Design & Monitorin

of Shellfish Restoration Project

A PRACTITIONERS GUIDE TO TH

AN ECOSYSTEM SERVICES APPROACH
Authors & Affiliations:

Robert D. Brumbaugh

The Nature Conservancy

University of Rhode Island Narragansett Bay Campus

South Ferry Road

Narragansett, RI 02882

Michael W. Beck

The Nature Conservancy

Center for Ocean Health

University of California Santa Cruz

100 Shaffer Road

Santa Cruz, CA 95060

Loren D. Coen

Marine Resources Research Institute

South Carolina Department of Natural Resources

217 Fort Johnson Road

Charleston, SC 29412

Leslie Craig

NOAA Restoration Center

263 13th Avenue South

St. Petersburg, FL 33701

Polly Hicks

I.M. Systems Group Inc./NOAA Restoration Center

7600 Sand Point Way NE

Seattle, WA 98115

communities that represent the diversity of life on Earth by protecting the lands and

waters they need to survive.
Acknowledgements

This Practitioner’s Guide grew out of a workshop convened by The Nature Conservancy and the NOAA Restoration Center in 20

at the Dauphin Island Sea Lab in Alabama. The authors would like to acknowledge the participants for their contributions in that

workshop as well as thoughtful comments on the early drafts of this publication: Diane Altsman, Dr. Marci Bortman, Cindy Brown

Mark Bryer, Raphael Calderon, Jeff DeBlieu, Mark Dumesnil, Patrick Ertel, Erika Feller, Wayne Grothe, Nina Hadley, Dr. Kenneth

Heck, Ted Illston, Carl LoBue, Betsy Lyons, Jay Odell, Dr. Dianna Padilla, Betsy Peabody, Dr. Sean Powers, Dr. LaDon Swann, Bar

Truitt, Dick Vander Schaaf, Nicole Vickey, Dr. Rick Wallace and Dr. Jacques White. In addition, Robin Bruckner, Lynne Hale,

Kerry Griffin and Dr. Mark Luckenbach provided valuable comments to this guide at various intervals throughout its preparati

Ultimately, the recommendations contained in this publication are only possible because of basic research, monitoring and care

documentation of outcomes from previous shellfish restoration projects by scores of other scientists, resource managers and restorati

practitioners whose work is referenced herein. We are particularly grateful for their contributions to this guide and to the field o

restoration science. Production of this guide was supported by the National Partnership between The Nature Conservancy and

National Oceanic and Atmospheric Administration Community-based Restoration Program.

1.

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Introduction: The case for shellfish restoration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

A lost resource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Engineers at work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

How shellfish work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Basic life cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Settlement substrate selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Getting to the bottom of it all: Restoration by design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

The “5-S” approach – an adaptive approach for designing projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Sources of stress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Strategies for restoration: Options based on stresses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Monitoring for ecosystem services and project outcomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Measuring recruitment of shellfish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Measuring habitat value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Measuring water quality impacts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Putting it all together . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Building effective partnerships . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Securing permits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Raising awareness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Footing the bill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Hope for the future . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Literature cited . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
A Lost Resource

Bivalve shellfish have historically been a prominent component

of benthic, or bottom dwelling, communities of temperate and

subtropical estuaries and coastal baysBivalves also have been and

continue to be an important food source for people throughout

the world, serving as both as a delicacy and a staple. In coastal

communities throughout the U.S., shellfish are cultural icons,

reflecting traditions and a way of life dating back generations. It is

not surprising therefore that until very recently resource management agencies have focused almost exclusively on maximizing

short-term returns from commercial and recreational bivalve harvest.

Once considered nearly inexhaustible, many shellfish populatio

around the world have declined precipitously – some to commerc

extinction - over the past two hundred years. These declines a

due in large part to over-exploitation as well as from the relat

overall decline in the condition of estuaries (Gross and Smyth

1946; Cook et al 2000; Jackson et al 2001; Edgar and Samson 200

Kirby 2004). In recent decades the translocation of shellfish

parasites and diseases between coastal areas has contributed 

to further losses and has exacerbated the effect of habitat lo

(Kennedy et at 1996).

2.

Bivalve shellfish restoration projects are becoming increasingly common in the United States, spurred by increased public awarenes

of their important ecological role in coastal waters and increases in funding (primarily federal) available for such efforts. Communi

groups, school classes and others interested in promoting healthier coastal ecosystems are joining forces with government agencies 

the local, state and federal level to help restore these important components of coastal ecosystems. This increased interest in restoratio

due, in part, to the dramatic declines in shellfish fisheries that were once the mainstay of many coastal communities. This is also lik

due to greater public awareness of the imperiled state of coastal environments in general, and a desire to restore the ecosystems suc

as oyster reefs, marshes, seagrass beds and mangroves that contribute to an overall healthier environment. The elements of shellfi

restoration may appear complex, especially for those who are unfamiliar with bivalve ecology or the basic tenets of restoration science

As a result, it may be difficult to know where to begin. 

This guide was written to help restoration practitioners design and monitor shellfish restoration projects that restore not only the

populations of target shellfish species – primarily clams, oysters, scallops – but also the ‘ecosystem services’ associated with healthy

populations of these organisms. As a primer for conservationists, resource managers and others interested in understanding basic

approaches to the design and implementation of shellfish restoration projects, this publication provides advice on:

1. Making the case for shellfish restoration

2. Identifying candidate species and an appropriate restoration strategy (or strategies)

3. Choosing sites for restoration projects

4. Monitoring project outcomes

5. Creating effective partnerships for restoration projects

II. Introduction: The case for shellfish restoration
failed to sustain shellfish populations or the fisheries that depended

on them. Few bivalve fisheries, if any, have been managed with

any evidence of long-term sustainability, both in the U.S. and in

many other parts of the world. Oysters and mussels in particular

have posed a unique challenge to fishery managers since fishing

activities for these species, unlike most fish and other mobile

organisms, tends to simultaneously remove their habitat. Various

approaches for countering fishery declines have been implemented,

ranging from hatchery based put-and-take fisheries to introductions

of non-native species, often with mixed results. By managing

bivalves and their habitats almost exclusively for recreational and

commercial fishing, many facets of their ecology that contribute

to maintaining the overall condition of our coastal bays and estuaries

have been ignored. 

Engineers at Work

With the decline of shellfish populations we have lost more than

the fisheries and economic activity associated with fishing. A

growing body of research in recent decades has illuminated the

profoundly important ecological roles that shellfish play in coastal

ecosystems. These roles include filtering water as bivalves feed

on suspended algae, providing structured habitat for other species,

and protecting shorelines from erosion by stabilizing sediments

and dampening waves. In fact, many bivalve shellfish have been

labeled ‘ecosystem engineers’ (Jones et al 1994; Lenihan 1999)

in recognition of the multiple roles they play in shaping the

environments in which they live. Restoring shellfish populations

to our coastal waters, therefore, represents a powerful way to restore

the integrity and resilience of these ecosystems.

The Water Filter

Shellfish are suspension-feeders that strain microscopic algae

(phytoplankton) that grow suspended in surrounding waters.

In some coastal systems shellfish, through their feeding

activity and resultant deposition of organic material onto

the bottom sediments, were abundant enough to influence

or control the overall abundance of phytoplankton growing

in the overlying waters. This control was accomplished both

by direct removal of suspended material and by controlling

the rate that nutrients were exchanged between the sediments and overlying waters (Officer et al 1982; Dame 1996;

Newell 2004). For example, it is widely touted that in the

late 19th century oysters were so abundant in the Chesapeake

Bay that they likely filtered a volume of water equivalent to

the entire volume of the Bay in less than a week (Newell

1988). This feeding activity contributed to greater water

clarity and allowed seagrasses to thrive in more areas of the

estuary than is observed today (Newell and Koch 2004). 

Similar ecological impacts have been attributed to other species

of bivalves as well. Hard clams in Long Island’s Great South

Bay were likely abundant enough, until about two decades

ago, to prevent outbreaks “brown tides” caused by planktonic

algae that cloud the water and prevent light from reaching

seagrasses growing in the bay. As these algae die, sink to the

bottom and decay, they also rob the Bay of oxygen (Kassner

1993; Cerrato et al 2004). The uptake of nutrients and

localized impacts on water quality documented for blue

mussels, Mytilus edulis, using flume experiments (Asmus a

Asmus 1991) and field observations in European estuarie

suggest that robust populations of mussels are capable of

consuming a considerable fraction of the phytoplankton

from overlying waters (Haamer and Rodhe 2000).

Ecosystem modeling and mesocosm studies have indicate

that restoring shellfish populations to even a modest fract

of their historic abundance could improve water quality a

aid in the recovery of seagrasses (Newell and Koch 2004

Ulanowicz and Tuttle 1992). Field studies have also revea

positive feedback mechanisms from shellfish populations th

promote greater seagrass productivity (Peterson and Heck 199

The Habitat Provider

In addition to their impacts as filter feeders, some specie

of bivalve shellfish such as oysters and mussels form reefs 

complex structures that provide refuge or hard substrate 

other species of marine plants and animals to colonize. F

example, the eastern oyster Crassostrea virginica, forms

three-dimensional reefs as generations of oysters settle an

grow attached to one another (Zimmerman et al 1989; Har

and Haven 1999; Steimle and Zetlin 2000). Reefs can oc

subtidally, often associated with edges of channels, as wel

in intertidal habitats, keeping pace with sea-level rise (DeAlte

1988; McCormick-Ray 1998 and 2005; Hargis and Have

1999). These reefs represent a temperate analog to coral

reefs that occur in more tropical environments. Both kin

of reefs are “biogenic”, being formed by the accumulation 

colonial animals, and both provide complex physical structu

and surface area used by scores of other species as a tempor

or permanent habitat. A single square meter of oyster ree

3.
shelter for an array of plants and animals (Bahr and Lanier

1981). Given the variety of species and complex interactions of

species associated with oyster reefs, they have been suggested

as “essential fish habitat,” which is an important distinction

for fisheries management in the U.S. (Coen et al. 1999).

Unfortunately, many of the reefs that were once so prevalent

have been mined away through fishing and dredging activities,

and their remnant ‘footprints’ have been silted over in the

past century (Rothschild et al. 1994, Hargis and Haven 1999). 

The Shoreline Protector

In some regions, intertidal oyster reefs and, likely, mussel

beds serve as natural breakwaters that can stabilize shorelines and reduce the amount of suspended sediment in the

adjacent waters. This reduction in suspended sediment

improves water clarity and protects shellfish, seagrasses and

other species. Shellfish restoration, therefore, offers a way to

recapture this important ecosystem service (Meyer et al 1997)

in some locations.

Given the increased understanding of the various roles that

shellfish play in nearshore ecosystems, there is increasing

interest in re-establishing robust and self-sustaining native

shellfish populations as a component of coastal ecosystems.

Indeed, the restoration of shellfish is increasingly invoked as

a key strategy for rehabilitating and conserving marine and

estuarine systems because of these anticipated ecosystem

services. However, surprisingly little effort has been made to

document the degree to which these ecosystem services are

provided through restoration activities in actual practice.

returns from restoration activities to garner the long term

support necessary for large scale restoration efforts. 

To balance the many services provided by shellfish and th

objectives of multiple stakeholders and agencies, we must

incorporate into our restoration and management goals t

many ecological linkages between shellfish and the surround

sediments, waters, and other species within coastal system

(Coen and Luckenbach 2000; Peterson et al 2003). Desp

an incomplete knowledge of these linkages it is reasonabl

to conclude that the ultimate goals of restoration – whet

for economic or ecological gain – depend to some degree 

increasing the abundance and overall biomass of a targete

shellfish population (Coen and Luckenbach 2000; French

McCay et al 2003; Newell 2004). 

Of course, not all shellfish provide the same kinds or deg

of ecosystem services and there are many ways that shellf

biomass can be increased without returning all of the desi

ecosystem services or even cause additional environment

stress. Intensive shellfish aquaculture, for example, may prov

filtration benefits but may not provide much in the way o

habitat (Newell 2004) and the extensive use of nets, doc

cages, and mechanical harvesters can create significant env

ronmental stress. Non-native species that are brought in t

new environments may indeed exert a top-down control 

phytoplankton biomass (Cloern 1982) but can also compete w

native species, negatively affect food webs (Kimmerer et 

1994; Strayer et al 1999), and bring in new diseases and oth

undesirable species (NRC 2004).
Basic Life Cycle

Most bivalve shellfish have separate sexes (i.e., they are dioecious)

and many change sex during their lifetime (i.e., they are hermaphroditic). For example, the eastern oyster begins life as a male

and becomes female as it ages and grows larger (see Kennedy

1996 for thorough review). The typical bivalve shellfish lifecycle

involves a planktonic (free-floating) larval stage, and a sedentary

benthic (bottom dwelling) juvenile and adult stage (Figure 1). 

Eggs and sperm are released into overlying waters where fertilization occurs. The eggs hatch and rather quickly develop into a

larval stage called a ‘veliger’ that spends days (scallops) to weeks

(oysters) drifting with currents, feeding and growing while suspended in the water. The larval stage bears little resemblance to

the adult stages, and is well adapted for this planktonic phase in

their life cycle. While their swimming ability is generally limited,

they are equipped with tiny hairs called ‘setae’ that they use to

control their depth in the water column. Beyond a basic ability

to control their depth, they are largely at the mercy of wind and

tidal driven currents that transport them horizontally and this

larval stage is essentially the only period during the bivalve life

cycle that allows any significant horizontal movement from one

location to another. Juvenile and adult clams can burrow into

sediments with their muscular foot, scallops can ‘swim’ by clapping

their valves together, and mussels can even jockey for position

within a mussel bed by manipulating the tiny byssal threads used

for attachment to surfaces. However, the distances traveled are

much shorter by comparison than the distances traveled as larvae.

The actual distance that shellfish larvae travel depends on many

factors, including behavior that affects their placement within

currents moving in various directions, and the overall pattern

and strength of local currents and tides.

Significance for Restoration Project Design: a general knowledge

of local tidal current patterns can be useful for predicting where larvae

might be transported to–or from–and in turn can help with selection

of a restoration site.

Settlement and Substrate Selection

When shellfish larvae have grown large enough (days to week

they begin the benthic portion of the life cycle and settle to th

bottom. At this point, they select an appropriate habitat in respo

to both chemical and physical cues from the environment. Cues c

include substances exuded by adult shellfish of the same specie

vegetation associated with their preferred habitat, and physica

characteristics such as surface roughness (Rodriguez et al 199

Upon settlement the larvae undergo metamorphosis and tran

form into juvenile stages that more closely resemble the adult

Since most bivalve species have only a limited ability, if any, to m

after settlement, it is critical that larvae select the habitat that

provides the best chance of growth and survival to adult stage

Significance for Restoration Project Design:It is important to kn

what kind of settlement substrate – or bottom material – is preferr

by the species under restoration. Providing the correct kind of mater

can help to attract and protect young shellfish that settle and accumu

there. Ideally, the substrate material can also serve as a refuge tha

protects newly settled shellfish from predators.

5.

To restore any species, it is important to understand its life cycle, and how various life stages interact with and are influenced by th

surrounding environment. Applying this information to shellfish restoration projects will aide practitioners in selecting appropriate

sites, understanding and abating threats and measuring progress.

* Exceptions to Every Rule:

Given the marvelous diversity of bivalve shellfish, it is

not surprising that there are several variations on this

generalized life cycle. Some species, such as the Olympia

oyster, Ostrea choncaphila, fertilize and brood their eggs in

the female oyster’s mantle cavity, rather than broadcasting them directly into the overlying waters. The larvae

of some species of freshwater mussels attach to the gills

of fish and are then transported upstream as ‘hitchhikers’ rather than drifting with currents as plankton.

Scallops use tiny hook-like hairs to attach to settle first

onto underwater grasses and seaweeds prior to settling

directly on the bottom.

FIGURE 1: Basic lifecycle diagram for the eastern oyster, Crassostrea virgin

Image reprinted courtesy of John Norton and MD Sea Grant.

http://www.mdsg.umd.edu/oysters/garden/seed.html
Systematic identification, design and monitoring of

shellfish restoration using The Nature Conservancy’s

“5-S Approach” 

The need for systematic approaches within a given region for the

identification, design and monitoring of conservation, management,

and restoration projects is widely recognized (e.g., Groves 2003;

Groves et al. 2002; Margules & Pressey 2000; Pressey et al 1993;

U.S. Commission on Ocean Policy 2004). The Nature Conservancy

uses such an approach, called ‘Conservation by Design’ (TNC

2000), to identify biodiversity conservation objectives at regional (Ecoregional) scales. As a systematic approach to defining restoration needs and identifying strategies for shellfish restoration

projects, Conservation by Design has four discrete steps: (1)

identifying priorities, i.e., compiling data and information to

identify representative sites that account for the full range of b

diversity across regional ecosystems (Beck and Odaya 2001,

Beck 2003), (2) developing site and multi-site strategies for pr

serving or restoring those sites to fullest functionality, (3) impl

mentation of those strategies, (4) measuring the effect of imple

mentation. This guide assumes that shellfish restoration is a con

servation strategy that has been identified through some form 

regional-scale assessment, and the balance of our discussion w

focus on the restoration strategies that are applicable at indivi

ual sites or multiple sites within an ecoregion.

6.

Perhaps the most fundamental step for successful shellfish restoration is to carefully consider and define restoration goals for a speci

project (Coen and Luckenbach 2000; Shumway and Kraeuter 2003; Luckenbach et al 2005). Given the commercial and social 

significance of many bivalve species, fishery production has been for decades the primary and often sole motivating factor in shellfi

enhancement projects. The literature describing techniques for enhancing commercial and recreational production of shellfish 

extensive (MacKenzie 1989; Kennedy et al 1996; Arnol et al 2002) and has typically focused on increasing short-term fisherie

production. In contrast, until very recently few restoration initiatives have defined as their primary goal the rebuilding of natural

capital – reefs and robust spawning populations capable of sustaining both fisheries and the health of coastal ecosystems (Breitbur

et al 2000). Given the multifaceted ecological roles played by bivalves in coastal systems, ecosystem restoration is becoming a prima

motivating force for at least small scale restoration projects (Brumbaugh et al 2000a & b; Hadley and Coen 2002). With these issue

in mind, we offer in this guide a suite of ‘Better Management Practices” to help practitioners design and monitor shellfish restorat

projects with ecosystem services in mind, i.e., to document and enhance the services provided by shellfish ecosystems.
Once a biodiversity conservation approach – e.g., shellfish

restoration – has been identified through an Ecoregional

Assessment, the specific actions to take at the site and multi-site

scale must be defined, implemented and monitored for their

outcomes. To accomplish these tasks, TNC employs a “5-S”

methodology to identify the System, Stresses and Sources of

stress to the system, Strategies for abating stresses, and Success

measures to determine whether a conservation or restoration

objective has been achieved. For the purposes of this guide the

System is the bivalve shellfish ecosystem – more specifically

oysters, clams, scallops and mussels and the other associated

species. It is recognized that these are connected to other types

of Systems (e.g., marshes and seagrass meadows) within estuaries

or coastal lagoons. 

The second and third “S” when embarking on a shellfish restoration

project is to identify the Stress and Sources of Stress affecting

the abundance of shellfish at a given site. Here we combine these

somewhat within three broad categories – fisheries mortality,

habitat limitation and recruitment limitation. At many sites,

all three types of stress are present. Later we will discuss potential

Strategies and appropriate Success measures (or indicators) to

track the outcome of restoration activities.

Sources of Stress: Fishing mortality, habitat loss,

recruitment limitation

The Sources of stress affecting shellfish populations can include

fishing, channel dredging and destruction of habitat, and

degraded water quality (i.e., anoxia, sedimentation, harmful algal

blooms). Depending on the source of stress it is helpful to view

restoration activities within a ‘hierarchy of intervention actions’ that

represent the range of potential strategies to be considered when

designing a project (Shumway and Kraueter 2003). 

Stress Category 1: Fisheries Mortality encompasses a group

of stresses that can depress and hold population biomass below

levels necessary to return economic or ecological benefits. There

are many stresses within this category such as excessive take

7.

Identify areas where reefs or target shellfish populations historically

existed. Data on historic distributions can be obtained from published

accounts, fishing records, and navigation charts or other bottom surveys.

It is predicted that these sites are the most likely to be able to further

support shellfish.

Evaluate bottom conditions to determine if the bottom will support

addition of shell or other materials used for habitat enhancement. It

may be necessary to restore the bottom for example by removing excess

sediments or other debris such as wood waste from logging operations.

Determine whether this area is a “sink” for larvae being transported in from

other areas. Populations have a higher chance of recovering most rapidly

in areas that are “sinks” for larvae (Crowder et al 2000). Deployment of

spat collectors - devices used to attract larvae to settle - or sampling

the bottom within areas that are known for supporting shellfish can

help to gauge the level of ‘recruitment’ likely for a given restoration site.

Assess the current velocity. Shellfish growth is generally higher where

currents are greater, delivering food and oxygenated water and carrying

away waste by-products. 

Determine what threats exist in areas formerly populated by shellfish.

Examples include sources of sedimentation (e.g., erosive banks, poorly

buffered shorelines), stormwater or other point sources of pollution.

Determine whether the overlying waters are well oxygenated. Small,

poorly flushed coves may become sub-oxic or anoxic, particularly in

the summer when the water is warmest. This can affect shellfish

directly (e.g., reduce recruitment and survival, Breitburg 1992) and

indirectly (e.g., fish and crabs escaping areas of low oxygen may converge

on reefs or nearby shellfish populations and alter community structure

through predation or competition, Lenihan et al 2001).

Consider locating restoration projects within small, replicable sub-estuaries.

Such areas are sometimes referred to as “trap estuaries” (Pritchard 1953),

denoting areas with a high degree of retention of water circulation, which

can help promote recruitment of shellfish larvae and other colonizing

species. These small systems can serve as testing grounds for measuring

potential ecosystem service impacts to water clarity and quality.

Consider placement of restoration projects in areas where illegal impacts

can be deterred. For example projects can be placed where shellfish harvest

is banned for human health reasons. Such areas represent de-facto

sanctuaries. Other areas may lend themselves to enforcement such

as areas where there have been well established lease or ownership

rights or areas near bridges, research stations and nature preserves

where there are potential partners to monitor the project. These are

also likely to be urban areas where community support and involvement

in restoration for strictly environmental reasons may be garnered

(Brumbaugh 2000b).

Consider using submerged lands that are privately leased or owned

to maintain investments in restoration on project sites. Submerged

lands are available for lease and ownership in all coastal states (Marsh

et al 2002; Beck et al 2005). Many of these lands have traditionally

been used to grant exclusive access for shellfishing. They can however

also be used to protect investments in restoration and allow groups

greater stewardship opportunities for the natural resources that they

have enhanced at sites.
may be as “simple” as reducing fishing pressure or modifyin

other activities such as dredging and filling (see Habitat

Limitation below) that damages or removes shellfish (Abad

and Poirrier 2000; Maguire et al. 2002). The reduction of

fishing mortality can promote an increase in the numbers o

adult shellfish that help to bolster the spawning population

over time, assuming that habitat (e.g., bottom characteristic

and water quality) remains abundant and in good condition 

allow young shellfish to accumulate and grow. As an examp

of this approach, Jordan and Coakley (2004) have postulat

based on results of a population dynamics modeling exercise th

eliminating fishing pressure on the Chesapeake Bay’s remaini

oyster populations would allow for a 10-fold expansion of t

population in less than ten years. 

Of course, the political will necessary to amend fishing regulati

can be challenging to build. It should also be noted that reductio

in fishing effort need not involve absolute closures or prohibitio

of fishing activity. Rather, reductions may be achievable throu

some combination of controls on overall harvest numbers, s

limits, locations, or timing of harvest depending on the over

status of the population. Fundamentally, restoration efforts th

are intended to enhance the total value of ecological service

must first and foremost reduce stresses that are affecting th

population and not just consider how to maximize landings

Stress Category 2: Habitat limitation is a stress that occu

when there is no longer a sufficient amount of habitat to supp

all life history stages of the population and, as a result, the po

ulation cannot be sustained over long periods of time. Relev

subcategories of stress include habitat modification, degradat

and loss. For example, physical degradation of three-dimension

oyster reefs throughout much of the eastern oyster’s range i

considered a limiting factor for populations throughout it

range. Since the 1800s, the three-dimensional reef habita

has been destroyed leaving only rubble ‘footprints’ of oyst

reefs (Rothschild et al 1994; Hargis and Havens 1999). Th

reduction of vertical relief has relegated oysters to living low

in the water column where dissolved oxygen levels cause str

that increases their susceptibility to diseases (Lenihan an

Peterson 1998). As another example, the global decline of

seagrasses as a result of nutrient over-enrichment and disea

(Orth and Moore 1983, Green and Short 2003, Short and

Wyllie-Echeverria 1996, Duarte 2002) likely limits populatio

of shellfish species such as hard clams and scallops that recr

first as juveniles to these beds of vegetation (Pohle et al 199

Heck and Crowder 1991; Irlandi et al 1995, 1999). 

To abate the stress of habitat limitation, therefore, it may b

necessary to develop and implement strategies that involve dir

manipulation of the habitat available to juvenile or adult shellf

Habitat manipulation, such as placement of shells on the botto

or restoration of seagrass beds, represents a much higher deg

of intervention than just regulating harvest alone and care shou

be taken to select the appropriate sites for habitat enhanceme

(See Box 1 for some considerations). 

8.

Because there are potential genetic consequences when using stock enhancement as

a strategy to restore shellfish populations, there are several fundamental guidelines

for reducing these potential risks (Allen and Hilbish 2000):

Transplant wild broodstock animals collected from local sources.

Shellfish that are collected in the immediate vicinity or purchased

from fishermen working nearby can be transplanted at higher

densities to improve the likelihood of reproductive (fertilization)

success. This is a way to tap into the local gene pool and minimizes

the chances of “genetic bottlenecking”.

Use locally collected broodstock for spawning in hatchery-based stock

enhancement. It may be necessary to collect wild shellfish for artificial

propagation if little natural settlement is occurring in local waters, and

when importing large numbers of shellfish from another location

would produce undesirable results (e.g., would diminish the ecosystem

services or fishery stock in a given location). Collecting broodstock

from an area close to your project can reduce the loss of local genetic

characteristics (Peter-Contesse and Peabody 2005).

Use pair-wise crossings of animals in the hatchery to maximize ‘effective

population size’ (Ne) and to minimize “genetic bottlenecking”. Maximizing

the number of animals spawned in the hatchery (i.e., getting close

to Ne) and using pair-wise crosses can maximize the chances of

maintaining genetic diversity in a broodstock enhancement program.

Characterize the genetics of broodstock (for wild and hatchery-origin

stocks) to aid in the tracking of progeny in the field. This is an

expensive and time consuming process (both the genetic characterization and the identification of offspring in field samples), but

allows for ‘proof of restoration impact’ and also for monitoring of

genetic changes over time. Efforts to use genetic markers to track the

offspring of oysters transplanted to selected Chesapeake Bay

restoration reefs are underway and are intended to provide a

quantitative basis for improving future restoration projects (Mann

2004; Millbury et al 2004).

of Stock Enhancement Programs
Stress Category 3: Recruitment limitation occurs when an

insufficient number of offspring are added to the population

on an ongoing basis to offset losses of larger, older members of

the population. Several factors can contribute to this condition,

including an overabundance of predators, excessive fishing

pressure that reduces the number of spawners in the population,

degraded water quality that affects survival of larvae, and diseases

or parasites that affect the ability of adults to spawn successfully.

Given the depleted status of many shellfish populations, an

insufficient abundance – and density - of spawning age animals

in the population is not uncommon. The overall abundance and

size of adults in the population will determine the maximum

number of eggs and larvae produced, and the density (i.e.,

proximity to one another) affects the relative fertilization success,

since bivalves release eggs and sperm cells directly into the water.

Strategies for Restoration: Options based on stresses

There is an array of strategies available for abating the stresses

outlined in the previous section. Each project is unique and

appropriate strategies must be based on knowledge of the target

species, geography, social and political framework. The Strategies

outlined below give examples of approaches that have been

proven broadly applicable at many sites.

Strategies to address Fishing Mortality

No-take areas or sanctuaries: A basic intervention strategy

to reduce stress associated with excessive fishing mortality

is to set aside areas where fishing is curtailed – essentially,

‘no take’ reserves for shellfish. By eliminating fisheries

mortality, the presumption is that shellfish will live longer,

grow to larger sizes, and occur at higher densities thereby

producing more offspring (Rice et al 1989; Breitburg et al

2000). ‘No take’ reserves are also useful for reducing

impacts from fishing gear on the bottom, which can alter the

distribution of shelly habitat and affect overall biodiversity

(Hewitt et al 2005). This approach may be employed with

all kinds of bivalve shellfish. 

Reducing effort and incidental take: While it is often

preferable to restrict harvest entirely at sites and this will

result in the greatest likelihood in restoring natural shellfish

9.

All life stages of bivalve shellfish are susceptible to some degree of predation, from

larvae (Breitburg et al 1995) to adult (Virnstein 1977). Losses to predators can 

significantly reduce the effectiveness of stock enhancement programs and should b

factored into restoration planning. Predation is a part of the natural functionin

of ecosystems. Nonetheless it is often desirable to reduce these levels as naturally 

as possible initially in order to successfully establish new shellfish reefs and beds:

Broodstock Size: Predation mortality tends to decrease with increasin

shellfish size (Bisker and Castagna, 1989; Eggleston 1990). For

oysters, a minimum size of 40 mm is recommended as field and

laboratory studies have shown that blue crabs can readily consume

smaller oysters (e.g., Krantz and Chamberlain 1978). Clams may

fair well at a somewhat smaller size than oysters, but in general th

larger the bivalve, the less susceptible it is to predation. Minimizing

rather than eliminating, losses of animals added for broodstock

enhancement is a reasonable objective, since even the largest shel

fish are vulnerable to some level of predation.

Time of Year: Generally, it may be most advantageous to transplan

broodstock immediately prior to the spawning season as it is desirab

to have individuals spawn successfully prior to significant predation

Factors such as (1) predator abundance and activity (Bishop et al

2005), (2) recruitment of other competing species (Osman et al

1989) and (3) physiological stress of temperature extremes (high

or low) are factors that may determine how far in advance of spawnin

season you might want to transplant broodstock. 

Consider Spatial Arrangement: It may be possible to minimize

predation by siting the project away from sources of predators. Fo

example, blue crabs are a significant predator on juvenile oysters

and they are abundant in marshes and sea grass beds. Crabs may

move between these different ecosystems as they forage (Michel

and Peterson 1999) so restoring an oyster reef some distance awa

from marsh edges or seagrass beds may minimize the likelihood o

crab predation on young oysters (Grabowski et al 2005).

Predator Control: Numerous studies have been undertaken to evaluat

methods for controlling predators affecting aquaculture production

Typically, these methods involve exclusion devices (cages or nets) o

predator removal regimens. Exclusion devices require maintenanc

and likely require additional permits. Direct predator control in th

field is expensive, time consuming and may not be consistent with

restoration goals in the long term. A more ecosystem-based approac

may be to sustain or increase the abundance of other associated specie

such as toadfish that prey on crabs and other bivalve predators (Bisk

and Castagna 1989). Curbing fishing pressure or providing habita

for such species in association with restoration projects, predation

on stocked shellfish may be reduced. 

Increase the Number of Animals Stocked: It may be possible to

adjust the stocking density to compensate for anticipated levels of

predation. Increasing the number of shellfish added to a sanctuary sit

may compensate for losses to predators assuming that the increase

number of shellfish does not attract additional predators or cause

density-dependent problems such as competition between shellfi

for food or space.

Use Substrate as a Predator Deterant: Placing a thin layer of she

or other material on the bottom, or even on top of the shellfish themselve

may reduce the ability of predators to find and consume shellfish

added to a restoration site.
10.

capital, even just reducing or redirecting effort can still be

helpful. In places where many non-native shellfish are present

(e.g., Puget Sound) it may be possible to direct harvest to

these species to avoid fishery pressure in areas of restoration

with native species. Where there are practices that are too

efficient at removing shellfish (e.g. dredging), less efficient

methods could be mandated (e.g., tonging or diving).

Strategies to address Habitat Loss

When the overall abundance of shellfish in a system is limited

by the availability of suitable habitat, it may be desirable to

enhance or alter the bottom to promote greater recruitment

of young bivalves and to enhance their survival. This is a

‘passive’ approach to restoration, and assumes that adequate

spawning and larval supply is occurring at a given location.

When restoring habitat for shellfish, as with many kinds of

wildlife, it is important to consider the placement of the

restoration project in the context of the larger landscape

(Scott et al 2001). For example, an oyster reef placed in

the vicinity of areas that periodically experience low oxygen

conditions may result in mobile organisms – fish and crabs

– seeking refuge on the reef and causing elevated rates of

predation on the shellfish being restored, or on other organisms

residing on the reef (Lenihan et al 2001). Similarly, the

placement of oyster reefs near vegetated areas such as marsh

edges or seagrass beds may encourage greater use by mobile

organisms such as crabs and fish (Grabowski et al 2005).

While this may expose the shellfish on the reef to predation

by crabs and other predators, this may be acceptable if the

intent of the project is to convey benefits such as shoreline

stabilization or habitat corridors for mobile organisms. These

and other considerations relevant to site selection are addressed

in Text Box 1.

Restoration of seagrass habitat is an activity that can be

useful – if not a prerequisite for restoring scallops and to

some extent hard clams as well. Seagrasses are an important

sizes (Pohle et al 1991). Being off the bottom presumably

helps to protect the youngest scallops from predators tha

might be foraging below. The physical complexity of seagr

habitat is also thought to reduce the ability of predators t

prey on scallops within the beds (Irlandi et al. 1995, 1999

Talman et al 2004).

Construction of 3-dimensional reefs has become a wid

used approach for enhancing the recruitment of and survi

of oysters and their associated reef community, particular

from Pamlico Sound northward along the east coast of th

U.S. Materials used for reef creation should provide a sig

nificant degree of ‘interstitial space’ within the reef matr

This complexity increases survival of young oysters (Bart

and Mann 1997) and provides refuge from predation for

other species that inhabit the reef (Breitburg 1999; Posey 

al 1999). Typically, oyster shells are the preferred materia

for use in oyster reef projects since they most closely emula

the natural reef matrix and interstitial space in a natural r

when they are piled on the bottom (O’Beirn et al 2000).

Limestone marl rock has been successfully used to crea

settlement habitat for oysters in Louisiana (Haywood e

1999; Soniat and Burton 2005). TNC and the North

Carolina Department of Marine Fisheries are also usin

this material to create spawner sanctuary reefs in Pamli

Sound with much success (Figure 2 and Case Study 2).

Construction of intertidal ‘fringing reefs’ may be a mo

appropriate approach for restoring oysters in the souther

portion of its range, particularly along the southeastern U

coastline. This approaches focuses on providing substrate f

settlement and 3-dimensional ‘relief’ in the intertidal zon

For oysters growing in the intertidal zone, the significance 

shell orientation (i.e., vertical vs. horizontal) is still poorl

understood, but may play a role in growth and survival.

Intertidal oysters tend to grow vertically, which may be a mea

of reducing exposure to solar radiation and, by extension,

moderating temperature (Bahr and Lanier 1981). Restoratio

efforts should strive to provide vertical relief on both larg

scales (reefs) and micro-scales (individual oyster shells). 

Broad scale placement of shell or shell fragments at hi

density on the bottom has been shown to increase recruitm

of hard clams (Kraeuter et al 2003) and this kind of patc

habitat also serves to increase biodiversity (Hewitt et al 200

Shells for projects can be obtained from oyster processin

facilities or from shell recycling programs (Hadley and Co

2002). South Carolina has a well-developed program tha

enables people to return shells from oyster roasts for use 

reef restoration projects: 

www.dnr.state.sc.us/marine/regs/sfrecycling.html. 

One cautionary note, however, is that shells should be allow

to ‘age’ or dry out on land for a period of at least one mo

prior to deployment in the water to minimize the likeliho
Strategies to address Recruitment Limitation

Populations that are extremely depleted may in some cases

gradually rebound on their own without supplementation

of “broodstock,” or reproductively capable adults. However,

in some cases the population has declined below a point of

recovery, when recruitment of offspring will not overcome

the mortality of adults in the population (“Allee effect,”

Gascoigne and Lipcius 2004). In this instance, it may be

necessary to artificially increase the abundance and density

of adults in the population through “stock enhancement”.

This differs from stocking clams, oysters or scallops in support

of ‘put-and-take’ fisheries since (1) the stocked animals are

never re-harvested, and (2) the stock enhancement strategy

(location, density, genetic composition) is specifically

intended to encourage maximum reproductive contribution

to the population.

Broodstock Enhancement: To address recruitment limitation,

it may be necessary to add shellfish to the population to

increase the production of offspring. Stocking adult shellfish in relatively high densities is likely to improve the

chances of successful spawning and reproductive success.

This strategy may be useful for ‘jump starting’ populations

from a range of bivalve species including scallops (Peterson

et al 1996), oysters (Brumbaugh et al 2000a & b; Southworth

with broodstock enhancement efforts, ranging from genet

considerations to predation on transplanted bivalves.

Additional information about these topics is provided in

Text Boxes 2 and 3.

For many shellfish species, both availability of habitat and

recruitment are limiting factors, and a combination of

restoration strategies involving both habitat manipulation

and stock enhancement is required to restore the shellfish

population (Caddy and Defeo 2003). Clearly this represen

the highest degree of intervention, and increases the complexi

of the project. Mann and Evans (2004) have summarized

some of the significant factors that can affect the success 

restoration involving both habitat rehabilitation and stock

enhancement and advocate taking a population dynamics

approach to planning such activities. In particular, they

recommend that restoration efforts be informed by demo

graphic modeling that takes into account egg production

losses of larvae to advection, and factors contributing to

recruitment success (e.g., habitat availability). To accomplis

this requires fairly specific knowledge of the system under

going restoration, including (i) temperature and salinity, whic

can be determined from regional water quality monitorin

programs, (ii) circulation patterns, which can be inferred

from drifter studies and (iii) risk of predation (see Box 3)

11.

V. Monitoring for Ecosystem Services

Aquatic ecosystem restoration, in general, is a relatively new field and unfortunately many restoration projects undertaken to date h

been poorly monitored and documented (Bernhardt et al. 2005). Without adequate documentation, it is not possible to know the

ecological impact and whether the goals or objectives of a project have been met. Conversely, a well designed monitoring plan provid

opportunities for adaptive management – essentially mid-course corrections – that enables practitioners to achieve project goals a

importantly, to improve future projects. Ultimately, well documented projects increase the knowledge base that can be used to impro

the outcome of projects over time and increase the public support and funding available for additional restoration. This publication

provides a starting point and a broad overview of methods that are available for monitoring shellfish projects. More comprehensive

guides to monitoring methods are available to practitioners seeking to expand on this introduction (e.g., Thayer et al. 2005). 

Figure 2: Limestone marl has successfully been used to create oyster reefs in North Carolina's Pamlico Sound (Ashley Harraman, TNC; Rob Brumbaugh, TN
The methods applied to monitoring will depend on the particular

Success Measures (one of TNC’s “5-S’s”) or indicators identified

to help quantify project outcomes. Of course, success measures

chosen for a shellfish restoration project depend on the original

goals of the project (Coen and Luckenbach 2000). In general,

success measures relevant to ecological services fall into four

broad categories:

1. recruitment and growth of the shellfish population

undergoing restoration

2. provision of habitat for other associated species

3. direct and indirect effects on local water quality

4. shoreline protection

The scale at which each of these services is measurable will depend

on the particular ecosystem service being measured, as well as on

the system within which the project is being undertaken (Figure

3). For example, it may be possible to discern an increase in

recruitment at relatively large distances from the reef or bed

being restored, depending on the water circulation patterns that

govern, in part, the distance their larvae are able to travel.

Conversely, measuring the service of habitat enhancement may best

be accomplished directly at the site being restored with appropriate

replication and comparison to reference sites.

that occurs as a result of restoration activities. The basic desig

for such monitoring, known as Before-After-Control-Impact

(BACI), has been well established in the ecological literature

(e.g., Underwood 1991, Schroeter et al 1993 and 2001). In ou

case the better acronym is BACR to include actions from

Restoration rather than ecological impacts (e.g., sewage outfal

BACR is relatively easy to implement. Though it may appear

obvious, the most difficult quantity is forethought; as control

and restoration sites need to be monitored before any treatme

are established. Moreover, it is best to monitor these areas sever

times before and after shellfish are restored. Incorporating BAC

designs into restoration planning will be important for describ

the net return on restoration investment and for developing

predictive models for scaling restoration up to ecosystem scale

Measuring Recruitment to the Shellfish Populatio

Clearly, to generate ecosystem services the shellfish populatio

under restoration must expand to the point that it becomes se

sustaining. Basic measures such as abundance, density (number p

unit area) and size frequency of the shellfish should be monitor

over time to determine whether the population and biomass i

growing, declining or staying relatively unchanged. Studies of wetla

restoration projects have revealed that it can take a decade or lon

for a restored site to resemble a natural reference marsh site

(reviewed by Callaway 2005). Similarly, the accumulation of fis

biomass within marine protected areas can occur over vario

timescales from years to decades (Russ et al 2005). The reestablis

ment of shellfish populations and their ecosystem services will

likely require similar timescales. Baseline monitoring of shellfis

abundance and size should be repeated annually for a minimu

of 5 years.

Quadrat samples can be used to provide quantitative estimat

of shellfish abundance in both the intertidal zone and in the

subtidal zone. On oyster reefs, samples are obtained from variou

elevations (e.g., reef crest, slope, base) to gauge the variation i

recruitment with depth. Usually 0.25m2 quadrats, excavated to 

depth of 10 – 15 cm, provide a reasonable sample volume for

estimating population parameters (Bartol and Mann 1997)

(Figure 4). For each sample, count all live oysters and articula

shells (dubbed “boxes,” articulated shells are a measure of rec

mortality), and measure all live shellfish (or a minimum rand

sample of 50 individuals for large sample sizes) to the neares

mm. These data will help to characterize the changes in the

population density and size classes of animals (and, by inferen

age classes) over time. If the reef material is not conducive to

sampling with quadrats or if non-destructive sampling is preferr

trays filled with reef substrate (e.g., shells, marl limestone, etc

can be embedded in the reef surface at random locations an

retrieved repeatedly or at the end of the recruitment season

Similar data for clams infaunal bivalves (i.e., organisms livin

within the sediment) can be collected by divers placing quadr

at random intervals along transects or within a grid on the botto

Excavate all clams and place within mesh bags for counting an

measuring at the surface.

Benthic grab samplers can also be used to quantify clams and

other organisms living within the sediment. These devices are

Figure 3: Theoretical array of ecosystem services to measure around restoration

project sites

12.
13.

An advantage of this method is that it provides a quantitative

(area-based) measure of abundance. A disadvantage is that only

a relatively small area is sampled (unless a very large sampler is

used, which requires a crane and larger vessel to deploy). These

samplers also tend to be specific to the kinds of sediments they

sample most effectively. For example, heavily weighted Ponar-style

grab samplers are effective for sampling in gravel, sand or consolidated sediments, while lighter Van Veen- and Ekman-style

samplers are more suited for softer sediments. 

Artificial settlement substrates or settlement collectors provide a

simple and inexpensive means of gauging relative settlement

patterns across an array of sites. Artificial settlement substrates

can be used to help with siting reefs and beds as well as identifying

if settlers are being attracted to restoration sites, a key condition

for success. Collectors can be deployed from docks or shorelines

or by boat using buoys and small anchors to hold the gear in place

for a prescribed period of time. Ceramic tiles or other materials

that are readily colonized by marine invertebrates can be used to

determine the timing and magnitude of settlement of oysters

(Michener and Kenny 1991; Roegner and Mann 1995; Bartol

and Mann 1997). Mesh bags containing nylon monofilament

mesh (e.g., gill net material) can be used to gauge the timing and

magnitude of scallop settlement. There are sampling artifacts

associated with nearly any type of artificial substrate – e.g., 

differences in predation rates, fouling, and competition for

space. These data can be used to infer relative magnitudes of

abundance and general distribution patterns but should not be

assumed to represent actual settlement rates on the bottom.

Measuring Habitat Value for Associated Species

A common and rarely monitored goal for the restoration of

shellfish (and seagrasses and marshes) is re-establishment of 

of view, the return of naturally, diverse assemblages of species 

re-established shellfish habitats and ecosystems should always 

a primary goal. In general, restoration is often approached wi

a “more biomass is better” perspective (French-McKay et al 20

also, with caveats, Newell 2004), only recently have investigat

attempted to discern the relationship between species diversi

and biomass or abundance measures (Coen and Luckenbach

2000; Luckenbach et al 2005). Some studies have document

the fauna - resident and transient fish and invertebrates – tha

inhabit shellfish reefs (Breitberg 1995; Wenner et al 1996; Co

et al 1999; Harding and Mann 2001). Such studies are ofte

designed in ways that allow for effective comparisons wit

adjoining habitat such as salt marshes and vegetated or unvegeta

bottom (Glancy et al 2003). 

Various approaches exist to qualitatively or quantitatively mon

or sample the organisms associated with shellfish restoratio

projects and shallow intertidal environments. These method

include lift nets (Wenner et al 1996), drop nets and enclosur

(Minello et al 2003), haul seines and gill nets (Harding and Man

2001), sampling trays embedded in reefs or beds (O’Beirn et 

2000; Coen and Luckenbach 2000; Luckenbach et al. 2005)

video surveys, and diver surveys/fish counts. Different approac

will lend themselves to projects under different conditions

Video surveys and diver surveys are most appropriate for doc

menting larger or highly mobile species where water clarity i

reasonably good, while nets, sampling trays and other enclosu

are more useful for quantifying smaller or more cryptic organism

A common misconception that explains why species and com

munity change are rarely monitored in restoration projects is

that they are perceived to be time consuming to measure in t

field and difficult to analyze. For example, it can be difficult i

the field to measure abundances of all species in a community

Figure 4: For oyster reefs constructed from unconsolidated materials such as shells or small pieces of rock, samples can be collected from quadrats to 

determine the number of live shellfish and other organisms on the reef. (Rob Brumbaugh, TNC; Lisa Drake, U.S. Coast Guard Academy)
14.

These issues can be minimized, because often it may be possible

to measure and analyze changes in biodiversity and communities

by measuring just presence/absence. These measures (either

presence/absence or abundance) can be analyzed with statistics

that are remarkably robust at detecting community change.

These statistics are known as Analyses of Similarity (Anosim)

and are part of an easy to use statistics package, Primer

(www.pml.ac.uk/primer/). These measures and statistics are

widely used (see Primer website). Presence-absence data can

also be used to document differences in overall biodiversity

between different kinds of habitats, or reefs in different locations

(i.e., Beta diversity, see http://cnx.rice.edu/content/m12147/latest/)

Measuring Direct and Indirect Effects on Water Quality

Laboratory and field studies have documented the capacity of

filter-feeding shellfish to reduce concentrations of suspended

particulates in overlying waters (Verwey 1952; Haven and

Morales-Alamo 1971; Asmus and Asmus 1991; Dame 1996).

Typically, these studies measure changes in Total Suspended

Solids (TSS) and chlorophyll_a (Chl_a) in water before and

after it has passed over shellfish beds (Haamer and Rhode

2000; Cressman et al 2003; Nelson et al 2004). More work is

needed to develop methods that are robust and capable of measuring

subtle changes in these parameters on appropriate spatial and

temporal scales. A combination of flow-through fluorometry

and analysis of whole water samples is one approach being tested

as a means of providing such high resolution information to

document filtration effects of shellfish populations (Ray Grizzle,

University of New Hampshire, personal communication).

Simpler approaches to monitoring water clarity using Secchi disks

are also worth considering, although they are less likely to detect

subtle changes in clarity that might be attributable to the filtering of nearby shellfish. This method provides a relative measure

of water clarity and light transmission within the water column,

but is more subjective than the methods described above because

the depth that the disk disappears from view can depend on variety

of factors in addition to water clarity, including time of day, ambient

light levels and water surface conditions. Different observers, too,

can report different readings for the same time and location, so it

can be more effective for the data to be collected by the same

observer over time. Despite the subjectivity of this method, Secchi

to increases in shellfish populations over time (Abadie and Poirr

2000). Instructions for the use and interpretation of Secchi di

are available in “Volunteer Estuaries Monitoring: A Methods

Manual” at: 

http://www.epa.gov/owow/estuaries/monitor/.

Lastly, an indirect and somewhat anecdotal means of gauging

the effect of shellfish restoration on water clarity is to monito

changes in seagrass presence and abundance in areas adjacent 

your project site. There is increasing evidence that shellfish ca

enhance the productivity of seagrass beds through both filtrati

of water as well as by changes in sediments resulting from the

deposition of organic matter and waste by-products (Peterson

and Heck, 1999; Newell and Koch 2004). Examining aerial

photos is one approach to monitoring changes to seagrass bed

over time. Other methods include recording shoot densities a

grass canopy height within quadrats placed at random interva

along transects (McKenzie and Campbell 2002; Short et al 200

see: http://www.seagrassnet.org/global.html). Care should be

taken when attributing observed changes in seagrass abundan

to nearby shellfish restoration activities, however, since there 

many other factors such as rainfall, suspended sediments an

temperature are also major factors affecting the health and 

productivity of seagrass beds. As with the shellfish restorati

site itself, having a reference site for comparison and collectin

baseline data as part of the ‘Before’ stage of a BACR monitor

plan can help with interpreting your observations. 

Measuring the Value of Oyster Reefs as Shorelin

Protection

Aerial photography and GIS/image analysis approaches have

also been used to provide landscape scale analysis of intertida

oyster reef habitat (Grizzle et al 2002). While oyster reefs ar

subject to erosive forces from boat wakes and wave action (Griz

et al. 2002) they can also, by dampening and absorbing wave ene

gy, be an effective means of stabilizing erosive shorelines (Me

et al 1997). Stakes planted along the shoreline at restoration si

provide a baseline for measuring shoreline migration relative 

reference sites. The change in vegetative cover behind fringin

reefs is also a useful metric for assessing performance relative 

reference sites and can be measured by estimating the percen

cover of vegetation or shoot density (number of stems per squ

meter) in quadrat samples within the marsh.
Local, state and federal agencies have legal jurisdiction and can help

facilitate or even take the lead on securing permits needed for habitat

enhancement. The necessary permits will vary depending on the

location, type of restoration activity being proposed, project scale and

other factors. Agency partners also typically possess the long term

data sets that can help with site selection and setting restoration targets.

Fishing industry representatives have both knowledge and infrastructure to help with projects. Involving industry stakeholders

not only helps to ensure buy in and support, but can prove

invaluable for tackling tasks like hauling and deploying shells on

restoration sites, or transporting and transplanting clams or oysters.

Non-profit organizations have various strengths that can aid in

the development and implementation of a project. Small locallyfocused organizations that have close ties to a community and may

be instrumental at securing permission to use coastal property as

either a staging area or a restoration site. Recruiting volunteers

for hands-on components of a project is another forte of local

non-profit organizations. Land trusts serve as a catalyst by securing

and holding leased areas used for restoration. Larger organizations

may have the capacity to help research and write proposals or even

provide matching funds.

Academic partners can provide the technical expertise as well as

the facilities and equipment (e.g., boats, labs, instrumentation)

to support the monitoring necessary for measuring project ou

comes. Involving academic partners early in the process is also 

good way to solicit input on the design to ensure that meanin

ful data can be collected to document results of a project. For

academic partners, the benefits of being involved with restorat

include community service, increased visibility, opportunities 

students to hone research skills, and having a platform for inqu

based education. 

Volunteers are vital connections to the local community and c

provide many services that would otherwise have to be contract

Build an Effective Partnership 

There are many stakeholders that care, for various reasons, about activities – including restoration – that affect the waterways ne

where they live, work or recreate. Engaging these stakeholders is an important step in the development of a project as the right mix o

partners can be a tremendous help in designing and implementing a successful restoration project and ensuring a sustainable result

(Brumbaugh 2000a). Different organizations or agencies possess different strengths, resources or capabilities, so building an effec

coalition of partners is perhaps the best way to facilitate a project. The exact mix of partners and their roles in the project will va

from project to project. Here are some general considerations for what various different agencies or stakeholders have to offer:

15.

V. Putting it all together
a tremendous leveraging opportunity. For federal grants, such as

those available through NOAA’s Community-based Restoration

Program (http://www.nmfs.noaa.gov/habitat/restoration), volunteer

time is valued at rates equivalent to contractors or staff hired to

perform similar tasks. Volunteers with appropriate training and 

2000b; Hadley and Coen 2002). It helps to have an academ

or research institution involved for advice and oversight to ens

appropriate methods are used for gathering the data and analyz

the project outcomes.

Securing Permits 

Soliciting input from local, state and federal agencies early on 

the design process will be helpful for identifying which permi

if any, are needed for a shellfish restoration project. Generally

speaking, anything that involves placing material such as oyster sh

or shell material on the bottom will involve a state or federal

permit under the Federal Clean Water Act. Often the author

for evaluating projects and issuing permits under the Clean

Water Act has been delegated to a state agency, although fede

oversight is still in force as well. Likewise, placing shell or oth

structures (e.g., aquaculture cages, predator control nets, etc.) 

likely also regulated by the Federal Rivers and Harbors Act

through the U.S. Army Corps of Engineers. In any event, it 

important to investigate permitting requirements early in th

design process to identify which actions are regulated, how lon

might require to secure permits, and what kind of environmen

monitoring requirements might accompany a permitted activ

Raising Awareness 

An often overlooked part of restoration projects is the media

outreach strategy. This is an invaluable part of any restoration

project because it helps to ensure that the project is supporte

by those who live, work and recreate in the vicinity of the proj

Again, a diverse partnership can be helpful for providing acce

to media contacts and assistance in preparing and distributing

press releases. Such partnerships also make for attractive stori

which can increase the chances of having the media highlight yo

project. Restoration projects are tremendous vehicles for calli

attention to not only to specific places and objectives (e.g., restor

shellfish to your local waterway), but they are also invaluable

opportunities for drawing attention to larger, related issues 

habitat conservation, water quality, and coastal management

Integrating these themes into your press releases and com

munication with the media is a great way to raise public

awareness of these other broad topics.

Footing the Bill 

While funding for habitat restoration has been increasing (Bernha

et al. 2005), finding the right funding source or combination 

sources is still a time consuming process. All of these partner

can help to bring funding or in-kind donations to support the

project, and it is important not to overlook the monetary valu

of their contributions (e.g., capturing volunteer hours as in-ki

match to use as leverage for grant funds). Most funders of

restoration activities, whether they are public agencies or priv

foundations, are interested in seeing their funds leveraged a

much as possible. Look for ways to leverage partner’s contributio

whether this is a direct financial contribution or an in-kind servi

As mentioned in the previous section, volunteer-time is a

important and valuable source of in-kind match that can be u

in many instances.

16.
17.

Private ownership provides a platform for ecosystem-based conservation, restoration and partnership

Project Synopsis:

Great South Bay, a shallow tidal lagoon inside Long Island’s south shore, was once known as the “clam factory”. In the 1970s, fishermen

pulled more than 700,000 bushels of wild hard clams (Mercenaria mercenaria) from the sandy bottom of the Bay, and supplied more

than 50 percent of the annual catch in the U.S. However, the fishery was not sustainable and as clam populations declined in the

late 20th century, the harvest dwindled to just 1 percent of the peak level seen in the 1970s. In addition to local economic losses,

profound changes to the ecosystem have become apparent as well. Without enough clams to filter the bay’s waters, brown tides

caused by microscopic algae became prevalent. The blooms killed additional shellfish and prevented sunlight from reaching underwater

grasses that provide a refuge for young fish, crabs and other organisms.

Since 2002, The Nature Conservancy has acquired 13,000 acres of submerged lands in Great South Bay from the Bluepoints

Oyster Company, representing about 20 percent of the bottom of the Bay. The Conservancy’s Conservation by Design planning

process has guided the formation of the Bluepoints Bottomlands Council, a group of

stakeholders, local state and federal agencies and scientists, that is committed to creating

and implementing a plan “to restore Great South Bay to a thriving, healthy, naturally

productive, self-sustaining estuary that supports native shellfish, seagrass, and other

essential ecosystem components.” TNC and its partners have embarked on a restoration

plan that has the following elements:

• Establish a network of spawner sanctuaries to allow clams to accumulate, grow

and reproduce, thereby supplying offspring to other parts of the Bay.

• Stock approximately one million adult clams per year for several years to increase

the overall level of clam reproduction in the Bay.

• Measure survival and reproduction of clams transplanted into sanctuaries.

• Maximize survival of clams in sanctuary areas through ecosystem-based

approaches to managing predators.

• Identify nutrient sources and understand their broad ecological effects on 

the ecosystem.

The restoration activities on the Bluepoints property are being closely monitored by The

Nature Conservancy and its partners. Results to date have increased our understanding

of clam reproduction in the Bay, and are leading to improvements in transplanting

approaches. The broad involvement of stakeholders is intended to foster greater sense

of community stewardship of the estuary and its resources, and should ensure that 

future harvest management and enforcement efforts are consistent with long-term 

sustainability of a more functional ecosystem.

Hard clam restoration in

Great South Bay, New York

Carl LoBue, a scientist with The Nature Conservan

adult hard clams to a sanctuary located on TNC’s ‘B

Property’ in Great South Bay. Stacy Goldyn-Moller, 

< The Nature Conservancy is using its ownership stake in Great South

Bay to bring stakeholders together to restore the entire ecosystem.
18.

Pamlico Sound oyster reef projects demonstrate strategies for large scale restoration

Project Synopsis: 

Like so many coastal embayments from Nova Scotia to the Gulf of Mexico,

the Sounds behind North Carolina’s Outer Banks once supported tremendous

populations of the eastern oyster, Crassostrea virginica. Extensive areas of

oyster reef habitat were formed by these populations and supported

diverse assemblages of fish, crustaceans and other marine life. Tragically, the

oyster population and extensive oyster reef structure in North Carolina

has declined to only a small fraction of what it once was, and with it the

fisheries that shaped coastal communities until well into the 20th century. 

In 2001 The Nature Conservancy, in partnership with the NOAA

Community-based Restoration Program and the NC Division of Marine

Fisheries, began working to develop and refine new approaches for restoring the eastern oyster (Crassostrea virginica) to Sounds of

coastal North Carolina. Since then, TNC and its partners have taken the following actions since to address the decline of native oyste

populations in the Sound:

• Created multiple spawner sanctuaries to allow oysters to accumulate, grow to lar

sizes, reproduce and supply larvae to other parts of the Sound.

• Constructed large three-dimensional oyster reefs within sanctuary areas using

Class-B rip-rap marl (limestone rocks about the size of basket balls). The reef

structure mimics historic shape of reef habitat that once occurred in the Sound.

• Monitored the settlement, growth and survival of oysters on newly constructed

reefs and documented the use of restored reefs by other species.

The monitoring data collected on reefs constructed since 2001 verifies what had

been hypothesized by researchers – that oyster growth and survival is enhanced b

the three-dimensional reef structure, and that a diverse array of species will use

restored reefs. Validation of these concepts has been a key to inspiring state and

federal agencies to look to larger scale application of this strategy in the Sound. T

facilitate this work, additional questions remain to be addressed: What spatial co

figuration of reef sanctuaries is optimal for achieving Sound-wide benefits? Wh

size and spacing of reefs within sanctuaries provides the optimal biodiversity and

habitat benefits? Restoration at larger scales, along with continued monitoring, w

help to address these questions and provide lessons to export for shellfish restorati

in other locations.

Eastern oyster restoration in 

Pamlico Sound, North Carolina

< Oyster sanctuaries in North Carolina. The Nature Conservancy

Careful monitoring is key to understanding the effects of

restoration. Rob Brumbaugh, TNC

Limestone marl is used to restore oyster reef structure within sanctuaries. NC Division of Marine Fisheries
19.

A systematic approach leads to development of restoration strategy

Project Synopsis: 

At one time, Puget Sound was home to large populations of the Olympia oyster, Ostreola chonchaphila, the only oyster native to the regio

Overharvest and pollution led to dramatic declines in Olympia oyster populations between the mid-1800s to the early-1900s, to th

point where the commercial shellfish industry now depends on non-native oysters introduced to the region in the early 20th centu

With support from the NOAA Community-based Restoration Program and other funders The Puget Sound Restoration Fund

(PSRF) and Washington Department of Fish and Wildlife (WDFW) set out in 2004 to revitalize the native Olympia oyster on a

site in Liberty Bay, a small embayment in Puget Sound that once had a robust native oyster population. A systematic approach has

been used to determine the best strategies to pursue for restoration. 

• Baseline surveys were conducted to identify any existing native oysters in Liberty Bay, and to determine how much habitat wa

available for settlement of new oysters

• The abundance and population structure of the local oyster population was assessed using quadrat samples (i.e., noting how

many larger, older oysters exist relative to smaller, younger oysters).

• The timing and extent of oyster reproduction was measured by sampling oysters

at various times and examining gonads to look for signs of eggs and sperm cells.

• Additional reef habitat was constructed adjacent to existing oyster reefs using

oyster shells purchased from commercial shellfish companies. Shells were

deposited in layers thick enough to ensure an adequate settlement habitat was

created on the bottom of the Bay.

The baseline surveys conducted by PSRF and WDFW informed the later steps in this

project. Multiple size classes of Olympia oysters were present at the site, indicating that

oyster settlement was occurring on a regular basis in Liberty Bay. However, surveys also

revealed that clean shell habitat for oysters was in short supply. Armed with this information, PSRF and WDFW along with their additional project partners, Suquamish

Tribe, U.S. Navy and Hood Canal Oyster Company, focused their subsequent restoration

efforts on construction of new oyster reef habitat. Plots of clean shell were created

adjacent to existing reefs and monitored for settlement of juvenile oysters. An expansion

is planned to take advantage of the more than 10 acres of tidelands identified as suitable

for restoration. Next steps also include monitoring of other fish or invertebrates that

use the restored habitat, and evaluating the potential impacts of predators, including an

introduced snail, on the project’s overall outcome.

Native oyster restoration in

Puget Sound, Washington

< Betsy Peabody, Executive Director of PSRF, measures oyster size

and abundance along transect in Liberty Bay. Kay McGraw, NOAA

Oyster shells are sprayed from the deck of a bardge 

new oyster habitat in liberty Bay. Tristan Peter-Conte
20.

Temperate marine and estuarine ecosystems are places of significant biodiversity and threat. The lands around these systems have bee

the centers of human habitation with landscapes that have been dramatically altered by human activities, so it is not entirely surpris

to find them in poor condition throughout much of the world. From a societal standpoint, returning these systems to a more desirab

prior condition (NRC 1992) will require a significant commitment of funding and other resources, coupled with a management paradigm

that recognizes the value of ecosystem services provided by various habitats and other components of these systems (Breitburg et a

2000). From a scientific standpoint, this will require a more interdisciplinary approach to understanding how the various componen

of marine and estuarine ecosystems interact to allow species or habitats targeted for restoration to persist (Peterson and Lipcius 200

Given their multi-faceted role within nearshore marine systems, the

conservation and restoration of bivalves is emerging as a priority for

state and federal agencies as well as the conservation community in

general. Benefits to commercial and recreational fishery stakeholders

make these groups a natural ally in this endeavor, but the broad

suite of ecological benefits should attract even greater public

support. While the perceived benefits of restoration seem clear,

and some effort has been placed on describing the general

attributes and community structure of shellfish ecosystems, the

approaches to documenting ecosystem benefits from restoration

are still very much in their infancy. Modeling exercises have been

used to explore the theoretical relationships between bivalve

population size and certain ecological functions, but there have

been few tests of these relationships in the field to validate

assumptions or findings.

Shellfish landings have served as a primary metric used to gauge

the impact of restoration efforts (NRC 2004). While fisheries

production is certainly a valuable service, it is important to recognize that it may be years or decades for some shellfish ecosystems

to recover to the point of sustaining higher shellfish fishery yields.

For restoration to gain the momentum needed to achieve the

gains in biomass necessary to deliver the many ecosystem services

we deem important, we must redouble our efforts to measure 

document the ecological, not just the economic, performance 

projects at every scale. Restoration practitioners should seek t

elevate ecosystem services such as provision of habitat and wa

quality as priorities for shellfish projects and should strengthe

collaborations with research scientists to refine monitoring

approaches to adequately document these services. Results

should be communicated broadly within scientific, manageme

and public forums to develop a broader base of support for

shellfish restoration and protection. Communicating more

directly with the public, through effective media outreach, 

also an important component of restoration as this helps to

build support for your restoration project specifically, but a

for improved long-term coastal management overall.

Finally, it is important to note that shellfish restoration is still

very much in its infancy and there is much room for further

innovation and improvement to the approaches identified her

To that end, we hope this document helps to spur new restorati

projects that, with effective monitoring, will advance the field 

restoration and help to build support for expanded restoratio

activities in the future.
21.

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27.

Some relevant web sites related to shellfish, restoration and monitoring

EPA’s Shellfish Web Site:

http://www.epa.gov/ost/shellfish/

Interstate Shellfish Commission:

http://www.issc.org/

Maryland Seagrant Oyster Page:

http://www.mdsg.umd.edu/oysters/

Virginia Institute of Marine Science shellfish restoration atlas:

http://www.vims.edu/mollusc/oyrestatlas/oramaptoc.htm

Gulf of Maine Restoration Goals:

http://www.gulfofmaine.org/habitatrestoration/

SCORE! South Carolina Oyster Restoration and Enhancement Web Site:

http://www.csc.noaa.gov/scoysters/

South Carolina DNR Shellfish Research:

http://www.dnr.sc.gov/marine/mrri/shellfish/index.htm

Oyster Shell Recycling in South Carolina

http://saltwaterfishing.sc.gov/oyster.html

Restore America’s Estuaries Principles of Estuarine Habitat Restoration:

http://www.estuaries.org/assets/documents/Principles.pdf

Society or Ecological Restoration International (Primer on Ecological Restoration):

http://www.ser.org/content/ecological_restoration_primer.asp

NOAA Community-based Restoration Program

http://www.nmfs.noaa.gov/habitat/restoration/

Army Corps of Engineers

http://www.usace.army.mil/

U.S. Fish and Wildlife Service

http://www.fws.gov/coastal/

http://www.fws.gov/partners/

EPA Office of Welands, Oceans and Watersheds:

http://www.epa.gov/owow/

Geological Survey

http://www.usgs.gov/

National Park Service:

http://www.nps.gov/

Natural Resources Conservation Service:

http://www.nrcs.usda.gov/

EPA Volunteer-based Monitoring Web Site:

http://www.epa.gov/owow/estuaries/monitor/

EPA’s Principles of Habitat Restoration

http://www.epa.gov/owow/wetlands/restore/principles.html

National Sea Grant:

http://www.nsgo.seagrant.org/

South Carolina oyster reef monitoring workgroup

http://www.coastal.edu/marine/sgoyster/
28.

Front cover: Barry Truitt, The Nature Conservancy; Rob

Brumbaugh, The Nature Conservancy; Carl LoBue, The Nat

Conservancy; Debbie Dalton Welch, NY/NJ Baykeeper; Bet

Peabody, Puget Sound Restoration Fund 

Cover Background: Alan Power, G.E.O.R.G.I.A. Project 

Inside front cover: Carl LoBue, The Nature Conservancy 

Page 2: Rob Brumbaugh, The Nature Conservancy

Page 3: Tristan Peter-Contesse, Puget Sound Restoration Fun

Page 4: Betsy Peabody, Puget Sound Restoration Fund 

Page 5: Barry Truitt, The Nature Conservancy 

Page 6: Stephanie Hunt, NOAA Restoration Center 

Page 7: Carl LoBue, The Nature Conservancy 

Page 8: Nicole Vickey, The Nature Conservancy 

Page 9: Barry Truitt, The Nature Conservancy 

Page 10: Carl LoBue, The Nature Conservancy 

Page 12: Betsy Lyons, The Nature Conservancy 

Page 14: Rob Brumbaugh, The Nature Conservancy; Aaron

McCall, The Nature Conservancy 

Page 15: Alan Power, G.E.O.R.G.I.A. Project; Rob Brumbau

The Nature Conservancy 

Page 16: Debbie Dalton Welch, NY/NJ Baykeeper; Rob

Brumbaugh, The Nature Conservancy 

Page 20: Debbie Dalton Welch, NY/NJ Baykeepe; 

Page 28: Alan Power, G.E.O.R.G.I.A. Project 
Brumbaugh, R.D., M.W. Beck, L. D. Coen, L.Craig and P. Hicks. 2006. A Practitioners' Guide to the Design and Monitoring of S

Restoration Projects: An Ecosystem Services Approach. The Nature Conservancy, Arlington, VA.

Contact:

Robert D. Brumbaugh

Global Marine Initiative The Nature Conervancy

University of Rhode Island Narragansett Bay Campus

South Ferry Road

Narragansett, RI 02882

rbrumbaugh@tnc.org
“A disposition to preserve and an ability 

to improve, taken together, would be 

my standard of a statesman.” 

- Edmund Burke