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USGS Circular 1316

Synthesis of U.S. Geological Survey Science for the Chesapeake Bay Ecosystem and Implications for Environmental Management

Chapter 1: Introduction and Overview of Findings
By Scott W. Phillips

USGS Chesapeake

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 mid- 1980s, 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 restoration 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 writing 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.

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.

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 implement, 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.

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

Findings Related to the Chesapeake Bay Program (CBP) Chesapeake 2000 Goal for Sound Land Use

CBP Management Goal & Information Need USGS Scientific Findings Management Implications Application

Goal: Reduce the rate of harmful sprawl in the watershed.
Need: Develop methods to document and monitor harmful sprawl.

The USGS analyzed different indicators for harmful sprawl, recommended the CBP use impervious surface as an indicator, and analyzed changes in impervious surface. Analysis of impervious surface in the watershed showed impervious surface accounts for 21 percent of all urban lands in the watershed. Impervious surfaces increased 41 percent during the 1990s compared to an 8-percent increase in population. (See Chapter 2)

The rate of increase of impervious surface implies there will be a more rapid delivery of nutrients to streams and an increase in sediment erosion. State and local governments are using the results to conserve habitats to reduce runoff, increase implementation of stream-restoration actions, and develop policies to reduce impacts of impervious surfaces.

Goal: Preserve 20 percent of land in the watershed.
Need: Identify high value lands to help guide preservation efforts.

USGS collaborated with CBP partners on the Resource Lands Assessment, which identified lands that have high ecological, water-quality, economic, and cultural value. The USGS conducted a vulnerability assessment to predict the risk of conversion of these high-value lands to urban areas by 2010.  The results identified several areas under high development pressure including the Delmarva Peninsula, southern Pennsylvania, and the I-95 corridor. (See Chapter 2)

Land-use change due to population increase will continue to cause loss of high-value lands. State agencies and land-preservation organizations have used the methods from the vulnerability assessment to better target land acquisition and conservation programs.

Goal: Assess potential nutrient and sediment loads in the future due to population increase.
Need: Forecasts of nutrient and sediment loads to the Bay.

The USGS began to develop a land-use change model to predict the impacts of population growth. The model will be linked with the CBP watershed model to provide scenarios of nutrient and sediment loading during 2010-30. (See Chapter 2)

The predictions of nutrient and sediment loads during 2010-30 will be used to formulate additional strategies needed to remove the Bay from the impaired waters list.

Findings Related to the CBP Chesapeake 2000 Goal for Water Quality—Nutrients.

CBP Management Goal & Information Need USGS Scientific Findings Management Implications Application

Goal: Implement the CBP tributary strategies to reduce nutrients to the Bay and improve water-quality conditions for living resources.
Need: Better define the spatial distribution of the sources and transport of nutrients entering the Bay.

The USGS provided a better understanding of nutrient sources and their transport to streams and the estuary using a watershed model application know as SPAtially Referenced Regressions On Watershed attributes (SPARROW). The SPARROW model results have shown the spatial distribution of high priority nutrient sources (agriculture, urban lands, and point sources) and their delivery to the Bay.  The SPARROW model results were also used to improve the spatial resolution of the CBP Phase V watershed model and to design the CBP nontidal water-quality network (see Chapter 3)

Resource managers have identified several nutrient sources (agriculture, urban lands, and point sources) as a high priority for nutrient-reduction actions. The SPARROW model results are being used to identify priority areas for geographic targeting of management actions.

Goal: Reduce nutrients to remove the Bay from the impaired waters list by 2010.
Need: Better define the transport time of nutrients being delivered to the Bay.

The USGS determined that on average, ground water was found to contribute about 50 percent of the water and nitrogen to the streams and rivers that enter the Bay. The highest concentration of nitrogen in ground water occurred in areas overlain by agricultural land. The age of ground water, which affects the time it takes for nitrogen to travel through shallow aquifers from the land to a stream, varies from modern to over 50 years old. About 50 percent of the total water to streams is modern, with 90 percent moving from its source to a stream in less than 15 years. (See Chapter 4)

The hydrologic pathways of nutrients in the watershed (surface water or ground water) will influence the lag time between implementing management actions 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.

Goal: Reduce nutrient delivery to remove the Bay from the impaired waters list by 2010.
Need: Improve monitoring and better define the factors affecting the delivery of nutrients entering the Bay.

The USGS worked with the U.S. Environmental Protection Agency (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. The USGS has improved techniques to assess water-quality change in the Bay watershed and explain the factors affecting the change. Results from the analysis show streamflow variability has a large influence on the annual and seasonal loads in the watershed and their delivery to the Bay. When techniques are used to compensate for the effect of flow variability, there has been a decrease in nitrogen and phosphorus concentrations at a majority of the sites in the watershed. (see Chapter 5)

The watershed monitoring information was used to help assess progress in meeting goals to remove the Bay from the impaired waters list by 2010. Concentrations are not decreasing at a rate that would reduce nutrient loads sufficiently to remove the Bay from the impaired waters list by 2010. The USEPA has recently revised the timeline for delisting the Bay to be beyond 2010.

Findings Related to the CBP Chesapeake 2000 Goal for Water Quality—Sediment

CBP Management Goal & Information Need USGS Scientific Findings Management Implications Application

Goal: Reduce sediment to improve water clarity for submerged aquatic vegetation (SAV) and remove the Bay from the impaired waters list.
Need: Understand the sources of sediment in the watershed and their delivery to the Bay.

USGS analysis of historical sediment data found the highest yields in the Piedmont, with lowest yields in the Coastal Plain. Based on results from three research studies, the portion of sediment from land erosion and stream corridor erosion varies in individual watersheds and needs to be defined for local areas. There is a significant amount of sediment and associated nutrients that are being stored in the forest and wetland assemblages on the Coastal Plain prior to their delivery to the estuary. Sediment is also being stored in stream corridors and in reservoirs. (See Chapter 6)

Sediment-reduction actions need to be implemented both in the watershed and in near-shore areas to improve stream and estuary conditions. In the watershed, practices should be emphasized in the Piedmont to decrease sediment to tidal-fresh areas of the estuary. Protecting and restoring forest and wetland assemblages in Coastal Plain stream corridors can be another effective approach to minimizing the transport of sediment to the estuary. Maintaining the sediment storage capacity of reservoirs and dams will also slow the delivery of sediment from the watershed to the estuary.

Goal: Reduce sediment to improve water clarity for SAV and remove the Bay from the impaired waters list.
Need: Better document the sediment sources and factors affecting delivery to the Bay.

USGS synthesis of sediment information found that sediment sources to the Bay include watershed inputs, erosion of shorelines and wetlands, and ocean inputs. The relative importance of the sources varies in different regions of the Bay. Watershed sources affect the tidal fresh regions of the estuary. Below the estuarine turbidity maximum, which is the area of mixing between freshwater and saline water, erosion from shorelines is a primary source. The ocean and shoreline erosion are primary sources of sediment in the southern Bay. Sea-level rise is an important process affecting sediment erosion from low-lying shoreline areas. Sediment travel times from the watershed to the estuary may be decades to centuries. (See Chapter 7)

In addition to watershed management actions, practices to improve water clarity in the estuary should be focused at shoreline sources. Practices to address shoreline erosion must also consider the sediment erosion due to continued sea-level rise and climate warming. 

Findings Related to the CBP Chesapeake 2000 Goal for Water Quality—Contaminants

CBP Management Goal & Information Need USGS Scientific Findings Management Implications Application

Goal: Have a “toxics free” Bay to improve conditions for aquatic- dependent wildlife.
Need: Define the occurrence of contaminants in the Bay watershed.

Synthetic organic pesticides, along with certain degradation products, have been widely detected in ground water and streams in the Bay watershed. The most commonly detected pesticides are herbicides used on corn, soybeans, and small grains. Pesticides were also detected in urban areas, including insecticides and the herbicide prometon. Pesticides are present year round but changes in concentrations reflect application rates and properties affecting their movement. Emerging contaminants such as pharmaceuticals and hormones are also being detected in the Bay watershed, with the highest number being detected in municipal effluent. (see Chapter 8)

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. The occurrence of emerging contaminants and their environmental consequences needs to be better defined.

Goal: Have a “toxics free” Bay to improve conditions for aquatic- dependent wildlife
Need: Document the effect of contaminants on water birds and wildlife.

Concentrations of DDT and its breakdown products and other organochlorine pesticides have declined since their ban in the 1970s but PCB concentrations remain unchanged. Results from USGS and U.S. Fish and Wildlife studies indicate that pesticide concentrations are below thresholds that cause adverse reproductive effects for some water in the "toxic areas of concern" in the Bay watershed (Baltimore Harbor, Anacostia River, and Elizabeth River). (See Chapter 9)

Management actions in the 1970s and 1980s restricting the use of chlorinated pesticides have had several results for wildlife. The populations of many fish-eating birds, such as the bald eagle, have rebounded. However, other contaminants that are slow to break down remain a threat to wildlife.

Findings Related to the CBP Chesapeake 2000 Goal for Vital Habitats—Estuary Habitats

CBP Management Goal & Information Need USGS Scientific Findings Management Implications Application

Goal: Restore water-quality conditions to support fisheries.
Need: Understand the effect of long-term changes in climate variability on estuary water quality.

The USGS found that climate variability over the past several thousand years has affected the salinity, temperature, and dissolved oxygen conditions in the Bay. Changes in these parameters show that the 20th century is characterized by anomalous climate variability when compared to the last 2,000 years. Water temperatures in the Bay during the late 19th and 20th centuries exhibited greater extremes than those of the previous 2,000 years. Hypoxia and anoxia were much most extensive and severe during the past four decades than at any time in the past 2,500 years. (See Chapter 10)

The results imply that management actions to address climate variability and associated global warming need to be incorporated into current strategies to restore the estuary. Management actions that address delivery of nutrient and sediment loads under varying river-flow conditions will need to be emphasized to help address the impacts of climate change and variability.

Goal: Restore 185,000 acres of submerged aquatic vegetation (SAV) in the estuary.
Need: Define the factors affecting water clarity and SAV.

Investigations showed that the factors affecting water clarity vary in different areas of the estuary. Total suspended solids, which include both organic matter and inorganic solids (clay, silt) are the primary factor affecting water clarity in the mid-channel sites in the estuary. At shallow water sites, organic solids were the primary factors affecting clarity during a low-flow year. Investigations revealed SAV has returned in some areas of the Potomac, including increased in both native and non-native species. (See Chapter 11)

The results imply that managers need to further define the primary cause of degraded water clarity to select the types on sediment- and nutrient-reduction strategies needed in different areas of the estuary.

Goal: Restore 25,000 acres of wetlands.
Need: Define the factors affecting wetlands loss and restoration.

Sea-level rise, due to climate change, will impact tidal wetlands during the coming century. USGS forecasts of wetland change in the Blackwater National Wildlife Refuge reveal that marsh will convert will continue to convert to open water for the next century.  Additional factors influencing marsh loss include grazing of vegetation by nutria and waterfowl, altered flooding and salinity patterns, and annual prescribed burning of vegetation. (See Chapter 12) Coastal wetland loss and landward migration will continue due to sea-level rise. Managers need to consider land-use policies that allow for landward migration of wetlands to help preserve and restore tidal wetlands. 

Goal: Restore 25,000 acres of wetlands.
Need: Science to support restoration and conservation.

The presence of an existing seed bank is important for wetland restoration. Tidal wetland creation from dredged sediments is an effective method for restoring wetland habitats when the proper intertidal soil elevations are established and maintained. Controlling competition and predation from non-desired species affects the function and structure of restored wetlands. (See Chapter 12) The presence of an existing seed bank, and understanding the seed dispersal pathways, can increase success and reduce costs of wetland restoration projects. The success of the restoration efforts will also depend on controlling competition and predation from non-desired species, which also attempt to colonize a restored wetland.

Findings Related to the CBP Chesapeake 2000 Goal for Living Resources

CBP Management Goal & Information Need USGS Scientific Findings Management Implications Application

Goal: Restore, enhance and protect fisheries.
Need: Define the factors affecting lesions on menhaden and relation to Pfiesteria.

The USGS and collaborators determined lesions on menhaden were caused by a fungal pathogen (Aphamonyces invadans). The same organism was demonstrated in menhaden from Delaware to South Carolina. It is now recognized that A. invadans is a serious pathogen of both estuarine and freshwater fishes worldwide. (See Chapter 13)

The USGS findings 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.

Goal: Restore, enhance and protect fisheries.
Need: Determine the cause of lesions in striped bass.

The USGS and collaborators identified the cause of the skin lesions in striped bass as mycobacteriosis, which are species of bacteria that can impact both marine and freshwater fish. The USGS co-hosted a workshop with National Oceanic and Atmospheric Administration (NOAA) to summarize information about mycobacteriosis. Bacteria affect relatively high numbers of striped bass, with external lesions in up to 28 percent of the fish caught and internal lesions in more than 62 percent. (See Chapter 13)

The findings imply 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 environmental conditions in the Bay could improve the ability of striped bass to resist the impact of mycobacteria.

Goal: Restore, enhance and protect fisheries.
Need: Develop methods to assess fish health. 

The USGS conducted tributary health assessments from 1998–2003 to understand fish health in the Bay and its tributaries. The assessments included developing new methods to document fish health and use the information to compare the “health” of various tributaries. Findings from the assessments showed the suppression of the white perch’s immune system occurred in several tributaries and changed seasonally. (See Chapter 13)

The National Ocean Service of NOAA is implementing these methods in a program to monitor fish health in the Chesapeake Bay tributaries.

Goal: Restore, enhance and protect fisheries
Need: Assess cause of “intersex” conditions of fish in the Potomac basin.

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. During more comprehensive fish health assessments, the presence of testicular oocytes, a form of intersex, was noted in the male bass. Reproductive abnormalities in fish have been strongly linked with a variety of contaminants that have endocrine-modulating activity. (See Chapter 13)

Management agencies are awaiting the results from research to assess causes of intersex and fish kills in the watershed to begin to formulate actions and policies.

Department of Interior (DOI) Goal: Manage populations of waterbirds.
Need: Understand decline in waterfowl populations.

The USGS has focused on the factors affecting the declines in seaduck 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 suggest these declines could be from changes in diversity and abundance of shellfish and other benthic foods. (See Chapter 14).

The findings imply that management efforts to increase oyster populations could also benefit seaduck populations.

DOI Goal: Manage populations of waterbirds.
Need: Understand impacts of exotic species.

Food sources and habitats of waterbirds also are affected by exotic and invasive species. Although data on the reduction of SAV by nesting mute swans and their offspring during the spring and summer are limited, studies on their food habits show that mute swans rely heavily on SAV during these months. USGS findings revealed a major decline of wild rice in tidal marshes of the Patuxent River due to consumption by resident Canada geese (See Chapter 14).

These findings imply a better understanding of factors affecting food sources and habitat of waterbirds will provide managers with more reliable information to manage and regulate populations.

Photo of the view looking south along the mouth of the Elk River.

View looking south along the mouth of the Elk River. In the foreground is recent development. Photograph by Jane Thomas, IAN Image Library (

Figure 1.2 shows different ecoregions in the Chesapeake Bay watershed.

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.


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.

Grassed waterways are an agricultural bes management practice

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 (

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