Cover. Clockwise from upper left: [1] satellite image of Chesapeake Bay, [2] collection of sediment samples using the USGS 
 

hoverprobe, [3] storm event at the Conowingo Dam, and [4] osprey landing in nest. All photographs courtesy of USGS.
 


Inside Cover. The Minnie T. Phillips was built in Baltimore, Maryland in 1873. At 100 feet and 137 tons, she was primarily engaged in the 
 

coasting trade to the Bahamas. Photograph from Chesapeake Bay Schooners by Snediker and Jensen, 1992.
 

Synthesis of U.S. Geological Survey Science 

for the Chesapeake Bay Ecosystem and 

Implications for Environmental Management 

Scott W. Phillips, Editor 

Chapters written by: 

Scott W. Ator, Vicki S. Blazer, John W. Brakebill, Donald R. Cahoon, 
 

Peter R. Claggett, Thomas M. Cronin, Judith M. Denver, Christine L. Densmore, 
 

Allen C. Gellis, Cliff R. Hupp, Jurate M. Landwehr, Michael J. Langland, 
 

Christopher A. Ottinger, Milan J. Pavich, Matthew C. Perry, Scott W. Phillips, 
 

Stephen D. Preston, Jeff P. Raffensperger, Barnett A. Rattner, Nancy B. Rybicki, 
 

and Debra A. Willard
 


Circular 1316 

U.S. Department of the Interior 

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

DIRK KEMPTHORNE, Secretary 

U.S. Geological Survey 

Mark D. Myers, Director 

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

For product and ordering information:
 


World Wide Web: http://www.usgs.gov/pubprod
 


Telephone: 1-888-ASK-USGS
 


For more information on the USGS—the Federal source for science about the Earth, its natural and living resources, 
 

natural hazards, and the environment:
 


World Wide Web: http://www.usgs.gov
 


Telephone: 1-888-ASK-USGS
 


Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the 
 

U.S. Government. 

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

reproduce any copyrighted materials contained within this report.
 


Suggested citation:
 


Phillips, S.W., ed., 2007, Synthesis of U.S. Geological Survey science for the Chesapeake Bay ecosystem and implica ­


tions for environmental management: U.S. Geological Survey Circular 1316, 63 p.
 


Library of Congress Cataloging-in-Publication Data 

Synthesis of U.S. Geological Survey science for the Chesapeake Bay ecosystem and implications for environmental 

management / Scott W. Phillips, editor.

 p. cm. -- (Circular ; 1316)


 ISBN 978-1-4113-2021-5 (pbk. : alk. paper)


 1. Estuarine ecology--Chesapeake Bay (Md. and Va.) 2. Environmental management--Chesapeake Bay (Md. and Va.) 

3. 	Chesapeake Bay (Md. and Va.)--Environmental conditions. 	I. Phillips, Scott W. II. Geological Survey (U.S.) 

QH104.5.C45S96 2008

 577.7’347--dc22

 2007048562 
Chesapeake Bay Bridge. Photograph by Jane Thomas, IAN Image Library (www.ian.umces.edu/imagelibrary/). 
iv 

Acknowledgments 

The authors wish to thank the USGS scientists, programs, and partners that have collaborated 

on these investigations during 2001–06. USGS scientists who provided significant contributions 

to the investigations include Betty K. Ackerson, Julie M. Baldizar, William S.L. Banks, 

Joel D. Blomquist, John-Karl Böhlke, Eurybiades Busenburg, Owen P. Bricker, John F. Bratton, 

William C. Burton, Virginia Carter, Douglas B. Chambers, Jonathan B. Cohen, Robert Clark, 

Robert D. Darber-Delach, Karen M. Eisenreich, R. Michael Erwin, Michael J. Focazio, Nancy H. 

Golden, Glenn R. Guntenspergen, Richard Hammerschlag, G. Michael Haramis, Jeff S. Hatfield, 

Debra C. Iwanowicz, Luke R. Iwanowicz, David M. Kidwell, Daniel E. Kroes, Elise A. Larsen, 

Curtis E. Larsen, Bruce D. Lindsey, Sarah K. Martucci, Moira A. McKernan, Mark J. Melancon, 

Douglas L. Moyer, Wayne L. Newell, Gregory B. Noe, L. Niel Plummer, Gregory E. Schwarz, 

Edward R. Schenk, Nancy S. Simon, Gary K. Speiran, Kathy Spring, and Daniel B. Stotts. 

The authors are grateful to the USGS programs from all four disciplines (Biology, Geology, Geography, and Water) that provided resources to conduct the investigations and to David P. Russ for 

enhancing collaboration between USGS programs for Chesapeake Bay studies. Additionally, the 

authors wish to thank Susan Russell Robinson, Robin Shrock, and Matthew G. Pajerowski for 

their technical reviews of the report. 

The authors appreciate the collaboration with the following partners to conduct these investigations: U.S. Environmental Protection Agency Chesapeake Bay Program Office, Center of Conservation Biology of the College of William and Mary, Maryland Department of Natural Resources, 

Maryland Geological Survey, Metropolitan Washington Council of Governments, National 

Park Service, University of Maryland, Pennsylvania Department of the Environment, U.S. Army 

Corps of Engineers, U.S. Department of Agriculture, U.S. Fish and Wildlife Service, U.S. Naval 

Research Laboratory, Virginia Department of Environmental Quality, Virginia Department of 

Game and Inland Fisheries, Virginia Institute of Marine Sciences, Washington, D.C., Fisheries 

Division, and the West Virginia Department of Natural Resources. 
Contents 

Chapter 1: Introduction and Overview of Findings 

By Scott W. Phillips..................................................................................................................................................... 2
 


Chapter 2: Human Population Growth and Land-Use Change 

By Peter R. Claggett...................................................................................................................................................10
 


Chapter 3: Factors Affecting the Distribution and Transport of Nutrients 

By John W. Brakebill and Stephen D. Preston ................................................................................................14
 


Chapter 4: Transport of Nitrogen in Ground Water 

By Scott W. Phillips....................................................................................................................................................18
 


Chapter 5: Assessing Changes in Streamflow and Nutrients 

By Jeff P. Raffensperger and Michael J. Langland........................................................................................22
 


Chapter 6: Sources and Transport of Sediment in the Watershed 

By Allen C. Gellis, Cliff R. Hupp, Jurate M. Landwehr, and Milan J. Pavich..........................................28
 


Chapter 7: Sediment Sources and Deposition in the Estuary 

By Thomas M. Cronin................................................................................................................................................32
 


Chapter 8: The Occurrence of Pesticides in the Bay Watershed 

By Judith M. Denver and Scott W. Ator .............................................................................................................36
 


Chapter 9: Contaminant Exposure and Impacts on Waterbirds and 

Selected Wildlife 

By Barnett A. Rattner................................................................................................................................................40
 


Chapter 10: Long-Term Changes in Climate and Water Quality 

By Debra A. Willard ...................................................................................................................................................42
 


Chapter 11: Submerged Aquatic Vegetation and Water Clarity 

By Nancy B. Rybicki and Jurate M. Landwehr................................................................................................46
 


Chapter 12: Factors Affecting Coastal Wetland Loss and Restoration 

By Donald R. Cahoon.................................................................................................................................................50
 


Chapter 13: Factors Affecting Fish Health 

By Vicki S. Blazer, Christopher A. Ottinger, and Christine L. Densmore .................................................54
 


Chapter 14: Changes in Food and Habitats of Waterbirds 

By Matthew C. Perry .................................................................................................................................................60
 

2 Chapter 1:Chapter 1: Introduction and Overview of Findings Introduction and Overview of Findings

By Scott W. Phillips 

The U.S. Geological Survey (USGS), the science agency for the Department of the Interior (DOI), has 

the critical role of providing scientific information that is utilized to document and understand ecosystem condition and change in the Chesapeake Bay and its watershed. The findings are used by resource managers 

and policy makers to assess the effectiveness of restoration actions and adapt improved strategies for the future. 

The Chesapeake Bay, the Nation’s largest estuary, has been affected by human-population increase resulting in 

degraded water quality, loss of habitat, and declines in populations of biological communities. Since the mid1980s, the USGS has been a partner of the Chesapeake Bay Program (CBP), a multi-agency partnership working 

to restore the Bay ecosystem. The CBP created Chesapeake 2000, an agreement that established over 100 restora 

tion commitments to be achieved during 2000–10. The major goals of the agreement are related to: (1) land use, 

(2) water quality, (3) vital habitats, (4) living resources, and (5) stewardship. 

To support the expanded technical needs of the Chesapeake 2000 agreement, the USGS summarized its 

previous research (Phillips, 2002) and interacted with CBP partners to develop science goals for 2001–06: 

•	 Improve watershed and land-use data and analysis. 

•	 Enhance the prediction, monitoring, and understanding of nutrient delivery to the Bay. 

•	 Understand the sources and impact of sediment on water clarity and biota. 

•	 Assess the occurrence of toxic constituents and emerging contaminants. 

•	 Assess the factors affecting the health of fish, waterbirds, and their habitats. 

•	 Disseminate information and develop decision-support tools. 

The purpose of this report is to present a synthesis of the USGS Chesapeake Bay science related to the 

2001–06 goals and provide implications for environmental management (fig. 1.1). The report provides USGS 

findings that address the science needs of the CBP restoration goals and includes summaries of: (1) land-use 

change; (2) water quality in the watershed, including nutrients, sediment, and contaminants; (3) long-term 

changes in estuarine water quality; (4) estuary habitats, focusing on submerged aquatic vegetation (SAV) and 

tidal wetlands; and (5) factors affecting fish and waterbird populations. A summary of the major CBP restoration 

goals and associated USGS scientific findings and their management implications is presented in table 1. 

The USGS is also meeting the future needs of the CBP partners. In 2005, which represented the mid-point 

of the Chesapeake 2000 agreement, there was growing concern at all levels of government and by the public that 

ecological conditions in the Bay and its watershed had not significantly improved. The slow rate of improvement, coupled with the projected human-population increase in the Bay watershed, implied that many desired 

ecological conditions will not be achieved by 2010. The Government Accountability Office (2005) recommended 

that the CBP complete efforts for an integrated assessment approach of ecosystem conditions and developed a 

comprehensive, coordinated implementation strategy. To address these challenges, the CBP partners are writ 

ing a strategic implementation plan (SIP) to more accurately define the degree to which restoration goals can be 

achieved by 2010, and the most effective approach to achieve the goals. The USGS findings and their implications provide critical information that will be used by the CBP partners to prepare the SIP and develop improved 

management strategies. 

Given the evolving needs of the CBP partners, the USGS revised its Chesapeake Bay Science Plan for 

2006–11 (Phillips, 2005) to provide integrated science for effective ecosystem conservation and restoration, 

which are being addressed through four primary themes: 

•	 The causes and consequences of land-use change; 

•	 Factors affecting water quality and quantity; 

•	 Ability of habitat to support fish and bird populations; and 

•	 Synthesis and forecasting to improve ecosystem assessment, conservation, and restoration. 

­

­
Figure 1.1. U.S. Geological Survey conceptual approach for studies of the Chesapeake Bay and its watershed 

during 2001–06 and relation to Chesapeake Bay Program issues. 

3 

The USGS has implemented projects to address each science theme through a combination of monitoring, 

modeling, research, assessment, and synthesis. The USGS is emphasizing an adaptive management approach for 

conducting its projects over the next 5 years so resource managers can use the findings to more effectively imple 

ment, assess, and adapt management actions in different landscape settings (fig. 1.2). The USGS results will: 

•	 Provide an improved understanding of the ecosystem to better target implementation of conservation and 

restoration strategies; 

•	 Assess ecosystem change to help evaluate the effectiveness of management activities; 

•	 Forecast the potential impacts of population growth and climate change; and 

•	 Provide implications and decision-support tools to help policy makers and resource managers adopt 

improved approaches for ecosystem assessment, conservation, and restoration. 

Implementing USGS projects to address the science themes is achieved through collaboration between 

multiple USGS National Programs, Science Centers, and partners (Phillips, 2006). Projects are designed by 

scientists to meet the objectives of the USGS Chesapeake Bay science themes and missions of the collaborating 

USGS National Programs and partners. Appropriate Federal, State, local, and academic CBP partners work with 

USGS to jointly conduct monitoring, modeling, research, and assessment activities associated with each science 

theme. The USGS interacts with resource managers and policy makers to help them make informed decisions for 

conservation and restoration of the Chesapeake Bay and its watershed. 

­
4 

Table 1. Summary of U.S. Geological Survey (USGS) Chesapeake Bay findings and management implications. 

Chapter 1 

55 

Table 1. Summary of U.S. Geological Survey (USGS) Chesapeake Bay findings and management implications.—Continued 

Chapter 1 

6 

Table 1. Summary of U.S. Geological Survey (USGS) Chesapeake Bay findings and management implications.—Continued 

Chapter 1 

Table 1. Summary of U.S. Geological Survey (USGS) Chesapeake Bay findings and management implications.—Continued 

77 Chapter 1 


View looking south along the mouth of the Elk River. In the foreground is recent development. Photograph by 

Jane Thomas, IAN Image Library (www.ian.umces.edu/imagelibrary/). 
8 Chapter 1 


Figure 1.2. Different landscape settings in the Chesapeake Bay watershed (modified from Phillips, 

2005). The movement of nutrients, sediment, and contaminants in the watershed and their delivery 

to the estuary are influenced by the different landscape settings, which have unique combinations 

of physical and biological characteristics. The USGS is providing a better understanding of the 

influence of landscape settings on water quality, habitat, and fish and bird populations to improve 

implementation and assessment of conservation and restoration activities. The USGS will conduct 

the majority of its activities in the watershed because (1) human-population growth and land-use 

change will continue to be the greatest threats to the ecosystem, and (2) the majority of conservation 

and restoration actions will be implemented on land. The USGS will work with partners to relate the 

changes in the watershed to the changes in the Bay and its tidal estuaries. 
References 

Bachman, L.J., Lindsey, B.D., Brakebill, J.W., and Powars, D.S., 1998, Ground-water discharge and base-flow 

nitrate loads of nontidal streams, and their relation to a hydrogeomorphic classification of the Chesapeake Bay 

watershed: U.S. Geological Survey Water-Resources Investigations Report 98–4059, 71 p. 

Government Accountability Office, 2005, Chesapeake Bay Program: Improved strategies are needed to better 

assess, report, and manage restoration progress: Washington, D.C., Government Accountability Office 

Report 06–96, 88 p. 

Phillips, S.W., ed., 2002, The U.S. Geological Survey and the Chesapeake Bay—The role of science in environmental restoration: U.S. Geological Survey Circular 1220, 32 p. 

Phillips, S.W., 2005, The U.S. Geological Survey Chesapeake Bay science plan, 2006–2011: U.S. Geological 

Survey Open-File Report 2005–1440, 53 p. 

Phillips, S.W., 2006, U.S. Geological Survey Chesapeake Bay Studies: Scientific solutions for a healthy bay and 

watershed: U.S. Geological Survey Fact Sheet 2006–3046, 4 p. 

Woods, A.J., Omernik, J.O., and Brown, D.D., 1999, Level III and IV ecoregions of Delaware, Maryland, 

Pennsylvania, Virginia, and West Virginia: U.S. Environmental Protection Agency, National Health and 

Environmental Effects Laboratory, 24 p. 

9 Chapter 1 

Grassed waterways are an agricultural best management practice that helps slow down the flow of runoff 

and absorb nutrients before they reach streams or ground water. Photograph by Jane Thomas, IAN Image 

Library (www.ian.umces.edu/imagelibrary/) 
10 Chapter 2:Chapter 2: Human Population Growth and Land-Use Change Human Population Growth and Land-Use Change

By Peter R. Claggett 

Human activities and their associated impact on the landscape have significantly affected the condition of 

the Chesapeake Bay and its watershed. The Bay watershed is one of the most populous coastal estuaries in the United States and over the past 20 years has experienced the largest increase in population compared to 

all other coastal watersheds in the United States (Crossett and others, 2004). The population of the Chesapeake 

Bay watershed grew from 8.1 million in 1950 to almost 16 million in 2000, greatly expanding urban and suburban areas. To help address the impacts of population growth, the Chesapeake 2000 agreement includes a goal to 

“develop, promote, and achieve sound land-use practices which protect and restore watershed resources, maintain 

reduced pollutant loadings for the Bay and its tributaries, and restore and preserve aquatic living resources.” Two 

specific restoration commitments for this goal include (1) by 2012, reduce the rate of urban sprawl by 30 percent, 

and (2) permanently preserve from development 20 percent of the land area in the watershed by 2010. To support 

these commitments, the USGS established a related goal during 2001–06 to improve watershed and land-use data 

and analysis. This chapter synthesizes the USGS findings about the rate of urban sprawl in the watershed and 

outcomes from a vulnerability assessment. 

The USGS cooperated with the CBP partners to quantify the rate of urban land change as an approach to 

quantify the rate of urban sprawl. The USGS had previously conducted analysis that documented the increase 

of urban land use in the Baltimore-Washington area over the past 200 years and provided future projections 

(Acevedo, 1999). The USGS worked with the CBP partners to evaluate different methods to characterize urban 

sprawl and determined that impervious surface change would provide the best surrogate to track the rate of urban 

development. Analysis of land-cover information produced by the University of Maryland’s Regional Earth Science Application Center (Goetz and others, 2004) revealed that during the 1990s, the expansion of suburban areas 

was a major contributing factor to a 41-percent increase in impervious surface in the Bay watershed compared 

to an 8-percent increase in population (U.S. Environmental Protection Agency, 2004). Some of the contributing 

factors to the dispersed pattern of growth were consumer preferences for houses on large lots and commercial 

preferences for less expensive office and retail space. Further USGS analysis of satellite imagery and road data 

indicates that impervious surfaces compose about 18 percent of all urban lands in the Bay watershed. The majority of impervious surfaces results from the construction of roads, buildings, and parking lots; driveways, sidewalks, and other sources typically make up less than 20 percent of the impervious surfaces in a watershed (Tilley 

and Slonecker, 2006). 

The environmental consequences of impervious surfaces include increased water runoff from the land 

leading to higher peak streamflows, increased streambank and bed erosion, and downstream flooding (Konrad, 

2003). Impervious surfaces also cause more rapid delivery of nutrients, sediment, and contaminants from 

the land to streams by routing runoff directly into streams and bypassing the filtration and retention services 

provided by wetlands and riparian forest buffers. Biological and chemical impairment of streams can occur 

when the proportion of impervious surfaces in a watershed exceeds 5 to 6 percent (Couch and Hamilton, 2002). 

The dispersed development patterns in the Bay watershed have resulted in a loss of forests and agricultural 

lands, which typically provide a combination of water quality, wildlife, and aesthetic benefits. State and local 

governments are using the data on development patterns to focus land conservation and restoration activities to 

reduce runoff and to develop policies that reduce the impacts of impervious surfaces. 

State population projections indicate that population increases in suburban and exurban counties will continue to occur. Over the past 30 years, the population of the Bay watershed increased by over 1 million persons 

per decade, and if these trends continue through the year 2030, the area of developed land will increase by more 

than 60 percent (Boesch and Greer, 2003). As part the CBP Resource Lands Assessment (RLA), which was 

developed to help identify lands for preservation, the USGS conducted a vulnerability assessment (Claggett and 

Bisland, 2004). The vulnerability assessment evaluated the relative potential risk of future land conversion to 

urban areas by 2010 based on proximity to the urban growth areas of the 1990s (fig. 2.1). The findings from the 

assessment imply that land-use change will continue to impact valuable lands and habitats in the Bay watershed. 

The vulnerability assessment is useful for evaluating development patterns and has been used by State resource 

agencies, together with other information, to more strategically prioritize lands for protection. The USGS also 

began to develop approaches to link different land-use change models with the CBP watershed model to predict 
11 

nutrient and sediment loads through the year 2030. The USGS will develop a Chesapeake Bay Land Change 

Model that will also be a prototype for a National Land Change Community Modeling system. The predictions 

of nutrient and sediment loads for the period 2010–30 will be used to formulate additional strategies needed to 

improve the Bay ecosystem. 

Figure 2.1. Potential urban land growth in the Chesapeake Bay watershed by 2010 

(modified from Claggett and Bisland, 2004). The USGS conducted a vulnerability 

assessment to predict the risk of conversion of high value lands to urban areas by 2010. 

The results are being used to better target land acquisition and conservation programs. 
Chapter 2 

12 

View of the Patapsco River, Baltimore, including oil tank farms and the Patapsco Wastewater 

Treatment Plant. Curtis Creek is in the background. Photograph by Jane Thomas, IAN Image 

Library (www.ian.umces.edu/imagelibrary/). 

Great Blue Heron fishes alongside road runoff culverts in Easton, Maryland. Photograph by Jane 

Hawkey, IAN Image Library (www.ian.umces.edu/imagelibrary/). 
References 

Acevedo, W., 1999, Analyzing land-use change in urban environments: U.S. Geological Survey Fact 

Sheet 188–99, 4 p. 

Boesch, D.R., and Greer, J., (eds.), 2003, Chesapeake futures, choices for the 21st Century: Edgewater, Mary 

land, Scientific and Technical Advisory Committee publication no. 03–001, Chesapeake Research Consortium, 

160 p. 

Claggett, P.R., and Bisland, C., 2004, Assessing the vulnerability of forests and farmlands to development in the 

Chesapeake Bay Watershed, in Proceedings of the IASTED International Conference on Environmental Modeling and Simulation, November 22–24, 2004, St. Thomas, U.S. Virgin Islands. 

Couch, C., and Hamilton, P., 2002, Effects of urbanization on stream ecosystems: U.S. Geological Survey Fact 

Sheet 042–02, 2 p. 

Crossett, K.M., Culliton, T.J., Wiley, P., and Goodspeed, T.R., 2004, Population trends along the Coastal United 

States, 1980–2008: Silver Spring, Maryland, National Oceanic and Atmospheric Administration, National 

Ocean Service, 47 p. 

Goetz, S.J., Jantz, C.A., Prince, S.D., Smith, A.J., Varlyguin, D., and Wright, R.K., 2004, Integrated analysis 

of ecosystem interactions with land use change: the Chesapeake Bay watershed, pages 263–275 in DeFries, 

R.S., Asner, G.P., and Houghton, R.A., eds., Ecosystems and land use change: Washington, D.C., American 

Geophysical Union, Geophysical Monograph Series. 

Konrad, C.P., 2003, Effects of urban development on floods: U.S. Geological Survey Fact Sheet 076–03, 4 p. 

Tilley, J., and Slonecker, T., 2006, Quantifying the components of impervious surfaces: U.S. Geological Survey 

Open-File Report 2007–1008, 40 p. 

U.S. Environmental Protection Agency Chesapeake Bay Program, 2004, Resource lands assessment, October 

2005: Annapolis, Maryland, [variously paged]. 

­

13 Chapter 2 
Chapter 3:Chapter 3: Factors Affecting the Distribution and Factors Affecting the Distribution and 

Transport of Nutrients ransport of Nutrients

14 

By John W. Brakebill and Stephen D. Preston 

I

n the Chesapeake 2000 agreement, the goal for water quality is to “achieve and maintain the water 

quality necessary to support aquatic living resources of the Bay and its tributaries and to protect human 

health.” Related to this goal is a commitment to correct nutrient- and sediment-related problems in the Bay and 

its tributaries in order to remove the Bay from the impaired waters list by 2010. This chapter summarizes USGS 

efforts to better understand the distribution and transport of nutrients using a watershed modeling application, 

known as SPAtially Referenced Regressions On Watershed attributes (SPARROW). 

SPARROW models use a nonlinear regression approach to define relations among nutrient sources, 

stream nutrient loads, and the environmental factors that potentially affect nutrient transport (Smith and others, 

1997; Schwarz and others, 2006). Results from the SPARROW models provide (1) a statistical basis for 

estimating stream nutrient loads in unmonitored locations, and (2) the statistical significance of nutrient sources, 

environmental factors, and transport processes in explaining predicted nutrient loads. 

The distribution and transport of nutrient sources in the Chesapeake Bay watershed have been evaluated 

by the USGS using the SPARROW methodology. Models of total nitrogen and total phosphorus were developed for the Chesapeake Bay watershed, estimating water-quality conditions for three snapshots in time: the 

late 1980s-Version 1.0 (Preston and Brakebill, 1999; Brakebill and Preston, 1999), the early 1990s-Version 2.0 

(Brakebill and others, 2001), and the late 1990s-Version 3.0 (Brakebill and Preston, 2004). Spatial data representing nutrient source quantities for each specified time period were compiled and include: atmospheric deposition, 

point-source locations, septic systems (Version 2.0 only), land use, land cover, and agricultural sources including 

commercial fertilizer and manure applications. Environmental characteristics datasets representing factors that 

affect the transport of nutrients (land-to-water delivery) also were compiled. 

The fate and transport of nitrogen within a drainage catchment are influenced by watershed characteristics 

(such as slope, lithology, and geologic structure) and processes within the stream channel. Soil permeability 

(Version 1.0) and area within the Coastal Plain Physiographic Province (Versions 2.0 and 3.0) were identified in 

the SPARROW models as statistically significant watershed characteristics that affect the transport of nitrogen 

to streams. These factors may reflect the potential for nitrogen to flow through ground-water pathways that are 

slower and provide more potential for loss through denitrification (Brakebill and Preston, 2004). Additionally, 

the effect of in-stream loss processes, represented as a function of stream traveltime based on various streamflow 

classes and the presence of reservoirs, is a significant factor affecting the transport of nitrogen in streams 

(Brakebill and Preston, 2004; Preston and Brakebill, 1999). Smaller streams (those less than 200 cfs, or cubic 

feet per second), tend to have higher nitrogen loss than larger streams—those greater than 1,000 cfs. Smaller, 

shallower streams have more contact with bottom sediments and have a greater potential for total nitrogen loss 

due to biological processing and denitrification. 

Resource managers have identified three nutrient sources—point sources, agriculture, and urban lands— 

as high priorities for nutrient-reduction actions. The spatial distribution of the amount of nitrogen delivered 

(expressed as yield) from each major source as it is transported to the Chesapeake Bay estuary is shown in 

figure 3.1. This information is being used to identify geographic areas where management actions designed to 

reduce nitrogen to the estuary should be implemented. The USGS also has provided the SPARROW model results 

for each of the tributary strategy basins, which are the geographic areas with specific nutrient and reduction 

goals, so resource managers can identify local areas with the highest delivery of nutrients to local streams and 

the estuary. An example of the SPARROW model results for the Shenandoah Valley tributary strategy basin is 

shown in figure 3.2. The amount of nitrogen that is generated locally and transported to streams (“incremental 

yield”) is shown in figure 3.2A, and the amount of nitrogen that is generated locally and would be transported 

to the estuary (“delivered yield”) is shown in figure 3.2B. The maps can be used together to better define areas 

where management actions may improve water quality both in local streams and the estuary. Information from 

the SPARROW models was also used to refine the segmentation for the CBP Phase V watershed model (Martucci 

and others, 2005), and to help design the CBP nontidal water-quality network (Brakebill and Preston, 2003). 

Results from the network for nutrient and sediment trends are provided in Chapter 5. 
15 

Figure 3.1. Distribution of nitrogen yields delivered to Chesapeake Bay from (A) point sources, (B) agricultural sources, 

and (C) urban lands (modified from Brakebill and Preston, 2004). The USGS developed watershed models (SPARROW 

models) that provide a finer resolution of nutrient sources and their transport to streams and to the estuary. The 

SPARROW model results are being used to identify priority areas for implementing management actions. 

The Cambridge wastewater treatment plant, with downtown Cambridge in the background 

and the Choptank River Bridge on the right. Photograph by Jane Thomas, IAN Image Library 

(www.ian.umces.edu/imagelibrary/). 
Figure 3.2. Distribution of total nitrogen yield in the Shenandoah Valley tributary strategy basin. (A) Incremental yield 

of total nitrogen is the amount generated in a local watershed and transported to a stream reach, and (B) delivered yield 

of total nitrogen is the amount that is generated in a local watershed and is reduced by instream loss as it is transported 

to the Bay. The results are being used to further delineate areas where management actions can benefit both the 

estuary and local water quality. 

16 Chapter 3
 


View of Harpers Ferry, West Virginia at the confluence of the Shenandoah and Potomac Rivers. 

Photograph by U.S. Geological Survey. 
References 

Brakebill, J.W., and Preston, S.D., 1999, Digital data used to relate nutrient inputs to water quality in the Chesapeake Bay watershed, Version 1.0: U.S. Geological Survey Open-File Report 99–60, [variously paged]. 

Brakebill, J.W., and Preston, S.D., 2003, A digital hydrologic network supporting spatially referenced regression modeling in the Chesapeake Bay watershed, in Proceedings of the U.S. Environmental Protection Agency 

EMAP Symposium 2001: Coastal Monitoring Through Partnerships, Environmental Monitoring and Assessment, April 24–27, 2001, Pensacola, Florida, [81:1–3] 73–84, 403 p. 

Brakebill, J.W., and Preston, S.D., 2004, Digital data used to relate nutrient inputs to water quality in the Chesapeake Bay watershed, Version 3.0: U.S. Geological Survey Open-File Report 2004–1433, [variously paged]. 

Brakebill, J.W., Preston, S.D., and Martucci, S.K., 2001, Digital data used to relate nutrient inputs to water quality in the Chesapeake Bay, Version 2.0: U.S. Geological Survey Open-File Report 01–251, [variously paged]. 

Martucci, S.K., Krstolic, J.L., Raffensperger, J.P., and Hopkins, K.J., 2005, Development of land segmentation, 

stream-reach network, and watersheds in support of Hydrological Simulation Program–Fortran (HSPF) modeling, Chesapeake Bay watershed, and adjacent parts of Maryland, Delaware, and Virginia: U.S. Geological 

Survey Scientific Investigations Report 2005–5073, 15 p. 

Preston, S.D., and Brakebill, J.W., 1999, Applications of spatially referenced regression modeling for the evaluation of total nitrogen loading in the Chesapeake Bay watershed: U.S. Geological Survey Water-Resources 

Investigations Report 99–4054, 12 p. 

Smith, R.A., Schwarz, G.E., and Alexander, R.B., 1997, Regional interpretation of water-quality monitoring data: 

Water Resources Research, v. 33, no. 12, p. 2,781–2,798. 

Schwarz, G.E., Hoos, A.B., Alexander, R.B., and Smith, R.A., 2006, The SPARROW water-quality model: 

Theory, applications, and user documentation: U.S. Geological Survey Techniques and Methods 6B3, 248 p., 

CD-ROM. 

17 Chapter 3 
18 Chapter 4:Chapter 4: Transport of Nitrogen in Ground W ransport of Nitrogen in Ground Water

By Scott W. Phillips 

The hydrologic pathways for nutrients have important implications for the lag time between implementing management actions and detecting water-quality changes in surface water. Previous USGS studies 

documented that on average, just over 50 percent of the total volume of water in streams is from ground water, 

with a range of 16 to 92 percent for different streams (Bachman and others, 1998). Estimates of the amount of 

nitrogen delivered to a stream through ground water range from 17 to 80 percent, with an average of 48 percent 

(Bachman and others, 1998). Additional analysis by Sprague and others (2000) found similar percentages (15 to 

65) of total nitrogen in streams from nitrate contributed through ground water. This chapter summarizes USGS 

findings about the factors affecting the occurrence and residence time of nitrogen in ground water and its discharge to streams. 

The presence of nitrogen in ground water, which occurs mostly as nitrate, is related primarily to nutrient 

application in different land-cover settings and natural factors including rock type and denitrification that also 

influence the amount of nitrate occurring in ground water and its discharge to streams (Lindsey and others, 2003). 

Previous USGS studies determined that the average concentration of nitrate in ground water under different types 

of land cover ranged from about 5.0 mg/L (milligrams per liter) in agricultural areas, to 2.0 mg/L in urban areas, 

and less than 0.1 mg/L in forested areas (Ator and Ferrari, 1997). Results from USGS collaboration with USEPA 

to assess ground-water vulnerability to nitrogen (Greene and others, 2005) also were used to assess the spatial 

distribution of nitrate in ground water. The probability of nitrate concentrations exceeding 3 mg/L in the MidAtlantic area is shown in figure 4.1. The probability of nitrate exceeding 3 mg/L is greatest in parts of the Coastal 

Plain, in the northern part of the Piedmont Physiographic Province, and in the carbonate rocks of the Valley and 

Ridge. This information is useful for resource managers to better understand where ground-water discharge will 

more likely affect water-quality change in streams in response to management actions. 

Once nitrate is in ground water, denitrification can be an important process in controlling the amount of 

nitrogen discharging to streams in some areas of the Bay watershed. In the Coastal Plain, areas with the highest 

potential denitrification correspond to poorly drained, impermeable soils with abundant organic matter (Ator and 

others, 2000, 2005). In much of the non-Coastal Plain areas of the watershed, Peper and others (2001) identified 

near-surface rock formations that contain high amounts of carbon and sulfur that promote denitrification. To 

better understand the relation between rock type and denitrification, the USGS studied four small watersheds 

in the major rock types within the Bay basin (Lindsey and others, 2003). Results from this study revealed that 

denitrification was occurring in the watersheds underlain by unconsolidated rocks (Coastal Plain) and sandstone, 

shale, and siltstone of the Valley and Ridge, but was not as common in crystalline (Piedmont) or carbonate rocks 

(Valley and Ridge). Further, the denitrification was significant in ground water with residence times greater 

than 20 years, but younger, more locally recharged water was not greatly affected by denitrification (Lindsey 

and others, 2003). Therefore, the influence of denitrification varies greatly throughout the watershed and has 

implications for management actions. In areas where denitrification is occurring in ground water, resource 

managers may focus actions to reduce nitrogen in overland runoff from reaching streams. 

The age of waters being delivered to a stream will be influenced by the relative contribution of surface 

runoff, soil water, and ground water. Runoff and soil water both have very young ages (hours to months, respectively) and supply, on average, about half of the water to a stream (Phillips and Lindsey, 2003) (fig. 4.2). The 

remainder of the water supplied to a stream moves through the ground-water system and has a range of modern 

to over 50 years, with a median age of 10 years. The overall result is that about half of the water entering a typical stream in the Bay watershed can be considered modern, and about 90 percent is less than 15 years old. The 

relative contribution of surface water, soil water, and ground water will influence the response of the stream to 

changes in nutrient sources and management actions in a watershed. 

The USGS prepared a ground-water model of the East Mahantango Creek watershed, a predominantly 

agricultural basin underlain by fractured rock, to predict the change in nitrate concentration in a stream over time 

(Lindsey and others, 2003). The model used information on the amount of nitrogen applied to the land surface 

over time in the basin, assumed a ground-water age of about 10 years, and estimated a response of the base-flow 

(the amount from ground water) nitrate concentrations in a stream (fig. 4.3). The model results indicate that 

the base-flow nitrate concentration of the stream increased during the last several decades (curve a in fig. 4.3) 

because of increases in the concentrations discharging from ground water. The increase in nitrogen sources used 
19

Figure 4.1 The probability of nitrate concentrations in ground water exceeding 3 miligrams per liter in 

the Mid-Atlantic region (modified from Greene and others, 2005). Having an understanding of nitrogen 

concentrations in ground water helps managers consider different options for implementing management 

actions to reduce nutrients to streams and the estuary.
Chapter 4 

20 

Figure 4.2. Distribution of ages from runoff, soil 

water, and ground water entering a typical stream 

in the Bay watershed (from Phillips and Lindsey, 

2003). About 50 percent of the water contributed to 

streams is modern, with 90 percent of water moving 

to a stream in less than 15 years. The hydrologic 

pathways of nutrients in the watershed (surface 

water or ground water) will influence the lag time 

between implementing a management action and 

seeing a water-quality response. Watersheds with 

a higher percentage of the nitrogen transported 

through surface-water runoff will have more rapid 

improvements in water quality than those with a 

higher portion of nitrogen in ground water. 

in the model is typical of many agricultural regions within the Chesapeake Bay watershed. Two future scenarios 

were examined with the model: (1) continuation of nitrogen applications at current levels, and (2) elimination of 

all nitrogen applications. The scenario with nitrogen applications at current levels results in a continued increase 

in concentration of base-flow nitrate in the stream over the next several decades (curve b in fig. 4.3). The scenario 

with complete elimination of nitrogen applications shows that a 50-percent reduction in nitrate base-flow concentrations could occur in the first 5 years, with a decrease likely to continue until 2040 (curve c in fig. 4.3). Baseflow nitrate concentrations over time in many streams in the Chesapeake Bay watershed likely will be bounded 

by these two scenarios depending on the amount of nonpoint-source reductions and the relative contribution 

and age of surface and ground water to a stream. The relative contribution of flows to a stream and their respective ages will influence the lag time between implementation of management actions and improvement in water 

quality. Streams with a higher portion of surface water and young ground water will have more rapid improvement than streams with higher proportions of ground water of older ages. Knowledge of these differences at local 

scales can be used to help choose the types of management actions needed and better assess their effectiveness. 

Figure 4.3. Predicted 

nitrate concentrations 

of base flow to a stream 

in the East Mahantango 

Creek watershed in 

Pennsylvania (from Phillips 

and Lindsey, 2003). A model 

was used to predict the 

stream concentrations 

based on nitrogen-source 

reductions and the influence 

of ground water in an 

agricultural watershed. 

The model results indicate 

that the base-flow nitrate 

concentration of the stream 

increased during the last several decades (curve a) because of increases in the concentrations discharging from 

ground water that are related to increases in nitrogen sources. Two future scenarios were examined with the model: 

(1) continuation of nitrogen applications at current levels, and (2) elimination of all nitrogen applications. Scenario 

(1) results in a continued increase in concentration of base-flow nitrate in the stream over the next several decades 

(curve b), while scenario (2) shows that a 50-percent reduction in nitrate base-flow concentrations could occur in about 

5 years, with a decrease likely to continue until 2040 (curve c). Base-flow nitrate concentrations over time in many 

streams in the Chesapeake Bay watershed likely will be bounded by these two scenarios. 
References 

Ator, S.W., Denver, J.M., and Hancock, T.C., 2000, Relating shallow ground-water quality to surfical hydrogeol 

ogy in the Mid-Atlantic Coastal Plain, in Proceedings of the National Water-Quality Monitoring Conference, 

April 25–27, 2000, Austin, Texas, p. 409–423. 

Ator, S.W., Denver, J.M., Krantz, D.E., Newell, W.L., and Martucci, S.K., 2005, A surficial hydrogeologic frame 

work for the Mid-Atlantic Coastal Plain: U.S. Geological Survey Professional Paper 1680, 44 p., 4 pls. 

Ator, S.W., and Ferrari, M.J., 1997, Nitrate and selected pesticides in ground water of the Mid-Atlantic Region: 

U.S. Geological Survey Water-Resources Investigations Report 97–4139, 8 p. 

Bachman, L.J., Lindsey, B.D., Brakebill, J.W., and Powars, D.S., 1998, Ground-water discharge and base-flow 

nitrate loads of nontidal streams, and their relation to a hydrogeomorphic classification of the Chesapeake Bay 

watershed: U.S. Geological Survey Water-Resources Investigations Report 98–4059, 71 p. 

Greene, E.A., LaMotte, A.E., and Cullinan, K.A., 2005, Ground-water vulnerability to nitrate contamination 

at multiple thresholds in the Mid-Atlantic Region using spatial probability models: U.S. Geological Survey 

Scientific Investigations Report 2004–5118, 24 p. 

Lindsey, B.D., Phillips, S.W., Donnelly, C.A., Speiran, G.K., Plummer, L.N., Böhlke, J.K., Focazio, M.J., Burton, 

W.C., and Busenberg, E., 2003, Residence times and nitrate transport in ground water discharging to streams in 

the Chesapeake Bay watershed: U.S. Geological Survey Water-Resources Investigations Report 03–4035, 

202 p. 

Peper, J.D., McCartan, L.B., Horton, J.W., Jr., and Reddy, J.E., 2001, Preliminary lithogeochemical map show 

ing near-surface rock types in the Chesapeake Bay watershed, Virginia and Maryland: U.S. Geological Survey 

Open-File Report 01–187, Version 1.0, available online at http://pubs.usgs.gov/of/2001/of01-187/ 

Phillips, S.W., and Lindsey, B.D., 2003, The influence of ground water on nitrogen delivery to the Chesapeake 

Bay: U.S. Geological Survey Fact Sheet FS-091-03, 6 p. 

Sprague, L.A., Langland, M.J., Yochum, S.E., Edwards, R.E., Blomquist, J.D., Phillips, S.W., Shenk, G.W., 

and Preston, S.D., 2000, Factors affecting nutrient trends in major rivers of the Chesapeake Bay watershed: 

U.S. Geological Survey Water-Resources Investigations Report 00–4218, 108 p. 

­

­

­

21 Chapter 4 
22 Chapter 5:Chapter 5: Assessing Changes in Streamflow and Nutrients Assessing Changes in Streamflow and Nutrients

By Jeff P. Raffensperger and Michael J. Langland 

Monitoring and assessing streamflow and nutrient concentrations in the watershed provide critical information toward evaluating the progress of management actions to reduce nutrient and sediment loads 

in the watershed and their delivery to the estuary. This chapter summarizes USGS findings related to change in 

streamflow and nutrients in the watershed and the factors affecting water-quality change. 

Streamflow and water-quality monitoring in the watershed is conducted using three primary networks—the 

USGS stream-gaging network, the River-Input Monitoring (RIM) Program, and the CBP nontidal water-quality 

network. The stream-gaging network has multiple partners and purposes—computation of total river flow to 

the Bay and support of water-quality monitoring are the two primary applications for Chesapeake Bay studies. 

The USGS, in partnership with the Maryland Department of Natural Resources and the Virginia Department of 

Environmental Quality, began comprehensive water-quality monitoring in the 1980s through the RIM Program 

to estimate nutrient loads from the watershed to the estuary and assess concentration change over time. The RIM 

sites are at the head-of-tide on the nine major tributaries entering the Chesapeake Bay and collectively monitor 

approximately 80 percent of the Bay watershed (fig. 5.1). In 2004, the USGS partnered with USEPA and the six 

states in the watershed to establish the CBP Nontidal Water-Quality Network (fig. 5.1). The primary goal of the 

network is to identify the status and trends in water-quality conditions to help assess progress of the CBP tributary strategies to reduce nutrients and sediment to meet water-quality criteria in the estuary (U.S. Environmental 

Protection Agency, 2003). The partners in the network are using compatible sampling and analysis protocols to 

collect nutrient and sediment samples over a range of flow conditions at existing USGS stream-gaging sites. As 

of 2006, about one-third of the 200 proposed sites for the network had been fully implemented. 

The USGS has developed (Cohn and others, 1989; Hirsch and others, 1991; Helsel and Hirsch, 1992) and 

enhanced techniques (Langland and others, 2000, 2004, 2006) to better document changes in streamflow and 

nutrient concentrations over time. The water-quality changes are affected by the natural variability in streamflow 

and the changes in nutrient sources over time. The natural variability in streamflow (fig. 5.2) has greatly impacted 

the transport of nutrients and sediment through the watershed and their delivery to the Bay (Langland and 

others, 2006). Between 1940 and 1959, the majority of annual river flow to the Bay was within the normal range 

(defined as the 25th to 75th percentile). A dry period occurred during the 1960s, followed by wetter conditions 

in the 1970s. The 15 years between 1990 and 2004 exhibited extreme variability. Since 1990, the annual nitrogen 

loads computed for the RIM stations have varied from 100 to over 350 million pounds with additional amounts 

of nitrogen being contributed from point sources and runoff from the areas not monitored at these stations 

(Langland and others, 2006). The combination of wetter conditions in the 1970s, along with increased nutrients 

and sediment from human activities, were two primary factors that caused the decline in water quality in the 

estuary that is still evident (Phillips and others, 2002). The findings indicate that even with reductions in nutrient 

and sediment concentrations, natural variability in streamflow will greatly influence the seasonal and annual 

delivery of loads to the estuary and influence its water quality. The CBP partners use a 3-year average of estuary 

water-quality data to assess attainment of water-quality standards to help address the influence of streamflow 

variability and loads on estuary water quality. The partners may also need to emphasize specific management 

actions to more effectively reduce nutrient and sediment loads from high-flow events. The flow-adjusted trend for 

a site is also estimated as a continuous percent change over time. Examples from three different sites are shown 

in figure 5.3. The pattern of change over time at a site can be used to further assess the influences of population 

growth and management actions in a watershed. Some watersheds continue to show downward trends in nutrients 

and sediment due to management actions, whereas other sites are starting to show increasing concentrations of 

nutrients and sediment due to continued population growth. 
23

Figure 5.1. Monitoring sites of the Chesapeake Bay Program (CBP) Nontidal Water-Quality Network and River-Input 

monitoring sites. The USGS worked with the USEPA and the six states in the Bay watershed to establish the CBP 

Nontidal Water-Quality Network. Data from the network are used to document water-quality change that is related to 

land use, implementation of management actions, and climate variability. 
Chapter 5 

24 

Figure 5.2. Annual total streamflow into the Chesapeake Bay, water years 1938–2006. Streamflow variability has 

increased since 1970 and has a large influence on the annual nutrient and sediment loads delivered to the Bay. 

Documenting the variability helps explain and forecast water-quality and ecological conditions in the estuary. 

The USGS uses another approach, known as flow-adjusted trends, to provide an estimate of changes in 

nutrients due to human activities in the Bay watershed. This technique removes the influences associated with 

streamflow and seasonal variability to better estimate changes due to human activities. At sites where monitoring 

has been conducted since at least 1990, significant decreasing trends were detected at 72 percent of sites for total 

nitrogen (fig. 5.4), 81 percent of the sites for total phosphorous, and 43 percent of the sites for sediment (Langland and others, 2006). These results indicate that management actions are reducing the concentration of nutrients 

and sediment in parts of the watershed. 

There are multiple factors affecting the occurrence and change of nutrients over time including the natural 

variability in streamflow, changes in nutrient sources and land use, influence of ground water, and implementation of management actions (Sprague and others, 2000; Phillips and others, 2006). More recent USGS analysis 

further documented the effect that the predominant land use and changes in land-use activities over time have 

on nutrient concentrations and trends throughout the Chesapeake Bay watershed between 1985 and 2005. Mean 

concentrations of total nitrogen and total phosphorus in stream water were highest in agricultural and urbanized basins, whereas lower concentrations occurred in streams draining areas dominated by forests, wetlands, 

and grasslands. Reductions in point-source loads of nitrogen and phosphorous, through the phosphate detergent 

ban and wastewater treatment plant improvements, contributed to improving water quality in some areas of 

the Bay watershed. In other areas, however, increasing urban or suburban population and other factors resulted 

in increased point-source loads and increasing trends of nutrients at some sites. Changes in nonpoint sources, 

including land-use changes, implementation of nutrient management plans, and changes in fertilizer and manure 

application rate, were also factors affecting nutrient loads and trends in surface water throughout the Bay watershed. The implication of these findings is that reducing nutrient and sediment loads to meet the water-quality 

criteria in the Bay by 2010 will not be achieved. The USEPA has used these findings, and other information on 

the rate of implementation of management actions, to revise the expectations for load reductions that will likely 

occur by 2010. 
25

Figure 5.3. Examples of continuous flow-adjusted trend plots. The patterns of change over time at sites can be used 

to further assess the influences of population growth and management actions in a watershed. Some watersheds 

continue to show downward trends in nutrients and sediment due to management actions, whereas other sites are 

starting to show increasing concentrations of nutrients and sediment due to continued population growth.

Chapter 5
26 Chapter 5 


Figure 5.4. Change in flow-adjusted trends for total nitrogen in the Chesapeake Bay watershed (modified from 

Langland and others, 2006). There has been a decrease in nitrogen and phosphorus at a majority of sites in the 

watershed. However, concentrations are not decreasing at a rate that would reduce the nutrient loads sufficiently to 

remove the Bay from the impaired waters list by 2010. 
References 

Cohn, T.A., Delong, L.L., Gilroy, E.J., Hirsch, R.M., and Wells, D.K., 1989, Estimating constituent loads: 

Water Resources Research, v. 25, no. 5, p. 937–942. 

Helsel, D.R., and Hirsch, R.M., 1992, Statistical methods in water resources: Amsterdam, Elsevier Science 

Publishers, Studies in Environmental Science, v. 49, 522 p. 

Hirsch, R.M., Alexander, R.B., and Smith, R.A., 1991, Selection of methods for the detection and estimation of 

trends in water quality: Water Resources Research, v. 27, no. 5, p. 803–813. 

Langland, M.J., Blomquist, J.D., Sprague, L.A., and Edwards, R.E., 2000, Trends and status of flow, nutrients, 

and sediments for selected nontidal sites in the Chesapeake Bay watershed, 1985–98: U.S. Geological Survey 

Open-File Report 99–451, 46 p. 

Langland, M.J., Phillips, S.W., Raffensperger, J.P., and Moyer, D.L., 2004, Changes in streamflow and 

water quality in selected nontidal sites in the Chesapeake Bay Basin, 1985–2003: U.S. Geological Survey 

Scientific Investigations Report 2004–5259, 50 p. 

Langland, M.J., Raffensperger, J.P., Moyer, D.L., Landwehr, J.M., and Schwarz, G.E., 2006, Changes in streamflow and water quality in selected nontidal basins in the Chesapeake Bay watershed, 1985–2004: U.S. Geo

logical Survey Scientific Investigations Report 2006–5178, 75 p., 1 CD. 

Phillips, S.W., (ed.), 2002, The U.S. Geological Survey and the Chesapeake Bay—The role of science in environmental restoration: U.S. Geological Survey Circular 1220, 32 p. 

Phillips, S.W., Lindsey, B.D., Preston, S.D., Brakebill, J.W., Raffensperger, J.P., and Shedlock, R.J., 2006, 

The influence of ground water and watershed processes on nutrient delivery to the Chesapeake Bay: [abs.] 

in Proceedings of the Joint Assembly, May 26–30, 2006, Baltimore, Maryland. 

Sprague, L.A., Langland, M.J., Yochum, S.E., Edwards, R.E., Blomquist, J.D., Phillips, S.W., Shenk, G.W., 

and Preston, S.D., 2000, Factors affecting nutrient trends in major rivers of the Chesapeake Bay watershed: 

U.S. Geological Survey Water-Resources Investigations Report 00–4218, 109 p. 

U.S. Environmental Protection Agency, 2003, Ambient water-quality criteria for dissolved oxygen, water clarity, 

and chlorophyll-a for Chesapeake Bay and its tidal tributaries: Annapolis, Maryland, U.S. Environmental 

Protection Agency Report 903-R-03-002. 

­

27 Chapter 5 
28 Chapter 6:Chapter 6: Sources and T Sources and Transport of Sediment in the W ransport of Sediment in the Watershedatershed

By Allen C. Gellis, Cliff R. Hupp, Jurate M. Landwehr, and Milan J. Pavich 

Sediment has an adverse impact on the health of streams in the Bay watershed, SAV, and living resources 

in the estuary. The CBP partners have commitments to reduce sediment to the estuary to improve waterclarity conditions for SAV and conduct watershed planning to improve the health of streams. The USGS led a 

synthesis of sediment information by the CBP partners (Langland and Cronin, 2003) and conducted additional 

studies. This chapter provides a synthesis of USGS findings about sediment sources and transport in the watershed; the following chapter synthesizes sediment sources and deposition in the estuary. 

The USGS used several methods to assess the sources of sediment in the watershed including (1) analyzing historical data to evaluate areas with the highest sediment loads, yields, and concentrations, (2) assessing the 

distribution of sediment erosion rates, and (3) using geochemical tracers to determine sediment sources. Gellis, 

Banks, and others (2004) examined historical annual suspended-sediment loads (tons per year), yields (tons per 

square mile per year), discharge-weighted concentrations (mg/L), and instantaneous suspended-sediment concentrations (mg/L) for 65 USGS sediment stations operating in the Chesapeake Bay watershed. The highest sediment 

loads entering the Bay were from the Potomac and Susquehanna River Basins. The sediment loads were highly 

correlated to drainage area and river discharge, so larger basins usually had larger sediment loads. Sediment 

yields, which are loads divided by basin area, are used for assessing and comparing sediment generation in different areas of the Bay watershed. The sediment yields ranged from just over 1,000 tons per square mile to under 

10 tons per square mile for sediment stations operating from 1985–2001 (fig. 6.1). Some of the highest yields 

were in the Conestoga River, a tributary of the Susquehanna River. Agriculture is the predominant land use in the 

Conestoga watershed and therefore is probably an important contributing factor to the high amount of sediment 

in this watershed. 

Sediment yields computed by Gellis, Banks, and others (2004) were further examined to assess the distribution of sediment erosion in the different physiographic regions in the watershed. The sites were classified to fall 

within six physiographic regions (Coastal Plain, Valley and Ridge, Piedmont, Mesozoic Lowlands, Blue Ridge, 

and Appalachian Plateau) in the Chesapeake Bay watershed. Watersheds that had a majority of their contributing 

areas draining the Piedmont had the highest sediment yields, whereas Coastal Plain sites had the lowest sediment 

yields. The amount of eroded sediment from any one area depends on multiple factors including geology, land 

use, climate variability, and vegetation. The Piedmont Physiographic Province has a high degree of land disturbance (urban and agricultural land use) and topographic relief that promotes erosion. While the Coastal Plain has 

similar land disturbance, it has much lower topographic relief (especially on the Eastern Shore) and therefore, 

less sediment erosion. These findings imply that management actions to reduce sediment to the upper reaches of 

the estuary would be most effective if they are implemented in the Piedmont Province. 

These analyses of historical data are fairly consistent with another study approach that was first developed 

by Brown and others (1988) using a cosmogenic isotope 10Beryllium (10Be) to assess the relative disturbance 

and acceleration of erosion from upland soils. This technique was used to estimate erosion from 48 basins in the 

eastern United States, including 10 basins that drain to the Chesapeake Bay. The highest rates of erosion were 

observed in the Piedmont streams, and the lowest rates were observed in Coastal Plain streams. More recently, 

the USGS applied this technique to produce erosion indices based on 10Be for selected watersheds in the Susquehanna River Basin (Gellis, Pavich, and others, 2004; Reuter and others, 2005). Many of the higher values indicating significant erosion are clustered in the lower Susquehanna Basin, including the Conestoga watershed. The 

Conestoga also had some of the higher sediment yields (fig. 6.1), indicating that the 10Be approach is useful in 

assessing erosion rates in the Bay watershed. 

The relative contribution of the erosion of sediment from the land surface rather than from stream corridors is not well understood in the Chesapeake Bay basin. The USGS conducted research in three watersheds 

using a “sediment fingerprinting” approach to identify the sources of fluvial sediment. Sediment fingerprinting 

approaches were developed by Walling (2005), and the USGS developed a new algorithm and made use of several geochemical tracers, namely the relative composition of total carbon, nitrogen, and phosphorous in a sample, 

the stable isotopes carbon 13, nitrogen 15, and two radionuclides (cesium 137, and lead 210) to better identify 

sources of sediment. Preliminary results show that samples from the Pocomoke watershed on the Eastern Shore 

of Maryland were found to have up to 75 percent of the sediment eroded from within stream corridors (Gellis and 

Landwehr, 2006). Land erosion appears to be a higher contributor in other watersheds. The implication of these 
29 

Figure 6.1. Distribution of sediment yields in the Chesapeake Bay watershed, 1985–2001 (from Gellis, Banks, and 

others, 2004). USGS analysis of historical sediment data found the highest yields in the Piedmont, with the lowest 

yields in the Coastal Plain, indicating that management actions to reduce sediment to tidal fresh areas should be 

targeted in the Piedmont. Protecting and restoring forest and wetland assemblages is another effective approach to 

minimize sediment transport to the estuary. 
Chapter 6 

30 

findings is that detailed information will be needed in local watersheds to identify the primary source of erosion 

(stream corridors or land erosion) to properly plan and implement sediment-reduction actions. 

The time required to transport sediment from the watershed to the estuary depends on the amount of stor ­

age in different areas of the watershed. Sediment is stored and trapped in stream corridors, behind dams, and in 

Coastal Plain flood plains and wetlands adjacent to the estuary. The sediment stored in stream corridors includes 

a large amount of sediment eroded during land clearance in the 1700s and 1800s, known as “legacy” sediment 

(Langland and Cronin, 2003). Merritts and others (2004) proposed that impoundment of sediment behind tens of 

thousands of mill dams in the Mid-Atlantic Region was the dominant cause of sediment accumulation in streamchannel corridors. As these mill dams were breached or removed, sediment stored behind the dams was eroded 

and transported. Previous studies by the USGS revealed that dams on large rivers also store large amounts of 

sediment. Reservoirs on the lower Susquehanna River, for example, trap 70 percent of sediment being transported 

in the river (Langland and Hainly, 1997). The investigators also found that two of these dams have reached their 

sediment storage capacity and the lowermost reservoir (Conowingo) may fill in 20 to 25 years. 

Coastal Plain flood plains and their bottomland hardwood systems remain a critical landscape element 

for the maintenance of water quality by trapping and storing large amounts of sediment and associated 

contaminants (Hupp, 2000). These flood plains are among the last places for sediment storage and natural 

biogeochemical remediation of nutrients and contaminants before entering critical estuarine nursery areas for 

fish and wildlife. Preliminary USGS results show large amounts of nitrogen and phosphorus are also trapped 

in sediment in the Chesapeake Bay Coastal Plain flood plains prior to entering tidal waters because of much 

lower stream gradients and a large amount of flood-plain area (Noe and Hupp, 2005). Therefore, maintaining the 

ability of the flood plains to retain sediment and associated nutrients is a critical management action for the CBP 

partners to consider. 

References 

Brown, L., Pavich, M.J., Hickman, R.E., Klein, J., and Middleton, R., 1988, Erosion of the eastern United States 

observed with 10Be: Earth Surface Processes and Landforms, v. 13, no. 5, p. 441–457. 

Gellis, A.C., Banks, W.S.L., Langland, M.J., and Martucci, S.K., 2004, Summary of suspended-sediment data for 

streams draining the Chesapeake Bay watershed, water years 1952–2002: U.S. Geological Survey Scientific 

Investigations Report 2004–5056, 59 p. 

Gellis, A.C., and Landwehr, J.M., 2006, Identifying sources of fine-grained suspended sediment in the Pocomoke 

River, an Eastern Shore tributary to the Chesapeake Bay, in Proceedings of the Joint 8th Federal Interagency 

Sedimentation Conference and 3rd Federal Interagency Hydrologic Modeling Conference, April 2–6, 2006, 

Reno, Nevada, Paper 5C-1 in CD-ROM file ISBN 0-9779007-1-1, 9 p. 

Gellis, A.C., Pavich, M.J., Landwehr, J.M., Banks, W.S.L., Bierman, P.R., and Reuter, J.M., 2004, Identifying 

watershed sediment sources in the Chesapeake Bay: EOS Transactions, American Geophysical Union, Fall 

Meeting Supplement, v. 85, Abstract H51C-1159. 

Hupp, C.R., 2000, Hydrology, geomorphology, and vegetation of coastal plain rivers in the south-eastern USA: 

Hydrological Processes, v. 14, nos. 16–17, p. 2,991–3,010. 

Langland, M.J., and Cronin, T.M., eds., 2003, A summary report of sediment processes in Chesapeake Bay and 

watershed: U.S. Geological Survey Water-Resources Investigations Report 03–4123, 109 p. 

Langland, M.J., and Hainly, R.A., 1997, Changes in bottom-surface elevations in three reservoirs on the Lower 

Susquehanna River, Pennsylvania and Maryland, following the January 1996 flood—Implications for nutrient and sediment loads to Chesapeake Bay: U.S. Geological Survey Water-Resources Investigations Report 

97–4138, 34 p. 

Merritts, D., Walter, R., Lippincott, C., and Siddiqui, S., 2004, High suspended and sediment yields of the Conestoga River watershed to the Susquehanna River and Chesapeake Bay are the result of ubiquitous post-settlement mill dams: EOS Transactions, American Geophysical Union, v. 85, no. 47, p. 903. 
Noe, G.B., and Hupp, C.R., 2005, Carbon nitrogen, and phosphorus accumulation in floodplains of Atlantic 

Coastal Plain Rivers, USA: Ecological Applications, v. 15, no. 4, p. 1,178–1,190. 

Reuter, J.M., Bierman, P.R., and Pavich, M.J., 2005, Using GIS to select drainage basins for sampling: An 

example from a cosmogenic 10Be study of erosion rates within the Susquehanna River Basin: Geological 

Society of America Abstracts with Programs, v. 37, no. 1, 32 p. 

Walling, D.W., 2005, Tracing suspended sediment sources in catchments and river systems: Science of the Total 

Environment, v. 344, p. 159–184. 

31 Chapter 6 

Plume of sediment-laden runoff, possibly from an adjacent construction area, near Annapolis, Maryland. 

Photograph by Jane Thomas, IAN Image Library (www.ian.umces.edu/imagelibrary/). 
32 Chapter 7:Chapter 7: Sediment Sources and Deposition in the Estuary Sediment Sources and Deposition in the Estuary

By Thomas M. Cronin 

During the past 10 years, integrated studies of sediment in Chesapeake Bay and its tributaries have been 

carried out by a team of USGS scientists, in collaboration with researchers from several universities, 

the Maryland Geological Survey, the U.S. Naval Research laboratory, the USEPA, and other institutions. The 

USGS worked with these investigators to prepare a comprehensive review of sediment processes in the Bay and 

its watershed (Langland and Cronin, 2003). The current chapter, along with the chapter by Willard on the longterm water-quality changes in the Bay, summarizes the highlights of these studies. 

Sediment input into the Chesapeake Bay comes from four main sources: riverine input, shoreline erosion, 

oceanic sediment, and in situ biological (biogenic) sources generated by organisms living in the bay (Langland 

and Cronin, 2003). The USGS used its understanding of geologic processes controlling sediment to map the 

probable locations of different sources of sediment entering the estuary (Newell and others, 2004). Although 

estimates of the relative contributions of different sediment sources vary, the rivers draining the Piedmont and 

Appalachian Physiographic Provinces are the main sources of sediment to the northern Bay and tidal fresh zones 

of the major tributaries (fig. 7.1). Shoreline and marsh erosion of Coastal Plain sediments are the primary sources 

in the central part of the Bay and below the zone of maximum turbidity in major tributaries. Both shoreline 

erosion and ocean input are major sources of sediment in the southern part of the Bay. Tidal re-suspension 

of existing sediment on the Bay floor through tides, currents, and waves also produces suspended material, 

especially in the turbidity maximum zones of the main stem and larger tidal tributaries. Among these sources 

and processes, sediments from the watershed and shoreline erosion have the greatest potential for reduction by 

management actions. 

The USGS examined sediment cores to better understand the amount of sediment delivered from the watershed to the Bay. Analysis indicates a four-to-five fold increase in sediment accumulation in some parts of the 

Bay since the 1800s, whereas other areas showed no change in sediment rates (fig. 7.2) (Langland and Cronin, 

2003). In general, evidence indicates that sediment transport from the watershed to the Bay is not uniform and 

varies according to local watershed characteristics, storage conditions, and climate variability. As mentioned in 

the previous chapter, sediment storage greatly influences the transport time in the watershed. Sediment transport 

from the watershed to the estuary can take decades to centuries (Langland and Cronin, 2003) and contributes to a 

substantial lag time between watershed erosion (and associated management controls) and improvements in water 

clarity in the estuary. As a result, the CBP partners are considering emphasizing land-based practices nearer the 

tidal parts of the Bay to improve water clarity. 

Sediment erosion from shorelines also varies spatially and temporally because of multiple factors. The 

amount of sediment erosion from shorelines varies depending on climate conditions (wet or dry years), local 

geology, shoreline slope and geomorphology, offshore bathymetry, winds, and tides. The Western Shore of the 

Bay, for example, where headlands and large tidal tributaries draining the uplands are predominant, has different 

erosion processes than the Eastern Shore, where low-lying tidal marshes are extensive. Since sea level continues to rise in the Bay region at a rate of approximately 1.0 to 1.4 feet per century, and because the rate may be 

accelerated due to climate warming, shoreline erosion in response to rising sea level is an important process 

affecting low-lying areas (Langland and Cronin, 2003). The findings imply that, without management of coastal 

zones, a greater contribution of sediment to the Bay will come from shoreline erosion in the future. The states of 

Maryland and Virginia are considering sediment management of coastal areas as part of their tributary strategies. 

Overall, these findings imply that controlling sediment sources in the Piedmont Province of the watershed will be 

important to improve conditions for the tidal fresh regions of the estuary, and shoreline management actions will 

be needed to improve water clarity in more saline regions of the estuary. 
33
Chapter 7

34

Figure 7.2. Rates of sediment deposition in the Chesapeake Bay estuary (modified from Langland and Cronin, 

2003). Sediment deposition is influenced by land-based activities and factors affecting delivery of sediment from the 

watershed to the estuary. Sediment traveltimes from the watershed to the estuary may be decades to centuries. In 

general, sediment-reduction practices to improve water clarity in the estuary should be focused on sources that 

are closest to tidal waters. Practices to address shoreline erosion must also consider the sediment erosion due to 

continued sea-level rise and climate warming.

References

Langland, M.J., and Cronin, T.M., eds., 2003, A summary report of sediment processes in Chesapeake Bay and 

watershed: U.S. Geological Survey Water-Resources Investigations Report 03–4123, 109 p.

Newell, W.L., Clark, I., and Bricker, O., 2004, Distribution of Holocene sediment in Chesapeake Bay as interpreted from submarine geomorphology of the submerged landforms, selected core holes, bridge borings and 

seismic profiles: U.S. Geological Survey Open-File Report 2004–1235, Version 1.0, available online at 

http://pubs.usgs.gov/of /2004/1235.
3535 Chapter 7

Photograph showing the high suspended-sediment concentrations caused by a large storm, Hurricane Ivan, 

which affected parts of the Chesapeake Bay Watershed from September 17–18, 2004. (NASA Terra satellite 

image of the Chesapeake Bay Watershed region taken on September 21, 2004, obtained from NASA Internet 

site http://earthobservatory.nasa.gov/NaturalHazards/shownh.php3?img_id=12456; accessed October 21, 

2004). Note the brownish turbid waters of the Susquehanna and Potomac Rivers, and upper Chesapeake 

Bay. A sample collected at the Susquehanna River at Conowingo, Maryland on September 20, 2004 at 0900 

yielded a suspended-sediment concentration of 3,685 milligrams per liter.
36 Chapter 8:Chapter 8: The Occurrence of Pesticides in the Bay W The Occurrence of Pesticides in the Bay Watershedatershed

By Judith M. Denver and Scott W. Ator 

One of the CBP’s restoration goals is “to achieve and maintain the water quality necessary to support 

the aquatic living resources of the Bay and its tributaries and to protect human health.” The CBP 

developed a toxics reduction strategy to address contaminants as part of this goal. Some of the information 

needs of the toxics reduction strategy include (1) documenting the sources and occurrence of contaminants, and 

(2) understanding the potential for contaminants to adversely impact aquatic-dependent wildlife. The USGS 

had a science goal in 2001–06 to address the occurrence of selected contaminants to provide information to 

the CBP and also to support DOI needs about the impact of contaminants on wildlife. The USGS science goal 

mainly addressed pesticide occurrence in surface and ground water in the watershed by utilizing results of the 

USGS National Water-Quality Assessment (NAWQA) Program studies that were conducted during 1992–2004. 

Additionally, more recent results from USGS studies of emerging contaminants are presented. The USGS goal 

also addressed the impacts of selected contaminants on waterbirds and wildlife species. This chapter summarizes 

findings about pesticides and some selected emerging contaminants in the watershed. It provides an overview of 

the occurrence of pesticides in ground water and surface water, their relation to land use and other factors, and 

changes over time, followed by a summary of emerging contaminants. The next chapter focuses on the impact of 

contaminants on waterbirds and wildlife. 

Results from NAWQA studies in the Susquehanna River Basin (Lindsey and others, 1998), Potomac River 

Basin (Ator and others, 1998), and the Delmarva Peninsula (Denver and others, 2004) revealed that synthetic 

organic pesticides, along with certain degradation products, have been widely detected at low levels (typically 

less than 1 microgram per liter) in ground water and streams in the Chesapeake Bay watershed. Pesticides and 

their degradates are generally detected more frequently in streams than in ground water; an example from the 

Delmarva Peninsula is shown in figure 8.1. The most commonly detected pesticides are herbicides used on corn, 

soybean, and small grain crops. Atrazine, metolachlor, and simazine are the most commonly detected pesticides 

in surface water, whereas atrazine is the most commonly detected pesticide in ground water (Hainly and Kahn, 

1996; Ator and Ferrari, 1997; Ferrari and others, 1997; Denver and others, 2004). Pesticides also are detected in 

urban areas, where the use and detection of insecticides—such as diazinon, carbaryl, and chlorpyrifos—and the 

herbicide prometon are more common. Herbicides common to agricultural areas have also been widely detected 

in urban areas, though typically at lower concentrations. Pesticides are less commonly detected in forested areas; 

infrequent, low-level detections in such areas may be attributable to local use or to atmospheric transport from 

agricultural or urban areas (Majewski and others, 1998). Degradation products of pesticides also are found in 

ground water and streams, often at concentrations higher than those of their corresponding parent compounds 

(Ator and others, 2005; Denver and others, 2004). The occurrence and distribution of pesticides in the Bay water 

shed reflect usage patterns, environmental conditions, and the chemical and physical properties of the pesticides. 

Given that pesticide occurrence is closely tied to nutrient practices on agricultural and urban lands, these results 

could be used by resource managers to better integrate actions to reduce nutrients and pesticides to improve water 

quality in the Bay and its watershed. 

The occurrence and distribution of pesticides in ground water are related to natural geologic and soil condi 

tions, as well as usage patterns. Where applied, pesticides usually occur at higher concentrations in ground water 

in areas underlain by permeable soils and aquifer material than in areas underlain by less permeable materi

als (Ator and Ferrari, 1997; Lindsey and others, 1998; Debrewer and others, 2007). Results from these studies 

showed that concentrations were generally higher in agricultural areas overlying limestone or fractured crystal 

line bedrock (such as in the Great Valley or parts of the Piedmont Physiographic Provinces) or sandy sediments 

in the Coastal Plain. Lower concentrations were found in agricultural areas overlying unfractured sandstone and 

shale of the Piedmont and Appalachian Mountains or in fine-grained sediments underlying fine-grained, organicrich soil in the Coastal Plain. Once pesticide compounds enter ground water, they often take years to decades to 

be carried through the flow system and discharge to local streams and rivers. 

Pesticides are present year round in streams of the Bay watershed, but the changes in pesticide concentra 

tions over time generally reflect changes in application rates, as well as physical and chemical properties that 

control the movement of these compounds in the environment (Gilliom and others, 2006). Increasing or decreasing use of pesticides may cause relatively rapid corresponding changes in concentrations in overland runoff and 

streams during runoff periods. Changes in pesticide use will be more slowly reflected in ground water and, 

­

­

­

­

­
37 

Figure 8.1. Pesticides detected in 

surface water and ground water in 

the Delmarva Peninsula, 1999–2001 

(modified from Denver and others, 

2004). Synthetic organic pesticides, 

along with certain degradation 

products, have been widely detected 

in ground water and streams in the Bay 

watershed. Pesticide occurrence is 

closely tied with nutrient land practices 

on agricultural and urban lands, so 

there is potential to better integrate 

management actions to reduce both 

nutrients and contaminants to the Bay. 

Over-application of herbicides on farm fields can result 

in excess toxins and nutrients reaching the waterways. 

Photograph by Jane Hawkey, IAN Image Library (www.ian. 

umces.edu/imagelibrary/). 
Chapter 8

38

Figure 8.2. Changes in diazinon 

concentrations in Accotink 

Creek, a small urban stream near 

Washington, D.C., 1997–2004 

(modified from Phillips and others, 

2007). Pesticides are present 

year round, but changes in 

concentrations reflect application 

rates and properties affecting their 

movement.

therefore, in streams during base-flow periods, however. Diazinon concentrations decreased 39 percent between 

1998 and 2004 in Accotink Creek, in an urban area near Washington, D.C., coincident with reductions in 

diazinon use (fig. 8.2) (Phillips and others, 2007). No trends were apparent, however, between 1993 and 2002 in 

concentrations of several commonly used herbicides (atrazine, metolachlor, prometon, and simazine) or desethylatrazine in ground water in agricultural areas of the Great Valley underlain by carbonate bedrock (Debrewer and 

others, 2007), which indicates that usage of these compounds did not change significantly during the corresponding ground-water recharge period. The implication of these findings is that there will be varying lag times 

between management practices to reduce pesticides and improvements in water quality. For pesticides in the 

dissolved phase that are transported in runoff directly from a field to a stream, a very short response time between 

management actions and water-quality improvements may be expected. There will be a longer response time 

if the compound has been transported through ground water. Pesticides associated with sediment will have the 

longest lag time between management actions and improvements in water quality.

In addition to pesticides, pharmaceuticals, hormones, and other organic wastewater compounds, are also of 

concern in the Bay watershed and the Nation. The USGS conducted a national study of emerging contaminants 

that included sites in the Bay watershed (Kolpin and others, 2002). During the study, samples were analyzed 

for 95 different emerging contaminants, including human and veterinary drugs, hormones, detergents, disinfectants, insecticides, and fire retardants. At least one of these contaminants was found in 80 percent of the Nation’s 

streams, with mixtures of the chemicals occurring at 75 percent of the sites. The most common groups detected 

were steroids, nonprescription drugs, and insect repellent. Only 14 compounds have human or ecological health 

criteria, and measured levels rarely exceeded any of the standards or criteria. However, little is known about the 

majority of the compounds or their mixtures. 

The USGS also published results of a study on pharmaceutical compounds having antibiotic resistance to 

bacteria and their relation to nutrient cycling in sediments (Simon, 2005). The antibiotic oxytetracycline (OTC) 

was found in bottom sediments in two streams that were studied on the Eastern Shore of the Chesapeake Bay. 

OTC can produce changes in antibiotic resistance of indigenous bacteria and change the reaction rates of nitrate 

oxidation by soil and sediment bacteria. These results indicate that OTC in sediments decreases the ability of 

bacteria to alter nitrogen and phosphorous, which could result in increased loads of nutrients being delivered to 

the estuary. 

Studies have recently begun to document the potential relation between emerging contaminants and the 

disruption of the endocrine system of fish in parts of the Bay watershed. Reconnaissance sampling for emerging 

contaminants at several sites in the West Virginia part of the Potomac River Basin detected antibiotics in 

municipal wastewater, aquaculture, and poultry-processing effluent (Chambers and Leiker, 2006). The highest 

number and the greatest concentrations were found in municipal effluent. Previous results from USGS sampling 

of the Potomac Basin by the NAWQA Program detected chlordane, DDT, and PCBs in streambed sediment and 

aquatic tissues (Ator and others, 1998). Sediment from over one-half of the sites contained concentrations that 

may pose adverse effects on aquatic life. There is a limited amount of information on these contaminants in the 

Bay watershed and their impact on the stream ecosystems and fish populations, however. Therefore, the USGS 

is beginning a more extensive study of the issue in the Bay watershed. More information can be found in the 

chapter on fish health. 
References 

Ator, S.W., Blomquist, J.D., Brakebill, J.W., Denis, J.M., Ferrari, M.J., Miller, C.V., and Zappia, H., 1998, Water 

quality in the Potomac River Basin—Maryland, Pennsylvania, Virginia, and West Virginia and the District of 

Columbia, 1992–96: U.S. Geological Survey Circular 1166, 38 p. 

Ator, S.W., Denver, J.M., and Brayton, M.J., 2005, Hydrologic and geochemical controls on pesticide and nutrient transport to two streams on the Delmarva Peninsula: U.S. Geological Survey Scientific Investigations 

Report 2004–5051, 34 p. 

Ator, S.W., and Ferrari, M.J., 1997, Nitrate and selected pesticides in ground water of the Mid-Atlantic Region: 

U.S. Geological Survey Water-Resources Investigations Report 97–4139, 8 p. 

Chambers, D.B., and Leiker, T.J., 2006, A reconnaissance for emerging contaminants in the South Branch Potomac River, Cacapon River, and Williams River Basins, West Virginia, April–October 2004: U.S. Geological 

Survey Open-File Report 2006–1393, 28 p. 

Debrewer, L.M., Ator, S.W., and Denver, J.M., 2007, Factors affecting spatial and temporal variability in nutrient 

and pesticide concentrations in the surficial aquifer on the Delmarva Peninsula: U.S. Geological Survey Scien 

tific Investigations Report 2005–5257, 44 p. 

Denver, J.M., Ator, S.W., Debrewer, L.M., Ferrari, M.J., Barbaro, J.R., Hancock, T.C., Brayton, M.J., and 

Nardi, M.R., 2004, Water quality in the Delmarva Peninsula—Delaware, Maryland, and Virginia, 1999–2001: 

U.S. Geological Survey Circular 1228, 30 p. 

Ferrari, M.J., Ator, S.W., Blomquist, J.D., and Dysart, J.E., 1997, Pesticides in surface water of the Mid-Atlantic 

Region: U.S. Geological Survey Water-Resources Investigations Report 97–4280, 8 p. 

Gilliom, R.J., Barbash, J.E., Crawford, C.G., Hamilton, P.A., Martin, J.D., Nakagaki, Naomi, Nowell, L.H., 

Scott, J.C., Stackelberg, P.E., Thelin, G.P., and Wolock, D.M., 2006, Pesticides in the Nation’s streams and 

ground water, 1992–2001: U.S. Geological Survey Circular 1291, 172 p. 

Hainly, R.A., and Kahn, J.M., 1996, Factors affecting herbicide yields in the Chesapeake Bay watershed, 

June 1994: Water Resources Bulletin, v. 32, no. 5, p. 965–984. 

Kolpin, D.W., Furlong, E.T., Meyer, M.T., Thurman, E.M., Zaugg, S.D., Barber, L.B., and Buxton, H.T, 2002, 

Pharmaceuticals, hormones, and other organic wastewater contaminants in U.S. streams, 1999–2000: A 

national reconnaissance: Environmental Science and Technology, v. 36, no. 6, p. 1,202–1,211. 

Lindsey, B.D., Breen, K.J., Bilger, M.D., and Brightbill, R.A., 1998, Water quality in the Lower Susquehanna 

River Basin, Pennsylvania and Maryland, 1992–95: U.S. Geological Survey Circular 1168, 38 p. 

Majewski, M.S., Foreman, W.T., Goolsby, D.A., and Nakagaki, N., 1998, Airborne pesticide residues along the 

Mississippi River: Environmental Science and Technology, v. 32, no. 23, p. 3,689–3,698. 

Phillips, P.J., Ator, S.W., and Nystrom, E.A., 2007, Temporal changes in surface-water insecticide after the 

phaseout of diazinon and chlorpyrifos: Environmental Science and Technology, v. 41, no. 12, p. 4,246–4,251. 

Simon, N.S., 2005, Loosely bound Oxytetracycline in riverine sediments from two tributaries of the Chesapeake 

Bay, 2005: Environmental Science and Technology, v. 39, no. 10, p. 3,480–3,487. 

­

39 Chapter 8 
Chapter 9:Chapter 9: Contaminant Exposure and Impacts on W Contaminant Exposure and Impacts on Waterbirdsaterbirds 

and Selected Wildlife

40 

By Barnett A. Rattner 

The impact of selected contaminants on waterbirds and wildlife in the Chesapeake Bay ecosystem has 

been addressed with USGS studies and use of ecotoxicological information for wildlife that has been 

extracted from the Contaminant Exposure and Effects—Terrestrial Vertebrates (CEE-TV) database (Rattner and 

others, 2005). Currently, the CEE-TV database contains 839 data records (representing about 9,500 individuals) 

for the Chesapeake Bay region, with sample-collection dates ranging from 1966 to 2005. Contaminant exposure 

and effects data are available for 109 species of terrestrial vertebrates, with the majority of records from birds 

(79 percent) and mammals (12 percent). Exposure and effects data are available on 92 unique contaminants, with 

most information focused on legacy organochlorine contaminants (including DDT, chlordane, endrin, dieldrin, 

and polychlorinated biphenyls, or PCBs) and heavy metals (including lead, mercury, cadmium, and chromium). 

Concentrations of p,p’-DDE (a metabolite of DDT that caused eggshell thinning and decimated populations 

of fish-eating birds) and other organochlorine pesticides and metabolites have declined since they were banned in 

the 1970s, whereas PCB values in eggs seem to have remained unchanged (fig. 9.1). One recent USGS study of 

ospreys documented their reproduction in the most highly polluted parts of the Bay (Rattner and others, 2004). 

In 2000 and 2001, a “sample egg” was collected from many osprey nests in or near the CBP “toxic regions of 

concern” (Baltimore Harbor, Anacostia River, Elizabeth River), and the fate of eggs remaining in each nest was 

monitored. Concentrations of organochlorine pesticides, total PCBs, and arylhydrocarbon receptor-active PCB 

congeners were often greater in sample eggs from regions of concern compared to the reference area (South, 

West, and Rhode Rivers). Productivity of ospreys in or near Baltimore Harbor and the Anacostia River was 

marginal (observed success less than 1 fledgling/active nest) for sustaining local populations. In addition, tumors 

in bullhead catfish have been found in these very same regions (Pickney, Harshberger, May, and Reichert 2004; 

Pickney, Harshberger, May, and Melancon, 2004). Overall, management actions in the 1970s and 1980s restricting the use of chlorinated compounds and some metals have had several results for wildlife. Decreased use of 

chlorinated pesticides contributed to improved conditions and population recovery of many fish-eating birds. 

Populations of many species, including the bald eagle, have rebounded to numbers observed before the advent 

and use of organochlorine pesticides. However, concentrations of other contaminants such as PCBs in wildlife 

appear unchanged and remain a concern. 

Several emerging contaminants are being detected in Chesapeake Bay wildlife, but the associated threat 

to wildlife is not known at this time. Environmental concentrations of polybrominated diphenyl ether (PBDE) 

flame retardants (commonly used in polymers, textiles, and electronics) are increasing; on a global basis, some 

of the highest levels in bird eggs have been found in ospreys nesting in the Chesapeake (Hale and others, 2004). 

Since little is known about the toxicity thresholds of PBDEs in wildlife, it is difficult to predict the hazards they 

pose to biota in the Bay. USGS studies have been initiated to determine potential embryo-toxicity of these flame 

retardants using wild bird eggs. Other compounds of contemporary interest include alkylphenol, ethoxylate, and 

perfluorinated surfactants, pharmaceuticals, and personal care products. Finally, rising mercury concentrations 

in the environment and widespread fish consumption advisories are of national concern (U.S. Geological Survey, 

2006). Although fish consumption advisories due to mercury contamination are widespread, adverse effects have 

not been documented in wildlife associated with the estuary. Data from the CEE-TV database show that mercury 

concentrations in bird eggs, and in livers and kidneys of terrestrial vertebrates collected in the Chesapeake estuary, are generally well below known adverse effect levels. 
41 

Figure 9.1. Changes in DDE and PCB 

concentrations in the Bay ecosystem from the 

1970s to present day. Concentrations of DDT and 

its breakdown products have declined since their 

ban in the 1970s, but PCB concentrations remained 

unchanged. The populations of many fish-eating 

birds, such as the bald eagle, have rebounded 

with the decline in DDT and DDE. However, other 

contaminants that are slow to break down remain 

a threat to wildlife. 

References 

Hale, R.C., LaGuardia, M.J., Harvey, E., Rattner, B.A., Watts, B.D., and Potter, K.E., 2004, Are PBDE congener 

profiles useful indicators of source? in Proceedings of the 25th Annual Meeting of the Society of Environmental Toxicology and Chemistry, November 14–18, 2004, Portland, Oregon, PM042. 

Pinkney, A.E., Harshbarger, J.C., May, E.B., and Melancon, M.J., 2004, Tumor prevalence and biomarkers of 

exposure in brown bullhead (Ameiurus nebulosus) from Back River, Furnace Creek, and Tuckahoe River, 

Maryland: Archives of Environmental Contamination and Toxicology, v. 46, no. 4, p. 492–501. 

Pinkney, A.E., Harshbarger, J.C., May, E.B., and Reichert, W.L., 2004, Tumor prevalence and biomarkers of 

exposure and response in brown bullhead (Ameiurus nebulosus) from the Anacostia, Washington, D.C. and 

Tuckahoe River, Maryland, USA: Environmental Toxicology and Chemistry, v. 23, no. 3, p. 638–647. 

Rattner, B.A., Eisenreich, K.M., Golden, N.H., McKernan, M.A., Hothem, R.L., and Custer, T.W., 2005, Retrospective ecotoxicological data and current information needs for terrestrial vertebrates residing in coastal habi 

tat of the United States: Archives of Environmental Contamination and Toxicology, v. 49, no. 2, p. 257–265. 

Rattner, B.A., McGowan, P.C., Golden, N.H., Hatfield, J.S., Toschik, P.C., Lukei, R.F., Hale, R.C., SchmitzAfonso, I., and Rice, C.P., 2004, Contaminant exposure and reproductive success of ospreys (Pandion haliaetus) nesting in Chesapeake Bay regions of concern: Archives of Environmental Contamination and Toxicology, v. 47, no. 1, p. 126–140. 

U.S. Geological Survey, 2006, Fish consumption advisories for mercury, accessed June 5, 2007, at 

http://minerals.usgs.gov/mercury/advisories.html. 

­

Osprey nest atop channel marker in the Tred Avon River in 

Easton, Maryland. Photograph by Jane Hawkey, IAN Image 

Library (www.ian.umces.edu/imagelibrary/). 
42 Chapter 10:Chapter 10: Long-Term Changes in Climate and W erm Changes in Climate and Water Qualityater Quality

By Debra A. Willard 

The CBP has restoration goals to increase dissolved oxygen and water clarity in the Bay to improve 

water-quality conditions for fisheries and SAV. Because land-use practices in the Chesapeake Bay 

watershed have a great influence on estuarine water quality and its biota, most of the restoration actions focus on 

changing land-use practices to reduce nutrient and sediment loads. Regional climate variability also has a significant impact on water quality. Precipitation and river flow into the Bay directly affect salinity stratification within 

the estuary, which in turn influences the timing and extent of seasonal hypoxia, independent of nutrient loads. 

Likewise, a climatically induced fluctuation in river flow to the Bay affects the amount of suspended sediment 

in the water column. Therefore, the proposed management strategies to improve estuarine water quality need to 

consider the impacts of natural climatic fluctuations on nutrient and sediment loads. The USGS has summarized 

results from a series of integrated studies designed to document the long-term variability of Chesapeake Bay 

water quality (salinity, temperature, and dissolved oxygen). 

The Chesapeake Bay is underlain by a thick sequence of sediments that provide an archive of past 

ecosystem response to a series of climatic and land-use changes. These sediments have been deposited 

continuously throughout the approximately 7,000-year history of the modern Bay, and previously when the 

paleo-Susquehanna River flowed through the valley that ultimately was flooded by sea-level rise to form the 

modern Chesapeake Bay. Biological and geochemical indicators are analyzed from sediment cores, which serve 

as proxies for environmental parameters (temperature, salinity, and dissolved oxygen), to assess water-quality 

changes during the past several thousand years. Age models of the cores are developed using radiogenic isotope 

methods (carbon 14, lead 210, cesium 137) and pollen biostratigraphy (see Willard and others, 2003, for a 

complete discussion). Reconstruction of the history of temperature, salinity, and dissolved oxygen in the Bay 

is based on quantitative analysis of microfossils of pollen, ostracodes, foraminifers, mollusks, dinoflagellates, 

diatoms, and sediment geochemistry. 

An understanding of the natural variability in river flow, which is strongly influenced by precipitation, is 

important for developing sustainable management plans to limit nutrient and sediment loads in the Bay. The 

relation among rainfall, river flow, and Chesapeake Bay salinity over the past 175 years was quantified by USGS 

researchers using instrumental records, and established foraminiferal and ostracode indicators for salinity made 

it possible to reconstruct past variability in salinity and river flow during the last 7,000 years (Cronin and others, 

2000). Examination of the sediment records reveals a significant difference between Chesapeake salinities of the 

early Holocene (7,200 to 5,000 years before present, or yrBP), when mean was 28 ppt (parts per thousand) and 

the last 2,000 years, when salinity averaged 20 ppt (Cronin and others, 2005). The persistent occurrence of multidecadal salinity and temperature oscillations (every 20–40 years) during the entire history of the Bay indicates 

that climate variability is an inherent component of the North Atlantic climate system (Cronin and others, 2005). 

Over a shorter time scale, detailed records spanning the last 1,500 years document both extended periods of drier 

than average conditions (during the Medieval Warm Period ranging from 1200–600 yrBP), and wetter than average conditions during the Little Ice Age (from 500–100 yrBP). The 20th century is characterized by a series of 

precipitation extremes that indicate anomalous behavior of the climate system. The occurrence of such extreme 

variability in river flow over annual to decadal periods can have a much greater influence on delivery of nutrient 

and sediment loads to the estuary than the management actions designed to reduce these loads. The results imply 

that managers need to better account for natural variability when assessing progress in reducing nutrient and sediment loads to the estuary and assessing attainment of water-quality standards. 

Seasonal and interannual temperatures of Chesapeake Bay surface waters are influenced both by inflowing 

waters from the continental shelf and regional atmospheric temperatures. The potential for 21st century warming related to greenhouse gas concentrations also is likely to affect estuarine temperatures. Using magnesium/ 

calcium ratios from ostracode shells from sediment cores, USGS researchers, in collaboration with colleagues at 

Duke University, reconstructed long-term, estuarine surface-water temperatures over the past 2,000 years. These 

records indicate that surface-water temperature maxima occurred approximately every 70 years during the interval between 2200 yrBP and 250 yr (fig. 10.1A). This pattern indicates the long-term persistence of multi-decadal 

processes such as the North Atlantic Oscillation (Cronin and others, 2000; Cronin and Vann, 2003). Temperatures 

during the late 19th and 20th centuries exhibited greater extremes (fig. 10.1B) than those observed during the previous 2,000 years, including the relatively warm Medieval Warm Period (MWP) and cooler Little Ice Age (LIA) 
Figure 10.1. (A) Water temperature patterns for Chesapeake Bay, and (B) change from long-term mean compared 

with (C) Northern Hemisphere atmospheric temperature changes from long-term mean. Water temperatures in the Bay 

during the late 19th and 20th centuries exhibited greater extremes than those of the previous 2000 years. The results 

imply that management actions to address climate variability and associated global warming need to be developed to 

restore the estuary. 

43
Chapter 10 

44 

(fig. 10.1A). These results are consistent with other studies in the North Atlantic region that indicate anomalous 

20th century climate variability when compared to the past 2,000 years (fig. 10.1C). The implications of these 

findings are that long-term changes in climate, due to both natural variability and increasing greenhouse gases 

from human sources, and changes in land-use practices have to be addressed to improve water-quality conditions 

in the Bay. 

Seasonal oxygen depletion in waters of the Chesapeake Bay has been documented for much of the 20th 

century by a number of research efforts. Research by USGS scientists has focused on reconstruction of dissolved 

oxygen trends in Chesapeake Bay during the past 2,500 years (Bratton and others, 2003; Cronin and Vann, 2003; 

Karlsen and others, 2000; Willard and others, 2003) and indicates that the deep channel of the Bay may have 

been briefly hypoxic (concentrations less than 2 mg/L) during relatively wet periods prior to European colonization (prior to 1600 AD). Seasonal anoxia (a lack of dissolved oxygen lasting weeks to months) probably occurred 

periodically during the relatively wet periods between 1600 AD and 1960 AD, and became more frequent after 

1970 (fig. 10.2). These findings, together with earlier research, clearly indicate that hypoxia and anoxia were 

much more severe and extensive in Chesapeake Bay and its tributaries during the past four decades than at any 

time in the past 500–2,500 years. 

Figure 10.2. Long-term 

changes in dissolved 

oxygen (DO) conditions in 

Chesapeake Bay. Since 

the 1970s, both population 

growth and a period of 

extreme climate variability 

contributed to dissolved 

oxygen occurring at 

the worst levels of the 

past 500–2,500 years. 

Management actions 

that address delivery of 

nutrient and sediment 

loads under varying river 

flow conditions will need 

to be emphasized to help 

address climate variability. 
References 

Bratton, J.F., Colman, S.M., and Seal, R.R., II, 2003, Eutrophication and carbon sources in Chesapeake Bay over 

the last 2,700 years: Human impacts in context: Geochimica et Cosmochimica Acta, v. 67, p. 3,385–3,402. 

Cronin, T.M., Thunell, R., Dwyer, G.S., Saenger, C., Mann, M.E., Vann, C., and Seal, R.R., II, 2005, Multiproxy 

evidence of Holocene climate variability from estuarine sediments, eastern North America: Paleoceanography, 

v. 20, PA4006, doi: 10.1029/2005PA001145. 

Cronin, T.M., and Vann, C.D., 2003, The sedimentary record of climatic and anthropogenic influence on the 

Patuxent estuary and Chesapeake Bay ecosystems: Estuaries, v. 26, no. 2, p. 196–209. 

Cronin, T., Willard, D., Karlsen, A., Ishman, S., Verardo, S., McGeehin, J., Kerhin, R., Holmes, C., Colman, S., 

and Zimmerman, A., 2000, Climatic variability in the eastern United States over the past millennium from 

Chesapeake Bay sediments: Geology, v. 28, no. 1, p. 3–6. 

Karlsen, A.W., Cronin, T.M., Ishman, S.E., Willard, D.A., Holmes, C.W., Marot, M., and Kerhin, R., 2000, 

Historical trends in Chesapeake Bay dissolved oxygen based on benthic foraminifera from sediment cores: 

Estuaries, v. 23, no. 4, p. 488–508. 

Willard, D.A., Cronin, T.M., and Verardo, S., 2003, Late-Holocene climate and ecosystem history from Chesa 

peake Bay sediment cores, USA: The Holocene, v. 13, no. 2, p. 201–214. 

­

45 Chapter 10 

The USGS Hoverprobe is used to collect sediment cores to study long-term ecosystem history. Photograph 

by Daniel J. Phelan, U.S. Geological Survey 
46 Chapter 11:Chapter 11: Submerged Aquatic V Submerged Aquatic Vegetation and W egetation and Water Clarityater Clarity

By Nancy B. Rybicki and Jurate M. Landwehr 

Underwater grasses, known as submerged aquatic vegetation (SAV), provide food for waterfowl populations as well as vital habitat for juvenile fish and shellfish. Historically, the Chesapeake Bay supported 

a diverse and abundant community of SAV; however, the acreage has declined substantially since the 1960s. The 

decline has been linked to poor water clarity due to a combination of increased suspended sediment and persistent algal blooms. The CBP has a goal to double the number of SAV acres by 2012. The USGS summarized its 

findings related to (1) water clarity, and (2) the influence of exotic species on SAV acreage. 

USGS research on SAV minimum light requirements has identified the water-clarity conditions needed to 

support SAV in different salinity zones of the Bay. The minimum light requirements, defined as the amount of 

surface light reaching the bottom, are 13 percent for the freshwater SAV community and 22 percent for the more 

brackish waters (Carter and others 2000; Kemp and others, 2004). Many fluctuating factors, such as quantity of 

river flow and suspended matter in the water column, contribute to the variability in water clarity (fig. 11.1). To 

determine which water column constituents best explain variation in water clarity during the SAV growing season 

(April to October), the USGS analyzed factors influencing water clarity at 63 mid-channel water-quality-monitoring stations (fig. 11.2) throughout the Chesapeake Bay (Landwehr, 2005). The analysis indicated that the most 

important factor affecting water clarity is total suspended solids (TSS), which includes organic matter (phytoplankton, other planktonic organisms, bacteria, and organic detritus) and inorganic solids (clay, silt, and sand). 

For the Potomac River and the eight major tributaries, TSS was the primary explanatory variable for water clarity 

at 54 of the 63 stations. At eight stations in the more saline portions of the York, Rappahannock, Patuxent, and 

Choptank Rivers (fig. 11.2), chlorophyll-a concentration (an indicator of phytoplankton biomass) was the primary explanatory variable. Assuming that the inorganic component of TSS is greater than the organic component 

Figure 11.1. Conceptual diagram of factors affecting water clarity. Impacts of sediment, nutrients, algal 

blooms, and epiphytic growth on submerged aquatic vegetation (SAV) can affect the amount of sunlight 

reaching the plants. USGS research on the light requirements for SAV in different salinity zones was used 

to help set the water-quality standards in the estuary. 
Figure 11.2. Water-clarity monitoring sites in the Chesapeake Bay estuary. Investigations have shown that factors 

affecting water clarity vary in different areas of the estuary. The results indicate that managers need to further utilize 

information about the primary cause of degraded water clarity to better focus sediment- and nutrient-reduction 

strategies. 

47 
Chapter 11 

48 

in most regions of the Bay and that the attenuation from inorganic solids exceeds attenuation from organic solids 

(Cerco and Moore, 2001), these results indicate that strategies to reduce sediment loads could improve water clarity more than strategies to reduce nutrient loads in most locations. At the other eight locations, these data would 

indicate that water clarity could improve with nutrient reduction and subsequent reduction in phytoplankton. 

The USGS also analyzed information from both shallow water sites (nearer the shoreline) and mid-channel 

sites (further from the shoreline) to assess factors affecting water clarity in these different areas. In 2002, 

the Maryland Department of Natural Resources (MD DNR), in partnership with the USGS, measured water 

quality at 10 shallow water sites within the Chesapeake and Maryland Coastal Bays (fig. 11.2). Regression 

analysis showed that in 2002, a dry and low-flow year, nutrients and organic suspended solids best explained 

light attenuation at the shallow water monitoring sites (Baldizar and Rybicki, 2006). These results indicate that 

nutrient reduction and subsequent reduction of organic solids would have a greater impact on water clarity than 

reduction of sediments (inorganic solids) during low-flow conditions. The regression analysis of the mid-channel 

data from the nine Bay tributaries showed a different result. The results of mid-channel analysis indicate that TSS 

is the dominant factor impacting water clarity at most sites in the estuary. Given these results, managers should 

remain focused on both sediment- and nutrient-reduction strategies to improve water clarity in the estuary. The 

results also indicate that additional data analysis is needed to evaluate factors affecting water clarity during other 

flow conditions. 

The USGS also addressed the occurrence of invasive aquatic plants in the estuary (Rybicki and Landwehr, 

2007). Exotics are expanding their range annually, yet few studies have summarized the conditions and impacts 

of this expansion within the context of water-quality restoration efforts. Hydrilla, the dominant exotic species in 

the upper tidal Potomac River, occurs in rivers, lakes, and estuaries throughout the world. The USGS conducted 

a long-term, quantitative study of SAV diversity following the colonization of hydrilla to the fresh and upper 

oligohaline part of the Potomac Estuary between Washington, D.C. and Maryland Point. Using information 

from annual field surveys and aerial photographs, USGS scientists created a database to document which 

species occurred in SAV beds in different sections of the Potomac River system. They recorded the percentage 

of total coverage and biomass each species attained annually. In comparing species coverage with water-quality 

composition, they discovered that, with the reduction of nitrogen concentration, hydrilla coverage expanded but 

so did the diversity of plant species. Hydrilla did not crowd out native species; indeed, native species increased. 

In addition, hydrilla is a good winter food source for waterfowl communities, which have increased significantly 

over this period. 

Seagrass in Round Bay in the Severn River, Annapolis, Maryland. Photograph by Jane Thomas, 

IAN Image Library (www.ian.umces.edu/imagelibrary/). 
References 

Baldizar, J.B., and Rybicki, N.B., 2006, Primary factors influencing water clarity at shallow water sites throughout the Chesapeake and Maryland Coastal Bays, in Proceedings of the Joint 8th Federal Interagency Sedimentation Conference and 3rd Federal Interagency Hydrologic Modeling Conference, April 2–6, 2006, Reno, 

Nevada, in CD-ROM file ISBN 0-9779007-1-1. 

Carter, V., Rybicki, N.B., Landwehr, J.M., and Naylor, M.D., 2000, Light requirements for SAV survival and 

growth, in Kemp, M., Batiuk, R., and others, eds., Chesapeake Bay submerged aquatic vegetation water quality 

and habitat-based requirements and restoration targets: A second technical synthesis: U.S. Environmental 

Protection Agency 903-R-00-014, 217 p. 

Cerco, C.F., and Moore, K., 2001, System-wide submerged aquatic vegetation model for Chesapeake Bay: Estuaries, v. 24, no. 4, p. 522–534. 

Kemp, W.M., Batiuk, R., Bartleson, R., Bergstrom, P., Carter, V., Gallegos, C.L., Hunley, W., Karrh, L., Koch, 

E.W., Landwehr, J.M., Moore, K.A., Murray, L., Naylor, M., Rybicki, N.B., Stevenson, J.C., and Wilcox, D.J., 

2004, Habitat requirements for submerged aquatic vegetation in Chesapeake Bay: Water quality, light regime, 

and physical-chemical factors: Estuaries, v. 27, no. 3, p. 363–377. 

Landwehr, J.M., 2005, Determining the “Best” model for explaining water clarity variation during SAV seasons within the tidal tributary rivers of the Chesapeake Bay watershed, [abs] in the Proceedings of Estuarine 

Research Federation Meeting, October 16–20, 2005, Norfolk, Virginia. 

Rybicki, N.B., and Landwehr, J.M., 2007, Long-term changes in abundance and diversity of macrophyte and 

waterfowl populations in an estuary with exotic macrophytes and improving water quality: Limnology and 

Oceanography, v. 52, no. 3, p. 1,195–1,207. 

49 Chapter 11 

Floating mats of green algae and horned pondweed on the North Fork of the Tred Avon River in Easton, 

Maryland. Photograph by Jane Hawkey, IAN Image Library (www.ian.umces.edu/imagelibrary/). 
Chapter 12:Chapter 12: Factors Affecting Coastal W Factors Affecting Coastal Wetland Lossetland Loss 

and Restoration

50 

By Donald R. Cahoon 

Tidal and nontidal wetlands in the Chesapeake Bay watershed provide vital hydrologic, water-quality, and 

ecological functions. Situated at the interface of land and water, these valuable habitats are vulnerable 

to alteration and loss by human activities including direct conversion to non-wetland habitat by dredge-and-fill 

activities from land development, and to the effects of excessive nutrients, altered hydrology and runoff, contaminants, prescribed fire management, and invasive species. Processes such as sea-level rise and climate change also 

impact wetlands. Although local, State, and Federal regulations provide for protection of wetland resources, the 

conversion and loss of wetland habitats continue in the Bay watershed. Given the critical values of wetlands, the 

Chesapeake 2000 Agreement has a goal to achieve a net gain in wetlands by restoring 25,000 acres of tidal and 

nontidal wetlands by 2010. The USGS has synthesized findings on three topics: (1) sea-level rise and wetland 

loss, (2) wetland restoration, and (3) factors affecting wetland diversity. 

Chesapeake Bay is a drowned-river-valley estuary where emergent tidal wetlands migrate landward 

(upslope) in response to sea-level rise through the accumulation of mineral sediments and plant matter. Wetlands 

convert to shallow, open-water habitat (such as ponds) through interior marsh breakup if they do not build vertically at a pace equal to sea-level rise, which is currently about 3 mm/yr (millimeters per year) in the Bay (Douglas, 2001). The majority of tidal marsh in Chesapeake Bay is in the lower part of Maryland’s Eastern Shore. 

Extensive areas of submerged upland marshes in the Blackwater River-Fishing Bay region of Dorchester County, 

Maryland have converted to open water over the past century, particularly those marshes at Blackwater National 

Wildlife Refuge (BNWR). 

The rate of sea-level rise is predicted to increase two- to four-fold during the next century (Church and 

others, 2001). To determine what impact this sea-level change would have on wetland resources and to improve 

land-use planning within the immediate vicinity of BNWR for the next century, USGS scientists developed 

a digital elevation model (DEM) of BNWR land surfaces from LIDAR (Light Detection And Ranging) data 

collected in March 2002 (fig. 12.1A) (Larsen and others, 2004). DEM simulations using current sea-level rise 

rates (approximately 3 mm/yr) reveal that high marsh will convert to low marsh and low marsh will continue 

to convert to open water for the next century, assuming 2002 surface elevations remain unchanged (fig. 12.1B). 

Marsh loss rates will be higher, and the area impacted larger, for predicted future rates of sea-level rise (about 

6 mm/yr) (fig. 12.1C). Measurements of marsh vertical accretion, marsh-surface elevation change, and shallow 

soil subsidence made by USGS scientists over 5 consecutive years reveal that marsh-surface elevations are 

not static but are actually decreasing at most sampling stations at BNWR (G. Guntenspergen, U.S. Geological 

Survey, written commun., 2007). The declining marsh surface elevations at BNWR indicate that the DEM 

projections likely underestimate the extent of future marsh loss. 

The BNWR marsh system is characterized by low mineral sediment supply. Although major storms, 

such as Hurricane Isabel in 2003, deposit mineral sediments on the marsh every few decades, the increase in 

marsh elevation is often minimal. This soil organic matter accumulation comprised mostly of plant roots plays 

an important role in vertical soil development. Several factors affect the ability of the marshes at BNWR to 

build vertically through soil matter accumulation and therefore likely influence the rate of ongoing interior 

marsh breakup. These factors include grazing of vegetation by muskrat and nutria, altered flooding and salinity 

patterns, annual prescribed burning of vegetation, overabundance of nutrients, subsidence, and changes in the 

rate of sea-level rise (fig. 12.2). For example, intense grazing of marsh vegetation by nutria, an exotic species 

introduced to the United States from South America, severely reduced plant production at BNWR. Following 

the removal of more than 9,000 nutria from the region between 2002 and 2004, there has been strong recovery of 

marsh vegetation (M. Haramis, U.S. Geological Survey, written commun., 2007). These findings imply that the 

combination of sea-level rise and factors affecting sediment accumulation rates will govern the rate of wetland 

loss along the estuary. Thus, resource managers will have to fully understand the combination of factors affecting 

marsh loss at a particular site for successful wetland restoration. 

Sediments dredged from Chesapeake Bay navigation channels are being used to restore degraded wetland 

habitats within the Bay. During the past decade, several wetland restoration projects using dredged sediments 

have been undertaken, including Poplar Island, Anacostia River, and Barren Island. USGS investigations at 

Poplar Island brackish marshes in the central Bay (Erwin and others, 2003) and Kenilworth and Kingman tidal 

freshwater marshes in the Anacostia River, Washington, D.C. (Hammerschlag and others, 2006), revealed some 
51 51

Figure 12.1. Digital elevation model (DEM) forecasts of sea-level rise at Blackwater National Wildlife Refuge, 

Dorchester County, Maryland (A) 2002, (B) 2100 assuming a 3-millimeter-per-year rise in sea level, and (C) 2100 assuming 

a 6.2-millimeter-per-year rise in sea level (modified from Larsen and others, 2004). Sea-level rise during the coming 

century will impact tidal wetlands throughout the estuary. 
Chapter 12 

52 

Figure 12.2. Conceptual 

diagram of processes 

affecting wetland 

loss. Multiple factors 

influence marsh loss, 

including grazing of 

vegetation by muskrat 

and nutria, altered 

flooding and salinity 

patterns, annual 

prescribed burning of 

vegetation, and the 

rate of sea-level rise. 

Managers need to 

identify which factors 

are occurring, including 

continued sea-level 

rise, at a site to plan 

for successful wetland 

restoration. 

of the important processes controlling and limiting habitat quality in these reconstructed wetlands. At Kingman 

and Kenilworth marshes, studies showed there is a large, functionally diverse seed bank of wetland species in 

the Anacostia River available to colonize dredged sediment deposits (Neff and Baldwin, 2005). The combination 

of natural colonization and vegetative planting efforts facilitated rapid development of vegetated marsh habitats 

wherever restored soil elevations were suitable (Hammerschlag and others, 2006). However, marsh establishment at several sites was affected by grazing from an overabundance of resident Canada geese. USGS scientists 

also found geese herbivory to be an important factor in the decline of wild rice along the tidal Patuxent River 

(Haramis and Kearns, 2007). Removal of geese by hunting, and efforts to protect and re-establish rice by fencing 

and planting, led to successful restoration of this marsh type. The results imply that tidal wetland creation from 

dredged sediments is an effective method for restoring wetland habitats when the proper intertidal soil elevations 

are established and maintained and herbivory is managed. The results also imply the presence of an existing 

seedbank may enhance the success of wetland restoration. 

USGS studied the correlation between wetland restoration and changes in bird populations at Poplar 

Island, which eroded to less than 5 acres in 1996, and is undergoing wetland restoration that will include 550 

or more acres of constructed tidal wetlands, creeks, ponds, and mudflats. USGS found that the restored habitat 

is attracting desired common terns, least terns, snowy egrets, cattle egrets, American black ducks, and osprey 

(Erwin and others, 2003). This site is the only nesting area for common terns in the Maryland part of the Bay 

and thus, is critical to species survival in Maryland. However, constructed upland habitats also attract undesirable 

bird species such as gulls and great horned owls and mammal predators (red foxes) that harass or prey upon the 

desired bird species. 

USGS studies showed the diversity of coastal and nontidal wetlands are affected by multiple factors. Grazing by exotic species such as resident Canada geese at Anacostia River marshes (see above) can prohibit plant 

development and change vegetation composition. Exotic colonizers, such as Phragmites, can out-compete native 

vegetation and cause a loss in diversity and in habitat value and function. USGS studies of native and invasive 

varieties of Phragmites reveal that the invasive variety can grow in saltwater concentrations at which the native 

varieties cannot survive. They also produce more shoots per gram of rhizome tissue and have a higher relative 

growth rate than the native varieties (Vasquez and others, 2005). These findings imply that the diversity of a tidal 

wetland will depend on controlling competition and predation from non-desired species, which also attempt to 

colonize restored and native wetlands. 
In forested wetlands, patterns of plant zonation and diversity are strongly influenced by physical conditions, 

such as flooding patterns related to variations in river flows and local geomorphology (such as hydrogeomorphology). Nontidal riparian and flood-plain wetland communities are typically highly diverse areas in the landscape, 

but the reasons for this are poorly understood. Although plant diversity and composition can be attributed in part 

to hydrologic conditions (such as seasonal flooding patterns), recent USGS investigations reveal that hydrologic conditions alone do not describe forested wetland plant patterns (Alexander-Augustine and Hupp, 2002). 

Plant diversity is strongly impacted by hydroperiod (the period during which wetlands are flooded), micro-scale 

changes in relief, and upstream-downstream position within the stream corridor. More importantly, however, the 

influence of hydrogeomorphology on species richness varies with spatial scale. Species richness was described 

by hydrogeomorphic variables (downstream position, river discharge, stream power, and topographic relief) at the 

plot scale (400 square miles). Tree diversity was best explained at the site scale (1 hectare), and hydrogeomorphic 

variables were best explained at the watershed scale (Alexander-Augustine and Hupp, 2002). Thus, a combination of spatial, hydrologic, and geomorphic conditions explains plant diversity patterns in forested wetlands. 

These findings imply that the diversity of a tidal and forested wetland will depend on controlling competition and 

predation from non-desired species, which also attempt to colonize a restored wetland. Resource managers need 

to understand these conditions when developing management plans for riverine wetlands. 

References 

Alexander-Augustine, L.E., and Hupp, C.R., 2002, Process and pattern: Hydrogeomorphology and biodiversity 

in forested wetlands on the Chesapeake Bay Coastal Plain, in Proceedings of the 87th Annual Meeting of the 

Ecological Society of America and the 14th Annual International Conference of the Society for Ecological 

Restoration, August 4–9, 2002, Tucson, Arizona. 

Church, J.A., Gregory, J.M., Huybrechts, P., Kuhn, M., Lambeck, K., Nhuan, M.T., Qin, D., and Woodworth, 

P.L., 2001, Changes in sea level, in Climate Change 2001: The scientific basis. Contribution of Working 

Group I to the Third Assessment Report of the Intergovernmental Panel on Climate Change, Houghton, J.T., 

Ding, Y., Griggs, D.J., Noguer, M., van der Linden, P.J., Dai, X., Maskell, K., and Johnson, C.A., eds.: 

Cambridge, United Kingdom and New York, New York, USA, Cambridge University Press, p. 639–693. 

Douglas, B.C., 2001, Sea level change in the era of the recording tide gauge, p. 37–64, in Douglas, B.C., 

Kearney, M.S., and Leatherman, S.P., eds., Sea level rise: History and consequences: San Diego, California, 

Academic Press, 272 p. 

Erwin, R.M., Brinker, D., and Fruh, B., 2003, Poplar Island environmental restoration project: Build it and they 

(wildlife) will come, but are all welcome?, in Proceedings of the 13th Biennial Coastal Zone Conference, 

Baltimore, Maryland, July 13–17, 2003, NOAA/CSC/20322-CD. CD-ROM. 

Hammerschlag, R.S., Baldwin, A.H., Krafft, C.C., Paul, M.M., Brittingham, K.D., Rusello, K., and Hatfield, J.S., 

2006, Final Report—Five years of monitoring reconstructed freshwater tidal wetlands in the Urban Anacostia 

River, accessed June 6, 2007, at http://www.pwrc.usgs.gov/resshow/hammerschlag/anacostia.cfm. 

Haramis, G.M., and Kearns, G.D., 2007, Herbivory by resident Canada geese: The loss and restoration of wild 

rice along the tidal Patuxent River, Maryland: Journal of Wildlife Management, v. 71, p. 788–794. 

Larsen, C., Clark, I., Guntenspergen, G.R., Cahoon, D.R., Caruso, V., Hupp, C., and Yanosky, T., 2004, The 

Blackwater NWR inundation model. Rising sea level on a low-lying coast: Land use planning for wetlands: 

U.S. Geological Survey Open File Report 04–1302, available online only at http://pubs.usgs.gov/of/2004/1302/ 

Neff, K., and Baldwin, A., 2005, Seed dispersal into wetlands: Techniques and results for a restored tidal fresh 

water marsh: Wetlands, v. 25, no. 2, p. 392–404. 

Vasquez, E.A., Glenn, E.P., Brown, J.J., Guntenspergen, G.R., and Nelson, S.G., 2005, Salt tolerance underlies 

the cryptic invasion of North American salt marshes by an introduced haplotype of the common reed 

Phragmites australis (Poaceae): Marine Ecology Progress Series, v. 298, p. 1–8. 

­

5353 Chapter 12 
54 Chapter 13:Chapter 13: Factors Affecting Fish Health Factors Affecting Fish Health

By Vicki S. Blazer, Christopher A. Ottinger, and Christine L. Densmore 

The CBP has a restoration goal in the Chesapeake 2000 agreement to “restore, enhance, and protect 

finfish, shellfish, and other resources, their habitats and ecological relationships to sustain all fisheries 

and provide for a balanced ecosystem.” To address this restoration goal, the USGS had a science goal to “address 

the factors affecting the health of fish, wildlife, and their habitats.” This chapter summarizes USGS findings 

about fish health in the Bay and its watershed; the following chapter presents findings on waterbird populations. 

The USGS addressed four primary topics related to fish health including (1) menhaden and ulcerative lesions, 

(2) striped bass and mycobacteria, (3) tributary health assessments, and (4) intersex conditions in the Potomac. 

Multi-species management plans are being prepared by the National Oceanic and Atmospheric Administration 

(NOAA) and state partners for menhaden and striped bass as part of the CBP restoration goal for fisheries. 

In 1997, USGS scientists were asked to assist in research directed toward understanding the causes of the 

high incidence of skin lesions and kills of Atlantic menhaden in a number of Chesapeake Bay tributaries. Men 

haden are both ecologically critical and commercially valuable species. The lesions and fish kills were thought 

to be associated with the presence of Pfiesteria, which is believed to produce a toxin that affects fish as well as 

humans. However, the chronic nature of the lesions (fig. 13.1A) and the consistent presence of an invasive fungal 

pathogen (fig. 13.1B) raised many questions as to the actual cause of these lesions and the associated environ 

mental stressors (Blazer and others, 1999). 

­

­

Figure 13.1. Photographs 

of (A) ulcerative mycosis 

of menhaden, and (B) 

microscopic appearance of 

ulcers illustrating the invasive 

fungal hyphae and chronic 

inflammatory response 

within muscle tissue, 

underlying skin. The USGS 

and collaborators determined 

lesions on menhaden were 

caused by a fungal pathogen 

Aphanomyces invadans. 

It is now recognized that 

A. invadans is a serious 

pathogen of both estuarine 

and freshwater fishes 

worldwide. 
55 

Figure 13.2. Photograph of 

mycobacteriosis lesions in striped 

bass (courtesy of Maryland 

Department of Natural Resources). 

The USGS and collaborators 

identified the cause of skin lesions in 

striped bass to be mycobacteriosis, 

which are species of bacteria 

that can impact both marine 

and freshwater fish. Improving 

environmental conditions in the 

Bay could improve the ability of 

striped bass to resist the impact of 

mycobacteriosis. 

Research conducted by USGS scientists and collaborators resulted in the isolation and identification of the 

fungal pathogen Aphanomyces invadans, based on morphology, temperature and salinity growth characteristics, 

infectivity, and DNA sequence. Using the polymerase chain reaction (PCR) method, the same organism was 

found in menhaden with lesions from Delaware to South Carolina, and in similar lesions in selected freshwater fish species in Georgia and Louisiana (Blazer and others, 2002). Once isolated, the infectivity and relation 

of A. invadans to the skin ulcers of menhaden were investigated. Using injection of the infective zoospores, a 

dose-response in ulcer development and mortality was shown, with only about 10 spores needed to cause death 

in 50 percent of exposed menhaden (LD50). Injection of as few as one zoospore was sufficient to induce lesions 

in 31 percent of the fish (Kiryu and others, 2003). Experiments using bath exposure to the infective zoospores 

indicated that a low percentage of unstressed menhaden developed ulcers; however, stressed (net-handled) and 

traumatized menhaden had significantly higher mortality and incidence of ulcerative lesions (Kiryu and others, 

2002, 2003). These findings suggest that a high incidence of menhaden with lesions in the wild may be a result 

of environmental factors that favor the proliferation of the pathogen, as well as damage the skin and/or cause 

immunosuppression. 

Many factors, including water-quality parameters (temperature, dissolved oxygen, salinity, and nutrients), 

contaminants, toxins including algal toxins such as Pfiesteria, and other infectious agents may play a role in 

predisposing menhaden to A. invadans infections (Blazer and others, 1999; Reimschuessel and others, 2003). It 

is now recognized that A. invadans is serious pathogen of both estuarine and freshwater fishes worldwide. USGS 

scientists have worked with international colleagues to reexamine causal factors, describe a case definition, and 

attempt to standardize nomenclature for a number of syndromes associated with this pathogen (Baldock and others, 2005), as well as review existing knowledge (Blazer and others, 2005). The USGS findings imply that understanding the multiple factors that contribute to the occurrence of pathogens affecting fish will allow for more 

comprehensive multi-species ecosystem management plans to be developed to protect and restore fisheries in the 

Bay. The USGS findings also suggest that improving environmental conditions for menhaden, such as improved 

dissolved oxygen and lower contaminant concentrations, will make them less susceptible to A. invadans infections and other toxic algae. 

Striped bass are a highly prized sport and commercial fish in the Chesapeake Bay and along the eastern 

coast of the United States. They are also one of the five targeted species for which the CBP partners are developing Ecosystem-Based Fisheries Management Plans. The striped bass population has increased in the Bay after 

a moratorium helped provide relief from overfishing. In the late 1990s, however, fishermen and field biologists 

began to report a high incidence of emaciated striped bass, many with skin lesions (fig. 13.2). The USGS and 

collaborators identified the cause of the skin lesions to be mycobacteriosis, which are species of bacteria that can 
Chapter 13 

56 

USGS investigator processing fish for health evaluations. Fish are bled, organs cultured for 

bacteria and viruses, and pieces of tissue removed and fixed for microscopic evaluation. 

(Photograph by U.S. Geological Survey.) 

impact both marine and freshwater fish. A variety of previously described species of mycobacteria have been 

isolated from diseased Chesapeake Bay striped bass (Rhodes and others, 2004, 2005); some of these are potential 

human pathogens (Ottinger and others, 2005). The bacteria affects relatively high numbers of striped bass caught 

in the Chesapeake Bay with external lesions observed in up to 28 percent of bass caught and internal lesions in 

more than 62 percent (Ottinger and others, 2005). The multiple factors that promote the presence of mycobacteria 

and lower the resistance of striped bass to the bacteria are still not well understood. In 2006, the USGS co-hosted 

a workshop with NOAA to summarize the state of the knowledge and prioritize next steps to address the issue 

(Ottinger and Jacobs, 2006). The USGS and NOAA findings imply that the resistance of striped bass populations 

to disease appears to have been lowered due to multiple environmental conditions including low dissolved oxygen, contaminant concentrations, and improper diet. Improving these environmental conditions in the Bay could 

improve the ability of striped bass to resist the impact of mycobacteria. 

Given the problems with lesions in key fish species of the Chesapeake Bay, the USGS conducted tributary 

health assessments from 1998 to 2003 to better understand fish health in the Bay and its tributaries. The assessments included developing new methods to document fish health and to use the information to compare the 

“health” of various tributaries. White perch were selected as a sentinel species because they are less migratory 

than menhaden or striped bass. Several methods to assess fish health were enhanced (Blazer, 2000; Smith and 

others, 2002), while new methods were developed (including cellular and subcellular assays) to better identify 

immunosuppression (Gauthier and others, 2003; Harms and others 2000; Iwanowicz and others, 2004). Findings from the assessments showed that the suppression of the white perch’s immune system occurred in several 

tributaries and increased from the spring to the summer. The immunosuppression that occurred in the summer coincided with the finding of lesioned menhaden in the same tributaries (Harms, Ottinger, and KennedyStoskopf, 2000). The new techniques that USGS developed for fish-health assessments could be adopted by 
resource management agencies to provide a more thorough understanding of the health of fisheries in the Bay. 

The National Ocean Service (NOS) of NOAA is implementing these methods in a program to monitor fish health 

in Chesapeake Bay tributaries. 

Since 2002, USGS has been involved with numerous cooperators in examining potential causes for skin 

lesions and kills of various fish species in the watershed, particularly smallmouth bass and redbreast sunfish. The 

presence of various pathogens, including multiple bacteria, fungi, and parasites, indicated these fishes suffer from 

immunosuppression. During more comprehensive fish-health assessments, the presence of testicular oocytes, a 

form of intersex, was noted in the male bass. As previously stated, the CBP has a restoration goal “to achieve and 

maintain the water quality necessary to support the aquatic living resources of the Bay and its tributaries and to 

protect human health.” The toxic reduction strategy requires information on (1) the sources and occurrences of 

contaminants, and (2) the potential for contaminants to adversely impact aquatic-dependent wildlife. Reproductive abnormalities in fishes have been strongly linked with a variety of contaminants that have endocrine-modulating activity. Intersex, specifically testicular oocytes, has been linked to exposure to estrogenic compounds, 

which also have immunomodulatory activity. A preliminary assessment of the occurrence of testicular oocytes 

in smallmouth bass indicates that (1) it is widespread within the Potomac drainage, and (2) the prevalence and 

severity may increase as human population and agricultural intensity increase. Further research is underway to 

assess causes of intersex and fish kills in the watershed, document the spatial distribution, and compare species 

and life stages to determine the population effects. 

57 Chapter 13 

Fish kill in Choptank River, suspected to be from toxic algal bloom entrapped in floating seagrass mat. 

Photograph by Adrian Jones, IAN Image Library (www.ian.umces.edu/imagelibrary/). 
Chapter 13 

58 

References 

Baldock, F.C., Blazer, V.S., Callinan, R.B., Hatai, K., Karunasagar, I., Mohan, C.V., and Bondad-Reantaso, M.G., 

2005, Outcomes of a short expert consultation on epizootic ulcerative syndrome (EUS): Re-examination of 

causal factors, case definition and nomenclature, p. 553–586 in Diseases in Asian aquaculture V, Walker, P.J., 

Lester, R.G., and Bondad-Reantaso, M.G., eds.: Manila, Phillippines, Fish Health Section, Asian Fisheries 

Society, 633 p. 

Blazer, V.S., 2000, Necropsy-based fish health assessment, in Schmitt, C.J., and Dethloff, G.M., eds., Biomoni 

toring of Environmental Status and Trends (BEST) Program: Selected methods for monitoring chemical con

taminants and their effects in aquatic ecosystems: U.S. Geological Survey Information and Technology Report 

USGS/BRD-2000-0005, p. 18–22. 

Blazer, V.S., Bondad-Reantaso, M.G., Callinan, R.B., Chinabut, S., Hatai, K., Lilley, J.H., and Mohan, C.V., 

2005, Aphanomyces invadans (= A. piscicida): A serious pathogen of estuarine and freshwater fishes, 

p. 24–41 (chapter) in Health and Diseases of Aquatic Organisms: Bilateral Perspectives, Proceedings of the 

Second Bilateral Conference between Russia and the United States, Cipriano, R.C., Shchelkunov, I.S., and 

Faisal, M., eds.: East Lansing, Michigan, Michigan State University. 

Blazer, V.S., Lilley, J.H., Schill, W.B., Kiryu, Y., Densmore, C.L., Panyawachira, V., and Chinabut, S., 2002, 

Aphanomyces invadans in Atlantic menhaden along the east coast of the United States: Journal of Aquatic 

Animal Health, v. 14, no. 1, p. 1–10. 

Blazer, V.S., Vogelbein, W.K., Densmore, C.L., May, E.B., Lilley, J.H., and Zwerner, D.E., 1999, Aphanomyces 

as a cause of ulcerative skin lesions of menhaden from Chesapeake Bay tributaries: Journal of Aquatic Animal 

Health, v. 11, no. 4, p. 340–349. 

Gauthier, D.T., Cartwright, D.D., Densmore, C.L., Blazer, V.S., and Ottinger, C.A., 2003, Measurement of in 

vitro mitogenesis in fish: ELISA-based detection of the thymidine analogue 5’-bromo-2’-deoxyuridine: 

Fish and Shellfish Immunology, v. 14, p. 279–288. 

Harms, C.A., Ottinger, C.A., Blazer, V.S., Densmore, C.L., Pieper, L.H., and Kennedy-Stoskopf, S., 2000, Quan 

titative polymerase chain reaction for transforming growth factor-β applied to a field study of fish health in 

Chesapeake Bay tributaries: Environmental Health Perspectives, v. 108, no. 5, p. 447–452. 

Harms, C.A., Ottinger, C.A., and Kennedy-Stoskopf, S., 2000, Correlation of transforming growth factor-β messenger RNA (TGF-β mRNA) expression with cellular immunoassays in Triamcinolone-treated captive hybrid 

striped bass: Journal of Aquatic Animal Health, v. 12, no. 1, p. 9–17. 

­

­

­
Iwanowicz, L.R., Densmore, C.L., and Ottinger, C.A., 2004, A Calcein, AM based cytotoxic-cell assay for fish 

leucocytes: Fish and Shellfish Immunology, v. 16, no. 2, p. 127–137. 

Kiryu, Y., Shields, J.D., Vogelbein, W.K., Kator, H., and Blazer, V.S., 2003, Infectivity and pathogenicity of the 

oomycete, Aphanomyces invadans, in Atlantic menhaden, Brevoortia tyrannus: Diseases of Aquatic Organisms, v. 54, no. 2, p. 135–146. 

Kiryu, Y., Shields, J.D., Vogelbein, W.K., Zwerner, D.E., and Kator, H., 2002, Induction of skin ulcers in Atlantic 

menhaden by injection and aqueous exposure to the zoospores of Aphanomyces invadans: Journal of Aquatic 

Animal Health, v. 14, no. 1, p. 11–24. 

Ottinger, C.A., Blazer, V.S., Densmore, C.L., Gauthier, D.T., Kator, H., Panek, F.M., Rhodes, M.W., and Vogelbein, W., 2005, Mycobacteriosis in Chesapeake Bay striped bass (Morone saxatilis), p. 238–243 in Health 

and Diseases of Aquatic Organisms: Bilateral Perspectives, Proceedings of the Second Bilateral Conference 

between Russia and the United States, Cipriano, R.C., Shchelkunov, I.S., and Faisal, M., eds.: East Lansing, 

Michigan, Michigan State University. 

Ottinger, C.A., and Jacobs, J.M., 2006, USGS/NOAA workshop on mycobacteriosis in striped bass, May 7–10, 

2006, Annapolis, Maryland: U.S. Geological Survey Scientific Investigations Report 2006–5214, 42 p. 

Reimschuessel, R., Gieseker, C.M., Driscoll, C., Baya, A., Kane, A.S., Blazer, V.S., Evans, J.J., Kent, M.L., 

Moran, J.D.W., and Poynton, S.L., 2003, Myxosporean plasmodial infection associated with ulcerative lesions 

in young-of-the-year Atlantic menhaden in a tributary of the Chesapeake Bay, and possible links to Kudoa 

clupeidae: Diseases of Aquatic Organisms, v. 53, no. 2, p. 143–166. 

Rhodes, M.W., Kator, H., Kaattari, I., Gauthier, D., Vogelbein, W., and Ottinger, C.A., 2004, Isolation and char 

acterization of mycobacteria from striped bass (Morone saxatilis) from Chesapeake Bay: Diseases of Aquatic 

Organisms, v. 61, no. 1–2, p. 41–51. 

Rhodes, M.W., Kator, H., McNabb, A., Deshayes, C., Reyrat, J., Brown-Elliott, B.A., Wallace, R., Jr., Trott, 

K.A., Parker, J.M., Lifland, B., Osterhout, G., Kaattari, I., Reece, K., Vogelbein, W., and Ottinger, C.A., 2005, 

Mycobacterium pseudoshottsii sp. nov., a slowly growing chromogenic species isolated from Chesapeake Bay 

striped bass (Morone saxatilis): International Journal of Systematic and Evolutionary Microbiology, v. 55, 

p. 1,139–1,147. 

Smith, S.B., Donahue, A.P., Lipkin, R.J., Blazer, V.S., Schmitt, C.J., and Goede, R.W., 2002, Illustrated field 

guide for assessing external and internal anomalies in fish: U.S. Geological Survey Information and Technology Report 2002–2007, 46 p. 

­

59 Chapter 13 
60 Chapter 14:Chapter 14: Changes in Food and Habitats of W Changes in Food and Habitats of Waterbirdsaterbirds

By Matthew C. Perry 

The Chesapeake Bay is an important area for waterbirds because it is located in the Atlantic Flyway. 

The Bay winters over one million ducks, geese, and swans annually, provides stopover habitat to 

thousands of migrating marsh, shore, and wading birds, and maintains substantial breeding populations of 

colonial waterbird species. While migratory bird protection is not one of the goals in Chesapeake 2000, the DOI 

has the responsibility to restore populations under the North American Waterfowl Management Plan. The USGS 

supported the DOI management need through studies addressing the factors affecting waterbird populations and 

their habitats. The synthesis of USGS findings is focused on loss of food sources and alteration of habitat for 

waterbird populations. 

During 2001–06, USGS focused on the factors affecting the declines in sea duck populations, which are a 

group of ducks not frequently seen by the public due to the fact that they feed in deep water in the Bay. USGS 

findings indicate that these declines could be from changes in diversity and abundance of shellfish and other 

benthic foods (Kidwell and Perry, 2005; Perry and others, 2005; Niven and others, 2005). The declines of food 

sources, such as mussels and other invertebrates, and changes in foodweb and habitat relations (fig. 14.1) have 

possibly contributed to the declines in sea ducks. The findings imply that the collapse of the once vast native 

oyster population has possibly had a major impact on sea ducks by removing mussels and other invertebrates 

associated with the oyster bars. Decline in these communities represents a major loss in foods and foraging habitat available to a variety of waterbirds. The findings imply that if oyster populations and other invertebrates are 

restored in the Bay, populations of waterbirds that depend on them as a food source could also increase. 

Food sources and habitats of waterbirds also are affected by exotic and invasive species. The exotic 

mute swan has increased its population size in Chesapeake Bay (Maryland and Virginia) to approximately 

4,500 since 1962, when five swans were released in the Bay (Perry, 2004). The Bay population of mute swans 

now represents 30 percent of the total Atlantic Flyway population (12,600), and had a phenomenal increase of 

1,200 percent from 1986 to 1999. Unlike the tundra swans that migrate to the Bay for the winter, the mute swan 

is a year-round resident. There are concerns about their impact on nesting native waterbirds and the consumption 

of SAV. Although data on the consumption of SAV by nesting mute swans and their offspring during the spring 

and summer are limited, USGS studies of their food habits show that mute swans rely heavily on SAV during 

these months (Perry and others, 2004). It has been reported that a mute swan can consume about 8 pounds of 

SAV per day, raising concerns among resource managers (Perry and others, 2004). 

While concern grows over the increasing number of exotic mute swans on the Chesapeake Bay, less attention seems to be given to the highly familiar and native Canada goose, which has developed unprecedented 

non-migratory, or resident, populations over time. Although nuisance flocks of Canada geese have been well 

developed at city parks, athletic fields, and golf courses over the past three decades, recent expansion of populations to an estimated one million birds in the Atlantic Flyway, and to over 500,000 in Maryland, carries a threat 

of broader ecological consequences. USGS findings revealed that herbivory by invasive resident Canada geese 

has led to a major decline of wild rice in tidal marshes of the Patuxent River and probably in other areas (Haramis and Kearns, 2004). Wild rice is a critical fall resource to a variety of migrating wetland birds, especially 

sora rails, and rails have declined in abundance with loss of these habitats. Chesapeake Bay historically provided 

valuable habitat for wintering rails and several species have supported hunting seasons. These findings imply that 

better understanding of factors affecting food sources and habitat of waterbirds will give managers more reliable 

information to manage and regulate waterbird populations. Monitoring the effectiveness of management plans 

of bird populations that are considered invasive or problematic (such as mute swans and resident geese) will be 

needed to determine if strategies need to be revised. 
61

Figure 14.1. Generalized food web for some of the major waterbirds that frequent the Chesapeake Bay 

(modified from Perry and others, 2005). Food sources and habitats of waterbirds are affected by multiple factors, 

including exotic and invasive species. A better understanding of these factors will provide managers with 

stronger information to manage and regulate populations.
Chapter 14 

62 

Collection of benthic samples which are used to help determine food sources for sea ducks in 

Chesapeake Bay. (Photograph courtesy of Matthew Perry, U.S. Geological Survey.) 

References 

Haramis, G.M., and Kearns, G.D., 2004, Invasive herbivory: Resident Canada geese and the decline of wild rice 

along the tidal Patuxent River, p. 37–38 in Perry, M.C., ed., Mute swans and their Chesapeake Bay habitats, in 

Proceedings of a symposium, U.S. Geological Survey Information and Technology Report 2004–0005, 59 p. 

Kidwell, D.M., and Perry, M.C., 2005, Delineation of surf scoter habitat in Chesapeake Bay, Maryland: Macrobenthic and sediment composition of surf scoter feeding sites, [abs.] in Perry, M.C., Second North American 

Sea Duck Conference, November 7–11, 2005, Annapolis, Maryland, Program and Abstracts, USGS Patuxent 

Wildlife Research Center, Maryland, 123 p. (p. 91). 

Niven, D.K., Sauer, J.R., and Butcher, G.S., 2005, Population trends of North American sea ducks based on 

Christmas bird count and Breeding Bird Survey data, [abs.] in Perry, M.C., 2005, Second North American 

Sea Duck Conference, November 7–11, 2005, Annapolis, Maryland, Program and Abstracts, USGS Patuxent 

Wildlife Research Center, Md., 123 p. (p. 101) 

Perry, M.C., ed., 2004, Mute swans and their Chesapeake Bay habitats, proceedings of a symposium: U.S. Geological Survey Information and Technology Report 2004–0005, 59 p. 

Perry, M.C., Osenton, P.C., and Lohnes, E.J.R., 2004, Food habits of mute swans in Chesapeake Bay, p. 31–36 in 

Perry, M.C., ed., Mute swans and their Chesapeake Bay habitats, proceedings of a symposium: U.S. Geological Survey Information and Technology Report 2004–0005, 59 p. 

Perry, M.C., Osenton, P.C., Wells-Berlin, A.M., and Kidwell, D.M., 2005, Food selection among Atlantic Coast 

sea ducks in relation to historic food habits, [abs.] in Perry, M.C., Second North American Sea Duck Conference, November 7–11, 2005, Annapolis, Maryland, Program and Abstracts, USGS Patuxent Wildlife Research 

Center, Maryland, 123 p. (p. 105). 
63 Chapter 14 

Birds on the water at Blackwater National Wildlife Refuge. Photograph by Heather Lane, IAN Image Library 

(www.ian.umces.edu/imagelibrary/). 
Prepared by Publishing Service Centers 3 and 1.
 


Edited by Valerie M. Gaine.
 


Graphics by Timothy W. Auer.
 


Layout by Ann Marie Squillacci.
 


For additional information, contact:
 


USGS Chesapeake Bay Coordinator 
 

MD-DE-DC Water Science Center
 


U.S. Geological Survey 

5522 Research Park Drive 

Baltimore, MD 21228 

or visit our Web site at: 

http://chesapeake.usgs.gov