed in southeastern New York, 2000-01.

[mi2, square miles, in/yr, inches per year, ton/mi2, tons per square mile per year. Sites in boldface are index sites and were sampled more frequently than other 

sites. Sampling-site and subbasin locations are shown in fig. 1.] 

Site 

name*

USGS 

Station 

Number 

Stream

 Name

Drainage 

area 

(mi2)

Runoff

(in/yr)

Average 

basin 

slope

(ft/mi)

Septicsystem 

density

(units 

per mi2)

Annual application 

or production 

rate (ton/mi2) 

Percentage of 

subbasin area

Road 

salt

Livestock 

manure

Row 

crop Forest

ANAND 1414840 Gladstone 

Hollow Brook 

near Andes 

5.79 25.5 1,111 13.3 17.6 3.63 1.2 62.2

ANCBH 1414860 Campbell 

Hollow Brook 

0.90 23.3 1,306 2.2 2.5 4.43 0.00 49.6

ANGLH 1414835 Gladstone 

Hollow Brook 

north of Andes

2.56 26.0 1,086 6.6 9.7 5.33 0.89 62.2

ARTIL 1414290 Mill Brook 

Tributary 

1.96 27.8 1,301 1.5 0.5 0.00 0.00 93.7

DNCTH 1416870 Cat Hollow 

Brook 

3.75 24.4 1,244 9.3 33.5 0.00 0.00 94.5

DNPP2 1416895 Pepacton 

Reservoir 

West End 

Tributary

0.38 24.0 1,178 5.3 0.0 0.00 0.00 98.1

FLLRK 1413343 Little Red Kill 0.79 25.9 714 29.1 7.5 0.00 0.00 85.5

FLRDK 1413346 Red Kill 5.52 26.0 1,143 11.6 2.7 0.00 0.00 85.5

MRBYB 1413990 Bryants Brook 4.39 24.1 1,238 9.1 26.1 1.92 0.00 77.3

MRSNH 1413930 Sanford Hollow 

Brook 

2.50 25.9 1,207 23.2 3.1 0.03 0.00 77.3

MRWRH 1413920 Winter Hollow 

Brook 

3.46 26.2 1,023 22.5 8.0 1.78 1.50 67.8

MRWVH 1413950 Weaver Hollow 

Brook 

3.13 25.0 1,403 10.2 6.5 1.79 0.00 79.1

RXBTK 141309740 Batavia Kill 9.02 26.5 1,310 13.2 1.9 0.37 0.17 65.7

RXMGH 1413085 Montgomery 

Hollow 

3.67 26.2 1,544 10.1 2.5 0.59 0.00 81.1

RXVGA 141309730 Tributary to 

Batavia Kill

1.67 26.1 1,098 20.4 3.0 0.00 0.00 46.9

SEHMB 1414280 Mill Brook 1.41 36.3 1,521 0.0 0.0 0.00 0.00 99.8

SEMNH 1413274 Rider Hollow 

Brook East of 

Mapledale

1.69 35.6 1,713 0.0 0.0 0.00 0.00 99.8

SERDH 1413276 Rider Hollow 

Brook near 

Mapledale 

4.07 34.2 1,549 5.7 3.2 0.00 0.00 98.4

WKJSH 1413303 Vly Creek above 

Halcott Center 

3.25 27.5 1,447 4.0 2.1 0.39 0.36 88.9

WKVLY 1413306 Vly Creek near 

Halcott Center 

10.23 28.2 1,276 8.8 2.5 0.62 0.12 82.2

*Site Name - first two letters are an abbreviation of the USGS topographic quadrangle map in which site is located; last

three letters are an abbreviation of the stream-valley (hollow) name or that of the nearest hamlet.

Topographic map names and abbreviations are as follows:

Andes (AN) Fleischmans (FL) Seager (SE)

Arena (AR) Margaretville (MR) West Kill (WK)

Downsville (DN) Roxbury (RX)

 Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
sustains streamflow. Ground-water chemistry, in turn, reflects 

the chemical changes along flow paths from water-rock 

interactions and from chemical additions to ground water 

from human activities (especially nonpoint sources). Water 

chemistry was evaluated by major-ion water type and by 

selected constituents associated with nonpoint sources within 

the study area.

Major-Ion Water Type 

 Major-ion concentrations of water samples classified 

as water types provide a useful framework for interpretation 

of the waters sampled in this study. Differences in relative 

ion concentrations among basins and within basins over time 

can indicate differences in relative ground-water residence 

time and changes in contributions to base flow from hillslope 

areas. These characteristics reflect the hydrogeologic 

framework underlying a stream basin. Water types are named 

for predominant ions (from highest to lowest concentration) 

that constitute at least 10 percent of the total cations or 

anions, respectively, in milliequivalents per liter. For example, 

calcium-magnesium-bicarbonate-sulfate (Ca-Mg-HCO3-SO4) 

waters are the most common water type identified in the study 

area. Water types determined at each stream site during each 

of the four sampling periods are shown in fig. 3.

Acid neutralizing capacity (ANC) values are 

herein converted to bicarbonate (HCO3) concentrations for 

determination of chemical water-type. The pH range of the 

samples indicated that bicarbonate was the primary source of 

acid-neutralizing capacity.

Hydrogeologic and Human Controls on 

Water Type

Ground-water chemistry, and by inference, the water 

chemistry observed in base flow, evolves as water moves 

through a ground-water flow system (for example, Back, 

1966; Wunsch, 1993; Stuyfzand, 1999) (figs. 4A and 4B). This 

chemistry can be altered (especially in shallow ground-water) 

by downward leaching of contaminants from human activities, 

such as application of salt to roads.

Natural factors that control the degree of change in 

ground-water chemistry include the mineral composition, 

surface area, and permeability of the rock materials, and 

the hydraulic gradients and fracture interconnection within 

these materials. These factors affect the reactivity of the 

rock material and the residence or contact time of the ground 

water flowing through it. In general, unreactive materials 

and short contact times minimize changes in ground-water 

composition. Streams that maintain the same base-flow water 

type year-round (fig. 3) indicate short ground-water residence 

times and (or) unreactive rock material. Reactive materials 

and long residence times promote changes in ground-water 

composition.

Fractured bedrock is considered less reactive than 

unconsolidated deposits in the shallow ground-water flow 

Figure 2. Streamflow at the East Branch Delaware River at Roxbury, N.Y. stream-gaging station (01413088) and sampling dates of 

network surveys and additional index-site surveys. (Site locations are shown in fig. 1.)



















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Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination 
Figure 3. A. Major-ion water types and selected chemical concentrations for samples from four base-flow surveys, December 2000 

through October 2001, compared with B. streamflow at the reference stream-gaging station. (Locations are shown in fig. 1.)

 Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3

ARTIL

SEHMB

WKVLY

RXMGH

RXBTK

ANCBH

DNPP2

SEMNH

SERDH

WKJSH

MRWVH

FLRDK

ANGLH

MRSNH

MRWRH

FLLRK

RXVGA

ANAND

MRBYB

DNCTH

Dec 4-7,

2000

May 3,

2001

July 19-20,

2001

Oct 22-23,

2001

EXPLANATION

Water Types – each ion listed represents 10

percent of total cations or anions, respectively,

in milliequivalents per liter. Sites in boldface are

index sites.

Dilute mixed-ion waters

Calcium - Bicarbonate - Sulfate

(Ca-HCO3-SO4)

Calcium - Magnesium - Bicarbonate

- Sulfate (Ca-Mg-HCO3-SO4)

Evolved bicarbonate waters

Calcium - Bicarbonate (Ca-HCO3)

Calcium - Magnesium - Bicarbonate

(Ca-Mg-HCO3)

Road-salt-affected waters

Chloride and (or) sodium are 10 percent

total cations or anions, but are not

the most abundant ions

Same as above except chloride 

is the most abundant anion

Selected Chemical Concentrations –

Chloride r2 mg/L

Bicarbonate 25 mg/L

STREAMFLOW, IN CUBIC

FEET PER SECOND 10

0

20

Average base flow at East Branch

Delaware River, Roxbury, NY,

stream-gaging station (01413088)

STREAMFLOW NETWORK SAMPLE SITE

10

17

2.5 3.1

Naturally occuring waters, or waters

minimally affected by road salt

Specific conductance, in

microsiemens/cm at 25oC

51

Dec 4-7,

2000

May 3,

2001

July 19-20,

2001

Oct 22-23,

2001

rgreater than or equal to

36

48

48

47

50

38

28

32

40

48

43

64

47

65

44

73

78

83

42

68

32

38

39

39

45

33

26

30

35

44

33

58

43

58

47

57

74

92

39

69

45

56

51

56

68

57

31

39

48

70

52

93

69

107

72

95

107

185

53

99

38

64

56

62

75

55

30

36

49

77

42

115

77

109

65

102

135

227

55

93

A. WATER TYPES AND SELECTED CHEMICAL CONCENTRATIONS

SAMPLE SURVEY DATE

B. STREAMFLOW AT REFERENCE STREAM-GAGING STATION (ROXBURY)
Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination 

Figure 4. A. Conceptual model of shallow ground-water evolution from base-flow water-type determinations, starting with dilute 

mixed-ion water types and proceeding through natural and human-induced changes. B. Generalized stream basin depicting 

the hydrogeologic framework with ground-water flowpaths and the distribution of major-ion water types in ground water that 

discharges to the stream.

Ca-Mg-HCO3-SO4

Long groundwater flow path

or reactive

aquifer material

Dilute mixed-ion waters

Evolved

bicarbonate waters

Ca-HCO3-SO4 Ca-HCO3

Ca-Mg-HCO3

Ca-Mg-HCO3

Lime application

on agricultural

fields

Cl is most

abundant anion

Cl and (or) Na

are defining ions

Cl and (or) Na

are defining ions

Road salt

application Road salt

application

Natural Ground-Water Evolution

Human-Induced Changes

greater than 

or equal to 

r

Limed Field 

 Salted Roadway 

Stream

EXPLANATION

Ground-water types − listed ions are 10 percent of total

cations or anions, respectively, in milliequivalents per liter.

Naturally Occurring 

Dilute mixed-ion waters (Ca-HCO3-SO4)

Evolved bicarbonate waters (Ca-HCO3)

Human Affected 

Limed fields in agricultural areas 

(Ca-Mg-HCO3)

Road-Salt affected (Cl and Na 

are defining ions) 

Subsurface flow 

Spring discharge 

BEDROCK

UNCONSOLIDATED

MATERIAL

A. GROUND-WATER TYPE EVOLUTION

B. GROUND-WATER TYPE DISTRIBUTION AND FLOW
systems within the Pepacton watershed for several reasons. 

Fractures in bedrock have much less surface area than do pore 

spaces in unconsolidated materials, so there is less opportunity 

for water-rock reactions. In addition, minor amounts of 

(reactive) calcite in the bedrock (Gale and Siever, 1986) have 

likely been leached from the surfaces of shallow fractures. 

Till and other glacial deposits, however, may contain reactive 

materials such as carbonate-rock fragments transported 

from source areas to the north. Fractured bedrock is the 

primary pathway for ground-water movement on the upper, 

and typically steepest, slopes of most stream basins; steep 

gradients and high numbers of shallow, conductive fractures 

(Heisig, 1999) imply relatively rapid ground-water flow and 

short residence (or contact) times with aquifer material in 

these areas. 

Bedrock at high elevations is probably the least reactive 

of all because large quantities of water flush the system and 

because soil leaching rates from acid rain are high. Total 

runoff, the part of precipitation available for ground-water 

recharge or overland flow within a basin, generally increases 

with basin elevation. The highest total annual runoff values 

among basins are nearly 50 percent greater than lowest values. 

High elevation also correlates with high soil leaching rates 

(losses of exchangeable base cations on soil exchange sites) 

in forest soils (Lawrence and others, 1999). Thus, large fluxes 

of water and high leaching rates in forest soils, coupled with 

thin till deposits and high hydraulic gradients in underlying 

fractured bedrock resulted in relatively dilute (and stable) 

ground-water and base-flow chemistry from the high-elevation 

subbasins (ARTIL, SEHMB, SEMNH, SERDH; fig. 1).

In contrast, the thickest unconsolidated deposits typically 

are on lower hillslope or valley-bottom areas, and low 

gradients in these deposits increase the likelihood of changes 

in water chemistry. Large subbasins in the network (8-10 mi2; 

RXBTK, WKVLY; fig. 1) have the longest ground-water 

flow paths because the valley bottoms are relatively wide 

and are permeable enough to conduct most hillslope water to 

the stream through subsurface flow rather than surface flow. 

Flow through valley-bottom deposits with high surface area 

increases contact time with rock fragments, which increases 

the likelihood of a change to a more evolved water type prior 

to discharge as base flow. 

The primary human control on base-flow water types 

is the addition of substances to the land surface that can be 

dissolved by precipitation, infiltrate through the soil, and 

join the shallow ground-water flow system. These substances 

include salt applied to roadways, manure applied to farm fields 

and, to a lesser extent, lime applied to farm fields (fig. 4B).

Naturally Occurring Water Types

Four natural water types were identified in base-flow 

samples. These water types consist of two water-type pairs, 

each pair including a dilute and an evolved water type. The 

difference between the pairs is the presence or absence of 

magnesium as a dominant cation (figs. 3 and 4). In both 

figures, the calcium-only pair is represented by shades of blue 

and the calcium-magnesium pair is represented by shades of 

green. The dilute components, calcium-bicarbonate-sulfate 

(Ca-HCO3-SO4) and calcium-magnesium-bicarbonate-sulfate 

(Ca-Mg- HCO3-SO4) waters, are mixed-ion water types with 

relatively low specific-conductance values (figs. 3, 4A). 

Mixed-ion waters are typical of an initial water composition in 

ground-water flow systems (Back, 1966; Wunsch, 1993) and 

represent relatively short residence times and (or) flow through 

unreactive soil and aquifer material. The remaining two types, 

calcium-bicarbonate (Ca-HCO3) and calcium-magnesiumbicarbonate (Ca-Mg-HCO3

), are evolved ground waters 

that represent increased residence times or short residence 

times in contact with more reactive soil or aquifer material. 

Dissolution of carbonate minerals (calcite or dolomite) in 

unconsolidated deposits, bedrock, or in the soil (associated 

with lime application) increase bicarbonate concentrations in 

these waters (reported as acid-neutralizing capacity (ANC)) to 

the point where bicarbonate becomes the only dominant anion 

(figs. 3, 4A).

 Stream samples with Ca-HCO3-SO4 and Ca-HCO3

water types drain basins with relatively high average slopes, 

high total runoff, high elevation, and thin, discontinuous till 

coverage. These basins border the eastern and southeastern 

edges of the watershed. The water type in two basins with 

these characteristics (SEMNH, SERDH; fig. 1) are exceptions; 

they are both characterized as a Ca-Mg-HCO3-SO4 water 

type (fig. 3). However, magnesium is a dominant cation 

only because calcium concentrations (3.2 – 4.6 mg/L) are 

exceedingly low in these subbasins of high total runoff, little 

till, high forested area, and high leaching rates. Waters from 

these basins are among the most dilute in this study (see 

specific-conductance data in fig. 3).

Samples of evolved Ca-HCO3 water from site RXVGA, 

collected during high base-flow conditions, are unusual 

because the drainage basin is small. The basin is no longer 

farmed and has low-density residential development. 

Apparently, there is a more reactive natural or human-derived 

carbonate source in this area compared with other parts of 

the Pepacton watershed. Streams that drain two other small 

nearby basins (not part of this network) had similarly high 

calcium and bicarbonate concentrations, but their land uses 

were different. One basin had a lower density of residential 

development than RXVGA and the other was farmed. 

Stream samples with Ca-Mg-HCO3-SO4 and 

Ca-Mg-HCO3 water types drain subbasins in the northern and 

central areas of the watershed that have relatively low average 

basin slopes, which generally correspond to a high degree 

of till cover and, potentially, additional reactive carbonate 

minerals. In general, bicarbonate, calcium, and magnesium 

increased with decreasing average basin slope in the Pepacton 

watershed. Base flows from forested subbasins, however, 

consistently had lower bicarbonate values than subbasins with 

low percentages of forest area. Till appears to be a natural 

source of carbonate minerals, but in agricultural areas, liming 

of fields is an additional human-derived source. Elevated 

10 Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
magnesium concentrations in base flow from a forested 

subbasin such as DNPP2 (fig. 1) indicate that the magnesium 

is likely derived from a natural source. 

 Lime periodically applied to farm fields in the form 

of crushed limestone (D. Dewing, Cornell Cooperative 

Extension, Delaware County, oral commun., 2002) gradually 

dissolves and can infiltrate to the water table. Most farm 

fields tend to be in the lower elevations of a given agricultural 

subbasin (similar to roadways) so that the greatest influence 

of lime application on base-flow chemistry is during dry 

summer periods, when the forested-hillside area contributions 

to base flow are at a minimum. A farmed subbasin (such as 

ANGLH) shows greater increases in bicarbonate, calcium, and 

magnesium during these periods than an adjacent, formerly 

farmed basin (MRSNH; fig. 5). Addition of a reactive 

carbonate source to a basin can result in the development of 

a mature Ca-Mg-HCO3 water type within a relatively short 

residence time (figs. 4A and 4B). Large bicarbonate increases 

(100+ percent) from high to low base-flow samples from 

farmed subbasin sites ANGLH and MRWRH suggest that lime 

is an additional source of carbonate. The May to July increase 

in bicarbonate at subbasin MRWRH was sufficient to change 

the water-type definition from a salt-affected type to a Ca-MgHCO3

 type (fig. 3); a similar shift is evident at site ANGLH in 

fig. 5.

Chloride- and Sodium-Affected Water Types

The fundamental difference among water types shown in 

figure 3 is the presence or absence of sodium and chloride as 

dominant ions (orange and red boxes). Sodium and chloride 

were not dominant ions in base-flow samples from forested, 

undeveloped areas; concentrations were typically less than 1 

milligram per liter (mg/L). Human activities contribute most 

of the sodium and chloride detected in stream samples from 

this area. Application of rock salt (sodium chloride) on roads 

for deicing purposes is the primary source of these ions. Salt 

applied to roads dissolves and infiltrates soils with meltwater 

or rainwater in roadside areas. The water moves through the 

soil to the water table and joins the shallow ground-water 

flow system. As the ground water flows downgradient and 

ultimately discharges to the local stream, sodium and chloride 

are transported with it (fig. 4B). Chloride and sodium are 

among the dominant ions in water types from subbasins 

with state or county roads. The persistence of these water 

types at some sites throughout the year suggests that sodium 

and chloride are partly retained in the unsaturated zone 

and that subsequent recharge continues to transport these 

ions downward to the shallow ground-water flow system. 

Toler and Pollock (1974) documented retention of road-salt 

chloride in the unsaturated zone adjacent to a salted road, and 

other studies, among them Granato and others (1995) and 

Figure 5. Bicarbonate (HCO3) concentration at the three index sites over time, with the major-ion water type, chloride concentration, 

and corresponding daily mean streamflow from the reference stream-gaging station keyed to each sample. (Locations are shown in 

fig. 1.) 

10

12

14

16

18

20

BICARBONATE CONCENTRATION,

IN MILLIGRAMS PER LITER

STREAMFLOW, IN CUBIC FEET PER SECOND

DATE

ANGLH

MRSNH

SEMNH

EXPLANATION

WATER TYPES – Number adjacent

to square is chloride concentration,

in milligrams per liter

Evolved bicarbonate waters

(Ca-HCO3)

Dilute mixed-ion waters

(Ca-Mg-HCO3-SO4)

Affected by Cl and(or) Na 

Discharge of East Branch

Delaware River at Roxbury

stream-gaging station

(01413088)

0

2

4

6

8 2.8

1.7

0.6

6.3

7.1

0.6

3.0

2.5

0.4

4.5

3.4

0.5 0.6

0.4

0.6

0.5

4.5

5.9 5.9 5.9 5.9

4.6

4.2

7.7

7.4 7.9

0

10

20

30

40

50

2000

DEC

2001

JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV

(farmed)

(formerly farmed)

(forested)

STREAMFLOW –

Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination 11
Jones and Sroka (1997), have documented the persistence 

of elevated chloride concentrations throughout the year in 

shallow ground water downgradient of salted roads. Stream 

base flows affected by the discharge of road-salt-contaminated 

ground water are discussed by Howard and Haynes (1997), 

Rosenberry and others (1999), and Heisig (2000).

Elevated sodium and chloride concentrations are not 

limited to the sites shown in red and orange on figure 3. 

All subbasins with salted roads have higher sodium and 

chloride concentrations in stream base flow than in streams 

from undeveloped subbasins. Samples that contain chloride 

concentrations of 2 mg/L or greater, regardless of water type, 

are likely affected by road-salt contamination and are noted 

in figure 3. Chloride and sodium concentrations are related to 

the salt-application rate (see following discussion of chloride 

and sodium; p. 13). 

Chloride and sodium data effectively link land-use 

activities (source areas) and shallow ground-water quality 

to stream-base-flow quality, despite low concentrations. For 

example, the roadway in figure 4B shows the primary location 

of salt input within a hypothetical basin. Because most roads 

in the region parallel the local stream, road-salt-affected 

ground water is typically limited to an area between the 

road(s) and the local stream. Increases in chloride and sodium 

during dry periods imply that the percentage of ground-water 

contribution to streamflow from valley-bottom areas increases 

relative to that from forested hillside areas.

Implications of Spatial and Temporal 

Water-Type Variation

Changes in base-flow water type at network sites were 

common during the course of the study (fig. 3). Most of these 

changes paralleled a decrease in streamflow from high flows 

in the winter and spring to low flows in the summer and fall. 

Average daily discharges at the Roxbury, N.Y. station ranged 

from 2.5 to 17 cfs (fig. 3) for the four seasonal surveys and 

from 0.36 to 17 cfs for more frequent samples at the three 

index sites (fig. 5). Streamflow measurements at sampling 

sites were limited to the winter and summer surveys. Low 

discharges from the summer survey were a fraction (5 to 48 

percent) of corresponding measurements from the winter 

survey. Summer-survey streamflow was 25 percent of the 

winter-survey streamflow at the Roxbury, N.Y. reference 

station. 

Streams usually had mixed-ion water types during the 

winter and spring surveys; the remainder were moderately 

affected by road salt (chloride and sodium were among the 

dominant ions, but were not the most abundant) (fig. 3). As 

streamflows decreased during an especially dry summer 

and fall of 2001, about half the streams that started out with 

dilute, mixed-ion waters shifted to evolved waters or waters 

moderately affected by road salt; the other half remained the 

same water type. Streams moderately affected by road salt 

typically remained the same type or became highly affected 

(chloride was the most abundant anion). 

Variations in base-flow water type resulted from changes 

in hillside and valley-bottom contributions to base flow 

and from the presence or absence of human activities. Two 

source areas of ground-water flow to streams are springs 

that drain hillside areas and diffuse ground-water seepage 

from valley-bottom deposits. Valley bottoms are narrow in 

V-shaped valleys (DNCTH, MRBYB) and are relatively broad 

in U-shaped valleys (MRWVH, MRWRH; fig. 1). The valley 

bottoms of larger subbasins (RXBTK, WKVLY) contain 

stratified deposits. Hillside springs represent ground water 

derived primarily from high-gradient flow (short residence 

time) in fractured bedrock. This geochemical environment 

is relatively unreactive, resulting in a dilute mixed-ion 

contribution to streamflow. Hillside areas are also generally 

forested, which minimizes human activities and associated 

chemical changes. Thus, in small subbasins dominated by 

hillside sources and with little human activity (SEMNH, 

for example), base flow consistently was a dilute mixed-ion 

water type (figs. 3 and 5). Seven of the twenty streams in the 

network (fig. 3) had a single water type during this study. 

Base flow in most larger subbasins became an evolved 

water type or a water type affected by human sources as the 

relative contribution from hillside source-areas decreased 

and valley-bottom source areas increased. Water in hillside 

(upland) areas, which account for the majority of the land area 

in all subbasins, is the dominant source of water (mixed ion) to 

streams during high base-flow periods (late fall, early winter, 

and spring; fig. 3). Permeable shallow bedrock in hillsides 

progressively drains as conditions become drier during the 

growing season, which reduces the hillside source contribution 

to the local stream. Direct upland-flow contributions to mainvalley streams are also diminished by infiltration through 

streambeds as tributaries enter larger valleys (Randall, 1978). 

Ground-water contributions to base flow from valley-bottoms 

therefore increase (as a percentage of base flow) as upland 

water sources decrease. Base flow from the largest subbasins 

without major roadways shifts to an evolved water in which 

bicarbonate is the single dominant anion. This change occurs 

through either natural ground-water evolution along a flow 

path or possibly through dissolution of lime on agricultural 

fields (figs. 4A and 4B). Base flow from other large subbasins 

with more heavily salted roadways shifts to a salt-affected 

water type. 

Selected Constituents Associated with 

Nonpoint Sources

Nonpoint-source contributions from four sets of 

constituents were evaluated with respect to their production 

or application rates within the subbasins in an effort to define 

relations between base-flow quality and land-use practices. 

The constituents included: chloride and sodium, nitrogen 

species, orthophosphate, and herbicides. Chloride and sodium 

were chosen because they are widely applied as road salt 

and because chloride, a conservative ion, provides a basis 

for comparison with less conservative constituents. Nutrients 

12  Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
(nitrogen species and orthophosphate) are indicators of animal 

and human wastes and commercial fertilizers and can cause 

nuisance algal growth in streams and lead to eutrophication of 

lakes and reservoirs. Nutrient inputs from streams are a waterquality issue for several of New York City’s water-supply 

reservoirs, including the neighboring Cannonsville Reservoir 

(New York City Department of Environmental Protection, 

2002). Herbicides are associated with row-crop cultivation and 

are of concern because they can adversely affect aquatic life 

and drinking-water quality. No samples exceeded any state or 

federal drinking-water standards.

Four nonpoint sources were quantified within each 

subbasin: 1) deicing salt applied to roadways, 2) domestic 

wastewater disposed of in septic systems, 3) livestock waste 

applied to land surface (primarily from dairy farms), and 4) 

herbicides applied to row-crop fields. Each constituent was 

plotted in relation to subbasin production or application rates 

and the results are discussed in the sections that follow.

Chloride and Sodium

Leachate from road salt applied during the winter can 

infiltrate the unsaturated zone, reach the water table, and flow 

to nearby streams, resulting in elevated chloride and sodium 

concentrations in base flow throughout the year (figs. 3, 4A, 

and 4B). The annual rate of road-salt application in each 

subbasin was calculated from data provided by the New York 

State Department of Transportation (NYSDOT), Delaware 

County, and six town highway departments. The data 

included road-salting practices, annual salt usage, road types, 

and road mileage.

Because it is relatively inexpensive, sodium chloride 

(rock salt) is the primary road-deicing product used by all 

highway departments in the Pepacton watershed. Some 

departments use other types of salt as a supplement; for 

example, NYSDOT and one town use liquid magnesium 

chloride as a “dressing” on mixtures of sand and salt to 

prevent it from freezing and to provide immediate deicing 

action on roads. The Delaware County Department of Public 

Works uses solid calcium chloride as an additive on county 

roads (W. Reynolds, Commissioner, Delaware County 

Department of Public Works, oral commun., 2001). All 

departments except NYSDOT use sand or cinders mixed with 

salt on paved roads; NYSDOT uses salt only. The highest 

annual road-salt-application rates per mile of two-lane paved 

road were 40 ton/mi by NYSDOT and 32 ton/mi by Delaware 

County; the lowest rates were between 1 and 12 ton/mi by 

the towns.

Dirt roads are common in most towns, but salt application 

varies among highway departments. Some departments use 

only sand because salted dirt roads can become rutted; others 

apply the same amount of salt as on paved roads.

Estimation of the total salt tonnage annually applied in 

each subbasin was limited to sodium chloride because it was 

the most extensively used deicing material and was the most 

easily quantified. Annual application rates for each type of 

road (state highway, county road, or town road (paved and 

dirt)) were multiplied by the respective road lengths and 

summed for each subbasin. These totals were then divided by 

the corresponding subbasin areas to determine the annual salt 

application (tons) per square mile of each subbasin (table 1) to 

facilitate comparisons among subbasins. Subbasins SERDH 

and ARTIL were omitted from the calculations because the 

reported application practices and amounts of salt usage were 

uncertain; this, coupled with low road density, would have 

given unreliable estimates. Also omitted were the subbasins 

with no roads (SEMNH, DNPP2, SEHMB) because zero 

values could not be plotted on the natural log scales used in 

the scatterplots.

Log base-flow concentrations of chloride and sodium are 

positively correlated with the log of annual salt-application 

rates per square mile of subbasin in each of the four network 

base-flow surveys (fig. 6). This not only corroborates the more 

general water-type results presented earlier—it indicates that 

road-salt leachate entering a local, shallow ground-water flow 

system has a predictable effect on stream base-flow chloride 

(and sodium) concentrations. Sodium concentrations are 

similar to those of chloride where little or no salt is applied 

and less than chloride in basins with the highest application 

rates (fig. 6). Cation exchange of sodium primarily for calcium 

likely accounts for the relatively low sodium concentrations in 

basins with the highest salt application rates (Shanley, 1994).

Although sodium and chloride concentrations in all 

base-flow samples were not of concern from a drinking-waterquality perspective, the correlation between salt-application 

rates and the concentrations of sodium and chloride in 

streams (fig. 6) indicates a direct link between human-derived 

nonpoint-source contaminants applied at land surface and the 

quality of shallow ground-water discharge and stream water. 

This link provides a basis for evaluating the potential for 

transport of other nonpoint-source contaminants to streams.

Base-flow chloride concentrations increased with each 

sampling survey from December 2000 through October 2001 

(fig. 7). In general, the lowest concentrations corresponded to 

the highest base flows (December and May), and the highest 

concentrations corresponded to the lowest base flows (July 

and October). High base flows include a larger component 

of flow from mostly forested hillside areas than do low base 

flows, which are primarily derived from valley bottom areas, 

where road-salt application is typically concentrated.

The May chloride concentrations in subbasins with high 

salt-application rates equaled or exceeded those of December, 

even though the May discharges exceeded the December 

discharges, and thus provided a greater potential for dilution. 

In contrast, the May concentrations in subbasins with low saltapplication rates were similar to the December concentrations 

(fig. 7). Chloride concentrations from stream basins with high 

salt-application rates were higher in May than December 

because recharge of water containing road salt near streams is 

likely saltier after the winter period of salt application (May) 

than before it (December). The low (background) December 

and May concentrations in basins with low salt-application 

Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination 13
rates are consistent with the relatively small amount of 

salt applied and the large amount of dilution provided by 

uncontaminated water from forested hillside areas. 

In summary, the strong relations between road-salt use 

and base-flow chloride and sodium concentrations imply that 

land use, shallow ground-water quality, and stream baseflow quality are intimately connected within the Pepacton 

watershed. Flow-based variations of base-flow chloride reflect 

the predominance of roads (and road-salt inputs) in valleybottom areas and the natural variation of base-flow water 

contributions from hillside areas.

14  Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3

Figure 6. Base-flow concentrations of chloride and sodium as a function of annual road-salt-application rate in each subbasin 

during the four network sample surveys, Pepacton Reservoir watershed, southeastern New York, December 2000 through 

October 2001.

5

20

30

40

50

1

10

1 5 10 20 30 40

5

20

30

40

50

1

10

1 5 10 20 30 40

5

20

30

40

50

1

10

1 5 10 20 30 40

5

20

30

40

50

1

10

1 5 10 20 30 40

BASE-FLOW CONCENTRATION, IN MILLIGRAMS PER LITER

TONS OF SALT APPLIED ANNUALLY PER SQUARE MILE OF SUBBASIN

December 4-7, 2000 

Chloride log(y)=0.653 (log x)-0.120 r2=0.87

Sodium log(y)=0.448 (log x)-0.043 r2=0.77

May 3, 2001 

Chloride log(y)=0.829 (log x)-0.167 r2=0.87

Sodium log(y)=0.629 (log x)-0.137 r2=0.82

July 19-20, 2001 

Chloride log(y)=0.867 (log x)-0.011 r2=0.82

Sodium log(y)=0.620 (log x)-0.095 r2=0.74

October 22-23, 2001 

Chloride log(y)=0.790 (log x)-0.187 r2=0.77

Sodium log(y)=0.577 (log x)-0.185 r2=0.61
Nitrogen Species

Nitrogen (N) cycling in the environment is complex, as 

there are many biologically mediated pathways for uptake 

and transformation. The nitrogen (as N) analyses of base-flow 

samples encompassed (1) nitrite and nitrate, (2) nitrite, (3) 

ammonia and organic nitrogen (organic N), and (4) ammonia. 

All nitrite and ammonia concentrations were below the 

minimum reporting levels (0.06 and 0.04 mg/L, respectively) 

except at the farmed site ANGLH on June 28, 2001, when 

nitrite was detected. Therefore, the nitrite-and-nitrate analyses 

and the ammonia-and-organic-N results are referred to as 

“nitrate” and “organic N”, respectively. 

Characterization of Nitrogen Sources

Sources of N to ground water and stream base flow in 

the Pepacton watershed include: 1) atmospheric deposition, 

modified by vegetation, 2) leachate from septic systems, and 

3) manure and other fertilizers applied to land surface. All are 

considered nonpoint sources and are described further on in 

relation to base-flow N concentrations. 

Figure 7. Comparison of base-flow chloride concentration as a function of subbasin annual salt application rate among the four network sample surveys, Pepacton Reservoir watershed in southeastern 

New York, December 2000 through October 2001. BASE-FLOW CHLORIDE CONCENTRATION, IN MILLIGRAMS PER LITER 

TONS OF SALT APPLIED ANNUALLY PER SQUARE MILE OF SUBBASIN 

50

40

30

20

15

10

9

8

7

6

5

4

3

2

1

0.9

0.8

1.5

1 2 3 4 5 6 7 8 9 10 20 30 40 50

December 4-7,2000

May 3, 2001

July 19-20, 2001

October 22-23, 2001

See figure 6 for regression equations 

Oct.

July

May

Dec.

Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination 15
Atmospheric Deposition, Nitrogen Saturation, and 

Nitrogen Depletion

The northeastern United States has high rates of 

atmospheric N deposition, and the Catskill Mountains 

have among the highest N-deposition rates in the Northeast 

(Ollinger and others, 1993). The N is derived from many 

pollution sources, including powerplant and automobile 

emissions, and is deposited on the land surface as wetfall and 

dryfall. A state of N saturation can be reached if the deposition 

rate exceeds the demand of the forest vegetation (Agren and 

Bosatta, 1988; Aber and others, 1998). N saturation results in 

the leaching of excess nitrate to streams. 

Forested watersheds with a history of forest cutting 

or burning can apparently have long-term N deficits (Aber 

and Driscoll, 1997; Goodale and others, 2000). Lovett and 

others (2000) suggested that differences in forest tree-species 

composition, which may be a response to forest history, 

may also affect nitrogen output to streams in the Catskill 

Mountain region. They found the lowest nitrate levels in 

forested watersheds where red oak is a dominant species. 

These watersheds were probably subject to long-term human 

disturbance (harvesting, fire) because they were accessible, on 

the fringes of the Catskill Mountains and at low elevations.

In general, mature or declining forests are more likely to 

show N saturation and high rates of leaching than growing, 

immature forests or open fields on former farmland (Aber 

and others, 1998). Former farmlands, which make up a 

large part of the watershed, are likely to have N deficits and 

contribute low N concentrations to streams after many years 

of crop harvests followed by forest regrowth (Zak and others, 

1990). Thus, atmospheric N deposition most likely increases 

N in streams that drain predominantly forested subbasins 

within the Pepacton watershed. These increases in base-flow 

concentrations were likely to be small because most N export 

occurs under high-flow conditions. The percent forested 

area of each subbasin is listed in table 1. Base-flow nitrate 

concentrations in forested subbasins were expected to be lower 

than in subbasins with agricultural or septic-system N sources. 

Septic-System Wastewater

Human waste that enters the unsaturated zone from septic 

systems is a source of nitrogen to ground water (Robertson 

and others, 1991). Septic effluent initially contains reduced 

forms of nitrogen (ammonia and organic N), but these are 

largely transformed to nitrate through microbial action in the 

presence of oxygen within the unsaturated zone if allowed 

sufficient time. Nitrate is relatively stable in oxygenated, 

shallow ground water and, barring denitrification, particularly 

in organic-rich near-stream sediments, it is eventually 

discharged to local streams. A recent study of small streams 

in New York City’s Croton watershed indicated that septicsystem density (up to 1,000 systems/mi2

) in stream drainage 

areas was positively correlated with base-flow nitrate 

concentration (up to about 3 mg/L as N (Heisig, 2000).

Estimates of septic-system density (number of systems 

per square mile of drainage basin) within each of the 

subbasins (table 1) were derived from digital-ortho-quarterquad imagery (DOQQs) and field verification. All subbasins 

had low septic-system densities of fewer than 30 systems per 

square mile. This density (30 systems/mi2) did not raise nitrate 

concentration in base flow above the range of background 

concentrations (for zero or near-zero system densities) in 

the Croton watershed (Heisig, 2000). Estimates of nitrate 

concentration in base flow based on septic-system-density 

within the Pepacton watershed also would exaggerate the 

nitrate contribution in base flow because many of the homes 

are second homes that have only periodic use. Despite no 

measurable basinwide response in base-flow nitrate to low 

septic-system densities, the quality of shallow ground water 

immediately downgradient from individual septic systems 

(acting as point sources) is degraded by septic effluent 

(Robertson and others, 1991; Ptacek, 1998; Wilhelm and 

others, 1994; and Morrill and Toler, 1973). 

Manure and Commercial Fertilizers

 Manure (livestock waste) and commercial fertilizers 

can be important sources of nutrients to streams draining 

agricultural watersheds (Gburek and Folmar, 1999; Jordan 

and others, 1997; and Owens and others, 1992). Nitrate is the 

dominant form of N exported in stream base flow. The most 

commonly used fertilizer within the Pepacton watershed is 

manure from dairy farms; this constitutes about 90 percent of 

the total amount of fertilizer applied within the watershed (D. 

Dewing, Cornell Cooperative Extension, Delaware County, 

oral commun., 2002). Commercial fertilizers account for 

the remaining 10 percent. Herein, manure refers to livestock 

waste, in solid and liquid forms. Manure generated in barns 

during the nongrowing season is spread on row-crop fields 

or on pastures. Feedlots likely receive manure year-round. 

Pastures also receive manure directly from grazing cattle 

during the growing season, as do streams that flow through 

pastures or between barns and pastures. 

The assessment of livestock density within the subbasins 

entailed sending survey forms to dairy farmers and following 

up as necessary with phone calls or field visits. Other types 

of livestock were assessed through field surveys. Estimates 

of annual manure production for different age and size cows 

and other livestock were based on, or interpolated from, data 

presented in Midwest Plan Service (2000). Annual manureproduction estimates for all livestock within each subbasin 

(in tons) were totaled and divided by the number of square 

miles within the respective subbasin, to obtain the annual rate 

(table 1). Manure production was highest among subbasins 

with dairy farms, because dairy cows are the primary source of 

manure. The highest annual rate was about 5 tons per mi2.

16  Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
Biological Uptake and Transformation of 

Nitrogen in Streams

Nitrogen concentrations in stream base flow represent 

source concentrations decreased to varying extents by 

biological processing during: (1) infiltration from source 

areas to the ground-water table, (2) ground-water transport, 

and (3) discharge to streams through streambeds (the 

hyporheic zone, which is immediately beneath or adjacent 

to the stream channel). Microbially mediated denitrification, 

with net transformation of nitrate to nitrogen gas (lost to 

the atmosphere), is possible within aquifer material or the 

hyporheic zone where sufficient organic material is present. 

Once in streams, nutrients such as nitrate can be removed 

through uptake by macrophytes, algae, and microbes. The 

degree of growth and nutrient uptake by autotrophs, such 

as diatoms, green algae, and cyanobacteria, is dependent on 

factors such as: scour, light, nutrients, temperature, current, 

and substrate (Allen, 1995). Microbial activity increases 

with increased organic matter (leaf litter) entering streams 

(Mulholland and others, 1985). Seasonal changes in these 

factors result in variable N removal from stream water and 

thus variable N concentration in base flow over an annual 

cycle. Burns (1998) estimated in-stream nitrate losses, 

with some seasonal variation, in two reaches of a Catskill 

Mountain stream.

Base-flow N that is retained in stream biomass is most 

likely transported by stormflows that induce scour and 

dislodge algae, leaf litter, and microbes.

Base-flow concentrations of nitrate in streams of the 

Northeast show a seasonal pattern that appears to be generally 

consistent, regardless of local land use. Base-flow nitrate 

concentrations tend to be highest from December through 

April, when low temperatures and minimal daylight suppress 

biological activity. Nitrate concentrations from May to early 

October are generally lower than in the winter period and may 

progressively decrease as temperatures warm and biological 

activity increases (denitrification, uptake of nutrients). The 

lowest concentrations of the year typically occur during the 

few weeks immediately after leaf fall (Murdoch and Stoddard, 

1992; Allen, 1995), when the addition of leaf organic matter 

spurs microbial activity in streams. This seasonal pattern has 

been observed in a variety of settings in the Northeast—in 

forested watersheds (Murdoch and Stoddard (1992) and 

Goodale and others (2000)), in agricultural watersheds 

(Owens and others (1991), Owens and others (1992), Wall and 

others (1998), and Pionke and others (1999)), and in suburban 

watersheds (D. Borchert, New York City Department of 

Environmental Protection, written commun., 2000). 

Dissolved Organic Nitrogen and Nitrate in 

Base Flow

Different seasonal variations in organic-N and nitrate 

concentrations are evident in the base-flow samples. Nitrate 

concentrations show the seasonal pattern described above 

and show the strongest correlation with manure production 

in the December 2000 stream survey. Organic-N and nitrate 

concentrations were relatively low; the highest organicN concentration was 0.29 mg/L as N. The highest nitrate 

concentration was 1.1 mg/L as N. This nitrate concentration 

is much lower than the maximum base-flow nitrate (about 3 

mg/L) measured in suburban subbasins with high densities 

of septic systems in the Croton Watershed (Westchester and 

Putnam Counties, New York (Heisig, 2000)). A base-flow 

nitrate concentration of 1.1 mg/L (as N) would correspond 

to a suburban subbasin with a low to moderate septic density 

(about 300 septic systems/mi2).

Nitrate, organic-N, and stream-temperature base-flow 

data for the three index subbasins are shown in figure 8 along 

with corresponding flow data from the East Branch Delaware 

River station at Roxbury, N.Y. The subbasins represent the 

best examples of three distinct land-use associations within 

the Pepacton watershed: 1) SEMNH represents forested, with 

no development, 2) ANGLH represents farmed (dairy farms), 

with some forest and residential development, and 3) MRSNH 

represents former farmland, with low-density residential 

development, forested areas, and minor (non-dairy) livestock. 

Organic Nitrogen

Elevated organic-N concentrations in surface water 

or ground water are generally considered an indicator of 

organic waste (Hem, 1985) or a wetland source. Organic N 

was detected only in samples from the farmed index subbasin 

(ANGLH), except for one winter sample from the formerly 

farmed index subbasin (MRSNH). No organic-N was detected 

in the samples from the forested index subbasin (SEMNH). 

The primary source of organic N in the ANGLH samples is 

probably manure because this subbasin contains no wetlands. 

Seasonal concentrations in this subbasin varied by as much as 

100 percent. The highest concentrations were in winter and 

summer samples, and the lowest were in the spring and fall 

samples (fig. 8). 

The seasonal changes in organic-N concentration at 

the ANGLH site (fig. 8) reflect the seasonal changes in 

contributions to base flow and in microbial activity. The 

high winter concentrations presumably resulted from the 

suppression of microbial decomposition by low temperatures, 

and the spring decrease probably resulted from dilution 

by the large, dilute upland base-flow component, which 

would have contained no manure. In addition, the rising 

stream-water temperature in May (fig. 8) would have 

spurred microbial activity and thereby lowered the organicN concentrations. The summer organic-N concentrations 

were highest in late June and July, then decreased until early 

October, when they reached a secondary peak. The lowest 

concentrations of organic N were reached during late October 

and early November, when microbial activity increased in 

response to leaf litter in the stream (Murdoch and Stoddard, 

1992; Allen, 1995).

Warm-weather increases in organic-N concentration 

coincided with (1) the proportionate increase in the groundStream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination 17
Figure 8. Nitrate concentration, organic 

nitrogen concentration, and stream-water 

temperature at the three index sites (ANGLH, 

MRSNH, and SEMNH) during base-flow 

conditions, and discharge of the East Branch 

Delaware River at the reference streamgaging station at Roxbury, N.Y., December 

2000 through November 2001. (Locations are 

shown in fig. 1.)

ANGLH (farmed)

MRSNH (formerly farmed) 

East Branch Delaware 

River Discharge 

SEMNH (forested) 

Minimum Reporting Limit (0.05) 

1.2

1.1

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

NITRATE, AS N, IN MILLIGRAMS PER LITER

20

15

10

5

0

20

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

15

10

5

0

East Branch Delaware 

River Discharge 

ANGLH (farmed) 

MRSNH (formerly farmed) 

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

0.25

0.20

0.15

ORGANIC NITROGEN, AS N, IN MILLIGRAMS 

PER LITER 

20

15

10

5

0

ANGLH (farmed) 

MRSNH (formerly farmed) 

SEMNH (forested) 

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

2001

East Branch Delaware 

River Discharge 

STREAM TEMPERATURE, IN DEGREES C 

DISCHARGE AT EAST BRANCH DELAWARE RIVER AT ROXBURY, NY, IN CUBIC FEET PER SECOND

24

22

20

18

16

14

12

10

8

6

4

2

0

Minimum Reporting Limit (0.10) (concentrations 

between 0.05 and 0.09 are estimated) 

(No detections at

SEMNH (forested) site)

18  Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
water contribution to base flow from valley-bottom areas 

as the hillside contributions decreased, and (2) increased 

livestock defecation close to or directly into the stream 

during grazing or while moving to pasture. Increases in 

dissolved manganese, iron, and DOC (dissolved organic 

carbon, possibly from manure) at ANGLH during late June 

and July indicated the discharge of anoxic ground water 

from at least part of the valley bottom area to the stream. 

The organic-N concentration was positively correlated with 

DOC concentration. 

The data from this study indicate a direct association 

between organic-N concentrations in streams and farmed 

subbasins. The maximum organic-N concentrations were 

in December 2001, but elevated concentrations were most 

widespread in July. Organic N constituted the smallest 

percentage of total dissolved N (nitrate plus organic N) 

in May, when nitrate concentrations were decreasing, and 

drainage from uncontaminated hillside sources was greatest, 

and constituted the largest percentage of total N in October, 

when nitrate concentration was at a minimum. The month in 

which the largest number of nonfarmed subbasins (three) had 

measurable organic-N concentrations was December. One of 

these subbasins (FLLRK, table 1) contains a small wetland 

that could be the source of organic N (and DOC). Organic 

N was detected most frequently at the six farmed subbasins 

in which annual manure production was greater than 1.75 

ton/mi2. Measurable concentrations of organic N were detected 

in samples collected from three or four (50 or 66 percent) 

of these six sites in December, May, and October, and in the 

samples collected from all (100 percent) of these sites in July.

Nitrate

Nitrate concentrations varied among the three index sites 

(fig. 8). The highest concentrations occurred at the farmed 

index site (ANGLH) during the relatively high flows of winter 

and early spring, when biological activity was at a minimum. 

The highest concentration, in March, may have been partly 

due to prior snowmelt from farmed areas of the subbasin. 

Nitrate concentrations at the formerly farmed and forested 

index sites were similar to one another through the winter, and 

these concentrations were among the highest measured at the 

formerly farmed site. 

Nitrate concentrations in the high early-May base flows 

that followed snowmelt were similar among the three index 

sites; therefore, the dominant streamflow component in all 

three subbasins at that time probably was drainage from the 

forested hillside areas. Increases in stream-water temperature 

and growth of algae before leaf-out may partly account for the 

subsequent early-spring decrease in nitrate concentrations at 

the farmed subbasin. 

The farmed and formerly farmed index sites (ANGLH 

and MRSNH) showed a progressive decrease in nitrate 

concentrations from summer to early fall, but the forested 

index site (SEMNH) showed a gradual increase (fig. 8). The 

decrease at the farmed and formerly farmed index sites may 

be due to the open fields and minimal shade, which would 

allow sunlight to increase the water temperature and in turn 

enhance algal growth and promote other biological activity, 

both of which decrease nitrate concentrations (fig. 8). Algal 

growth at the farmed index site would be further favored by 

a greater supply of nutrients than at the other sites; biological 

uptake at this site lowered the nitrate concentrations to below 

the reporting limit from late August through early October. In 

contrast, the base-flow nitrate concentration at the formerly 

farmed index site was below the minimum reporting limit only 

in early October. 

The forested index site, which receives minimum light 

and had the lowest water temperature and the poorest nutrient 

availability, showed a slight increase in nitrate concentrations 

during the summer and early fall. This observation may reflect 

a relative increase in headwater spring contributions during 

dry periods. Late fall or spring recharge that has flushed 

excess soil nitrate to shallow, fractured bedrock (Murdoch and 

Stoddard, 1992) results in relatively stable summer headwater 

spring discharges (Burns and others, 1998) with somewhat 

elevated nitrate concentration. Stable or increasing nitrate 

during the summer at the forested index site (SEMNH), whose 

subbasin has high relief and headwater springs, suggests little 

net uptake of nitrate by algal growth in the stream.

The seasonal patterns in base-flow nitrate concentrations 

at the index sites were also observed at the other streams 

in the network—a general decrease from December 2000 

through October 2001. The largest decline was after leaf 

fall during late October, when nitrate concentrations were at 

or below the minimum reporting limit of 0.1 mg/L as N in 

60 percent of the samples. 

Nitrate Concentrations in Relation to Nonpoint Sources

Base-flow nitrate concentrations for each of the four 

sampling surveys were plotted in relation to annual manureproduction rates (fig. 9), and all sites were grouped by 

amount of forested subbasin area (table 1)—greater than 90 

percent, 75 to 90 percent, or less than 75 percent. Subbasins 

with the highest percentages of forest area are most likely to 

be N-saturated and export excess nitrate. Base-flow nitrate 

concentrations are affected by manure production, although 

the effects are masked by biological activity during the 

warm weather months and following leaf off in the fall. The 

regression lines shown for December 2000 and May 2001 in 

figure 9 are based on only farmed-subbasin data (basins with 

manure production) and are included for comparison with 

the forested- and formerly farmed-subbasin nitrate data. The 

results from each of the four sample surveys are discussed in 

chronological order below. 

December 4-7, 2000. These samples provided the closest 

representation of nitrate concentrations in shallow ground 

water because biological activity was minimal in the streams 

at this time (fig. 9). The predominant source of nitrogen was 

manure, and the base-flow nitrate concentration showed a 

positive linear correlation with annual manure-production 

Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination 19
Figure 9. Base-flow nitrate concentration as a function of annual manure-production rate in sampled subbasins of the 

Pepacton Reservoir watershed in southeastern New York during four sample surveys, December 2000 through October 

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20 Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
rate. Nitrate concentrations in most of the forested subbasins 

were lower than in farmed subbasins but showed an equally 

wide concentration range that probably reflects differences 

in forest history. For example, streams in high-relief, poorly 

accessible subbasins with mature forests (SEHMB, fig. 1) had 

the highest nitrate concentrations among forested subbasins. 

Those in subbasins with low relief and greater accessibility 

(DNPP2, fig. 1) and a probable history of tree harvesting, 

possibly followed by regrowth of different tree species (Lovett 

and others, 2000), had low nitrate concentrations. The lowest 

base-flow nitrate concentrations were generally in formerly 

farmed basins; this is consistent with the low nitrification rates 

found in abandoned farm fields by Zak and others (1990) and 

histories of long-term nutrient loss from cultivated fields and 

nitrogen uptake during forest regrowth. 

May 3, 2001. May 2001 samples were collected during 

the highest base-flow conditions of the study—10 days after 

a peak flow caused by the final spring snowmelt. Base-flow 

nitrate concentrations at farmed subbasins continued to be 

positively correlated with manure-production rates, but the 

maximum concentrations were only about half of those 

measured in December 2000. This decrease is attributed to a 

combination of nitrate uptake or nitrate removal through algal 

growth and denitrification in the streams, and dilution of nearstream nutrient sources by discharge from springs that drain 

unfarmed hillside areas. The May nitrate concentrations in 

forested subbasins were generally about 0.1 mg/L greater than 

in the December sample survey and equaled or exceeded those 

at the farmed-subbasin sites. Base-flow nitrate concentrations 

were below 0.1 mg/L at most formerly farmed subbasins and 

in the low-relief forested basin (DNPP2).

July 19-20, 2001. This sampling survey occurred during 

the lowest base flows and the highest water temperatures of 

the four sampling periods. The July nitrate concentrations 

in nearly all streams had decreased since May, presumably 

in response to increased uptake by algae and plants, and to 

denitrification. Little correlation was discernible between 

manure-production rate and the July base-flow nitrate 

concentrations in the farmed subbasins as the nitrate values 

approached the minimum reporting limit (fig. 9). Base-flow 

nitrate concentrations at forested subbasins exceeded those at 

most of the farmed subbasins because nitrate concentrations in 

forested subbasins remained stable during the summer, while 

all others decreased, as described earlier. Baseflow nitrate 

concentrations at two farmed subbasins that were more than 

80 percent forested with low manure-production rates were 

similar to those of the forested subbasins (fig. 9).

October 22-23, 2001. The October nitrate concentrations 

were the lowest of the four sampling surveys. The 

concentrations at half of the sites were at or below the 

minimum reporting limit. The October samples were collected 

during the leaf-off period, when microbial activity (nutrient 

uptake, nitrification) was spurred by leaf litter in the streams. 

No correlation was evident between manure-production rate 

and base-flow nitrate concentrations. Two of the farmed 

subbasins had nitrate concentrations that were among the 

highest in this survey, but the forested-subbasin samples had a 

greater number of nitrate detections.

Effects of Seasonal Changes on Nitrogen Concentrations

The seasonal changes in nitrate concentrations in 

general, and in the relation between nitrate concentration and 

manure-production rate, appear to reflect the strong effect 

of biological processes in streams or within streambeds (the 

hyporheic zone). Therefore, identification and evaluation of 

the ground-water sources of base-flow nitrate is best done 

with winter data, which represent the period when biological 

activity is minimal. In other seasons, nitrate retention by algae 

and plants and nitrate loss through denitrification reduce the 

nitrate-source contributions to a greater degree in farmed 

subbasins than in forested subbasins (figs. 8 and 9). High N 

retention in farmed subbasins is the result of greater nutrient 

availability, less forest area, and thus, more light reaching 

streams and warmer stream-water temperatures than in 

forested watersheds. Increased organic-carbon loading from 

animal waste in farmed subbasins may also facilitate loss of 

nitrogen through denitrification. Nitrogen from ground-water 

discharge that is retained in biomass is most likely transported 

in stormflows (as dissolved and particulate forms) rather than 

in base flow, because scour can remove algae, leaf litter, and 

microbes. Thus, use of base-flow nitrate during the growing 

season for comparison of nitrogen sources among basins with 

different land uses gives a false impression of nitrogen-source 

contributions. Greater retention of nitrogen in biomass in 

productive streams (farmed subbasins) than in less productive 

streams (forested subbasins) can make forested subbasins 

(by default) a greater source of base-flow nitrate during 

the growing season (figs. 8 and 9). However, total nitrogen 

(all dissolved and particulate species) exported during all 

streamflow conditions is almost certainly greatest from farmed 

subbasins with manure production. 

Phosphorus 

Phosphorus (P) is a nutrient of concern in New York City 

reservoir watersheds because it can spur algal growth, which 

in turn can lead to eutrophic conditions in reservoirs (Correll, 

1998). Phosphorus is one of the principal nutrients in manure 

(Midwest Plan Service, 2000) and is the primary source of P 

(initially organic P) in streams that drain farmed areas in the 

Pepacton watershed. Another source of P is chemical-fertilizer 

supplements; these are a much smaller source than manure, 

however, and their application rates were not quantified in this 

study. A third P source is septic wastewater (Robertson, 1995; 

Robertson and others, 1998), but its contribution to base-flow 

concentrations was not considered important because of low 

septic-system densities within the subbasins selected for the 

study (table 1). Therefore, nonpoint-source P contributions 

were estimated only from manure-production data in each 

subbasin, as shown earlier for nitrate (fig. 9 and table 1). 

Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination  21
Orthophosphate was the form of P selected for this 

analysis because it typically is the dominant dissolved form 

in streams. It also is the primary P species that is sorbed onto 

sediments and that is directly available for uptake by aquatic 

biota (Ryden and others, 1973; Correll, 1998). OrganicP is probably the predominant form of P in manure, but 

subsequently can be chemically or biologically transformed 

to orthophosphate.

Mobility of Orthophosphate and Organic Phosphorus 

Orthophosphate transport in sediments is limited 

by sorption-desorption processes. Materials that have a 

strong affinity for P include: iron (Fe), aluminum (Al), and 

manganese (Mn) oxide or hydroxide precipitates, clays, 

carbonates, and organic matter (Sims and others, 1998; 

Fox, 1993). Desorption of P from sediments can occur 

where P concentrations in the surrounding waters are low. 

Phosphorus release from metal oxides and hydroxides can 

occur under anaerobic conditions (Allen, 1995; Hendricks and 

White, 2000; Sallade and Sims, 1997b) when the metal ions 

(particularly Fe) are reduced through bacterial decomposition 

of organic matter. This process is a potential means of P 

release from three sources—P-rich (manured) seasonally 

saturated soils (Vadas and Sims, 1998), sediment that is 

washed into drainage ditches from cultivated fields during 

storms (Sallade and Sims, 1997a, b), and hyporheic zones 

along streams (Hendricks and White, 2000).

Organic forms of P may have greater mobility than 

orthophosphate. The leaching and loss of P from agricultural 

areas are most commonly reported where many years of 

manure applications have increased the P content of the 

soil beyond the amount required by crops (Sims and others, 

1998). Decreases in the P-sorption capacity of soils have 

been linked to manure application by Bache and Williams 

(1971) and Mozaffari and Sims (1996). P that is derived from 

manure has been reported to have greater downward mobility 

than P derived from chemical fertilizer through a soil layer 

with a high P-sorption capacity (calcium carbonate; Eghball 

and others, 1996); organic forms of P were surmised to have 

greater mobility than inorganic forms. Organic P that reaches 

streams can be converted to orthophosphate by streambed 

microbial communities that produce exoenzymes (Hendricks 

and White, 2000). Phosphorus transport to streams can be 

a serious issue at dairy farms, where the need to dispose of 

manure is constant, regardless of soil conditions (Sims and 

others, 1998). 

Transport of P through soils and from local ground-water 

systems to streams is facilitated by high soil permeability and 

by artificial drainage in the soils and underlying saturated 

deposits. In general, transport is also favored in coarsegrained sediments with low metal-oxide and clay content, 

although some fine-grained soils contain macropores that can 

facilitate rapid downward movement. Artificial drainage, such 

as subsurface drains, represents a short circuiting of local 

hydrologic systems, which enhances P export (both dissolved 

and particulate-P) by accelerating drainage from the farm 

fields to surface waters (Ryden and others, 1973; Gaynor and 

Findlay, 1995).

Orthophosphate concentrations in streamflow are 

affected by stream biota. Increased uptake is likely during 

periods of algal growth that typically peak under optimal light 

conditions—before leaf-out in the spring—and possibly again, 

although to a lesser degree, in the fall (Allen, 1995). Stream 

biota can release dissolved organic or inorganic P through 

excretion from cells or during cell lysis (Allen, 1995). 

Orthophosphate in Base Flow

Orthophosphate detection in stream base flow was 

closely associated with manure production in farmed basins 

(fig. 10). Orthophosphate concentrations at the farmed index 

site (ANGLH) were equal to or greater than the minimum 

reporting level (0.007 mg/L as P) in all samples except those 

from the leaf-off period in late October and mid-November 

2001. The maximum concentration was 0.077 mg/L as P. 

In contrast, all samples from the formerly farmed index 

site (MRSNH) were at or below the MRL. Concentrations 

at the forested subbasin index site (SEMNH) exceeded the 

MRL only from mid-July through early October (maximum 

concentration 0.011 mg/L as P). 

The fluctuations of orthophosphate concentration in 

samples from the farmed index site (ANGLH) indicated 

a nonconservative behavior unlike that of nitrate (and 

unlike the conservative behavior of chloride). Relatively 

low concentrations occurred during higher base flows in 

December, March, and early May—that is, high base flows 

with large upland flow contributions had low orthophosphate 

concentrations. The most striking feature of orthophosphate 

occurrence was a period of maximum concentrations from at 

least late June through mid-July (fig. 10). Nearly all farmed 

subbasin samples exhibited a similar pattern. Summertime 

elevated concentrations of soluble P in a small, farmed 

watershed in Pennsylvania also have been reported by 

Gburek and Heald (1974) and Pionke and others (1999). 

Orthophosphate concentrations from late August through early 

October (lowest flows) were similar to those from the spring 

period (highest flows). Samples from late October through 

early November were below the MRL, and this, like nitrate, 

is attributed to uptake by microbial activity in the presence of 

leaf litter.

The early to mid-summer 2001 peak in orthophosphate 

concentrations may have resulted from a combination of 

hydrologic, biological, and chemical factors: 

1. First, the peak spring concentrations coincided with a 

period of transition from elevated spring base flows with 

a strong hillside component to relatively stable, low 

summer base flows (mid-August) in which valley-bottom 

or near-stream ground-water contributions to base flow are 

enhanced (fig. 10). Springtime recharge in valley-bottom 

areas of subbasins in which manure has been applied would 

probably provide a downward flush of organic carbon, 

22  Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
Figure 10. Concentrations of orthophosphate, iron, atrazine, 

metolachlor ESA, manganese, dissolved organic carbon, and sulfate 

at the three index sites, and discharge at the reference streamgaging station (Roxbury, N.Y.), December 2000 through November 

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

EXPLANATION 

Farmed site (ANGLH) 

Formerly farmed site (MRSNH) 

Forested site (SEMNH) 

Discharge at reference gage 

at Roxbury 

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

0.08

0.06

0.04

0.02

Orthophosphate

MRSNH

(formerly farmed) 

ANGLH (farmed) 

SEMNH (forested)

Minimum Reporting Limit (.007)

2001

DISCHARGE AT EAST BRANCH DELAWARE RIVER AT ROXBURY, NY, IN CUBIC FEET PER SECOND

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

MILLIGRAMS PER LITER 

Iron

MRSNH

(formerly farmed) 

ANGLH (farmed) 

Minimum Reporting Limit (10)

100

90

80

70

60

50

40

30

20

10

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

MICROGRAMS PER LITER 

Atrazine

ANGLH (farmed) 

Minimum Reporting Limit

0.016

0.015

0.014

0.013

0.012

0.011

0.010

0.009

0.008

0.007

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

0.08

0.06

0.14

0.12

MICROGRAMS PER LITER 

Metolachlor ESA 

ANGLH (farmed) 

Minimum Reporting Limit (0.05)

0.10

0.16

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

MICROGRAMS PER LITER 

Manganese

MRSNH

(formerly farmed) 

ANGLH (farmed) 

Minimum Reporting Limit (3.2) 

180

160

140

120

100

80

60

40

20

20

15

10

5

0

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

3.0

2.5

2.0

1.5

MILLIGRAMS PER LITER, AS C 

Dissolved Organic Carbon 

MRSNH

(formerly farmed) 

ANGLH (farmed) 

SEMNH (forested) 

1.0

0.5

0.0

20

15

10

5

0

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

8

7

6

5

MILLIGRAMS PER LITER 

Sulfate

MRSNH

(formerly farmed) 

ANGLH (farmed) 

SEMNH (forested) 

4

3

20

15

10

5

0

2001

DISCHARGE AT EAST BRANCH DELAWARE RIVER AT ROXBURY, NY, IN CUBIC FEET PER SECOND

20

15

10

5

0

MILLIGRAMS PER LITER, AS P 

20

15

10

5

0

20

15

10

5

0

20

15

10

5

0

Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination  23
nutrients (including organic forms of P), and herbicides 

to a rising water table. Organic P may be more readily 

transported than orthophosphate (Eghball and others, 1996). 

 2. Periodic springtime rises of the water table into 

orthophosphate-bearing soil horizons would provide at least 

an intermittent potential source of phosphorus to the ground 

water flowing to the stream. Two large storms (greater 

than 1 in. of precipitation) occurred in June 2001, one of 

which was 4 days before the June index-site sample survey.

The peak concentration of the herbicide atrazine, which is 

applied in late spring, in the June samples indicated that 

recent ground-water recharge to valley-bottom deposits was 

entering the stream. 

 The movement of organic carbon to ground water, and its 

subsequent decomposition by bacteria, could create local 

anoxic conditions in the shallow ground water, which is 

at its highest water level in the spring. The spring peak in 

orthophosphate concentration also coincided with a peak 

in dissolved iron (Fe) concentration, which decreased 

thereafter much more slowly than the orthophosphate 

concentrations (fig. 10). Iron in solution in ground-water 

discharge suggests at least local anoxic conditions. The 

simultaneous occurrence of Fe and orthophosphate peaks 

may indicate the dissolution of P-bearing metal oxides 

or hydroxide precipitates. Periodic submergence and 

dissolution of P-bearing metal oxides and hydroxides 

in soils by high ground-water levels might explain the 

relatively brief orthophosphate peak. The ground-water 

transport of dissolved orthophosphate by sorptiondesorption processes is typically slow, but phosphorussaturated soils near streams or linked to subsurface drainage 

systems may enhance orthophosphate transport (fig. 10). 

3. Streambed sediments with sorbed P, washed from farm 

fields and deposited within streams, could be a potential 

source of P in stream water (Sallade and Sims, 1997a,b). 

P sorbed to soil particles could be brought into solution 

through (1) dissolution of metal oxides and hydroxides 

under anoxic conditions, such as in stagnant, organic-rich 

waters or in streambeds where anoxic ground water is 

discharging, (2) desorption from clay or organic material, or 

(3) microbial transformation of organic P to orthophosphate.

Trends in the concentrations of other chemical species 

affected by redox conditions at the ANGLH site also indicated 

the discharge of anoxic ground water during the summer; they 

included organic N, dissolved organic carbon (DOC), sulfate, 

and manganese (Mn). For example, the peak in organic-N 

concentrations coincided with the orthophosphate and Fe 

peaks (figs. 8, 10), but the concentrations decreased more 

gradually over the summer and fall. DOC concentrations 

increased, and sulfate concentrations decreased, during 

this flow-transition period, and then remained relatively 

stable during the low flows of late summer and early fall 

(fig. 10). In contrast, Mn concentrations increased steadily 

from midsummer to midfall. The observed manganeseoxide coatings on streambed rocks indicated the discharge 

of anoxic ground waters containing dissolved Mn and the 

subsequent precipitation of Mn as it became oxidized within 

the stream. The brevity of the P peak relative to those of other 

chemical species associated with anoxic conditions may 

indicate temporary sources of P (such as the unsaturated zone 

during periods of high ground-water levels) or depletion of 

available P in near-stream areas or in streambed sediments. P 

concentrations in streams can be decreased by nutrient uptake 

by algae and bacteria.

The trends in orthophosphate concentrations at the 

ANGLH subbasin were generally consistent with those at 

the other farmed-subbasins, especially those with extensive 

dairy farming. An increase in orthophosphate concentrations 

at site ANCBH throughout the study period was anomalous, 

however, and the reasons for it are unknown.

The orthophosphate concentrations obtained during 

each of the four sampling periods were compared with the 

manure-production estimates (fig. 11) in the same manner 

as for nitrate. The highest orthophosphate concentrations 

of each sampling period were at farmed-subbasin sites with 

high manure-production rates. The farmed-subbasin samples 

showed positive linear correlations with manure production 

in July and, to a lesser extent, in May, but little correlation 

in October or December. The orthophosphate concentrations 

at predominantly forested sites and formerly farmed sites 

were at or only slightly above the MRL (.007 mg/L) from 

July to October. All concentrations from forested and 

formerly farmed sites were at or below the MRL during the 

other sampling periods. Thus, a general seasonal pattern 

was observed in which orthophosphate was elevated in all 

subbasins from July through October, with farmed subbasins 

peaking in concentration in July and showing the best 

correlation of orthophosphate with annual rates of manure 

production. 

Herbicides

Corn is grown in the Pepacton watershed to support 

dairy farming and cultivated fields are typically treated with 

herbicides during late spring. Studies in several agricultural 

areas of New York (Phillips and others, 1999, 2000a, 2000b; 

Eckhardt and others, 2000; Phillips and Heisig, 2004) have 

detected herbicides, generally at low concentrations, in ground 

water and surface waters, including the Pepacton Reservoir. 

Herbicide concentrations were determined for all indexsubbasin samples and for the December 2000 and July 2001 

sample surveys.

Herbicide concentrations in base-flow samples showed a 

strong association with corn cultivation within the respective 

subbasins (fig. 12). A relatively weak relation between the 

intensity of corn cultivation and total herbicide base-flow 

concentration probably was the result of several factors, 

including the generally low herbicide concentrations in all 

samples, and the small percentages of subbasin area under 

cultivation (0 to 1.2 percent, table 1).

Three herbicides (atrazine, metolachlor, and simazine) 

and three herbicide degradates (alachlor ESA (ethanesulfonic 

24  Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
Figure 11. Orthophosphate concentrations as a function of annual manure-production rate in sampled subbasins of the 

Pepacton Reservoir watershed in southeastern New York during four sampling surveys, December 2000 through October 

2001. 

MANURE PRODUCTION, IN TONS PER SQUARE MILE OF SUBBASIN PER YEAR

0.045

0.040

0.035

0.030

0.025

0.020

0.015

0.010

0.005

0 1 2 3 4 5 6

December 4-7, 2000 

Minimum Reporting Limit (0.07) 

ORTHOPHOSPHATE, AS P, IN MILLIGRAMS PER LITER

0.045

0.040

0.035

0.030

0.025

0.020

0.015

0.010

0.005

0 1 2 3 4 5 6

May 3, 2001 

Regression equation only for stream 

basins with manure production: 

y=.0070+.0019x

r2=0.57

Minimum Reporting Limit 

0 1 2 3 4 5 6

July 19-20, 2001 

Minimum Reporting Limit 

0 1 2 3 4 5 6

October 22-23, 2001 

Minimum Reporting Limit 

>90 percent forested 

75-90 percent forested 

<75 percent forested 

EXPLANATION 

< less than 

> greater than 

0.045

0.040

0.035

0.030

0.025

0.020

0.015

0.010

0.005

0.045

0.040

0.035

0.030

0.025

0.020

0.015

0.010

0.005

Regression equation only for stream 

basins with manure production: 

y=.0092+.0050x

r2=0.80

Stream Base-Flow Chemistry - Responses to Hydrogeologic Factors and Nonpoint Sources of Contamination  25
acid), deethylatrazine, and metolachlor ESA) were detected in 

base-flow samples during this study. Atrazine and metolachlor 

are used on cornfields, and simazine (detected only once) has 

a variety of uses, including corn crops. Metolachlor ESA was 

detected the most often and at the highest concentrations; the 

maximum concentration was 0.42 mg/L. The concentrations of 

the other five compounds were less than 0.10 mg/L.

The ratio of metolachlor ESA to its parent compound 

(metolachlor) was calculated for all Pepacton watershed 

subbasins; results are given in Phillips and Heisig (2004). All 

base-flow samples had high ratios that were within the range 

typical of ground water rather than surface runoff (Phillips 

and others, 1999); this is consistent with the assumption that 

the samples collected in this study were derived solely from 

ground-water discharge. 

The frequency of herbicide and herbicide-degradate 

detection was strongly associated with row-crop (corn) 

production at the three index sites. All nine samples from the 

farmed-subbasin index site (ANGLH) from December 2000 

through November 2001 contained at least one herbicide 

(including the values estimated for concentrations below 

the MRL; Childress and others, 1999). No samples from 

the forested-subbasin index site contained any herbicide or 

herbicide degradate. Only two samples from the formerly 

farmed-subbasin index site contained an herbicide or 

herbicide degradate (Phillips and Heisig, 2004); one contained 

deethylatrazine (a degradate), and one contained simazine, an 

herbicide that has other applications in addition to corn crops.

The pattern of atrazine occurrence at the farmed index 

subbasin (ANGLH) paralleled that of orthophosphate. Only 

the late-June concentration was above the MRL (fig. 10). 

The winter, spring, and late-summer concentrations were 

estimated values (below the MRL), and no atrazine was 

detected in the fall samples (Phillips and Heisig, 2004). The 

similarity between the patterns of atrazine and orthophosphate 

occurrence may indicate similar hydrologic pathways—both 

constituents are applied to row-crop fields, and both reached 

their peak concentrations in base flow just after a postapplication storm. Subsurface drains are not widespread in 

this subbasin but, where present, may provide local short 

circuits from the soil to the stream. Soil-water herbicide and 

orthophosphate contributions to ground water and base flow 

presumably decrease through the summer as the water table 

declines and the soils drain. 

Metolachlor ESA occurrence at the farmed index 

subbasin stream was nearly the opposite of atrazine (fig. 10). 

It was detected in all samples but the May 2001 sample and 

was highest during the lowest base-flow conditions. This 

pattern suggests a strong association with ground water from 

the valley bottom, where most farm fields are located. Nondetection in the May sample is consistent with dilution of 

valley-bottom ground-water concentrations by high base-flow 

contributions from forested upland areas.

All basins with any degree of corn row-crop area (table 

1) and two basins formerly under corn cultivation had the 

only detections of herbicides or herbicide-degradates in the 

December 2000 and July 2001 surveys. Herbicide occurrence 

in streams was related to agricultural land use in the stream 

basins by comparing total herbicide concentrations with the 

percent of basin area used for corn cultivation (fig. 12). Total 

herbicide concentrations were used rather than individual 

concentrations because 1) the three herbicides detected are 

nonconservative, 2) use of any one herbicide may not be 

uniform among the farmed basins, and 3) concentrations of 

A. December 2000 B. July 2001 

PERCENTAGE OF SUBBASIN AREA UNDER CORN CULTIVATION

TOTAL HERBICIDE CONCENTRATION,

IN MICROGRAMS PER LITER

0.5

0.4

0.3

0.2

0.1

0.0

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6

WKVLY 

WKJSH

MRSNH

MRBYB

RXBTK

ANGLH

ANAND

MRWRH

WKVLY

WKJSH

MRSNH

MRBYB

RXBTK

ANGLH

ANAND

MRWRH

0.5

0.4

0.3

0.2

0.1

0.0

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6

Figure 12. Total herbicide concentration (sum of atrazine, metolachlor, simazine, and associated degradates) in base flow as a function 

of basin area under cultivation. Trend lines are drawn among nested or adjacent subbasins. (Site locations are shown in fig. 1.)

26  Hydrogeology and Water Quality of the Pepacton Reservoir Watershed in Southeastern New York Part 3
individual compounds were low. Estimates of percent subbasin 

area in corn cultivation were derived from a 2001 field survey. 

Phillips and Heisig (2004) found significant positive Spearman 

nonparametric correlations between total herbicides in base 

flow and percent subbasin area in corn cultivation for the 

December 2000 and July 2001 surveys. 

The relation between total herbicide concentration in 

base flow and the percentage of subbasin area used for corn 

cultivation differs among subbasins (fig. 12), probably as a 

result of differences in (1) herbicide-application history, types 

of herbicides used, and application rate; (2) soil properties 

such as permeability, organic carbon content, and clay content; 

(3) annual runoff, slope, proximity to a stream, groundwater flow paths, and residence time; and (4) uncertainties 

associated with measurement of extremely low herbicide 

concentrations (near the detection limits). The herbicideapplication history may be a major factor, in that land use 

has shifted away from agriculture over the past few decades. 

For example, the relation of total-herbicide concentration to 

percentage of subbasin used for row crops differs sharply 

between the eastern part of the watershed and the north-central 

part; subbasins WKJSH and WKVLY in the eastern part (fig. 

1) have much smaller percentages of cropland than subbasins 

in the north-central part (ANGLH, ANAND, MRWRH), yet 

subbasins WKJSH and WKVLY have similar total herbicide 

concentrations in base flow (fig. 12). 

Summary and Conclusions

In 2000-01, the USGS, in cooperation with NYSDEC, 

investigated the effects of hydrogeologic factors and land use 

on the quality of ground-water that discharges to local streams 

in the Pepacton watershed in southeastern New York. Baseflow samples were collected from 20 subbasins throughout 

the watershed from December 2000 through November 2001 

and were analyzed for major ions and selected nonpointsource constituents (nutrients, herbicides) that reflect local 

land use. Samples were collected seasonally (December, May, 

July, and October) at all sites, and as many as five additional 

times at three index sites that were selected to represent three 

end-member land-use categories—farmed land (mostly dairy 

farms), formerly farmed land with low-density residential 

development, and forested land with little or no residential 

development. Temporal changes in base-flow composition 

at the index sites were plotted, as were the relations between 

concentrations of selected constituents and corresponding 

measures of nonpoint-source intensity. 

Base flow (dry-weather streamflow) in the Pepacton 

watershed consists of ground water that discharges from 

seeps, springs, and directly to streams from the valley-bottom 

deposits. Base-flow chemistry, therefore, reflects subbasin 

lithology, hydraulic flow paths, and land use. Base flow 

was categorized by major-ion water type as either naturally 

occurring or affected by road salt. Road-salt-affected waters 

were widespread. The naturally occurring waters (unaffected 

by salt) were designated as dilute or evolved on the basis of 

the predominant ions. Dilute waters are mixed-ion types with 

low specific conductance and short residence times and (or) 

short flow paths within the ground-water system, generally 

along high-gradient upland flow paths through fractured 

bedrock. Evolved waters have bicarbonate as the single 

dominant anion and higher specific conductance than most 

dilute waters. Evolved water composition indicates longer 

flow paths and (or) greater contact with reactive material in 

the valley-floor material than dilute waters. Seasonal changes 

in water type at a given sampling site over the study period 

are attributed to seasonal decreases or increases in the dilute 

ground-water contribution from uplands in relation to the more 

highly evolved contributions from valley-bottom areas. 

Base-flow concentrations of chloride and sodium from 

road salt, and of nitrate, orthophosphate, and herbicides from 

agricultural practices, showed a positive correlation with 

their application rate, production, or areal occurrence within 

the respective subbasins. This correlation indicates a strong 

link between contaminants from nonpoint sources in valley 

bottoms or lower hillside areas, the local ground-water flow 

system, and base-flow water quality. 

The concentrations of chloride and sodium (conservative 

ions) were correlated with the rate of road-salt-application 

rates in all four sampling periods. The highest concentrations 

occurred during the summer and fall, when the ground-water 

contributions from valley-bottom areas (with most of the 

roadways) were the greatest of the year. 

Nitrate concentrations in base flow decreased seasonally 

through processes of denitrification or biological uptake near 

or within the stream. These processes are minimized by low 

temperatures; therefore, winter nitrate concentrations are the 

highest of the year and give the closest approximation of the 

concentrations in ground-water discharge. Two identified 

sources of nitrate in base flow of the study area are livestock 

manure and nitrogen from atmospheric deposition. Base-flow 

nitrate concentration showed a positive linear correlation 

with annual rates of manure application in the December 

2000 samples, but not in the samples collected during warm 

weather or after leaf-off in the fall, when biological uptake 

or chemical transformation in and near the stream lowered 

the concentrations. Nitrate uptake in streams within farmed 

subbasins was enhanced by the greater amounts of sunlight 

reaching the streams, and by warmer water temperatures 

and higher phosphorus concentrations than in the forested 

subbasins. The relatively low retention of atmospheric 

nitrogen by vegetation in forested subbasins, and the low 

nitrate uptake in shaded forest streams, resulted in relatively 

stable nitrate concentrations through the summer in those 

subbasins.

The primary source of phosphorus in base-flow samples 

from farmed subbasins was manure. Orthophosphate was 

detected in all but one sample from the farmed-subbasin 

index site; the latter sample was collected during the fall 

leaf-off period, when biological activity is spurred by leaf 

Summary and Conclusions  27
organic carbon in the streams. Maximum orthophosphate 

concentrations at that site occurred in the early summer and 

midsummer, when the nitrate concentrations were minimal. 

Orthophosphate concentrations at the forested and formerly 

farmed subbasin index sites were low and were detected only 

in samples collected from July through October. 

The peak orthophosphate concentration at the farmed 

index subbasin occurred at the end of June 2001, shortly 

after two storms, and coincided with the atrazine peak and 

with broader peak concentrations of dissolved iron, organic 

nitrogen, and DOC. The simultaneous occurrence of peak 

concentrations suggested association with recent recharge 

from the storms. The occurrence of recent recharge (high 

ground-water levels) with the DOC peak and with reducing 

conditions in base flow (as indicated by the dissolved iron) at 

the farmed index subbasin suggested that the orthophosphate 

could have been released from the nearby soils or streambed 

sediments as the metal oxides were reduced. The July 2001 

samples from farmed subbasins indicated a positive linear 

relation between base-flow orthophosphate concentration and 

manure-production rate. 

The pattern of herbicide and herbicide-degradate 

occurrence was positively correlated with corn cultivation in 

subbasins, but the relations with area under cultivation were 

inconsistent among the subbasins. Atrazine concentration 

was highest during high early-summer base flows, but 

metolachlor ESA concentrations peaked during low base 

flows in the summer and fall, when valley-bottom groundwater contributions were greatest. Differences in the timing 

of concentration peaks, and the concentrations themselves, in 

base flow suggest seasonal factors that affect the movement of 

these constituents, or their release to streams.

The results of this study indicate that base-flow 

chemistry from small, well-drained stream basins reflects 

local hydrogeologic factors and the intensity of nonpoint 

sources within the basins. Shifts in relative water contributions 

from hillside and valley-bottom areas are evident from majorion water type and from selected constituents associated with 

nonpoint sources in the valley bottoms. Seasonal or consistent 

correlations among chloride, sodium, nitrate, orthophosphate, 

and herbicides and the measures of the intensity of 

nonpoint sources provide information on the interaction of 

these constituents with soil or aquifer material, biota, and 

hydrologic conditions.

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