U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2008–5057

Prepared in cooperation with New York City Department of Environmental Protection

Effects of Forest Harvesting on Ecosystem Health in 

the Headwaters of the New York City Water Supply, 

Catskill Mountains, New York
Cover. Aerial view of the Dry Creek watershed during the fall of 1998, 18 months after it was clearcut. 

Photograph by Aerial Dimensions.
Effects of Forest Harvesting on Ecosystem 

Health in the Headwaters of the New York 

City Water Supply, Catskill Mountains, 

New York

By Michael R. McHale, Peter S. Murdoch, Douglas A. Burns, 

and Barry P. Baldigo

Prepared in cooperation with 

 New York City Department of Environmental Protection 

Scientific Investigations Report 2008–5057

U.S. Department of the Interior

U.S. Geological Survey
ii

U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2008

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Suggested citation:

McHale, M.R., Murdoch, P.S., Burns, D.A., and Baldigo, B.P., 2008, Effects of forest harvesting on ecosystem health in 

the headwaters of the New York City water supply, Catskill Mountains, New York: U.S. Geological Survey Scientific 

Investigations Report 2008–5057, 22 p., also available online.
iii

Figures

1. Map showing the location of the four study watersheds in the Catskill Mountains

 of southeastern New York..........................................................................................................2

2. Diagram showing interaction of biogeochemical components of a 

forested landscape.......................................................................................................................3

3–9. Graphs showing—

3. Concentrations of (A) nitrate, (B) sulfate, and (C) calcium plus magnesium 

in O- and B-horizon soil water in the Dry Creek watershed (DC57) in response 

to the clearcut of 1996–97 ..................................................................................................7

4. (A) Nitrate and (B) inorganic monomeric aluminum concentrations in stream 

water before, during, and after the harvests in the Dry Creek - DC57 (clearcut) 

and Shelter Creek - SC40 (selectively harvested) watersheds in southeastern 

New York, 1992–2001...........................................................................................................9

5. Three hypothetical relations (dotted lines) between mean stream water 

nitrate concentration and percentage of watershed biomass harvested during 

the first year after the clearcut (DC57) and the selective harvests (SC40) in 

southeastern New York ....................................................................................................11

Contents

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

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

A Changing Approach to Forest Management ................................................................................3

Study Area..............................................................................................................................................4

Methods...........................................................................................................................................................4

Effects of Forest Harvesting on Ecosystem Health..................................................................................4

Forest Soils and Soil Water.................................................................................................................4

Soil Chemistry...............................................................................................................................5

 Soil Microbial Processes ..........................................................................................................5

Soil-Water Chemistry ..................................................................................................................7

Nitrate and Sulfate .............................................................................................................7

Calcium and Magnesium...................................................................................................8

Stream-Water Chemistry.....................................................................................................................8

Forest Regrowth and Aquatic Communities after the Harvests ...................................................9

Nutrient Uptake and Tree Regrowth.........................................................................................9

Macroinvertebrate Communities ............................................................................................11

Fish Communities.......................................................................................................................12

Conclusions...................................................................................................................................................16

Acknowledgments.......................................................................................................................................16

References Cited..........................................................................................................................................16

Appendix 1. Selected Photographs of the Dry Creek and Shelter Creek Forest 

Harvesting Study ............................................................................................................................19
iv

6. (A) Species richness, (B) EPT richness, and (C) Hilsenhoff Biotic Index in 

relation to New York State thresholds for “slightly impaired” site conditions 

as defined by (Smith and Bode, 2004) at four stream sites in the study area 

before, during, and after experimental tree harvests..................................................13

7. Mean sample values for (A) Percent Gatherers, (B) Percent Shredders, and 

(C) Metals Tolerance Index at the Dry Creek gage (DC57) before and after 

the clearcut..................................................................................................................................14

8. Brook-trout mortality during 30-day exposure experiments in the spring of each 

year 1995–2000 at: (A) the clearcut site (Dry Creek, DC57), (B) the selectively 

harvested sites (North and South Shelter Creek, SC40), (C) the confluence of Dry 

Creek and Shelter Creek (SC20), and (D) Clear Creek (the control stream, CL25)...........15

Tables

1. Mean chemical properties of soil horizons in Dry Creek watershed before and 

after clearcut of 1996–97 .............................................................................................................6

2. Stream-water chemistry in Dry Creek (clearcut, DC57), Shelter Creek (selectively 

harvested watersheds, SC40), and Clear Creek (the control watershed, CL25) 

before, during, and after forest harvests conducted from 1995–97 ...................................10
v

Conversion Factors, Datum, and Abbreviations

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft)

kilometer (km) 0.6214 mile (mi)

Area

square meter (m2) 0.0002471 acre

hectare (ha) 2.471 acre

square kilometer (km2) 247.1 acre

hectare (ha) 0.003861 square mile (mi2)

square kilometer (km2) 0.3861 square mile (mi2)

Volume

liter (L) 1.057 quart (qt)

Flow rate

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

Application rate

kilograms per hectare 25.49 tons per square mile

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

°F = (1.8×°C) + 32

Horizontal coordinate information is referenced to the North American Datum of 1983 

(NAD 83).

Abbreviated water-quality units used in this report

μmol/L micromoles per liter
This page has been left blank intentionally.
Effects of Forest Harvesting on Ecosystem Health in 

the Headwaters of the New York City Water Supply, 

Catskill Mountains, New York

By Michael R. McHale, Peter S. Murdoch, Douglas A. Burns, and Barry P. Baldigo

Abstract 

The effects of forest clearcutting and selective harvesting 

on forest soils, soil and stream water chemistry, forest 

regrowth, and aquatic communities were studied in four 

small headwater catchments. This research was conducted 

to identify the sensitivity of forested ecosystems to forest 

disturbance in the northeastern United States. The study area 

was in the headwaters of the Neversink Reservoir watershed, 

part of the New York City water supply system, in the Catskill 

Mountains of southeastern New York. Two sub-catchments 

of the Shelter Creek watershed were selectively harvested, 

one in its northern half and one more heavily in its southern 

half in 1995–96, the Dry Creek watershed was clearcut in the 

winter of 1996–97, and the Clear Creek watershed was left 

undisturbed and monitored as a control site. Monitoring was 

conducted from 4 years before the harvests until 4 years after 

the harvests. Clearcutting caused a large release of nitrate 

(NO3

-

) from watershed soils and a concurrent release of 

inorganic monomeric aluminum (Alim), which is toxic to some 

aquatic biota. The increased soil NO3

-

 concentrations measured 

after the harvest could be completely accounted for by the 

decrease in nitrogen (N) uptake by watershed trees, rather 

than an increase in N mineralization and nitrification. The 

large increase in stream water NO3

-

 and Alim concentrations 

caused 100-percent mortality of caged brook trout (Salvelinus 

fontinalis) during the first year after the clearcut and adversely 

affected macroinvertebrate communities for 2 years after the 

harvest. Nutrient uptake and biomass accumulation increased 

in uncut mature trees after the two selective harvests. There 

was no increase in stream-water NO3

-

 or Alim concentrations, 

and so there were no adverse affects on macroinvertebrate or 

trout communities. The amount of tree biomass that can be 

removed without causing a sharp increase in stream-water 

NO3

-

 and Alim stream-water concentrations is unknown, but 

probably depends on the history of forest-disturbance and 

acid deposition and the level of soil acidification. Results of 

this study indicate that macroinvertebrate and brook trout 

communities were sensitive to clearcutting and that deer 

browsing may affect water quality by suppressing forest 

regeneration and nutrient uptake. Further studies of selective 

harvests could identify the harvesting threshold below which 

changes in water quality and soil chemistry are minimized, 

and nutrient retention is maximized, thus reducing the damage 

that logging can inflict on stream and aquatic communities.

Introduction

Forest-harvesting studies have indentified several 

variables that are directly affected by forest harvesting 

including: vegetation, soil chemistry, soil physical properties, 

soil microbial communities, and ground-water and streamwater quantity and quality (Vitousek, 1981; Hornbeck and 

Kropelin, 1982; Dahlgren and Driscoll, 1994). Furthermore, 

changes in these components can adversely affect forest 

regeneration and aquatic communities in surface waters that 

receive drainage from harvested areas. The Catskill Mountain 

region of southeastern New York (fig. 1) is about 85 percent 

forested and contains six reservoirs that are the principal 

drinking-water supply for New York City. Land-use managers 

in the region need forest-harvesting guidelines that will ensure 

the continued vigor of the forest-products industry while 

preventing water-quality degradation. The effects of harvesting 

on the sustainability and health of forest and aquatic 

ecosystems have been the subject of research for many years 

(Likens and others, 1969; Vitousek and others, 1979; Bormann 

and Likens, 1994; Reynolds and others, 1995); of particular 

interest have been the effects of harvesting on the nitrogen (N) 

cycle in forest soils and adjacent surface waters (Vitousek, 

1981; Hornbeck and Kropelin, 1982).

Since 1982 the U.S. Geological Survey (USGS) has been 

studying stream-water quality in forested Catskill watersheds 

in relation to acid rain (Murdoch and Stoddard, 1992, 1993; 

Murdoch and Shanley, 2006), climate change (Murdoch and 

others, 1998; Murdoch and others, 2000; Burns and others, 

2007), nitrogen cycling (Burns, 1998; Welsch and others, 

2001), hillslope hydrology (Brown and others, 1999), and 

logging (Baldigo and Murdoch, 1997; Baldigo and others, 

2005; Burns and Murdoch, 2005; McHale and others, 2007). 
2 Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City Water Supply

West

Branch Neversink River

EXPLANATION

Light selective cutting

Heavy selective cutting

Clearcut

Surface water sampling site

DC57

SC20

Soil water sampling site

1-hectare unfenced clearcut

Clear

Creek

Dry

Creek

South

Shelter

Creek

North

Shelter

Creek

CL25

SS20

SC40

NS25

Control

Watershed

NEW YORK

Study Area

74°31' 30'

41°

59'

58'

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

Universal Transverse Mercator Projections, Zone 18

0 1,500 FEET

0 500 METERS

Figure 1. Location of the four study watersheds in the Catskill Mountains of southeastern New York.
Introduction 3

In 1992, the USGS, in cooperation with the New York City 

Department of Environmental Protection, began a 9-year study 

of the ecological effects of two forest-harvesting methods—a 

clearcut and a selective harvest (timber stand improvement) 

in the headwaters of the Neversink Reservoir watershed in 

the Catskill Mountains of southeastern New York (fig. 1). 

The harvests were conducted during the winters of 1995–96 

and 1996–97; stream-water and soil-water chemistry were 

monitored for 4 years before and after the harvests, and tree 

regrowth, macroinvertebrate communities, and brook-trout 

(Salvelinus fontinalis) mortality were used as indicators of the 

ecological effects of forest harvesting. This report describes 

the harvesting and monitoring methods used and summarizes 

the effects of the harvests on soil chemistry, soil- and streamwater chemistry, macroinvertebrate communities, and brooktrout mortality. More detailed findings from this study, 

published in peer-reviewed scientific journals, are referenced 

throughout this report.

A Changing Approach to Forest Management

Traditionally, forest-management decisions have been 

based mainly on the observed physical condition of trees 

in a forest stand. A new, broader perspective on forest 

management has emerged in recent years from the field 

of watershed biogeochemistry, the study of biological and 

geochemical processes and element cycling within a given 

drainage basin (fig. 2). A biogeochemical approach to 

forest management takes into account a suite of interrelated 

indicators of ecosystem health. These include the rate of 

atmospheric deposition (wet and dry chemical deposition), 

climatic conditions, chemical and physical properties of 

the soil, stream-water and ground-water quality, and the 

possible effects of changes in these factors on stream biota 

in addition to traditional silvicultural considerations such as 

the physical condition of the forest. For example, if logging 

were conducted in an area where soils had been depleted of 

Forest

Floor

Fixation to Surfaces

Mineral

Soil

Soil Water

Wet and Dry Deposition

Nutrient and Base Cation Leaching

Litterfall

Cation Exchange

Organic Decomposition

Root Uptake

Figure 2. Interaction of biogeochemical components of a forested landscape. (Modified from Lawrence and Huntington, 1999, fig. 1.)
4 Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City Water Supply

base cations such as calcium (Ca2+) and magnesium (Mg2+), a 

biogeochemical assessment might indicate a lighter harvest to 

minimize the ecological effects of harvesting, than would be 

suggested by standard silvicultural methods.

Study Area

 The study area (fig. 1) is characterized by steep slopes 

interrupted by flat terraces. Thin soils overlie thin till (1–3 m 

or ~3–10 ft thick) that was deposited by glaciers about 

14,000 years ago on sandstone and conglomerate interbedded 

with siltstone and shale. Forests are mixed northern hardwoods 

of primarily Fagus grandifolia (American beech), Betula 

alleghaniensis (yellow birch), Acer saccharum (sugar maple), 

and Acer rubrum (red maple); Tsuga canadiensis (L.) Car. 

(eastern hemlock) dominates in many riparian zones. Mean 

annual air temperature is 5oC (41°F), and annual precipitation 

averages 1.6 m (63 inches).

Methods

Three watersheds were harvested during the study, and a 

fourth was used as a control in which no harvesting was done 

(fig. 1). The North Shelter Creek (NS25, 33 ha) and South 

Shelter Creek (SS20, 51 ha) catchments form the Shelter 

Creek watershed (109 ha), which is monitored at site SC40 

(fig. 1). The combined areas of the NS25 and SS20 catchments 

are less than the entire area of the Shelter Creek watershed at 

SC40 because the catchment gages are well upstream from 

the SC40 gage (fig. 1). The Dry Creek watershed (DC57, 

24 ha) lies just south of the Shelter Creek watershed; Dry 

Creek flows into Shelter Creek upstream from gaging station 

SC20 (161 ha). The Clear Creek watershed (CL25, 48 ha) was 

used as a control and is located just west of the Dry Creek 

watershed (fig. 1).

Several environmental indicators such as atmosphericdeposition chemistry, soil chemistry, soil-water chemistry, 

stream-water and ground-water chemistry, tree biomass 

and leaf chemistry, and biological nitrogen transformations 

(mineralization, nitrification, and denitrification) were 

monitored during 1992–97 before the experimental harvests. 

A “Timber Stand Improvement” (selective removal of sick or 

unmarketable trees to increase the growth rate of remaining 

trees) was done in parts of the Shelter Creek watershed 

(SC40) in two phases. Phase 1, termed the “light selective 

harvest,” entailed selective logging of the North Shelter Creek 

catchment (NS25, fig. 1) during the winter of 1995–96 to 

provide a 7-percent decrease in tree basal area within the 

logged area; this resulted in a 2-percent decrease in basal area 

within the entire North Shelter Creek catchment. Phase 2, 

termed the “heavy selective harvest,” entailed logging of the 

South Shelter Creek catchment in the fall of 1996 to provide a 

29-percent decrease in tree basal area within the logged area; 

this resulted in an 8-percent decrease in basal area within the 

entire SS20 catchment. About 5.6-percent of the basal area 

was removed from the entire Shelter Creek watershed (SC40), 

68 ha of the Shelter Creek watershed was left untouched 

because it is part of the New York State forest preserve. 

During the following winter (1996–97), 18 ha of the 24-ha 

Dry Creek watershed (DC57, fig. 1) was clearcut, leaving only 

a few scattered seed trees for regeneration; 6 hectares in the 

southwestern portion of the watershed were left undisturbed 

because that area is also part of the New York State forest 

preserve (fig.1). Slash (branches and tree tops) was left on the 

ground and arranged along temporary skidder trails to create a 

“corduroy” surface to minimize soil disturbance. The clearcut 

decreased the basal area of the harvested area by 97 percent 

and amounted to an 80-percent decrease in the basal area of 

the entire watershed. The fourth watershed (CL25, 48 ha) was 

monitored as an untreated reference site. The heavy selective 

harvest in the South Shelter Creek watershed and the clearcut 

area of the Dry Creek watershed were enclosed with 2.5 m 

high game fence to prevent deer browsing which can inhibit 

forest regrowth. One additional 1-ha forest plot, adjacent 

to the Dry Creek watershed, was clearcut and left unfenced 

to assess the effect of deer browsing on forest regeneration 

(fig. 1). Monitoring at all sites continued from October 1, 1992 

through September 30, 2001 (water years 1993–2001).

Effects of Forest Harvesting on 

Ecosystem Health

The effects of forest harvesting on soils and soil 

microbial communities, soil-, stream-, and ground-water 

chemistry, and stream aquatic communities are often used as 

indicators of the effects of a tree harvest on ecosystem health. 

The following sections describe the effects of the experimental 

harvests on soils and soil-water chemistry, stream-water 

chemistry, macroinvertebrate communities, caged brook trout, 

and tree regrowth after the harvests.

Forest Soils and Soil Water

 Soil samples and soil-water samples were collected in 

the Dry Creek watershed to evaluate the effects of harvesting 

on watershed soils. Soil samples were collected from several 

depths at each of 43 locations and were air-dried, sieved, and 

analyzed with standard soil-analysis methods. Soil-water 

samples were collected monthly from zero-tension lysimeters, 

also referred to as “gravity lysimeters,” because they collect 

water that drains through the soil by gravity (as opposed to 

suction lysimeters, which use negative pressure to collect soil 

water). Additional samples were collected during storms and 

spring snowmelt with sequential lysimeters. This technique 

linked zero-tension lysimeters to an automated sampler to 
Effects of Forest Harvesting on Ecosystem Health 5

allow frequent sampling and provide more detailed data on 

changes in soil-water chemistry than would be possible with 

monthly, biweekly, or even weekly fixed-interval sampling.

Soil Chemistry

Soils provide the nutrients and water that trees and 

other vegetation require to survive and host the macro- and 

microorganisms that cycle those nutrients and make them 

available to plants. Soils are also the medium through which 

rain and snowmelt percolate and through which shallow 

ground water flows. Soil water is a significant component of 

stream flow and so changes in the chemistry of soil water can 

have a direct affect on stream-water chemistry. An assessment 

of soil chemistry prior to forest harvesting can indicate how 

harvesting may affect soil chemical pools, nutrient cycling, 

soil- and stream-water chemistry and ultimately the rate of 

forest regrowth. 

Forest harvesting typically results in soil acidification 

because tree removal decreases N uptake creating an excess 

of N in the soil; that N is then transformed to nitrate (NO3

-

) 

through a microbial process known as nitrification. The NO3

-

then passes through the soil as nitric acid (HNO3), which can 

deplete neutralizing cations such as Ca2+, Mg2+, sodium (Na+), 

and potassium, (K+) (collectively referred to as base cations). 

This leaching of soil base cations causes a decrease in soil 

pH and is often accompanied by a release of soil aluminum 

(as Al3+) (McHale and others, 2007), which is detrimental 

to tree growth and toxic to some fish and other aquatic biota 

(Schofield and Trojnar, 1980; Shortle and Smith, 1988; Cronan 

and Grigal, 1995; Baldigo and Murdoch, 1997; Baldigo and 

others, 2005).

Changes in soil chemistry can be difficult to detect 

at time scales shorter than a decade because the pool of 

chemicals held in the soil greatly exceeds the amount that 

is cycled by biota annually. Nonetheless, the clearcut was 

followed by a decrease in the amount of exchangeable 

base cations (positively charged ions attached to negatively 

charged soil particles) in the upper part of the forest floor 

(the Oi horizon), which is rich in organic matter (table 1) 

(McHale and others, 2007). This decrease was insignificant 

at greater depths. Percent base saturation—the amount of 

exchangeable base cations relative to the amount of all 

exchangeable cations (hydrogen and aluminum plus base 

cations)–decreased within the Oa horizon (the organic 

soil layer) after the clearcut. Exchangeable base cation 

concentrations and percent base saturation are important 

measures of the base cation pool available in the soil and base 

cations are essential nutrients for forest regrowth.

In general, the concentrations of exchangeable base 

cations in the study area were low, even before the clearcut, 

relative to those of forests elsewhere in the northeastern 

United States (David and Lawrence, 1996); this is because the 

sandstone bedrock from which Catskill soils are derived has 

a relatively slow weathering rate and consists largely of silica 

(Rich, 1934). These soils were highly acidic even before the 

forest harvest as a result of natural soil-forming processes and 

several decades of acidic atmospheric deposition (Lawrence 

and Huntington, 1999). The clearcut resulted in a further 

decrease in exchangeable base cations and a coincident 

increase in exchangeable Al concentration within the soil 

(table 1).

 Soil Microbial Processes

The N cycle in forest soils reflects the competition 

among plant roots and microbes for available ammonium 

(NH4

+

) and NO3

-

. Plants need soil microorganisms to convert 

N stored in organic matter into inorganic forms that they can 

assimilate through their roots (although recent research has 

shown that some plants take up organic forms of N directly). 

The effects of forest disturbances such as tree harvesting, 

soil freezing, and insect infestations can shift the balance 

between roots and microorganisms and thereby alter the rate 

of N accumulation and movement in soils (Likens and others, 

1969; Groffman and others, 2001; Lovett and others, 2002). 

Forest harvesting causes an increase in NO3

-

 concentrations 

in soil water, stream water, and ground water. What is unclear 

is whether the increase is caused primarily by tree removal 

and the consequent decrease in N uptake or increased rates of 

microbial N cycling that result from higher soil moisture and 

temperature. To investigate this question, net N-mineralization 

and nitrification rates (the processes by which N is converted 

from organically bound N to NH4

+

 and NO3

-

) were measured 

before and after the clearcut and compared to estimates 

of N uptake by vegetation before the clearcut and streamwater N export after the clearcut. Net N-mineralization and 

nitrification rates in Catskill soils before the clearcut were 

among the highest recorded in northeastern forests and did 

not change significantly as a result of the clearcut (Burns 

and Murdoch, 2005). Rather, the increase in stream-water N 

export in Dry Creek after the clearcut roughly equaled the 

preharvest uptake of N by trees in the watershed; therefore, 

the increase in stream-water N export is attributed mostly to 

a decrease in uptake by trees, rather than to a temperature- or 

moisture-stimulated increase in rates of N mineralization 

and nitrification. This conclusion may also apply to other 

forested watersheds that receive N deposition in amounts 

greater than required by watershed biota. Previous studies 

have documented significant increases in N-mineralization and 

nitrification rates after forest harvesting in other northeastern 

watersheds, however, those watersheds were leaching much 

less inorganic N to streams than the Dry Creek watershed 

was prior to harvesting (Matson and Vitousek, 1981; Gordon 

and Van Cleve, 1983; Vitousek and Matson, 1985; Frazer and 

others, 1990; Pierce and others, 1993).
6 Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City Water Supply Table 1. Mean chemical properties of soil horizons in Dry Creek watershed before and after clearcut of 1996–97. [Ca, calcium; Mg, magnesium; K, potassium; Na, sodium; Al, aluminum; H+, hydrogen ion; m, meter. Site location is shown in fig. 1] Soil horizona No. of samples (n) b Soil properties Exchangeable-cations, in centimoles of charge per kilogram Percent base saturation Ca:Al ratio Soil- water pH Soil pH (as CaCl2) c Percent LOI d Percent carbon Percent nitrogen Ca Mg K Na Al H+ Cation- exchange capacity A. Preharvest—12 samples collected at 0.1-m depth increments and 31 bulk samples from each horizon during 1996 Oi 11 4.50 3.88 88 47.8 2.69 23.55 4.70 3.83 0.09 Oa 16 3.83 3.21 34 17.7 1.03 3.53 0.87 0.63 .03 4.73 4.09 13.87 35.79 0.75

B 79 3.90 3.38 5 2.5 0.18 0.38 .12 .11 .02 5.34 1.74 7.72 7.98 .07C 47 4.40 3.78 2 0.9 .14 .15 .04 .06 .01 3.53 0.48 4.27 6.11 .04

B. Postharvest—27 samples collected from soil pits at 0.1-m depth increments during 1998

Oi 27 4.06 3.38 78 41.9 2.23 13.88 2.69 1.63 .05Oa 26 3.77 3.13 43 24.2 1.38 3.96 .82 .71 .04 7.82 4.80 18.15 29.73 .51B 98 4.13 3.46 4 3.7 .25 .26 .08 .12 .01 5.48 1.54 7.49 6.66 .05C 34 4.40 3.71 2 .9 .07 .11 .03 .07 .01 3.65 0.42 4.29 5.19 .03

a Oi, Organic material that shows little decomposition, mostly leaves.a Oa, Organic material that is well decomposed.a B, Mineral soil that shows little or no evidence of the original sediment or rock structure and has a low organic matter content.a C, Undeveloped soil composed of the material from which the soil is formed; includes materials in various stages of weathering.b Differences in n values between horizons reflect the number of 0.1-m depth intervals within each horizon.c Soil pH after extraction with a 0.02 M CaCl2 (calcium chloride) solution.d Percent Weight Loss on Ignition (LOI) gives a measure of the organic matter in the sample; it denotes the percent weight lost when the sample is combusted.
Effects of Forest Harvesting on Ecosystem Health 7

Soil-Water Chemistry

Water enters forest soils as dilute rainwater, snowmelt, 

or throughfall (precipitation that has passed through the 

forest canopy). Upon entering the soil, the water percolates 

downward where it can be taken up by plants, recharge ground 

water, or drain to streams. The chemistry of the water changes 

considerably as it interacts with the soil mainly through 

exchange reactions with ions bound to soil particles; as a result 

soil water chemistry reflects conditions in the soil. Soil water 

chemistry can be a more sensitive indicator of changes in soil 

chemistry than stream water or ground water because stream 

water is composed of soil water, groundwater, and (during 

storms) precipitation and changes in ground water chemistry 

occur over much longer time periods than soil water. Soil 

water was sampled as a part of this study to measure changes 

in the soil caused by the harvests.

Nitrate and Sulfate

Previous studies of forest harvesting have documented 

a large increase in soil-water NO3

-

 concentrations and have 

attributed that change to decreased uptake by trees and to 

increased rates of N mineralization and nitrification (Vitousek 

and Melillo, 1979; Matson and Vitousek, 1981; Vitousek, 

1981; Hornbeck and Kropelin, 1982). Within a few years 

soil-water NO3

-

 concentrations typically decrease to preharvest 

concentrations or lower as the demand for N by vegetation 

increases during the early stages of forest regrowth. Soil 

water in the Dry Creek watershed before the 1996–97 clearcut 

was acidic and contained measurable amounts of sulfate 

(SO4

2-) and NO3-

 throughout the year. Soil-water chemistry 

did not change immediately after the clearcut, which was 

completed in April 1997; rather, it remained at preharvest 

levels for 3 months until mid-July, when it changed sharply 

A Nitrate

0

200

400

600

800

1,000

1,200

1,400

1,600

1,800

B Sulfate

CONCENTRATION, IN MICROMOLES PER LITER

0

20

40

60

80

100

120

140

C Calcium plus Magnesium

Date

1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 

0

100

200

300

400

500

O horizon

B horizon

Clearcut Completed Clearcut Completed Clearcut Completed

Figure 3. Concentrations of (A) nitrate, (B) sulfate, and (C) calcium plus 

Magnesium in O- and B-horizon soil water in the Dry Creek watershed 

(DC57) in response to the clearcut of 1996–97. (Location is shown in fig. 1.)
8 Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City Water Supply

(fig. 3). During the fall of 1997 NO3

-

 concentrations exceeded 

1,100 μmol/L in O horizon soil water, 1,600 μmol/L in B 

horizon soil water, and were as high as 1,390 μmol/L in 

stream water (McHale and others, 2007). Those concentrations 

were much higher than NO3

-

 concentrations measured after 

clearcuts in other northeastern watersheds with lower rates of 

atmospheric N deposition, for example the whole-tree harvest 

at Hubbard Brook, N.H. in 1983–84 produced maximum 

soil-water NO3

-

 concentrations of ~825 μmol/L (Dahlgren 

and Driscoll, 1994). In contrast to the Hubbard Brook study 

there was still measurable NO3

-

 in soil water during the 

growing season as long as 4 years after the Dry Creek clearcut. 

Sulfate concentrations in B-horizon soil water decreased from 

45 μmol/L to 20 μmol/L during the first 8 months after the 

clearcut because a decrease in soil pH increased the adsorption 

of sulfate onto soil particles (fig. 3) (Welsch and others, 2004).

After the clearcut, soil-water samples from the sequential 

lysimeters often showed 2 peaks in NO3

-

 concentration during 

storms, the first peak typically occurred early in the storm, 

the second after the storm hydrograph peak. Water table 

elevation data collected at a shallow well located adjacent 

to the sequential lysimeters revealed that the first peak in 

NO3

-

 occurred when the water table was below the lysimeters 

as soil water was percolating down through the soil column. 

The second peak in NO3

-

 concentration occurred when the 

water table had risen above the elevation of the lysimeters and 

shallow ground water was flowing laterally into the lysimeters. 

This dual peak in NO3

-

 concentrations only occurred during 

storms in which the water table overtopped the lysimeters. 

Storms that occurred after long, dry periods resulted in high 

NO3

-

 and NH4

+

 concentrations because, in the absence of 

vegetative uptake, those dry periods allowed NO3

-

 to buildup 

in the soil through N mineralization and nitrification. When 

storms occurred in rapid succession there was a dilution of 

NO3

-

 and NH4

+

 in soil water from one storm to the next. Thus, 

the moisture conditions in the watershed before storms had a 

large effect on the release of NO3

-

 from watershed soils.

Calcium and Magnesium

Concentrations of Ca2+ and Mg2+ in soil water increased 

sharply after the clearcut and returned to preharvest levels 

within 4 years (fig. 3). Clearcutting in these Ca-poor soils 

resulted in a decrease in the exchangeable-base-cation pool 

and the percent base saturation, both of which are indicators of 

the amount of base cations available to support forest regrowth 

(table 1). Continued monitoring of soil-water chemistry and 

tree regrowth is expected to reveal the long-term effect of 

decreased exchangeable Ca2+ and Mg2+ on forest regeneration 

in these Catskill watersheds.

Stream-Water Chemistry

Stream-water chemistry reflects all of the watershed 

processes discussed thus far and is often used to represent the 

response of an entire watershed to natural disturbances as well 

as to forest-management activities. The study was divided 

into three time periods for water-quality comparisons among 

watersheds—the preharvest period (1993–96), the harvest 

period (1997–99), and the postharvest period (2000–01). The 

NO3

-

 and base-cation concentrations in Dry Creek increased 

sharply after the clearcut, but there was only a small response 

in Shelter Creek after the two selective harvests (fig. 4). This 

is consistent with results of previous studies, which have 

also documented the leaching of NO3

-

 and base cations after 

forest harvests (Vitousek and Melillo, 1979; Hornbeck and 

Kropelin, 1982; Dahlgren and Driscoll, 1994). As NO3

-

 passes 

through the soil th cidity it produces is neutralized first by 

base cations and then by inorganic monomeric Al (Alim), 

as a result Alim concentrations in Dry Creek also increased 

markedly after the clearcut, but not in Shelter Creek after the 

selective harvests (gaging stations NS25, SS20, or SC40) 

(fig. 4, table 2). In general, NO3

-

 and Alim concentrations 

in Dry Creek were much higher than those reported for the 

whole-tree harvest at Hubbard Brook (Hornbeck and Kropelin, 

1982; Lawrence and others, 1987; Dahlgren and Driscoll, 

1994). High Alim concentrations are toxic to some fish species, 

including brook trout (Schofield and Trojnar, 1980; Baker 

and Schofield, 1982; Baldigo and Murdoch, 1997; Kaeser 

and Sharpe, 2001; Baldigo and others, 2005); they also can 

inhibit the uptake of calcium by tree roots (Shortle and Smith, 

1988; Cronan and Grigal, 1995) and thereby increase forest 

vulnerability to disease, insect infestation, and mortality from 

other stresses such as drought.

Ground-water seepage into Dry Creek mitigated the 

effect of the clearcut on stream-water chemistry to a degree, 

in that the high base-cation concentrations in ground water 

neutralized some of the stream acidity produced by soilwater HNO3. Nonetheless, the large amount of NO3

-

 released 

from watershed soils after the clearcut overwhelmed the 

neutralizing capacity of the ground water and the sharp 

decrease in soil-water and stream-water pH coincided with a 

large release of Alim from O- and especially B-horizon soils to 

the stream (fig. 4, table 2) (McHale and others, 2007). Forest 

regeneration began during the first year after the clearcut 

(fencing around the clearcut area prevented deer browsing 

on young trees), and stream-water NO3

-

, Alim, and basecation concentrations returned to or fell below pre-harvest 

concentrations by the fifth year after the clearcut. 

The large release of NO3

-

 and the coincident release of 

Alim from watershed soils after the clearcut, produced streamwater Alim concentrations well above the 3.7 μmol/L threshold 

that is considered toxic to some aquatic biota (fig. 4, table 2). 

In contrast, the selective harvests in the north and south 

Shelter Creek catchments did not cause an increase in the 

concentrations of stream-water NO3

-

 or Alim (fig. 4, table 2). 

Further research is needed, however, to define the harvesting 

threshold above which nutrient and base-cation losses greatly 

increase, and below which nutrient retention is maximized, to 

ensure minimal effects on stream-water quality and aquatic 

biota (fig. 5).
Effects of Forest Harvesting on Ecosystem Health 9

Forest Regrowth and Aquatic Communities after 

the Harvests

Soil chemistry and microbial processes are the principal 

factors that affect the rate of forest regrowth while streamwater quality and flow conditions are the principal factors 

that affect the health of stream aquatic communities. As 

discussed in the previous section, stream water quality 

integrates the effects of soil chemistry, soil microbial activity, 

and soil-water chemistry as well as other factors such as 

atmospheric deposition, soil- and ground-water flowpaths, 

and the effects of vegetation and, therefore, is often used to 

represent the response of the entire watershed to an ecosystem 

disturbance such as forest harvesting. An increase in streamwater acidity and Al concentrations can affect the survival of 

individual organisms, species distribution, and the structure 

and function of aquatic communities. Many of these factors 

can be represented by biological indicators which are used to 

quantify the severity of a disturbance within an affected stream 

ecosystem. Therefore, part of this study entailed monitoring of 

forest regrowth, macroinvertebrate communities, and mortality 

of brook trout as indicators of the effects of forest harvesting 

on biological communities.

Nutrient Uptake and Tree Regrowth

From a forest management perspective the critical 

question regarding forest regrowth is whether the physical, 

chemical, and hydrologic conditions in the watershed after the 

harvest will sustain healthy regeneration. Those conditions 

determine the rate and vigor of forest regrowth and they 

depend on the pre-harvest state of the watershed and the 

severity of the disturbance. For this study forest regrowth 

was assessed by measuring nutrient uptake and biomass 

NITRATE CONCENTRATION,

IN MICROMOLES PER LITER

0

200

400

600

800

1,000

1,200

1,400

1,600

Clearcut (DC57)

Selective cut (SC40)

Date

1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 

INORGANIC MONOMERIC

ALUMINUM CONCENTRATION,

IN MICROMOLES PER LITER 

0

20

40

60

80

100

Heavy Selective Harvest Completed (SS20)

 Clearcut Completed (DC57) 

Light Selective Harvest Completed (NS25)

Heavy Selective Harvest Completed (SS20)

 Clearcut Completed (DC57) 

Light Selective Harvest Completed (NS25)

A Nitrate

B Inorganic monomeric

 aluminum 

Figure 4. (A) Nitrate and (B) inorganic monomeric aluminum concentrations in stream 

water before, during, and after the harvests in the Dry Creek - DC57 (clearcut) and 

Shelter Creek - SC40 (selectively harvested) watersheds in southeastern New York, 

1992–2001. (Locations are shown in fig. 1.)
10 Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City Water Supply Table 2. Stream-water chemistry in Dry Creek (clearcut, DC57), Shelter Creek (selectively harvested watersheds, SC40), and Clear Creek (the control watershed, CL25) before, during, and after forest harvests conducted from 1995–97. [Concentrations are means, in micromoles per liter. pH is given in pH units, ANC given in microequivalents per liter. ANC, acid-neutralizing capacity; Ca, calcium; Mg, magnesium; K, potassium; Na, sodium; Cl, chloride; NO3, nitrate; SO4, sulfate; DOC, dissolved inorganic carbon; SiO4, silica; Almon, monomeric aluminum; Alorg, organic momomeric aluminum, Alim, inorganic monomeric aluminum, ND = not detected. Watershed locations are shown in fig. 1] Watershed pH ANC Ca Mg K Na Cl NO3 SO4 DOC SiO2 Almon Alorg Alim Preharvest (1993–96) Clearcut 5.91 28.22 55.86 25.87 8.48 16.29 15.83 22.85 55.23 192.77 35.95 1.97 0.79 1.18 Selective cut 5.40 2.75 41.49 24.95 6.97 13.84 16.09 12.33 55.20 299.93 40.31 3.00 1.58 1.40 Control 5.97 20.02 47.81 29.28 6.50 13.57 16.05 12.24 60.37 150.66 44.94 1.34 .61 0.74 Harvest (1997–99) Clearcut 5.59 6.34 85.47 53.17 17.37 17.20 16.07 206.85 41.73 162.81 35.26 7.76 .71 6.99 Selective cut 5.46 6.52 41.03 24.06 7.36 12.63 12.77 13.73 49.63 312.66 36.16 2.88 1.63 1.25 Control 6.04 20.14 49.29 29.92 6.53 14.33 13.54 27.27 53.66 146.76 39.57 1.17 .37 .72 Postharvest (2000–01) Clearcut 6.17 42.34 56.48 26.52 13.62 15.72 13.03 24.97 52.28 202.84 37.34 0.88 .15 .56 Selective cut 5.63 11.65 40.05 24.32 6.29 15.24 15.53 13.95 51.00 184.77 38.47 1.22 .39 .79 Control 6.14 27.67 47.05 29.03 6.24 14.55 14.54 16.45 53.28 141.43 40.27 .45 ND .38
Effects of Forest Harvesting on Ecosystem Health 11

accumulation in 20 x 20-m plots established throughout 

the clearcut watershed (DC57), the selectively harvested 

watersheds (SS20 and NS25), and the reference watershed 

(CL25) (Yorks, 2001; Yorks and others, 2003) (fig. 1). 

In addition, the effects of deer browsing on vegetation 

regrowth was assessed by comparing regrowth in a 1-ha 

unfenced clearcut area established outside of the Dry Creek 

watershed to the fenced 18-ha clearcut area within the Dry 

Creek watershed.

Biomass and nutrient accumulation were greater in the 

Shelter Creek selectively harvested catchments than in the 

Dry Creek clearcut during the first 2 years after the harvests, 

but this pattern reversed during the next 2 years (Yorks, 

2001). Trees with a diameter-at-breast-height greater than 

5 cm showed the greatest amount of nutrient and biomass 

accumulation in the selectively harvested areas, whereas in 

the Dry Creek clearcut the greatest amount of nutrient and 

biomass accumulation initially occurred in woody stems 

less than 1.4 m tall, and later in saplings, as regeneration 

progressed (Yorks, 2001). Biomass accumulation and nutrient 

uptake increased after the harvests in uncut mature trees in the 

selectively harvested watersheds and stream-water chemistry 

indicated that light tree thinning can be done without adversely 

affecting stream-water quality (Yorks, 2001).

The two selectively harvested areas showed minimal new 

growth of striped maple (Acer pensylvanicum) and American 

beech (Fagus grandifolia), whereas the clearcut watershed 

showed substantial regeneration of pin cherry (Prunus 

pensylvanica), sugar maple (Acer sacharum), yellow birch 

(Betula alleghaniensis), and several shrub species (Yorks, 

2001). Deer browsing suppressed regeneration, biomass 

accumulation, and nutrient uptake by vegetation in the 1-ha 

unfenced clearcut area; N uptake in the unfenced area 4 

years after the clearcut was only 6.3 kg/ha—one-fifth of 

that measured in the fenced clearcut where N uptake totaled 

30.4 kg/ha (Yorks, 2001). These results confirm that deer 

browsing suppresses forest regeneration and nutrient uptake in 

Catskill forests and imply that deer browsing may affect soiland stream-water quality.

Macroinvertebrate Communities

Benthic macroinvertebrates are reliable indicators of 

stream-water quality because many species are fairly immobile 

and vary widely in their sensitivity to common toxins; also 

their moderately long life span generally allows exposure to 

rare or episodic toxic disturbances (Bode and others, 1991, 

1996; Lazorchak and others, 2003). Nevertheless, no recent 

studies have documented the effects of forest harvesting on 

macroinvertebrate communities despite evidence that it can 

alter the chemistry of soil and stream water (Driscoll and 

others, 1989; Dahlgren and Driscoll, 1994; Burns and others, 

1997). For this study macroinvertebrate communities were 

sampled at four sites—the Dry Creek gage (DC57) at the 

outlet of the clearcut watershed, the upper Shelter Creek gage 

(SC40) at the confluence of the two streams that drain the 

selectively harvested catchments, the lower Shelter Creek gage 

(SC20) downstream from the confluence of Dry Creek and 

Shelter Creek, and the outlet of the control watershed (CL25) 

(fig. 1).

Sampling was done in the late summer 1 or 2 years 

before and 4 or 5 years after each harvest to evaluate the 

PERCENTAGE OF WATERSHED BIOMASS REMOVED

0 20 40 60 80 100

0

50

100

150

200

250

Clearcut (DC57)

MEAN NITRATE CONCENTRATION,

IN MICROMOLES PER LITER

Selective

harvests (SC40)

Figure 5. Three hypothetical relations (dotted lines) between mean stream water nitrate 

concentration and percentage of watershed biomass harvested during the first year after 

the clearcut (DC57) and the selective harvests (SC40) in southeastern New York. The actual 

relation is unknown. (Locations shown in fig. 1.)
12 Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City Water Supply

resulting changes in macroinvertebrate communities. 

Macroinvertebrates were sampled by the method of Surber 

(1970). Six indices were used to represent the response of 

macroinvertebrates to the effects of forest harvesting: 

1. Total species richness, the total number of species or taxa 

found in the sample. 

2. EPT richness, the number of species of mayflies 

(Ephemeroptera), stoneflies (Plecoptera), and caddisflies 

(Tricoptera) found in an average 100 organism subsample; 

these are considered clean-water organisms. 

3. The Hilsenhoff Biotic Index (HBI), a measure of the 

tolerance of organisms in a sample to organic pollution 

such as sewage effluent or animal waste. 

4. Percent gatherer feeding groups, the percentage of 

macroinvertebrate species that feed on items found on 

surface deposits. Percent gatherer feeding groups are 

sometimes lower in toxic conditions. 

5. Percent shredder feeding groups, the percentage of 

macroinvertebrate species that shred organic material. The 

percentage of shredder feeding groups usually increases 

when organic matter in the water increases which would 

be typical immediately after a clearcut. 

6. MTI, the metals-tolerance index which is an index of the 

number of species present that are tolerant of high metals 

concentrations in water (Bode and others, 2002).

Three of these indices—total species richness, EPT 

richness, and HBI—exceeded the New York State Department 

of Environmental Conservation thresholds that denote “slight 

impairment” of the site after the clearcut during 1998 or 1999 

(fig. 6) (Bode and others, 1996; Smith and Bode, 2004). In 

addition, there was a decrease in the HBI and the percent 

of gatherer feeding groups and an increase in the percent 

of shredder feeding groups and the MTI after the clearcut 

(figs. 6, 7). None of the indices were affected by the selective 

harvests at Shelter Creek (SC40) or downstream from the 

clearcut and selective harvests at lower Shelter Creek (SC20) 

(fig. 6). The low index values for Clear Creek (CL25) during 

1996 were probably caused by a highly acidic snowmelt 

during a thaw in January. The decrease in the HBI and the 

increase in the MTI, at Dry Creek after the clearcut reflect a 

large decrease in the numbers of metal-sensitive Microspectra 

sp. and an increase in the numbers of other metals-tolerant 

species (figs. 6, 7). Most of the indices at Dry Creek had 

returned to near preharvest conditions by August 2000 

(figs. 6, 7).

Fish Communities

While other studies have shown that forest harvesting can 

affect the chemical quality of stream water (Likens and others, 

1970; Dahlgren and Driscoll, 1994; Burns and others, 1997), 

the effects of forest harvesting on fish survival (or mortality) 

and fish communities in acid-sensitive streams have not been 

well documented. For this study young-of-the-year brook 

trout from the New York State Department of Environmental 

Conservation hatchery in Rome, N.Y., were exposed (in cages) 

to stream water in Dry Creek (DC57), Shelter Creek (at the 

SC40 gage), lower Shelter Creek (at the SC20 gage), and 

the reference stream (CL25) for 30-day periods during each 

spring from 1995 through 2000 to evaluate the effects of the 

selective harvests and the clearcut on this acid-tolerant species 

(Baldigo and Lawrence, 2001). As discussed previously the 

clearcut in the Dry Creek watershed caused a sharp increase 

in stream-water Alim concentrations to levels that are toxic to 

brook trout and many other fish species (fig. 4, table 2) (Baker 

and others, 1990; Baker and Christensen, 1991; Baldigo and 

Murdoch, 1997). 

A small percentage of brook trout mortality was 

measured at Dry Creek (DC57), Shelter Creek (SC40), and 

Clear Creek (CL25) during the spring of 1996 (fig. 8) as a 

result of unusually high and acidic stream flow during spring 

melt that mobilized some Alim, however, that was the only 

year mortality occurred at the control watershed. Dry Creek 

(DC57) was the only site where there was mortality of brook 

trout as a result of the forest harvest (fig. 8). Trout mortality 

at this site ranged from 0 to 15 percent in the spring of 1995 

and 1996 (before the clearcut) and during the first spring after 

the clearcut (1997), but all caged brook trout died during the 

first 7 days of the test in the spring of 1998, and 85 percent 

died during the 30-day test in 1999. No mortality occurred 

during the 30-day test in 2000. Although exposure tests were 

not conducted during the fall, stream water Alim concentrations 

in Dry Creek during the fall of 1997 indicate that toxicity was 

greater and trout mortality would have occurred sooner than 

in the spring test of 1998 (fig. 4). The brook-trout mortality 

appears to have been caused by the Alim concentrations that 

reached toxic levels during the first year after the clearcut as 

the lack of N uptake by trees allowed excess N to become 

nitrified and increase the soil-water acidity, which in turn 

mobilized soil Alim which was transported to the stream (Burns 

and Murdoch, 2005; McHale and others, 2007).

Findings from this study and related investigations in 

the Northeast (Gagen and others, 1993; Simonin and others, 

1993; Van Sickle and others, 1996; Baldigo and Murdoch, 

1997) confirm that Alim in stream water is acutely toxic to 

juvenile brook trout when concentrations exceed 3.7 μmol/L. 

Several laboratory and field investigations have found brook 

trout to be more tolerant of acidic, high-Alim conditions than 

many other fish species that inhabit headwater streams of the 

Northeast (Johnson and others, 1987; Baker and Christensen, 

1991; Gagen and others, 1993; Simonin and others, 1993; 

Baldigo and Lawrence, 2001). Therefore, the toxic conditions 

produced by the clearcut would probably have killed other 

fish species that may have been present, such as slimy sculpin 

(Cottus cognatus), and the brook-trout mortality reported 

here may represent only some of the detrimental effects 

that clearcutting could have on fish communities and the 

downstream ecosystem.
Effects of Forest Harvesting on Ecosystem Health 13

1994 1995 1996 1997 1998 1999 2000 2001

RICHNESS,

IN NUMBER OF SPECIES

20

25

30

35

40

45

1994 1995 1996 1997 1998 1999 2000 2001

EPT RICHNESS,

IN NUMBER OF SPECIES

8

10

12

14

16

18

20

22

1994 1995 1996 1997 1998 1999 2000 2001

HBI INDEX1

2.5

3.0

3.5

4.0

4.5

5.0

5.5

New York State Threshold

for Slight Impairment

EXPLANATION

Clearcut (DC57)

Confluence of DC57 and SC40 (SC20)

Selective Harvest (SC40)

Control (CL25)

A Species Richness

B EPT Richness

C Hilsenhoff Biotic Index

Clearcut Completed

Heavy Selective Harvest Completed

Light Selective Harvest Completed

Figure 6. (A) Species richness, (B) EPT richness, and (C) Hilsenhoff Biotic Index in relation to New York State thresholds for 

“slightly impaired” site conditions as defined by Smith and Bode (2004) at four stream sites in the study area before, during, 

and after experimental tree harvests. (Locations are shown in fig. 1.) 
14 Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City Water Supply GATHERERS

0

20

40

60

80

100

PERCENTAGE OF COMMUNITY

SHREDDERS

0

20

40

60

80

100

1995 1996 1997 1998 1999 2000

METALS TOLERANCE

INDEX (MTI)

IN NUMBER OF SPECIES

0

1

2

3

4

5

6

Clearcut Completed Clearcut Completed Clearcut Completed

Figure 7. Mean sample values for (A) Percent Gatherers, (B) Percent 

Shredders, and (C) Metals Tolerance Index at the Dry Creek gage (DC57) 

before and after the clearcut. (Location is shown in fig. 1.)
Effects of Forest Harvesting on Ecosystem Health 15

MORTALITY, IN PERCENT

100

80

60

40

20

0

0 5 10 15 20 25 30

DAYS OF EXPOSURE

D Clear Creek (CL25)

C Confluence of streams draining selectively

harvested and clearcut watersheds (SC20)

100

80

60

40

20

0

B Selective harvests (SC40)

100

80

60

40

20

0

A Clearcut (DC57)

100

80

60

40

20

0

1995

1996

1997

1998

1999

2000

Figure 8. Brook-trout mortality during 30-day exposure experiments in 

the spring of each year 1995–2000 at: (A) the clearcut site (Dry Creek, 

DC57), (B) the selectively harvested sites (North and South Shelter Creek, 

SC40), (C) the confluence of Dry Creek and Shelter Creek (SC20), and 

(D) Clear Creek (the control stream, CL25). (Locations are shown in fig. 1.)
16 Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City Water Supply

Conclusions

This study evaluated the effects of clearcutting and 

selective harvesting on nutrient retention, soil chemistry, 

soil-water chemistry, stream-water quality, fish and 

macroinvertebrate communities, and forest regrowth in three 

small, forested watersheds in the Catskill Mountains of 

southeastern New York. All of these factors were included to 

evaluate the effect of harvesting on the health of the ecosystem 

rather than focusing on one component. Several general 

conclusions can be drawn from this research:

•	 Soil chemical pools are large relative to the changes 

in soil chemistry that resulted from clearcutting so 

significant long-term changes in soil chemistry are 

unlikely. Nevertheless, a reduction in the base cation 

pool in the upper soil horizons could inhibit forest 

regrowth since that is where vegetation gets the 

majority of the nutrients it needs for growth.

•	 The clearcut resulted in a large release of NO3

-

 from 

watershed soils and a coincident release of Alim, 

which was toxic to brook trout and adversely affected 

macroinvertebrate communities. 

•	 The selective harvests, which removed far fewer 

trees than the clearcut, did not cause an increase in 

stream-water NO3

-

 or Alim concentrations. Nutrient 

uptake and biomass accumulation in the uncut mature 

trees increased after the selective harvest, and stream 

water quality changed little—an indication that 

tree thinning can be done with minimal effect on 

stream-water quality. 

•	 Deer browsing severely limited tree regrowth in the 

1-ha unfenced clearcut area; a lack of regrowth can 

limit nutrient uptake and lead to prolonged soil N 

leaching and the resultant adverse effects on stream 

water quality.

•	 Selective harvesting of about 5 percent of the basal area 

had little effect on stream-water chemistry or on brooktrout survival. 

•	 The percentage of tree basal area that can be harvested 

without a large release of NO3

-

 and Alim is unknown 

but probably is variable, depending on the amount of 

previous forest disturbance, the acidity of the soil, and 

the history of acid deposition at the site.

Results of this study indicate that brook trout and 

macroinvertebrates in many Catskill streams, particularly 

in the highly acidic Neversink River basin, are likely to be 

adversely affected by clearcutting. Further research is needed 

to define the harvesting threshold below which soil nutrient 

loss is minimized to limit the adverse effects of logging on 

stream-water quality and aquatic biota.

Acknowledgments

The authors thank Tom Suleski, James Anderson, 

Deborah Horan-Ross, Gretchen Wall, and Hannah Ingleston 

for assistance with field work and the staff at the US 

Geological Survey Laboratory in Troy, N.Y. for chemical 

analyses. Financial support for this research was provided by 

the New York City Department of Environmental Protection 

and the US Geological Survey. The Frost Valley YMCA 

owns the land this research was conducted on and Frost 

Valley foresters conducted the forest harvest; their support is 

greatly appreciated. 

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Appendix 1 19

Appendix 1. Selected Photographs of the Dry Creek and 

Shelter Creek Forest Harvesting Study
20 Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City Water Supply

1. The Dry Creek clearcut during October, 1998—18 months after the clearcut was completed.

2. The Dry Creek and Shelter Creek watersheds and the approximate locations of the NS25, SS20, DC57, 

SC40, and SC20 gaging stations.
Appendix 1 21

3. View of the clearcut facing east about halfway up the Dry Creek watershed, fall 1998.

4. View of the clearcut facing east 

just outside the deer fence from the 

southwest corner of the Dry Creek 

watershed, fall 1998.
22 Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City Water Supply

5. Clearcut facing north, fall 1998. 6. Clearcut facing northeast, fall 1998.

7. Clearcut facing northwest, fall 1998.
For additional information write to: 

New York Water Science Center

U.S. Geological Survey

425 Jordan Road 

Troy, NY 12180

Information requests:

(518) 285-5602

or visit our Web site at:

http://ny.water.usgs.gov
McHale and others—Effects of Forest Harvesting on Ecosystem Health in the Headwaters of the New York City 

 Water Supply, Catskill Mountains, New York

—Scientific Investigations Report 2008–5057