EPA/600/R-15/287 | May 2017 

www.epa.gov/ord

Implementing the Biological Condition

Gradient Framework for Management 

of Estuaries and Coasts 

Office of Research and Development

National Health and Environmental Effects Research Laboratory
EPA/600/R-15/287

May 2017

www.epa.gov/ord

Implementing the Biological Condition Gradient Framework 

for Management of Estuaries and Coasts

by

Giancarlo Cicchetti

Marguerite C. Pelletier

Kenneth J. Rocha

Patricia Bradley (retired)

Atlantic Ecology Division

National Health and Environmental Effects Research Laboratory

Narragansett, RI

Deborah L. Santavy

Gulf Ecology Division

National Health and Environmental Effects Research Laboratory

Gulf Breeze, FL

Margherita E. Pryor

Region 1, 

Boston, MA

Susan K. Jackson

Office of Water

Washington, DC

Susan P. Davies (retired)

Maine Department of Environmental Protection

Augusta, ME

Christopher F. Deacutis

RI Department of Environmental Management

Jamestown, RI

Emily J. Shumchenia

Great Lakes Environmental Center

Traverse City, MI

National Health and Environmental Effects Research Laboratory

Office of Research and Development

U.S. Environmental Protection Agency

Atlantic Ecology Division

Narragansett, RI
Implementing the Biological Condition Gradient Framework

ii

Notice and Disclaimer

The EPA Office of Water’s Biological Condition Gradient method was originally developed for 

application to freshwater streams. This document adapts that approach for use in larger and more 

complex estuarine and coastal systems. The discussions in this document are intended solely to 

provide information on advancements in the field of biological assessment. The EPA through its Office 

of Research and Development, Office of Water, and Region 1 funded and collaborated in the research 

described here. This document has been subjected to the Agency’s peer and administrative review 

and has been approved for publication as an EPA document. Mention of trade names or commercial

products does not constitute endorsement or recommendation for use. While this manual describes

EPA’s scientific recommendations regarding biological assessment to help protect aquatic life in 

coastal and estuarine ecosystems, it does not substitute for CWA or EPA regulations, nor is it a 

regulation itself. Thus, it cannot impose legally binding requirements on EPA, states, territories, 

tribes, or the regulated community and might not apply to a particular situation or circumstance. 

EPA may change this guidance in the future. All environmental data in this document are reported in 

the published literature and are used here to illustrate the Biological Condition Gradient development 

process. This is a contribution to the EPA Office of Research and Development’s Safe and Sustainable 

Waters Research Program.

The appropriate citation for this report is:

Cicchetti, G., M.C. Pelletier, K.J. Rocha, P. Bradley, D.L. Santavy, M.E. Pryor, S.K. Jackson, S.P. Davies, 

C.F. Deacutis, and E.J. Shumchenia. 2017. Implementing the Biological Condition Gradient Framework 

for Management of Estuaries and Coasts. U.S. Environmental Protection Agency, Office of Research 

and Development, Atlantic Ecology Division, Narragansett RI. EPA/600/R-15/287.

This document can be downloaded from:

https://www.epa.gov/nscep

Cover photos, clockwise from upper left: 1) Entrance to Point Judith Pond, Narragansett, RI. 

2) Scientist collecting data, La Parguera reefs, PR. 3) Shipping cranes, San Pedro Harbor, Los 

Angeles, CA. 4) Kayakers enjoying Caribbean coastal waters. 5) Elkhorn coral, Dominican Republic. 

6) Mary Donovan Marsh, Little Compton, RI. 
Table of Contents

iii

Table of Contents

Notice and Disclaimer...............................................................................................................................ii

Figures......................................................................................................................................................iv

Tables........................................................................................................................................................ v

List of Acronyms ...................................................................................................................................... vi

Acknowledgments .................................................................................................................................. vii

Executive Summary ............................................................................................................................... viii

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

2. The BCG in freshwater systems........................................................................................................... 5

2.1. Key terms for BCG......................................................................................................................... 7

2.2. Overview of BCG........................................................................................................................... 7

3. Estuarine and coastal BCG implementation........................................................................................ 9

3.1. How can the BCG be implemented in estuarine and coastal settings?........................................ 9

3.2. Development of estuarine/coastal BCG guidance......................................................................12

4. Components of the estuarine/coastal BCG .......................................................................................23

4.1 Attributes and measures .............................................................................................................23

4.2. BCG levels....................................................................................................................................29

4.3. The Generalized Stress Axis........................................................................................................36

5. Application of the approach: details and examples..........................................................................39

5.1. Classification ...............................................................................................................................39

5.2. How can the BCG improve management of estuaries and coastal waterbodies?.....................42

5.3. The BCG as part of larger social/ecological/economic management approaches.....................44

5.4. Overall estuary or waterbody condition.....................................................................................49

5.5. Sustainability and the estuarine/coastal BCG ............................................................................56

6. Results from early pilots....................................................................................................................61

6.1. Narragansett Bay ........................................................................................................................61

6.2. Tampa Bay...................................................................................................................................66

6.3. Mobile Bay ..................................................................................................................................71

6.4. Lower Columbia River.................................................................................................................74

6.5. Puerto Rico coral reefs................................................................................................................77

7. Summary and next steps ...................................................................................................................85

References..............................................................................................................................................89

Appendix A. Attributes and narratives to assign BCG levels in streams ................................................97

Appendix B. The BCG for estuaries and coasts: FAQs ..........................................................................102

Appendix C. Attendees at the 2008 workshop.....................................................................................109

Appendix D. Attendees at the 2009 workshop ....................................................................................110
Implementing the Biological Condition Gradient Framework

iv

Figures 

Figure 1-1. Docks, roads, commercial fishing vessels, marine transportation, and industry in 

Point Judith Harbor, RI ...................................................................................................................... 1

Figure 1-2. Charleston Harbor, SC, an important low-lying urban southeastern estuary....................... 3

Figure 2-1. Freshwater stream, Yosemite National Park, CA. ................................................................. 5

Figure 2-2. Conceptual model of the BCG as developed for streams ..................................................... 6

Figure 3-1. Researcher collecting scientific data for a coral reef BCG, La Parguera, PR. ........................ 9

Figure 3-2. The Providence River in Narragansett Bay, RI, after 400 years of post-colonial 

development. .................................................................................................................................. 10

Figure 3-3. Woods Hole, MA, a complex coastal system. ..................................................................... 11

Figure 3-4. SNA map of collaborations within the Piscataqua River Estuary Program......................... 14

Figure 3-5. Estuarine benthic invertebrates, often the basis of estuarine assessment........................ 15

Figure 3-6. Scientists collecting the new data required to construct a coral reef BCG, 

southwestern PR ............................................................................................................................. 16

Figure 3-7. Steps for calibration of a quantitative BCG......................................................................... 18

Figure 3-8. Oceanic influence near the mouth of Narragansett Bay, RI................................................ 20

Figure 3-9. Taskinas Creek, part of the Chesapeake Bay NERR in Virginia............................................ 22

Figure 4-1. Seagrass is a biotope and a sensitive indicator of condition .............................................. 24

Figure 4-2. Non-native taxa: dead man’s fingers................................................................................... 25

Figure 4-3. Sediment profile image ....................................................................................................... 26

Figure 4-4. Hydrological evidence for poor connectance–Watchemoket Cove, RI............................... 27

Figure 4-5. HICO satellite image of the Columbia River, OR and WA.................................................... 28

Figure 4-6. Thicket of Acropora cervicornis (staghorn coral) and reef fishes indicative of 

coral reef BCG levels 1 and 2........................................................................................................... 32

Figure 4-7. Seagrass with barracuda...................................................................................................... 33

Figure 4-8. Small cove in Black Rock Harbor, CT.................................................................................... 37

Figure 5-1. Two adjacent lagoonal estuaries (Green Pond and Great Pond, Cape Cod, MA)............... 39

Figure 5-2. An anthropogenic estuary built behind breakwaters (San Pedro Bay and Long Beach, 

Los Angeles, CA) .............................................................................................................................. 40

Figure 5-3. Entrance to a small riverine estuary (Narrow River, RI)...................................................... 41

Figure 5-4. Large charismatic animals appeal to public sentiment, and are often dependent on 

high water quality and suitable habitat availability........................................................................ 45

Figure 5-5. Charismatic brown pelican in Tampa Bay, FL ...................................................................... 48

Figure 5-6. West Falmouth Harbor, MA ................................................................................................ 49

Figure 5-7. Seagrass habitat is important for the settling and development of juvenile conch........... 51

Figure 5-8. Aerial views of heads of two sub-estuaries showing biotopes........................................... 52

Figure 5-9. Migrating coho salmon show connectance between oceans, estuaries, and streams ...... 54

Figure 5-10. Northeast corner of Greenwich Bay, RI............................................................................. 55

Figure 5-11. Economy: investment in recreational fishing. Columbia River, OR and WA.................... 57
Figures and Tables

v 

Figure 5-12. Environment: seagrass and staghorn coral, both sensitive species, 

in the Florida Keys Marine Sanctuary ............................................................................................. 57

Figure 5-13. Society: public enjoyment of the seashore. Town Beach, Charlestown, RI..................... 58

Figure 6-1. Narragansett Bay, RI............................................................................................................ 61

Figure 6-2. Greenwich Bay, RI, located mid-bay on the western shore of Narragansett Bay............... 63

Figure 6-3. The ecological and cultural history of Greenwich Bay ........................................................ 64

Figure 6-4. Habitat structure BCG model for Greenwich Bay ............................................................... 65

Figure 6-5. Tampa Bay, FL...................................................................................................................... 66

Figure 6-6. TBEP graphic to describe ‘Restoring the Balance’............................................................... 68

Figure 6-7. Biological gradient for biotopes of Tampa Bay ................................................................... 69

Figure 6-8. Be Floridian sign................................................................................................................... 70

Figure 6-9. Road sign showing FL DOT support of the Be Floridian campaign...................................... 70

Figure 6-10. Mobile Bay, AL ................................................................................................................... 71

Figure 6-11. Create a Clean Water Future campaign−changing public attitudes ................................. 72

Figure 6-12. Natural beauty of Three Mile Creek, Mobile Bay, AL........................................................ 72

Figure 6-13. Another image from Three Mile Creek, Mobile, AL, illustrating the need to change 

public actions .................................................................................................................................. 73

Figure 6-14. The Columbia River............................................................................................................ 74

Figure 6-15. Prairie Channel (WA) and the natural beauty of the Lower Columbia Estuary ................ 75

Figure 6-16. Stakeholder investment: paddlers on the Lower Columbia Estuary................................. 76

Figure 6-17. The stretch of reefs from La Parguera to Guánica Bay, southwestern PR........................ 77

Figure 6-18. Diagram showing ecosystem connectance ....................................................................... 78

Figure 6-19. EPA coral reef sites reflect a range of coral reef conditions............................................. 79

Figure 7-1. Photo montage of public/stakeholder interest in estuaries and coasts............................. 85

Figure 7-2. Eroding marsh edge............................................................................................................. 87

Figure B-1. Conceptual model of the BCG as used in freshwater ....................................................... 103

Figure B-2. Excerpt from Buzzards Bay Report Card output ............................................................... 107

Figure B-3. 2012 Chesapeake Bay Report Card output ....................................................................... 108

Tables

Table 4-1. Five attributes and potential measures for application to estuarine and coastal BCGs 

at different scales ........................................................................................................................... 23 

Table 4-2. Attributes and potential measures developed at the 2008 Estuarine BCG workshop ........30

Table 4-3. Strengths and weaknesses of various methods used to determine undisturbed or 

minimally disturbed conditions ......................................................................................................32

Table 6-1. Summary descriptions of four coral reef condition categories (very good to poor) 

based on expert assessments of individual stations.......................................................................80

Table A-1. Ecological attributes and possible measures paired with example narratives for 

BCG levels........................................................................................................................................97

Table A-2. Detailed matrix of Taxonomic Composition and Structure Attributes I-V for streams .....101
Implementing the Biological Condition Gradient Framework

vi

List of Acronyms

ALU Aquatic Life Uses

AUV Autonomous Underwater Vehicle

BCG Biological Condition Gradient

CMECS Coastal and Marine Ecological Classification Standard

CMSP Coastal and Marine Spatial Planning

CPUE Catch Per Unit Effort

CWA Clean Water Act

CWA 303(d) Clean Water Act List of Impaired Waters

DPSIR Drivers-Pressures-State-Impacts-Responses 

EBM Ecosystem-Based Management

EPA Environmental Protection Agency

EU European Union

FGDC Federal Geographic Data Committee

GSA Generalized Stress Axis

HICO Hyperspectral Imager for the Coastal Ocean

IBI Index of Biological Integrity

LCEP Lower Columbia Estuary Partnership

MBNEP Mobile Bay National Estuary Program

NBEP Narragansett Bay Estuary Program

NCCA National Coastal Condition Assessment 

NEP National Estuary Program

NERR National Estuarine Research Reserve

NGO Non-Governmental Organization

NOAA National Oceanic and Atmospheric Administration

RPB Regional Planning Body

SCCWRP Southern California Coastal Water Research Project

SDM Structured Decision Making

SNA Social Network Analysis

TBEP Tampa Bay Estuary Program

TALU Tiered Aquatic Life Uses

TMDL Total Maximum Daily Load

USCRTF United States Coral Reef Task Force

WFD Water Framework Directive

WQS Water Quality Standards
Acknowledgements

vii

Acknowledgements

This work was inspired by the earlier work of those scientists who developed the foundational 

concepts of integrity, condition, bioassessment, biocriteria, and related topics. We thank the many 

scientists who participated in our 2008 and 2009 workshops for their insights and contributions to 

this effort. We are grateful to Holly Greening of the Tampa Bay Estuary Program for her continued 

support. We recognize Catherine Corbett of the Lower Columbia Estuary Partnership as well as 

Tom Herder and Roberta Swann of the Mobile Bay Estuary Program for their BCG work and insightful 

comments. Marnita Chintala of the U.S. EPA Atlantic Ecology Division promoted these efforts, 

while Naomi Detenbeck, Dan Campbell, and Elizabeth Watson (also of the Atlantic Ecology Division) 

provided thoughtful reviews of this document.
Implementing the Biological Condition Gradient Framework

viii

Executive Summary

Estuaries and coastal systems are areas of confluence and connection. The river and the land meet 

the ocean here, resulting in steep gradients of habitat change, a diversity of life, and high biological 

productivity. People also meet the ocean here and have been attracted to coastlines for many 

thousands of years. Human populations are expanding rapidly on our coasts; this leads to increased 

environmental stressors (including excess nutrients, habitat alteration, and toxic pollution) and the 

need for more effective management of these valuable areas. 

Living organisms respond to the cumulative impacts of all stressors, and natural populations of biota 

have been affected for centuries. These biological changes can be addressed with bioassessments–

evaluations of the biological condition of a waterbody using surveys of the structure and function of 

biotic elements. Bioassessment puts a spotlight on biology and allows managers to address the 

cumulative impacts that degrade environmental condition. Bioassessment in estuaries and coasts 

integrates many of the upstream stressors in the larger watershed as well as stressors within the 

waterbody and is a vital part of managing at the waterbody and watershed levels. 

The Biological Condition Gradient (BCG) is a conceptual scientific framework for interpreting biological 

response to increasing effects of stressors on aquatic ecosystems (U.S. EPA 2016). The framework was 

developed from common patterns of biological response to stressors observed empirically by aquatic 

biologists and ecologists in different geographic areas of the United States. The framework describes 

how attributes of aquatic ecosystems change in response to increasing levels of stressors, from an “as 

naturally occurs” condition (e.g., undisturbed or minimally disturbed) to a severely altered condition.

The highest level of condition, level 1, represents natural or undisturbed biological communities and 

anchors the starting point for defining five levels of change or departure from this condition with level 

6 representing conditions that have been severely altered due to anthropogenic stress. Each level is 

defined by a narrative description that can be consistently interpreted regardless of biology, location, 

or sampling method. These narratives are translated into quantitative decision rules for specific local 

areas through expert consensus. The BCG end product is a set of well-vetted and transparent decision 

rules that can be readily interpreted and implemented by state water quality program managers and 

scientists, and can be easily understood by stakeholders, the public, and higher levels of management. 

This process provides the conceptual basis for comparable interpretation of assessments and for 

clear communication of condition, because the levels have the same basic meaning wherever BCG 

is applied. Level 4 for fish in a New Jersey estuary describes the same relative biological condition 

as level 4 for invertebrates in a Maine stream, although in practice the different datasets used in 

analyses will introduce variability. The BCG provides a tool for effective comparisons of condition 

across time and among waterbodies, allowing managers to support Clean Water Act (CWA) and 

Total Maximum Daily Load (TMDL) programs, communicate relative condition, develop thresholds, 

set goals, and monitor progress towards these goals. The BCG framework was initially developed 

for application in freshwater streams and has been applied in these environments for years as a 

management tool to interpret baseline conditions, identify high quality waters, and define attainable 

goals for improvements in degraded waters. 
Executive Summary

ix

This document expands the stream BCG framework and proposes guidance for estuarine and coastal 

BCG implementation as a sequence of actions or steps to assist estuarine and coastal scientists and 

managers as they plan and implement environmental decisions. The initial Steps (1–7) walk scientists 

and managers through identifying stakeholders, problems, goals, and relevant biological indicators

to develop a descriptive BCG. This phase establishes a common understanding among potential users 

on the role of a BCG in meeting their specific resource management needs. For example, a 

descriptive (qualitative) BCG can be used to refine stakeholder visions, improve narrative designated 

use categories, set broad goals, and communicate biological condition to motivate the public. The 

last set of actions or Steps (8–11) guide development of a more rigorous quantitative BCG that can 

help establish numeric thresholds for assessing biological condition, inform CWA decisions, track

changes in condition, develop biological criteria, and monitor to evaluate management actions. 

The approach is flexible–coastal and estuarine managers can choose to develop any of the steps that 

would best meet their requirements, and in any order. National Estuary Programs (NEPs) were the 

first groups to adopt this BCG implementation guidance, and the approach is well suited to address 

many of their needs. Implementation steps of estuarine/coastal BCG development are:

1. Define problems, engage partners and stakeholders

2. Collaborate to define management goals, visions, and objectives

3. Determine the biological components, stressors, measures, and attributes most relevant 

to management objectives 

4. Delineate and classify the waterbody and watershed of interest 

5. Organize and analyze existing data for the identified measures, collect new data if needed 

6. Define BCG level 1 conditions for the identified attributes

7. Develop narrative descriptions of the biology expected at each BCG level as a narrative 

BCG model; apply to management needs

8. Convert narrative descriptions to quantitative metrics and thresholds, calibrate the BCG

9. Develop a stressor gradient and stressor-response relationships 

10. Organize, interpret, and report results 

11. Develop decision support, communication, and monitoring tools; assist management 

partners. 

These BCG implementation steps provide a path for scientists and managers to identify and solve 

environmental problems. The methods and outputs can be tailored to larger well-funded programs 

such as state and federal agencies or to smaller programs with fewer resources including NEPs, 

National Estuarine Research Reserves, town or county governments, and local Non-Governmental 

Organizations (NGOs) or coalitions.

The estuarine and coastal BCG offers an easily understood method for communicating biological

condition in a way that engages the public and other stakeholders. BCG levels can be used at the 

waterbody scale to define current biological conditions for determining attainment of CWA goals; 

set non-regulatory goals and targets for attaining a desired biological or ecological condition; 

and track environmental progress towards achieving targets and goals. NEPs who have used the 

estuarine and coastal BCG identify the ability to set meaningful targets for habitat protection and 
Implementing the Biological Condition Gradient Framework

x 

restoration, and the ability to positively engage the public and other stakeholders as primary benefits 

of the approach. At the national scale, consistent interpretation of biological assessments in 

estuaries and coasts allows for comparisons across waterbodies and better reporting of condition 

in national surveys, including documentation of successes in restoring or protecting these critical 

resources. This application of the BCG to estuaries and coasts is adaptable and can be modified for 

other waterbody types that are studied and managed as individual systems. The process is well 

underway for estuaries and coral reefs and could also be applied to large rivers, lakes, and other 

waterbodies.

This document serves as technical guidance for scientists and managers taking on projects that would 

benefit from use of bioassessment to manage complex coastal systems. BCG methods are described

in a logical order of development steps, with recommendations for different uses of BCG in 

management. Case studies illustrate applications of this approach to waterbodies in a variety of

geographic and ecological settings.
1. Introduction

1 

1. Introduction

Cumulative impacts and bioassessment

Estuaries and other coastal systems are among the environments most influenced by human 

activities. These waters are affected by a variety of stressors that act at several scales, including 

localized point sources of contaminants, anthropogenic inputs from the watershed and the ocean, 

habitat destruction, widespread or diffuse non-point sources of contaminants, biological harvesting, 

and larger scale impacts such as sea level rise (Figure 1-1). These valued ecosystems, and their biota, 

are significantly altered by the cumulative impacts of multiple stressors. Over time, this has led to 

“severe, long-term degradation of near-shore marine systems worldwide” (Lotze et al. 2006). 

Effective management of cumulative impacts on any scale requires coordination among management 

entities and a variety of tools to quantify degradation, identify causes, address those causes, and 

track progress. No single approach can address all of these issues, but evaluations of biology are very 

often used to characterize and communicate the extent of anthropogenic degradation. Biological 

condition integrates the effects of all the stressors that living organisms are exposed to and can be 

an effective tool in managing cumulative impacts. Many different methods and indices to quantify 

biological condition have been developed and applied by scientists, local resource managers, states, 

and federal agencies. Most bioassessments evaluate changes in quality or quantity of ecologically or 

economically defined condition or value of habitats, communities, or species, relative to a defined 

reference state.

Figure 1-1. Docks, roads, commercial fishing vessels, marine transportation, and industry in Point Judith 

Harbor, RI, an illustration of estuarine uses and stressors. 
Implementing the Biological Condition Gradient Framework

2 

Consistent bioassessment

These assessments, when applied in different estuaries, often evaluate very different aspects of 

biology and use different reference conditions, usually for the good reason that biology differs among 

estuaries. Nonetheless, independent bioassessments do not allow comparisons among estuaries on 

statewide, regional, or national levels. Estuarine managers have little context for how biological 

condition in their waterbody compares to that in nearby estuaries, and larger-scale managers cannot 

easily provide area-wide condition reports or analyses with which to focus priorities for protection or 

restoration.

One approach to common assessment is to employ an Index of Biological Integrity (IBI), which may be 

developed for different assemblages (e.g., fishes, invertebrates) in local or regional areas. IBIs tend 

to be well calibrated and effective for their local area of development, but results are generally not 

applicable to other areas. The issue of regional comparability has led to development of a nationwide 

estuarine benthic index using invertebrates (Gillette et al. 2015). However, nationwide indices for 

other assemblages have not been developed, and local managers may not have the appropriate data 

or resources to apply these approaches.

Other nationwide approaches, described in the Coastal and Marine Ecological Classification Standard 

(CMECS), can be based on analyses standardized to infaunal community successional stage (FGDC 

2012), or on image-based indices of condition, e.g., sediment profile cameras but these measures 

may be less sensitive than well-tuned local indices. Further, the widespread use of different 

bioassessment endpoints leads to reports that are not comparable among waterbodies, states, 

or federal agencies. A common framework for interpreting data and assessment results and 

communicating this information to stakeholders would enhance collaboration within and among 

different agencies and assist in coordination of management actions.

The Clean Water Act

Certain regulatory actions require consistent assessments. Within the U.S. EPA, the vision of the 

1972 Clean Water Act (CWA) provides a long-term national objective to “restore and maintain the 

. . . chemical, physical, and biological integrity of the Nation's waters”. Under the Act, states are 

responsible for water quality management programs to assess the condition of their waters, set 

designated uses, establish criteria in their Water Quality Standards (WQS), and then monitor

attainment of the uses. The CWA has led to tremendous environmental improvements, largely by 

regulating point sources and individual chemicals (U.S. EPA 1986). The path to biological integrity, 

however, has not been as clear cut. Biological integrity has been defined as “the capability of 

supporting and maintaining a balanced, integrated, adaptive community of organisms having a 

composition and diversity comparable to that of the natural habitats of the region” (Frey 1977), 

but the term is not specifically defined in the CWA itself. Nor does the CWA define the ecological 

components, or attributes, that constitute biological integrity (Davies and Jackson 2006).
1. Introduction

3 

Given this lack of specificity, a way to interpret biological condition consistently and independently 

of assessment methods would more clearly communicate the current status of aquatic resources and 

their potential for restoration (Davies and Jackson 2006), allowing scientists and managers to better 

assess aquatic resources. These gaps in the available management tools led the U.S. EPA Office of 

Water Biocriteria Program to develop the concept of a BCG. The BCG framework (U.S. EPA 2016) is 

a scientific model for consistent interpretation of biological response to increasing effects of stressors 

on aquatic ecosystems. This bioassessment tool supports CWA and other decisions in freshwater 

streams and is now being applied to coastal and estuarine systems. The BCG anchors biological 

condition to natural or undisturbed conditions (level 1) and describes five declining levels of condition 

from that starting point, with level 6 representing severe alteration from undisturbed condition. 

These level assignments are defined by consistent narratives and methods, allowing comparisons 

of condition across sampling methods, biological endpoints, waterbodies, and time. 

A flexible BCG approach for estuaries and coasts

The objective of this document is to propose an approach for applying the BCG framework to 

improve management of estuaries and coasts. This is presented as a toolbox of steps or actions that 

take scientists and managers from identifying environmental problems to applying BCG for solutions. 

Early steps lead scientists, stakeholders, and managers through the process of defining management 

needs and goals. Next steps develop a narrative BCG to communicate condition, create visions, and 

set targets. In the final steps, a more rigorous quantitative BCG is developed to better support 

management and regulatory actions to protect or improve estuarine and coastal ecosystems. The 

guidance is not prescriptive, the steps need not be approached in any defined order, and coastal or 

estuarine scientists and managers can develop any step 

or steps they deem valuable for their specific needs. 

This flexible approach can benefit states in regulating

water quality, NEPs in developing goals, plans and

actions or national and regional managers in comparing

condition among estuaries and waterbodies. All steps 

are consistent with the essential tenets of the BCG 

framework as developed for freshwater streams by 

the U.S. EPA’s Office of Water Bioassessment Program 

(U.S. EPA 2016).

Figure 1-2. Charleston Harbor, SC, an important low-lying urban southeastern estuary. 

Image: Google Earth, data from SIO, NOAA, U.S. Navy, NGA, GEBCO
Implementing the Biological Condition Gradient Framework

4 

Roadmap

This document describes the BCG framework as applied to streams in Chapter 2, then defines 

and explains the estuarine and coastal BCG guidance in Chapter 3. Chapter 4 provides more detail 

on the key components of the guidance, Chapter 5 discusses how to apply the guidance, and 

Chapter 6 presents BCG pilots. A summary and discussion of next directions can be found in 

Chapter 7. This report is authored by a workgroup of scientists and managers who have been 

developing and promoting BCG applications in estuaries, coral reefs, and other complex systems

since 2008.
2. The BCG in freshwater systems

5 

2. The BCG in freshwater systems 

Figure 2-1. Freshwater stream, Yosemite National Park, CA. 

BCG fundamentals

The BCG framework was developed as a conceptual model for consistent interpretation and 

communication of bioassessment information to improve management of freshwater streams 

and wadeable rivers (U.S. EPA 2016). The model is based on a scientific understanding of how 

ecosystems respond to increasing levels of human disturbance or stress. As shown in Figure 2-2, 

the BCG describes a gradient in biological condition that ranges from a natural or undisturbed 

condition (level 1) to a severely altered condition (level 6).

These changes in biology are evaluated through attributes, which are measurable and ecologically 

important characteristics of the ecosystem. These attributes include measures of biological 

and ecological structure, non-native taxa, organism condition, ecosystem function, spatial and 

temporal extent, and connectance (U.S. EPA 2016). The BCG provides consistent and comparable 

interpretation of assessments, because all evaluations are relative to the same fixed starting point 

(or anchor) of undisturbed conditions, and because consistent narratives define every level for each 

attribute regardless of waterbody or method. In practice, the BCG approach synthesizes existing 

data, observations, and expert interpretations to document the response of aquatic biota to 

increasing levels of anthropogenic stress. This approach helps identify environmental targets 

and develop biological criteria that support conservation, restoration, monitoring, and 

management activities.
Implementing the Biological Condition Gradient Framework

6 

Figure 2-2. Conceptual model of the BCG as developed for streams with narratives for levels 1–6. 

The actual relationships between multiple stressors and their cumulative impacts on biology are not likely 

to be linear, although they are presented here as such to better illustrate BCG concepts. 

Graphic: U.S. EPA 2016
2. The BCG in freshwater systems

7 

2.1. Key terms for BCG

Aquatic Life Uses: Beneficial use designations (for state water quality standards) describing 

how the waterbody should provide suitable habitat for survival and reproduction of native 

aquatic organisms.

Attributes: Characteristics of structure, non-native taxa, condition, function, landscape, or 

connectance that reflect biological or ecological condition and represent biological integrity. 

Used to organize measures and standardize narratives for each of (up to) six levels of 

biological condition. 

Bioassessment: The use of biological indicators to evaluate environmental condition. 

Biological Condition Gradient (BCG): A conceptual scientific framework for interpreting biological 

response to increasing effects of stressors on aquatic ecosystems.

Biological Condition: Levels of biological status defined by narrative or numeric decision rules 

that are derived from empirically observed patterns of biological response to stressors. 

The patterns associated with each BCG level are described by ecosystem characteristics or 

attributes (see above).

Ecology: The relationship between living things and their environment. In a BCG, ecology 

includes the interactions among organisms and with their physical/abiotic environments.

Estuarine and Coastal BCG: A conceptual scientific framework (BCG) for interpreting biological 

response to increasing effects of stressors on complex, multi-habitat aquatic ecosystems, 

adapting the freshwater BCG to include larger scale processes. This may also be referred to 

as the Estuarine/Coastal BCG or the Estuarine BCG.

Estuarine and Coastal BCG Implementation: A set of steps to assist estuarine and coastal scientists 

and managers from stakeholder engagement and problem formulation (Steps 1–3) through 

BCG development and application (Steps 4–11).

Metric: As used in this document, a calculated term or enumeration that represents a quantifiable 

biological feature that changes in a predictable way with increased human influence.

Measure: As used in this document, any quantitative, calculated, qualitative, narrative, or 

descriptive evaluation of a biological feature that changes in a predictable way with 

increased human influence. Measures include metrics.

2.2. Overview of BCG

The major components of the BCG framework (U.S. EPA 2016) are as follows:

1. Biological attributes are used to assess biological condition.

2. The BCG defines six levels of biological response to increasing stress (Figure 2-2, page 6).

3. The highest level of condition (level 1) is anchored in undisturbed conditions as naturally

occur. BCG level 2 represents minimally disturbed conditions. In many places undisturbed

conditions no longer exist and cannot be determined, so BCG levels 1 and 2 are combined

and considered comparable to naturally occurring conditions. The poorest condition (level 6)

is defined as severely altered and heavily disturbed by high levels of multiple stressors.
Implementing the Biological Condition Gradient Framework

8 

4. Expert best professional judgment and consensus in an empirically-based process

(U.S. EPA 2016) lead to development of narrative decision rules for assigning sites to

BCG levels. Application of independent data sets turns these decision rules into quantitative

thresholds using statistically based methods, modeling, or other technical approaches.

5. The BCG process is based on scientific data. Thresholds are calibrated and validated with data,

and development steps are documented. This creates a transparent, testable, and defensible

assessment method with the clear thresholds needed to determine impairment and likely

trajectories of condition.

What does the BCG do, and how?

BCG levels 1–6 provide a ‘common language’ for assessment because the repeatable scientific 

process can be applied anywhere that a full range of biological condition can be described with 

any method of characterizing biology. These levels are used to interpret biological assessments, 

then apply this information to management decisions in a way that is easily communicated to the 

public. The BCG identifies both improvements and degradations to biological and ecological 

condition and can help managers set targets in a transparent way and track environmental progress 

towards these targets. Further, comparisons among waterbodies allow managers to understand

the success of efforts in different systems and to perhaps anticipate the effects on their own 

systems if stressor levels change to more closely resemble those of other systems.

In practice, expert panels are used in stream BCG development to synthesize biological data, 

assemble guidelines to define levels for each attribute (e.g., narrative and then numeric decision 

rules, algorithms and models), and determine level thresholds for designated use assignments. 

Stream ecosystems across the country have a long history of monitoring for macroinvertebrate, 

fish, and periphyton communities, although different sampling techniques have been used. Stream 

ecologists have a good understanding of how these biological communities respond as stressors 

increase, and in many areas can identify level 1 and 2 sites (Figure 2-2, page 6) as examples of 

undisturbed or minimally disturbed environments.

The BCG is based on elements of both science and management, with a focus on translating scientific 

thinking and available data into clear quantitative thresholds for management decision-making. 

A gap between research and management can occur when the greater understanding of pattern 

and process sought by scientists does not directly lead to the easily communicated answers that 

managers need. The BCG bridges this gap through expert scientist workshops and workgroups that 

distill complex science into six consistent levels of condition that are easily understood and easily 

communicated to the public. 
3. Estuarine and coastal BCG implementation

9 

3. Estuarine and coastal BCG implementation

3.1. How can the BCG be implemented in estuarine and coastal settings? 

Applying the BCG to estuarine and coastal areas relies on the concepts described above, but 

requires a broader ecological approach to address the many different types of coastal waters

(Figure 3-1). This adaptation of the freshwater BCG takes a system-level view of the waterbody 

and modifies attribute descriptions to cover larger scales of assessment. For example, it expands 

the stream organism condition attribute to include habitat condition, e.g., wetland condition indices 

which evaluate a variety of plant species, marsh ponding, and other wetland-specific features. 

The estuarine/coastal BCG provides guidance for management groups to involve stakeholders 

in defining problems and setting goals and allows a more flexible BCG that can be tailored to the 

specific problems of an individual waterbody. This BCG can be used to assess condition of coastal 

waterbodies in the past and present, and can be used to develop visions for desired future 

conditions. It can assist in a variety of management applications including goal setting by NEPs

and regulatory actions by states, and can be applied by small programs with fewer resources.

Figure 3-1. Researcher collecting scientific data for a coral reef BCG, La Parguera, PR. 

How is managing estuaries different from managing streams?

Estuaries and coastal waterbodies are very different from the stream reaches that are monitored 

and assessed in many state water quality management programs and so require different assessment 

and management strategies. Estuaries and coastal systems represent a large diversity of waterbody 

types, from small lagoons to coral reefs. Many are characterized by rapidly changing natural 

conditions (e.g., salinity and temperature shifts over a tidal cycle or along the estuarine gradient) 

and most have a large diversity of habitats, each contributing to overall waterbody function. 
Implementing the Biological Condition Gradient Framework

10

Many estuarine species are extremely tolerant of stressors and environmental variability yet recent 

anthropogenic changes have severely disturbed estuarine organisms, communities, and habitats

(Cloern et al. 2016). Worldwide, estuaries and coasts are among the areas most densely settled 

over long periods of time. Narragansett Bay, for example, has seen over 400 years of post-colonial 

development and thousands of years of Native American settlement before that (Figure 3-2). 

Most estuaries show significant degradation from the cumulative effects of anthropogenic stressors, 

including shoreline development, nutrient inputs, habitat alteration, and overfishing (Lotze et al. 

2006, Bricker et al. 2007, Bolster 2012). 

Figure 3-2. The Providence River in Narragansett Bay, RI, after 400 years of post-colonial development.

Estuaries and stream reaches also differ from a management perspective. Estuarine and 

coastal management often involves several different entities at national, state, and local scales, 

including organizations with different scopes and different mandates. Historic, natural, or 

undisturbed conditions may be less common in estuaries due to these cumulative historic stresses, 

and the characteristic variability of estuaries can make assessments difficult. Estuarine programs 

such as NEPs and National Estuarine Research Reserves (NERRs) often work with limited budgets and 

staff, so the coastal approach offers guidance for simplified development and use of narrative BCGs, 

as well as of quantitative BCGs. 

Estuaries and coasts are, in general, less intensively monitored than streams and the BCG 

implementation steps can be used to organize whatever data are available and identify gaps. 

While many stream reaches can be assessed in aggregate in the context of regional condition, 

estuaries and coastal systems are usually managed as unique waterbodies requiring individual 

attention and many different approaches have been used in various estuaries. In order to assess 

and manage these coastal systems, estuarine/coastal BCG implementation keeps the advantages of 

the BCG as originally developed for streams but provides management steps and greater flexibility to 

address the complexity of estuarine and coastal biology (Figure 3-3). 
3. Estuarine and coastal BCG implementation

11

Figure 3-3. Woods Hole, MA, a complex coastal system.

Origins of the estuarine and coastal BCG

The estuarine and coastal approach was proposed and launched at a 2005 estuarine workshop 

hosted by the U.S. EPA (Office of Water and Region 1) in Providence, RI. Concepts were developed 

further at workshops in Maine during the winter of 2006 and spring of 2007. The approach was 

solidified when the EPA Office of Water, Region 1, and Office of Research and Development 

co-sponsored a November 2008 workshop in Narragansett, RI, inviting many national estuarine 

experts and managers (Appendix C). The goal of these efforts was to develop and refine a nationally 

applicable, integrative estuarine BCG approach to enable meaningful comparisons among measures 

and waterbodies. Another workshop in 2009 gathered Narragansett Bay experts and managers 

(Appendix D) to begin an estuarine BCG for that area. The work has evolved and been further 

refined by a standing estuarine/coastal BCG workgroup and by pilot BCG work in Mobile Bay, AL; 

the Lower Columbia River, OR and WA; Greenwich Bay, RI; and Puerto Rico coral reefs. This 

document summarizes work to date on development and application of guidance for estuarine 

and coastal BCG implementation and provides a basis for further work to refine, test and apply 

the approach.
Implementing the Biological Condition Gradient Framework

12

3.2. Development of estuarine/coastal BCG guidance 

Discussions at the Narragansett workshops and afterwards led to a sequence of eleven possible steps 

or actions as guidance for scientific and management groups developing and applying the BCG to an 

estuarine system. To address the variety of system types and needs, each group can review the steps 

and create a path that works for their specific case and may choose to apply one, several, or all of 

these implementation steps. While these are presented as separate steps, groups can merge these 

concepts in their actual development process. Collaborative approaches to these steps might range 

from informal discussions, to expert workgroups, to hosted workshops. 

Eleven useful steps - outline

The first implementation steps of the guidance (1–3) do not involve an actual BCG per se, but 

apply management decision tools to involve stakeholders and evaluate environmental problems 

in preparation for BCG work. In the next steps (4–7) a BCG is built to solve these problems by 

developing narratives for BCG levels used for communication, engaging stakeholders, and nonregulatory approaches including assessment of condition, goal-setting, evaluating management 

alternatives, and monitoring to track progress toward goals. In the final stages (8–11) a rigorous 

and quantitative BCG is developed through expert consensus to define ALU thresholds and baseline 

conditions, track changes in condition, and assess effectiveness of non-regulatory and regulatory 

actions. Public/stakeholder engagement and hosted workshops can be critical throughout the 

process. Steps:

 1. Define problems, engage partners and stakeholders

2. Collaborate to define management goals, visions, and objectives

3. Determine the biological components, stressors, measures, and attributes most relevant 

to management objectives 

4. Delineate and classify the waterbody and watershed of interest 

5. Organize and analyze existing data for the identified measures, collect new data if needed 

6. Define BCG level 1 conditions for the identified attributes

7. Develop narrative descriptions of the biology expected at each BCG level as a narrative 

BCG model; apply to management needs

8. Convert narrative descriptions to quantitative metrics and thresholds, calibrate the BCG

9. Develop a stressor gradient and stressor-response relationships 

10. Organize, interpret, and report results 

11. Develop decision support, communication, and monitoring tools; assist management partners.
3. Estuarine and coastal BCG implementation

13

Eleven useful steps - details

The implementation steps should not be seen as prescriptive, but rather as a series of choices that 

can be selected to deliver the desired benefits of a BCG for a coastal system or estuary. Some of 

these steps may already have been accomplished for some systems or may not be necessary for 

certain objectives. Every coastal group using a BCG approach will have different problems, 

different goals, and different solutions. The eleven steps can serve as thinking and planning 

points for BCG development. 

Steps 1–3: Initial collaborative management for effective BCG outcomes 

1. Define problems, engage partners and stakeholders. Scientists, managers, and stakeholders

should first address fundamental questions: What are the problems to be solved? What are the 

stressors of concern? Who will use or care about the results? Identifying and involving stakeholders

(including partners, state and federal agencies, communities, industry, businesses, and the public)

early in the process leads to effective application of a developed BCG later on. Well-established 

management frameworks (Section 5.3, pages 44–48) including Structured Decision Making (SDM) 

or Drivers-Pressures-State-Impacts-Responses (DPSIR) are effective tools for working with partners 

to produce a BCG that will be used in environmental decision-making. Social Network Analysis (SNA) 

is an advanced method of identifying stakeholders, connections among groups, and participation 

gaps (Figure 3-4). Forming relationships with stakeholders at the start of a project can be critical, 

as outlined in Steps 1, 2, and 3 of this BCG guidance. 

2. Collaborate to define management goals, visions, and objectives. What are the ecological, 

economic, and social outcomes that should be achieved relative to the management problems? 

What are stakeholder visions for a desired future estuary? Relative to BCG, what are the 

environmental objectives? As above, these questions are best addressed in partnerships 

with stakeholders, and SDM or DPSIR can be very helpful.
Implementing the Biological Condition Gradient Framework

14

Figure 3-4. SNA map of collaborations within the Piscataqua River Estuary Program (PREP). Partner 

types are shown with different colors based on participation in past projects and collaborative groups 

(gray circle). Size of the nodes and thickness of the lines are proportional to the number of organizations 

and projects represented. Graphic: Kate Mulvaney

3. Determine the biological components, stressors, measures, and attributes most relevant to 

management objectives. The most effective components of biology, e.g., benthos (Figure 3-5), 

seagrass, saltmarsh birds, fishes, are: 1) relevant to the management objectives, 2) susceptible to 

human disturbance and affected by controllable stressors, 3) ecologically important, 4) important 

to stakeholders, and 5) easily assessed with effective measures (e.g., benthic IBI scores, seagrass 

acres, bird diversity indices, and fish Catch Per Unit Effort (CPUE) statistics). Evaluating candidate 

components/measures/attributes and their stressors may require conceptual ecological models, 

examination of species lists, habitat lists, guild lists, public/stakeholder workshops, information on 

ecosystem services/values, etc. In many cases, proxies or models may be used to evaluate desired 

attributes that are difficult to measure; for example, structural measures such as measured depth 
3. Estuarine and coastal BCG implementation

15

of bioturbation may be used as proxies for functional attribute processes such as benthic 

biogeochemical cycling. Any application of proxies or modeled measures should explain the 

logic behind this use. Final selection of measures and attributes will also depend on the data that 

are available for each, as described in Step 5 below. Measures are organized into the BCG estuarine/ 

coastal attributes described in Table 4-1 (page 23). This last step is critical because the narrative 

descriptions used to consistently assign BCG levels are tied to specific attributes.

Figure 3-5. Estuarine benthic invertebrates, often the basis of estuarine assessment. 

Scale shows one centimeter.

Steps 4–7 A narrative BCG model to identify and communicate condition, 

develop visions, set goals and targets, and motivate stakeholders

: 

4. Delineate and classify the waterbody and watershed of interest. Bounding the research area 

will streamline and improve this and later work. The estuary or area of interest should be defined, 

identifying landward and seaward boundaries. The watershed of the estuary should also be 

delineated. Areas of heightened interest should be identified, and a variety of spatial tools are 

available to assist with all these tasks. Classifying the systems into types of estuaries lets managers 

make comparisons among similar systems, including comparisons of methods to determine 

undisturbed or minimally disturbed conditions. Classifications can also address specific issues 

including conservation status or nutrient susceptibility. Within a waterbody, classification by 

substrate, salinity, habitat, or other factors can reduce apparent natural variability in biological 

data by grouping analyses within ecologically relevant types. Classification improves the BCG process 

and clarifies links to stressors. Many established classification schemes exist for various purposes, 

and this is covered in Section 5.1 (pages 39−42). 

5. Organize and analyze existing data for the identified measures, collect new data if needed. 

Practitioners might consider three actions for each of the measures identified in Step 3 above:
Implementing the Biological Condition Gradient Framework

16

- Identify the spatial and temporal coverages that are required to answer the scientific 

and management questions, identify existing data, identify data gaps, and determine if 

new data collection is advisable. 

- Develop data acceptance criteria (for existing data) and/or sampling design (for new 

data). If helpful, texts and resources are available to assist with sampling design, 

including Gibson et al. (2000) and U.S. EPA (2002). 

- As appropriate, if new data are required, define sample collection, sample processing, 

data management, and Data Quality Objectives (U.S. EPA 2006b).

Different estuarine systems have been studied in various ways, and the types of data that exist in 

each differ widely. For some estuaries, the type, quantity, quality, and organization of existing and 

available data on biology and on stressors will be excellent. For many estuaries, some data will be 

available but a considerable effort will need to be invested in finding, deciphering, and organizing 

these data. Other estuaries will be relatively unstudied, and basic assessments may need to be 

conducted. For every estuary, it is important to evaluate the types of data that exist, the resources 

that are available to collect new data, and the types of new data that would be most useful 

(Figure 3-6). 

Figure 3-6. Scientists collecting the new data required to construct a coral reef BCG, southwestern PR. 

6. Define BCG level 1 conditions for the identified attributes. An important element of BCG 

development is that assessment is consistently linked to natural or undisturbed condition as level 1. 

This reference is anchored to reduce problems associated with ‘’shifting baselines” (Pauly 1995), 

where what is perceived as ‘good’ condition declines over decades as humans collectively forget what 

was ‘good’ 50 years ago. Methods to define this level 1 anchor are discussed in detail in Section 4.2
3. Estuarine and coastal BCG implementation

17

(pages 29–35). Conceptually, an undisturbed baseline will relate to both biological condition and 

stressor levels and so can be identified in several ways. An undisturbed coastal or estuarine condition 

can be defined as a biological state through structural or functional descriptors, as an ecological

narrative, as a time period, as a stressor level, or in some other manner. Undisturbed or natural

condition should be described as accurately as possible for each assessed waterbody, but methods 

to determine an undisturbed state will differ among waterbodies depending on the data that are 

available, on the local history of development, and on other factors. In some cases, level 1 cannot 

be well defined, and levels 1 and 2 conditions are combined to describe an undisturbed/minimally 

disturbed baseline. In all cases, baseline conditions can be defined by assembling panels of experts

to find consensus on biological conditions that would be expected in a waterbody under undisturbed 

conditions given the data that are available.

7. Develop narrative descriptions of the biology expected at each BCG level as a narrative BCG 

model; apply to management needs. Once level 1 is defined, narrative or conceptual descriptions 

of expected biological structure, condition, and function at levels 2 through 6 can be developed for

each of the identified attributes. For consistency among BCG efforts in different areas, BCG narrative

for different levels should follow established level descriptions for each attribute. For estuaries and 

coasts, see Table 4-2 (pages 30–31). These narratives were adapted from those developed and 

tested in streams (U.S. EPA [2016], Tables A-1 and A-2 of this document). Building on Table 4-2,

developing more specific narrative descriptions for each attribute in a particular waterbody better

defines the biology characterizing BCG levels. These level descriptions are a narrative BCG model

that assigns BCG levels to observed biology. Adding a Generalized Stress Axis (e.g., human 

population, year for a historical BCG) would add value and context (see step 9 below).

Hosted workshops, panels of invited experts, or expert workgroups have been a successful approach 

to develop these specific narratives. The basic process is formalized as BCG calibration in Step 8 

below. Experts should be well prepared before the workshop, should arrive already familiar with the 

basic concepts of BCG, and should have a clear vision of workshop expectations. Pre-analysis of data 

can assist in this process. For example, in streams, biotic assemblage data were analyzed with 

stressor data to produce empirically derived high stress and low stress indicator taxa; these data 

were brought to the workshop and compared to expert conception of high and low stress indicator 

taxa. In developing a BCG for coral reefs, experts were presented with a selection of representative 

unlabeled photos and videos collected along a condition gradient, which helped facilitate discussion 

and consensus. The descriptions of coral condition at each level were then used effectively in reef 

evaluation and goal setting (Bradley et al. 2014). The essential elements of BCG calibration (Step 8 

below) were used to develop this BCG model. 

In the coral reef example above, a narrative BCG was used for assessment and for setting goals and 

targets. A narrative BCG is an effective tool for public communication and can support a variety of 

management needs. For non-regulatory approaches a narrative BCG can take management groups 

through the entire process of engaging stakeholders, describing past and present conditions, 

developing a vision for a desired future estuary, defining management goals and targets, evaluating 

possible actions, and monitoring progress towards targets. 
Implementing the Biological Condition Gradient Framework

18

Steps 8−11: A fully developed BCG model to support both regulatory 

and non-regulatory needs

8. Convert narrative descriptions to quantitative metrics and thresholds, calibrate the BCG. 

Building on narrative descriptions of the selected measures, numeric metrics (e.g., IBI scores, acres 

of habitat, density of valued species) can be developed to better define thresholds between levels. 

This can improve the ability of a narrative BCG to set numeric targets, track progress, prioritize

actions, refine stressor-response relationships, or support CWA regulations.

The BCG is calibrated when expert workgroups use consistent BCG level guidelines (Table 4-2) and 

a consensus process to develop decision rules for assigning thresholds to BCG levels, then test these

rules with data and modify as needed. A narrative non-regulatory BCG model can and should be 

calibrated, but a model intended to support CWA and other regulations must be quantitative, 

rigorous, based on sufficient data and well-calibrated with the required testing and iteration.

U.S. EPA (2016) provides a

detailed, tested, and wellestablished calibration 

process for convening 

experts, using scientific 

consensus with available 

data (e.g., stressorresponse relationships from 

monitoring programs), 

calibrating the BCG, and 

assigning biological metric 

scores to BCG levels (U.S. 

EPA 2016). Figure 3-7 

outlines the steps in 

calibrating a BCG for 

quantitative or regulatory 

use by states, tribes, 

territories, and counties in 

supporting CWA and other 

decisions.

Figure 3-7. Steps for calibration of a quantitative BCG. Graphic: U.S. EPA 2016
3. Estuarine and coastal BCG implementation

19

In Step 1 of calibration, data are assembled to cover the full range of condition and stress within one 

or more estuaries or coastal settings. Calibration for regulatory application requires sufficient highquality data. In Step 2, these data are processed to describe stressor-response relationships, and 

are put in a format that is useable by workshop participants. Step 3 (identifying and inviting an 

appropriate range of experts) is critical to the success of the project because in Step 4 these experts 

will use the data to develop a quantitative BCG, i.e., numeric decision rules for BCG levels in selected 

attributes. In Step 5, the quantitative model and process are tested against data and recalibrated 

until the BCG is consistent, scientifically defensible, transparent, well-documented, and ready for 

use in CWA decision-making or other regulatory and non-regulatory applications. At this point, 

the decision rules can be applied into the future without further consulting the expert panel.

These calibration steps were designed for development of BCG models for regulatory application 

under the CWA and rely on quantitative data, but most estuarine or coastal BCG models are 

developed by non-regulatory programs such as NEPs, and are not intended as a basis for regulation. 

Further, the sparse data typical of estuaries may not be sufficient to support calibration and testing

for CWA decisions. However, the expert workgroup process described above improves any BCG 

model, even when extensive testing and iteration are not possible. As before, coral reef BCG 

practitioners used this expert calibration process with narrative descriptions of coral condition 

to create a much-needed management tool. Expert panels are a central element in developing 

any BCG model.

9. Develop a stressor gradient and stressor-response relationships. The Generalized Stress Axis

(GSA, the BCG x-axis of Figure 2-2, page 6) aggregates stressors on the assumption that biology 

(the y-axis) responds to the cumulative impacts of all stressors (see U.S. EPA 2016, Chapter 5). 

Anthropogenic stress to the estuary can be considered in general terms to address many BCG goals, 

and better characterizations of GSA stressors may include human population numbers, loadings 

from point sources, ambient pollutant levels, or time, as a surrogate for increasing anthropogenic 

stress. An analysis of changes in land-use patterns in the estuarine watershed over time (e.g., 

changes in percent of impervious surface) or use of a landscape development index (Oliver et al.

2011) or other watershed index may be an effective tool for improving a generalized stressor 

gradient. Many estuarine and coastal impacts are based on stressors within the watershed, 

e.g., nutrient or sediment loads.

A stress gradient that identifies individual stressors allows development of specific thresholds 

for these stressors and so leads to a more effective BCG. Diagnostics and control of stressors 

may involve more detailed stressor characterization and additional analysis using specific 

stressor-response data sets and diagnostic tools such as stressor identification and causal analysis 

(www.epa.gov/rps/stressor-indicators, www3.epa.gov/caddis). Specific stressor-response models 

linking stressor levels to BCG condition are extremely valuable for stressor control.

Oceanic stressors may also play a significant role (Figure 3-8). Temperature changes and rising sea 

levels are stressors that influence biotic distribution and condition. If these larger-scale stressors 

are not considered, local restoration (e.g., of saltmarshes) may not be effective. To best relate all 

biological and stressor measures to a common anchor point, programs can include undisturbed 

stressor levels in the definition of reference condition. Also, the human-caused component of 
Implementing the Biological Condition Gradient Framework

20

stressors should be separated from natural stressor variability. In many cases, for the more widelyused indices, basic stressor-response relationships for the assessment measures will already have 

been developed through established monitoring programs or through the published literature. 

In other cases, e.g. measures of function and connectance, stressor-response relationships may be 

estuary-specific and may need more development. In all cases, a stressor gradient that associates 

biological condition with individual stressors is critical for managing specific stressors. 

Figure 3-8. Oceanic influence near the mouth of Narragansett Bay, RI. 

10. Organize, interpret and report results. BCG attribute levels and a GSA can be organized as a 

BCG model to evaluate environmental data and communicate estuarine condition in a meaningful 

way. Analyses may focus on specific areas or on the entire waterbody to reveal what the overall 

condition of the estuary is, which biotic components of the estuary are doing well, what the 

significant biological problems are, what specific locations within the estuary are doing well 

(or poorly), and how that estuary is faring in comparison to other estuaries. Stressor-response 

linkages to biological condition can be reported for the GSA and for specific manageable 

stressors. 

Data should be presented in ways that the public can easily understand and relate to. Although not 

conducted using a BCG, the Chesapeake Bay Program provides helpful examples of data presentation, 

having worked with the issues of summarizing multiple assemblages at multiple scales. They report 
3. Estuarine and coastal BCG implementation

21

data at the embayment level, whole-bay and watershed level. Various measures are examined 

separately, and averages are combined into an overall health index. The experiences of Chesapeake 

Bay (and of other estuaries with long-term data such as Buzzards Bay or Tampa Bay) are useful 

models for data presentation (See Appendix B, FAQ sheet). Many of these analyses focus on the 

relationship of the parts to the whole, e.g., evaluating the overall current condition of estuaries 

relative to the condition of estuarine components, and relative to the conditions of the past. 

11. Develop decision support, communication, and monitoring tools; assist management partners. 

Work in pilot systems provides several excellent examples of applying BCG to management, and 

Section 6 (pages 61–84) describes these efforts in detail. Different uses of BCG can be explored 

to meet the objectives of each program: 

• Explicitly incorporating biology into estuarine and coastal management for greater public appeal 

and for better addressing both cumulative impacts and specific stressors.

• Using scientific and stakeholder consensus to improve interpretation of assessment and develop 

environmental visions, goals, and targets. This can benefit National Estuary Program (NEP) 

management plans; assist National Estuarine Research Reserve (NERR) programs (Figure 3-9), 

Non-Governmental Organizations (NGOs) and other self-motivated stakeholders. 

• Communicating conditions, goals, progress towards goals, and other aspects of ecology and 

management. Different forms of communication are usually needed to reach a wide range 

of audiences and stakeholders. A motivated public can contribute to environmental success 

in many ways, e.g., reducing inputs from lawns or generating political will.

• Organizing and reporting results from existing monitoring programs; this improves assessments 

of environmental conditions both nationally and locally. 

• Supporting CWA and other regulatory goals for environmental action by states, tribes, territories, 

counties, and federal agencies. Regulatory goal-setting requires a rigorous calibrated BCG−

these goals are usually subject to a higher level of scrutiny than are the non-regulatory goals 

described above. 
Implementing the Biological Condition Gradient Framework

22

Figure 3-9. Taskinas Creek, part of the Chesapeake Bay NERR in Virginia. Photo: April Bahen, 

CBNERRVA NOAA, courtesy of NOAA

As above, applying the coastal and estuarine BCG guidance can allow better assessment, goal-setting, 

monitoring, and communication/reporting. It can also contribute to refinement of designated uses 

so they are directly linked to biological measures. The guidance can be used to improve biological 

criteria for management of nutrient inputs, assess the overall condition of the waterbody for better 

communication, prioritize local land-planning decisions, interpret national monitoring programs, 

communicate a need for protection of nature, or set numeric targets in a way the public can easily

understand.

The focus of the BCG approach is on developing the scientific underpinnings needed to assign BCG 

level numbers to biological conditions. The issues of determining what conditions are or are not 

acceptable for a specific waterbody are management questions, informed by BCG levels, but decided 

through a process that considers public and stakeholder interests, environmental regulation, 

ecological goals, and societal goals. NEPs and similar management groups are well positioned to 

take BCG through the entire process, from initial stakeholder investment to BCG development 

to stakeholder involvement in setting and achieving specific goals and targets. 
4. Components of the estuarine/coastal BCG

23

4. Components of the estuarine/coastal BCG

4.1. Attributes and measures

How and Why Do We Group Biological Responses?

Biology responds to stressors in predictable ways that can be divided into types of response. Here we use 

changes in structure, non-native taxa, condition, function, and connectance as five meaningful groupings 

of biological response, termed ‘attributes’ in the BCG approach. This is important because attributes respond 

differently to stressors; increasing stress may affect species composition (structure) before it affects 

bioturbation (function). Assigning levels of biological condition within attributes improves resolution 

and consistency. 

This BCG approach organizes important estuarine and coastal biological responses into ecological 

attributes (Table 4-1). This table serves as a guide for a wide range of applications, is designed to be 

useful at multiple spatial scales, and incorporates a variety of biological and ecological measures. 

The stream attributes (see Appendix A, also U.S. EPA 2016) were used as the foundation for the table, 

but were adapted to include estuarine and coastal features.

Table 4-1. Five attributes and potential measures for application to estuarine and coastal BCGs at different 

scales, developed through expert consensus at a 2008 BCG workshop. This table provides an ecological 

organization of measures but does not include all relevant measures and does not provide specific direction on

which ones to use in a given waterbody. Attribute and measure selection needs to consider the management 

questions, the important stressors, and the data that exist or that can realistically be collected. 

Attribute Potential Measures and Description

Structure 

Measures of waterbody, community, or habitat structure and complexity, also recognizing loss of 

habitats or species due to human activities

Examples include macroinvertebrate or fish indices, phytoplankton or zooplankton community 

measures, epifaunal measures, biotope mosaics, presence/quantity of sensitive or susceptible taxa or 

biotopes, measures of seagrass or macroalgae

Non-Native 

Taxa

Measures of non-native species, including intentionally introduced species

May include measures of the impact of introduced and non-native species

Examples include estimated numbers of species or individuals, biomass measures of natives and 

non-natives, or replacements of native species

Condition

Measures of the condition (‘health’) of waterbodies, habitats, or species. Also includes measures of 

resiliency 

Examples include harmful algal blooms, disease outbreaks, outbreaks of other harmful taxa, measures 

of habitat or biotope health such as seagrass condition or wetland condition, fish pathology or shellfish 

bed condition, measures of reproductive success

Function

Measures of energy flow, trophic linkages, and material cycling, including proxy or snapshot measures

that correlate to functional measures 

Examples include photosynthesis:respiration ratios, benthic:pelagic production rates, chlorophyll a

concentrations, benthic bioturbation, and form/extent of primary production

Connectance

Measures of exchanges, movements, predation, migrations or recruitment of biota between 

watersheds, waterbodies or habitats; measures may be strongly affected by factors adjacent to or 

larger than the immediate study area 

Proxies may be used as measures, including habitat landscape metrics, biological watershed inputs, 

anadromous fish data, or hydrological measures
Implementing the Biological Condition Gradient Framework

24

Three basic attributes

The structure, non-native taxa, and condition attributes are often used in building BCG models. 

These attributes are ecologically important, meaningful to stakeholders, and relatively easy to 

measure. The structure attribute can be applied to almost all BCGs, and measures of these three 

attributes can also serve as proxies for function and connectance.

Structure

The estuarine/coastal ‘structure’ attribute described in Table 4-1 considers structural patterns of 

biology at several scales including community structure (e.g., IBIs and other measures), habitat 

structure (e.g., patterns of primary and secondary production within seagrass beds), or waterbody 

structure (e.g., numeric analyses of the mosaic of living habitats [biotopes] within the waterbody). 

This attribute may further include biological features at the watershed scale (e.g., landscape measures 

of terrestrial biology to evaluate the living watershed/waterbody complex).

Figure 4-1. Seagrass is a biotope and a sensitive indicator of condition. 

Channel Islands National Marine Sanctuary, CA. Photo: NOAA

Non-native taxa

The coastal/estuarine ‘non-native taxa’ attribute evaluates the populations of invasive species in a 

waterbody and their effects on native species. This is essentially identical to the stream non-native 

taxa attribute, although different species are involved (Figure 4-2). 
4. Components of the estuarine/coastal BCG

25

Figure 4-2. Non-native taxa: dead man’s fingers (Codium fragile), a branching green seaweed, was first 

seen in the U.S. in 1957 and has spread extensively since then. Codium displaces seagrasses, kelp, and 

other native flora. Codium has washed up on shores in Massachusetts in such large quantities that beaches 

have had to be closed to the public (Donohue 2006).

Condition

The estuarine ‘condition’ attribute mirrors the stream condition attribute in evaluating the anatomical 

or physiological characteristics of an organism through disease, tumors, and deformities, but the 

estuarine version may also consider ecological condition of a larger habitat or area. Coastal or 

estuarine condition measures include coral or seagrass disease, multi-metric saltmarsh condition 

indices, or outbreaks of destructive native taxa (e.g., predatory native urchins or starfish).

Higher-level attributes

In general, measures of biological structure, non-native taxa, and condition (described above) are 

more available than measures of biological function and connectance as described below (Davies 

and Jackson 2006). Yet, these higher attributes may better address concepts of sustainability and 

resilience, and may help identify and predict critical ecosystem shifts and tipping points such as 

system-level anoxia or coral reef loss. Some effective functional measures have been developed, 

often based on surrogates or proxies. Structural measures may serve as proxies for function and 

connectance when logic and assumptions are clearly explained. 
Implementing the Biological Condition Gradient Framework

26

Function

The ‘function’ attribute is very similar in both stream and coastal/estuarine BCGs. Both evaluate 

ecosystem processes including primary production, respiration, and benthic biological exchange, 

also, both use the evidence of structural proxies as measures of functions. To illustrate, the Southern 

California Coastal Water Research Project (SCCWRP) and collaborators have developed a macroalgal 

biomass measure for California coastal lagoons that indicates major shifts in ecological condition and 

function (Sutula et al. 2014). Macroalgal biomass was linked to bioturbation depth (measured with a 

sediment profile camera, Figure 4-3) which served as the more direct proxy for evaluating ecological 

condition and functional shifts.

Figure 4-3. Sediment profile image showing shells on the sediment surface and a 15 cm deep section of 

the sediment below the shelly surface. The light brown or reddish area nearest to the sediment surface 

has been oxidized by the activities of burrowing animals. The depth of this area is an approximation of 

benthic bioturbation, which controls many sediment processing rates and is a structural proxy for function. 

The large brown vertical sediment disturbance just right of center is evidence of tunneling by a larger 

benthic creature, likely a mantis shrimp (Squilla empusa) as they are abundant in this part of the Taunton 

River (MA).

Other potential measures or proxies of function include system metabolism, form and quantity of 

primary production, and sediment biogeochemical processing rates. Metrics quantifying changes 

to the extent, proportion, and distribution of biotopes (living habitats) in an estuary or other area 

(the biotope mosaic approach, see Section 5.4.1.c on pages 51−53) are structural proxies for function 
4. Components of the estuarine/coastal BCG

27

at a larger scale: each biotope provides a unique set of functions, so when the mix of biotopes is 

changed from the undisturbed condition, so too is the overall function of the waterbody. When high 

functioning naturally-occurring biotopes (e.g., oyster reefs) are replaced with low functioning biotopes 

(e.g., shell hash with small tube-building fauna), the overall function and biological condition of the 

waterbody will be diminished−and this is a concept that engages public sentiment.

Connectance

‘Connectance’ in estuaries occurs more broadly than in streams: estuaries are not linear, and water 

movements are multi-directional. Connectance in estuaries, coastal habitats, and coral reefs includes 

habitat exchanges (Figure 6-18, page 78), linkages within the estuary, and connections to streams, 

coastal waters, and watersheds or watershed integrity. Proxies may include abundance of 

anadromous or catadromous fishes (e.g., eels, salmon, and herring) or other taxa known to 

depend on habitat connections. 

Biological watershed inputs (e.g. phytoplankton chlorophyll a, prey species, salt-tolerant freshwater 

taxa) may be used as proxies for watershed connectance. Within-estuary connectance can be 

evaluated through spatial analyses of biotope mosaics, e.g., measures of landscape structural 

connectedness, isolation, or fragmentation (Rutledge 2003). Similarly, hydrologic data (e.g., effects

of dams, culverts, causeways) when combined with biological data can be used as surrogates 

for connectance (Figure 4-4). 

Figure 4-4. Hydrological evidence for poor connectance–Watchemoket Cove, RI, is connected to 

Narragansett Bay only under a small bridge on an old railroad causeway. 

The coastal and estuarine BCG adaptation does not use stream attribute IX (spatial and temporal 

extent of detrimental effects). Draft narratives for all estuarine attributes follow U.S. EPA (2016) 

stream narratives (Appendix A) to allow comparability in level assignments among BCG approaches 

in different types of waterbodies.
Implementing the Biological Condition Gradient Framework

28

New methods

Moving forward, advanced new sampling technologies and analysis tools will lead to new or improved 

measures to characterize the informative attributes of function and connectance. Evaluating and 

monitoring coastal and estuarine systems can be difficult due to high levels of complexity and 

variability. Yet, innovative remote sensing technologies (including acoustic imaging, aerial 

photography, underwater still and video imagery, autonomous underwater vehicles [AUVs], 

and satellite imagery) are now available for acquiring large amounts of data.

Satellite ocean color data (such as that previously provided by the Hyperspectral Imager for the 

Coastal Ocean [HICO] on the International Space Station) offer high quality spectral data at global 

scales and high spatial resolutions (Figure 4-5). While the HICO hyperspectral sensor with 90 m pixels 

was damaged in a solar storm, other orbiting sensor platforms are currently providing multispectral 

data (e.g., Operational Land Imager with 30 m pixels, Ocean and Land Color Instrument with 300 m 

pixels). Several other hyperspectral sensors are planned for the future with 2020 and later launch 

dates. Satellite remote sensing presents opportunities to link anthropogenic stressors to biological

responses in coastal and inland waters. EPA is developing spectral algorithms that better determine 

chlorophyll levels, biological productivity (e.g., plankton blooms), and other water quality measures 

in coastal waters. These could serve as proxies for BCG attributes of function and connectance.

Figure 4-5. HICO satellite image of the Columbia River, OR and WA. Image: HICO image gallery: 

http://hico.coas.oregonstate.edu/gallery/gallery-scenes.php, accessed 5-23-2016

While these developing technologies may enhance our 

ability to better characterize and manage estuarine and 

coastal resources, no single sampling method or tool 

can successfully address all attributes relevant to a 

waterbody. Incorporating several measures at 

multiple scales in a BCG leads to a more comprehensive 

understanding of condition, which should improve the 

ability to engage the public, to set and track meaningful 

environmental goals, and to understand the dynamic 

conditions that exist within coastal waters. BCG is a way 

to bring different attributes and lines of evidence together 

with academic and scientific expertise to evaluate large 

systems, e.g., the managed waterbody and its associated 

watershed and coastal or oceanic systems.
4. Components of the estuarine/coastal BCG

29

4.2. BCG levels 

Once attributes and measures have been selected and the necessary data have been acquired, the 

BCG is assembled by assigning narrative or numeric thresholds and decision rules for levels 1 through 

6 for each measure. This will usually occur in separate stages of effort. The key to this process is the 

consistent guidance of Table 4-2, which provides narrative to define all six levels for each estuarine/

coastal BCG attribute. Table 4-2 was developed through a panel of national estuarine experts at the 

2008 BCG workshop (Appendix C), and the first two columns of Table 4-2 (‘Attributes’ and ‘Potential 

Measures’) are identical to those in Table 4-1 (page 23). The six ‘Examples of BCG Level Narratives’

columns present a flexible set of estuarine and coastal narratives that are closely aligned with stream 

narratives (U.S. EPA 2016, Appendix A of this document), but have been modified to include estuarine 

aspects including complexity, biotopes, and estuarine taxa.

The strength of the estuarine and coastal BCG level narratives as shown in Table 4-2 is their 

consistency with the accepted freshwater level narratives. Level 2 in a Midwest stream should have 

the same basic ecological meaning as level 2 in a Florida lagoon. BCG levels 1 - 6 provide a common 

language for assessment because the methods and the narratives can be applied whenever a full 

range of biological condition can be described using any characteristic of biology. Applications in 

different estuaries will include different measures; the measure-specific narratives of Table 4-2 are 

put forth as examples that could be modified for use with different approaches and measures. All 

measures and narratives of this Table can be adapted as needed. Further, levels can be compressed 

or eliminated as dictated by the available data or by management needs, e.g., combining levels 1 & 2, 

3 & 4, and 5 & 6 as three units of reporting. Each estuarine or coastal BCG program should consider 

their own uses of Table 4-2, but the basic guidelines provided by the freshwater stream narratives 

should be followed. The left column of Figure 2-2 (the BCG conceptual model, page 6) shows stream 

narratives applicable to all attributes, and Appendix A provides stream narratives for each individual 

attribute. These narratives are discussed in U.S. EPA (2016). 
Implementing the Biological Condition Gradient Framework

30

Key table: Consistent narratives to define BCG levels

Table 4-2. Attributes and potential measures developed at the 2008 Estuarine BCG workshop 

(left two columns) paired with examples of narratives for BCG levels (right 6 columns). 

Attribute Potential Measures

and Descriptions

Examples of Estuarine BCG Level Narratives, based on recommendations of a panel of experts

and U.S. EPA (2016)

Level 1 Level 2 Level 3 Level 4 Level 5 Level 6

Structure

Measures of waterbody, 

community, or habitat 

(i.e., biotope) structure 

and compositional 

complexity; may also 

recognize loss of biotopes 

or species due to human 

activities. 

Examples include 

macroinvertebrate or fish 

indices, phytoplankton or 

zooplankton community 

measures, epifaunal 

measures, biotope mosaic 

measures, and presence, 

quantity, or arrangement 

of sensitive taxa or 

biotopes, including large 

long-lived benthic species, 

seagrass, coral reefs, 

macroalgae, or wetland 

vegetation. 

Community or 

biotope 

composition is 

as naturally 

occurs except 

for global 

extinctions; 

patterns of 

primary 

producers, 

biotope mosaic 

measures, and 

communities or 

areas with large, 

long-lived and 

sensitive species 

or biotopes are 

as naturally 

occurs

Minor 

changes in 

natural 

occurrences 

of biotopes, 

patterns of 

primary 

producers, 

or other 

measures; 

slight 

changes in 

abundances 

of sensitive 

or tolerant 

species or 

biotopes

Evident changes in 

biological measures; 

decreases in 

sensitive species or 

biotopes and 

increases in tolerant 

species or biotopes; 

evident changes in 

patterns of primary 

producers and 

estuarine biotope 

mosaics

Significant 

changes in 

biological 

measures; 

marked decreases 

in sensitive 

species, including 

large or long-lived 

taxa; increases in 

tolerant species. 

Evident changes 

in patterns of 

primary 

producers and 

estuarine biotope 

mosaics, which 

are altered with 

replacement of 

natural biotopes 

by tolerant or 

non-naturally 

occurring 

components

Most sensitive, large 

and/or long-lived 

taxa are absent, with 

a dominance in 

abundance of 

tolerant taxa; 

significant shifts in 

species diversity, size 

and densities of 

remaining species; 

patterns of primary 

producers and 

estuarine biotope 

mosaics significantly 

altered; many 

sensitive natural 

biotopes lost with 

replacement by 

tolerant or nonnaturally occurring 

components

Sensitive, large 

and/or long-lived 

taxa are largely 

absent with 

possible 

extremes in 

abundance of 

remaining taxa; 

marked shifts in 

diversity, sizes, 

and densities of 

remaining 

species; near 

complete loss or 

alteration of 

estuarine biotope 

mosaic; marked 

losses in natural 

biotope area 

Non-Native 

Taxa

Status of non-native 

species. May include 

measures of the impact of 

invasive and non-native 

species. 

Examples include 

estimated numbers of 

species or individuals, 

relative densities or 

biomass measures of 

natives and non-natives, 

or replacements of native 

species. 

Non-native taxa, 

if present, do 

not significantly 

reduce native 

taxa or alter 

structural or 

functional 

integrity

Non-native 

taxa

may be 

present, but

occurrence 

has a nondetrimental

effect on 

native

taxa

Non-native taxa may 

be prominent in 

some assemblages 

(e.g., benthic 

invertebrates, 

crustaceans, algae, 

bivalves, fishes); 

some sensitive 

native taxa may be 

reduced or replaced 

by functionally 

equivalent nonnative species

Increased

abundance of

tolerant nonnative species; 

non-natives 

prominent in 

many 

assemblages

Some assemblages 

(e.g., benthic 

invertebrates, algae, 

bivalves, 

crustaceans, fishes, 

epifauna) are 

dominated by 

tolerant and/or 

invasive non-native 

taxa

Same as level 5

Condition

Measures of the condition 

of waterbodies, biotopes, 

communities, populations, 

or organisms. Some 

measures may serve as 

proxies for resiliency. 

Examples include harmful 

algal blooms, disease 

outbreaks, outbreaks of 

harmful native taxa (e.g., 

starfish), fish pathology, 

and measures of specific 

biotopes or communities, 

e.g., indices of 

invertebrate, coral, 

wetland, or shellfish bed 

condition.

Diseases, 

harmful algal 

blooms, other 

outbreaks of 

harmful taxa, 

and biotope or 

community 

measures are 

consistent with

naturally 

occurring

incidents and

characteristics

Same as 

level 1

Incidences of 

diseases, harmful 

algal blooms, and 

other outbreaks may 

be slightly higher 

than expected; 

biotope or 

community 

measures may be 

slightly lower than

expected

Incidences of 

diseases, harmful 

algal blooms, and 

other outbreaks 

are slightly higher 

than expected 

(e.g., coral

bleaching events 

occur sporadically 

and result in 

slightly elevated 

mortality), and 

other indices are 

slightly lower than 

expected 

Incidences of 

diseases, blooms, 

and other outbreaks 

are increasingly 

common, 

particularly affecting 

long-lived taxa 

where biomass may 

also be reduced, e.g.,

coral bleaching 

events are frequent 

and result in 

mortality. Other 

indices are 

significantly lower 

than expected

Diseases, harmful 

algal blooms, and 

other outbreaks 

are common and 

serious, biotope 

or community 

condition 

measures are 

extremely low, 

Disease, 

outbreaks, etc. 

may occur across 

multiple

biotopes, 

communities, 

taxa groups, or 

populations 
4. Components of the estuarine/coastal BCG

31

Table 4-2. (continued)

Attribute Potential Measures

and Description

Examples of BCG Level Narratives, based on recommendations of a panel of experts and U.S. EPA (2016)

Level 1 Level 2 Level 3 Level 4 Level 5 Level 6

Function

Measures of energy flow, 

trophic linkages and 

material cycling, including 

proxy or snapshot 

structural metrics that 

correlate to functional 

measures.

Examples include

production:respiration 

ratios, benthic:pelagic 

production ratios, extent 

of benthic bioturbation, 

export rates, and 

form/extent of primary 

production, e.g., 

chlorophyll a concentrations, macroalgal 

biomass.

Energy flows, 

material cycling, 

and other 

functions are as 

naturally occur, 

typically 

characterized by 

complex 

interactions and 

trophic links 

supporting large, 

long-lived 

organisms

Energy flows,

material 

cycling, and 

other 

functions are 

within the 

natural range 

of variability;

characterized 

by complex

interactions 

and trophic 

links 

supporting 

large, longlived 

organisms

Virtually all

functions are

maintained through

operationally

redundant system

attributes. Minimal

changes to export

and other indicative 

functions. Some

functions (e.g.,

production,

biomass,

respiration) may 

have increased

due to organic 

pollution or low 

levels of disturbance 

Most functions 

are maintained 

through

operationally

redundant system

attributes, though 

evidence shows 

loss of efficiency

or complexity, 

and some 

functional rates 

may shift

Losses of some

ecosystem 

functions

are manifested as

changed export or

import of 

resources, changes 

in energy and 

material processing 

rates, production: 

respiration ratios, 

benthic:pelagic

production ratios,

or respiration/

decomposition

rates

Most functions

show extensive 

and persistent

disruption, 

including shifts in

primary production, microbial

dominance, fewer

and shorterlength trophic 

links and highly 

simplified trophic 

structure, marked 

shifts in benthic: 

pelagic 

production ratios

and in energy and 

material 

processing rates

Connectance

Measures of exchanges, 

movements, predation, 

migrations, or 

recruitment of biota 

between watersheds, 

waterbodies, or habitats. 

Measures within the area 

being studied may be 

strongly affected by 

factors adjacent to or 

larger than the immediate 

study area. 

Structural measures may 

be used as proxies, 

including hydrological 

metrics, presence of dams

or causeways, biotope 

landscape metrics such as 

fragmentation or nearestneighbor analyses, 

biological watershed 

inputs, or characteristic 

migratory species, e.g., 

anadromous or 

catadromous fish 

abundance. 

System is 

naturally

connected or

disconnected* in

space and time - 

exchanges, 

movements, 

predation, 

migrations, or 

recruitment 

between

watersheds, 

waterbodies, or 

habitats are as 

naturally

occurs

*Note that some 

systems are 

naturally closed 

off, and this is 

the Level 1 state

Same as

level 1

Slight loss, or

increase, in

connectance

between

watersheds, 

waterbodies, or 

habitats, but

colonization

sources, refugia,

and other

mechanisms mostly

compensate

Some loss, or

increase, in

connectivity

between 

watersheds, 

waterbodies, or 

habitats, but

colonization

sources, refugia,

and other

mechanisms

prevent complete

disconnects or

other failures

Significant loss or 

increase in 

ecosystem 

connectance 

between 

watersheds, 

waterbodies, or 

habitats is evident; 

alternative 

pathways and 

recolonization 

sources do not 

exist for some 

biotopes or taxa; 

some nearcomplete 

disconnects or 

connects exist; 

significant 

reductions in highly 

connected 

biotopes 

For many groups, 

a complete loss 

(or maximum 

increase) in 

ecosystem

connectance in at

least one 

dimension (either 

spatially or

temporally) 

lowers

reproductive or

recruitment 

success and 

prevents (or fully 

allows)

exchanges, 

movements, 

predation, or 

migrations 

between

watersheds, 

waterbodies, or 

habitats. 

Disconnects or

other failures are 

frequent. Most 

naturally 

occurring 

biotopes are 

eliminated

Defining BCG level 1: 

The BCG is anchored in level 1 as natural or undisturbed conditions. This ties back to the CWA 

requirement to protect the biological integrity of waterbodies, and the Frey (1977) definition of 

biological integrity as grounded in natural condition. Quantitative data representing natural

conditions exist in some locations for some measures. In the absence of these data, narrative 

descriptions from historic records prior to significant human influence (and other methods) may be 

applied (Table 4-3). 
Implementing the Biological Condition Gradient Framework

32

Figure 4-6. Thicket of Acropora cervicornis (staghorn coral) and reef fish indicative of coral reef BCG 

levels 1 and 2, very good to excellent conditions. Photograph from 1975, Florida Keys, FL. 

In practice, four basic methods can be considered for determination of level 1 (or combined level 1 

and 2) conditions, based on Gibson et al. (2000): use of historical data, use of current data from 

‘reference’ areas, use of predictive models, and use of expert consensus. Each method has strengths 

and weaknesses (Table 4-3), and is discussed further below. These methods can also be combined.

Table 4-3. Strengths and weaknesses of various methods used to determine undisturbed or 

minimally disturbed conditions (Table 4-1 from Gibson et al. 2000).
4. Components of the estuarine/coastal BCG

33

Historical data

Historical data have been used to describe undisturbed or minimally disturbed conditions in a 

number of U.S. estuaries. The Chesapeake Bay Program set many conservation and restoration 

goals on historic baselines, using 1994 for oysters and the 1930s for seagrass (CBP 2000). Seagrass 

is frequently used as an indicator of historic conditions because early charts, records, or photographs 

often show seagrass and because of its sensitivity and value (Figure 4-7). Historic conditions and 

subsequent changes over time were also described for Greenwich Bay, Rhode Island (Pesch et al. 

2012, Shumchenia et al. 2015). The Buzzards Bay Coalition compared biological data to a historical 

baseline of pre-colonial conditions. The Lower Columbia Estuary Partnership (LCEP) used historical 

habitat conditions (the 1870s) as a baseline to set targets for habitat acreage to restore historic 

habitat diversity (LCEP 2012). Similarly, the Tampa Bay Estuary Program identified 1900 as minimally 

disturbed conditions for bay habitats, and used historical conditions of 1950 as acreage targets both 

for restoring seagrass and for restoring the historical balance (proportions) of multiple habitats in the 

estuary (Greening and Janicki 2006, Cicchetti and Greening 2011). In Puget Sound, historical baselines 

from the 19th century were incorporated into management of wetlands, bald eagles and resident killer

whales (Samhouri et al. 2011). Historical data can correct the misinterpretation of “natural” 

conditions caused by shifting baselines, and have a solid track record in representing undisturbed 

conditions for estuarine and coastal management.

Figure 4-7. Seagrass with barracuda.
Implementing the Biological Condition Gradient Framework

34

Current reference data

Present day biology in areas believed to reflect least disturbed reference conditions is also regularly 

used to develop baselines, especially when applying indices of biological condition to distinguish 

between unimpaired and impaired condition. Use of reference sites to define reference condition 

is the preferred technique for setting baseline conditions in the U.S. as well as in areas managed by 

the European Union (EU) (EC 2002). However, present day best condition may already be significantly 

degraded from natural, and shifting baselines of human perception can obscure this. Best existing 

reference may represent a range from undisturbed to minimally or moderately disturbed, so defining 

the quality and meaning of the reference condition is important (Stoddard 2006), particularly for use 

in BCG. In severely degraded estuaries, relatively unimpaired areas in a similarly classified estuary 

may be used as a surrogate measure. Data from existing reference areas have been used extensively 

in the Chesapeake Bay Program, sometimes supplemented by use of best professional judgment 

(Weisberg et al. 1997). In BCG developments to date, expert panels have assigned present-day 

reference sites to BCG levels 2, 3, and 4, reflecting opinions that the reference sites have been 

exposed to some degree of disturbance. While subject to changes in natural stressors, BCG level 1 

is considered anthropogenically unstressed. This is equivalent to the ‘Biological Integrity Reference’ 

(Stoddard et al. 2006). 

Predictive models

Predictive models have often been used in freshwater systems to approximate biological condition 

in the absence of environmental impact (Hawkins et al. 2000). These methods, however, have not 

been widely tested or used to assign minimally disturbed conditions in estuaries and near coastal 

waters either in Europe (Muxika et al. 2007) or in the United States, although see ‘combined 

approaches’ on the next page. This is an area in need of further development and evaluation. 

Expert consensus 

Expert consensus, panels of experts, or expert workshops can be used together with historical 

information and/or data to describe the biota expected in undisturbed or minimally disturbed 

conditions. This combination of methods has been used to narratively describe level 1 in freshwater 

BCG applications, and is well suited to BCG work in providing an anchored baseline. This approach 

was used to predict the biological assemblages (fish and macroinvertebrates) expected in 

undisturbed/minimally disturbed coral reefs in Puerto Rico (Section 6.5, pages 77–82). Expert 

consensus is also valuable in adjusting best existing condition to more closely match naturally 

occurring conditions. As a cautionary note, expert consensus may not succeed where data are sparse 

and conceptual understanding of how the system responds to stress is poor (Thompson et al. 2012). 
4. Components of the estuarine/coastal BCG

35

Combined approaches 

Combinations of methods will also be effective. A BCG level 1 condition for fish assemblages has been 

proposed for the Upper Mississippi River based on historical data combined with a statistical modeling 

approach (U.S. EPA 2016 Appendix B1). The Upper Mississippi (like many estuaries) is so altered that 

undisturbed or minimally disturbed conditions no longer exist, yet conditions have more recently been 

improving under better environmental management. To apply a BCG with a full range of condition, 

a synthetic historical fish community was developed for level 1. Known ecology and habitat needs

of fishes that were abundant early in European colonization were combined with large data sets of 

modern fish species occurrences linked to a gradient of chemical, physical, and biological stressors. 

Statistically pairing the living requirements of historically abundant fish to this gradient of stressors 

led to the synthetic historical fish community, which quantitatively anchored the undisturbed end of 

the stressor gradient as BCG levels 1 and 2. The full gradient of condition was then used to derive BCG 

thresholds for existing fish index measures, and these thresholds were used to assess ALU attainment 

under the CWA. Further, the science-based quantitative descriptions of abundant historical fish 

species (together with the fact that many of these species are still present) provides context and 

motivation for restoration in the direction of BCG levels 1 and 2, even if these levels are unattainable. 

This approach to historic data, while still in development, may be valuable for application to estuarine 

and coastal aquatic ecosystems―the Upper Mississippi River system is similar to many estuaries in 

complexity and extent of degradation. Other combinations of the four basic methods to determine 

reference could also be helpful, and expert consensus contributes to all methods.

Regardless of methods used, development of level 1 (or combined level 1 and 2) undisturbed 

conditions is a critical part of BCG in setting the anchor point from which other levels will be derived. 

When BCG levels are distributed over the full range of condition, consistent level narratives allow valid 

comparisons among measures and attributes at different sites or waterbodies, and at different times 

from the past, present, and future. This is the foundation for many of the benefits of the BCG 

approach.

Thresholds and decisions 

Level thresholds: After specific attributes and measures have been selected, level 1 has been 

described, and data from the full range of condition have been prepared for analysis, an expert panel 

should be convened to develop narrative and then numeric decision rules for assigning sites to BCG 

levels (U.S. EPA 2016) following attribute guidelines in Table 4-2, pages 30–31. This ‘consensus of 

experts’ approach brings different scientific viewpoints together to assign local measures to BCG levels 

in a well-documented and transparent manner. Expert consensus integrates divergent scientific 

thinking and imperfect or limited data into numeric thresholds for determining impairments or 

trajectories of condition. Clear and quantitative threshold values will best determine trajectories of 

impairment and improvement. Managers gain clear and defensible scientific answers backed by 

expert consensus, while scientists gain understanding and insight from discussions and consensusbuilding, and see their work and perspectives incorporated into the management process. 
Implementing the Biological Condition Gradient Framework

36

Documentation of process: The BCG focus on transparency and consistent communication of data, 

methods, expert logic, and assessments has been extremely helpful to managers. Clear 

documentation of the entire development process includes:

- Defining how undisturbed conditions were identified, including the basis for assuming that these 

conditions approximate “as naturally occurs”

- Describing how and why biological measures, attributes, and attribute narratives were selected

- Describing the decision rules and numeric thresholds for levels and how these were developed 

by experts in workgroups or workshops

- Identifying any limitations of the science or of the scientific tools that were used. 

This transparency provides the rationale for decision-making, addresses any perception that 

management decisions are random, and provides rigor for defense in any legal proceedings that 

may follow.

Decision-making: The BCG provides mechanisms to help translate biology into useful information 

for management decision-making. The BCG can be used together with societal values and economic 

considerations to inform management decisions, as in the non-regulatory goals and targets developed 

by NEPs. In regulation under the CWA, states and territories must establish designated uses for each 

water body and describe the conditions that are acceptable for these uses, including scientific, social 

and economic factors. Specific management applications are discussed in Section 5.2 (pages 42–44). 

4.3. The Generalized Stress Axis (GSA) 

Multiple stressors

Stressors, in the BCG construct, include any or all anthropogenic events, actions, and outcomes that 

decrease biological integrity. These are addressed on the X axis of the BCG Gradient (Figure 2-2, 

page 6) as the Generalized Stress Axis (GSA). The GSA is a conceptual description of the full range 

(or gradient) of all anthropogenic stressors that affect the biology of the waterbody in question. This 

full range can then be parsed into a set of specific controllable stressors with known stressor-response 

relationships. The GSA can be quantified using proxies for cumulative human impacts in a watershed, 

for example human population, land use/land cover metrics, or time in years from undisturbed or less 

disturbed conditions (e.g., early in European colonization).

A GSA based on more detailed statistical analyses of land use/land cover data leads to a useful 

understanding of how and where stressors are generated. Further, these data support identification 

of specific controllable land-based stressors that contribute to cumulative impacts (U.S. EPA 2016). 

This is valuable for linked watershed-estuary analyses, but since estuaries and coasts are also 

impacted by oceanic and in-estuary processes, land use analysis alone may not be able to capture

all of the important stressors impacting coastal waters.
4. Components of the estuarine/coastal BCG

37

Natural stressors are not considered in the BCG as causing detrimental effects because they are a 

part of the natural environments under which biota evolved. As is typical in estuaries, strong natural 

abiotic gradients (e.g., salinity, flow, abiotic habitat) may be clearly related to the observed biological 

gradient. Here, classification (Section 5.1, pages 39–42) can remove the influence of the natural 

gradient by defining undisturbed conditions within each class. For example, an estuary may be 

classified into mesohaline and polyhaline areas. Some natural stressors may be influenced or 

exacerbated by anthropogenic actions. In these cases, the change to natural stressor levels is 

characterized as the anthropogenic component of that stressor.

Stressors in the BCG are considered in aggregate as part of the GSA (U.S. EPA 2016) because 

biological communities integrate the influence of multiple stressors (Figure 4-8). The GSA is helpful 

in addressing cumulative impacts and as part of the decision rules used to calibrate the BCG. The GSA 

also supports state CWA actions and is useful in goal-setting, communication, long-range planning, 

and other applications in coastal management. The GSA can be evaluated using a variety of methods 

and at any level of detail.

Figure 4-8. Small cove in Black Rock Harbor, CT, an estuary known for high levels of stressors including 

toxicity, nutrients, sediment input, and habitat alteration. The GSA (BCG X-axis) represents the 

synergistic aggregation of all these stressors; the BCG Y-axis evaluates their cumulative impacts on biology. 
Implementing the Biological Condition Gradient Framework

38

Individual stressors

Many environmental efforts (such as the TMDL program) identify one or more stressors that should 

be reduced. Restoration may also focus on a single stressor (e.g., nitrogen) to promote recovery of

resources such as seagrass. Specific stressors of concern should be identified when defining

waterbody problems, selecting attributes and measures, and characterizing biological response to

an overall stressor gradient. The GSA captures the cumulative effects of stressors and serves as 

an organizing framework for individual controllable stressors. The Greenwich Bay historical BCG

(Shumchenia et al. 2015) examined overall change in biological response over time, but also identified

the specific stressors impacting the embayment. Identifying the specific causal stressor or stressors 

can also allow use of the diagnostic decision process (U.S. EPA 2010 [http://www.epa.gov/caddis], 

Ho et al. 2012) that allows further management and improvement of the waterbody.

More sophisticated use of the stressor gradient has taken place in streams when large data sets 

are available. Kashuba et al. (2012) used a Bayesian network model to identify the probability of 

achieving a desired BCG level given a defined management action. For example, if management 

actions reduced flashiness and specific conductance to certain levels in an urban stream, the 

probability of receiving a BCG level 3 or better designation would increase from 24% to 70%. 

Thus, BCG stressor work adds greater scientific understanding of the impacts to biological 

communities while providing critical information and targets for TMDL work, other load reduction 

efforts, and restoration. Stressor-response models linked to BCG levels are necessary for 

management of specific stressors in the BCG framework. The GSA serves as a conceptual basket 

that holds individual stressor-response models and captures their cumulative effects in a quantifiable 

way. See U.S. EPA (2016) Chapter 5 and Appendix A for more information and detailed examples.
5. Application of the approach

39

5. Application of the approach: details and examples

5.1. Classification

Why classify?

Developing a basic understanding of the waterbody (or waterbodies) in question is fundamental 

to coastal and estuarine management. Coastal systems across the U.S. occur in different sizes and 

shapes, with varying bathymetry, tidal influence, volume of river inflow, circulation patterns, etc. 

Within any given system, high spatial and temporal variability support multiple habitats and biological 

communities. This complexity has led scientists and managers to treat each coastal and estuarine 

system as a unique entity (Kelly 2008). Yet, these diverse and complex systems can be described 

and classified through basic sets of geomorphologic, hydrologic, and physical characteristics 

(Engle et al. 2007). Classification allows coherent groups to be identified so as to inform or simplify 

a management question (Kurtz et al. 2006). Classification further allows information from one 

estuary or coastal area to be applied to another, minimizing the need for intensive individual studies 

of similar coastal systems (Figure 5-1). 

Figure 5-1. Two adjacent lagoonal estuaries (Green Pond and Great Pond, Cape Cod, MA). 
Implementing the Biological Condition Gradient Framework

40

Classification of estuaries

Many classification schemes have been developed for dividing estuaries into similar groups. 

Geomorphic classifications (e.g., Pritchard 1967, Dyer 1973) use geologic origin or geology to define 

estuary classes. Estuaries can be classified as drowned river valleys, fjords, deltas, lagoons, and 

tectonic estuaries. Hydrodynamic classifications (e.g., Strommel & Farmer 1952, Hansen & Rattray 

1966) use circulation and stratification to define estuary classes. Briggs (1974) developed a 

classification based on zoogeographic regions used by the U.S. EPA’s National Coastal Condition 

Assessment (NCCA). On a smaller within-waterbody scale, habitat classification allows descriptions 

and inventories of habitats and communities. Classifying data by sediment type, habitat, latitude, 

salinity, or other influencing factors reduces variability in analysis and is valuable for evaluating 

changes over time or space. One of the best known habitat classifications is the Cowardin et al. 

(1979) scheme, which is hierarchical, starting with system (e.g., marine, lacustrine), and then using 

physical and habitat features along with modifiers to classify habitat type. This model has been 

further developed into the federally approved Coastal and Marine Ecological Classification Standard 

or CMECS (FGDC 2012), which has been adopted and is used by many state agencies, several federal 

agencies, and a number of academic and management groups. This standard assists in classifications 

of habitats, estuaries, and coastal areas of all types (Figures 5-1, 5-2, and 5-3). 

Figure 5-2. An anthropogenic estuary built behind breakwaters (San Pedro Bay and Long Beach, 

Los Angeles, CA). Image: Google Earth, data from Landsat
5. Application of the approach

41 

Figure 5-3. Entrance to a small riverine estuary (Narrow River, RI).

Classification to meet different needs

More recently, estuarine classification systems have been developed for specific purposes. Edgar 

et al. (2000) developed a system to identify conservation status. Estuaries were assigned to groups 

based on geomorphology and hydrology. Fish and benthic invertebrate community structures were

used to validate and refine these estuary groupings, which were then ranked based on catchment 

stressors (e.g., population, land use). Biological data were examined for biodiversity and endangered 

species, allowing the individual estuaries to be categorized into one of six conservation levels. Bricker 

et al. (1999) classified estuaries by their susceptibility to nutrient over-enrichment using physical 

measures of dilution and flushing. In a study in Chesapeake Bay, Boynton and Kemp (2000) suggested 

that classification may allow normalization of important factors so as to develop stressor-response 

relationships that could be applied in multiple estuaries. 

Classification can be used for many purposes, including “describing and inventorying communities 

and habitat types, examining differences and similarities between groups, identifying and prioritizing 

conservation efforts, managing resources, and guiding research” (Engle et al. 2007). The type of 

classification chosen in a project will be determined by the questions being asked. If the priority 

is to describe and inventory habitats and communities within an estuary, then geomorphic, 

hydrodynamic, or habitat classification may be most appropriate. Assessment within groups 

of similar biological expectation determined by (for example) salinity, depth, or substrate type 

can improve the quality of assessments by eliminating data from different environmental regimes. 

Managing resources, especially for TMDL or nutrient reduction work, may require identification of 

susceptibility (Bricker et al. 1999) and/or normalization (Boynton and Kemp 2000) so that appropriate 
Implementing the Biological Condition Gradient Framework

42

load-response relationships can be developed. If the differences and similarities between coastal 

estuaries need to be examined or if conservation efforts need to be prioritized, then further 

examination of conservation status groups as in Edgar et al. (2000) could be helpful. 

For BCG application, the European Water Framework Directive (WFD) may be particularly relevant. 

Here, estuaries and coastal waters are defined into types or classes based on physical and chemical 

factors that determine the structure and function of biological communities. Waters are assigned

using (primarily) biology into one of five status (condition) categories (equivalent to BCG levels) 

using a reference condition that is based on high status in other waters as the preferred method 

(EC 2002). Reference conditions are determined within the same type or class of estuary (U.S. EPA 

2011b) so that expectations are appropriate to the physical constraints of the system. For example, 

reference conditions from an open embayment would not be applied to a lagoon. The extensive 

work applying the WFD to European estuaries and coasts provides methods and lessons helpful to 

the application of BCG to U.S. estuaries and coasts. See also the “Six required steps for managing 

European estuaries” text box on page 83. 

Grouping or classification allows better transfer of data, models, and lessons learned from one 

estuarine or coastal system to another. Although our estuaries and coastal systems are unique 

resources valued in different ways by their residents and stakeholders, classification creates 

management opportunities to better protect a specific or unique system through comparisons 

to other similar systems. Classification within an estuary streamlines and focuses biological 

assessments. Classification of nature is a well-developed scientific field that can provide benefits 

to all forms of environmental management.

 

5.2. How can the BCG improve management of estuaries and coastal waterbodies? 

This BCG guidance provides a flexible approach that can be adapted to fit the unique characteristics 

and management needs of an individual estuarine or coastal waterbody (or a classified set of 

waterbodies) and then developed to make best use of the resources and data that are available. 

The ability to make valid comparisons across measures, space, and time provides many benefits. 

The estuarine and coastal BCG was designed to provide national, regional, state, and local managers 

with scientific information needed to improve the environmental condition of their waterbodies. 

Who can benefit?

National managers (e.g., the U.S. EPA Ocean and Coastal Protection Division) benefit from consistent 

assessments of estuaries and estuarine biology. This improves communication and allows more 

comparable national reports on the condition of estuaries and estuarine resources. State managers 

benefit from the ability of the BCG to help with CWA goals: refine designated uses, develop 

biocriteria, identify high-quality waters and watersheds, and document biological response to 

stressors (U.S. EPA 2011a). Consistent assessments guide development of thresholds for Aquatic Life 

Uses, TMDLs, the management of single or multiple stressors, and the communication of condition 

to define goals and monitor progress. The BCG provides rigorous and transparent results that can be 

used in regulation. This has been demonstrated in streams, and the concepts are equally applicable 
5. Application of the approach

43

to management of estuaries. Applications of the BCG to state management and regulatory goals 

are discussed in U.S. EPA (2016). 

Local and regional non-regulatory management groups including NEPs, NGOs, Regional Planning 

Bodies (RPBs), municipal planners, and others are assisted in communicating with stakeholders, 

determining agreed-upon vision statements for desired future conditions, setting goals and targets, 

prioritizing actions, and tracking progress towards targets and goals. The estuarine/coastal BCG 

approach (or any part of it) can also be applied within a larger management program, for example 

EPA’s Healthy Watersheds Initiative, which embraces many of the same principles. Managers will 

also find other advantages in using the BCG.

How can the BCG help?

The estuarine and coastal BCG implementation approach considers waterbodies at several scales, 

and extends several uses of the stream BCG approach to the management of larger systems:

1. Assessing (consistently interpreting the environmental conditions that exist). The BCG defines 

undisturbed conditions, then BCG levels consistently evaluate existing conditions relative to 

those undisturbed conditions using data from any relevant biological measure at scales ranging 

from organisms to waterbodies. Consistent assessments are the basis for effective management 

from goal setting to monitoring to CWA decisions. 

2. Developing visions, goals, and targets (providing information to support consensus on desired 

environmental conditions). Comparing existing conditions of valued biological resources to 

higher quality (more natural) conditions expected with stressor reductions can help develop a 

stakeholder vision of what is desirable and attainable for the future. Levels of condition linked 

to specific attributes and measures can lead to both narrative and quantitative targets towards 

visions and goals. Ultimately, a compelling vision of a desired future can engage stakeholders 

to take action and generate the political will to protect and improve their waterbody; for added 

motivation this vision can also be compared to the ‘do nothing different’ future (see number 5 

below).

3. Informing specific management actions (identifying and prioritizing the stressors most relevant 

to achievement of goals). Additional development of the GSA and stressor identification (see 

www3.epa.gov/caddis) can help parse out the stressors (including stressors in the watershed)

that most contribute to cumulative impacts. This may also provide information to: identify the 

specific and generalized stressor values that determine biological condition levels; develop actions 

to manage those stressors; and evaluate whether environmental targets and goals are realistic. 

4. Monitoring progress (providing measures and levels to track progress towards desired 

conditions). The same measures, attributes, and levels that were used to set targets for an 

individual waterbody are then used to track progress towards those targets. Direct methods 

to evaluate improvement or degradation lead to more effective adaptive management.

 
Implementing the Biological Condition Gradient Framework

44

5. Predicting future scenarios (projecting current or alternative trajectories into the future). In many 

cases the consequences of a ‘do nothing different’ management option can be predicted with

historic BCGs by extending the existing condition trajectory into the future (Cicchetti and Greening 

2011). This may help management groups and communities prevent or prepare for undesirable

future conditions. 

6. Communicating (translating ecology into terms that are more easily understood and 

communicated). BCG levels are easily understood as six grades of condition for what we have, 

what we have lost, and what we can restore, relative to the natural state. The concept of restoring 

valued resources that once existed can resonate with the public and stakeholders (Cicchetti and 

Greening 2011). Further, BCG addresses issues specific to an estuary and includes resources that 

are valued by local stakeholders. BCG levels can easily be converted into another form that may 

appeal to certain groups (report cards, bar graphs, color codes, etc.). The BCG is a basis for 

communication with many different audiences.

A goal of an estuarine and coastal BCG is to consider the estuary or coastal area and its stressors 

in a comprehensive manner by combining consistent assessments at multiple scales. The BCG can 

serve as a conceptual ‘box’ that is capable of capturing a wide range of scales and sub-regions from 

watershed headwaters to the near coastal edge. This provides an ecological foundation for 

integrating environmental and socioeconomic management. 

5.3. The BCG as part of larger social/ecological/economic management approaches

All of the above benefits, however, presume that scientists and managers are well-informed as to 

the underlying science of how their estuary functions, the human stressors that most alter that 

function, the environmental, social and economic priorities of the local communities, and the 

resulting management problems that need to be addressed (i.e., estuarine BCG implementation 

Step 1). It will be difficult to develop a useful BCG model unless it is clear what needs to be assessed 

and why. On the other hand, certain aspects of BCG development can assist with this process; for 

example, an understanding of the historical distributions of biological resources may help clarify 

goals and objectives. 

In situations where objectives are uncertain, initial actions can be taken to apply larger socioecological management approaches that better define environmental, social, and economic needs; 

incorporate stakeholder values; clarify desired objectives; identify stressors; and balance opposing 

goals. This allows BCG assessments to address those issues most relevant to stakeholders and 

managers. In some cases, values articulated by stakeholders (e.g., protect charismatic megafauna, 

figures 5-4 and 5-5) can be addressed through more tractable BCG measures (e.g., habitat quantity 

and quality). Larger social frameworks used together with BCG can address these and other issues.
5. Application of the approach

45

Figure 5-4. Large charismatic animals appeal to public sentiment, and are often dependent on high 

water quality and suitable habitat availability. Manatee calf resting chin on mother’s back, Weeki 

Wachee River, FL. Manatees require abundant aquatic vegetation for food and access to clean fresh water 

for osmoregulation. Photo: N. Cicchetti

These larger approaches include Structured Decision Making (SDM) (Gregory et al. 2012), EcosystemBased Management (EBM) (McLeod and Leslie 2009), Drivers-Pressures-State-Impacts-Responses 

(DPSIR) (OECD 1994), and Coastal and Marine Spatial Planning (CMSP) (White House Council for 

Environmental Quality 2010). BCG levels can also be linked to ecosystem service values. Of these, 

SDM, DPSIR, and EBM have been used directly with BCG (Carriger et al. 2013, Corbett 2013, Yee et al. 

2014, Shumchenia et al. 2015). These larger methods are valuable in any decision-making process, 

and a better understanding of the ecological-social-economic landscape can benefit any BCG effort, 

even after objectives and assessment goals have been established.

Structured Decision Making

Structured Decision Making is an approach that applies human benefits and stakeholder values 

to identify clear objectives and evaluate management alternatives. The basic organization of SDM 

(USFWS 2008, Gregory et al. 2012, Carriger et al. 2013, Yee et al. 2014, Bradley et al. 2015) 

is as follows:

1. Clarify the decision context – identify the significant problem(s) to be solved, and the 

stakeholders involved. 

2. Define objectives and performance measures – develop environmental, social, and economic 

objectives (usually in the form of ‘more X, and less Y’) that reflect stakeholder values. An 

objectives hierarchy is used to organize this from broad values or ‘fundamental objectives’, 
Implementing the Biological Condition Gradient Framework

46

to specific objectives (‘means objectives’), to actions, to performance measures that track 

progress towards the objectives. 

3. Develop alternatives – propose different management approaches, methods, or thresholds 

through which objectives may be achieved, involving stakeholders in the process. 

4. Evaluate alternatives and select management actions; predict likely outcomes and 

consequences of alternative approaches, in general applying scientific methods. Evaluate

tradeoffs with stakeholder input. Select the best approaches and actions as a management 

decision that is informed by science and stakeholders. 

5. Implement, monitor, and review − initiate actions, monitor results using quantitative measures, 

and review to support adaptive management.

In Puerto Rico (Section 6.5, pages 77–82), SDM was used prior to development of a coral reef BCG 

to identify the fundamental objectives of managers and stakeholders, along with potential measures 

in an objectives hierarchy (Carriger et al. 2013, Bradley et al. 2015). This objectives hierarchy 

provided a clear list of desired goals and performance measures. For example, a fundamental 

objective was ‘maximize ecological integrity’. A sub-objective was ‘living habitat condition (seagrass, 

mangroves, corals).’ Performance measures were ‘living habitat condition indices’. Once objectives 

had been defined, a means-ends network was used to develop those objectives (ends) and link them 

to proposed actions (means) from a watershed management plan (Carriger et al. 2013). SDM 

provides a clear understanding of linkages between objectives and management actions, engages 

stakeholders, helps identify gaps, and facilitates evaluation of alternatives. 

DPSIR

As part of SDM in Puerto Rico, the DPSIR framework provided further management context for BCG 

development (Bradley et al. 2015, 2016). DPSIR is a comprehensive human-focused decision-making 

framework that integrates humans, management, socioeconomics, and ecology. The DPSIR terms 

have been defined in slightly different ways, especially with regard to ‘Pressures’, but in a general 

form DPSIR includes five stages. ‘Drivers’ are basic human needs and their influences (e.g., need for 

sustenance, living space, removal of waste), and ‘Pressures’ are the human activities and stresses 

that Drivers place on the environment (additions of nutrients and toxins, destruction of natural 

habitat). ‘State’ then describes the resulting environmental conditions (macroalgal biomass, 

dissolved oxygen levels, seagrass acres, and benthic faunal indices). ‘Impacts’ describe the 

resulting losses or changes to ecosystem services (valuable resource losses, fish kills, unsustainable 

environments, loss of enjoyment of nature). ‘Responses’ are the actions taken by management 

to address Impacts and changes in State (regulation of Pressures, restoration of State). DASEES 

(www.dasees.org), described along with other SDM tools in Bradley et al. (2015, 2016), is an 

online user-friendly platform to help practitioners use both SDM and DPSIR. For projects exploring 

environmental links to human health, EPA has expanded the basic ecological version of DPSIR to 

include human health/social issues on a parallel track. This Eco-Health DPSIR model better integrates 

the relationships between humans and the environment, and is thoroughly discussed in Bradley and 

Yee (2015).
5. Application of the approach

47

The BCG stressor-response approach is embedded in the D-P-S-I portion of the ecological DPSIR 

framework. Anthropogenic BCG stressors can be DPSIR Drivers (e.g., need for living space and 

urbanization), Pressures (e.g., nutrient additions, filling of wetlands, increased siltation) or States 

(e.g., low dissolved oxygen levels, sediment toxicity). Biological BCG responses can be DPSIR States 

(diversity measurements, benthic condition indices, seagrass abundance) or Impacts (decreased 

biodiversity, loss of societally valued seagrass), noting that in the BCG approach, ‘response’ is used 

in a stressor-response construct, and has a different meaning than does ‘Response’ in DPSIR, where 

the term is used to describe management actions. In Puerto Rico, DPSIR was used to organize 

scientific knowledge, stakeholder values, and conceptual linkages in a transparent way, and to help 

establish the decision context with which to identify fundamental objectives (Yee et al. 2014, 

Bradley et al. 2015). Within SDM and DPSIR, the coral reef BCG was valued for its ability to provide 

the Pressure to State linkages and identify indicators. BCG allows a consistent determination of reef 

condition that informs management actions across many reefs and reef areas, and plays an important 

role within both SDM and DPSIR. 

In the Greenwich Bay (RI) BCG (see this document Section 6.1 [pages 61–65] and Shumchenia et al. 

2015) the DPSIR framework was used to build a conceptual model of the complex pathways among 

Drivers (human needs), the resulting Pressures (which were BCG stressors), State (which captured the 

cumulative effects of stressors), and Impacts (which were linked to the biological response indicators 

used in the BCG). These response indicators were eelgrass loss and replacement, benthic community 

changes, and primary production/shellfish−which are connected in Greenwich Bay. This combination 

of indicators addressed shallow substrates, deeper substrates, the water column, and valued species, 

representing major components of estuarine biology. The DPSIR model organized the ecosystem, 

included humans, identified BCG stressors, and linked them to meaningful indicators of biological 

condition. Combining DPSIR and BCG better clarified the workings of the human-ecological system 

(Shumchenia et al. 2015).

A vision of a desired future state

As a complementary management approach, managers, scientists, and stakeholders can work to 

develop a consensus-based vision of a desired future state for the waterbody of concern. This is an 

effective tool for initiating and guiding environmental efforts. The concept of building desired future 

conditions into management is critical to both SDM and EBM (Carriger et al. 2013). National Ocean 

Council guidance for regional marine planning (National Ocean Council 2013) also includes a visioning 

step. Visioning is aligned with the BCG approach, and can take place before, during, and after BCG 

development. An early or pre-BCG vision can inform selection of the biological condition measures 

that are most relevant to the desired future state. A developed BCG can be used to derive or refine 

a stakeholder vision by describing changes to estuarine condition over time. What was our estuary 

like in the past (levels 1 and 2)? What is our estuary like now? What do we want our estuary to be 

like in the future? This last leads to the vision, in the context of what we had, what we have, and 

what we want. If no new actions are taken, forward projections of current environmental trajectories 

can suggest possible future conditions–perhaps levels 5 or even 6.
Implementing the Biological Condition Gradient Framework

48

A BCG visioning approach can be applied to a specific sub-area or to the overall condition of a coastal 

waterbody or estuary. Public and stakeholder outreach and workshops can lead to an agreed-upon

vision for a desired estuarine condition that resonates with and motivates the public. Objectives, 

BCG attributes, measures, BCG level targets and actions can be chosen to address the vision. 

Environmental effects of these actions and progress towards targets, objectives, and the vision

can then be monitored and reported using the same measures and consistent BCG levels. 

The Tampa Bay Estuary Program (Section 6.2, pages 66–70) used these concepts very effectively, 

developing a simple and unifying vision to protect and restore certain valued biological attributes 

to conditions experienced in the 1950s. This vision of a desired future motivated the public and led 

to specific goals and targets that drove management actions (Cicchetti and Greening 2011). In 2015, 

the Tampa Bay Estuary Program achieved (and then exceeded) their original goal of restoring 

seagrass to the historic acreage present in 1950 (TBEP 2015). The vision of moving Tampa Bay 

ecosystems back towards earlier conditions and to ‘restore the balance’ of Tampa Bay habitats led 

to an engaged public, which was a critical element in the success of the program. 

Figure 5-5. Charismatic brown pelican in Tampa Bay, FL. Photo: NOAA

Larger decision-making approaches like SDM and DPSIR, visioning, and BCG are valuable tools that 

can benefit states, NEPs, NGOs and similar organizations in their roles as conveners of different 

management and stakeholder interests. This work aligns with principles of integrated management 

(e.g., EBM): evaluating and managing the waterbody and watershed to achieve ecological, societal, 

and economic goals through involvement of many different groups and partners. This broad

participation is an effective way to address the continuing degradations caused by cumulative 

impacts of multiple stressors. 
5. Application of the approach

49

5.4. Overall estuary or waterbody condition

Why evaluate overall condition?

The public and stakeholders are often very concerned about the overall condition or health of their 

particular waterbody, whether that is a cove or bay where they live, swim, or fish, or an entire 

estuary or coastal area. This concern is best addressed with an assessment of the overall condition 

of that system and the multiple stressors that affect it. The BCG makes the appealing concept of 

waterbody ‘health’ meaningful through consistent comparisons to past conditions, and to conditions 

in other locations. Moreover, evaluating overall condition helps prioritize stressors to best address 

waterbody-level problems. 

Figure 5-6. West Falmouth Harbor, MA, a small lagoonal estuary located down-flow from a groundwater 

injection sewage treatment facility. Note abundant seagrass in 2002. A good candidate for BCG 

monitoring of overall condition over time.

How to evaluate overall condition

Overall condition of an estuary (or other waterbody) is difficult to measure. First, overall condition 

or state derives from the conditions of the major subcomponents, their connections, and their 

combined functions. Consequently, the waterbody should be considered as a system to include these

interactions. Classifying the waterbody (Section 5.1, pages 39–42), then assembling a conceptual 

ecosystem model or diagram of the physical, chemical, and biological processes that structure the 

system helps understand overall condition. Estuaries are spatially and temporally variable, with 
Implementing the Biological Condition Gradient Framework

50

notable differences in structure and function along the axis between head and mouth, and along 

transects from intertidal to deep waters.

Several methods and proxies have been developed to evaluate overall condition of the estuary or 

coast, all of which could be included in a coastal and estuarine BCG through comparisons to 

undisturbed or minimally disturbed conditions. Ideally, the set of biological measures chosen would 

cover as much of the entire estuarine gradient as possible, and incorporate several components of

the estuary (e.g., intertidal and subtidal; primary and secondary production; benthos and nekton). 

In practice, this will be limited by data availability. Different approaches (which can be combined)

to assess overall biological condition are described below. 

5.4.1. Structural measures (e.g., number and type of organisms, acreage of habitats). The structure 

attribute is often used in BCG for practical measurements and repeatable assessments of biological 

condition.

The waterbody is good if a critical part of it is good

5.4.1.a. Assessment with a single structural measure of condition: in some cases, one well-chosen 

measure may meet management requirements for evaluating overall condition.

Keystone species, which have large and disproportionate effects on the ecosystem relative to their 

abundance (Power et al. 1996), may be monitored to assess overall ecosystem condition. An example 

is the U.S. west coast sea otter. In the absence of otters, sea urchins can completely graze down a 

kelp forest, leaving a barren seafloor. The otter feeds on the urchins, keeping their population in 

check, and maintaining the kelp forest (Estes and Palmisano 1974). However, recent work suggests 

that the influence of keystone species may be context specific (Power et al. 1996), densitydependent, or show lags in response (Dean et al. 2000, Konar 2000). Keystone species should be 

used cautiously as a sole measure of overall condition. 

Individual species or assemblages may also be assessed as indicators of overall condition when they 

respond predictably to environmental stressors over a range of impact. Seagrass, for example, is 

very sensitive to water quality (Dennison et al. 1993) and has been used as an indicator in many 

estuaries. In general, plentiful beds of healthy seagrass in shallow areas of an estuary indicate 

good overall condition, and the beds further provide important habitat for valued fauna 

(Figure 5-7). Benthic invertebrates have also been used to assess the overall health of coasts and 

estuaries. EPA has consistently collected benthic invertebrate data in estuaries since 1990 (U.S. EPA 

2001, 2004, 2008, 2012) and summarizes estuarine condition using area-weighted benthic index 

values (U.S. EPA 2006a). SCCWRP uses benthic invertebrate data and locally developed indices 

to assess coastal health in southern California (http://www.sccwrp.org/ResearchAreas/ 

RegionalMonitoring). Other common indicator assemblages include wetlands, shellfish reefs, 

and fishes. 
5. Application of the approach

51

Figure 5-7. Seagrass habitat is important for the settling and development of juvenile conch. 

The waterbody is good if several critical parts of it are good

5.4.1.b. Assessment with multiple structural indicators of condition: several species, communities, 

or habitats may be used together for a more robust overall evaluation that is less prone to annual 

or seasonal variability.

This approach has been used to evaluate and communicate condition in many estuaries and waterbodies. The Massachusetts Estuaries Project (http://www.oceanscience.net/estuaries/about.htm)

uses both seagrass and infaunal invertebrates as indicator species. The Chesapeake Biotic Index 

(http://ian.umces.edu/ecocheck/report-cards/chesapeake-bay/2011/indicators/biotic_index) jointly 

assesses seagrass, benthic invertebrate communities, and phytoplankton communities to provide 

an overall measure of condition for the entire Chesapeake Bay or for specific spatial areas of the 

Bay. The health of the living resources of Buzzards Bay is determined by assessing present 

condition of eelgrass, bay scallops and river herring in comparison to historic (pre-1900) condition 

(http://www.savebuzzardsbay.org). Similarly, the Greenwich Bay (RI) BCG (Section 6.1, pages 64−65) 

evaluated seagrass, benthos, and a combined primary production/shellfish measure. Assessment 

with multiple indicators depends on the availability of data for each indicator and may not be 

practical in poorly studied waterbodies.

The waterbody is good if its mix of habitats is good

5.4.1.c. Assessment of the extent, composition, or arrangement of living habitats (biotopes): the mix 

of critical living habitats within a waterbody reflects waterbody-scale changes due to anthropogenic 

stressors and these habitat mixtures can be evaluated with statistical tools.
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Biotopes are repeating combinations of physical features and biological communities, named after 

the dominant biota (see Appendix B, Question 9). Productive estuaries in a natural state are a mosaic 

of biotopes (Henningsen 2005), including seagrass beds, oyster reefs, mussel reefs, salt marshes, 

mangrove forests, clam flats, and specific soft-bottom benthic communities. The biotope mosaic 

approach is a relatively new structural metric that evaluates the condition of a waterbody through 

the mix of biotopes it contains (Figure 5-8), just as the condition of a faunal community is evaluated 

through the mix of species it contains. This method considers biotopes as critical elements of 

estuarine biology, and quantifies extent (acreages), composition (proportions), or arrangement 

(spatial distributions) of the important biotopes within an estuary relative to minimally disturbed 

conditions from a previous or historic state.

Anthropogenic stress to an estuary leads to destruction and alteration of natural biotopes through

removal (e.g., filling a wetland) or replacement with other biotopes (e.g., soft sediment fauna

replaces a seagrass biotope). A basic tenet of the approach is that restoration towards the mosaic 

that would naturally occur will provide the greatest benefit for the native communities of organisms 

that have evolved in that setting over millennia, thereby improving biological integrity. Use of 

the biotope concept in management is described in Cicchetti and Greening (2011), and biotopes 

are incorporated into classifications of biology in CMECS, a federal standard (FGDC 2012). 

Figure 5-8. Aerial views of heads of two sub-estuaries showing biotopes. Left: a sub-estuary on Martha’s 

Vineyard (MA) showing seagrass, salt marsh, and maritime forest. Right: a sub-estuary in Long Island 

Sound (CT) with no natural biotopes identifiable in the shallow subtidal, intertidal, or adjacent uplands.

Historical and present-day habitat distribution data are often available for estuaries through early 

and recent maps, charts, photos, or habitat acreage studies. GIS methods are extremely helpful, and 

this waterbody-scale evaluation can be very useful in showing major degradations and improvements 
5. Application of the approach

53

over long time periods in a BCG. Biotope measures (e.g., extent, relative proportions, diversity, and 

fragmentation) are inherently quantitative, and loss of certain habitats may identify specific stressors 

of concern, e.g., loss of seagrass may identify poor water clarity as a stressor while loss of salt marsh 

may identify filling or sea level rise as stressors.

Perhaps most importantly, the method tells a compelling and intuitive story for public and

stakeholder communication. This is described for the Tampa Bay example in Section 6.2 (pages 

66−70). While the term ‘biotope mosaic’ provides a clear link to biological integrity and the BCG, 

the synonymous term ‘habitat mosaic’ (or any other language) may be used for more immediate 

understanding by public audiences.

Structure and function

Many of these structural measures (Sections 5.4.1.a, b, and c above) are assumed to be surrogates 

for function and condition. Because species (Sections 5.4.1.a and b) occupy specific niches, they 

have specific functional roles. For example, benthic invertebrates are involved in nutrient cycling, 

oxygenation of sediments, and building seafloor structures. Structural measures such as species 

abundance and diversity are often evaluated, but feeding type or pollution sensitivity metrics based 

on species abundance can also been used to assess condition. An expansion of this approach is 

biological traits analysis, which uses the life history characteristics of individual species to assess 

ecosystem function (Bremner et al. 2006). Biodiversity is also related to ecosystem function 

(Naeem et al. 1999). Here, a decrease in ecosystem function is likely related to the species that 

become locally extinct (Cardinale et al. 2006), the functional characteristics of those species, and 

the types of ecosystem and functional pathways within the system (Hooper et al. 2005). A similar 

structure and function assumption can be made about biotopes (Section 5.4.1.c) in the larger 

estuary. Since each biotope provides a unique set of species and functional contributions, the 

overall function of the estuary is expected to change when the extent and relative proportions of the 

individual biotopes change. 

The waterbody is good if it works as it should

5.4.2. Measures of ecosystem function and connectance. Biological measures that quantify

processes of ecosystem function include evaluations of energy flows, trophic webs and linkages, 

carbon or nutrient fluxes, production of diverse biomass, nutrient processing, rates, or resilience 

to changes. Measures that capture complex interactions in the entire estuary may be particularly 

valuable. These larger processes are often assessed using proxies that are easier to evaluate, 

including structural measures as mentioned above.

Measurements and proxies of functional processes include photosynthesis:respiration ratios;

benthic-pelagic exchange and production rates; benthic bioturbation and nutrient cycling; 

chlorophyll a concentrations; macroalgal biomass; biodiversity; other comprehensive measures of 

biological organization; exchange, export, sedimentation, or migration rates; or results from flux 

chamber work and trophic analyses. Bioturbation is a proxy for benthic ecosystem function (Solan et 

al. 2004, Teal et al. 2010) and is relatively easy to assess as the depth of the color discontinuity in the 
Implementing the Biological Condition Gradient Framework

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upper layers of sediment. Similarly, chlorophyll a may serve as a proxy for ecosystem function and 

is also relatively easy to assess, particularly given new methods of remote sensing. Together, these 

proxies can cover the vertical profile of an estuary from surface to bottom.

Connectance can refer to the connections of populations among patches, the relationships between 

habitat patches and the organisms that move between them, or the extent to which the system 

allows movement of organisms (Kindlmann and Burel 2008). As with ecosystem function, this 

attribute is more easily measured using proxies, such as landscape ecology metrics from a biotope 

mosaic approach (when estuarine data allow spatial GIS analyses). These proxies include nearestneighbor analyses, evaluations of corridors or fragmentation, and other approaches to measure 

spatial dispersion and arrangement of habitats. Other proxies for connectance may include analyses 

of metapopulation stability, anadromous fish runs (Figure 5-9), or hydrodynamic and current data 

(Figure 4-4, page 27) which can be used to help predict isolation or dispersal capacity. As in all cases, 

the logic behind selection of proxies should be clearly explained.

Figure 5-9. Migrating coho salmon show connectance between oceans, estuaries, and streams. 

Photo: NOAA

The waterbody is good if biology is good and stressors are low

5.4.3. Combining biological condition and stressors. This is an often used and effective assessment 

and communication tool that supports the use of stressor-response models in management. Any of 

the above measures of biology can be combined with a stressor evaluation. The GSA (Section 4.3, 

pages 36−38) links directly to BCG levels in evaluating the sum of the cumulative stressors to which

biota is exposed. The GSA can be characterized with proxies for anthropogenic stress including 
5. Application of the approach

55

human population numbers, ambient pollutant levels, combinations of primary individual stressor

levels, or time. Analyses of changes in watershed land use over time (e.g., changes in percent of 

impervious surface or use of a landscape development index) relate to BCG levels and provide 

information on the nature and distribution of cumulative stressors and their sources (U.S. EPA 2016). 

These spatial analyses are useful for communicating stressor information and for managing at the 

watershed level. Further, the GSA can be parsed into the individual stressors that contribute to 

cumulative impacts and can help to prioritize these stressors. 

In one example of this approach, overall health of Chesapeake Bay is calculated by combining the 

biotic index mentioned above (Section 5.4.1.b, page 51) with a water quality stressor index that 

includes water clarity, chlorophyll a, and dissolved oxygen measures. Overall health can be 

calculated bay-wide or for individual sections of the bay. Similarly, overall status of Buzzards Bay 

is determined by combining living resource indicators with indicators of pollution (nitrogen, bacteria, 

and toxics) and watershed health (forest, streams, and wetlands). In developing the Puerto Rico coral 

reef BCG, investigators combined measures of the reef and associated biological communities with 

water clarity to define different levels of condition.

In a BCG for Greenwich Bay RI (Figure 5-10), information from three biological indicators and several 

attributes was put together with information on a GSA and on specific stressors. This produced an 

integrated estuary-wide Biological Condition Gradient with an analysis of stressors and their 

cumulative effects over historical time (Section 6.1, pages 63−65). The approach is valuable in

describing the current state of the estuary together with the significant events and processes that 

have shaped it over time. This provides context and information for scientists and managers working 

on any question or issue within the estuary, helps prioritize the stressors most important to the 

waterbody, and reinforces public and management perceptions of a thorough and meaningful 

research effort.

Figure 5-10. Northeast corner of Greenwich Bay, RI. 
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More on overall condition

The EU approach (see text box on page 83) uses the overall condition of waterbodies as the primary 

basis for regulatory decisions. In brief, a set of rules is used to develop status (condition) levels for 

each of four biological elements: phytoplankton, flora, benthos and fish. Overall waterbody status is 

determined as the lowest status among the four elements, and regulatory requirements start in with 

a status below ‘Good’ for any one element, secondarily considering hydrogeomorphological elements 

(e.g. dams, dredging) and physico-chemical elements (e.g. toxicants, nutrients). DPSIR is used to 

evaluate alternative management methods to restore ‘Good’ status. This somewhat prescriptive 

approach is used to ensure that Member States are effectively and consistently regulating their 

waterbodies.

Generally speaking, the public and stakeholders care about the overall condition of their 

estuary. This is a scale at which people think about waterbodies, and think about waterbody 

improvement. This scale is also effective for evaluating and managing the biological effects of 

cumulative impacts, because these effects manifest throughout the entire estuary. For practical 

application, developing a BCG for the overall condition of an estuary together with a stakeholder 

vision for a desired overall future estuarine condition is an effective approach to management, 

and may be of particular benefit to NEPs. Although estuarine and coastal ecosystems are used to 

illustrate this, these methods can apply to overall assessment of any defined ecosystem. A BCG 

may be developed to assess and manage areas of high ecological importance within a larger setting, 

including large rivers, oyster reefs, or rocky outcrops in otherwise soft-sediment areas. Here, the 

estuarine and coastal BCG may assess overall condition of the ecosystem or area of interest using 

any of the methods described above, or other more specific approaches.

5.5. Sustainability and the estuarine/coastal BCG 

Sustainability

Sustainability has been adopted by the U.S. EPA as a major goal for research, management, and longrange planning. The Agency defines sustainability as “meeting the needs of the current generation 

while preserving the ability of future generations to meet their own needs” and recognizes the three 

pillars of sustainability as “economy, environment, and society” (Anastas 2012, see Figures 5-11, 5-12, 

and 5-13). In the estuarine and coastal BCG, environmental sustainability evaluates the ability of a 

functioning ecosystem to maintain those functions given past, existing, and future levels of stress 

and disturbance. The BCG can address the societal pillar of sustainability through stakeholder 

involvement and stakeholder-driven visions of a desired future estuary−thus exploring the needs 

of future generations (Section 5.3, pages 47−48). Information on economic sustainability can be 

provided though an ecosystem services analysis linked to BCG levels. However, the BCG is 

strongest in characterizing environmental sustainability; other tools can better evaluate 

economic and societal sustainability.
5. Application of the approach

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Figure 5-11. Economy: investment in recreational fishing. Columbia River, OR and WA. Photo: NOAA

Figure 5-12. Environment: seagrass and staghorn coral, both sensitive species, in the Florida Keys 

Marine Sanctuary. Photo: NOAA
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Figure 5-13. Society: public enjoyment of the seashore. Town Beach, Charlestown, RI. 

The historical investigations that often accompany an estuarine BCG are useful in evaluating 

sustainability in coastal systems, because trends over time show trajectories that may or may not 

lead to support of future needs. Historical evaluations of Tampa Bay habitat mosaics showed that 

the estuary continuously degraded from 1900 through 2005, and so the environment and associated 

ecosystem services were not sustained−and would not be sustainable into the future given that 

trend. In recent years, after concerted public and private efforts that began in the 1970s, trends 

were reversed, sustainability of valued habitats has improved by way of meeting the needs of 

future generations, and habitat measures have been trending up (Cicchetti and Greening 2011, 

TBEP 2015). Yet, continued sustainability of the Tampa Bay estuary is threatened by projections 

of greatly increased human populations and associated stressors by 2050.

BCG analyses of changes over time can also show year-to-year consistency in ecosystem state, 

another indicator of stability and sustainability. Ecosystems that are highly variable from one year 

to the next may be more likely to cross a tipping point that would dramatically alter ecological state. 

In conditions of high yearly variability in macroalgal bloom biomass, state change may be caused by 

an inability of the biological system to recover from low dissolved oxygen, sulfides and other 

macroalgal-related toxins (Sutula et al. 2014) when high algal biomass years occur back-to-back. 

Incremental changes and feedback loops associated with high macroalgal biomass (Sutula et al. 2014) 

or other stressors may also lead to state change. 
5. Application of the approach

59

Resilience

Sustainable systems have high resilience and low susceptibility. Resilience is defined as, “the capacity 

of an ecosystem to absorb disturbance without shifting to an alternative state and losing function 

and services” (Holling 1973, Côté and Darling 2010). Using BCG terminology, resilience is the ability 

to maintain biological attribute levels when stressors increase, particularly attributes of function 

and connectance. Resilient estuaries are characterized by high biodiversity of species and habitats 

(relative to expectation for that estuary type). In systems with high species diversity, loss of sensitive 

species is compensated by expansions of other species that fill the same ecological roles, and overall 

function is retained (Tilman and Downing 1994, Godbold and Solan 2009). High natural connectance 

within an estuary may enhance recruitment, recolonization, and movement of species from areas of 

high abundance to areas of low abundance, providing a buffering capacity within the estuary to avoid 

localized extinctions. The BCG approach offers measures that can serve as proxies for resilience, 

e.g., species or habitat-level biodiversity and high connectance.

Susceptibility

Susceptibility, when used to describe waterbodies in a BCG approach, is an estimate of the ability 

of a waterbody to resist stress based upon physical factors such as hydrodynamics and flushing time 

(Bricker et al. 1999, 2007). Waterbody susceptibility may also be affected by temperature, physical 

energy, tidal range, depth, or other factors. Some other definitions of susceptibility (often when 

resilience is not also considered) do include biological factors (Scavia and Liu 2009). However, in the 

BCG construct biology is included in resilience and so susceptibility is limited to non-biological factors 

in order to maintain a useful distinction between the two terms. Estuarine BCG levels of condition 

use a locally-derived reference for minimally disturbed, so level assignments remain comparable 

among estuaries of different physical susceptibilities. Further, estuarine classification by physical 

susceptibility (Bricker et al. 1999, 2007) allows BCG comparisons among estuaries of similar 

susceptibilities (Section 5.1, page 41). 

Recovery potential

Recovery potential is a term used to predict the ability of degraded systems to recover, and the 

probability of success in ecological restoration projects. Indicators of recovery potential consider 

ecology, stressors, and social factors to evaluate the likelihood that efforts at a specific location will 

actually lead to an improved environment. The biological and ecological aspects of recovery potential 

consider current and projected stressor loads, stressor-response relationships, resilience, and 

susceptibility. Social aspects include political will, community support, funding sources, and existing 

infrastructure. Information on recovery potential can be found at 

http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/recovery/indicators.cfm. 
Implementing the Biological Condition Gradient Framework

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Summary

Sustainability, resilience, susceptibility and recovery potential are interrelated concepts that can be 

important to environmental planning and communication. These concepts can be examined through 

indices or proxies (e.g., biodiversity), or through rates (and variability) of ecosystem change in the 

past, present, or predicted future. The BCG approach helps by providing consistent measurements 

of biological and stressor changes over space and time in a waterbody. 
6. Results from early pilots

61

6. Results from early pilots 

BCG and BCG-like approaches for estuaries and coasts are in use or in development by NEPs on all 

three marine coasts of the U.S. and in the Caribbean. These NEPs have identified significant benefits 

of BCG through the ability to set targets for habitat protection and restoration, and the ability to 

engage stakeholders and managers. This section describes NEP efforts as examples of BCG 

application and finishes with a sidebar on a very similar approach taken by the European Union. 

6.1. Narragansett Bay

Figure 6-1. Narragansett Bay, RI. Note the city of Providence at the northern end of the bay. 

Image: Google Earth, data from Landsat
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Workshops

Narragansett Bay (Figure 6-1) extends almost the full length of RI and is characterized by a strong 

north-south stressor gradient from high anthropogenic impacts in Providence and the northern bay 

to less development and significant oceanic influence in the southern Bay. A group of EPA scientists 

has been working with the Narragansett Bay Estuary Program (NBEP) and other partners on BCG 

development since 2008. A 2009 workshop was attended by representatives of many scientific and 

management groups from Rhode Island and Massachusetts including federal and state agencies, 

NGOs and private groups, NBEP, and academic organizations (Appendix D). The workshop brought 

out tremendous historical knowledge of Narragansett Bay and explored a number of environmental 

trends within the Bay. It was a successful starting point by way of gathering information important 

to a BCG. However, the diversity of opinion at the workshop together with some misunderstandings 

of BCG principles held back a consensus description of a minimally disturbed Narragansett Bay− 

which was a workshop goal. A lesson learned from this was that oversight and management of the 

Narragansett Bay system was somewhat fragmented, with several influential groups arguing for 

different approaches.

The workgroup concluded that building a Narragansett Bay BCG would need to include discussions to 

identify common goals of the different user groups. The workgroup also concluded that a next expert 

workshop to build consensus on BCG issues would benefit from a narrow set of workshop goals, and 

from better informing participants about BCG approaches before the meeting. The Narragansett Bay 

workgroup looks at the Puerto Rico Coral Reef workshops as a very successful model, particularly 

regarding the instructions and materials that were sent to participants ahead of the meeting to 

frame the discussions (Bradley et al. 2014).

Moving forward from the 2009 workshop, the BCG workgroup expanded into a discussion group 

and community of practitioners to include EPA scientists working on the coral reef BCG together with 

more EPA and non-EPA scientists and managers working in Narragansett Bay. These are the authors 

of this document. Within this larger and more national group, the subset of scientists most 

interested in Narragansett Bay turned to Greenwich Bay (Figure 6-2, a sub-estuary of Narragansett 

Bay) to develop an estuarine BCG demonstration and to test the approach described in this 

document. Greenwich Bay has a rich history of change, a high level of public interest, and relatively 

abundant social and environmental data.
6. Results from early pilots

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Greenwich Bay historical timeline

Figure 6-2. Greenwich Bay, RI, located mid-bay on the western shore of Narragansett Bay. 

Image: Google Earth, data from Landsat

Historical research on Greenwich Bay and the surrounding area led to a historic reconstruction and 

trajectory of Greenwich Bay that included cultural history, ecological resources, and stressor impacts

(Pesch et al. 2012). This instructive story was published as an EPA report for a broad public and 

scientific audience, and includes guidance for historical research. Figure 6-3 shows a composite of 

changes and significant events in natural and anthropogenic stressors in Greenwich Bay together 

with qualitative eelgrass abundance, all on the same historic timeline. This merged the natural 

and anthropogenic history of the embayment and provided information on a baseline of ‘as naturally 

occurred’. The biological and stressor data uncovered through this effort were used to develop a 

demonstration BCG for Greenwich Bay. 
Implementing the Biological Condition Gradient Framework

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Figure 6-3. The ecological and cultural history of Greenwich Bay, describing the baseline of undisturbed

together with historic trajectories of stressors and biological responses. Graphic: Pesch et al. 2012

Greenwich Bay BCG

This BCG demonstration (Shumchenia et al. 2015) is a detailed historical account of stressors and 

ecological responses over the last two centuries in Greenwich Bay, crafted into a qualitative BCG 

using stressor changes over time as the GSA (Figure 6-4). BCG development included

1) evaluating and selecting biological measures and attributes 

2) defining a minimally disturbed reference condition

3) synthesizing available data to set thresholds for the six levels of biological response

to stress for each measure/attribute, and 

4) communicating results using the BCG stressor-response diagram (Figure 2-2, page 6). 

Consistent narratives for BCG levels (e.g., Appendix A, page 97; Table 4-2, pages 30–31) were used for 

thresholds. This allows comparability with new efforts to develop a BCG for all of Narragansett Bay.
6. Results from early pilots

65

Figure 6-4. Habitat structure BCG model for Greenwich Bay. EG = eelgrass extent; BH = benthic habitat; 

PS = primary productivity and shellfish, which are linked in Greenwich Bay. The stressor axis is based on

time periods (top label) that correspond to stressors in Figure 6-3 (page 64); the response axis shows BCG 

levels together with narrative threshold guidelines that are consistent with accepted BCG standards. 

Graphic: Shumchenia et al. 2015

The BCG development process itself also led to ecological insights. Evaluating seagrass, benthic 

communities, primary production and shellfish showed the benefits of including multiple 

assemblages. Had the assemblages been examined separately this sub-estuary would have been 

evaluated at different BCG levels, showing the importance of more holistic large scale approaches. 

Shumchenia et al. (2015) was written to educate managers on the value of BCG for integrating

historical and biological information in setting goals that are supported by the public, and for 

supporting decisions on how to achieve those goals. It also serves as an example for practitioners 

applying BCG to other waterbodies. The Narragansett Bay group is using this paper to build

management support for a habitat mosaic BCG covering the entire estuary.
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6.2. Tampa Bay

Figure 6-5. Tampa Bay, FL. Image: Google Earth, data from SIO, NOAA, U.S. Navy, NGA, GEBCO 

Early public involvement and a BCG-like approach

Tampa Bay (Figure 6-5) is Florida’s largest open-water estuary. In the late 1970s environmental 

managers and the public grew concerned about macroalgae covering their beaches, phytoplankton 

blooms, and loss of marsh, seagrass, birds, fish, and manatees. This led to efforts to better the 

condition of the Bay. In 1992, the Tampa Bay Estuary Program (TBEP) was formed to build on this 

previous work and serve as a convener to organize different efforts, providing oversight for improving 

the Bay. Starting their work before BCG concepts were formalized, TBEP and partners applied a 

science-based management approach that is very similar to the estuarine and coastal BCG; in fact, 

this estuarine/coastal BCG implementation document drew from key elements of the Tampa Bay 

approach, including: 

1. Expert consensus and stakeholder outreach to identify biological measures that are important 

to both estuarine function and the public

2. An overall management approach with a focus on moving the system towards a less disturbed 

condition that is closer to the ecological settings under which valued native species evolved

3. Use of less disturbed time periods in the past as management restoration goals

4. Expert workshops to assemble data and science for estimating past biological conditions
6. Results from early pilots

67

5. Stakeholder consensus workshops to assist in decision-making, e.g., for setting attainable goals 

that move the environment closer to a more natural state, while recognizing societal values

6. A strong investment in public outreach and engagement. 

Many of these elements involve the public and other stakeholders. TBEP has used a variety of 

methods to engage, include, educate, and motivate these stakeholders, including hosted meetings, 

events, public media, informational materials, volunteer opportunities, contests, newsletters

(http://archive.constantcontact.com/fs003/1101662914468/archive/1107152227015.html) 

and economic valuations of the bay area (TBEP and TBRPC 2014).

Biotope mosaics and goals

An important TBEP contribution was the development of the biotope mosaic approach (Section 

5.4.1.c, pages 51−53) where bioassessment is based on waterbody-wide changes to quantity (acres) 

and distributions (relative proportions) of biotopes over time. Establishing 1900 as a minimally 

disturbed historic condition for habitat acres, ecological priorities for Tampa Bay were to restore 

the balance of critical biotopes to a less disturbed historic benchmark of 1950, with a specific goal 

to restore seagrass acreage to that present in 1950 through improvements in water quality. The 1900 

minimally disturbed condition and the 1950 goal were developed through consensus of scientists 

and stakeholders in 1995. 

Restoring the balance – a simple unifying vision

Tampa Bay stakeholders and the public were invested in the quantity and diversity of valued habitats, 

and the concept of ‘Restoring the Balance’ (Figure 6-6) resonated with this community as a simple 

unifying vision. The intuitive appeal of this message was effective at communicating estuarine 

condition and developing stakeholder visions and goals, which led to management actions and 

environmental results. This method can be used together with other approaches as an important 

component in the management of estuaries. TBEP has been working with these concepts for many 

years (Lewis and Robison 1995).
Implementing the Biological Condition Gradient Framework

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Figure 6-6. TBEP graphic to describe ‘Restoring the Balance’. Graphic: TBEP 2012

A biological gradient

TBEP developed a stressor-response relationship for valued intertidal and subtidal biotopes using 

1900 as the minimally disturbed anchor point (Cicchetti and Greening 2011). The stressor gradient 

was based on time as Tampa Bay became more developed and exploited, while response was 

characterized as percent change in biological condition metrics relative to 1900. This provided a 

common language (percent change from minimally disturbed) for comparisons within this estuary 

in a manner that would allow easy translation into a BCG. Figure 6-7 shows changes in metrics of 

biological condition (specific habitat areas) since 1900, including the general decline in habitat area 

up to 1990. This was followed by improvements to the estuary after 1990, following restoration 

and protection efforts that began in earnest during the 1980s. These data suggest an initial lag 

in environmental changes after the implementation of management actions, then document 
6. Results from early pilots

69

subsequent improvements and progress towards goals. In 2015, Tampa Bay achieved their goal

(set in 1995) of restoring seagrass to the acreage present in 1950, shown as a red star in Figure 6-7. 

A historic BCG (or BCG-like approach) offers many insights of value to scientists and managers. Going 

further, assigning levels 1 through 6 to Tampa Bay metrics would have led to a BCG framework and 

introduced a common language to improve comparisons among Tampa Bay and other waterbodies. 

Figure 6-7. Biological gradient for biotopes of Tampa Bay. The 2015 attainment of the 1950 seagrass 

goal is marked with a star. Graphic: modified from Cicchetti and Greening 2011

Be Floridean

Following water quality and seagrass acreage gains from improved sewage treatment, reduced 

atmospheric deposition from power plant upgrades, and improved industrial practices, TBEP turned 

to lawn and landscape fertilization as a significant source of nutrient pollution in urban areas of the 

Tampa Bay watershed. Reducing these non-point inputs would depend on changing the mindsets 

and actions of the individuals and communities who own or maintain outdoor spaces. So, the 

“Be Floridian” campaign (Figure 6-8) was launched to positively engage the public to change their 

landscaping practices. In “calling on all Southwest Floridians to help protect what makes Florida so 

fun”, the campaign uses billboards, news releases, community outreach, a flock of travelling painted 

flamingos, even Florida DOT (Department of Transportation) road signs (Figure 6-9) that call for 

residents to “skip the fertilizer during the summer rainy season”, “protect our fun”, “Floridify your 

lawn”, and similar. The program has buy-in from a number of cities, counties, organizations and 

communities, the state DOT, and countless individuals. An expansive website with gardening guides 

and tips, photo galleries, FAQs, lists of resources, and more can be found at www.befloridian.org. 
Implementing the Biological Condition Gradient Framework

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Figure 6-8. Be Floridian sign: “This summer I will skip fertilizing my lawn and do the responsible 

thing instead: GO HAVE FUN”. Image: TBEP, www.befloridian.org

Figure 6-9. Road sign showing FL DOT support of the Be Floridian campaign. Photo: TBEP, 

www.befloridian.org

Summary

TBEP efforts, based on a combination of approaches to achieve a simple and unifying vision, have 

led to habitat gains in Tampa Bay that are widely regarded as a management and restoration success

(Cloern 2001; Tomasko et al. 2005; Duarte 2009; Duarte et al. 2015). In 2015, Tampa Bay achieved 

and exceeded their seagrass restoration target of 1950s acreage (TBEP 2015) in large part due to 

20-plus years of active engagement and reach-out to involve and motivate stakeholders including 

the public, managers, commerce, and other partners (Holly Greening, pers. comm.).
6. Results from early pilots

6.3. Mobile Bay

71

Figure 6-10. Mobile Bay, AL. Image: Google Earth, data from Landsat and NOAA

The Mobile Bay BCG

Mobile Bay (Figure 6-10) is a relatively shallow estuary with a highly variable salinity regime and a 

major deepwater port at the northern head of the Bay. Building a BCG approach for coastal Alabama 

is one of the objectives of the Mobile Bay National Estuary Program (MBNEP) in their 2013–2018 

Comprehensive Conservation & Management Plan (MBNEP 2013), and the Estuary Program has been 

working on BCG well before that. The Mobile Bay BCG assesses changes in estuarine condition based 

on indices of habitat distribution and quality along a continuum of anthropogenic stress (Thibaut et 

al. 2014). Condition is evaluated and communicated in three levels (good, fair, poor) that are aligned 

with BCG narrative. The Estuary Program and partners will use the BCG for monitoring status and 

trends, communicating with the public, developing numeric criteria for condition, tracking 

management effectiveness, and informing coastal restoration efforts.

Create a clean water future

Along the lines of the TBEP ‘Be Floridian’ project, MBNEP developed the ‘Create a Clean Water 

Future’ outreach program (Figure 6-11). This is a public service campaign to raise awareness of 

stormwater runoff and its impacts, increase political demand for management actions, clean up 

trash, and empower individuals and communities with information and tools to reduce polluted 
Implementing the Biological Condition Gradient Framework

72

runoff from their homes, lawns, and streets. The program promotes the desire for a better future as 

an inspirational message and provides a number of resources that communities and individuals can 

use to reach out to others (see www.cleanwaterfuture.com). MBNEP recognized that changing the 

day-to-day actions of residents is critical for reduction of non-point source pollution and that 

motivated citizens are a powerful force in environmental improvement (Figures 6-11, 6-12, and 6-13). 

Public outreach and incorporating the priorities and values of local stakeholders are central tenets of 

the Estuary Program’s work.

Figure 6-11. Create a Clean Water Future campaign−changing public attitudes to protect Mobile Bay. 

Image: MBNEP

Figure 6-12. Natural beauty of Three Mile Creek, Mobile Bay, AL. Photo: MBNEP
6. Results from early pilots

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Figure 6-13. Another image from Three Mile Creek, Mobile, AL, illustrating the need to change 

public actions, and the need for the Clean Water Future campaign. Photo: MBNEP

Habitats, ecosystem services, and restoration

MBNEP, in partnership with The Nature Conservancy and NOAA, used NOAA’s Habitat Priority 

Planner to identify priority habitats throughout coastal Alabama. Through a year-long process of data 

gathering and evaluation, MBNEP’s Coastal Habitats Coordination Team identified 10 priority habitats 

in need of preservation or restoration. During 2010 planning for the current CCMP, the MBNEP’s 

Science Advisory Committee evaluated the ability of each of these habitats to provide ecosystem 

services at different levels of impact from a suite of stressors. Freshwater wetlands, streams, rivers 

and riparian buffers, intertidal marshes, and flats were most stressed, primarily due to habitat 

conversion. The BCG is used to measure changes in condition of these habitats due to restoration 

efforts. This BCG also includes ecosystem services analyses to communicate the importance and 

value of loss or improvement in habitat condition.

Going further

MBNEP is initiating a program for high resolution mapping of habitats to establish present-day 

baselines for acreage and distribution of critical habitats (including seagrasses), with continued 

monitoring for change. A later action would be to develop numeric criteria for habitat condition. 

Also, an existing restoration effort in Mobile Bay’s D’Olive watershed is being used as a pilot to 

develop and test a conceptual model to measure levels of ecosystem services as related to changes 

in stressor levels. Restoration success here may guide the re-establishment of once-present seagrass 

beds downstream. The BCG would be used to quantify this and other changes as well as to 

communicate results in a way that resonates with stakeholders and informs further restoration 

actions. MBNEP is building a comprehensive approach that effectively incorporates BCG into 

management of Mobile Bay, and is developing these tools for transferability to other areas on 

the Alabama coast. 
Implementing the Biological Condition Gradient Framework

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6.4. Lower Columbia River 

Figure 6-14. The Lower Columbia River, which forms much of the border between Oregon 

and Washington. Image: Google Earth, data from Landsat

The Lower Columbia River Estuary (Figure 6-14) is the 146 mile tidally-influenced reach of the 

Columbia River from the Bonneville Dam (which is about 100 river miles east of Figure 6-14) to the 

Pacific Ocean. The Lower Columbia Estuary Partnership (LCEP) uses the BCG to evaluate ecosystem 

condition and to develop quantitative environmental targets for different areas of the river, thus

improving management of this system.

Engaging stakeholders and developing a vision

LCEP actively engaged and involved communities and stakeholders throughout the process of

articulating a holistic vision, determining objectives, and setting quantitative management targets. 

Communicating and implementing the resulting plan was then a collaborative effort with these initial 

partners. LCEP now practices adaptive management by monitoring to ensure that environmental 

goals are met and reports results back to the involved communities and stakeholders. This approach 

adopts the principles of both EBM and SDM (Section 5.3, pages 45-46).

Through this process, biological integrity and habitat loss/modification were identified as 

management issues significant to the region, and were addressed in the Estuary Partnership’s 

Management Plan. A vision and goals (LCEP 2012) were developed as:

- Integrated, resilient, and diverse biological communities are restored and maintained in the 

Lower Columbia River and estuary.
6. Results from early pilots

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- Habitat in the Lower Columbia River and estuary supports self-sustaining populations of plants, 

fish, and wildlife. 

Moving to deliver on this vision, the Partnership has devoted significant time and resources to 

address biological integrity and habitats using a BCG approach.

LCEP BCG

LCEP organized a two-day workshop in April 2012 with EPA support to define ‘minimally disturbed’ 

and identify attributes specific to the estuary (Corbett 2012). Workshop participants specified 

attributes including 1) natural habitat diversity, 2) focal species (e.g., Pacific salmon and steelhead), 

3) water quality, and 4) ecosystem processes. While LCEP did not name their attributes in the 

terminology of BCG (e.g., Table 4-2, pages 30–31), they identify stakeholder management priorities

which could easily be translated into specific BCG attributes. To address LCEP attribute 1 (natural 

habitat diversity) the Partnership has identified priority habitats (including several classes of wetlands 

and vegetation-based shore habitats) for protection and restoration based on past habitat coverage; 

this is the BCG ‘Structure’ attribute and serves as a proxy for the ‘Function’ attribute.

Figure 6-15. Prairie Channel (WA) and the natural beauty of the Lower Columbia Estuary. Photo: LCEP

Quantitative targets

This group completed an extensive habitat change analysis comparing 1870 to 2009 land cover and

developed quantitative habitat coverage targets for native habitats based on past habitat extent 

using species-area curves (MacArthur and Wilson 1967). The targets include 1) no net loss of native 

habitats as of the 2009 baseline, 2) recover 30% of the historic coverage of priority habitats by 2030, 

and 3) recover 40% of the historic coverage of priority habitats by 2050. By meeting these targets

the Lower Columbia River will have regained between 46–88% of its historic habitat coverage by 

2050, depending on river reach, with an average of 60% historic habitat coverage. The Partnership’s 

next task is to identify “anchor areas” for larger protected reserves, a minimum number of reserves, 

and important locations for filling habitat gaps and migratory corridors (i.e., connectance). 
Implementing the Biological Condition Gradient Framework

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The Estuary Partnership is in the process of developing numeric and spatially explicit targets for the 

other three attributes. Focal species (LCEP attribute 2) were identified in the 2012 workshop, and the 

Partnership has been developing draft targets for this attribute, particularly for juvenile salmonids, 

a group of primary importance to the region (Corbett 2013).

Consensus and communication

The Partnership recognizes that quantitative targets, though they require a significant development 

effort, are very effective tools for environmental improvement. Further, quantitative targets 

promote Partnership goals within the larger competitive political landscape, and are an important 

communication tool both for managers and the public (Corbett 2013). The Estuary Partnership has 

made important strides in advancing BCG implementation, and continues to develop their plan, 

emphasizing consensus and communication among stakeholders so that science-driven targets 

are well-received and supported (Figure 6-16). 

Figure 6-16. Stakeholder investment: paddlers on the Lower Columbia Estuary. Photo: LCEP
6. Results from early pilots

6.5. Puerto Rico coral reefs

77

Figure 6-17. The stretch of reefs from La Parguera to Guánica Bay, southwestern PR, the area of data 

collection for the coral reef BCG. Note the heavily agricultural landscape. Image: Google Earth, data from 

SIO, NOAA, U.S. Navy, NGA, GEBCO

Coral reefs are unique ecosystems in decline

The southwestern Puerto Rico coast (Figure 6-17) is a patchy assortment of cays, coral reefs, 

mangroves, seagrasses, and beaches known for snorkeling, scuba diving, and nature tourism. 

Coral reefs, like estuaries, are complex coastal ecosystems made up of many closely linked habitats 

that interact with other adjacent habitats. Connectance is high in functioning coral reef systems. 

Mangroves and seagrasses, for example, strongly influence the community structure of fish on 

neighboring coral reefs (Figure 6-18, Mumby et al. 2004). These adjacent vegetated habitats also 

improve water quality on nearby reefs by trapping sediments, nutrients and pollutants (Grimsditch 

and Salm 2006). Coral reefs are the most biologically diverse marine ecosystems on earth and rely 

on the interaction of many species including hard and soft corals, marine invertebrates, and fishes 

(Sebens 1994, Odum 1997, Bradley et al. 2010).

Sadly, coral reef ecosystems are rapidly declining, in large part due to human activities including 

agriculture and land use practices that lead to polluted runoff, overfishing, temperature change, ship 

groundings and coastal development. Recognizing the importance and fragility of coral reefs, the 

United States Coral Reef Task Force (USCRTF) was established by Presidential Executive Order in 1998 

to conserve coral reefs, and includes 12 Federal agencies, a number of states and territories, and 

many other partners. The Task Force selected Guánica Bay, Puerto Rico, as the first pilot of their 

Watershed Initiative. 
Implementing the Biological Condition Gradient Framework

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Figure 6-18. Diagram showing ecosystem connectance between mangroves, seagrasses, and coral reefs 

for different life history stages of a species of grunt. Label (A) shows juvenile grunts in a seagrass bed. Upon 

reaching a certain size the fish move to mangroves (B). The mangroves serve as a nursery habitat as fish 

further increase in size and migrate to patch reefs (C), then shallow fore reefs (D), and finally high relief reefs 

(E). As adult grunts spawn on these high relief reefs their larvae (shown above in the upper water column) 

grow into juveniles that move into seagrasses (A). If mangroves (B) are not present, grunts on patch reefs 

(C) are smaller and significantly less abundant. Other species (F) including some parrotfishes (shown in orange 

and green here) are more dependent on mangroves, and are not seen when mangroves are absent. 

This connectance could be evaluated using a habitat mosaic approach. Graphic: Mumby et al. (2004), 

reprinted with permission from Nature. 

Workshop: Decision support, SDM, and DPSIR

Working with the USCRTF prior to developing a coral reef BCG for Guánica Bay, the EPA Office 

of Research and Development and colleagues co-hosted a decision support workshop in 2010, 

inviting decision makers, scientists, and stakeholders (Bradley et al. 2015). Goals were to facilitate 

participants to:

- Look at the watershed as a system

- Share a collaborative vision for sustainable coral reefs

- Initiate a systematic, deliberative process to analyze coastal and watershed decisions 

that impact coral reefs and other ecosystems that provide services to humans

- Advance an integrative framework to incorporate the ecological, social, economic and 

legal consequences of alternative decisions. 

This workshop used SDM and DPSIR to build consensus for management of the Guánica Bay 

watershed, using SDM tools including an objectives hierarchy (Section 5.3, pages 45–46) and 

a Social Network Analysis (Section 3.2, page 14) to better understand and improve stakeholder 

communications, and an advanced online SDM/DPSIR tool (DASEES, www.dasees.org) to organize 

the process. This work set the stage for development of a BCG. Bradley et al. (2015) present a 

detailed report on the process and outcomes of the workshop.
6. Results from early pilots

79

Coral reef BCG

Moving forward from this foundation, EPA developed a conceptual narrative model and BCG 

approach to describe how biological attributes of coral reefs change along a gradient of increasing 

anthropogenic stress. The approach also identifies the critical attributes of coral reefs and evaluates 

how each attribute changes in response to stress. This BCG assists decision-makers in understanding 

the current conditions of Puerto Rico coral reefs relative to natural, undisturbed conditions. Decision 

makers can then set realistic goals for their coral reefs, and establish monitoring (measurement) 

endpoints based on attributes identified by the scientific community (Bradley et al. 2014).

Workshop: Biological integrity and levels of condition

To develop this BCG, EPA hosted an expert consensus workshop in 2012 (Bradley et al. 2014). Invited 

scientists evaluated photos and videos collected by EPA and partners at 12 stations from Puerto Rico 

coral reefs exhibiting a wide range of conditions. The experts individually rated each station for 

observed condition (‘good’, ‘fair’ or ‘poor’) and documented their rationale for the assignment 

(Figure 6-19).

Figure 6-19. EPA coral reef sites reflect a range of coral reef conditions, from good (left) to fair (middle), 

to poor (right).

The group further identified the attributes that characterize high biological integrity (or natural 

condition) for Puerto Rico’s coral reefs. A BCG based on hard corals, fishes, gorgonians, sponges, 

and other critical biota was developed for shallow-water linear reefs of southwestern Puerto Rico 

(Bradley et al. 2014). The experts were able to identify and develop narratives for four distinct levels 

of condition: very good-excellent, good, fair, and poor as shown in Table 4-2 (pages 30–31), a 

qualitative but very useful approach. Going further, a quantitative BCG was later developed for 

fish species based on decisions of a BCG panel using analyses of numeric fish data.
Implementing the Biological Condition Gradient Framework

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Table 6-1. Summary descriptions of four coral reef condition categories (very good/excellent to poor) 

based on expert assessments of individual stations. The description of ‘very good/excellent’ condition is 

based on panelist determination of features expected in very good stations (Bradley et al. 2014). 

Condition Level Attribute descriptions

VERY GOOD –

EXCELLENT 

(Approximate 

BCG level 1-2)

Physical structure: High rugosity or 3D structure, substantial reef built above bedrock, many 

irregular surfaces provide habitat for fish, very clear water, no sediment, flocs or films

Corals: High species diversity including rare; large old colonies (Orbicella) with high tissue 

coverage; balanced population structure (old and middle-aged colonies, recruits); Acropora

thickets present

Sponges: Large autotrophic and highly sensitive sponges abundant 

Gorgonians: Gorgonians present but subdominant to corals 

Condition: Low prevalence disease, tumors, mostly live tissue on colonies

Fish: Populations have balanced species abundance, sizes and trophic interactions

Vertebrates: Large, long-lived species present and diverse (turtles, eels, sharks)

Other invertebrates: Diadema, lobster, small crustaceans and polychaetes abundant, some large 

sensitive anemone species

Algae/plants: Crustose coralline algae abundant, turf algae present but cropped and grazed by 

Diadema and other herbivores, low abundance fleshy algae

GOOD 

(Approximate 

BCG level 3)

Physical structure: Moderate to high rugosity, moderate reef built above bedrock, some irregular 

cover for fish habitat, water slightly turbid, low sediment, flocs or films on substrate

Corals: Moderate coral diversity; large old colonies (Orbicella) with some tissue loss; varied 

population structure (usually old colonies, few middle aged, and some recruits); Acropora thickets 

may be present; rare species absent

Sponges: Autotrophic species present but highly sensitive species missing

Gorgonians: Gorgonians more abundant than level 1-2

Condition: Disease and tumor presence slightly above background level, more colonies 

have irregular tissue loss

Fish: Decline of large apex predators (e.g. groupers, snappers) noticeable; small reef fish 

more abundant

Vertebrates: Large, long-lived species locally extirpated (turtles, eels)

Other invertebrates: Diadema, lobster, small crustaceans and polychaetes less abundant than 

level 1-2; large sensitive anemones species absent

Algae/plants: Crustose coralline algae present but less than level 1-2, turf algae present and 

longer, fleshier algae present than level 1-2

FAIR 

(Approximate 

BCG level 4)

Physical structure: Low rugosity, limited reef built above bedrock, erosion of reef structure 

obvious, water turbid, more sediment accumulation, flocs and films; Acropora usually gone, 

present as rubble for recruitment substrate

Corals: Reduced coral diversity; emergence of tolerant species, few or no large old colonies 

(Orbicella), mostly dead; Acropora thickets gone, large remnants mostly dead with long uncropped 

turf algae 

Sponges: Mostly heterotrophic tolerant species and clionids

Gorgonians: More abundant than Levels 1-3; replace sensitive coral and sponge species
6. Results from early pilots

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Condition Level Attribute descriptions

Table 6-1 (continued)

Condition: High evidence of diseased coral, sponges, gorgonians; evidence of high mortality, 

usually less tissue than dead portions on colonies

Fish: Absence of small reef fish (mostly damselfish remain)

Vertebrates: Large, long-lived species locally extirpated (turtles, eels)

Other invertebrates: Diadema absent; Palythoa overgrowing corals; crustaceans, polychaetes and 

sensitive anemones conspicuously absent

Algae/plants: Some coralline algae present but no crustose coralline algae; turf is uncropped, 

covered in sediment; abundant fleshy algae (e.g., Dictyota) with high diversity 

POOR 

(Approximate 

BCG level 5-6)

Physical structure: Very low rugosity, no or little reef built above bedrock; no or low relief for fish 

habitat; very turbid water; thick sediment film and flocs covering bottom; no substrate for recruits

Corals: Absence of colonies, those present are small; only highly tolerant species, little or no tissue

Sponges: Heterotrophic sponges buried deep in sediment, highly tolerant species

Gorgonians: Small and sparse colonies, mostly small sea fans, often diseased

Condition: High incidence of disease on small colonies of corals, sponges and gorgonians, 

if present

Fish: No large fish, few tolerant species, lack of multiple trophic levels

Vertebrates: Usually devoid of other vertebrates other than fishes

Other invertebrates: Few or no reef invertebrates, high abundance of sediment dwelling 

organisms such as mud-dwelling polychaetes and holothurians

Algae/plants: High cover of fleshy algae (Dictyota); complete absence of crustose coralline algae 

and rarely calcareous algae 

Lessons from this coral reef workshop that apply to other BCG workshops are:

1. The heightened contributions of motivated participants who care deeply about the 

resource and who are committed to bioassessment as a management tool.

2. The value of easily communicated measures of biology, e.g., visual assessment methods 

that can be distributed as images for participant review before the workshop.

3. The importance of thorough workshop pre-planning. 

This workshop is described and discussed in Bradley et al. (2014).

Public Values Forum: Involving stakeholders in management decisions

The EPA group positioned this BCG in the USCRTF pilot effort in Guánica Bay to communicate 

biological condition as part of a larger management effort. EPA further hosted a Public Values Forum 

for stakeholders in Guánica Bay during the summer of 2013. Goals of this forum were to identify 

stakeholder values, objectives, and performance measures, then prioritize management actions 

to address stakeholder and public values. Anonymous electronic voting tools were used to gather

immediate, individual, and inclusive feedback. Stakeholders also developed a preliminary 
Implementing the Biological Condition Gradient Framework

82

consequence table−a matrix of management alternatives vs. effects on values or concerns 

(Bradley et al. 2016). This allowed EPA and partners to frame the issues, understand citizen values 

and perceptions, engage stakeholders, clarify the decision landscape, and develop stakeholder 

objectives. Together with BCG and previous SDM work, this led to effective management decisions 

important to, and supported by, stakeholders. The forum is reported in Bradley et al. (2016) along 

with a section on decision support tools.

Summary – Puerto Rico

These efforts in Puerto Rico followed a clear logic path through a series of stakeholder workshops: 

first, the 2010 Decision Support workshop identified stakeholder objectives and measures using SDM, 

an objectives hierarchy, and DPSIR; next, a workshop in 2012 developed a BCG as the scientific basis 

for reef management; then, the Public Values Forum in 2013 elicited stakeholder values to further 

inform the decision process. This path closely parallels the BCG implementation steps we present 

here, but moves the process further into stakeholder-based management at a regional and watershed scale. These efforts are well documented in a number of U.S. EPA reports and publications 

which serve as detailed examples for estuarine and coastal BCG practitioners. The EPA played a 

very significant role in shaping decision-making in the Guánica Bay watershed as part of the large 

interagency USCRTF effort. This work takes implementation of the BCG to a high level in supporting 

management decision-making in coastal areas. While smaller management programs may not have 

the equivalent funding to replicate these efforts, the sequence of activities taken in Puerto Rico could 

be successfully enacted on a smaller scale with fewer resources. 

Another example - waterbody management in the European Union

The twenty-eight countries in the European Union (EU) have been using a BCG-like approach to 

manage their waters since the 2010 enactment of the EU Water Framework Directive (WFD), and 

this body of work is relevant and instructive to estuarine and coastal BCG development in the 

United States. EU Member States (countries) use the agreed-upon WFD to assess their coastal 

and estuarine waters. The Directive applies core BCG concepts in a series of steps.
6. Results from early pilots

83

Six required steps for managing European estuaries

1) The DPSIR framework with a ‘pressures and impacts assessment’ is used to evaluate 

environmental problems.

2) Waterbodies are classified into one of six ‘categories’ (rivers, lakes, estuaries, coasts, artificial 

waterbodies, and heavily modified waterbodies), then each category is further classified into 

‘types’ of similar systems to improve comparability. Types are determined using a hierarchy 

of classification factors. 

Obligatory Factors:

 - Ecoregion

 - Tidal Range

 - Salinity

Optional Factors for estuaries, in the following order if possible:

- Mixing

- Intertidal Area (%)

 - Residence Time

 - Other Factors (Depth, Current Velocity, Wave Exposure, etc.)

3) Biological elements (a bit more prescriptive than BCG attributes) can be evaluated using any 

method suited to the situation. All elements must be assessed.

Biological elements for estuaries:

 - Composition, abundance, and biomass of phytoplankton

 - Composition and abundance of other aquatic flora

 - Composition and abundance of benthic invertebrate fauna

 - Composition and abundance of fish fauna

4) Type-specific reference conditions for biological elements are defined using a hierarchy 

of methods, identical to those used in U.S. bioassessments (Gibson et al. 2000):

 - Comparison to an existing undisturbed site or

 one with only very minor disturbance (preferred) 

 - Use of historical data or information

 - Models

 - Expert Judgement

5) Assignment of ecological status classes (High, Good, Moderate, Poor and Bad) to biological 

elements is anchored in the type-specific reference condition and is based on consistently 

defined narratives. This is analogous to the BCG approach, although the WFD formalizes 

intermediate steps and applies an intercalibration process to assure that status class thresholds 

have consistent meaning among Member States.

6) The status classes are used with the DPSIR analyses (Step 1) in planning and decision-making. 

Overall ecological status of the waterbody is defined as the lowest status of any of the four 

biological elements, considering also (but to a lesser degree) status of hydromorphological and 

physico-chemical elements. Waterbody thresholds between Good and Moderate (also between 

High and Good) lead to sets of actions that must be taken by Member States to protect and 

improve their waters.
Implementing the Biological Condition Gradient Framework

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The WFD allows flexibility in methods for assessing condition and determining reference, but is 

designed for comparable assessment and regulation across Member States and so is significantly 

more prescriptive than the BCG we present here. The document (EC 2002) at 

http://www.eutro.org/documents/wfd%20cis2.4%20(coast)%20guidance%20on%20tcw.pdf 

is an excellent guidance report for the European approach, with many lessons for applying the 

BCG to estuaries and coasts on our side of the Atlantic. If you go to this document, take note of 

terminological differences, particularly with ‘typology’ and ‘classification’. Other WFD guidance 

documents describing every stage of the process in detail can also be accessed as pdfs on

the internet.

The coastal and estuarine BCG and similar approaches have been used to manage a number of 

waterbodies. Each case study is different, to address a variety of research and management needs. 

Together, they provide a tremendous resource of ideas and insight for those considering or 

implementing BCG methods.
7. Summary and next steps

85

7. Summary and next steps

Figure 7-1. Photo montage of public/stakeholder interest in estuaries and coasts. Clockwise from top left: 

1) Manatees are a boon to tourism, Weeki Wachee River, FL. Photo: N. Cicchetti 2) Shallow water coral reef 

scenes attract snorkelers, Florida Keys National Marine Sanctuary. Photo: NOAA 3) Recreational boating and 

fishing are popular activities, Everglades City, FL. Photo: NOAA 4) Young beachgoers and a swimmer enjoying 

the water, Charlestown, RI.

Biological tools for managing estuaries and coasts

The BCG is the U.S. EPA approach to bioassessment and positions biology as a central element in

environmental management and decision making. BCG levels provide a ‘common language’ that 

allows consistent biological assessment of waterbodies at different times, scales or locations. 

The BCG stressor axis helps identify and address degradations due to cumulative impacts of many 

stressors or due to specific impacts of individual stressors. This guidance document provides a 

toolbox of actions to address management needs and build a BCG to solve environmental problems 

in coasts and estuaries. 
Implementing the Biological Condition Gradient Framework

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Core aspects of developing an estuarine and coastal BCG for any system or area are to:

1. Build public and stakeholder consensus, evaluate environmental problems, important stressors, 

management needs, stakeholder needs, and available data to define the biological measures 

and attributes that will best assess biological condition for the problems at hand.

2. Apply expert consensus to define undisturbed and minimally disturbed conditions. Develop 

narratives for BCG levels and use the narratives to support non-regulatory management needs, 

including stakeholder engagement, visioning, target setting, assessments, and monitoring. 

3. Use expert best professional judgment to develop numeric decision rules and thresholds for 

each level. Apply the BCG to management needs, both non-regulatory (e.g., increased impact 

of all the above actions) and regulatory (e.g., state CWA actions or TMDLs). Use specific 

stressor-response models, further stakeholder input, adaptive management, and other tools 

as applicable. 

Future development of estuarine and coastal BCG

New and continued use of BCG by management programs is by far the most effective way to improve 

and expand this approach. Current adopters (Section 6 above) have shown many different ways to 

use these methods, and will continue to innovate. The estuarine and coastal BCG is intended as a 

flexible set of concepts and tools; new programs will select and develop those aspects best suited 

to their particular situations and needs. This adds to the experiences of a community of users and 

the approach will grow through a better understanding of what works in a variety of ecological, 

social, and political settings.

Moving forward, a workgroup of scientists and managers (including the authors of this document) 

continues to develop and promote BCG in estuaries, coral reefs and other complex systems. This 

group has been active and growing since 2008. BCG projects for managing specific coastal and 

estuarine waterbodies are underway in many areas across the country. Each application addresses 

a different set of problems and explores a different approach to environmental management but the 

goal for all projects is to improve decision-making by bringing biology and BCG methods into direct 

use by managers. The workgroup is also addressing priorities identified as important for further 

development of the estuarine and coastal BCG and its implementation. 

One priority is to better develop the GSA (the BCG X axis). A detailed stressor gradient can improve 

links between specific stressors and the resulting biological responses. When these relationships are 

quantitative, BCG can inform target setting for reduction of specific stressor levels and guide related 

management actions. Integrating these individual stressors-response measures into a welldeveloped quantitative GSA (with its own measures and proxies that evaluate cumulative impacts) 

would better define the entire stressor field to which biota is exposed and so improve both 

management and communication.

On the biological condition axis (the BCG Y axis) the workgroup continues to explore the use of 

higher attributes such as function and connectance to provide more comprehensive assessments
7. Summary and next steps

87

of waterbody condition. Developing more effective and easily attained measures of these attributes 

would allow EPA and others to better address questions of waterbody sustainability and resilience. 

This would be particularly applicable in degraded parts of estuaries where structure and composition 

are so severely altered that improving function becomes the priority for restoration and management. 

This information may in turn help human communities adapt to the effects of global change 

(Figure 7-2). 

Biotope mosaics are being explored as a way to evaluate function and connectance, and interest 

in this approach has been growing. New stressors leading to biotope losses, including sea level rise, 

are of growing concern. Mosaic measures are inherently quantitative, and work to consistently 

assign values of measures to BCG levels would be a valuable contribution to application of the 

method. This would require input from national experts working in different types of systems 

at different stages of degradation.

Figure 7-2. Eroding marsh edge, which can be a cause of marsh loss due to sea level rise. 

Lower Chesapeake Bay, VA.

Another interest is in improving tools that engage stakeholders in developing visions for desired 

future estuarine conditions and in setting environmental goals. Proven tools such as facilitated 

workshops and public fora may be supported by new tools such as electronic polling, Social Network 

Analyses (SNA), and outreach through electronic or visual media. Other priorities include exploration 

of more efficient sampling technologies including remote sensing of biology, which has potential 

to change the scale at which we assess our coasts and estuaries. Further, better approaches to 

estuarine classification−that specifically integrate the stressor field and biological response−could 

improve transfer of knowledge and practice among estuaries and estuarine managers.

Local or national expert workshops can refine implementation of the BCG to best meet management 

needs and will contribute to addressing the issues listed above. The coastal/estuarine BCG workgroup has started to evaluate the need for national workshops to assist all BCG practitioners and 

improve management applications. In fact, well-organized workshops have been indispensable in 

advancing local and national efforts from the very beginning of the Office of Water BCG program.
Implementing the Biological Condition Gradient Framework

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Conclusion

The estuarine and coastal BCG approach has an intuitive appeal to the public and other stakeholders. 

The focus on living things has a clear connection to the human experience, as does the concept of 

looking at changes over time. Linking stressor increases over historic time to losses of valued species, 

habitats, and functions leads to collaborative goal-setting as ‘what did we have, what do we have, 

and what do we want’, an approach that can resonate with people. Comparing existing condition 

to natural condition makes intuitive sense, and people like to see evaluations of an entire waterbody 

rather than just a part of it. This human appeal can engage citizens to participate in discussions 

to identify biological measures they value and set targets for improving the condition of those 

measures. A motivated public is a powerful driver of environmental change through their actions, 

communications, volunteerism, and ability to increase political will. Engaging the public and 

other stakeholders is a primary focus of the estuarine and coastal BCG.

Applicable at any scale or at multiple scales using one or several attributes, BCG is an effective and 

flexible approach to bioassessment and environmental management. The ability to consistently 

compare biology over time and location offers many advantages. The BCG is firmly entrenched 

and supported within the U.S. EPA Office of Water and can be used in combination with other 

management frameworks. A number of management groups have successfully applied the BCG 

(or similar methods) to address the problems facing their waterbodies.

Increased use of the BCG in programs around the nation has inspired other groups to look into the 

approach. This document proposes guidance for estuarine and coastal BCG implementation as a 

logical set of actions to engage stakeholders, scientists, and managers in solving problems and 

managing complex systems. NEPs, NGOs, states, and other interested parties are urged to contact 

current users, the authors of this report, or the Office of Water bioassessment program for further 

discussions and assistance.
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Appendix A

Appendix A. Attributes and narratives to assign BCG levels in streams 

Table A-1. Ecological attributes and possible measures (first three columns) paired with example narratives for BCG levels 

(last 6 columns), from U.S. EPA (2016).

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Table A-1 (continued) 

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Appendix A

Table A-1 (continued) 

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Table A-1 (continued) 

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Appendix A

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Table A-2. Detailed matrix of Taxonomic Composition and Structure Attributes I–V for streams

(compressed into ‘Structure’ in Table A-1), from U.S. EPA (2016).
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Appendix B. The BCG for estuaries and coasts: Frequently Asked Questions

1 - Why bioassessment? 

Bioassessment (the use of biological indicators to evaluate environmental condition) allows 

biology to be included in management. Living organisms respond to the cumulative impacts of 

many anthropogenic stressors, and this can be parsed into the impacts of individual stressors as 

well. Bioassessment allows managers to address these impacts through approaches ranging from

public engagement to Clean Water Act regulations. Bioassessment in estuaries integrates many 

of the upstream stressors in the larger watershed and is a vital part of managing at the waterbody 

and watershed level.

2 - What exactly is the Biological Condition Gradient or BCG? 

The BCG is a conceptual scientific framework for interpreting biological response to increasing 

effects of stressors on aquatic ecosystems (U.S. EPA 2016). This method was developed by EPA’s 

Office of Water (Office of Science and Technology) to evaluate the extent of biological impairment 

relative to a baseline condition of ‘as naturally occurs’ or ‘minimally disturbed.’ The BCG model 

defines up to six levels of biological condition along a trajectory of degradation in response to 

increasing anthropogenic stress (Figure B-1). The consistent narratives of condition on this 

trajectory can be used for comparable interpretation of biological assessment, support of Clean 

Water Act objectives, meaningful goal-setting, and coordinated management decision-making 

(Davies and Jackson 2006, U.S. EPA 2016).

3 - How does the BCG provide a common language for different biological measures? 

The levels of biological condition on the response axis of the BCG serve as a common language 

for assessment in comparing different biological measures such as benthic IBIs, seagrass acres, 

chlorophyll concentrations, etc. Levels of the BCG have the same inherent definitions for any 

biological measure in any setting, so that level 3 carries the same basic meaning e.g. for 

phytoplankton in a Vermont stream, benthos in a California lake, and fish communities in a 

Georgia estuary.

The descriptive gradient of biological response to stressors (Figure B-1) is the scientific 

underpinning behind a coastal and estuarine BCG. The gradient represents the full range of 

condition from the natural or undisturbed anchor (level 1) to most severely disturbed (level 6). 

Panels of experts bin the gradient into 6 levels using consistent descriptions of each level (left 

column of Figure B-1). This process can be applied to any biological setting because the entire 

range of biological condition can be defined anywhere and consistently divided into bins (levels).

In practice, U.S. EPA (2016) provides a detailed process for using expert consensus and available 

data (e.g., stressor-response relationships from comprehensive monitoring programs) to define 

the full range of condition, calibrate the BCG, and consistently assign biological metric scores to 

BCG levels. BCG levels 1–6 provide a common language for assessment because the repeatable

scientific process can be applied anywhere that a full range of biological condition can be 

described with any method of characterizing biology.
Appendix B

103

Figure B-1. Conceptual model of the BCG as used in freshwater. Graphic: U.S. EPA 2016

4 - What are the ecological attributes and how do they relate to the BCG concept?

Attributes are ecological characteristics used to organize biological response. In streams, the 

following ten attributes were tested and shown to be useful in environmental management:

Attribute I: Historically documented, sensitive, long-lived or regionally endemic taxa

Attribute II: Sensitive-rare taxa

Attribute III: Sensitive ubiquitous taxa

Attribute IV: Taxa of intermediate tolerance

Attribute V: Tolerant taxa

Attribute VI: Non-native or intentionally introduced taxa

Attribute VII: Organism condition

Attribute VIII: Ecosystem function

Attribute IX: Spatial and temporal extent of stressor effects

Attribute X: Ecosystem connectance
Implementing the Biological Condition Gradient Framework

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In estuaries, the Estuarine BCG Workgroup proposes five attributes to be evaluated at multiple 

scales, bundling Attributes I through V above into ‘Structural and Compositional Complexity’: 

- Structural and Compositional Complexity 

- Non-Native Taxa 

- Condition

- Function 

- Connectance

Identifying and focusing on one, a few, or all attributes simplifies and improves BCG development. 

Going beyond the more general definitions of levels in Figure B-1, each attribute provides more

precise definitions of each BCG level, tailored to the specific ecology of that attribute (Table A-1). 

5 – What is the estuarine and coastal BCG implementation approach? 

BCG implementation is proposed as a set of eleven actions or steps to assist coastal and estuarine 

scientists and managers in framing environmental problems and applying BCG methods towards 

solving those problems. The steps can be divided into three stages of development.

Steps 1–3. Initial collaborative management for effective BCG outcomes 

1. Define problems, engage partners and stakeholders

2. Collaborate to define management goals, visions, and objectives

3. Determine the biological components, stressors, measures, and attributes most relevant to

management objectives

Steps 4–7. A narrative BCG model to identify and communicate condition, develop visions, set goals 

and targets, and motivate stakeholders

4. Delineate and classify the waterbody and watershed of interest

5. Organize and analyze existing data for the identified measures, collect new data if needed

6. Define BCG level 1 conditions for the identified attributes

7. Develop narrative descriptions of the biology expected at each BCG level as a narrative BCG

model; apply to management needs

Steps 8–11. A fully developed BCG model to support both regulatory and non-regulatory needs

8. Convert narrative descriptions to quantitative metrics and thresholds, calibrate the BCG

9. Develop a stressor gradient and stressor-response relationships

10. Organize, interpret, and report results

11. Develop decision support, communication, and monitoring tools; assist management partners

Taken together, these steps can provide a full path for managing coastal waterbodies. However, 

the guidance and the steps are flexible, and managers should use any steps in any order and at 

the level of rigor that best meets their management needs. 
Appendix B

105

6 - Why is moving “up” BCG levels and closer to natural conditions a valuable environmental goal?

1. From an EPA point of view, the Agency’s mandate under the Clean Water Act is to “restore

and maintain the chemical, physical, and biological integrity of the Nation’s waters”, with 

integrity often defined in the sense of ‘as naturally occurs’.

2. A natural state, its beauty, and its associated biodiversity confer significant human well-being.

3. History has shown that deviations from the natural condition can lead to catastrophic

unforeseen consequences (building levees along the Mississippi, introducing rabbits to

Australia, building groins and jetties on beaches, etc.).

4. A historic benchmark of ‘as naturally occurs’ can be anchored at a defined point in the past,

which avoids problems associated with ‘shifting baselines’ where expectations of “good”

condition become lower over time.

5. For large-scale measures such as the biotope mosaic, natural biological condition describes

the relatively stable environments under which native biota evolved prior to rapid human

population growth. Restoring towards these conditions should favor the survival of valued

native organisms.

7 - How can this complement the ecosystem services/benefits work being done in many estuaries?

This BCG work can easily move forward in tandem with efforts to quantify ecosystem services and 

benefits. By assessing the values associated with BCG levels, ecosystem service analyses can 

demonstrate the importance and benefits of protecting or restoring an ecological state, and the 

costs of not doing so. Ecosystem benefits information helps decision-makers address stakeholder 

needs when setting goals and evaluating trade-offs between different management scenarios.

8 - What is the biotope mosaic method for bioassessment?

This bioassessment approach quantifies estuary-wide changes to living habitats (biotopes) and to 

mosaics of these biotopes over time. Scientists at the Tampa Bay Estuary program (TBEP) posited 

that the cumulative impacts of stressors manifest through destruction and conversion of 

biotopes, and that returning the proportions or balance of biotopes to a previous and lessdisturbed state would benefit the estuary as a whole by moving the estuary closer to the mosaic 

of biotopes under which native organisms evolved. Several quantitative metrics can be applied 

to evaluate the estuary-wide mosaic of biotopes. Tampa Bay stakeholders and the public valued

quantity and diversity of habitats, and this method proved effective at communicating estuarine 

condition and developing stakeholder visions and goals that led to management actions and 

environmental results. This approach was written into a paper (Cicchetti and Greening 2011) that

informs scientists and managers of a successful management program that has many parallels

to the coastal/estuarine BCG framework.

9 - How is biotope defined?

A biotope is an area that is relatively uniform in physical structure, and that can be identified by 

the dominant biota (Davies et al. 2004). A biotope is defined through the repeatable combination 

of an abiotic habitat and a strongly associated biological species or group, and the biotope is 

named after that species or group. Biotope can be used interchangeably with habitat when 

habitats specifically include biology: a sand bar is a habitat but not a biotope while seagrass is

both a habitat and a biotope. A more informative biotope name would include both the taxon 
Implementing the Biological Condition Gradient Framework

106

and the abiotic setting, e.g., ‘Zostera marina on subtidal sandy mud’. Bioassessment includes 

biotopes, but not physical habitats. However, the term ‘habitat’ is more familiar to a public

audience and may be used in that context for better communication to stakeholders: ‘the habitat 

mosaic’. Biological classifications in the Coastal and Marine Ecological Classification Standard 

(CMECS) document (www.csc.noaa.gov/cmecs) have a strong focus on the biotope concept, and 

CMECS is a federally approved national classification standard. 

10 - Where have BCG or similar approaches been applied to estuaries and coasts?

BCG approaches have been applied in Narragansett Bay, Mobile Bay, Lower Columbia River, 

Puerto Rico Coral Reefs, and Tampa Bay (essentially a BCG approach). Work in these estuaries 

is described in Section 6 of the EPA document “Implementing the Biological Condition Gradient 

Framework for Management of Estuaries and Coasts”. 

Other estuaries have been evaluated and managed with bioassessments and other methods 

using elements in common with the BCG approach. Two examples are described below:

Example 1: 

Buzzards Bay (MA) and its side estuaries have suffered from losses and alterations to natural 

species, communities, and habitats. The Buzzards Bay Coalition compared biological data to a 

historical baseline, in this case pre-colonial conditions. While Buzzards Bay has not developed 

a BCG, many of the critical elements exist – use of biology for assessment, determination of 

conditions ‘as historically occurred’, and use of expert consensus and best professional judgement

to evaluate data (Figure B-2).
Appendix B

107

Figure B-2. Excerpt from Buzzards Bay Report Card output. Trends of various measures are shown, 

as well as resource improvements or declines. Numbers represent the comparative value of the resource 

relative to historic reference value−a BCG concept. Graphic: Buzzards Bay Coalition 2015

Example 2: 

The Chesapeake Bay Program is a well-funded effort that has monitored biological condition 

for decades in several states. Many of their restoration targets are based on historic baselines 

(CBP 2000). A variety of biological endpoints are monitored on a routine basis, and biological 

condition is assessed by summarizing the data into indices based on information from reference 

sites. These indices are reported separately, for the entire Bay and for each sub-embayment, 

and can be compared to previous monitoring data for examination of trends. These indicators 

are also combined into an overall Bay Health Index (Figure B-3).
Implementing the Biological Condition Gradient Framework

108

Figure B-3. 2012 Chesapeake Bay Report Card output. Graphic: CBP 2000

Although work in the Chesapeake was not done for BCG development, many of the important 

elements of BCG are included. Biological data are used for assessment; reference conditions 

are defined; multiple levels of condition are identified (in some cases only good/fair/poor); 

and multiple assemblages are evaluated alone and in concert, at multiple scales, to determine 

estuary health.

While these programs successfully used BCG concepts to manage estuaries, the development 

of an actual BCG would allow unification of the indices used into a common language, better 

management of CWA goals related to “as naturally occurs”, comparability to sub-estuaries 

and to other estuaries, more consistent prioritization, management, and monitoring, and 

a more effective way to communicate condition to the public and other stakeholders in 

a meaningful way.

11 - How have NEPs most benefited from the estuarine and coastal BCG? 

NEPs that are using a BCG approach identify significant benefits in 1) setting meaningful targets 

for habitat protection and restoration and 2) engaging and motivating the public and other 

stakeholders to participate in waterbody management and to improve the environment 

by changing behaviors and actions.
Appendix C

109

Appendix C. Attendees at the 2008 workshop: A proposed organizing

framework for bioassessment of estuaries 

The goal of this effort was to develop and refine an integrative framework to provide a common 

language and enable meaningful comparisons among measures and waterbodies, thus allowing

better management of entire estuaries and watersheds.

Attendees:

Walter Berry1

Curtis Bohlen2

Claire Buchanan3

Lilian Busse4

Marty Chintala1

Giancarlo Cicchetti1

Bob Connell5

Susan Davies6

Chris Deacutis7

Naomi Detenbeck1

Ed Dettmann1

Jerry Diamond8

Walt Galloway1

Tim Gleason1

Diane Gould9

Holly Greening10

Susan Jackson11

Danielle Kreeger12

Chris Madden13

Tim O’Higgins14

Angela Padeletti12

Peg Pelletier1 

Margherita Pryor9

Richard Ribb7

Ed Sherwood10

Hilary Snook15

Martha Sutula16

1 U.S. EPA, Atlantic Ecology Division, Narragansett, RI

2 Casco Bay Estuary Partnership, Portland, ME

3 Interstate Commission on the Potomac River Basin, Rockville, MD 4 San Diego Water Board, San Diego, CA

5 New Jersey Department of Environmental Protection, Leeds Point, NJ

6 Maine Department of Environmental Protection, Augusta, ME 7 Narragansett Bay Estuary Program, Narragansett, RI

8 Tetra Tech Corporation, Owings Mills, MD

9 U.S. EPA, Region 1, Boston, MA

10 Tampa Bay Estuary Program, St. Petersburg, FL 11 U.S. EPA, Office of Water, Washington, DC

12 Partnership for the Delaware Estuary, Wilmington, DE

13 South Florida Water Management District, West Palm Beach, FL

14 U.S. EPA, Western Ecology Division, Newport, OR

15 U.S. EPA, Region 1, North Chelmsford, MA

16 Southern California Coastal Water Research Project, Costa Mesa, CA
Implementing the Biological Condition Gradient Framework

110

Appendix D. Attendees at the 2009 workshop: A biological condition 

gradient for Narragansett Bay

The goals of this workshop were to develop a concept and qualitative description of ‘minimally 

disturbed’ in the Narragansett Bay estuarine system, identify key indicators, and identify the existing 

historical and current data that are available for these key indicators.

Attendees:

Andrew Altieri1 

Tom Ardito2 

Walter Berry3 

David Borkman4 

Keryn Bromberg Gedan1

Carrie Byron5

Christopher Calabretta4

Rachel Calabro6 

Dan Campbell3 

Marty Chintala3

Giancarlo Cicchetti3

Earl Davey3 

Susan Davies7 

Chris Deacutis2 

Ed Dettmann3 

Walt Galloway3

Jonathan Garber3 

Jeroen Gerritsen8 

Susan Jackson11 

David Gregg9 

Alana Hanson3 

Carl Hershner10 

Susan Jackson11

Roxanne Johnson3

Q Kellogg12 

Sue Kiernan13 

Chris Krahforst14 

Lesley Lambert2 

Chris Melrose15 

Dave Murray1 

Candace Oviatt4 

Peg Pelletier3 

Carol Pesch3

Chris Powell16

Sheldon Pratt4

Warren Prell1

Margherita Pryor17

Paul Rees18

Richard Ribb2

Ken Rocha3

Rodney Roundtree19

Liz Scott13

Emily Shumchenia4

Ted Smayda4

Charlie Strobel3 

Diane Switzer20

Glen Thursby3

Sue Tuxbury21

Cathy Wigand3

1 Brown University, Providence, RI

2 Narragansett Bay Estuary Program, Narragansett, RI

3 U.S. EPA, Atlantic Ecology Division, Narragansett, RI

4 University of Rhode Island, Graduate School of Oceanography, Narragansett, RI

5 University of Rhode Island, Coastal Institute, Narragansett, RI

6 Save the Bay, Providence, RI 7 Maine Department of Environmental Protection, Augusta, ME

8 Tetra Tech Corporation, Owings Mills, MD

9 Rhode Island Natural History Survey, Kingston, RI

10 College of William and Mary, Virginia Institute of Marine Science, Gloucester Point, VA

11 U.S. EPA, Office of Water, Washington, DC

12 University of Rhode Island, Kingston, RI

13 Rhode Island Department of Environmental Management, Providence, RI

14 Massachusetts Bays Program, Boston, MA

15 NOAA, National Marine Fisheries Service, Narragansett, RI 

16 Rhode Island Department of Environmental Management, Providence, RI (retired)

17 U.S. EPA, Region 1, Boston, MA

18 University of Massachusetts, Water Resources Research Center, Amherst, MA

19 Marine Ecology and Technology Applications, Inc., Waquoit, MA

20 U.S. EPA, Region 1, North Chelmsford, MA

21 NOAA, National Marine Fisheries Service, Gloucester, MA
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