A Conceptual Framework for Lake Michigan 

Coastal/Nearshore Ecosystems, With Application to 

Lake Michigan Lakewide Management Plan (LaMP) 

Objectives

Open-File Report 2013–1138

U.S. Department of the Interior

U.S. Geological Survey
Cover photo. Sleeping Bear Dunes, Great Lakes National Program Office-Image Collection, 

U.S. Environmental Protection Agency, Robert De Jonge courtesy of Michigan Travel Bureau.
A Conceptual Framework for Lake Michigan 

Coastal/Nearshore Ecosystems, 

With Application to Lake Michigan Lakewide 

Management Plan (LaMP) Objectives

By Paul W. Seelbach, Lisa R. Fogarty, David Bo Bunnell, Sheridan K. Haack, and 

Mark W. Rogers

Open-File Report 2013–1138

U.S. Department of the Interior

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

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2013

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Suggested citation:

Seelbach, P.W., Fogarty, L.R., Bunnell, D.B., Haack, S.K., and Rogers, M.W., 2013, A conceptual framework for Lake 

Michigan coastal/nearshore ecosystems, with application to Lake Michigan Lakewide Management Plan (LaMP) 

objectives: U.S. Geological Survey Open-File Report 2013–1138, 36 p., http://pubs.usgs.gov/of/2013/1138/.
iii

Contents

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

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

An Ecosystem- and Process-Based Conceptual Framework to Support 

Great Lakes Resource Management Programs.................................................................2

Applying the Framework to Lake Michigan Lakewide Management Plan Goals ......................5

References.............................................................................................................................................5

We Can All Eat the Fish.................................................................................................................................6

Importance of Fish Consumption to Lake Michigan Communities ...............................................6

Contaminants, Sources, and Risks ....................................................................................................6

Fish Consumption Advisories and Monitoring .................................................................................7

Contaminant Trends..............................................................................................................................7

Identifying Key Processes and Uncertainties..................................................................................7

Geomorphic Processes ..............................................................................................................7

Hydrologic Processes.................................................................................................................8

Biological Processes ..................................................................................................................9

What We Know from Monitoring Efforts...........................................................................................9

Examples of Knowledge Gaps ............................................................................................................9

References...........................................................................................................................................10

We Can All Drink the Water.......................................................................................................................12

Importance of Drinking Water to Lake Michigan Communities..................................................12

Drinking-Water Monitoring ...............................................................................................................12

Identifying Key Processes and Uncertainties................................................................................13

Geomorphic Processes ............................................................................................................13

Hydrologic Processes...............................................................................................................13

Biological Processes ................................................................................................................14

What We Know from Monitoring Efforts.........................................................................................14

Knowledge Gaps and Uncertainties................................................................................................15

References...........................................................................................................................................15

We Can All Swim in the Water...................................................................................................................17

Importance of Swimming in the Water to Lake Michigan Communities ...................................17

Beach Monitoring...............................................................................................................................17

Identifying Key Processes and Uncertainties................................................................................18

Geomorphic Processes ............................................................................................................18

Hydrologic Processes...............................................................................................................18

Biological Processes ................................................................................................................18

What We Know From Monitoring Efforts........................................................................................19

Knowledge Gaps and Uncertainties................................................................................................19

References...........................................................................................................................................20

All Habitats Are Healthy, Naturally Diverse, and Sufficient to Sustain Viable Biological 

Communities....................................................................................................................................22

Importance of Healthy Habitats .......................................................................................................22

Habitats and Their Structure ............................................................................................................22

Habitat Trends .....................................................................................................................................23
iv

All Habitats Are Healthy, Naturally Diverse, and Sufficient to Sustain Viable Biological 

Communities (continued)

Identifying Key Processes and Uncertainty...................................................................................23

Geomorphic Processes ............................................................................................................23

Hydrologic Processes...............................................................................................................24

Biological Processes ................................................................................................................24

What We Know from Monitoring Efforts.........................................................................................25

Knowledge Gaps........................................................................................................................25

References...........................................................................................................................................25

Figures

1. Diagram of the proposed conceptual framework intended to 

support an ecosystem- and process-based approach to attaining 

the goals of the Lake Michigan Lakewide Management Plan (LaMP)................................3

Tables

1. Matrix of the primary ecosystem disciplines whose processes drive 

ecological structure and function within each of the primary aquatic zones 

that together constitute the Great Lakes ecosystem, and the key processes 

that fall within each zone ............................................................................................................4

Appendixes

Processes and components that impact the Great Lakes Lakewide Management Plan goal—

1. We Can All Eat the Fish................................................................................................................28

2. We Can All Drink the Water.........................................................................................................30

3. We Can All Swim in the Water. ...................................................................................................32

4. All Habitats are Healthy, Naturally Diverse, and Sufficient To Sustain 

Viable Biological Communities....................................................................................................34
v

Abbreviations and Acronyms

AOC Areas of Concern

BEACH Beaches Environmental Assessment and Coastal Health Act of 2000

CCL Contaminant Candidate List 

DDT dichlorodiphenyltrichloroethane 

EPA U.S. Environmental Protection Agency

FCAs fish consumption advisories 

FIB fecal indicator bacteria 

GLNPO Great Lakes National Program Office (EPA) 

GLFMP Great Lakes Fish Monitoring Program 

GLRI Great Lakes Restoration Initiative 

HAB harmful algal bloom 

HGM hydro-geomorphic 

LaMP Lakewide Management Plan 

NOAA National Oceanic and Atmospheric Administration 

PBBs polybrominated biphenyls

PBDEs polybrominated diphenyl ethers 

PCBs polychlorinated biphenyls 

qPCR quantitative polymerase chain reaction

SOLEC State of the Lakes Ecosystem Conference 

USGS U.S. Geological Survey
Darnell, NOAA Great Lakes Environmental Resrearcch Laboratory Image Gallery
A Conceptual Framework for Lake Michigan Coastal/

Nearshore Ecosystems, With Application to Lake 

Michigan Lakewide Management Plan (LaMP) Objectives

By Paul W. Seelbach,1 Lisa R. Fogarty,2 David Bo Bunnell,1 Sheridan K. Haack,2 and Mark W. Rogers1

1

 U.S. Geological Survey, Great Lakes Science Center.

2

 U.S. Geological Survey, Michigan Water Science Center.

Abstract

The Lakewide Management Plans (LaMPs) within the 

Great Lakes region are examples of broad-scale, collaborative resource-management efforts that require a sound ecosystems approach. Yet, the LaMP process is lacking a holistic 

framework that allows these individual actions to be planned 

and understood within the broader context of the Great Lakes 

ecosystem. In this paper we (1) introduce a conceptual 

framework that unifies ideas and language among Great Lakes 

managers and scientists, whose focus areas range from tributary watersheds to open-lake waters, and (2) illustrate how the 

framework can be used to outline the geomorphic, hydrologic 

biological, and societal processes that underlie several goals 

of the Lake Michigan LaMP, thus providing a holistic and 

fairly comprehensive roadmap for tackling these challenges. 

For each selected goal, we developed a matrix that identifies 

the key ecosystem processes within the cell for each lake zone 

and each discipline; we then provide one example where a 

process is poorly understood and a second where a process is 

understood, but its impact or importance is unclear. Implicit 

in these objectives was our intention to highlight the importance of the Great Lakes coastal/nearshore zone. Although the 

coastal/nearshore zone is the important linkage zone between 

the watershed and open-lake zones—and is the zone where 

most LaMP issues are focused—scientists and managers 

have a relatively poor understanding of how the coastal/nearshore zone functions. We envision follow-up steps including 

(1) collaborative development of a more detailed and more 

complete conceptual model of how (and where) identified 

processes are thought to function, and (2) a subsequent gap 

analysis of science and monitoring priorities.

Introduction

It is now broadly recognized that Great Lakes resource 

management programs must be based on an ecosystems 

approach. Such a holistic, systems-level approach identifies 

key driving processes that operate at different, often hierarchical, scales to influence selected ecosystem characteristics; for 

example, processes that sustain healthy and interconnected 

aquatic habitat mosaics. The Lakewide Management Plans 

(LaMPs) within the Great Lakes region are examples of broadscale, collaborative resource management efforts that require 

a sound ecosystems approach. Each LaMP has different 

endpoint goals, against which progress can be measured 

through time as specific management actions are implemented 

in selected areas by particular agencies. Yet, the LaMP process 

currently lacks a holistic framework that allows these individual actions to be planned and understood within the broader 

context of the Great Lakes ecosystem. This paper addresses 

two objectives that are meant to introduce and illustrate the 

use of an ecosystem-based framework for regional-scale 

resource management.

Our first objective is to introduce a conceptual framework 

that unifies ideas and language among Great Lakes managers 

and scientists, whose focus areas range from watersheds to 

open-lake waters. Our conceptual framework builds upon 

previous works, such as (1) the Coastal Habitat Classification 

Framework of the U.S. Geological Survey (USGS), Aquatic 

GAP Analysis Program (U.S. Geological Survey, 2013); 

(2) the U.S. Environmental Protection Agency (EPA) 

framework for “Assessing and Reporting on Ecological 

Conditions” (U.S. Environmental Protection Agency, 2002); 

and (3) the EPA “Conceptual Model of the Relationships 

Between Ecosystem Health, Stressors, and Sources of Stress” 

(Environment Canada and U.S. Environmental Protection 

Agency, 1997). The framework is a matrix that organizes 

driving ecosystem processes by aquatic eco-zones and key 

ecological disciplines (fig. 1). 
2

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

Our second objective builds on the first, in that we seek 

to illustrate how the framework can be used to outline the 

geomorphic, hydrologic, biological, and societal processes 

that underlie several goals of the Lake Michigan LaMP, thus 

providing a holistic and fairly comprehensive roadmap for 

addressing these goals. In this paper, we use four of the six 

Lake Michigan LaMP goals as examples of using this framework to address key Great Lakes ecosystem issues. The goals 

we focus on are the following:

1. “We can all eat the fish.” 

2. “We can all drink the water.”

3. “We can all swim in the water.” 

4. “All habitats are healthy, naturally 

diverse, and sufficient to sustain viable 

biological communities.” 

For each goal, we developed a matrix that identifies the 

key ecosystem processes within the cell for each lake zone 

and each discipline; we then provided one example where a 

process is poorly understood and a second where a process 

is understood, but its impact or importance is unclear. These 

examples are meant to be illustrative because we hope to 

stimulate more formalized expert- and partner-driven matrix 

development, project synthesis, and gap analysis in the future. 

Implicit in these objectives was our intention to highlight 

the importance of the Great Lakes coastal/nearshore zone. 

Although the coastal/nearshore zone is the important linkage 

zone between watershed and open-lake zones, scientists and 

managers have a relatively poor understanding of how the 

coastal/nearshore zone functions. This zone is the basin focus 

of (1) accumulation and chemical transformation of many 

human-derived loads, such as agricultural runoff, industrial 

waste, and urban storm and sewer outflows; (2) human economic uses of the Great Lakes, such as commercial harbors, 

water supply for industry and municipalities, and waste 

disposal; and (3) human enjoyment of the Great Lakes, such 

as for swimming, fishing, recreational boating, and viewing. 

Largely because of the diversity of habitats in this transitional 

zone between river and lake—including lowland rivers and 

their flood-plain wetlands, drowned-river-mouth lakes and 

embayments, deltaic wetlands, river plumes, and coastal 

wetlands—the coastal/nearshore zone is a productive biological hot spot where many Great Lakes fauna spend at least 

part of their life history. Finally, the coastal/nearshore zone is 

where most of the LaMP endpoint goals are measured. 

Our overall goal for this report is to help frame 

Lake Michigan management efforts under a unifying, 

ecosystem-based conceptual framework, where key processes 

underlying each endpoint goal will be explicitly considered. 

An Ecosystem- and Process-Based 

Conceptual Framework to Support Great Lakes 

Resource Management Programs

The conceptual ecological framework presented in this 

paper is a simple, but holistic, approach for identifying the 

processes critical to effective Great Lakes resource management. Because these inland seas are daunting in size and complexity, many aspects of the lake ecosystem have traditionally 

been studied and managed as local and narrowly focused 

issues, independent of other potentially related aspects—and 

some aspects have received little attention. 

The first major element of this conceptual framework 

outlines three geographic zones: the watershed, coastal/nearshore, and open lake; and the second major element identifies the key geomorphic, hydrologic, biological, and societal

processes that occur within each zone (fig. 1). We chose not 

to apply strict criteria to delineating the three zones, largely 

because in nature there are no simple and abrupt demarcations among these habitats. Thus, our framework embraces 

the inherent variation among zones and processes across 

Lake Michigan’s complex ecosystem. In simple terms, watershed includes the terrestrial drainage area surrounding the 

tributaries, open lake reflects waters deeper than 30 meters (m) 

or the depth at which the thermocline intersects the bottom of 

the lake, and coastal/nearshore represents the diverse habitats 

in between the watershed and the open-lake zones. Each of 

these zones is commonly studied and managed; however, each 

also transitions into, and thus influences, system processes in 

the adjacent zone. These areas of intersection and mixing are 

difficult to study, but they often are most critical to biological 

processes of interest. Instead of viewing these geographic 

zones as separate arenas, this framework highlights the 

importance of interconnections between them and the resulting influences on system processes and related ecological 

characteristics. 

The second major element represents important 

disciplinary subsystems within each geographic zone in 

the larger lake ecosystem. We use these major ecosystem 

disciplines to organize the process subsystems, which can 

be viewed as parallels to the human body’s subsystems; for 

example, the circulatory system.

Hydrologic processes circulate or move water, sediments, 

nutrients, and other materials into and through the zones. 

Watershed hydrology involves catchment-specific water 

budgets, as well as alternate flow routing via evapotranspiration, surface waters, or groundwater paths. Coastal/nearshore 

hydrology has been little studied, involving complexities 

of river- and lake-water mixing, lake seiche regimes, lake 

upwellings, and nearshore-current dynamics. Open-lake 

hydrology involves major water circulation patterns and 
Introduction

3

Figure 1. The proposed conceptual framework is intended to support an ecosystem- and process-based approach to attaining 

the goals of the Lake Michigan Lakewide Management Plan (LaMP). Building a detailed understanding of the geomorphic, 

hydrologic, and biological processes within the open lake, coastal/nearshore, and watershed ecosystem zones helps determine 

LaMP progress relative to specific management goals. In addition, societal values in each of the geographic lake zones weigh 

heavily in resource management decisions. The coastal/nearshore zone serves as the linkage (as orange arrows indicate) among 

the three habitats. Climate, geology, and the legacy human footprint are the overriding processes that influence all lake-zone 

processes at an ecosystem-wide scale. 
4

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

seasonal stratification of layers of water with different temperatures. Water characteristics such as nutrient concentrations 

or temperature are included under this “hydrologic” heading. 

Geomorphic processes include historical processes that 

have shaped the form and texture of the local landscape; current processes of sediment erosion, transport, and deposition; 

and patterns that influence local habitat character. Geomorphic 

processes influence numerous resource management issues, 

such as contaminant sources and dynamics. The characteristics of aquatic habitat are largely shaped by hydrologic and 

geomorphic processes, which are often referred to in wetland 

and stream ecology as hydro-geomorphic or “HGM” drivers. 

Peterson (2003) clarified that aquatic habitats generally 

include both “static” aspects (the local, historical geomorphic 

setting) and overlying “dynamic” aspects (the hydrologic and 

present-day geomorphic processes). 

Biological processes include fundamental nutrient and 

biogeochemical cycles governed by the ecology and activity of 

microorganisms, trophic energy (or food web) dynamics, and 

sometimes the presence of biological structure, such as aquatic 

plants or macrophytes. Biological processes overlay, and are 

driven and constrained by, the spatial physical template 

created by the HGM processes. 

Finally, we recognize the important influence of societal 

processes on the ecosystem as well, because societal perspectives and values that are in play at local and regional scales 

will determine the cost/benefit tradeoffs that ultimately drive 

resource management decisions. 

The geomorphic, hydrologic, and biological system 

processes all have natural characteristics that provide the 

basis for understanding that disciplinary subsystem, and each 

has then been changed, to some degree, by human actions 

within each of the three geographic zones. Thus, within each 

discipline-zone cell of the framework matrix, we further 

stratify processes as “natural” or “anthropogenic.” And 

we recognize that these human-influenced processes will 

often have ramifications across multiple zones or multiple 

disciplines.

The resulting ecological zone-discipline matrix allows us 

to examine selected topics, programs, and endpoints from a 

holistic, systems perspective. To examine each selected issue, 

a table based on the matrix template was built to identify 

specific, key driving processes that lie within each of the 

matrix cells, because often the issues that are observed or measured within a particular cell are in fact driven by processes 

in other cells. The resulting table (the general case shown 

in table 1) is a conceptual model of how the lake ecosystem 

works across space and disciplines to influence the issue of 

interest. Our framework is, at minimum, a sort of checklist 

reminding the user not to overlook processes in other lake 

zones or disciplines. The framework can be used to map and 

assess current or proposed science and management programs, 

and the results could then be used to identify program gaps or 

strategic directions. 

To begin to address the Lake Michigan ecosystem by 

means of a more holistic approach, we used the conceptual 

framework to develop a coarse outline of system processes 

important to several Lake Michigan LaMP goals. Examples 

of both natural and anthropogenic processes are identified in 

tables similar to table 1 (appendixes 1–4). We envision followup steps including (1) collaborative development of a more 

detailed and more complete conceptual model of how (and 

where) the identified processes are thought to function and 

(2) a subsequent gap analysis of science and monitoring needs. 

The gap analysis would establish priorities for subsequent 

science and monitoring efforts, adaptively moving us towards 

improved lake management. 

The intention of this framework is to encourage viewing 

the lake ecosystem as a system of multidiscipline processes 

that operate within and across different geographic areas. The 

focus of the framework is on the interacting processes and 

the need to understand the influence they have on reaching 

desired endpoints or causing undesirable results. With this 

framework, we hope to assist programs within the Great Lakes 

region to identify science and monitoring strengths and weaknesses, thus providing more complete information for making 

management decisions and prioritizing future research needs.

Table 1. Matrix of the primary ecosystem disciplines whose processes drive ecological structure and function within each of the 

primary aquatic zones that together constitute the Great Lakes ecosystem, and the key processes that fall within each zone.

Primary ecosystem disciplines Open lake Coastal/nearshore Watershed

Societal Key processes Key processes Key processes

Biological Key processes Key processes Key processes

Hydrologic Key processes Key processes Key processes

Geomorphic Key processes Key processes Key processes
Introduction

5

Applying the Framework to Lake Michigan 

Lakewide Management Plan Goals

The proposed conceptual framework was used to develop 

a process matrix to address four of the Lake Michigan LaMP 

goals: (1) we can all eat the fish, (2) we can all drink the 

water, (3) we can all swim in the water, and (4) all habitats 

are healthy, naturally diverse, and sufficient to sustain viable 

biological communities. Each of the following chapters briefly 

describes how the proposed conceptual framework can be 

used to support an ecosystem- and process-based management 

program and includes a table (as an appendix) of example 

processes critical for each LaMP goal. We offer the caveat 

that although we clearly recognize the importance of societal 

processes within the ecosystem scheme, we did not discuss 

these in the example chapters because our authorship lacked 

this expertise. We envision the conceptualization of societal 

process as part of the “subsequent steps” described above. 

References

Environment Canada and U.S. Environmental Protection 

Agency, 1997, State of the Great Lakes, 1997—The year of 

the nearshore: Chicago, Ill., Great Lakes National Program 

Office, EPA 905-R-97-013, 76 p.

Peterson, M.S., 2003, A conceptual view of environmenthabitat production linkages in tidal river estuaries: 

Reviews in Fisheries Science, v. 11, no. 4, p. 291–313.

U.S. Environmental Protection Agency, 2002, A framework 

for assessing and reporting on ecological condition—An 

SAB report: Washington, D.C., EPA-SAB-EPEC-02-009 

[variously paged].

U.S. Geological Survey, 2013, Coastal aquatic GAP 

analysis Web site, accessed March 19, 2013, at http://

www.glsc.usgs.gov/main.php?content=research_GAP_

coastal&title=Aquatic%20GAP0&menu=research_NCE_

GAP.
6

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

Rainbow smelt, Minnesota Sea Grant

We Can All Eat the Fish

Importance of Fish Consumption to Lake 

Michigan Communities

Over 30 percent of global fish production is in freshwater 

systems (Food and Agriculture Organization of the United 

Nations, 2010), and wild fish harvesting provides an important 

protein source for humans (Welcomme and others, 2010). 

Consuming harvested wild fish provides multiple health benefits, because fish are a good source of protein and are typically 

low in saturated fat (Gebhardt and Thomas, 2002). Estimated 

lakewide fish harvests in Lake Michigan have exceeded 

19 tons per year in recent decades (Brian Briedert, Indiana 

Department of Natural Resources, unpublished data); however, fish consumption advisories (FCAs) have been issued 

for all commercially and recreationally harvested fish species 

from Lake Michigan, except alewife (Alosa pseudoharengus). 

Alewife is not considered a food fish, but it is used as a protein 

source in livestock and aquaculture feeds, thus providing an 

indirect pathway for human consumption. 

Fish consumption can be a major source of human 

exposure to carcinogenic and toxicological contaminants 

(Sidhu, 2003) including methylmercury, polychlorinated 

biphenyls (PCBs), and organic pesticides and herbicides such 

as chlordane and dichlorodiphenyltrichloroethane (DDT). 

Contaminants of increasing concern include polybrominated 

biphenyls (PBBs) and polybrominated diphenyl ethers 

(PBDEs) and pharmaceuticals including chemicals that interfere with the body’s hormone system (endocrine disruptors), 

personal care products, and prescription drugs. Nevertheless, 

relationships between fish consumption and human health 

risks from these emergent contaminants are not understood 

well enough at the present time to invoke FCAs. 

Contaminants, Sources, and Risks

Mercury is a natural element released from processes 

such as volcanic eruptions and human activities such as 

the burning of fossil fuels. Bacteria convert mercury to an 

organic form in water, methylmercury, which can bioaccumulate within food webs. Methylmercury accumulates within 

fish muscle and causes neurological impairment to humans 

who consume the fish (Goyer and others, 2000). Similar to 

mercury, PCBs bioaccumulate within food webs and become 

concentrated in the lipids and tissues of top fish-eating 
We Can All Eat the Fish

7

carnivores or slow-growing fish that live near the bottom of 

the lake. PCBs had multiple industrial uses and were banned 

in 1979, because they have been suggested as a carcinogen 

and a cause of birth defects in humans (Mozaffarian and 

Rimm, 2006). Many FCAs are targeted towards limiting 

consumption of fish species with the high potential of PCB 

bioaccumulation by sensitive population groups such as young 

children, pregnant women, or women of childbearing age. 

A large group of organic chemicals identified as chemicals of 

emerging concern (CECs) also have been detected in Great 

Lakes surface waters, bottom sediments, and wastewaters 

entering the lakes (Lee and others, 2012). Among these CECs 

are PBDEs, which stem primarily from manufactured flame 

retardant chemicals commonly used in building materials and 

have characteristics similar to PCBs, whereas pharmaceuticals 

can disrupt hormone production and control in humans. 

Fish Consumption Advisories and Monitoring

Individual States and tribal entities are responsible for 

setting their own FCAs. Within the Great Lakes, the Great 

Lakes Sport Fish Consumption Advisory Task Force facilitates 

determination of FCAs and includes members from public 

health and natural resource agencies from each of the eight 

States bordering the Great Lakes, along with representatives 

from the EPA, Native American tribes, and Canadian agencies. 

FCAs originally were compared with risk standards developed 

by the Food and Drug Administration; however, the potential 

for increased consumption of contaminated fish by anglers 

relative to nonanglers resulted in modification of FCAs to 

decrease health risks to anglers. New advisories are based on 

cancer, reproductive, and developmental risks. Protocols have 

been developed by the Great Lakes Sport Fish Consumption 

Advisory Task Force to suggest consistent approaches for 

determining mercury- and PCB-driven FCAs across the 

Great Lakes.

Monitoring for determining “We can all eat the fish” 

relies primarily upon sampling of whole fish and fish flesh. 

The Great Lakes Fish Monitoring Program (GLFMP) within 

the Environmental Protection Agency Great Lakes National 

Program Office (EPA GLNPO) monitors bioaccumulative 

organic compounds in Lake Michigan by using lake trout 

(Salvelinus namaycush) as a biological monitor of contaminants in the open-lake area and Chinook and Coho salmon 

(Oncorhynchus tshawytscha and O. kisutch, respectively) for 

monitoring game fish fillets. The open lake has historically 

been sampled offshore at three sites that were selected to 

minimize nearshore influences: Saugatuck, Charlevoix, and 

Sturgeon Bay, Michigan. Game fish fillet monitoring by the 

GLFMP relies upon contaminant samples provided by States. 

Coho salmon are analyzed in even years, and Chinook salmon 

are analyzed in odd years. Game fish are sampled at approximately 10 rivermouths around the lake, and adults are targeted 

prior to spawning. The GLFMP also samples for contaminants 

in the water column and sediments. The EPA GLNPO and 

the Sport Fish Contaminant Monitoring Program in Ontario 

have collectively monitored contaminants in fish for over 

3 decades. Individual States often do additional sampling of 

other Lake Michigan fish species that are important to their 

constituents and their consumption preferences. For example, 

the Michigan Department of Natural Resources has tested for 

contaminants in 21 species since the mid-1980s; however, 

Chinook and Coho salmon and lake trout are the most continuously and regularly monitored species (Michigan Department 

of Natural Resources, unpublished data). 

Contaminant Trends

The 2009 “Nearshore Areas of the Great Lakes” report 

(U.S. Environmental Protection Agency and Environment 

Canada, 2009) determined the status of Lake Michigan 

contaminants in game fish as “fair” with an improving trend. 

Ongoing monitoring by the GLFMP and its partner State 

agencies has generally shown that contaminant levels in game 

fish have decreased since monitoring programs began, yet 

contaminant levels are still above levels requiring FCAs. For 

example, decreasing DDT and PCB concentrations in lake 

trout from the early 1970s to 2003 were reported by Carlson 

and others (2010), who also reported changes in first-order rate 

constants for multiple contaminants in lake trout that resulted 

in increased half-lives of contaminants between the mid-1970s 

and late-1990s. Carlson and others (2010) concluded that Lake 

Michigan contaminants may have reached stable concentrations and will persist within the Lake Michigan ecosystem for 

future decades. Persistence of contaminants within the ecosystem may be caused by internal recycling within the water near 

the lake bottom (Jeremiason and others, 1998).

Identifying Key Processes and Uncertainties

Monitoring programs for fish contaminants have focused 

on endpoint metrics, such as mercury concentration per meal 

portion, and an important next step is to better understand 

ecological processes that influence this LaMP restoration goal. 

Thus, there is a need to consider the primary drivers within the 

ecosystem that affect fish contamination and provide direction 

for restoration efforts. We used the framework to address this 

need; the following discussions are drawn from the example 

table, appendix 1.

Geomorphic Processes 

Geomorphic processes that affect the “We can all eat 

the fish” LaMP goal relate to distribution and retention of 

contaminants in the ecosystem. Important processes include 

the adherence of contaminants to substrate and the leaching 

of legacy contaminants that regulate bioavailability, as 

well the determination of watershed shape by landscape 

contours, which influences the distribution of depositional 
8

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

areas, shoreline energy, and shoreline erosion. Adherence to 

substrate is important because contaminants that are dissolved or weakly bound to substrate are more bioavailable 

than structurally complex contaminants. Retention and the 

subsequent dissolution of legacy contaminants from substrate 

into the water (leaching) is an important process because in 

high-energy coastal zones or large watersheds, contaminant 

transport tends to be dominated by surface runoff, current 

upwellings and downwellings, and nearshore currents; in lowenergy areas, by contrast, bed sediments are the major route 

of contaminant exposure to organisms (Burton and Johnston, 

2010). Thus, sediment attributes and landscape attributes create spatial variability in contaminants within Lake Michigan. 

Fine-scale processes of sediment transport and deposition 

regulate contact between sediment and contaminants, because 

suspended sediments provide large amounts of surface area for 

contaminant adsorption. The sizes of deposited sediment particles that make up the lake substrate influence the availability 

of the sediment pore space for transporting contaminants and 

subsequent contaminant exposure to bottom-dwelling animal 

species through ingestion or direct adsorption. MacDonald 

and others (2000) reported that PCBs were highly toxic to 

sediment-dwelling organisms, a finding that has implications 

for exposure and bioaccumulation for other animals that 

consume them. Contaminants within sediments in the coastal/

nearshore and watershed zones can be transferred to terrestrial 

species via food-web connections. For example, Raikow and 

others (2011) reported that lake-origin PCBs were detected 

up to 30 m inland in wasps. In that study, PCBs originated 

from contaminated emergent aquatic invertebrates inhabiting 

contaminated lake sediments that wasps consumed. The role 

of sediment contaminants is critical to the need for FCAs, 

but the fate of contaminants in both disturbed sediments and 

sediments that are subject to major disturbances is not well 

understood (Eggleton and Thomas, 2004). 

Anthropogenic modifications such as the construction of 

shoreline stabilization structures—or “shoreline hardening” 

—and dredging can alter geomorphic processes that determine 

contaminant retention and thus affect transport processes 

among lake zones. For example, channel construction can 

convert areas of sediment deposition to higher-flow, nondepositional areas and thus disturb historically settled contaminants and change distribution patterns of contaminants. 

Although anthropogenic modifications are of greater concern 

within the coastal/nearshore and watershed zones than in 

the open-lake zone, sites for disposing of dredging spoil are 

sometimes situated in the open-lake zone, and dredging-spoil 

disposal could potentially distribute contaminants that originated inshore to the open-lake zone. Riverbank alterations can 

also create opportunities for the movement of contaminants 

from recognizable “point” locations during rewetting events 

if contaminated sediments have been placed within erosional 

areas of the watershed (Burton and Johnston, 2010). The use 

and security of confined disposal facilities determine the risk 

of recontamination. 

Hydrologic Processes

Hydrologic processes also influence the loading 

and transport of contaminants within the Lake Michigan ecosystem. The manufacturing of many contaminants 

that are harmful to fish has been banned for decades—for 

example, PCBs were banned in the United States in 1979. 

Yet, there are legacy sources for most banned contaminants, 

and some contaminants are still actively produced—for 

example, mercury emissions from coal-fired power plants. 

Carlson and others (2010) reported that the major source 

for most contaminants within the Great Lakes is airborne 

deposition—a “nonpoint” source that cannot be traced to a 

single source—and the major contaminant deposition areas are 

sediments. Single, identifiable sources of contaminants (point 

sources) are now negligible sources of contaminants within 

the Great Lakes region (Carlson and others, 2010). Airborne 

deposition is the largest source of many contaminants, and 

mercury concentrations in fish are related to localized atmospheric concentrations across much of the United States (Hammerschmidt and Fitzgerald, 2006). Multiple models have been 

developed to explore atmospheric deposition and the exchange 

of contaminants, such as PCBs, between the atmosphere and 

the water surface (Meng and others, 2008); however, future 

dynamics and contaminant loadings are difficult to predict. 

In contrast, sources of CECs have been traced to agricultural, 

municipal, industrial, and sewage wastes (Lee and others, 

2012), thus creating opportunities to link hydrological processes to CEC contaminant loadings. 

The hydrologic transport of contaminants across and 

within ecosystem zones is complex and would benefit 

from additional research. Specific transport properties vary 

depending on individual contaminants and hydrologic setting 

in the Great Lakes. Within the open-lake zone, lake-water 

mixing and large-scale circulation patterns likely drive the 

deposition of contaminants. For example, fall turnover of 

different layers of water in Lake Superior could resuspend 

PCBs from sediment into the water column and increase 

their net residence time (Baker and others, 1985). Finer scale 

dynamics such as the deposition of contaminants in sediment, 

their burial, and then their localized resuspension have been 

modeled; one example is a mass-balance PCB model for 

Lake Ontario by Mackay (1989). Within the nearshore zone, 

contaminant loading is affected by surrounding landscape 

uses. For example, the Atmospheric Exchange Over Lakes and 

Oceans project hypothesized that increased urban emissions 

of hazardous air pollutants resulted in increased atmospheric 

depositional fluxes to adjacent Great Lakes waters (Simcik and 

others, 1999), and an “urban plume” of PCB-enriched precipitation affecting Lake Michigan that stemmed from Chicago 

has been documented (Offenberg and Baker, 1997). Within 

the coastal/nearshore zone, longshore currents—as well as 

episodic events such as upwellings, storm-induced surges, and 

spring runoff—act to distribute contaminants and disturb sediments, thereby resulting in contaminant resuspension in water. 
We Can All Eat the Fish

9

Studies of sediment trapping have measured contaminant 

settling and resuspension across a range of time scales, but we 

are not aware that anyone has related these measures to the 

bioavailability of contaminants. Contaminant loading and dispersion within the watershed is influenced by local population 

sizes, hydrologic flows, and flow seasonality.

Anthropogenic influences can exacerbate hydrological 

processes affecting loading and distribution of contaminants. 

Of greatest concern are human activities that magnify airborne deposition. Within the coastal/nearshore and watershed 

zones, both point and nonpoint loadings create concerns for 

contaminant loading. For example, Whittle and Fitzsimmons 

(1983) concluded that the Niagara River was a major source of 

contaminants and trace metals to Lake Ontario. Although point 

sources in the watershed have been greatly reduced via waterquality policies, infrequent accidents can result in punctuated 

loadings with long-term implications.

Biological Processes

Biological processes determine the transfer of contaminants into fish tissue. Given the bioaccumulative nature of 

most fish contaminants of concern in Lake Michigan, the 

need for FCAs is dependent on species-specific characteristics 

including the predator’s level in the food web, also referred 

to as “trophic level”; its primary prey type; its gross growth 

efficiency (that is, the proportion of food it consumes that goes 

towards growth); and its contaminant retention efficiency, 

meaning the proportion of contaminants it consumes that 

it does not excrete (Madenjian, Schmidt, and others 1999). 

For example, lake trout have 80-percent total PCB retention 

efficiency, whereas Coho salmon have 50-percent total PCB 

retention efficiency, although both fish species have very 

similar alewife-dependent diets (Madenjian, Schmidt, and 

others, 1999). Variations in the accumulation of contaminants 

within the same fish species can be explained by differences 

in gender, age, size, food-consumption rates, growth rates, and 

activity rates (Trudel and Rasmussen, 2006; Madenjian and 

others, 2010, 2011). Also important are contaminant concentrations in prey and contaminant toxicity (for example, PCB 

congener variability). 

The biological processes we identified that influence 

contaminant transfer through the food web are the same in all 

zones; however, the contributing components in each zone 

may differ. This difference is largely due to variations in 

biogeochemical activity, biological communities, and predator-prey interactions within the watershed, coastal/nearshore, 

and open-lake zones. Food-web linkages across these zones 

are not well understood. 

Anthropogenic influences can exacerbate processes that 

limit meeting the LaMP restoration goal of safe fish consumption. Introductions of low and middle trophic level invasive 

species can lengthen food chains, decrease energy transfer, 

and cause increased consumption needs for native top predators; thus potentially magnifying bioaccumulation of contaminants. Introductions of prey species can also shift predator diet 

compositions (for example, lake trout now commonly feed 

on benthic, invasive, round goby Neogobius melanostomus) 

causing the risk of contaminant exposure from eating any 

particular species to change through time. Human influences 

on climate can result in changes in exchange rates between 

atmospheric sources and water, as well as increases in the 

production rates of lower trophic level fish, and these changes 

would affect contaminant delivery to sediments and contaminant accumulation in predatory fish. Lastly, temperature 

changes would affect fish metabolic parameters, thus increasing predator feeding rates and potentially affecting contaminant elimination rates.

What We Know from Monitoring Efforts

Extensive diet analysis and bioenergetics modeling 

have provided much insight into Lake Michigan food-web 

processes influencing FCAs. Several intensive sampling 

opportunities every 5–10 years, such as the Lake Michigan 

Mass Balance Study, the Great Lakes Cooperative Science and 

Monitoring Initiative, and the Great Lakes Restoration Initiative, have provided support for investigating predator-prey 

interactions, food-web connections, and bioenergetics-based 

exploration of bioaccumulation within multiple fishery target 

species (for example, McCarty and others, 2004; Davis and 

others, 2007).

Studies of individual physical and chemical properties of 

contaminants create generalized expectations of contaminant 

half-lives and their behaviors within aquatic systems. Variations in contaminant physical and chemical properties within 

Lake Michigan should be expected given the range of energy, 

sediment, and transport processes across the ecosystem. 

Examples of Knowledge Gaps

Two examples of knowledge gaps that limit the ability 

to prioritize restoration actions for achieving the LaMP goal 

“We can all eat the fish” are provided below. The first shows 

that the process of contaminant loading to fish is understood, 

but data gaps limit our understanding of fish contaminant 

burdens in Lake Michigan. The second example illustrates a 

case where processes affecting circulation of contaminants and 

dispersal linkages among Lake Michigan zones are not well 

understood.

Because trophic-level influence on fish contaminant loads 

is well understood, increased monitoring could inform how 

spatial and temporal variability in fish diets affect contaminant 

burdens in their tissues. To further complicate the issue, recent 

evidence suggests that the contaminant burden of a prey fish 

can vary in response to changes in its diet. Altogether, these 

data gaps suggest that more regular monitoring of the diets 

of predatory fish under FCAs, as well as the diets and contaminant burdens of their primary prey, would help us better 

understand the primary sources of variation in contaminant 

loads for fishes under FCAs. Spatial variability in contaminant 
10

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

burdens is best exemplified by the finding that male walleye 

(Sander vitreus) had higher PCB concentrations than females 

in the Saginaw River system, because males spent more time 

in upstream areas where prey fish had high contaminant concentrations (Madenjian and others, 1998). Temporal variability 

in contaminant burdens of Chinook salmon would be detected 

by existing monitoring, but our understanding of this variation 

is limited. For example, Lake Michigan Chinook salmon diets 

consist of more than 75 percent alewife, and adult alewife had 

exponentially decreasing PCB loads from 4.5 milligrams per 

kilogram (mg/kg) in 1976 to 1.0 mg/kg in 1985 (Madenjian 

and others, 1993); PCB loads in alewife further declined to 

less than 0.5 mg/kg by 1994–95 (Madenjian and others, 1999). 

Declining alewife PCB concentrations coincided with 

declining alewife energy density, and thus total consumption of alewife had to increase to sustain the growth rates of 

their predators. How these changes influenced PCB loads 

of Chinook salmon over this same time period is unclear. 

Furthermore, recent species invasions have resulted in uncoupling of the Lake Michigan food web, resulting in fish diet 

changes that could influence the fishes’ contaminant burdens. 

For example, dreissenid mussels have recently become larger 

components of lake whitefish diets (Pothoven and Madenjian 

2008), but how this diet shift has influenced lake whitefish 

contaminant burden or contaminant retention has not been 

evaluated. Regular monitoring of prey-fish contaminant 

burdens—for example, monitoring every 2 years—along with 

regular evaluation of predator diet composition and investigations of food-web linkages would improve our understanding 

of trends in contaminant burdens in Lake Michigan fish and 

our ability to achieve this LaMP goal.

Dispersal processes that result in contaminant loadings 

within and across lake zones, such as those between the 

coastal/nearshore and offshore zones, are not well understood. 

Although we have identified plausibly important influences 

that are largely associated with hydrologic processes, we 

cannot identify the relative importance of these influences to 

contaminant dispersal. Biological processes also influence 

contaminant circulation; for example, riverine fish and invertebrates can become contaminated after eating the eggs of 

nonnative Pacific salmon species that reside for most of their 

lives within the open lake and return to Great Lakes tributaries 

to spawn (Merna, 1986). Evidence exists that contaminant 

concentrations in a Lake Ontario tributary increased in 

response to the death and decay of Chinook salmon after their 

spawning runs (O’Toole and others, 2006). Thus, fish behaviors can influence contaminant dispersal across zones, but 

their importance relative to hydrologic processes is not well 

understood. On a lakewide scale, we are not aware of knowledge that provides explicit, process-based linkages between 

localized contaminant hot spots” and resultant fish contaminant loads. Understanding processes that drive contaminant 

dispersal and within-lake sources would provide direction for 

restoration efforts.

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Hesselberg, R.J., 1999, Variation in net trophic transfer efficiencies among 21 PCB congeners: Environmental Science 

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Van Hoof, P., and Eadie, B., 2004. Results of the 

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12 A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

Chicago Lakefront, Daniel Schwen cc c

We Can All Drink the Water

Importance of Drinking Water to Lake Michigan 

Communities

Safe drinking water is of critical importance to 

Lake Michigan communities. Drinking water is taken from 

public-water-supply intakes tapping the nearshore zone, groundwater, or rivers or other surface water within the Lake Michigan 

basin. There are 31 direct Lake Michigan drinking-water intakes 

in Illinois, 25 in Wisconsin, 22 in Michigan, and 7 in Indiana. 

Water use for each Great Lakes basin has recently been compiled 

through 2005 (Mills and Sharpe, 2010), and the Lake Michigan 

basin accounted for 15 billion gallons per day (Bgal/day)—an 

estimated 12.3 Bgal/day was taken directly from Lake Michigan. 

This was 49 percent of all U.S. water withdrawn from the 

Great Lakes region, but much of this water was for uses other 

than public water supply, such as thermoelectric power or use. 

Within the Lake Michigan Basin, 1.5 Bgal/day from surface 

water was used for public water supply; from groundwater, 

295 million gallons per day (Mgal/day) was used for public 

water supply, and 178 Mgal/day was used for private (domestic) water supply, all sources together serving a population of 

about 7.7 million people. There are few estimates of the economic values associated with clean drinking water; however, 

the Cryptosporidium outbreak in Milwaukee, Wis., in 1993 

was estimated to cost $96.2 million: $31.7 million in medical 

costs and $64.6 million in productivity loss (Corso and others, 

2003). Austin and others (2007) estimated that operating costs 

for water-supply facilities using Great Lakes water totaled about 

$600 million in 2006 dollars and that the Great lakes Regional 

Collaboration goal of achieving a 40-percent reduction in 

sedimentation might reduce drinking-water treatment costs by 

$12 million annually. Many industries also rely on high-quality 

water for their processes.

Drinking-Water Monitoring

The U.S. Environmental Protection Agency (EPA) 

Office of Groundwater and Drinking Water has the primary role of ensuring that drinking water from public water 

supplies is protected. The EPA does not typically regulate 

private water supplies. In the States of the Lake Michigan 

basin, various agencies at several levels of government may 

require some tests of water quality when private water supplies are installed or when property is sold. These tests are 

rarely as extensive as those required by the EPA for public 

water supplies. The EPA has established National Primary 

Drinking Water Regulations, which are legally enforceable 

standards for public water systems. The EPA also maintains 

a database, the Safe Drinking Water Information System at 

http://water.epa.gov/scitech/datait/databases/drink/sdwisfed/

index.cfm, listing monitoring results and monitoring and 

standards violations for public water supplies (U.S. Environmental Protection Agency, 2012a). The EPA requires public 

water systems to be monitored for selected microbiological, 

inorganic, organic, and radiological contaminants listed at 

http://water.epa.gov/drink/contaminants/index.cfm#1. (U.S. 

Environmental Protection Agency, 2012b). Further, the EPA 

requires each community water system to generate an annual 

Consumer Confidence Report (http://cfpub.epa.gov/safewater/

ccr/; U.S. Environmental Protection Agency, 2012c) that is 

made available to all residents receiving water from that water 

system. Summary reports by year and state can be obtained at 

http://water.epa.gov/scitech/datait/databases/drink/sdwisfed/.

The contaminants required by the EPA to be monitored in 

public water supplies are typically those that have been identified to be of concern in source water for drinking-water supplies. Among these are many contaminants that are of general 
We Can All Drink the Water

13

concern in the Lake Michigan Basin, such as industrial contaminants and persistent organic chemicals, or the protozoan 

Cryptosporidium, which caused the largest drinking waterrelated outbreak of illness in U.S. history in Milwaukee, Wis., 

in 1993. In addition, some inorganic contaminants such as mercury and arsenic, which may have natural sources, or nitrate, 

which is often associated with excess fertilizer use or septicsystem contamination of groundwater, are also required to be 

monitored in public water supplies. The Safe Drinking Water 

Act includes a process that the EPA must follow to identify 

and list unregulated contaminants that may require a national 

drinking-water regulation in the future. The EPA must periodically publish a Contaminant Candidate List (CCL; http://

water.epa.gov/scitech/drinkingwater/dws/ccl/index.cfm; U.S. 

Environmental Protection Agency, 2012d) and decide whether 

or not to regulate at least five or more contaminants on the list. 

The newest CCL (CCL3) lists several endocrine-disrupting 

compounds such as hormones or hormone-like substances, 

and their addition to the CCL may have resulted from recent 

findings of pharmaceutical and personal care products in the 

Nation’s drinking-water supplies (Snyder and others, 2008). 

The Waterborne Disease and Outbreak Surveillance 

System is a national surveillance system maintained by the 

U.S. Centers for Disease Control and Prevention. This system 

receives data about waterborne disease outbreaks and summarizes and publishes the data. The most recent summary (for 

2005–6; Centers for Disease Control and Prevention, 2008) 

can be found at http://www.cdc.gov/mmwr/pdf/ss/ss5709.pdf. 

This summary notes a trend of increasing outbreaks caused by 

Legionella bacteria and also by contaminated groundwater.

Most States completed Source Water Assessments for 

their public drinking-water supplies in the early 2000s (http://

water.epa.gov/infrastructure/drinkingwater/sourcewater/

protection/sourcewaterassessments.cfm; U.S. Environmental 

Protection Agency, 2012e). Each assessment report defined a 

delineated protection area, identified an inventory of potential 

sources of contamination, and conducted an evaluation of the 

likelihood of the water system being contaminated.

Identifying Key Processes and Uncertainties

Current monitoring programs for drinking water are 

focused on public water supplies and on specific contaminants 

previously found to cause adverse health effects from drinking 

water. The EPA’s list of National Primary Drinking Water 

contaminants identifies the suspected sources for most of those 

constituents. Nevertheless, the sources of many contaminants 

are located at some distance from the drinking-water intake 

or well or are diffusely distributed across the landscape. For 

recently recognized contaminants, such as many microorganisms and constituents on the CCL, the sources and pathways to 

the drinking-water intake or well may be unknown. For many 

microbiological contaminants, the processes that govern their 

survival or persistence in the environment are poorly known. 

We used the framework to address this need; the following 

discussions are drawn from the example table, appendix 2.

Geomorphic Processes

The natural geology of an area surrounding a drinkingwater intake or well may influence the water quality of that 

water supply. For example, arsenic is a naturally occurring 

inorganic compound that has caused unacceptable quality 

of groundwater in parts of southeastern Michigan (http://

www.michigan.gov/documents/arsenicbroch_41426_7.pdf; 

Michigan Department of Community Health and Michigan 

Department of Environmental Quality, 2006) and Wisconsin (http://dnr.wi.gov/topic/Groundwater/arsenic/index.

html; Wisconsin Department of Natural Resources, no date). 

In addition, the natural geology may facilitate contamination 

of groundwater from surface sources. Porous or fractured 

limestone (karst) occurs on the western side of Lake Michigan 

and extends through the Door Peninsula and onto the Garden 

Peninsula in Michigan; this material is especially susceptible 

to contamination from surface sources such as agriculture, 

industry, or leaking septic systems (http://wi.water.usgs.gov/

gwcomp/find/door/susceptibility.html; University of Wisconsin 

Extension and U.S. Geological Survey, 2007) and will be an 

important concern for groundwater supplies both public and 

private (homeowner wells). Likewise, the vulnerability of 

shallow groundwater supplies—public or private—to nitrate 

contamination from agricultural fertilizer application has been 

evaluated (Chowdhury and others, 2003; Saad, 2008), and it 

again is a function of local geologic materials. For drinkingwater intakes that extend into Lake Michigan, geomorphic 

factors within the lake may be important. For example, currents and locations where sediments accumulate may influence 

the susceptibility of drinking-water intakes to contamination. 

Hydrologic Processes

Hydrologic processes that influence nearshore drinkingwater intakes include flow and transport from watersheds or 

storm drains, nearshore groundwater, longshore currents, interaction between nearshore and large lake currents, waves, and 

the effects of each of these on nearshore sediments or sands. 

Rao and Schwab (2007) reviewed hydrologic interactions 

between the open Great Lakes, the coastal boundary layer, 

and the surf and swash zones. They pointed out that we are 

“...still a long way from having predictive understanding of 

the dynamics of sediment, contaminant, and pathogen transport near beaches,” and this statement would also apply to the 

zone where drinking-water intakes are located. All of these 

complex hydrologic factors may be operational; however, the 

significance of each factor may vary from day to day. The 

final draft “Source Water Assessment Report for the City of 

South Haven, Mich.” noted a probable influence of the plume 

of water from the Black River when the wind direction was 

from the north-northeast and was sustained for 24 to 36 hours 

(U.S. Geological Survey and Michigan Department of Environmental Quality, 2003, at http://www.south-haven.com/

pages/public_works/pdf/Source-Water-Assessment-Report.

pdf). In addition, the amount of solid particles suspended in 
14

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

water (turbidity) was recorded to increase when wind was 

from the south through southwest; the increase was likely 

due to currents and sediment resuspension in Lake Michigan. 

Just this one example shows the importance of hydrology in 

Lake Michigan and in nearby rivers to a single drinking-water 

system. 

Public water supplies that draw from groundwater also 

are influenced by hydrologic characteristics, such as groundwater traveltimes and direction, which in turn influence the 

potential delivery of contaminants from surface or underground sources to their wells. Private drinking-water wells 

are similarly susceptible to surface or underground hydrologic 

transport processes, but they are rarely assessed. Finally, 

drinking water drawn from rivers is particularly susceptible 

to the hydrologic features of those rivers and the distance and 

traveltime to the intake from contaminant sources such as 

wastewater treatment plants, industrial outfalls, or agricultural 

wastes. 

Biological Processes

The vast majority of drinking-water-related outbreaks 

of disease or illness are caused by biological agents (Craun 

and others, 2006). For the period 1991–2002, 16 percent of 

outbreaks were due to chemical poisoning. (During 1971–90, 

only 10 percent were due to chemical poisoning.) The rest 

were caused by a variety of bacteria or viruses, although the 

“unidentified” cause category was the largest in both reporting periods, causing 38–52 percent of illness outbreaks. It is 

widely assumed that the true incidence of waterborne disease 

is underreported (Craun and others, 2006; Reynolds and 

others, 2008); 19.5 million cases of waterborne disease per 

year nationwide have been estimated (Reynolds and others, 

2008). 

The most frequently identified agents between 1991 and 

2002 were Cryptosporidium and Giardia protozoa. Ingestion 

of only a small number of these organisms can cause infection. 

They can survive not only long periods in cold water but 

also many types of water treatment, and their presence is not 

specifically indicated by tests for fecal indicator bacteria (FIB) 

such as fecal coliform bacteria or Escherichia coli—the most 

commonly used indicators of microbiological pollution. Likewise, viruses have many of the same survival characteristics 

as protozoa, but methods to analyze water for them are so difficult and costly that their prevalence is likely underestimated. 

Viruses such as reoviruses, enteroviruses, and adenovirusues 

have been detected in wastewater-treatment-plant influent 

and effluent in Milwaukee, Wis. (Sedmak and others, 2005). 

Additionally, 18 of 204 Lake Michigan source water samples 

for the Milwaukee drinking-water plant tested positive for 

reoviruses. Pediatric emergency diarrheal illness increased 

after release of undertreated sewage in Milwaukee, Wis. 

(Redman and others, 2007), and in two of six cases where 

undertreated sewage was released, there was a statistically 

significant increase in the number of hospital visits by people 

living in Lake Michigan ZIP codes. Septic-system density is 

associated with household infectious diarrhea for children less 

than 19 years old in households on private well-water supply 

in Wisconsin, according to a study by Borchardt and others 

(2003). This study and an additional study of groundwater and 

river-water supplies in Wisconsin showed no relation between 

the detection of viruses and the numbers of FIB (Borchardt and 

others, 2003, 2004). These few studies demonstrate that much 

more needs to be learned about the actual pathogens causing 

waterborne disease in the Lake Michigan Basin. 

In addition, taste and odor problems are a challenge for 

drinking-water systems, especially those that use surface water. 

If the taste and odor problem is an earthy or fishy smell, it 

may be due to the growth of cyanobacteria (sometimes called 

blue-green algae) that release odor-causing compounds. Large 

growths of cyanobacteria may also release more problematic 

compounds—toxins that affect the nervous system or liver 

function—and such a growth may be referred to as a “harmful 

algal bloom” (HAB). A recent study (Graham and others, 

2010) showed that in samples collected from 23 Midwestern 

lakes, taste- and odor-producing compounds co-occurred with 

microcystin (a cyanotoxin) in 91 percent of algal blooms. It is 

clear that blooms of cyanobacteria do occur in the Great Lakes 

(http://www.glerl.noaa.gov/res/Centers/HABS/index.html; 

National Oceanic and Atmospheric Administration, no date), 

but little is known about their origins and distributions or 

about the toxins released (Dyble and others, 2008). The 

National Oceanic and Atmospheric Administration (NOAA) 

Great Lakes Environmental Research Center has developed 

an experimental HAB forecast bulletin for Lake Erie, where 

HABs have become problematic (http://www.glerl.noaa.gov/

res/Centers/HABS/lake_erie_hab/lake_erie_hab.html; National 

Oceanic and Atmospheric Administration, 2012). This forecast 

system relies on an understanding of the biological factors that 

influence cyanobacteria growth and the hydrologic factors that 

allow blooms to concentrate. A recent study by the EPA (2009) 

recorded low levels of microcystin, one of the most common 

toxins produced by cyanobacteria, in many inland lakes of the 

Lake Michigan Basin. Still, there is no standard for microcystin in drinking water or recreational water in the United States; 

the World Health Organization (1998) recommends a concentration less than 1 microgram per liter of microcystin-LR 

(a particular form of microcystin) in drinking water. 

What We Know from Monitoring Efforts

From existing monitoring programs there is much information about the range of contaminants affecting public water 

supplies and about specific contaminants for which health 

effects have previously been determined. Each public water 

utility has completed a Source Water Assessment that identified many of the major potential threats to that supply. Data are 

widely disseminated for required contaminant monitoring, and 

most water supplies provide very good water as measured by 

current standards and constituents. Little is known about contaminants in private water supplies, and little is known about 

chemicals of emerging concern (CECs). 
We Can All Drink the Water

15

Knowledge Gaps and Uncertainties

One key uncertainty is the lack of epidemiological or analytic data for most pathogens that may be found in most water 

supplies, public or private. Substantial information is available 

about the causes and sources of outbreaks of contaminants in 

drinking water that are sufficiently large to attract attention; 

however, it is widely understood that the human disease 

burden due to contaminated drinking water is underestimated 

or not captured by current monitoring or outbreak-related data. 

Little is known about the influence of HABs in Lake Michigan 

on public health, there are no standards for cyanobacterial 

toxins in drinking water, and there is no monitoring program 

for HABs or for their toxins. 

Very little is known about the geomorphic, hydrologic, or 

biological factors that influence the concentration, transport, 

and health risk of recently recognized contaminants. In some 

cases, these contaminants may derive from sources not considered in Source Water Assessments. For example, chloride 

concentrations have been increasing over the past several 

decades in groundwater and surface water in and around the 

Lake Michigan Basin (Mullaney and others, 2009) and in 

the Great Lakes themselves (http://www.epa.gov/greatlakes/

monitoring/limnology/index.html); the assumed sources for 

chloride are road salt from stormwater runoff, wastewater or 

septic-system contamination, or agricultural practices. All 

these sources contain numerous CECs, but there has been little 

study of whether the increase in chloride concentrations may 

signal an associated increase in CECs in Great Lakes drinkingwater supplies. There is little monitoring for recently recognized contaminants, and only a few focused studies addressing 

drinking water in the Lake Michigan Basin.

References

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2007, America’s North Coast—A benefit-cost analysis of 

a program to protect and restore the Great Lakes, accessed 

April 17, 2013, at http://www.healthylakes.org/site_upload/

upload/America_s_North_Coast_Report_07.pdf.

Borchardt, M.A., Haas, N.L., and Hunt, R. J., 2004, 

Vulnerability of drinking-water wells in La Crosse, 

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Microbiology, v. 70, p. 5937–5946.

Borchardt, M.A., Bertz, P.D., Spencer, S.K., and 

Battigelli, D.A., 2003, Incidence of enteric viruses in 

groundwater from household wells in Wisconsin: Applied 

and Environmental Microbiology, v. 69, p. 1172–1180.

Centers for Disease Control and Prevention, 2008, 

Surveillance summaries: Morbidity and Mortality Weekly 

Report, v. 57, no SS–9, 72 p., accessed June 22, 2012, at 

http://www.cdc.gov/mmwr/pdf/ss/ss5709.pdf.

Chowdhury, S.H., Kehew, A.E., and Passero, R.N., 2003, 

Correlation between nitrate contamination and ground water 

pollution potential: Ground Water, v. 41, p. 735–745.

Corso, P.S., Kramer, M.H., Blair, K.A., Addiss, D.G., 

Davis, J.P., and Haddix, A.C., 2003, Cost of illness in the 

1993 waterborne Cryptosporidium outbreak, Milwaukee, 

Wisconsin: Emerging Infectious Disease, v. 9, p. 426–431.

Craun, M.F., Craun, G.F., Calderon, R.L., and Beach, M.J., 

2006, Waterborne outbreaks reported in the United States: 

Journal of Water and Health, v. 4, supp. 2, p. 19–30.

Dyble, J., Bienfang, P., Dusek, E., Hitchcock, G., Holland, F., 

Laws, E., Lerczak, J., McGillicuddy, D.J., Jr., Minnet, P., 

Moore, S.K., O’Kelly, C., Solo-Gabriel, H., and Wang, J.D., 

2008, Environmental controls, oceanography, and population dynamics of pathogens and harmful algal blooms—

Connecting sources to human exposure: Environmental 

Health, v. 7, supp. 2, article S5, 13 p.

Graham, J.L., Loftin, K.A., Meyer, M.T., and Ziegler, A.C., 

2010, Cyanotoxin mixtures and taste-and-odor compounds in 

cyanobacterial blooms from the Midwestern United States: 

Environmental Science and Technology, v. 44, no. 19, p. 

7361–7368, http://dx.doi.org/doi:10.1021/es1008938.

Michigan Department of Community Health and Michigan 

Department of Environmental Quality, 2006, Arsenic in 

well water, health information for well users: Michigan 

Department of Environmental Quality, 2 p., accessed 

June 21, 2012, at http://www.michigan.gov/documents/

arsenicbroch_41426_7.pdf.

Mills, P.C., and Sharpe, J.B., 2010, Estimated withdrawals and 

other elements of water use in the Great Lakes Basin of the 

United States in 2005: U.S. Geological Survey Scientific 

Investigations Report 2010–5031, 95 p., available online at 

http://pubs.usgs.gov/sir/2010/5031/.

Mullaney, J.R., Lorenz, D.L., and Arntson, A.D., 2009, 

Chloride in groundwater and surface water in areas underlain by the glacial aquifer system, northern United States: 

U.S. Geological Survey Scientific Investigations Report 

2009–5086, 41 p., available online at http://pubs.usgs.gov/

sir/2009/5086/.

National Oceanic and Atmospheric Administration [n.d.], 

Harmful algal blooms data & products: Center of Excellence for Great Lakes Human Health, accessed June 21, 

2012, at http://www.glerl.noaa.gov/res/Centers/HABS/index.

html.

National Oceanic and Atmospheric Administration, 2012, 

Supplemental information on experimental Lake Erie 

Harmful Algal Bloom bulletin: Great Lakes Environmental 

Research Laboratory, Bulletin 0, 2 p., accessed 

June 21, 2012, at http://www.glerl.noaa.gov/res/Centers/

HABS/lake_erie_hab/bulletin_2012-000.pdf.
16 A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

Rao, Y.R., and Schwab, D.J., 2007, Transport and 

mixing between the coastal and offshore waters in the 

Great Lakes—A review: Journal of Great Lakes Research, 

v. 33, p. 202–218.

Redman, R., Nenn, C., Eastwood, D., and Gorelick, M., 2007, 

Pediatric emergency department visits for diarrheal illness 

increased after release of untreated sewage: Pediatrics, 

v. 120, no. 6, p. 1472–1475.

Reynolds, K.A., Mena, K.D., and Gerba, C.P., 2008, Risk of 

waterborne illness via drinking water in the United States: 

Reviews of Environmental Contamination and Toxicology, 

v. 192, p. 117–158.

Saad, D.A., 2008, Agriculture-related trends in groundwater 

quality of the glacial deposits aquifer, central Wisconsin: Journal of Environmental Quality, v. 37, supp. 5, 

p. 209–225. 

Sedmak, G., Bina, D., MacDonald, J., and Couillard, L., 2005, 

Nine-year study of the occurrence of culturable viruses in 

source water for two drinking water treatment plants and 

the influent and effluent of a wastewater treatment plant in 

Milwaukee, Wisconsin (August 1994 through July 2003): 

Applied and Environmental Microbiology, v. 71, no. 2, 

p. 1042–1050.

Snyder, S.A., Trenholm, R.A., Snyder, E.M., Bruce, G.M., 

Pleus, R.C., and Hemming, J.C.D., 2008, Toxicological 

relevance of EDCs and pharmaceuticals in drinking water: 

American Water Works Association Research Foundation, 

121 p. plus 10 appendixes, available online at http://

environmentalhealthcollaborative.org/images/91238_

Toxicological_Relevance.pdf.

University of Wisconsin Extension and U.S. Geological 

Survey, 2007, Groundwater contamination susceptibility 

map, in Protecting Wisconsin’s groundwater through 

comprehensive planning: U.S. Geological Survey, accessed 

June 21, 2012, at http://wi.water.usgs.gov/gwcomp/find/

door/susceptibility.html.

U.S. Environmental Protection Agency, 2012a, Safe Drinking 

Water Information System, accessed June 22, 2012, 

at http://water.epa.gov/scitech/datait/databases/drink/

sdwisfed/index.cfm#1.

U.S. Environmental Protection Agency, 2012b, Drinking water 

contaminants, accessed June 22, 2012, at http://water.epa.

gov/drink/contaminants/index.cfm.

U.S. Environmental Protection Agency, 2012c, Where 

you live—Your drinking water quality reports online: 

U.S. Environmental Protection Agency Consumer 

Confidence Reports, accessed June 22, 2012, at 

http://cfpub.epa.gov/safewater/ccr/.

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regulatory determinations home, accessed June 22, 2012, at 

http://water.epa.gov/scitech/drinkingwater/dws/ccl/index.

cfm.

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Assessments, accessed June 22, 2012, at http://water.epa.

gov/infrastructure/drinkingwater/sourcewater/protection/

sourcewaterassessments.cfm.

U.S. Environmental Protection Agency, 2009 National Lakes 

Assessment—A collaborative survey of the Nation’s lakes: 

EPA 841–R–09–001, accessed July 3, 2012, at http://www.

epa.gov/owow/LAKES/lakessurvey/pdf/nla_report_low_res.

pdf.

U.S. Geological Survey and Michigan Department of 

Environmental Quality, 2003, Final draft of Source Water 

Assessment report for the City of South Haven water 

supply: Michigan Department of Environmental Quality, 

Water Division, Assessment Report 48, 18 p., accessed 

June 21, 2012, at http://www.south-haven.com/pages/

public_works/pdf/Source-Water-Assessment-Report.pdf.

Wisconsin Department of Natural Resources, 2003, Source 

Water Assessment for Sheboygan water utility: Wisconsin 

Department of Natural Resources, 19 p., accessed 

June 21, 2012, at http://dnr.wi.gov/org/water/dwg/swap/

surface/sheboygan.pdf.

Wisconsin Department of Natural Resources [n.d.], Arsenic in 

drinking water & groundwater, accessed June 21, 2012, at 

http://dnr.wi.gov/org/water/dwg/arsenic/.

World Health Organization, 1998, Cyanobacterial toxins—

Microcystin-LR in drinking-water: Originally published in 

Guidelines for drinking-water quality (2d ed.), addendum 

to v. 2, Health criteria and other supporting information,

accessed July 3, 2012, at http://www.who.int/water_

sanitation_health/dwq/chemicals/cyanobactoxins.pdf.
Importance of Swimming in the Water to Lake Michigan Communities 17

Importance of Swimming in the Water to 

Lake Michigan Communities

Lake Michigan has abundant beaches available for 

recreation, and 442 of them were monitored for recreational 

water quality in 2010: 24 in Indiana, 50 in Illinois, 78 in 

Wisconsin, and 290 in Michigan (http://water.epa.gov/type/

oceb/beaches/seasons_2010_index.cfm#states). Although 

there has been no systematic assessment of the importance 

of swimmable beaches, some examples indicate that beaches 

contribute profoundly to the economies of the States bordering 

Lake Michigan, and to the economic and physical well-being 

of their residents. One report indicated that in 1996, visitors 

to Indiana’s counties bordering Lake Michigan spent over 

$523 million and that beach closures due to unsuitable water 

quality cost as much as $5 million per day in lost revenue 

(http://www.great-lakes.net/humanhealth/lake/michigan.html; 

Great Lakes Commission, 2003). Rabinovici and others (2004) 

estimated a net economic loss among potential swimmers 

of $1,272–$37,030 (depending on assumptions) for 1 day 

of closure at a Lake Michigan beach; these costs include the 

value of recreation and the cost of health effects. 

Beach Monitoring

The frequency of Great Lakes beach monitoring and 

the consistency of monitoring targets have improved since 

passage of the Beaches Environmental Assessment and 

Coastal Health (BEACH) Act of 2000, which authorized the 

U.S. Environmental Protection Agency (EPA) to provide 

grants for monitoring and public notification to the marine 

and Great Lakes coastal States. In 2010, the EPA provided 

$960,000 in grants to the four States bordering Lake Michigan 

to implement beach monitoring and provide public notification. Currently, all States in the Great Lakes region, including 

those bordering Lake Michigan, monitor the majority of their 

priority beaches for the presence of Escherichia coli (E. coli), 

a fecal indicator bacterium (FIB) whose presence in water 

has traditionally been assumed to indicate fecal pollution and, 

hence, the potential for detrimental human and animal health 

effects due to actual pathogenic bacteria, viruses, or protozoa. 

Only beach water—not beach sand—is tested. Beach monitoring results are typically made public through Web pages such 

as http://www.deq.state.mi.us/beach/ for Michigan (Michigan 

Department of Environmental Quality, 2010). Each State 

also summarizes its yearly results for the EPA, and all reports 

are posted at the EPA Web site at http://water.epa.gov/type/

oceb/beaches/seasons_2010_index.cfm (U.S. Environmental 

Protection Agency, 2010a). In addition, the Natural 

Resources Defense Council (2011) publishes a yearly 

report that summarizes the State-provided data in different 

formats at http://www.nrdc.org/water/oceans/ttw/titinx.asp. 

Through initial funding from the EPA Great Lakes National 

Program Office (http://www.epa.gov/greatlakes/about.html; 

U.S. Environmental Protection Agency, 2012a) and subsequent 

funding from the Great Lakes Restoration Initiative (http://

www.epa.gov/greatlakes/index.html; U.S. Environmental 

Protection Agency, 2012b), beach managers have been encouraged to conduct sanitary surveys of their beaches as part 

of their monitoring efforts. In addition, the Alliance for the 

Great Lakes conducts a beach sanitary survey program, staffed 

by volunteers (Alliance for the Great Lakes, 2012), that has 

posted data from 2002 to the current date online at http://www.

greatlakes.org/adoptabeach. 

We Can All Swim in the Water

Kites Over Lake Michigan, Lester Public Library 
18

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

Identifying Key Processes and Uncertainties

Current monitoring programs for beaches are focused on 

periodic measurements of E. coli bacteria in beach water and are 

driven by regulatory mandates. Monitoring is typically carried 

out by various government health or recreation departments. 

Consensus is building that multiple complex processes, including those outlined below, need to be measured and understood 

before true protection of public health at beaches can be 

achieved (Dyble and others, 2008; Grant and Sanders, 2011; 

Zhu and others, 2011). Typical monitoring agencies do not have 

the scientific expertise, resources, or authority to investigate the 

geomorphic, hydrologic, or biological processes at the coastal/

nearshore scale, which likely influence beach microbiological 

water quality and, hence, this Lakewide Management Plan 

(LaMP) goal. Although there has been much leadership within 

the Great Lakes research community on beach issues—particularly with regard to E. coli dynamics and the development of 

models that can predict when E. coli concentrations exceed standards—research on geomorphic and hydrologic processes lags 

quite far behind similar research for marine coastlines. We used 

the framework to outline the relevant processes; the following 

discussions are drawn from the example table, appendix 3.

Geomorphic Processes

Beach geomorphology includes the shape and dynamics 

of such features as dunes, interdunal areas, the swash zone, the 

shallow water table, and sediment transport along beaches—

in other words, the factors that make a shoreline into a beach. 

Beaches take many forms in the Great Lakes, from flat and 

damp to high sand dunes with dry sands. The natural history of 

sand and gravel beaches and the types of beaches most likely to 

be used extensively by the public in Lake Michigan are profiled 

by the Michigan Natural Resources Inventory at http://mnfi.

anr.msu.edu/communities/index.cfm (Michigan State University 

Extension, no date). 

An extensive review of beach or coastal geomorphology 

is beyond the scope of this document. In any case, beach 

geomorphology has rarely been discussed with regard to the 

microbiology of beach water. Shoreline conditions throughout 

the Great Lakes are highly modified; for example, the south 

shore of Lake Erie is “severely sand-starved” compared to early 

settlement conditions, and almost 83 percent of that shoreline is 

hardened and protected from natural processes (Morang and 

others, 2011). Artificial embayments or structures that prohibit 

the natural flow of water along the shoreline may lead to concentration or focused deposition of bacteria-laden sediments 

(Ge and others, 2010). In municipal areas, it is not uncommon 

for sands to be brought to beaches and for a beach to be 

groomed, which changes the slope and type of beach materials. 

Beach-grooming methods affected E. coli concentrations at a 

Lake Michigan beach in Racine, Wis. (Kinzelman and others, 

2004), and a relation exists between natural and degraded beach 

conditions and E. coli concentrations in shallow groundwater 

below those beaches (Crowe and Milne, 2007). 

Hydrologic Processes

Hydrologic processes that influence beaches include 

those that affect nearshore sediments and sand, such as flow 

and sediment transport from river watersheds, creeks, and 

storm drains near or on the beach; runoff from the beach 

catchment (the area that contributes water directly to the beach 

during rainfall events); nearshore groundwater; longshore 

currents; interaction between nearshore and large lake currents; and waves. Hydrologic interactions between the open 

Great Lakes, the coastal boundary area, and the surf and swash 

zones were reviewed by Rao and Schwab (2007), who pointed 

out that we are “...still a long way from having predictive 

understanding of the dynamics of sediment, contaminant, and 

pathogen transport near beaches.” A “beach boundary layer 

model” has recently been defined (Grant and Sanders, 2011) 

that incorporates contributions of FIB from bird droppings, 

shedding of FIB by bathers, dry sources, and wet-weather 

runoff from the shoreline, shallow groundwater, beach sediments, nearshore waters, and marine embayments. The model 

includes growth, entrapment, and resuspension of FIB in 

marine sediments and sands. A similar model was defined for a 

Florida beach (Zhu and others, 2011), and the role of coupled 

physical-biological models in addressing human health risk 

at marine beaches has been described by Dyble and others 

(2008). In Lake Michigan, circulation patterns in an embayed 

beach led to entrainment of FIB and subsequent influence on 

beach water quality in the knee-deep and swash zones (Ge and 

others, 2010). Models developed for predicting when E. coli

may exceed water quality standards (Environmental Protection 

Agency, 2010b; Ohio Nowcast, at http://www.ohionowcast.

info/index.asp) have successfully demonstrated that largescale factors such as wind direction, wave height, and rainfall 

can be used to predict when E. coli concentrations will likely 

be high. Studies of beaches near large rivermouths have shown 

that rivers influence those beaches under specific weather conditions so that the river plume is directed to the beach (Nevers 

and others, 2008). All of these complex hydrologic factors 

may be operational at a given beach on a given day; however, 

the significance of each factor may vary from day to day. 

Nevertheless, there is no systematic effort to study, describe, 

and model the complex hydrologic and biological interactions 

that influence FIB and pathogens at Great Lakes beaches. 

Biological Processes

The biological processes that influence beach water 

quality are generally associated with the presence of bacteria, 

viruses, and other pathogens in beach water and sand. Beach 

water quality is determined by the abundance of FIB, typically 

E. coli. An analysis for E. coli takes 24 hours to complete and, 

therefore, the test results refer to the quality of yesterday’s 

water—a major limitation to protecting today’s swimmers 

from health hazards. Additionally, the monitoring programs 

of the States that surround Lake Michigan vary substantially in the frequency with which beaches are monitored; 
Importance of Swimming in the Water to Lake Michigan Communities

19

the monitoring program design may include the number of 

samples per beach, the timing of samples, and the depth at 

which samples are collected, and all influence E. coli concentrations and the policy choices regarding how and when 

to issue advisories or closures (Government Accountability 

Office, 2007; Nevers and Whitman, 2010). Even if the closure 

policy for a Lake Michigan beach could be implemented daily 

and without error, only about 42 percent of predicted illnesses 

would be avoided (Rabinovici and others, 2004). Possible 

reasons may include a lack of association between FIB and 

pathogens, spatial variability of FIB and pathogens that are 

not often accounted for, sources or pathogens other than water 

such as beach sand. Studies indicate that people swimming at 

Lake Michigan beaches influenced by human-sewage pollution contract gastrointestinal illnesses (Wade and others, 

2006, 2008) and that the illness rate is related to enterococci 

concentrations, as measured by quantitative polymerase chain 

reaction (qPCR). Human viruses have been reported at some 

Lake Michigan beaches influenced by human-sewage pollution (Wong and others, 2009), and human viruses have been 

implicated as the disease agents in Lake Michigan epidemiologic studies (Soller and others, 2010). Finally, one study 

has shown that playing in beach sand at two Lake Michigan 

beaches was associated with gastrointestinal illness (Heaney 

and others, 2009), although beach sand is not monitored 

for microbiological quality (Halliday and Gast, 2011). At 

locations not influenced by an identifiable source of human 

sewage (nonpoint-source contamination), the likelihood of 

contracting illness and the relation of illness rates to FIB 

remains unknown (U.S. Environmental Protection Agency, 

2009; Schoen and Ashbolt, 2010). Much recent research indicates that E. coli and other FIB, such as enterococci, may grow 

or persist in the environment or may be associated with nonfecal sources (Byappanahalli and others, 2003; Ishii and others, 

2010) and, therefore, do not indicate fecal pollution when the 

bacteria sources are not fecal. On the other hand, FIB from 

wildlife may indicate significant potential for human illness 

(U.S. Environmental Protection Agency, 2009). Pathogens 

may also persist, or grow, in the environment, and many may 

have different survival characteristics than FIB (Dyble and 

others, 2008). Unfortunately, the sources of E. coli or other 

FIB, and certainly of pathogens, are rarely known. Among the 

four States bordering Lake Michigan, 85 percent of Wisconsin 

beaches reported unknown sources of E. coli, and Michigan, 

Indiana, and Illinois did not report any sources for 2010 

(http://water.epa.gov/type/oceb/beaches/seasons_2010_index.

cfm#states). Nationally, the National Resources Defense 

Council reported that between 2000 and 2010, over half the 

beach closure or advisory days were due to unknown sources 

of E. coli bacteria (National Resources Defense Council, 

2011). The sources of the E. coli likely are unknown because 

current beach monitoring programs and sanitary surveys cannot capture the complex physical dynamics that bring source 

materials to the beach. 

What We Know From Monitoring Efforts

The enhanced monitoring of Great Lakes beaches for 

E. coli bacteria that followed the BEACH Act of 2000, 

plus the implementation of sanitary surveys through EPA 

and GLRI funding, has improved our understanding of the 

locations and beach conditions where E. coli concentrations 

are frequently or persistently high. The enhanced monitoring 

has allowed sufficient collection of data to permit predictive 

models of when E. coli may exceed safe swimming standards 

to be developed for some beaches. Sanitary surveys have 

improved local beach managers’ understanding of the factors 

that influence water quality at their beaches. In one case in 

Racine, Wis., better beach management—including modification of storm-drain outflows, planting of native beach 

vegetation, and altered beach grooming practices—has led to 

effective remediation of the causes of E. coli concentrations 

that exceed standards (http://www.glslcities.org/best-practices/

beaches/racine-beaches.cfm; Great Lakes and St. Lawrence 

Cities Initiative, 2003). Unfortunately, most monitoring 

programs are not using enhanced methods, and monitoring 

programs largely do not focus on the sources of contamination. Most routine monitoring programs are not designed to 

address the geomorphic, hydrologic, or biological processes 

that underpin and influence health risk at Great Lakes beaches. 

Knowledge Gaps and Uncertainties

One key uncertainty is the lack of epidemiological 

data for beaches (other than the select few that were chosen 

for their proximity to human-sewage influence) and a corresponding lack of actual pathogen data (except for a few 

limited studies). A second key uncertainty is fundamental 

knowledge on the primary sources of, and the processes that 

deliver, FIB and pathogens to Great Lakes beaches. Finally, 

as noted above, FIB are imperfect indicators of risk under all 

recreational-water situations. Although most beach managers 

and scientists could list an array of probable sources of FIB 

and pathogens for beaches, the degree to which any particular 

source plays a role at various types of beaches around the 

Great Lakes is unknown. Likewise, the geomorphic, hydrologic, and biological processes that deliver those FIB or 

pathogens to beaches remain poorly investigated. As a stark 

example, very few rivers in the Great Lakes are tested routinely, even for FIB; and if they were, very few river plumes 

and associated nearshore hydrodynamics have been successfully modeled in the Great Lakes (Rao and Schwab, 2007; 

Thupaki and others, 2013). Additionally, beach sands are an 

important contaminant source for beach water, and they have 

immediate health risks to beachgoers—but beach sands are 

rarely tested. 
20

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

References

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accessed June 22, 2012, at http://www.greatlakes.org/

adoptabeach.

Byappanahalli, M.N., Whitman, R.L., Shively, D.A., 

Ting, W.T., Tseng, C.C., and Nevers, M.B., 2003, 

Seasonal persistence and population characteristics of 

Escherichia coli and enterococci in deep backshore sand of 

two freshwater beaches: Journal of Water and Health, v. 4, 

no. 3, p. 313–320.

Crowe, A.S., and Milne, J.E., 2007, Relationship between 

natural and degraded beach ecosystems and E. coli 

levels in groundwater below beaches of the Great Lakes, 

Canada, in Selected papers in hydrogeology—International 

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22

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

Sleeping Bear Dunes, Michigan Sea Grant

All Habitats Are Healthy, Naturally Diverse, 

and Sufficient to Sustain Viable Biological Communities

Importance of Healthy Habitats

Diverse habitat mosaics are found across the Great Lakes, 

and when healthy and well connected, these support diverse 

and productive biota. Healthy habitats provide suitable— 

and sometimes preferred—physiological conditions for the 

survival, growth, and reproduction of plants and animals. 

Habitats are composed of linked physical and chemical 

(dynamic) and structural (stationary) components (Peterson, 

2003) that are created and sustained by both regional and local 

processes within a particular environmental setting or place. 

Habitats become limiting or impaired when their components 

become altered or the spatial connections among them become 

uncoupled in a way that reduces populations or causes local 

extinction (Schlosser, 1995; Schindler and Scheuerell, 2002). 

On a landscape scale or across neighboring habitats, impairments can result in system-level changes that increase the 

amount of (sink habitat (suboptimal, but accessible, habitat ) 

relative to the amount of (source habitat (habitat that is optimal for reproduction or growth). Thus, population productivity 

is reduced if source habitat becomes limiting (Dunning and 

others, 1992). 

Habitats and Their Structure

Here we use habitat in the sense of “place,” delineated 

by patterns in physical processes and physical and vegetative 

characteristics. Combinations of variable hydrologic and 

geomorphic processes result in physical and chemical characteristics with distinct features that set the stage for biological 

habitat components (Hayes and others, 1996). Habitats are 

often usefully described as a nested series of spatial units 

(Frissell and others, 1986). Overarching processes such as 

climate, geologic history, and large-scale lake currents affect 

landscape composition. Large or macro-scale processes 

include distinct localized processes and physical and chemical 

features, such as localized climates, river or lake currents, 

or geomorphic landforms. Macro-scale processes give rise 

to predictable intermediate or meso-scale patterns in habitat 

complexity, patchiness, and diversity, such as pools and 

riffles in streams (see Peterson, 2003, and references therein). 

Thus, understanding ecosystem habitat health and restoration 

requires considering the processes that determine habitat 

quantity and quality across different habitat scales. 
All Habitats Are Healthy, Naturally Diverse, and Sufficient to Sustain Viable Biological Communities

23

Great Lakes management programs have commonly 

emphasized aquatic habitats that are consistently or seasonally 

submersed. In this paper, for Lake Michigan, we have categorized aquatic habitats according to three ecosystem 

zones: (1) open lake, (2) coastal/nearshore, and (3) watershed 

(including tributaries). For Lakes Huron, Erie, and Ontario, 

we would also include a category of great connecting rivers. 

We explicitly include riparian terrestrial habitats within 

our coastal/nearshore and watershed zones, recognizing 

their dependence on and influence on neighboring aquatic 

habitats and importance to Lake Michigan ecosystem health. 

Connectivity among these zones contributes to ecosystem 

habitat diversity and function.

Habitat Trends

Noss and others (1995) considered the Great Lakes States 

among the 21 most endangered ecosystems in the United 

States. Lake Michigan has 10 Areas of Concern (AOCs) that 

have multiple impairments of beneficial use (Great Lakes 

Water Quality Agreement). The Great Lakes Restoration 

Initiative (GLRI) began in 2010 and is considered “the largest investment in the Great Lakes in two decades” (http://

greatlakesrestoration.us; Great Lakes Restoration Initiative, 2010). Urgent issues identified in the GLRI Action Plan 

include (1) habitat restoration focusing on toxic substances 

and areas of concern and (2) habitat and wildlife protection 

and restoration. The GLRI brought an increased focus to 

Great Lakes habitat issues and restoration needs; of specific 

importance is the coastal/nearshore zone, where much of the 

Great Lakes human population lives and works. 

Habitat trends in the coastal/nearshore zone may have 

great influence on habitat in the other zones. Mackey (2009) 

stated “the single most important anthropogenic factor 

disrupting coastal/nearshore processes and pathways is 

increasing shoreline development and the physical alteration 

of the land-water interface.” Cloern (2001) highlighted accelerated worldwide concerns about coastal eutrophication—the 

process of human mobilization of nutrients and other materials 

that are ultimately delivered to nearshore waters—resulting in 

excessive growth of aquatic plants and depletion of dissolved 

oxygen. Concerns about coastal eutrophication are fully applicable in the Great Lakes, as evidenced by current nuisance 

algal blooms. The Great Lakes currently are at a historic juncture for coastal management because earlier manufacturingbased coastal economies have become depressed in response 

to industrial life cycles and the national economy; thus, the 

region is potentially looking at a future period of redesigning, 

retrofitting, and redeveloping Lake Michigan’s coasts. Many 

watersheds may face similar developmental histories and 

future trajectories that will create opportunities to consider 

ecosystem health as it relates to changes in hydrologic and 

sediment regimes, nonpoint-source loadings, and future human 

uses of the region’s resources.

Identifying Key Processes and Uncertainty

Habitats arise from interactions between geomorphic, 

hydrologic, and biological processes. Thus, habitat restoration 

efforts for Lake Michigan should consider (1) how these 

processes structure or define habitat suitability, (2) how human 

activities influence these processes, and (3) how to devise and 

implement effective restoration activities that restore natural 

processes to provide healthy and diverse habitats. We used 

the framework to outline the relevant processes; the following 

discussions are drawn from the example table, appendix 4.

Geomorphic Processes

Glacial processes initially shaped lake depth and the 

form and texture of lake-bottom ridges, troughs, and plains. 

Such glacially sculpted patterns drive macro-scale processes 

affecting habitat character; for example, glacial ridges within 

the open-lake zone that provide shallow spawning reefs for 

native fish such as lake trout. Dynamic sediment-transport 

processes within the open-lake zone can influence localized 

bottom-sediment texture and sediment-exchange rates between 

coastal/nearshore and open-lake zones that may become 

increasingly important under high nearshore erosion conditions. Within the coastal/nearshore zone, glacial processes 

formed coastline shapes and textures that influence wave 

energy, sediment deposition and retention, and habitat suitability for aquatic biota. Glacial processes also resulted in 

coastline dunes and swamps that determine the composition 

and distribution of land-dwelling animals and plants. Glacial 

processes likewise shaped watersheds by influencing river 

catchment sizes, topography, sediment types, and valley 

structure. These effects carry over to determine valleyspecific shape and sediment dynamics that influence erosion, 

transport, and deposition of sediments and nutrients and the 

accumulation of woody debris. Variability in land form and 

texture among and with tributary watersheds creates diverse 

aquatic habitat availability at the landscape scale; for example, 

Lake Michigan tributaries range from (summer) slow-moving, 

warm streams with sand and silt bottoms to swift-flowing, 

cold streams with gravel and cobble bottoms. Further habitat 

variability is seen within individual river channels, in terms 

of proportions of riffle (shallow, swift, and turbulent water 

over rocks), pool (deep and slow water), and run (mid-depth, 

smooth-flowing water) habitats found.

Anthropogenic modifications to the natural glacial 

shaping of the lake alter sediment dynamics such as loading, 

erosion, transport, and deposition across all zones. Human 

modifications to coastline shape, such as piers and breakwalls, 

can change shoreline currents and alter water- and sedimentexchange rates between rivermouths and open-water zones. 

Breakwalls that reduce water-exchange rates can result in 

effectively isolated eddies with high risk for bacterial concentration and toxic algal blooms. Furthermore, shoreline 
24

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems

development that results in loss of coastal wetlands or naturalized shore areas reduces habitat suitability and diversity to 

wildlife species including juvenile fishes that find refuge in 

the coastal/nearshore zone and migratory birds that utilize 

midwestern flyways. 

Hydrologic Processes

Hydrologic processes influence habitat quality and diversity by determining flow sources of water to habitats, patterns 

of seasonal variations in water flow, and physical/chemical 

properties of water such as nutrient concentrations or water 

temperature. Large-scale currents and seasonal mixing of 

layers of lake water with different temperatures (stratification) 

influence nutrient availability for open-lake production, as 

well as water clarity and temperature regimes that are important to food availability. In winter, ice influences water stratification, and thermal and hydraulic refuges, and these effects 

carry over to spring production dynamics. Thermal habitat partitioning has been observed for open-lake fish species (Brandt, 

1980) and, thus, these hydrologic dynamics are important to 

open-lake habitat structure. Coastal/nearshore zone habitats 

can be especially dynamic because of storm surges, seiches, 

and upwellings that determine the stability of these habitats as well as nutrient delivery to plants for photosynthesis 

(Mortimer, 2004). This zone also encompasses lower energy 

habitats such as drowned lakes, wetlands, and bays. Hydrologic processes within the coastal/nearshore zone are complex because exchanges occur between open-lake waters and 

watersheds. Tributary habitats are driven by instream flows, 

suspended sediments, nutrients, and temperature conditions, 

along with anthropogenic influences on watersheds and stream 

channels. These characteristics are highly variable across Lake 

Michigan tributary watersheds. Groundwater contributions 

are very important to Lake Michigan tributaries, accounting 

for 51–81 percent of annual streamflow to the lake (highest 

contribution among the Great Lakes; Grannemann and others, 

2000; Neff and others 2005). Groundwater springs and seeps 

create localized thermal and water-quality refuges within 

streams across the basin, as well as within nearshore waters 

(Grannemann and others, 2000; Haack and others, 2005). 

Anthropogenic alterations to hydrologic processes can set 

off a chain of effects that result in debilitation of habitat quality. Air pollutants from inland sources can cause increases in 

airborne contaminant deposition to the lake and alter climates, 

thus changing seasonal thermal dynamics and ice conditions, 

which can result in spatial changes to species distributions 

or population reductions. Shoreline development alters the 

water exchange rate between the three ecosystem zones by 

re-directing wave energy and disconnecting coastal wetlands. 

Modifying landscape hydrology results in increased surface 

water runoff. Modifications at point locations within watersheds, such as water withdrawals and reservoir construction, 

alter flow rates and water temperatures, which can influence 

migratory fish movements and spawning and rearing habitat 

quality.

Biological Processes

Biological and biogeochemical processes are important 

to habitat quality and diversity and to provision of food 

resources, hydraulic refugia, and predator refugia. Within the 

open-lake and coastal/nearshore zones, one key biological process is the accumulation and dispersal of woody debris, which 

settles to the bottom and thus provides important structural 

habitat and complexity (Maser and Sedell, 1994; Elosegi and 

Johnson, 2003). Within the coastal/nearshore zone, submerged 

and emergent vegetation provide some species with refuge 

from predators and support periphyton growth and localized 

food production. Macro-scale habitats within the coastal/

nearshore zone can be quite variable in primary production 

because of localized temperature dynamics and nutrient 

loadings and, thus, provide differential quality habitat. Höök 

and others (2001) describe how macro-scale dynamics can 

structure habitat patchiness by highlighting that aquatic plants 

reduce the impacts of wave energy and alter local temperatures 

by reducing water circulation. Within these habitats, biogeochemical processes that drive nutrient and carbon cycling are 

important for biological growth and healthy diverse habitats.

Healthy and diverse habitats within the coastal/nearshore 

zone include riparian beaches, connecting wetlands, and the 

belt of shoreline development that influences habitat quality 

for terrestrial vegetation and wildlife. Important factors 

include seed banks and pollination dynamics for plants, 

structural cover for wildlife, and spatial distribution of habitat 

patches for aerial migrants. Terrestrial habitats in the coastal/

nearshore zone also interact with aquatic zones, and this 

interaction has implications for fish, wildlife, and humans. 

For example, foreshore sand can act as an Escherichia coli

source to Lake Michigan (Whitman and Nevers, 2003). 

Dynamic biological habitat drivers within the watershed 

include interactions with riparian flood-plain ecosystems and 

river-channel habitats; riparian complexity, such as the amount 

and quality of shading/canopy cover; and the accumulation 

of woody debris. Predation risk within the coastal/nearshore 

and watershed zones is influenced by influxes of nearshore 

spawning and anadromous fishes during spawning seasons, 

and by migratory bird populations. Connectivity among zones 

is critical to migrating fishes such as lake sturgeon (Smith 

and King, 2005) and for delivery of nutrients from watershed 

sources to open-lake habitats.

Anthropogenic effects modify biological processes 

influencing habitat quality; for example, human activities have 

modified the dynamics and distribution of woody debris in 

multiple ways. Today we see less large wood in river, rivermouth, and nearshore/beach habitats, because early 1900s 

logging removed the majority of older, larger trees and abundant dams captured most remaining wood that would naturally 

progress downriver to the lakes. And we are challenged by 

the large, underwater accumulations of polluting sawdust 

and debris that were deposited in rivermouths and bays by 

historical sawmills and other wood-processing operations. The 

introduction of quagga mussels has resulted in restructuring of 
All Habitats Are Healthy, Naturally Diverse, and Sufficient to Sustain Viable Biological Communities

25

the open-lake bottom by converting historically soft-sediment 

areas to a hardened bottom. Quagga and zebra mussels have 

influenced nearshore habitat by increasing water clarity and 

allowing the proliferation of Cladophora spp., a kind of green 

algae, at increasing depths. Nutrient additions within the 

nearshore zone have resulted in localized high algal concentrations that shade aquatic plants, and dredging has increased 

coastline slope, reducing suitable substrates for aquatic vegetation colonization. Within the watershed, modified riparian 

zones influence erosion rates and, thus, can cause siltation in 

historically suitable spawning substrates. Riparian alteration 

also influences shading from vegetation; thus, water temperatures may exceed lethal tolerances for some native fishes or 

could increase production capacity for warmer water fishes. 

What We Know from Monitoring Efforts

Habitat monitoring is conducted as part of small-scale 

studies, including focused work within AOCs and also through 

basinwide assessment efforts. Small, localized studies typically fall in one or two cells within the framework matrix 

(appendix 4), and findings have not been synthesized more 

broadly. Some ongoing, basin-scale initiatives include the following studies. 

1. The EPA State of the Lakes Ecosystem Conference 

(SOLEC) Indicators (http://www.epa.gov/solec/; 

U.S. Environmental Protection Agency, 2012), which do 

cover most geographic, disciplinary, and process aspects 

of our framework to some level and have been tracked for 

many years. 

2. The Environmental Indicators of the U.S. Great Lakes 

Coastal Region (Niemi and others, 2006). 

3. The Great Lakes Coastal Wetlands Monitoring Plan 

(Burton and others, 2008), which links coastal biological 

and hydrologic (water-quality) metrics to watershed and 

coastal landscape conditions. 

4. The USGS Great Lakes Coastal GAP Analysis (Morrison 

and others, 2005).

5. Other ongoing lake regionalization efforts (E. Rutherford, 

National Oceanic and Atmospheric AdministrationGLERL, Ann Arbor, Mich., personal commun., 2008) 

that are building fish habitat mapping and classification 

tools to aid coordination and interpretation of basin-level 

monitoring efforts (http://ifrgis.snre.umich.edu/projects/

GLGIS/index.htm). 

Therefore, habitat monitoring has provided snapshots of 

habitat condition in many of the zone-discipline cells of the 

ecosystems framework, sometimes across larger scales and 

sometimes consistently monitored through time. Collectively, 

we have our finger on the pulse of many habitat conditions 

across much of the Lake Michigan watershed. The impaired 

conditions of habitats across the basin have been cataloged, 

and the stressors within watershed and coastal zones have 

been mapped (Niemi and others, 2006; Wehrly and others, 

2010; Esselman and others, 2011; Allan and others, 2013).

Knowledge Gaps

Despite all of the substantial collective effort to monitor 

habitats for Lake Michigan, we still lack information for 

some key zone-discipline cells within the framework, and 

we have only begun to examine the underlying processes, 

within and across the zone-discipline elements, to provide 

a true ecosystems-based understanding of aquatic habitats 

of Lake Michigan. We have especially not recognized nor 

focused on the process linkages between the discipline cells 

for geographic zones (table 1); highlighting the interzone and 

interdisciplinary linkages will advance our understanding of 

habitats within a systems context. For the most part, these 

efforts are distinct and not cross-walked, and so “what we 

know” is difficult to compile.

The binational State of the (Great) Lakes Ecosystem 

Conference (SOLEC) indicators framework is designed to 

broadly cover many habitat aspects. As an example use of 

our framework, a careful overlay of SOLEC indicators on 

the ecosystems framework would prove useful to identify 

potential coverage and linkage gaps. 

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Michigan: Transactions of the American Fisheries Society, 

v. 134, p. 1159–1172.

University of Michigan, 2009, Great Lakes Environmental 

Assessment and Mapping Project: accessed June 22, 2012, 

at http://www.snre.umich.edu/greatlakesthreats/.

U.S. Environmental Protection Agency, 2012, State of the 

Lakes Ecosystem Conference (SOLEC), accessed June 22, 

2012, at http://www.epa.gov/solec/.

Whitman, R.L., and Nevers, M.B., 2003, Foreshore sand as 

a source of Escherichia coli in nearshore water of a Lake 

Michigan beach: Applied and Environmental Microbiology, 

v. 69, no. 9, p. 5555–5562.
Appendixes 1–4
28

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems Appendix 1. Processes and components that impact the Great Lakes Lakewide Management Plan goal: We Can All Eat the Fish.—Continued Disciplinary subsystem Geographic zone Open lake Coastal/nearshore Watershed Geomorphic (Retention of contaminants) Substrate adherence and leaching from substrate. Substrate adherence and leaching from substrate. Watershed soils. Sediment composition and interstitial spacing that drives bioavailability via contaminant burial or resuspension. Topography and hydraulics of lowest river-valley segment, embayment, and coastline influencing contaminant retention and exchange with open lake. Watershed area and slope. Coastal sediment dynamics driving erosion, transport, and deposition of contaminants within coastal/nearshore habitats. Substrate adherence and leaching from substrate. Geomorphic anthropogenic Siting of offshore spoil areas for contaminated dredging materials. Piers and breakwalls modifying shoreline processes, and lake influence and contaminant exchange with rivermouths and embayments. Channelization that modifies contaminant deposition versus dispersal to coastal/nearshore and offshore zones. Security of confined disposal areas to prevent reloading. Artificial reservoirs that store, transform, and potentially release contaminants and influence water-temperature regimes and other water-quality properties of tributaries. Hydrologic (Loading and transport of contaminants) Seasonal lake mixing that drives contaminant resuspension from sediments. Seasonal lake mixing that drives contaminant resuspension from sediments. Tributary flow regime driving instream dispersal and transport of chemicals and pathogens. Large-scale currents that drive contaminant and pathogen dispersion and deposition. Large-scale currents, upwellings, and storm-induced surges that drive contaminant and pathogen dispersion and deposition. Groundwater flows that contribute dissolved contaminants to tributaries. Persistence within the system due to physical and 

chemical properties determining contaminant half-lives.

Persistence within the system due to physical and 

chemical properties determining contaminant half-lives.

Surface runoff that may deliver or disturb sediments. 

Groundwater flow and delivery of contaminants and 

pathogens.

Hydrologic 

anthropogenic

Air- and precipitation-borne contaminants 

and chemicals.

Point-source runoff from industrial land use; 

infrequent accidental loadings.

Point-source runoff from industrial land use; 

infrequent accidental loadings.

Seasonal and climatic nonpoint runoff from local 

urban and agricultural landscapes.

Seasonal and climatic nonpoint runoff from local 

urban and agricultural landscapes.

Biological 

(Causing illness 

or disease)

Presence, survival, and reproducibility of 

pathogens.

Presence, survival, and reproducibility of pathogens. Presence, survival, and reproducibility of pathogens.
Appendix 1

29

Appendix 1. Processes and components that impact the Great Lakes Lakewide Management Plan goal: We Can All Eat the Fish.—Continued

Disciplinary 

subsystem

Geographic zone

Open lake Coastal/nearshore Watershed

Biological 

(Transformation 

of chemical 

contaminants)

Fish life history, foraging ecology, and metabolism. Fish life history, foraging ecology, and metabolism. Fish life history, foraging ecology, and metabolism.Methylation of mercury by bacteria. Methylation of mercury by bacteria. Methylation of mercury by bacteria.Bioaccumulation of contaminants due to compound 

properties.

Bioaccumulation of contaminants due to compound 

properties.

Acute and chronic (lethal and sublethal) toxicity 

from water- and sediment-related contaminants.

Settling phytoplankton that carry adhered 

contaminants to benthic zone.

Acute and chronic (lethal and sublethal) toxicity 

from water- and sediment-related contaminants.

Biological

anthropogenic

Fishery practices determining targeted species 

and locations.

Fishery practices determining targeted species 

and locations. 

Fishery practices determining targeted species 

and locations.

Catalytic impacts of invasive species on 

bioaccumulation.

Catalytic impacts of invasive species on 

bioaccumulation.

Catalytic impacts of invasive species 

onbioaccumulation.
30

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems Appendix 2. Processes that impact the Great Lakes Lakewide Management Plan goal: We Can All Drink the Water.—Continued Disciplinary subsystem Geographic zone Open lake Coastal/nearshore Watershed Geomorphic (Retention of contaminants) Substrate: inorganic sources (arsenic, metals). Substrate adherence and leaching from substrate. Substrate adherence and leaching from substrate. Watershed substrate. Topography and hydraulics of lowest river-valley segment, embayment, and coastline influencing contaminant retention and exchange with open lake. Watershed area and slope. Coastal sediment dynamics driving erosion, transport, and deposition of contaminants within coastal/nearshore habitats. Groundwater hydrogeology. Sediment dynamics. Geomorphic anthropogenic Atmospheric contamination. Substrate adherence and leaching from substrate. Altered sediment dynamics. Channelization and artificial reservoirs that modify contaminant deposition versus dispersal to coastal/ nearshore and offshore zones Enhanced erosion Hydrologic (Loading and transport of contaminants) Seiche. Currents that drive contaminant dispersion and deposition. Tributary flow regime driving instream dispersal. Large-scale currents that drive contaminant dispersion and deposition. Persistence within the system due to physical and chemical properties determining contaminant half-lives. Groundwater flow paths.

Seasonal lake mixing that drives contaminant 

resuspension from sediments.

Seasonal lake mixing that drives contaminant resuspension from sediments. Overland flow, infiltration, and associated contaminant transport to surface-water and 

groundwater systems.

Hydrologic

anthropogenic

Air- and precipitation-borne contaminants and 

chemicals.

Modified coastal hydrology. Modified hydrology (drains, wetland removal, 

impervious surfaces).

Placement of water intakes. Water-well placement.Point-source runoff from industrial land use; infrequent accidental loadings. Point-source runoff from industrial land use; infrequent accidental loadings.Nonpoint runoff from local urban and agricultural 

landscapes.

Nonpoint runoff from local urban and agricultural 

landscapes.

Groundwater pumpage
Appendix 2

31

Appendix 2. Processes that impact the Great Lakes Lakewide Management Plan goal: We Can All Drink the Water.—Continued

Disciplinary 

subsystem

Geographic zone

Open lake Coastal/nearshore Watershed

Biological 

(Causing illness 

or disease)

Development cycle of cyanobacteria Development cycle of cyanobacteria. Development cycle of cyanobacteria.

Natural sources, such as birds and wildlife. Natural sources, such as birds and wildlife.Survival and naturalization of fecal indicator bacteria 

and pathogens.

Survival, refugia, and naturalization of fecal 

indicator bacteria and pathogens.

Differential transport and persistence of different 

microbes.

Differential transport and persistence of different 

microbes.

Biological

anthropogenic

Boat and ship waste dumping. Storm drains that deliver biological contaminants. Manure application and runoff into nearby waters.

Shoreline septic systems that deliver biological 

contaminants.

Failing or leaking municipal sanitary waste systems, 

combined-sewer overflows, and sanitary-sewer overflows.

Human bathing as a source of pathogens or fecal 

indicator bacteria, or bathing activities that result in release of bacteria into the system.

Wastewater-treatment-plant effluent discharges.

Biological 

(Transformation 

of chemical 

contaminants)

Oxidation and reduction of chemicals and 

compounds.

Oxidation and reduction of chemicals and 

compounds.

Chemical pollutant degradation. Chemical pollutant degradation.

Biological

anthropogenic

Storm drains and urban runoff that deliver 

contaminants.

Chemical use (fertilizers, road salt, pesticides, 

industrial chemicals, chemicals of emerging concern).
32

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems Appendix 3. Processes that impact the Great Lakes Lakewide Management Plan goal: We Can All Swim in the Water.—Continued Disciplinary subsystem Geographic zone Open lake Coastal/nearshore Watershed Geomorphic (Retention of contaminants) Topography and hydraulics of lowest river-valley segment, embayment, and coastline influencing contaminant retention and exchange with open lake. Watershed substrate. Substrate adherence and leaching from substrate. Watershed area and slope. Coastal sediment dynamics driving erosion, transport, and deposition of contaminants within coastal/nearshore habitats. Groundwater hydrogeology. Sediment dynamics. Geomorphic anthropogenic Substrate adherence and leaching from substrate. Altered sediment dynamics. Channelization and artificial reservoirs that modify contaminant deposition versus dispersal to coastal/ nearshore and offshore zones Enhanced erosion Hydrologic (Fate and transport of fecal indicator bacteria and pathogens)) Seiche. Currents that drive contaminant dispersion and deposition. Tributary flow regime driving instream dispersal. Large-scale currents that drive contaminant dispersion and deposition. Persistence within the system due to physical and chemical properties determining contaminant half-lives. Groundwater flow paths. Seasonal lake mixing that drives contaminant 

resuspension from sediments

Differential transport and persistence of different 

microbes.

Differential transport and persistence of different 

microbes.

Dispersion and physical processing. Overland flow, infiltration, and associated 

contaminant transport to surface and groundwater systems.

Lake-groundwater interaction.

Hydrologic 

anthropogenic

Modified coastal hydrology. Modified hydrology (drains, wetland removal, 

impervious surfaces).

Point-source runoff from industrial land use; 

infrequent accidental loadings.

Point-source runoff from industrial land use; 

infrequent accidental loadings.
Appendix 3

33

Appendix 3. Processes that impact the Great Lakes Lakewide Management Plan goal: We Can All Swim in the Water.—Continued

Disciplinary 

subsystem

Geographic zone

Open lake Coastal/nearshore Watershed

Hydrologic 

anthropogenic

(continued)

Nonpoint runoff from local urban and agricultural 

landscapes.

Nonpoint runoff from local urban and agricultural 

landscapes

Impervious surfaces in beach catchment. Contaminated nearshore groundwater.

Biological 

(Source and 

behavior of fecal 

indicator bacteria 

and pathogens)

Natural sources, such as birds and wildlife. Natural sources, such as birds and wildlife.Survival and naturalization of fecal indicator bacteria 

and pathogens.

Survival, refugia, and naturalization of fecal indicator bacteria and pathogens.

Cladophora growth and decay.

Biological 

anthropogenic

Boat and ship waste dumping Storm drains that deliver biological contaminants. Manure application and runoff into nearby waters.

Shoreline septic systems that deliver biological 

contaminants.

Failing or leaking municipal sanitary waste systems, 

combined-sewer overflows, and sanitary-sewer overflows.

Human bathing as a source of pathogens or fecal 

indicator bacteria, or bathing activities that result in release of bacteria into the system.

Wastewater-treatment-plant effluent discharges.
34

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems Appendix 4. Processes that impact the Great Lakes Lakewide Management Plan goal: All Habitats are Healthy, Naturally Diverse, and Sufficient To Sustain Viable Biological Communities.—Continued Disciplinary subsystem Geographic zone Open lake Coastal/nearshore Watershed Geomorphic (Structuring of spawning, rearing, and refuge habitats) Glacial processes that shaped lake depth, and form and texture of lake-bottom terrain (ridges, troughs, plains). Glacial processes that shaped topography and texture of lowest river-valley segment, delta, embayment, and coastline. Glacial processes that shaped watershed size, topography, sediments, and valley structure. Sediment erosion, transport, and deposition dynamics influencing texture of lake-bottom sediments. Coastal sediment dynamics influencing erosion, transport, and deposition of sediments within coastal/nearshore habitats. Watershed- and valley-specific sediment dynamics driving erosion, transport, and deposition of sediments within channel and flood plain. Tributary dynamics influencing erosion, transport, and deposition of sediments within coastal/nearshore habitats. Interaction among hydrologic regime, geomorphic (hydrogeomorphic), and wood-recruitment processes that create patterns in mesohabitats (pools, riffles, runs). Topography and hydraulics of lowest river-valley segment, embayment, and coastline influencing sediment retention and exchange with open lake. Geomorphic anthropogenic Piers and breakwalls modifying shoreline processes, and lake influence and exchange with rivermouths and embayments. Altered watershed and valley sediment dynamics (loads, erosion, transport, deposition). Physical hardening and structuring of rivermouth and embayment shorelines. Diking and hardening of channel shorelines that reduces habitat complexity in channel and flood plain. Hydrologic (Flow sources and 

regimes; 

water mass 

characteristics)

Seasonal lake mixing (both vertical and with 

nearshore), and large-scale currents influencing clarity, nutrient, and temperature regimes.

Lake storm surges, seiches, upwellings influencing 

clarity, nutrient, and temperature regimes.

Watershed-driven, tributary flow regimes driving 

instream clarity, nutrient, and temperature regimes.

Winter ice-cover regimes. Tributary inflow regimes influencing clarity, nutrient, 

and temperature regimes.

Hydrologic sources to riparian ecosystems (river 

floodwaters, groundwater).

Dynamic hydrologic connectivity with coastal 

wetlands.

Topography and hydraulics of lowest river-valley 

segment, embayment, and coastline influencing water retention and exchange with open lake.

Hydrologic 

anthropogenic

Piers and breakwalls modifying shoreline currents, 

and lake influence and exchange with rivermouths and embayments.

Modified watershed landscape hydrology (for 

example, wetland loss, urbanization, agricultural drainage) changing instream clarity, nutrient, and temperature regimes.
Appendix 4

35

Appendix 4. Processes that impact the Great Lakes Lakewide Management Plan goal: All Habitats are Healthy, Naturally Diverse, and Sufficient To Sustain Viable Biological Communities.—Continued

Disciplinary 

subsystem

Geographic zone

Open lake Coastal/nearshore Watershed

Hydrologic 

anthropogenic 

(continued)

Air- and precipitation-borne contaminants and 

chemicals (acids).

Municipal and industrial wastewater discharges. Point- and nonpoint-source inputs of contaminants.

Climate change altering seasonal lake temperatures 

and ice regimes.

Nonpoint runoff from local or tributary watershed 

urban or agricultural landscapes.

Modified point hydrology (such as reservoir 

evaporation, dam release schedules, water withdrawals and diversions) influencing instream clarity, nutrient, and temperature regimes.

Reduced hydrologic connectivity with coastal 

wetlands.

Development within flood-plain valleys that 

eliminates wetland services.

Biological 

(Food 

resources, 

and hydraulic 

and predator 

refugia)

Distribution and dynamics of floating and sunken 

wood debris recruited from coasts and tributaries.

Distribution and dynamics of sunken wood debris 

recruited from coasts and tributaries.

Stream channel interactions with riparian flood-plain 

ecosystems and river-channel habitats; effects on shading, bank structure, recruitment of woody structure.

Distribution and dynamics of juvenile fishes 

produced in coastal/nearshore and tributary habitats.

Distribution and dynamics of juvenile fishes 

produced in open-lake, coastal/nearshore, and tributary habitats.

Instream dynamics of nutrient pulses in the form 

of fish eggs and fry (nutrients) imported from open-lake habitat.

Dynamics of adult fish (predators) migrating from 

open-lake habitat.

Instream distribution of sources of primary 

production.

Dynamics of aquatic and wetland macrophytes. Dynamics of aquatic and wetland macrophytes.Distribution of sources of aquatic primary 

production.

Dynamics of terrestrial plants.

Biological

anthropogenic

Removal of dead trees; commercial log harvest. Removal of dead trees; commercial log harvest. Instream removal of dead trees; commercial log 

harvest.

Restructuring bottom and altering nutrient pathways 

by nuisance dreissenid mussels.

Eutrophication-driven high algal concentrations 

shading bottom.

Modifications to riparian vegetation that effect floodplain and channel habitats.

Increased predation by hatchery-reared salmonids. Increased predation by hatchery-reared salmonids. Influx of hatchery-origin adult salmonids (predators) 

and their eggs and fry (nutrients) from open-lake habitat.

Nuisance effects from accidental species introductions. Nuisance effects from accidental species introduc- tions. Increased predation or nutrients from hatchery- reared, stream-resident trout.

Removal of aquatic and wetland macrophytes. Stocking of hatchery stream-resident trout, walleye, 

or other fishes.
36

A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems Appendix 4. Processes that impact the Great Lakes Lakewide Management Plan goal: All Habitats are Healthy, Naturally Diverse, and Sufficient To Sustain Viable Biological Communities.—Continued Disciplinary subsystem Geographic zone Open lake Coastal/nearshore Watershed Biological anthropogenic

(continued)

Elimination or disconnection of wetland habitats. Nuisance effects from accidental species 

introductions

Competition by nuisance terrestrial plants.Impacts of feral beach nest predators.

Seelbach and others—A Conceptual Framework for Lake Michigan Coastal/Nearshore Ecosystems—Open-File Report 2013–1138