A Review of Compensatory
Mitigation in Estuarine and
Marine Habitats


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Compensatory Mitigation in Estuarine and Marine Habitats

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Acknowledgements

Principle authors of this report were Emily French and Brian Topping (EPA Headquarters).
Thank you to the reviewers, including Steve Martin from USACE Institute for Water
Resources (retired); Susan Marie-Stedman from NOAA Headquarters; David O'Brien from
NOAA Fisheries; Jennifer Siu from EPA Region 9; Palmer Hough, Betsy Valente and Brittany
Bennett from EPA Headquarters; Aisling O'Shea from Massachusetts Department of Fish
and Game ILF Program; and Kristina Tong from USACE Seattle District. They offered their
expertise, including input on multiple drafts, and immeasurably improved this report.

Thank you also to the staff at the USACE's Seattle, San Francisco, Los Angeles, Galveston,
Jacksonville, Norfolk, and New England district offices for providing us with records on
permittee-responsible mitigation and assisting with interpreting ORM records.

Finally, we acknowledge the third-party mitigation providers who explained the landscape
and habitats at their sites and shared their monitoring methods and performance
standards. Thank you for the time that you took to exchange many phone calls and emails
with us.

We appreciate the assistance from all the aforementioned groups in writing this report and
are thankful for their commitment to improving estuarine and marine compensatory
mitigation.

Cover photo from Gulf Islands National Seashore (National Park Service) in Florida, an area
where the four habitats primarily featured in this report coexist. Photo by Emily French.

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Compensatory Mitigation in Estuarine and Marine Habitats

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'>i1 ¦'.•inn .

This review of compensatory mitigation in estuarine and marine habitats was conducted in
support of the Clean Water Act 404(b)(1) Guidelines including the 2008 Final Rule
Compensatory Mitigation for Losses of Aquatic Resources. It has been subjected to review
by EPA and approved for release. The mention of trade names or commercial products
does not constitute endorsement or recommendation for use. This review is not intended,
nor can it be relied upon, to create any rights enforceable by any party in litigation with the
United States. Anyone may decide to use the information provided in this document or not.
This document is not a regulation itself, nor does it change or substitute for statutory
provisions within EPA or USACE regulations. Thus, it does not impose legally binding
requirements on EPA, USACE, States, or the regulated community.

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Contents

Acknowledgements	1

Disclaimer	2

Glossary	5

Executive Summary	7

Introduction	8

Objectives	9

The focal habitats	10

Value and status of the focal habitats	12

Methods	14

Third-party mitigation	14

Permittee-responsible mitigation	15

Voluntary restoration and ambient monitoring	16

Results: Inventory	17

Third-party mitigation	17

Permittee-responsible mitigation	18

Voluntary restoration and ambient monitoring	19

Results: Seagrass	21

Third-party mitigation	21

Permittee-responsible mitigation	21

Monitoring and performance	22

Voluntary restoration and ambient monitoring	23

Results: Oysters	24

Third-party mitigation	24

Permittee-responsible mitigation	24

Monitoring and performance	25

Voluntary restoration and ambient monitoring	25

Results: Tidal flats	27

Third-party mitigation	27

Permittee-responsible mitigation	27

Monitoring and performance	27

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Voluntary restoration and ambient monitoring	28

Results: Shallow water	30

Third-party mitigation projects	30

Permittee-responsible mitigation projects	30

Monitoring and performance	31

Voluntary restoration and ambient monitoring	32

Discussion	33

Recommendations	38

Improving mitigation practices	38

Improving documentation and record-keeping	38

Next steps for research	39

Training opportunities	40

References	41

Appendix A- Data and tables	46

Table 1- Search Terms for third-party Mitigation in RIBITS	46

Table 2- Third-Party Mitigation Providers: Banks	47

Table 3- Third-Party Mitigation Providers: ILFs and Sites	49

Table 4- Department of the Army Permits	52

Table 5- Ambient monitoring programs	54

Table 6- California Eelgrass Mitigation Policy Performance Standards	55

Appendix B- Out-of-kind mitigation	56

Table 1- In-kind and out-of-kind mitigation	58

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Glossary

404 Program: A program established by Section 404 of the Clean Water Act regulating the
discharge of dredge and fill material into waters of the U.S. that is implemented primarily
by U.S. Army Corps of Engineers (USACE) or authorized states1 and the Environmental
Protection Agency (EPA).

Ambient monitoring site: A monitoring site that is not necessarily tied to a restoration
project; it may be a naturally-occuring population of organisms or a natural habitat area
monitored for preservation or research purposes.

Assessment methodology: The mechanism or tool used to evaluate either the loss of
functions or services at a permitted impact site or a gain in functions or services provided
at an associated compensation site.

Compensatory mitigation: Within the 404 Program, this refers to the restoration,
establishment (creation), enhancement, or preservation of wetlands, streams, or other
aquatic resources for the purpose of offsetting unavoidable adverse impacts.

Credits: A unit of measure representing the accrual or attainment of aquatic functions or
services at a compensatory mitigation site.

DARTER (Data on Aquatic Resources Tracking for Effective Regulation): EPA database
that receives data from the USACE ORM (OMBIL Regulatory Module) database.

District: Refers to a USACE district office.

ILF (In Lieu Fee): A sponsor that collects funds from multiple permittees in order to pool
the financial resources necessary to build and maintain the compensatory mitigation
site(s). The sponsor is a public agency or non-profit organization.

ILF site: A compensatory mitigation project developed by an ILF to offset permitted losses
of aquatic resource functions and services.

Impact: In this report, impact refers to the adverse effects of a discharge of dredge or fill
material into an aquatic resource.

In-kind: Compensatory mitigation that provides a resource of a similar structural and
functional type to the impacted resource.

Instrument: Refers to a mitigation bank or ILF's binding legal agreement and any
associated exhibits/attachments.

1 As of November 2022 Michigan, New Jersey and Florida has been authorized to implement the 404
permitting program for certain waters.

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IRT (Interagency Review Team): A group of federal, tribal, state, and/or local regulatory
and resource agency representatives that reviews documentation for and advises the group
chairs (USACE district and any other agency chairing the IRT) regarding establishment and
management of a mitigation bank or an ILF program or site.

Focal habitats: Seagrass, oysters, tidal flats, and shallow water.

Mitigation bank: A compensatory mitigation site with credits for sale that correspond to
habitat area. Mitigation banks collect funds from permittees that have impacted habitat at
another location. Mitigation bank sponsors are typically private organizations. Also
referred to as "bank" throughout report.

ORM (OBMIL Regulatory Module): An USAGE database that stores permit information,
including 404 Program permit information.

Out-of-kind: Compensatory mitigation that provides a resource of a different structural
and functional type than the impacted resource.

Oysters: Bivalve mollusks found in estuarine and marine, intertidal, and subtidal areas.

PRM (Permittee-responsible mitigation): Compensatory mitigation performed by the
permit applicant or their contractor.

Provider: Any entity providing compensatory mitigation or restoration services.

RIBITS (Regulatory In-Lieu Fee and Bank Information Tracking System): A national
web-based application used by multiple federal agencies to track mitigation bank and ILF
credits and details.

Seagrass: Rooted, vascular, salt-tolerant plants that exist in subtidal and intertidal areas.

Shallow water: Subtidal, vegetated or unvegetated estuarine or marine waters (see
introduction section for more information).

Sponsor: The entity that establishes and operates a bank or ILF program (i.e., mitigation
bank or ILF program sponsor).

Third-party mitigation: Compensatory mitigation performed by a mitigation bank or ILF
program.

Tidal flats: Intertidal, unvegetated, low-energy areas comprised of fine-grained material.
Waters of the U.S.: Aquatic resources regulated under the Clean Water Act.

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Executive Summary

Environmental restoration, the ecological improvement of natural resources, can be
voluntary or can be required by regulation. Section 404 of the Clean Water Act (CWA) is an
example of a regulation that requires environmental restoration (or compensatory
mitigation when used in this context) to be performed when certain unavoidable
environmental impacts occur. The CWA Section 404 Program regulates the discharge of
dredged or fill material into waters of the United States, including in coastal habitats.

Despite the efforts of voluntary and regulated restoration, coastal habitats continue to
diminish in area and ecosystem functioning. To help assess the state of these efforts and to
better inform mitigation decisions, this report reviews compensatory mitigation that has
taken place under the CWA Section 404 Program in estuarine and marine habitats. Broadly,
the report quantifies estuarine and marine third-party mitigation providers, then narrows
the focus to seagrass, oyster, tidal flat, and shallow water habitats to provide examples of
project types, monitoring methods, and performance standards. A review of large-scale
voluntary restoration projects involving seagrass, oyster, tidal flat, and shallow water
habitats is also included.

This report documents practices from across the country, which may be useful for federal
and state regulators who review permittee-responsible and third-party mitigation project
proposals, and for mitigation and other restoration providers. Based on available
information from the CWA Section 404 Program databases, permits, and mitigation bank
and ILF (In-Lieu Fee) program documentation, estuarine and marine mitigation projects
were found to comprise a small but significant proportion of all compensatory mitigation
projects: 2% of banks, 21% of ILF programs, 9% of ILF program sites, and 5% of PRM
(permittee-responsible mitigation). Compared to tidal flat and shallow water projects,
seagrass and oyster mitigation projects were found to have more comprehensive
monitoring methods and performance standards, and project area (size) may be more
commonly measured and tracked. Seagrass mitigation may also be occuring in-kind more
often than oyster, tidal flat, and shallow water mitigation. Preservation projects reviewed
generally had fewer monitoring methods or performance standards than restoration,
establishment, or enhancement projects.

From this baseline review of existing practices for estuarine and marine compensatory
mitigation, recommendations are made for future research and for CWA Section 404
program effectiveness. The challenges of providing compensation for impacts to, or in the
form of, unstructured habitats (i.e., tidal flats) are discussed, alongside recommendations
for record-keeping and development of assessment protocols.

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Introduction

Wetlands, streams, and other aquatic resources in the U.S. are intrinsically valuable and
essential to public health and well-being. However, humans are constantly modifying water
bodies, including those in coastal areas where high population densities occur. Although
statutes and regulations exist to protect aquatic resources, they also authorize impacts,
which lead to direct, indirect, and cumulative effects. In 1989, President George H. W. Bush
established the national "no net loss of wetlands" policy, which set the groundwork for
agencies across the federal government to begin balancing wetland loss with reclamation
and restoration efforts so the total acreage of wetlands across the U.S. would not decrease.
However, "no net loss" is a goal, and does not mean no losses occur; wetlands and other
aquatic resources are still lost through permit actions and unregulated activities. To offset
impacts, regulatory programs can require mitigation for impacts, and voluntary programs
also protect and restore wetlands, helping to pursue the goal of no net loss of wetlands
overall.2

The Clean Water Act Section 404 program (hereafter, 404 Program) uses compensatory
mitigation to not only protect against wetland loss, but also loss of other aquatic resources,
including streams and coastal aquatic habitats. Compensatory mitigation is the offsetting of
unavoidable impacts to wetlands or other aquatic resources resulting from a 404-
permitted activity with wetlands or aquatic resources that function similarly and are of
comparable size and value. Broadly, the 404 Program regulates the discharge of dredged
and fill material into waters of the United States3, unless the activity is exempt from Section
404 regulation (e.g., certain farming and forestry activities). When potential permittees
propose activities that will cause impacts to aquatic resources, they must show that steps
have been taken to avoid impacts, that the remaining potential impacts have been
minimized, and that compensation will be provided for all remaining unavoidable impacts4.
The U.S. Army Corps of Engineers5 (USACE) and Environmental Protection Agency (EPA)
jointly administer the 404 Program, through which USACE issues tens of thousands of
permits each year (Vanderbilt et al. 2015).

The National Oceanic and Atmospheric Administration (NOAA) National Marine Fisheries
Service (NMFS), Fish and Wildlife Service (FWS), and state and local agencies coordinate
and consult alongside EPA and USACE on 404 Program project reviews. Project size, impact
type, affected habitat, permit type, and permit conditions dictate whether compensatory
mitigation will be required. Compensatory mitigation can be provided though a third party
(a mitigation bank or In-Lieu-Fee [ILF] Program) or through a project initiated by the
permittee (permittee-responsible mitigation or PRM), and usually falls into one of four

2	For more information about federal funding sources for wetlands protection and restoration see
https://www.epa.gov/wetlands/federal-funding-wetlands.

3	For the definition of "waters of the United States," see: https://www.epa.gov/wotus.

4	For more information on the CWA Section 404 regulatory program, see: https: //www,epa.gov/cwa-
404/permit-program-under-cwa-section-404.

5	Michigan, New Jersey, and Florida have assumed the administration of the CWA Section 404 regulatory
program for many of the waters in their respective states. For more information about state and tribal
assumption of the Section 404 regulatory program, see: https://www.epa.gov/cwa404g.

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categories: restoration, preservation, establishment (creation), or enhancement. The 2008
Mitigation Rule, which revised and expanded rules governing how compensatory
mitigation projects are developed, reviewed, and implemented, requires performance
standards to be established for compensatory mitigation sites and monitoring reports to be
submitted to assess progress (33 CFR 332.4(c) and 40 CFR 230.94(c)). The 2008 Mitigation
Rule also includes a provision for difficult-to-replace resources, encouraging in-kind
compensation (33 CFR 332.3(e)(3)/40 CFR 230.93(e)(3)).

Despite the efforts of both regulatory and voluntary programs, aquatic resources in coastal
areas continue to diminish in area and ecosystem functioning. In back-to-back reports, FWS
and NOAA found that coastal wetlands have suffered considerable losses during the past 20
years (Stedman and Dahl 2008, Dahl and Stedman 2013). Coastal areas are not only
threatened by development but also by a suite of other stressors such as saltwater
intrusion, sea level rise, non-native species, and water quality impairment. A continuation
of such aquatic resource losses in coastal areas could result in an inability of coasts to
buffer water quality, increased flooding and vulnerability to storm surges, and extensive
habitat loss (Rezaie etal. 2020, Li etal. 2018).

This report reviews compensatory mitigation that has taken place in estuarine and marine
areas under the 404 Program. Although coastal wetlands and aquatic resources are diverse
and include freshwater and saltwater habitats, this report focuses exclusively on saltwater
habitats and specifically on seagrass, oysters, tidal flats, and shallow water (referred to as
'focal habitats' throughout), which are among the habitats referred to as "special aquatic
sites" under the 404(b)(1) Guidelines (EPA 1980)6. In the past, 404 Program staff at EPA
have noted that they had few examples to reference when compensation is needed for
impacts to these habitats, potentially because there are fewer permits involving these
habitats being issued (compared to freshwater wetlands and streams). To maximize
examples of projects involving seagrass, oysters, tidal flats and shallow water, a review of
voluntary restoration and ambient monitoring projects is also included in this report.

Objectives

The objectives of this report include the following:

1.	To understand how much estuarine and marine compensatory mitigation is occuring
across the U.S.;

2.	To better inform mitigation decisions for seagrass, oysters, tidal flats, and shallow
water habitats by (a) examining what types of compensatory mitigation projects exist
and what monitoring and performance criteria are used to evaluate them, and (b) by
providing references to voluntary restoration and ambient monitoring projects for the
same habitats.

6 The 404(b)(1) Guidelines (EPA 1980), a regulation central to the 404 Program, acknowledges that some
high-value habitats are especially difficult to replace and discourages the issuance of permits that would
result in their degradation or loss. The regulation identifies "special aquatic sites" that include seagrass (40
CFR 230.43), mudflats (40 CFR 230.42), and sanctuaries or refuges (40 CFR 230.40), which are often created
to protect oysters.

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Although there are other federal programs that require compensation for adverse impacts,
such as Natural Resource Damage Assessment or USACE Civil Works, only 404 Program
compensatory mitigation is evaluated in this report. This report provides information that
may be useful to federal and state regulators who review permittee-responsible and third-
party compensatory mitigation proposals, and to mitigation providers who develop and
implement compensatory mitigation projects.

The focal habitats

Oysters, seagrass, and tidal flats are found along shorelines nationwide and are common
features of estuaries and coastal bays. The three habitats co-occur in temperate areas of the
contiguous U.S., in shallow or intertidal waters.

Seagrasses are rooted vascular underwater or intertidal plants, distinguishing them from
algae (e.g., kelp) which do not have roots. Seagrasses grow in contiguous 'beds' or patches.
Seagrass beds or patches may fluctuate in size and location seasonally and from year to
year. Ten native seagrass species are found in the continental U.S.: Zostera marina
(commonly called eelgrass], Ruppia maritima, Halodule wrightii, Syringodium filiforme,
Thalassia testudinum, Halophila engelmannii, Halophila decipiens, Halophila johnsonii,
Phyllospadixscouleri, and Phyllospadix torreyi. One non-native seagrass species, Zostera
japonica, is featured in this report. The term 'seagrass' rather than 'submerged aquatic
vegetation' (SAV) is used here to identify salt-tolerant SAV species found in estuarine and
marine settings.

Oysters are bivalve mollusks found in areas with estuarine and marine salinities. They
grow in subtidal waters and sometimes intertidal areas depending upon climate (exposure
to extreme hot or cold air temperatures can desiccate or freeze oysters). There are two
oyster species native to the continental U.S.: Crassostrea virginica (commonly called
Atlantic oysters) found on the east and gulf coasts, and Ostrea lurida (commonly called
Olympia oysters) found on the west coast. Both species have been heavily exploited
commercially, with only a small percentage of their historic native populations remaining.
Although both species formed three-dimensional reef structures historically, few natural
reefs persist, and often, oysters are only found in patchy clumps. They are also found as
two-dimensional restoration projects, on reef balls or oyster castles as part of restoration
projects, or on shell bags or shell hash placed along living shorelines for restoration. For
the purposes of this report, and because few classic three-dimensional oyster reefs still
persist, all oyster presence was counted when searching for compensatory mitigation
projects. One non-native oyster species, Crassostrea gigas (commonly called Asian oyster),
is featured in this report.

Tidal flats can be broad, low-energy sheltered flats with fine-grained material; narrow,
fringing areas bordering salt marsh; or tidal creeks, which are unvegetated channels
exposed at low tide. Tidal flats occur in intertidal, estuarine or marine, relatively low-
energy areas. EPA regulations define mudflats as "broad, flat areas along the sea coast and
in coastal rivers...exposed at extremely low tides and inundated at high tides... substrate
containing organic material and particles smaller in size than sand... unvegetated or
vegetated only with algal mats" (40 CFR 230.42).

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Because the definition of tidal flats may vary, projects are only included in this report if
mitigation documentation or bank or ILF representatives self-identified as having tidal flat
(mudflat/sand flat) presence. Tidal flat areas that mitigation providers expected to become
vegetated in the future to produce tidal marsh are not included. Additionally, the term 'tidal
flat' is used throughout this report, as opposed to 'mudflat', to be inclusive of sand flats,
which are tidal flats located near high energy areas (e.g., oceans). However, sandy, high-
energy beaches are not included in this report.

Shallow water is defined in this report as subtidal (permanently covered by water)
estuarine or marine area, vegetated or unvegetated, with or without biogenic (e.g., oyster)
structures. 'Shallow' is a relative term; its definition changes depending on the region of the
U.S. and who is defining it. For instance, an EPA shallow water research conference defined
shallow water as "all marine and estuarine waters within four meters below mean low
water (MLW), including the intertidal zone" (Reilly et al. 1999), while other publications
have defined shallow water as between MLW and two meters deep (Bilkovic et al. 2009).

After consideration of the variability in turbidity and in light penetration depth in estuarine
and marine waters nationwide, three meters MLW was chosen as the cutoff depth for
'shallow water' for the purposes of this report. However, compensatory mitigation
documentation obtained for this research rarely stated water depth at mitigation sites,
making it difficult to say that every mitigation example featured in this report conforms to
this depth range (zero to three meters MLW). Ultimately, the authors' best professional
judgment was used, and the nature of mitigation projects included, for example creosote
piling removal or preservation of an embayment, seemed unlikely to exhibit water depths
greater than three meters.

Data on seagrass, oysters, tidal flats, and shallow water habitats can be collected using
aerial photography, sonar surveys, and in-situ diving and wading surveys. Common
methods for monitoring seagrass and oyster populations involve measuring the density
and size of plants or individuals. Tidal flat and shallow water monitoring may include water
quality measurements, sediment toxicity, grain size, infauna, fish communities, and other
wildlife presence.

Box 1- Habitat types explored in this report

Seagrass: Rooted, vascular, salt-tolerant plants that exist in subtidal and intertidal areas.
Not to be confused with seaweed or macroalgae such as kelp.

Oysters: Bivalve mollusks found in estuarine and marine, intertidal, and subtidal areas. Few
natural three-dimensional structures remain due to overexploitation.

Tidal flats: Intertidal, unvegetated, low-energy areas comprised of fine-grained material.
Present in estuarine and marine areas, and can appear as wide flats, salt marsh fringe or
intertidal channels.

Shallow water: Subtidal, vegetated or unvegetated estuarine or marine waters with or
without biogenic structures.

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Value and status of the focal habitats

Seagrass, oysters, tidal flats, and shallow water provide important habitat for both
commercially valuable species and small fish and invertebrates that are essential
components of the coastal ocean food web. Oysters and seagrasses are ecosystem
engineers, providing structure and refuge with their shells, canopies, and roots. Native and
migrating shorebirds use tidal flats to feed, and tidal flat and shallow water areas harbor
abundant infauna, including marine worms, clams, and crustaceans (Ray 2000). Tidal flats
and shallow water interspersed among structured habitats (like mangroves, salt marsh,
seagrass, or oysters) create a mosaic of foraging areas for predators (Orth et al. 1984,
Whitlow and Grabowski 2012, Kellogg et al. 2013).

All of the focal habitats improve water quality by functioning as coastal filters that trap and
remove excess nutrients and suspended sediments before they are exported to the ocean
(Mcglathery et al. 2007, Kellogg et al. 2018). Oysters and seagrasses assimilate nitrogen,
phosphorus, and carbon into their tissue and shell, sequestering it temporarily or
permanently depending upon the persistence of populations and whether the tissue and
shell are buried, consumed, or exported (Newell et al. 2004, Fourqurean et al. 2012).
Benthic microalgae, which occur at the sediment-water interface in intertidal and shallow
subtidal areas, function as a cap to retain sediment and nutrients (Pedersen et al. 2004).
Oysters and seagrasses create heterogeneity in sediments and aid in delivering organic
matter to the surface, both of which facilitate denitrification (removal of nitrogen from the
system) (Newell et al. 2005, Ward et al.1984, Aoki et al. 2019).

There is no nationwide analysis for how much seagrass, oyster, tidal flat, or shallow water
areas have decreased in acreage over time; however, some data and examples are available.
In the Chesapeake Bay, the largest estuary in the U.S., the oyster population is currently less
than 1% of historical levels (Wilberg etal. 2010). Eelgrass, one of two primary seagrass
species in the Chesapeake Bay, was historically abundant but has declined in area by 64%
over the last three decades (Richardson et al. 2018). In Maine, overfishing has significantly
reduced the abundance and diversity of species associated with tidal flats (Brown and
Wilson 1997). Along the Gulf of Mexico coast, several species of migratory shorebirds are
declining due to loss of coastal wetlands, including tidal flats and sandy beaches (Withers
2002). Shallow water losses in the Gulf of Mexico are being offset as storms and sea level
rise, causing the conversion of coastal marshes to shallow water habitat (Dahl 2011).

Aside from habitat conversion, a ubiquitous accelerant to the degradation of these habitats
is reduction of water quality, such as changes in water temperature, nutrients, and
alkalinity. Seagrasses and oysters are more vulnerable to mortality during sustained high
water temperatures (Moore and Jarvis 2008, Lowe et al. 2017, Green et al. 2019), and the
frequency of high-temperature events is predicted to rise. Excess nutrients from water
pollution may cause epiphytic algal growth on seagrass, which can prevent photosynthesis
(Dennison et al. 1993, Short and Burdick 1995). Oysters are threatened by rapidly
increasing acidity and CO2 levels in estuaries, which can decrease shell growth, size, and
strength (Hettinger et al. 2012, Waldbusser et al. 2011), leading to a reduction in the
number of juvenile oysters that survive into adulthood. Water quality impairment also has
negative effects on shallow water and tidal flats; the deposition of excess suspended solids

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can have cascading detrimental effects on tidal flat benthic communities (Reimer et al.
2015), and water contamination can cause fish kills and harm to shorebirds (Hargreaves et
al. 2011).

EPA's National Estuary Program (NEP), a network of 28 sites, and NOAA's National
Estuarine Research Reserve System (NERRS), a network of 29 sites, are among the
restoration and preservation programs around the country helping to conserve oysters,
seagrass, tidal flats, and shallow water habitat. These two programs preserve over one
million acres of estuaries. The National Park Service (NPS) also preserves thousands of
acres of estuaries. Examples of large-scale restoration include Chesapeake Bay's "10
Tributaries by 2025" program, which began restoring oysters in 10 rivers in 2013, and the
"Seagrass Restoration in Virginia's Coastal Bays" project, which began in 1999. These
efforts have respectively been called the largest oyster and seagrass restoration projects in
the nation. Tampa Bay is an example of a successful water quality improvement project. It
is a shallow bay with an average depth of 12 ft and includes oyster, tidal flat, and seagrass
habitat. Point source runoff reduction was part of a nutrient management strategy
implemented in the 1980s, and subsequently, the Bay has experienced a 60% reduction in
total nitrogen load and marked water quality improvements in shallow water habitat
(Greening et al. 2011).

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Methods

This report reviews compensatory mitigation implemented by third parties (mitigation
banks and ILF programs) and permittees, in addition to voluntary restoration and ambient
monitoring sites. The information is organized into subsections: third-party mitigation,
permittee-responsible mitigation, and voluntary restoration and ambient monitoring. The
results sections for each resource type also include a monitoring and performance
subsection in which third-party and PRM are discussed.

The aim of this report is to represent the most up-to-date and comprehensive information
available. However, some relevant information was inaccessible (e.g., monitoring reports).
To avoid potentially incomplete or misleading comparisons among specific projects, names
of third-party providers and Department of the Army permit numbers are not identified in
the body of this report. Instead, they are listed in Appendix A (Tables 2 and 3).

Third-party mitigation

RIBITS search- The USACE database RIBITS (Regulatory In-Lieu Fee and Bank Information
Tracking System)7 was queried for banks, ILF programs, and ILF sites where the focal
habitats were present. The search was conducted in March 2019 and was updated in
February 2021. The database was searched for third-party compensation in several ways.
First, the "Bank Summary Interactive" report was searched by the "Cowardin system list"
field for estuarine and marine sites (specifically, the search was performed using the
following string of terms: marine|estuarine|tidal|subtidal|intertidal|El|E2|Ml|M2). Then,
the "Bank Credit Classification Summary by Jurisdiction" report was searched, and the
"Credit Classification Type" and "Credit Classification" fields were filtered by the same
terms. Because some bank/ILF sites that were expected to appear in the search results but
did not, the reports for 23 keywords related to the focal habitats were also searched
(Appendix A Table 1). A few bank/ILF sites were also found by panning within the RIBITS
map viewer. Finally, through discussions with bank and ILF representatives, several ILF
sites were discovered that were not on RIBITS. If the ILF program was on RIBITS already,
these programs' sites were included.

These search methods returned banks and ILFs that are selling, have sold, or are approved
to sell estuarine and marine credits (statuses in RIBITS included "sold out," "approved,"
and "terminated"). Pending banks were not included because their status could change
before approval or could never be approved, and no umbrella banks appeared in the search
results. Several pending ILF sites were included because their programs were approved,
their sites secured, and their plans were available for Interagency Review Team (IRT)
review.

Documentation requests and analysis- At present, identifying third-party providers that
have seagrass, oyster, tidal flat, or shallow water habitat presence from RIBITS data is not
straightforward because credit types are named broadly (for example, "wetland" or
variants of Cowardin classes, like "El"). Other fields within RIBITS records also do not

7 https://ribits.ops.usace.army.mil/.

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

typically have specific habitat information. Therefore, studying instruments, mitigation
plans, and monitoring reports from the RIBITS cyber repository was necessary. These
materials were downloaded and reviewed for presence of the focal habitats, and for
compensatory mitigation project types, performance standards, and monitoring methods.
If none of the focal habitats were mentioned in this documentation, the bank or ILF
representative designated on RIBITS was contacted and asked if they knew of the presence
of these habitats on their sites. The bank/ILF was not included in the results section of this
report if the bank or ILF representative was unsure whether the habitats were present at
their sites.

Permittee-responsible mitigation

DARTER search- EPA's DARTER (Data on Aquatic Resources Tracking for Effective
Regulation) database was queried to find examples of compensatory mitigation projects
that involved the focal habitats in April 2019. DARTER houses information about USACE
decisions and milestones in the permitting process from the USACE ORM (OMBIL
Regulatory Module)8 database.

Permit actions were downloaded from DARTER and retained if any one of 22 mitigation-
related fields were filled out. The remaining projects were filtered by three fields:
mitigation type, regulation project was authorized under (e.g., Clean Water Act, Rivers and
Harbors Act, or blank) and Cowardin (Cowardin 1979) classification. Unlike RIBITS, which
has only third-party mitigation projects, DARTER has projects with compensation provided
by all three mitigation mechanisms (permittee-responsible, mitigation bank, or ILF).
Therefore, to avoid duplication from the third-party mitigation RIBITS search, only projects
with "permittee-responsible mitigation'" under the mitigation type field were retained.

Next, only projects authorized under CWA Section 404 were retained. Finally, projects were
filtered by Cowardin classification to retain only estuarine and marine projects. A small
number of projects were eliminated based on manual screening of the state field, for
example, for projects that occurred within inland states, the information in the Cowardin
classification field was assumed to be a typo. The resulting records were used to determine
states with the highest frequency of permits potentially requiring compensatory mitigation
in the focal habitats.

Permit requests and analysis- The five states with the most estuarine and marine
compensatory mitigation projects according to the search process were selected.9 Project
managers (hereafter, PMs) from each of the six corresponding USACE districts (hereafter,
districts) were established as points of contact and were emailed a request for permits,
mitigation plans, and any available monitoring reports for the projects. The documentation
received was reviewed to investigate whether it involved one of the focal habitats. If it did,
impacts and compensation details were noted.

Only projects that could be verified as having been permitted were included in this report.
Note, some projects are permitted but never built, and if the permitted impacts do not

8	httpsi//permits,ops,usace,army,mil/orm-public#.

9	Anticipating a large volume of permits, the PRM aspect of the study was limited to five states due to time and
resource constraints.

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Compensatory Mitigation in Estuarine and Marine Habitats

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occur, the compensatory mitigation does not occur either. Although mitigation information
was taken from the most recent information available for each project, in some cases only
the permit was available, which made it difficult to determine whether the mitigation
project occurred. In the results sections, the actions detailed in permits are referred to in
the past tense, unless documentation received indicated they are still in progress. Finally,
most project documentation referred directly to "compensatory mitigation," although some
referred to "mitigation." It was assumed that "mitigation" was used to mean "compensatory
mitigation," and all references in this report to "mitigation" are to compensatory mitigation.

Voluntary restoration and ambient monitoring

A review of voluntary restoration and ambient monitoring projects assisted with
understanding which monitoring methods and performance standards were typical for
seagrass, oysters, tidal flats, and shallow water. Ambient monitoring is monitoring that is
not necessarily connected to a restoration project, and such monitoring can occur on
natural populations of organisms or habitat areas. Voluntary restoration is restoration that
was not required by a regulatory program. Ambient monitoring and voluntary restoration
programs can help inform monitoring methods and performance standards developed for
compensatory mitigation projects. To find examples of these types of projects, an internet
search was performed, and the documentation retrieved was reviewed for project type and
monitoring and assessment information. In many cases, especially for national programs,
follow up and clarification with a program representative was necessary to ask for more
documentation and verify the methodology was current. The programs and projects
(Appendix A, Table 5) are global, regional, and local but are mainly large-scale.

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Compensatory Mitigation in Estuarine and Marine Habitats

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Results: Inventory

Third-party mitigation

Sixty-one IRT-approved mitigation banks and ILFs from RIBITS were categorized as
estuarine and/or marine. While vetting documentation, it became apparent that several of
the banks and ILFs had only freshwater habitats and were likely miscategorized.
Ultimately, 54 programs with estuarine or marine habitat were found in the search (38
banks and 16 ILF programs). The ILF programs include 111 sites (Figure la and b,
Appendix A Tables 2 and 3). The number of estuarine or marine ILFs and banks constitutes
2% of banks, 21% of ILFs, and 9% of ILF sites on RIBITS. Forty-four banks and ILFs across
18 states included seagrass, oyster, tidal flat, and/or shallow water (subtidal) habitats

Figure 1 - A: The number of banks with estuarine or marine habitats per state, B: The number of
ILF sites with estuarine or marine habitat per state.

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

State

Seagrass

Oysters

Tidal flat

Shallow
water

Alaska

2

-

5

2

California

2

-

2

4

Connecticut

-

1

-

-

Florida

4

2

1

6

Georgia

-

-

-

1

Louisiana

-

-

-

1

Maine

1

-

1



Massachusetts

1

1

-

1

Mississippi

-

-

-

1

New Hampshire

-

1

-

1

New Jersey

-

-

6



New York

-

-

1

1

North Carolina

-

1

1

1

Oregon

-

-

-

2

South Carolina

-

-

2

2

Texas

-

-

1

1

Virginia

1

2

2

2

Washington

1

1

2

-

Totals

12

9

24

32

Table 1- Third-party mitigation providers (ILF programs and banks) with focal habitats present by state (some
programs and banks have more than one focal habitat present].

A few unusual circumstances were revealed during the review process. Although four
banks had tidal flat habitat, bank representatives explained that it was not the final desired
habitat and that they were expected to vegetate, so they were not considered tidal flat for
the purposes of this report. There were also two banks in Florida where seagrass and tidal
flats were present within the bank boundaries, but sponsors were not issuing credits for
those areas, so those habitats were not counted as being present. Additionally, several
banks indicated uncertainty regarding oyster or seagrass presence as they did not conduct
monitoring of the underwater portions of the project site. Finally, in the results sections for
each resource type, area (in the form of acreage) is not given for third-party mitigation
projects, though it is for PRM projects; third-party mitigation projects were often mosaics
of habitats and did not provide area measurements for the focal habitats in their
properties.

Permittee-responsible mitigation

The initial search for projects that required compensatory mitigation in DARTER resulted
in 29,158 projects, which were then filtered and screened. Many records were not able to
be used because they were not labeled as a CWA Section 404 project (21% of 29,158) or
because they were not labeled as permittee-responsible (61%). There were 9051
remaining records, 487 of which had a Cowardin class of estuarine or marine (5%). The
remaining records, which spanned 21 states, were sorted by state and the five states with

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

the most records were selected for data collection. The states with the most projects were
Washington, Virginia, California, Florida, and Texas, with 260 projects total. The search was
performed on records from mid-2007 (ORM records began to be loaded into DARTER
starting in 2007) to April 2019.

PMs at corresponding district offices sent documentation on 214 of the 260 projects, and
studying the documents revealed that 55 of them involved the focal habitats (Table 2). PMs
reported some difficulty in locating and accessing records for various reasons. For instance,
some districts' records were digitized while others were not. The records provided for each
permit rarely contained a copy of each of the three requested documents (permit,
mitigation plan, and at least one monitoring report). PMs provided the following types of
documents: Nationwide Permit Verification letters, Letters of Permission, Department of
the Army Permits, Memorandum for the Record, mitigation compliance reports, monitoring
reports, mitigation plans, IRT correspondence, and USACE internal correspondence.
However, the project packets received rarely included more than a few of these document
types.

State

USACE
district

#

Projects

PMs
provided

# Permitted
projects
where
mitigation
involved

focus
habitats

Seagrass

Oysters

Tidal
flat

Shallow
water

California

LA

15

2

-

-

1

1

San
Francisco

21

8

5

-

2

1

Virginia

Norfolk

43

5

2

3

-

-

Texas

Galveston

7

2

-

1

-

1

Washington

Seattle

47

28

1

-

1

26

Florida

Jacksonville

81

11

5

1

-

5

Totals

214

56

13

5

4

34

Table 2- The number of permittee-responsible projects with focal habitats present at their mitigation sites by state and
USACE district [some projects have more than one focal habitat present].

Most mitigation project permits were issued post-2008 (Appendix A, Table 4), and most
involved restoration, establishment, or enhancement rather than preservation. In the
results section for each resource type, area is given (in the form of acreage) for permittee-
responsible mitigation as permit documentation usually included it.

Voluntary restoration and ambient monitoring

Although the internet search was not exhaustive, 17 examples of worldwide, national, and
regional restoration and ambient monitoring programs that monitor seagrass, oysters, tidal
flats, or shallow water were found (Appendix A Table 5). There was no shortage of

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Compensatory Mitigation in Estuarine and Marine Habitats	February 2023

academic studies with thorough monitoring and performance standards, but because those
studies' goals were research-oriented and more complex than the average mitigation
project, they were not included.

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Compensatory Mitigation in Estuarine and Marine Habitats

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Results: Seagrass

Third-party mitigation

There were 12 third-party mitigation providers
(three banks, nine ILFs) with seagrass presence at
their sites. The age of sites ranged widely, one
bank began restoring seagrass areas in the 1990s
while one bank and one 1LF have not yet
implemented their seagrass restoration
components (as of 2021). The seagrass at most
sites was eelgrass, though several programs in the
southeast worked with H. wrightii, S.filiforme and T, Lestudinum. Half of the providers were
preserving existing populations of seagrass at their sites, the remainder of the providers
were restoring, creating, or enhancing seagrass in a variety of ways. Several providers
transplanted seagrass from donor beds to restoration sites and one provider distributed
seeds to facilitate seagrass reestablishment. Three providers employed topographical
restoration techniques (removing fill or bringing propeller scars and other trenches up to a
suitable elevation for seagrass colonization), including one provider that used dredged
material. After topographical restoration, seagrass was either transplanted or expected to
recruit to the area naturally. One provider installed bird stakes, which are platforms for
birds to land on that enhance sediment nutrients and facilitate colonization of seagrass
populations (Fourqurean et al. 1995). Finally, one provider removed a tidal restriction,
which allowed seagrass to colonize part of the bank area.

Seagrass mitigation projects (third-party or PRM)
reviewed in this section occurred in the states in
shown in red.

Mitigation project types consisted of transplantation
from donor beds, topographical restoration, and seed
distribution. Topographical restoration projects
included excavating uplands, placing sediment tubes in
boat propeller scars (Figure 2), and filling in a channel
dredged though a historic seagrass flat. Multiple projects
mentioned the use of dredged material to construct the
mitigation area. Seed distribution projects involved a
university laboratory collecting flowering shoots of
seagrass, extracting mature seeds, and seeding
designated areas as compensatory mitigation. Impact

Permittee-responsible mitigation

There were 13 PRM projects, all of which restored, created, or enhanced seagrass beds
(there were no preservation projects) and were permitted or began somewhat recently,
between 2010-2018. The majority of projects took place in Florida and California. While all
of the seagrass mitigation projects in California, Washington, and Virginia involved
eelgrass, Florida's projects involved H. wrightii, S.filiforme•, R. maritima, and T. lestudinum.,
as well as the non-native llalophila ovalis. Projects
ranged in size from 0.005 to 2.61 acres, but most were
small, less than one acre.

Figure 2- Sediment tubes used for seagrass
restoration in St Joseph Bay, Florida. Photo by
Florida DEP.

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

types included public park projects in which boat ramps, jetties, trails, and culverts were
installed. Impacts also included installing poles for power lines, roadway and shoreline
improvement projects, dredging at a private residence, and a commercial dock installation.

Monitoring and performance

Most third-party and PRM seagrass projects were restoration, enhancement, or
establishment projects that had an acreage goal. A few projects had 'areal expansion of
seagrass beds' as a performance standard, although it was informal because there was no
set time limit or area goal. Monitoring methods and performance standards for the
restoration, enhancement, and establishment projects centered around canopy height,
shoot density, and percent cover. Most projects required in-situ monitoring, while a few
monitored seagrass beds via aerial surveys (these project types differed in that they used
seeds rather than transplants for restoration). One project used side-scan sonar for
monitoring its restored seagrass populations; although the sites were over ten years old,
the provider was interested in obtaining additional credits. Some third-party providers had
preservation sites, none of which had monitoring or performance standards for the
seagrass present. Several projects simply required noting land-use changes or landscape
alterations (on foot or by plane), and several required taking photos, some at established
locations (photo points).

The majority of restoration, enhancement, or establishment projects required reference
seagrass areas to be assessed in conjunction with monitoring the mitigation areas. These
projects usually required percent cover (and sometimes density and canopy height) at the
mitigation site to be equivalent to the reference site at the end of a monitoring period.
However, one project required percent cover to be equivalent to reference sites for two
consecutive years only within the monitoring period. Another required 80% cover and
density of reference site levels by the end of the monitoring period.

Seagrass mitigation projects in California follow performance standards established in the
California Eelgrass Mitigation Policy (or CEMP, NMFS 2014) or its predecessor, the
Southern California Eelgrass Mitigation Policy. The CEMP establishes a preference for in-
kind eelgrass compensatory mitigation, requires compensatory mitigation at a 1:1.2 ratio,
and requires at least five years of in-situ monitoring. Although the CEMP does not include a
suggested set of monitoring methods, it does have a suggested set of performance
standards for area, percent cover and shoot density at zero and six months and at years one
to five (Appendix A, Table 6).

Projects with in-situ monitoring used quadrats and transects to measure percent cover.
Several projects used the Braun-Blanquet method, which gives seagrass cover inside a
quadrat a score between one and five (Bell et al. 2008), while several estimated percent
cover using a grid within a quadrat (Rezek et al. 2019). Many projects used fixed transects,
while a few others selected transects or monitoring areas randomly. Performance
standards required that percent cover increase over time.

Several projects included informal (not quantitative) observance and notation of seagrass
epifauna (fish and invertebrates), epiphytes, macroalgae, and bioturbation. One project
also measured the prevalence of eelgrass wasting disease, which is caused by a pathogen
and periodically occurs in North American and European eelgrass populations

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

(Smithsonian 2018). A pending project proposes installing signage to increase seagrass bed
visibility to boaters. The associated performance standard is a decrease in the number of
boat scars over time. One project plans to measure sediment grain size within seagrass
beds. In Florida, because seagrass species are so numerous, the number species present
was also monitored in several projects.

Voluntary restoration and ambient monitoring

Mitigation projects retrieved in the search (Box 2) had similar monitoring methods to
voluntary restoration and ambient site monitoring programs. One difference between the
two was size: ambient and voluntary monitoring or restoration projects were typically
larger than compensatory mitigation sites and as a result could use aerial surveys rather
than in-situ monitoring. Ambient monitoring/restoration projects were also sometimes
more technical, measuring attributes like epifauna that live in seagrass beds. Voluntary
restoration and ambient monitoring projects did not typically assign performance
standards. Finally, no voluntary restoration projects modified the seafloor level to a depth
at which seagrass could grow; this was only seen in compensatory mitigation projects.

There are many examples of worldwide, national, regional, and local seagrass restoration
and monitoring programs. One program, Zostera Experimental Network, which was grant-
funded for six years but has been terminated, monitored ambient populations of eelgrass at
15 sites worldwide. Another worldwide monitoring program is SeagrassNet, which at one
time had 122 sites across 33 countries, although not all sites are currently operational. On a
national scale, NOAA's NERRS and EPA's NEP monitor seagrass at the reserves and sites
where it is present. For mapping resources, marinecadastre.gov hosts a national seagrass
layer that is a composite of data from state websites (NOAA and BOEM, 2019).

There are a few examples of regional seagrass monitoring programs. The Virginia Institute
of Marine Science has annual aerial surveys at sites across the Chesapeake Bay (Virginia
and Maryland). Some sites in this program have been monitored since the late 1980s. The
Florida Department of Environmental Protection (FL DEP) has an Aquatic Preserve
Program with 41 sites where seagrass is monitored where it is found. The Tampa Bay NEP
has been conducting aerial surveys and monitoring transects since the mid-1990s. Finally,
a large-scale eelgrass restoration project in Virginia's Coastal Bays monitors restored
populations and is billed as the world's largest seagrass restoration project.

Box 2- Common practices for monitoring seagrass mitigation sites

Common monitoring metrics: Percent cover, shoot density, area, canopy height

Other monitoring metrics: Wasting disease, water quality improvement, qualitative
assessments of epifauna, nekton, macroalgae, or bioturbation

Monitoring types: In-situ survey, aerial survey, sonar survey

Performance standards: Typically involved yearly documentation of progress toward an
acreage, percent cover and/or shoot density goal compared to reference site(s)

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

Results: Oysters

Third-party mitigation

Nine third-party mitigation providers (one bank,
eight ILFs) had oyster presence at their sites. Site
ages ranged from early 2000s to not-yet-completed
(as of 2021). The oyster species across all sites was
C. Virginia (or eastern oyster), except for one ILF site
which had C. gig as (Asian oyster). About half of the
providers were restoring, creating, or enhancing
oyster areas or reefs, while the other projects were
preserving existing populations or had created shoreline structure onto which wild oysters
had recruited (providers had not necessarily created the structures for this purpose).
Techniques used by the five providers restoring creating, or enhancing oyster areas
include deposition of oyster shell or other shell types (e.g., clam) for natural recruitment
(when wild oyster larvae attach to hard structures) or seeding reefs with 'spat-on-shell'
(juvenile oysters attached to shell, Figure 3).

Permittee-responsible mitigation

Five oyster PRM projects in Virginia, Texas, and Florida were permitted between 2005-
2019. All projects involved the eastern oyster. All projects were enhancement,
establishment, or restoration projects as opposed to preservation. Two projects were small
(<0.0.1 acre) while the other three ranged from 0.6 to 1.1 acres.

Oyster mitigation projects (third-party or PRM)
reviewed in this section occurred in the states in
shown in red.

projects (four of five) expected
natural recruitment, while one
project moved live existing
oysters. No spat-on-shell (Figure
3) were used. Impact types were
public (a city building a seawall, a
utility company installing poles
for power lines, and a military
base building a training facility) as
well as commercial (a dredged
material transfer facility,
bulkhead construction at a
restaurant, and two commercial
dock facilities).

Project iypes included constructing oyster areas using oyster shell and other materials like
crushed concrete, payments to a non-profit for the purchase of oyster shell for restoration
purposes, constructing a shoreline structure to which oysters recruited, and moving
existing oysters out of a project's impact footprint. The project that moved existing oysters
built a 15-inch reef base outside of the impact area that oysters and associated material
were transferred to. Most PRM

Figure 3- 'Spat on shell', juvenile oysters attached to a recycled oyster
shell in a hatchety setting. Photo by Emily French.

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

Monitoring and performance

Monitoring methods and performance standards for PRM and third-party projects were not
available for every oyster mitigation project. A few third-party preservation sites with
oyster presence did not do any oyster-focused monitoring. Several PRM projects either did
not have monitoring methods and performance standards or were unable to locate the
documents that would have had them. Across oyster mitigation projects that did have
monitoring methods and/or performance standards, common methods and standards were
related to oyster density, shell height, and area. All projects with methods and/or
standards required in-situ monitoring (no acoustic or aerial surveying). Among third-party
preservation sites with oyster presence, a few providers had chosen to measure density or
other attributes of the oysters present.

Only a few projects stipulated comparison of oyster mitigation areas with reference areas.
Performance standards for those projects required that the mitigation area must have
similar or better recruitment and survival to a nearby reference area.

In-situ monitoring required shell height measurements. Shell height is measured in
centimeters from the hinge to the top of the shell and measurements are used to bin
oysters into size classes (typically spat, juvenile, and adult or simply small and large).

Young (<6 months) oysters typically experience higher mortality rates than adult oysters
(Bartol et al. 1999), therefore collecting data on size classes can help gain insight into the
pressures a given population is experiencing.

Several projects took qualitative measurements of oyster-associated organisms, such as
fish, sessile organisms, oyster predators (in particular, oyster drills and boring sponges),
and fouling organisms. These projects also had qualitative performance standards, such as
'improving water quality and habitat in the area' or 'wild oyster recruitment and survival'.

One project tested for common oyster diseases caused by the parasites Haplosporidium
nelsoni and Perkinsus marinus. Another project measured volume of brown and black shell,
which is a proxy for whether reef substrate is buried and therefore unavailable for
colonization (black) or temporarily covered in mud (brown). Several projects had
construction-type performance standards, such as 'shell must be distributed across the
mound structure' or 'oyster bed establishment will be considered successful when the
concrete base is 18 inches high'. Finally, several projects measured the proportion of live to
dead oysters present.

Voluntary restoration and ambient monitoring

Although monitoring methods and performance standards were not available for every
oyster mitigation site, when sites did have them, methods and standards (summarized in
Box 3) were similar to those from voluntary restoration and ambient monitoring sites.
Additionally, unlike seagrass projects, several oyster ambient monitoring/voluntary
restoration projects had performance standards.

Examples of nationwide ambient monitoring programs include NOAA's NERRS program,
which monitors oysters on at least four of its 29 reserves. Although several reserves are
monitoring the eastern oyster, one west coast reserve is monitoring the Olympia oyster. In
terms of regional programs, in Chesapeake Bay, spurred by the Chesapeake Bay Agreement

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

(2014) and Executive Order 13508, oyster restoration in ten tributaries began in 2012 and
is currently ongoing. The restoration efforts differ by tributary. In some, juvenile oysters
and substrate (cultch or rock) are deployed. In others, only cultch is deployed for wild
juvenile oysters to attach to. Another large restoration project, Half Moon Reef, is located in
Matagorda Bay on the Texas coast. This project, which began in 2014, uses limestone as
substrate and has a hybrid approach: half the reef is a sanctuary, and the other half is open
to commercial harvest.

There were three other examples of statewide programs, all of which monitor ambient
populations: the Maryland Department of Natural Resources annual fall oyster recruitment
survey (a historic survey initiated in the 1950s), the North Carolina Department of Marine
Fisheries oyster sanctuary survey, and the FL DEP Aquatic Preserve program. The FL DEP
program has 41 sites and monitors many habitats, including oysters if they are present.
Across the nation, oyster restoration is popular and in the public eye; and there is no
shortage of smaller projects than those represented here that involve restoration or
monitoring of ambient populations.

Box 3- Common practices for monitoring oyster mitigation sites
Common monitoring metrics: Density, shell height, area

Other monitoring metrics: Proportion of live to dead oysters, amount of surface and
buried shell, oyster disease presence, natural recruitment, qualitative assessments of
associated reef organisms and fouling

Monitoring types: In-situ survey

Performance standards: Area and height goals for reef base (construction-type
specifications), density goals, similar recruitment and survival to a nearby reference reef

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

Results: Tidal flats

Third-party mitigation

There were 24 third-party mitigation providers
(17 banks, seven ILFs) with tidal flat presence at
their sites. The age of the sites ranged widely; one
bank was established in 1998 while another bank
is currently building their site (as of 2021). More
providers were restoring, enhancing, or creating
tidal flats as opposed to preserving them (about
15 as opposed to 9), and banks tended to restore, create, or enhance tidal flats while ILFs
tended to preserve them. Often, tidal flats were not the main focus of a given mitigation
project, but part of a mosaic of estuarine or marine habitats. For some projects, this made it
difficult to determine the compensatory mitigation method (restoration, enhancement,
establishment, or preservation).

Most of the providers that restored, created, or enhanced tidal flats were enhancing or
restoring them by removing a tidal restriction from a wetland complex. A few providers
had different approaches. One enhanced tidal flat by adding shell to enhance infauna and
epifauna plant and animal communities and another created tidal flat for salmon habitat.
Preservation sites with tidal flats ranged from marshes with intertidal channels, to barrier
island habitats known for being migratory bird habitat, to expansive tidal flats in areas with
a large tidal range.

Tidal flat mitigation projects (third-party or PRM)
reviewed in this section occurred in the states in
shown in red.

Monitoring and performance
Most third-party and PRM projects' tidal flat
components were not assigned distinct
monitoring methods or performance
standards. A few had performance standards

Figure 4- A mudflat in New Jersey, photo by Mark Renna.

Permittee-responsible mitigation

There were only four PRM sites with tidal flats, and all were establishment, enhancement,
or restoration projects. One of the sites also had a tidal flat preservation component. All
were permitted somewhat recently, between 2006 and 2017, and were in California and
Washington. Although two projects did not report the size of the tidal flats (or the
documentation obtained did not state it), the other two projects' tidal flat areas were large
(4.33 and 9.40 acres). Two projects created tidal wetland areas with salt marsh, fringing
tidal flats, and intertidal channels. One of the
projects used dredged material for
construction. Another project rehabilitated an
existing tidal flat but did not go into detail
about the methods (or the documentation
obtained did not state the methods). Impact
types included bridge replacement projects
and roadway improvement and re-grading
projects.

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

related to construction specifications (measuring acreage and hydrology by measuring
elevation and inundation). Tidal flats were often co-located with marsh restoration, which
required monitoring and had quantitative performance standards. Tidal flat preservation
projects had very limited monitoring; the extent of which was establishing photo points,
removing trash, looking for anthropogenic impacts on the site, and taking notes on general
site conditions. If tidal flats were monitored, it was usually in-situ, although a few projects
took aerial photos.

Other monitoring methods- Several tidal flat mitigation projects had more varied
monitoring methods, although they were often qualitative and most did not have
accompanying performance standards. A few projects sampled infauna, epifauna, surveyed
bird usage, and seined for fish when there was water overlying the tidal flats, and one
project compared these values to a reference site. A few projects measured water quality
when the flats were inundated with water. One project made observations of algal growth
on the flats. Three related sites (owned by the same mitigation provider) had performance
standards for hydrology and non-native plant presence. At two of the three sites, photo
points were established for time-lapse photos of a tidal cycle, a tidal gauge was placed to
monitor tide height, and observations of erosion were noted. Two sites sampled sediment
and fish and invertebrate tissue for heavy metals, in accordance with state guidance.

Voluntary restoration and ambient monitoring

No monitoring programs for which tidal flats were the sole focus were found within
voluntary restoration and ambient monitoring. Therefore, it was not possible to compare
monitoring methods and performance standards for tidal flats to compensatory mitigation.
There are several programs that use aerial survey data to map wetlands and soil types
(Fish and Wildlife Service's National Wetlands Inventory, Natural Resource Conservation
Service's soil survey, and NOAA's Coastal Change Analysis Program), and although the data
may capture tidal flats, they do not provide meaningful information about their
characteristics or condition. Regional examples were also sparse, but one restoration and
one research project were found. In southern California, a consortium of federal, state, and
non-profit partners is currently restoring mudflats in the San Elijo Lagoon. These groups
are planning to monitor the abundance and diversity of birds, fishes, and invertebrates, and
to monitor water quality overlying the intertidal flats (San Elijo Lagoon Restoration 2021).
Finally, U.S. Geological Survey (USGS) executed a tidal marsh sea level rise modeling survey
that required field data collection at nine sites in Washington and Oregon, some of which
included tidal flats. Monitoring included delineations of tidal mudflat area, gathering
elevation data, and inundation frequency (Thorne et al. 2015).

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Box 4- Common practices for monitoring tidal flat mitigation sites

Common monitoring metrics: Construction-type specifications (as-built area, tidal
hydrology), taking photos, informal monitoring for human disturbance

Other monitoring metrics: Infauna and epifauna abundance and diversity, water quality
measurements, fish population surveys, heavy metal presence in sediment and fish,
qualitative assessments of bird foraging

Monitoring types: In-situ survey, aerial survey

Performance standards: Mainly construction-related (area, hydrology)

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Results: Shallow water

Third-party mitigation projects
There were 32 third-party mitigation providers (22
banks, 10 ILFs) from states across the country with
shallow (subtidal) water at their sites. It was very
difficult to tell whether waters were subtidal at
providers' sites from RIBITS documentation, most
required follow-up with a bank or ILF
representative. The age of the sites ranged from
1996 to not-yet-completed (as of 2021). Most
providers restored, enhanced, or created shallow
water. There were few projects that preserved shallow water exclusively (about six of the
32). Most restoration, enhancement, and establishment projects involved reconnecting
waterways via removal of tidal restrictions by creating channels and removing fill.
Examples of tidal restrictions found in third-party documentation included mosquito
ditching, rice farming impoundments, dikes, and former roadway construction.

One provider improved benthic habitat and water quality of shallow water areas by
remediating sediment by neutralizing polyaromatic hydrocarbon (PAH) contaminants. A
few providers created shallow water by converting uplands. Several providers created
seagrass or oyster areas. When providers preserved shallow water habitat, it was generally
part of large, multi-acre wetland complexes.

Permittee-responsible mitigation projects
The 34 PRM projects that included shallow water
habitat were permitted between 2003-2019.

Projects occurred across Florida, Texas,

California, and Washington, though the majority
of the projects were in Washington (26 projects).

Of the Washington P RM projects, most were small
(<0.1 acre), although a few were larger (<1 acre).

Several of the Florida, Texas, and California
projects did not have sizes listed; the projects
that did ranged widely in size from 0.004 to 10
acres. One project removed derelict fishing gear
from a 581-acre open water area, however, the
actual mitigation footprint was not listed and
would have been much smaller. Like the third-party projects, most PRM projects restored,
enhanced, or created shallow water rather than preserving it.

In Washington, the most common compensatory mitigation project types were removal of
creosote-treated pilings, removal of subtidal or intertidal debris, removal of overwater
structures such as docks, and placement of gravel to enhance forage fish spawning habitat.
Creosote piling, intertidal and subtidal debris, and overwater structure removal frequently
occurred nearby or on the same site as the impact. Debris removal included items such as

30

Shallow water mitigation projects (third-party or
PRM) reviewed in this section occurred in the states
in shown in red.

Figure 5- Example of a shallow water impact- installation of
poles for power lines. Photo from a Jacksonville district
permit.


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fishing gear (nets, crab pots), old bulkhead and boat ramp material (concrete, other
rubble), tires, and a grounded vessel. One other mitigation project included establishment
of a 'shoreline cutback' to create shallow water. Compensatory mitigation projects from
Florida, Texas, and California involved rehabilitating a former dredged material storage site
and restoration of channels and lagoons that were part of wetland complexes. One
permittee planned to construct a stormwater treatment system, and two removed tidal
restrictions. Several projects removed derelict structures, including creosote pilings and
unused riprap.

The majority of the impacts were from the building of docks and associated structures at
private residences. There were also several public projects, including installing public
utility structures, building boat ramps, parks, seawalls, a military facility, bridge building
and repair projects, and one channel dredging project. Finally, the few commercial impacts
included bulkhead repair and pier-building projects.

Monitoring and performance

Many (about half) of the third-party mitigation providers did not have monitoring methods
or performance criteria for shallow water areas. Monitoring across PRM projects was
simple, and most projects did not have performance standards. The most common
monitoring methods and performance standards for PRM projects were taking photos and
requiring submittal of documentation that demonstrated compensatory mitigation was
complete. A few projects also required monitoring for adequate hydrology and collection of
qualitative information on wildlife use of the area (however, this was not always exclusive
to the shallow water habitat area present at the site). Water quality monitoring, fish
surveys, or other monitoring of shallow water characteristics were not required in any of
the PRM projects assessed.

Monitoring methods and performance standards for third-party providers' sites were often
written such that it was difficult to determine whether they applied to shallow subtidal
water areas exclusively, or to intertidal areas, tidal flats, vegetated areas, or the general
wetland complex. Following up with bank or ILF representatives did not always provide
clarification, so it is possible that some of the following monitoring methods and
performance standards may have been geared more toward intertidal than subtidal areas.

Most third-party monitoring and performance standards centered around hydrologic
conditions and water quality measurements. Providers measured hydrologic
characteristics by collecting water level, temperature, and salinity data from tide gauges
and sensors and by taking photos during the tidal cycle. A few providers took water quality
measurements using basic parameters (salinity, temperature, pH, dissolved oxygen) from
fixed stations or on surveys at regular intervals. Several providers monitored wildlife in the
shallow water areas at their sites. Fish population characteristics (diversity, abundance)
were measured using dip nets, traps, and seining. One provider divided fish present into
feeding guilds and tropic position. The same provider also monitored the wading bird
population. A different provider monitored salinity and fish populations to understand
whether hydrologic modifications offsite were affecting fish populations. Many of the
providers monitoring wildlife established performance standards and reference sites for
the comparison of compensatory mitigation site data.

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A few unique shallow water enhancement, restoration, and establishment projects are
highlighted herein. One provider that remediated sediment monitored the restoration area
by testing sediment samples and fish tissue for PAH concentrations and monitored benthic
infauna for abundance, diversity, and biomass. The performance standard was a sediment
PAH concentration below a set threshold. Another provider who was restoring a tidal
connection had the most complex monitoring methods and performance standards of any
shallow water mitigation project: the provider measured hydrology, water quality, fish and
wading bird populations, chlorophyll in the water column (as a proxy for algal presence),
light transmittance, and abundance and diversity of infauna. Each monitoring parameter
had a specific threshold to be met in relation to a reference site.

Voluntary restoration and ambient monitoring

A variety of project types within both compensatory mitigation and voluntary restoration
and ambient monitoring made it difficult to compare monitoring methods an performance
standards. Water quality improvement projects in shallow estuarine and marine waters are
being conducted across the U.S. at the national, regional, and local levels. Examples of
nationwide water quality testing programs that include monitoring in estuarine and
marine habitats include EPA's National Aquatic Resource Survey programs (National
Wetland Condition Assessment and the National Coastal Condition Assessment). The NOAA
NERRS and EPA NEP sites also measure water quality at many of their sites via fixed
stations or on surveys at regular intervals. Examples of regional water quality monitoring
programs include the NPS Eutrophication survey, the FL DEP Aquatic Preserve Program, as
well as many state-specific coastal water quality monitoring programs.

There are also many programs that purport to improve shallow water in ways other than
improving water quality, such as the Maryland Artificial Reef Program, which sinks
structures to create fish habitat in the Chesapeake Bay and in shallow coastal areas on the
ocean side of the state. Another example is the California Coastal Conservancy, which
maintains a program that removes creosote pilings from San Francisco Bay. Creosote-
contaminated sediments and pilings negatively affect fish by causing lesions and problems
with spawning (Malins et al. 1985, Vines et al. 2000).

Box 5- Common practices for monitoring shallow water mitigation sites

Common monitoring metrics: Water quality monitoring hydrologic monitoring via tide
gauges, fish diversity

Other monitoring metrics: Reef-associated organism species diversity and size class,
sediment toxicity, fish tissue toxicity, sediment infauna abundance and diversity, light
levels, oxidation/reduction potential

Monitoring types: In-situ survey, sonar survey

Performance standards: Varied from project to project and were not consistent

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¦ V . i. ¦ 111. i

The goal of this report was to review compensatory mitigation in estuarine and marine
habitats, which are less prevalent than freshwater wetlands and streams within the 404
Program. The search results showed that estuarine and marine habitats were present
across 21 of 23 coastal states at 2% of banks, 21% of ILF programs, 9% of ILF program
sites, and represent 5% of PRM permit actions.

Limitations of the search- This report represents a comprehensive compilation of
nationwide third-party mitigation that has been tracked in RIBITS and involves estuarine
or marine habitats. However, the goal of finding comprehensive PRM from five states was
not achieved. The search results could not generate a complete inventory of PRM involving
the focal habitats because of blank fields and missing information in the DARTER database
and incomplete documentation provided by USACE districts. Consequently, the permits
obtained likely represent only a fraction of the PRM that has occurred involving the focal
habitats. An example illustrates how many PRM projects may have been missed: Florida
Fish and Wildlife Service collected 130 USACE Jacksonville district permits over a five-year
period for seagrass impacts (personal communication with Margaret Hall; projects
referenced in Rezek et al. 2019); however, only 13 were obtained via this report's search
process, which spanned 12 years. As another example, the California Eelgrass Mitigation
Policy references 66 eelgrass mitigation projects in Southern California alone over the past
35 years (NMFS 2014), while only eight were found from this report's search. Therefore,
although the PRM results in this report can inform mitigation work and policy, they do not
provide a complete picture of estuarine and marine mitigation projects occurring
nationwide that involve seagrass, oysters, tidal flats, and shallow water.

The perception of the 404 Program as only wetlands- The 404(b)(1) Guidelines (EPA
1980) emphasize the value of habitats that are not traditionally considered to be wetlands,
such as vegetated shallows, sanctuaries, refuges, and mudflats. However, 404 Program
practitioners historically have tended to associate the CWA 404 Program with wetlands,
but not subtidal and unvegetated intertidal coastal areas. Perhaps consequently, and
because it has been common with wetland mitigation projects, the 404 Program has
historically focused on emergent vegetation when creating an estuarine or marine
compensatory mitigation project or assessing its success. A specific focus on emergent or
terrestrial vegetation for evaluating wetlands and riparian areas may be partially
responsible for the infrequent requirement for compensatory mitigation for submerged
and unvegetated habitats.

Several of the permits that were reviewed authorized discharges of dredged or fill material
that would impact tidal flats, but did not propose compensatory mitigation, stating that the
impact areas were not jurisdictional waters of the United States. One permit stated that the
proposed project, which was sited in shallow water, would not affect any aquatic resources
that would require compensatory mitigation. Many other projects found during this
research included CWA 404 permits issued for activities that would impact shallow water
and intertidal areas, and yet compensation did not appear to be required. Moreover, many
projects included monitoring methods and performance standards for vegetated intertidal

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or subtidal areas but excluded unvegetated areas that were part of the same compensation
project. Several compensatory mitigation projects converted tidal flat into salt marsh.
Finally, two permits that were reviewed identified tidal flats on the impact site as special
aquatic sites under the 404(b)(1) Guidelines, but the impacts were ultimately compensated
with out-of-kind mitigation. The exclusion of some estuarine and marine habitats from
requirements for compensatory mitigation, together with a broad lack of recognition of the
important functions of and compensation opportunities for these habitats, will continue to
result in impacts, habitat fragmentation, and cumulative degradation.

Credit types and categorization in RIBITS- At present, although a simple RIBITS search
for estuarine and marine credits will elicit many of the banks, ILFs, and ILF sites that exist
nationwide, it will not reveal every provider and site with estuarine or marine habitat. This
is because RIBITS uses a mixture of Cowardin Classification and more general terms (such
as 'wetland') to describe credit types. To find an up-to-date record of estuarine and marine
sites in RIBITS, several different searches were conducted, in addition to reading through
documentation from the cyber repositories and engaging in follow-up discussions with
bank and ILF representatives. This credit type issue is exacerbated when searching for
habitats more specific than just estuarine or marine, such as seagrass. For instance,
although 12 providers (banks or ILFs) had seagrass presence at their sites, a RIBITS search
revealed only one, and although 24 providers had tidal flat presence at their sites, none
were returned when "tidal flat", "mudflat," or "mud flat" was searched. The lack of
standardized naming conventions for habitat types in RIBITS made this type of
investigation more difficult, but more importantly, it creates a barrier for permittees
searching for in-kind compensatory mitigation for their estuarine and marine impacts.
Additionally, a small number of sites were not in RIBITS because they were old or simply
had never been uploaded.

Other barriers to mitigation for specific habitats- Documentation for third-party and
PRM sites often did not include a clear description of tidal flat or shallow water presence,
especially when these habitats were part of a mosaic of other habitats such as salt marsh.
These projects also did not measure area of these habitats, and instead, their presence was
recorded as part of the total area of the mitigation project. This practice precludes tracking
of how the habitat is changing over time and of its suitability for being used as
compensation. Oyster and seagrass area was measured more often than tidal flat and
shallow water in the projects analyzed.

Simple ratios, calculator tools, and assessment methods have been developed to assist
permittees and regulators translate impacts to compensatory mitigation required (e.g.
Chiavacci et al. 2022). There are calculator tools that recognize the presence of oysters,
seagrass, tidal flats, and shallow water (e.g., the Interim Hydrogeomorphic functional
assessment developed for Galveston District), and guidance documents that provide detail
on best mitigation practices, some of which include simple ratios (e.g., the California
Eelgrass Mitigation Policy and Florida's Guidance on Surveys for SAV Compensatory
Mitigation Projects). Despite these tools, however, the authors of this report are not aware
of any assessment methods that measure attributes of these habitats and attempt to
translate them into credits.

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Seagrass, oyster, tidal flat, and shallow open water assessment methods for compensatory
mitigation purposes should be developed. These assessments should calculate how much
compensation a mitigation site has provided or how much compensatory mitigation will be
required to offset a specific impact. At present, there are a few assessment methods that
acknowledge the presence of the focal habitats, but none that consider their attributes (for
example, density and shell height of oysters) for making mitigation decisions. There is a
wide body of seagrass and oyster restoration data available, as well as detailed state-level
seagrass mitigation guidance (Hinton A and B 2020, NMFS 2014) that would make
developing assessment methods a straightforward task. For tidal flats and shallow water,
assessment methods should be developed that consider a lack of traditional structure, and
instead emphasize other attributes, such as infauna presence or water quality thresholds.

Lack of monitoring and standards at preservation sites- Most third-party preservation
projects did not have quantitative performance standards or monitoring beyond photo
points and occasional surveillance. Although mitigation projects are designed to be self-
sustaining, the sustainability of a preservation site cannot be measured if baseline
information is not captured. Further, without habitat delineations and measurements such
as water quality, a site could become degraded such that compensation is no longer
equivalent to the impact, but no corrective actions would be required.

Seagrass mitigation observations- The information compiled in this study suggests that
compensatory mitigation for seagrass impacts is better established compared to the other
focal habitats. Seagrass mitigation projects' monitoring methods and performance
standards were usually thorough and aligned with typical monitoring and performance
standards used in voluntary restoration/ambient monitoring projects. Additionally,
multiple localities (FL, CA, OR, Chesapeake Bay, New England District) have developed
compensation guidance for SAV impacts (Hinton A and B 2020, Oregon Department of State
Lands 2019, USACE New England District 2020, NMFS 2014, and Chesapeake Bay Program
1995). In California, a state with many well-documented eelgrass mitigation projects, the
failure rate of transplantation is 13% (NMFS 2014), which prompted the California
Eelgrass Mitigation Policy (CEMP) to establish 1.2:1 as the minimum restoration threshold
for a mitigation area.

Oyster mitigation observations- Monitoring methods and performance standards for
oyster areas were not common among third-party sites, but several PRM sites did not
appear to have them. However, the PRM aspect of this report had a small sample size and
therefore it is unclear how often oyster PRM occurs without monitoring or performance
standards. Regardless, creating oyster habitat without establishing plans to monitor it first
is not recommended. Oyster restoration is complex, and factors for project failure include,
but are not limited to, predation, shell stock depletion, and lack of recruitment (Mann and
Powell 2007). Mitigation providers and restoration practitioners may view the
establishment of structure to be a net benefit whether wild oysters eventually recruit to it
or not; however, this hands-off approach precludes gauging the success of the project.

Tidal flat mitigation observations- Tidal flats were frequently present among third-party
providers with estuarine or marine habitat (24 of 54 providers), but very few had
associated monitoring methods or performance standards. Most projects (third-party and

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PRM) restored, enhanced, created, or preserved tidal flats as part of a mosaic of estuarine
wetlands rather than focusing on tidal flats exclusively. In permit documentation, several
permittees mentioned that existing tidal flat was previously disturbed and therefore low
value, especially if it was constructed from dredged material.

Tidal flats can be labeled as low-value resources because of their lack of structure (that is
visible to the human eye), which is thought of as the cornerstone of habitat. Media attention
is greater and therefore public perception is better for some coastal habitats compared to
others, which consequently makes them favored for protection and research (Duarte et al.
2008). Tidal flats rank low on this list, with some considering them "barren" or "stinky"
(Faris 1990 or Melinkoff 1990 for example). A decade ago, seagrass was labeled the "ugly
ducking" in this regard (Duarte et al. 2008). In this report's review of compensatory
mitigation projects, tidal flats were often characterized as secondary, less-desirable
habitats that are unable to sustain vegetation.

Shallow water mitigation observations- PRM documentation appeared to show that
compensatory mitigation requirements for shallow water impacts are inconsistent around
the country. Twenty-eight permits for shallow water projects in the Seattle district were
obtained, but only eight from the five other districts combined. If other districts were also
requiring compensatory mitigation for impacts to shallow water, a similar number of
projects should have been obtained. Additionally, in many of the reviewed projects, it was
difficult to discern whether shallow subtidal water was present because of a lack of
description of the mitigation areas and a lack of depth measurements.

It is not surprising that the 404 Program has struggled with marine and estuarine shallow
water compensation. First, because establishment of shallow water habitat would be at the
expense of other habitats (terrestrial or aquatic) and second, public perception is such that
unstructured habitats are often not regarded to be as desirable as structured habitats.
However, compensation, ideally in-kind, should be required for impacts to shallow water;
this could be carried out by improving existing subaqueous areas. The diverse suite of
projects reviewed in this report demonstrate a variety of options available for shallow
water improvement. For example, the Seattle district is allowing removal of over and in-
water structures, including creosote pole removal and derelict vessel removal, in areas
both on and off-site with respect to the impact. Two other districts approved large-scale
projects to remove derelict crab pots as compensatory mitigation. One ILF is remediating
sediment formerly contaminated with creosote. Other projects are installing stormwater
filtration devices to improve water quality and installing pea gravel to improve fish
spawning habitat. Tidal restriction removal projects are also common across the country.

Finally, mitigation providers have been authorized to add substrate (often to create
artificial reef structures) but also to remove substrate for the stated purpose of improving
shallow water areas. For example, one ILF is constructing an artificial reef from stone and
concrete with the intent of attracting fish and sessile invertebrates, while a PRM site
removed stone riprap and described it as "creation of benthic habitat." An important
consideration when deciding to add substrate is whether subtidal structure previously
existed in the area. A critical perspective of artificial reef programs would be that without

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rigorous monitoring and performance criteria, they are essentially a means of material
disposal.

Further challenges these habitats face- It is important to note that successful restoration
of seagrass, oyster, tidal flat, and shallow water habitat faces many challenges, including
sea level rise, non-native species presence, and warming temperatures. Although studying
sea level rise implications was not an objective of this report, several third-party providers
have pending projects that take sea level rise into account. One project involves high and
low salt marsh vegetation and the ability for the marsh to migrate landward. Another
project proposes to continually excavate uplands to match sea level rise for seagrass
mitigation, since the deeper edges of the beds would die off with increased depth of
overlying water. In the Pacific Northwest, regulators and mitigation providers are already
grappling with non-native species. One PRM applicant did not propose and was not
required to mitigate for impacts to non-native eelgrass [Z. japonica). A third-party provider
with extensive populations of a non-native oyster [C. gigas) is currently debating whether
to use the oyster areas for mitigation credits.

Future research- Interested researchers should continue compiling information on
marine and estuarine compensatory mitigation, as well as information about other, lesser-
known habitats that could be affected by the issuance of CWA Section 404 permits.
Documentation alone will not be enough to understand project and compensation
outcomes, and future researchers should plan to reach out to agency staff and mitigation
providers for additional details and context.

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Recommendations

Improving mitigation practices

The use of standardized assessment methods, monitoring metrics and performance
standards for oyster, seagrass, tidal flat, and shallow water habitat can lead to more
efficient review of permits and compensatory mitigation proposals in addition to improved
performance at mitigation sites. The following recommendations could also improve
compensatory mitigation outcomes:

1.	For tidal flat habitat:

•	Develop a clear definition of tidal flats (currently, there is confusion about
whether marsh edges, tidal creeks, unvegetated portions of living shorelines,
intertidal areas seaward of bulkheads, and other intertidal areas are tidal flats).

•	Identify and assess tidal flats at impact sites, and where appropriate require
compensatory mitigation.

•	Assess tidal flats at impact sites that are constructed of dredged materials, do not
assume they are degraded.

2.	For shallow water habitats:

•	Identify and assess shallow water at impact sites, and where appropriate require
compensatory mitigation.

•	Consider the many creative solutions for providing in-kind compensatory
mitigation for shallow water impacts that have been implemented, such as
sediment rehabilitation, removal of debris and creosote piles, placement of
habitat gravel, installation of stormwater treatment devices, and restoration of
tidal connections.

3.	Include monitoring and performance standards for seagrass, oysters, tidal flats, and
shallow water when they are present at preservation sites.

4.	For seagrass and oyster mitigation projects, draw project ideas, monitoring methods,
and performance standards from the wide body of literature and data that is available
from voluntary restoration projects.

5.	When seagrass, oysters, tidal flats, or shallow water habitat is part of a mosaic of
habitats affected by an impact OR established, restored, enhanced, or preserved for
compensatory mitigation, the footprint (area) of each of these habitats should be
measured to ensure accurate crediting.

6.	Consider the history of nonpoint sources and other unregulated impacts on an area's
current presence of oysters, seagrass, tidal flats, and shallow water.

Improving documentation and record-keeping

Including the appropriate markers for aquatic resource type (for instance, Cowardin
classification) when tracking permitted impacts and compensatory mitigation projects is
essential to enable anyone beyond those directly involved in the project to find it. The
ability to learn from compensatory mitigation practices over time also depends on the
availability of relevant information in project files, especially the approved mitigation plan,

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monitoring reports, and instrument or MFR. This report was made possible because of the
many regulators across the country who took the steps necessary to appropriately fill in
this documentation, even when it was not mandatory, however, many projects and their
lessons were missed.

Recommendations for ensuring that documentation will support future discovery by
regulators looking for examples or others studying regulatory practices are:

1.	Ensure the Cowardin classification field is populated for:

•	For PRM- Impacts and mitigation entries in the ORM database.

•	For third-party mitigation: all RIBITS credits.

2.	Make mitigation documentation digitally accessible, especially:

•	For PRM- the permit, mitigation plan, MFR, and monitoring reports

•	For third-party mitigation- the instrument, instrument modifications, mitigation
plans, and monitoring reports

3.	Monitoring reports should include the monitoring methods and performance criteria
that were required in the permit, mitigation plan or bank/ILF instrument, for reference
and in case documentation is seperated.

4.	Monitoring methods and performance criteria should be included in a defined
section(s) in the permit, mitigation plan or bank/ ILF instrument.

5.	Develop templates for bank or ILF instruments that include descriptions of all habitat
types present at mitigation sites, maps, and corresponding tables that clearly identify
credit types and the habitats they represent.

Next steps for research

Like the field of environmental restoration, the field of compensatory mitigation is
multifaceted and ever evolving. Advancements in research often lead to improvements in
compensatory mitigation practices and assessments. Compiling this report revealed an
array of agency staff, students, academics, and stakeholders who were in the process of
researching compensatory mitigation related topics. Future research to inform
compensatory mitigation practices for oyster, seagrass, tidal flat, and shallow water
habitats include:

1.	Develop assessment methods that can be used for regulatory purposes for seagrass,
oyster, tidal flat, and shallow water habitats. The methods must be able to assess
changes at impact and compensatory mitigation sites.

2.	Develop monitoring methods and performance standards unique to tidal flat
compensatory mitigation projects. Ideas include aerial photos and mapping, water
quality measurements when the area is submerged, area and elevation measurements,
sediment properties like grain size or toxic substance concentration, biological
properties such as algae or infauna presence, and/or wading or migratory bird usage.

3.	Develop monitoring requirements and performance standards unique to shallow water
mitigation projects. Ideas include tracking water quality (standard parameters like
salinity, temperature, dissolved oxygen, and pH but also chlorophyll and suspended

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solids, which may require laboratory analysis), toxic substance concentration of
sediments, light penetration, and fish abundance, diversity, and/or health.

4. Assess restoration success at a variety of locations to inform setting appropriate

mitigation ratios for different habitat types. For seagrass, success rates and mitigation
ratios are available in the California Eelgrass Mitigation Policy (NMFS 2014). Several
projects featured in this report buffered against seagrass variability by planting an area
greater than the impact site (a higher ratio of compensation to impact).

Training opportunities

Training on seagrass, oyster, tidal flat, and shallow water habitats is needed. Potential
training topics include functions and services, applicability of the CWA Section 404
requirements, and how to assess and compensate for impacts to each habitat.

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References

Aoki, L. R., McGlathery, K. J., Oreska, M. P. (2020). Seagrass restoration reestablishes the
coastal nitrogen filter through enhanced burial. Limnology and Oceanography, 65(1), 1-12.

Bartol, I. K., Mann, R., Luckenbach, M. (1999). Growth and mortality of oysters (Crassostrea
virginica) on constructed intertidal reefs: effects of tidal height and substrate level. Journal
of Experimental Marine Biology and Ecology, 237(2), 157-184.

Bilkovic, D. M., Herschner, C. H., Rudnicky, T., Nunez, K., Schatt, D. E., Kileen, S., Berman, M.
(2009). Vulnerability of shallow tidal water habitats in Virginia to climate change.

Bell, S. S., Tewfik, A., Hall, M. 0., Fonseca, M. S. (2008). Evaluation of seagrass planting and
monitoring techniques: implications for assessing restoration success and habitat
equivalency. Restoration Ecology, 16[3), 407-416.

Brown, B., Wilson Jr, W. H. (1997). The role of commercial digging of mudflats as an agent
for change of infaunal intertidal populations. Journal of Experimental Marine Biology and
Ecology, 218(1), 49-61.

Chesapeake Bay Program (1995). Guidance for Protecting Submerged Aquatic Vegetation
in Chesapeake Bay from Physical Disruption. Accessed 2-25-21:

https://www.chesapeakebay.net/what/publications/guidance for protecting submerged
afluat|c_veg	esaneakeJba^l.

Chiavacci, S.J., French, E.D., and Morgan, J.A., 2022, Database of biodiversity, habitat, and
aquatic resource quantification tools used for market-based conservation in the United
States (ver. 2.0, June 2022): U.S. Geological Survey data release,
https .org/10.5066/F79G5M3X.

Cowardin, L. M. (1979). Classification of wetlands and deepwater habitats of the United
States. Fish and Wildlife Service, US Department of the Interior.

Dahl, T.E. 2011. Status and trends of wetlands in the conterminous United States 2004 to
2009. U.S. Department of the Interior; Fish and Wildlife Service, Washington, D.C. 108 pp

Dahl, T.E. and Stedman, S.M. (2013) Status and trends of wetlands in the coastal
watersheds of the Conterminous United States 2004 to 2009. U.S. Department of the
Interior, Fish and Wildlife Service and National Oceanic and Atmospheric Administration,
National Marine Fisheries Service. (46 p.)

Dennison, W. C., Orth, R. J., Moore, K. A., Stevenson, J. C., Carter, V., Kollar, S., Bergstrom, P.
W., Batiuk, R. A. (1993). Assessing water quality with submersed aquatic
vegetation. Bioscience, 43(2), 86-94.

Duarte, C. M., Dennison, W. C., Orth, R. J., Carruthers, T. J. (2008). The charisma of coastal
ecosystems: addressing the imbalance. Estuaries and coasts, 31 (2), 233-238.

41


-------
Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

Faris, G. (1990, Jan 19). Disappearing coastal mudflats are 'the habitat of the overlooked'.
Los Angeles Times, https://www.latimes.com/archives/la-xpm-199C	e-144-

ston,

Fourqurean, J. W., Duarte, C. M., Kennedy, H., Marba, N., Holmer, M., Mateo, M. A.,
Aposotolaki, E. T., Kendrick, G. A., Krause-Jensen, D., McGlathery, K. J., Serrano, 0. (2012).
Seagrass ecosystems as a globally significant carbon stock. Naturegeoscience, 5(7), 505.

Fourqurean, J. W., Powell, G. V., Ken worthy, W. J., Zieman, J. C. (1995). The effects of long-
term manipulation of nutrient supply on competition between the seagrasses Thalassia
testudinum and Halodule wrightii in Florida Bay. Oikos, 349-358.

Green, T. J., Siboni, N., King, W. L., Labbate, M., Seymour, J. R., Raftos, D. (2019). Simulated
marine heatwave alters abundance and structure of Vibrio populations associated with the
Pacific Oyster resulting in a mass mortality event. Microbial ecology, 77(3), 736-747.

Greening, H. S., Cross, L. M., Sherwood, E. T. (2011). A multiscale approach to seagrass
recovery in Tampa Bay, Florida. Ecological Restoration, 29(1-2), 82-93.

Hargreaves, A. L., Whiteside, D. P., Gilchrist, G. (2011). Concentrations of 17 elements,
including mercury, in the tissues, food and abiotic environment of Arctic
shorebirds. Science of the Total Environment, 409(19), 3757-3770.

Hettinger, A., Sanford, E., Hill, T. M., Russell, A. D., Sato, K. N., Hoey, J., Forsch, M., Page, H. N.,
Gaylord, B. (2012). Persistent carry-over effects of planktonic exposure to ocean
acidification in the Olympia oyster. Ecology, 93(12), 2758-2768.

Hinton, J. (2020). A. Guidance on Surveys for Potential Impacts to Submerged Aquatic
Vegetation. Florida Department of Environmental Protection.

https://floridadep.gov/rcp/beaches-inlets-ports/docur	jance-survevs-potential-

impacts-submerged-aauatic-vegetation.

Hinton, J. (2020). B. Guidance on Surveys for Submerged Aquatic Vegetation Compensatory
Mitigation Projects. Florida Department of Environmental Protection.
https://floridadep.gov/rcp/beaches-inlets-ports/docur	jance-survevs-

submyergedbagyuat^^

Kellogg, M. L., Cornwell, J. C., Owens, M. S., Paynter, K. T. (2013). Denitrification and nutrient
assimilation on a restored oyster reef. Marine Ecology Progress Series, 480,1-19.

Kellogg, L., Brush, M., Cornwell, J. (2018). An Updated Model for Estimating the TMDL-
Related Benefits of Oyster Reef Restoration. Virginia Institute of Marine Science and
University of Maryland.

Li, X., Bellerby, R., Craft, C., Widney, S. E. (2018). Coastal wetland loss, consequences, and
challenges for restoration. Anthropocene Coasts, 1[ 1), 1-15.

Lowe, M. R., Sehlinger, T., Soniat, T. M., La Peyre, M. K. (2017). Interactive effects of water
temperature and salinity on growth and mortality of eastern oysters, Crassostrea virginica:

42


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Compensatory Mitigation in Estuarine and Marine Habitats

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a meta-analysis using 40 years of monitoring data .Journal of Shellfish Research, 36(3), 683-
697.

Malins, D. C., Krahn, M. M., Myers, M. S., Rhodes, L. D., Brown, D. W., Krone, C. A., McCain, B.
B., Chan, S. L. (1985). Toxic chemicals in sediments and biota from a creosote-polluted
harbor: relationships with hepatic neoplasms and other hepatic lesions in English sole
(Parophiys vetulus). Carcinogenesis, 6(10), 1463-1469.

Mann, R., and Powell, E. N. (2007). Why oyster restoration goals in the Chesapeake Bay are
not and probably cannot be achieved. Journal of Shellfish Research, 26(4), 905-917.

Melinkoff, E. (1990, Jan 6). Exposing the rich life in the mudflats. Los Angeles Times.

https://www.latimes.com/archives/la	0-01-06-vw-385-story.html.

McGlathery, K. J., Sundback, K., Anderson, I. C. (2007). Eutrophication in shallow coastal
bays and lagoons: the role of plants in the coastal filter. Marine Ecology Progress Series, 348,
1-18.

Moore, K. A., and Jarvis, J. C. (2008). Environmental factors affecting recent summertime
eelgrass diebacks in the lower Chesapeake Bay: implications for long-term
persistence. Journal of Coastal Research, (55), 135-147.

National Oceanic and Atmospheric Administration and Bureau of Ocean and Energy
Management (2019). Data Registry. Marine Cadastre.gov/data

National Marine Fisheries Service (2014). California Eelgrass Mitigation Policy and
Implementing Guidelines. Accessed 2-25-21:

https://media.fisheries.noaa.gov/dammigration/cemp_oct_2014_final.pdf

Newell, R. I., Fisher, T. R., Holyoke, R. R., Cornwell, J. C. (2005). Influence of eastern oysters
on nitrogen and phosphorus regeneration in Chesapeake Bay, USA. In The comparative
roles of suspension-feeders in ecosystems (pp. 93-120). Springer, Dordrecht.

Newell, R. I. (2004). Ecosystem influences of natural and cultivated populations of
suspension-feeding bivalve molluscs: a review. Journal of Shellfish research, 23(1), 51-62.

Oregon Department of State Lands (2019). A guide to the removal-fill permit process.
Accessed 3-1-21: https://www.oregon.gov/DSL/WW/Documents/Removal Fill Guide.pdf.

Orth, R. J., Heck, K. L., van Montfrans, J. (1984). Faunal communities in seagrass beds: a
review of the influence of plant structure and prey characteristics on predator-prey
relationships. Estuaries, 7(4), 339-350.

Pedersen M.F., Nielsen SL, Banta GT (2004). Interactions between vegetation and nutrient
dynamics in coastal marine ecosystems: an introduction. In: Nielsen SL, Banta GT, Pedersen
MF (eds) Estuarine nutrient cycling: the influence of primary producers, Kluwer Academic,
Dordrecht, p 1-16

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Compensatory Mitigation in Estuarine and Marine Habitats

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Richardson, J. P., Lefcheck, J. S., Orth, R. J. (2018). Warming temperatures alter the relative
abundance and distribution of two co-occurring foundational seagrasses in Chesapeake
Bay, USA. Marine Ecology Progress Series, 599, 65-74.

Ray, G. L. (2000). Infaunal assemblages on constructed intertidal mudflats at Jonesport,
Maine (USA). Marine Pollution Bulletin, 40(12), 1186-1200.

Reimer, J. D., Yang, S. Y., White, K. N., Asami, R., Fujita, K., Hongo, C., Shingo, I., Kawamura,
Maeda, I., Mizuyama, M., Obuchi, M., Sakamaki, T., Tachihara, A., Tamura, A., Tanahara, A.,
Yamaguchi, A., Jenke-Kodama, H. (2015). Effects of causeway construction on environment
and biota of subtropical tidal flats in Okinawa, Japan. Marine Pollution Bulletin, 94(1-2),
153-167.

Reilly, F. J., Spagnolo, R. J., Ambrogio, E. (1999). Marine and estuarine shallow water science
and management: The interrelationship among habitats and their
management. Estuaries, 22(3), 731-734.

Rezek, R. J., Massie, J. A., Nelson, J. A., Santos, R. 0., Viadero, N. M., Boucek, R. E., Rehage, J. S.
(2020). Individual consumer movement mediates food web coupling across a coastal
ecosystem. Ecosphere, 11[ 12), e03305.

Rezaie, A. M., Loerzel, J., Ferreira, C. M. (2020). Valuing natural habitats for enhancing
coastal resilience: Wetlands reduce property damage from storm surge and sea level
rise. PIoS one, 15[ 1), e0226275.

San Elijo Lagoon Restoration (2021). Nature Collective.

https://thenaturecollective.org/project/san-eliio-lagoon-restoration/.

Short, F. T., Burdick, D. M., Kaldy, J. E. (1995). Mesocosm experiments quantify the effects of
eutrophication on eelgrass, Zostera marina. Limnology and oceanography, 40(4), 740-749.

Smithsonian (2018). Eelgrass wasting disease has new enemies: Drones and artificial
intelligence. ScienceDaily. Retrieved December 16, 2020 from

www.scieiicedaily.com/releases/2018/09/18091811Q956.litiTi.

Stedman, S. M. and Dahl, T. E. (2008) Status and trends of wetlands in the coastal
watersheds of the Eastern United States 1998 to 2004. National Oceanic and Atmospheric
Administration, National Marine Fisheries Service and U.S. Department of the Interior, Fish
and Wildlife Service. (32 pages)

Thorne, K. M., Dugger, B. D., Buffington, K. J., Freeman, C. M., Janousek, C. N., Powelson, K.
W., Gutenspergen, G.R., Takekawa, J. Y. (2015). Marshes to mudflats—Effects of sea-level rise
on tidal marshes along a latitudinal gradient in the Pacific Northwest (No. 2015-1204). U.S.
Geological Survey.

U.S. Army Corps of Engineers New England District (2020). New England District
Compensatory Mitigation Guidance. Accessed 10-4-21:

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Compensatory Mitigation in Estuarine and Marine Habitats	February 2023

https://www.nae.usace.army.mil /Portals, ics/regulatory/Mitigation/Compensatory-
Mitigation-SQP-2020.pdf?ver=EWhCrK70ZfmPr—8x0K51g%3d%3d.

Vanderbilt, F., Martin, S., Olson, D. (2015). The Mitigation Rule Retrospective: A Review of
the 2008 Regulation Governing Compensatory Mitigation for Losses of Aquatic Resources.
U.S. Army Corps of Engineers Institute for Water Resources.

Vines, C. A., Robbins, T., Griffin, F. J., Cherr, G. N. (2000). The effects of diffusible creosote-
derived compounds on development in Pacific herring (Clupea paUasi). Aquatic
Toxicology, 51(2), 225-239.

Ward LG, Kemp W.M., Boynton W.R. (1984). The Influence of waves and seagrass
communities on suspended particulates in an estuarine embayment. Mar Geol 59:85-103

Waldbusser, G. G., Voigt, E. P., Bergschneider, H., Green, M. A., Newell, R. I. (2011).
Biocalcification in the eastern oyster (Crassostrea virginica) in relation to long-term trends
in Chesapeake Bay pH. Estuaries and Coasts, 34(2), 221-231.

Whitlow, W. L., and Grabowski, J. H. (2012). Examining how landscapes influence benthic
community assemblages in seagrass and mudflat habitats in southern Maine. Journal of
Experimental Marine Biology and Ecology, 411,1-6.

Withers, K. (2002). Shorebird use of coastal wetland and barrier island habitat in the Gulf
of Mexico. The Scientific World Journal, 2, 514-536.

Wilberg, M. J., Livings, M. E., Barkman, J. S., Morris, B. T., Robinson, J. M. (2011). Overfishing,
disease, habitat loss, and potential extirpation of oysters in upper Chesapeake Bay. Marine
Ecology Progress Series, 436,131-144.

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Compensatory Mitigation in Estuarine and Marine Habitats	February 2023

Appendix A- Data and tables

Table 1- Search Terms for third-party Mitigation in RIBITS

Habitat

Terms

Tidal flat

Tidal flat



Mud flat



Mudflat

Seagrass

Seagrass



Sea grass



Zostera



SAV



Submerged aquatic vegetation



Widgeongrass



Phyllospadix



Syringodium



Halodule



Thalassia



Halophila



turtle grass



eelgrass



eel grass



manatee grass



shoal grass



widgeon grass

Oyster

oyster



crassostrea virginica



ostrea lurida

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Compensatory Mitigation in Estuarine and Marine Habitats	February 2023

Table 2- Third-Party Mitigation Providers: Banks

Reference
#

State

Bank name

Year bank
established

Focal Habitats
Present

1

AK

Natzuhini Bay Mitigation Bank

2004

Tidal flat,
shallow water

2

AK

Trillium Mitigation Bank

2019

Tidal flat

3

CA

Colorado Lagoon Mitigation Bank

2020

Tidal flat,
seagrass,
shallow water

4

CA

Navy Region Southwest San Diego
Bay Eelgrass Mitigation Bank

2008

Seagrass,
shallow water

5

CA

Port of Los Angeles

2017

Shallow water

6

CA

San Francisco Bay Wetland
Mitigation Bank

2011

Tidal flat,
shallow water

7

FL

Bear Point Mitigation Bank

2004

None

8

FL

CGW Mitigation Bank

2008

None

9

FL

Florida Gulf Coast Mitigation Bank

2016

None

10

FL

FP&L Everglades Phase I Mitigation
Bank

2009

Seagrass,
shallow water

11

FL

Horseshoe Creek

2020

None

12

FL

Little Pine Island Mitigation Bank

1996

Shallow water

13

FL

Mangrove Point

2020

Tidal flat, oyster

14

FL

North Florida Saltwater Marsh
Mitigation Bank

2013

None

15

FL

Tampa Bay Mitigation Bank

2008

Shallow water

16

GA

T ronox

2008

None

17

GA

Tucker Mitigation Bank

2000

Shallow water

18

GA

Salt Creek Mitigation Bank

2017

None

19

LA

Chef Menteur Pass Mitigation Bank

2010

Shallow water

20

LA

Rockefeller Refuge A, B and C

2004

None

21

MS

Rhodes Lake Mitigation Bank

2008

Shallow water

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Compensatory Mitigation in Estuarine and Marine Habitats

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Reference

State

Bank name

Year bank

Focal Habitats

#

established

Present

22

NJ

Evergreen Abbot Creek Mitigation
Bank

2015

Tidal flat,
shallow water

23

NJ

Evergreen Great Bay Mitigation Bank

2018

Tidal flat,
shallow water

24

NJ

Evergreen MRI3 Mitigation Bank

2012

Tidal flat,
shallow water

25

NJ

Marsh Resources/Meadowlands

1999

Tidal flat,
shallow water

26

NJ

Richard P. Kane Wetland Mitigation
Bank

2010

Tidal flat,
shallow water

27

NJ

Evergreen Stipson's Island Mitigation
Bank

2011

Tidal flat,
shallow water

28

NY

NY City Small Business Services Saw

2018

Tidal flat,

Mill Creek Mitigation Bank

shallow water

29

OR

Wilbur Island Mitigation Bank

2008

Shallow water

30

SC

Clydesdale Mitigation Bank

2013

Shallow water

31

SC

Congaree Carton

2005

Tidal flat

32

SC

Murray Hill

2018

Shallow water

33

SC

SCDOT Huspa Creek East and West
Mitigation Bank Sites

1998

Tidal flat

34

TX

Gulf Coastal Plains Mitigation Bank

2016

Tidal flat,
shallow water

35

VA

Chesapeake Land Development Tidal
Bank

2004

T idal flat

36

VA

Goose Creek

1982

None

37

VA

New Mill Creek Tidal Mitigation Bank

2018

Tidal flat

38

WA

McHugh Demonstration Wetland
Bank

1999

None

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Compensatory Mitigation in Estuarine and Marine Habitats	February 2023

Table 3- Third-Party Mitigation Providers: ILFs and Sites

Reference
#

State

ILF name

Year ILF
established

Number of marine/
estuarine sites

Site Names

Focal
habitats
present

1

AK

Great Land Trust

2011

2

Fish Creek, Campbell Creek

Tidal flat

2

AK

Southeast Alaska
Land T rust

1998

25

Auk Nu Cove Conservation Easement,
Branta Lot 2, Crescent Bay Conservation
Easement, Eagles Reach Lot 2, Eagles View

Lot IB, Farragut Estuary Conservation
Easement, Gandercall Lot 3, Gandercall Lot
4, Great Horned Owl Lot 2, Grey Goose Lot
2, HAKALA Lot 2, Hilda Creek & Accretion
Conservation Easement, Hinz II Lot IB,
Honsinger Wetlands, King Conservation
Easement, Lazy G Acres Lot 2, Lobaugh
Conservation Easement, Moon Meadow Lot
2, Morning Meadow Lot 3, Morning
Meadow Lot 4, Nelson Homestead
Conservation Easement, Sherry Lot 2,
Sherry Lot 3, Sunny Point Park #3 Lot 1 &
Lot 2, Wigeon Ponds Lot 2 Deed Restriction

Seagrass,
tidal flats,
shallow
water

3

AK

The Conservation
Fund AK

2010

5

AR-4, AR-1, SW-2, SW-3, SW-4

Seagrass,
tidal flats

4

CT

CT ILF program

2011

1

Stratford Point

Oyster

5

FL

Keys
Environmental
Restoration Fund

1998

Between 3-10*

Lignumvitae Seagrass Scar 1999,
Lignumvitae Seagrass Stake Array 1999,
Lignumvitae Seagrass Sites 2005

Seagrass,
shallow
water

6

FL

Keys Restoration
Fund

2015

4

Bahia Honda A, Bahia Honda B, Crane Point
Hammock, Lignumvitae Seagrass

Seagrass,
shallow
water

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Compensatory Mitigation in Estuarine and Marine Habitats

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Reference
#

State

ILF name

Year ILF
established

Number of marine/
estuarine sites

Site Names

Focal
habitats
present

7

FL

Northwest
Florida Water
Management
District

2015

2

Dutex, Live Oak Point

Shallow
water,
seagrass,
oyster

8

MA

MA Dept. of Fish
and Game

2014

8

Upper Great Marsh, Rough Meadows, Town
Farm, Eelgrass Restoration, Parker River
Connector, Eelgrass restoration (Salem,
MA), Oyster Reef (Nantucket)

Seagrass,
shallow
water,
oyster

9

ME

Maine Natural

Resources
Conservation
Program

2011

22

Whiskeag Creek, Indian River, Meadow
Brook Wetlands, Brookings Bay, Maquoit
Bay, Basin Cove/Curtis Cove, St. George
River Tidal, Weskeag Wetlands, Mil Pond
Tidal Restoration, Kate Furbish
Restoration, Wallace Shore Road, Long
Cove Wetlands, Parker Head Road, Little
River Restoration, Old Pond- Demska,
Middle Bay-Liberty, Smelt Brook Intertidal
Restoration, Spring Point (Hog Bay), Fixing
Furbish (Phase 1), Rouse island,
Strawberry Creek, Willow Brook Culvert
Replacement

Tidal flat,
seagrass

10

NC

N.C. Dept of
Mitigation
Services

2010

9

Balance Farm, Hammock's State Park, Camp
Lejeune, Sturgeon City, Lengyel, Sawmill,
Bird Island, Maritime Museum, Pamlico
Sound Oyster Reef

Tidal flat,
oyster,
shallow
water

11

NH

NH Aquatic
Resources
Mitigation
Program

2018

2

Cutt's Cove, SALMON-PISC Oyster Reef

Oyster,
shallow
water

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

Reference
#

State

ILF name

Year ILF
established

Number of marine/
estuarine sites

Site Names

Focal
habitats
present

12

OR

OR Dept of State
Lands

2009

3

Pixieland, Kilchis River Preserve, Tamara
Quays

Shallow
water

13

VA

Living River
Restoration T rust

2018

2

Paradise Creek, Money Point

Oyster,
shallow
water

14

VA

Virginia Aquatic
Resources Trust
Fund

1995

19

Cumberland Marsh, Rappahannock
Phragmites Control, Crows Nest (Phase 1],

Crows Nest (Phase 2), VCU, Northwest
River (Kellam Rigato), Dragon Run (Milby),
Thompson, Hampton, Dameron Marsh, SAV
Beds, SAV Beds 2, Virginia Coast Reserve
(oyster restoration), New Point Comfort,
Eastern VA Phragmites Control, Dameron
Marsh, Church Neck, VMRC oyster reef,
Lower Chickahominy River

Seagrass,
oyster,
shallow
water

15

WA

Hood County
Coordinating
Council

2012

4

Anderson, Big Beef, Olson, Dewatto

Tidal flat,
seagrass,
oyster

16

WA

King County
Mitigation
Reserves

2011

1

Chinook Wind Mitigation Project

Tidal flat

*For the official tally of ILFsites, three rather than ten was used to be conseivative

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Compensatory Mitigation in Estuarine and Marine Habitats	February 2023

Table 4- Department of the Army Permits

Reference
#

State

DA NUMBER

Mitigation habitat

Year permit
issued

1

FL

SAJ-1999-03746

Shallow water

2003

2

FL

SAJ-2003-04783

Shallow water

2015

3

FL

SAJ-2004-01945

Seagrass

2010

4

FL

SAJ-2004-08169

Shallow water

2007

5

FL

SAJ-2005-05399

Shallow water

2018

6

FL

SAJ-2008-04801

Seagrass

2012

7

FL

SAJ-2010-00817

Seagrass

2013

8

FL

SAJ-2013-00319

Oyster, shallow water

2013

9

FL

SAJ-2014-02406

Seagrass

2015

10

FL

SAJ-2014-03521

Seagrass

2017

11

TX

SWG-2012-00203

Shallow water

2013

12

TX

SWG-2 014-00905

Oyster

2014

13

CA

SPL-2010-00028

Shallow water

2010

14

CA

SPL-2010-01129

Seagrass

2011

15

CA

SPL-2011-00463

Seagrass

2012

16

CA

SPL-2012-00172

Tidal flat

2017

17

CA

SPL-2013-00146

Seagrass

2013

18

CA

SPL-2015-00569

Seagrass

2017

19

CA

SPL-2015-00651

Seagrass

2016

20

CA

SPL-2016-00825

Tidal flat

2017

21

CA

SPN-2005-293680

Tidal flat

2006

22

CA

SPN-2016-00053

Shallow water

2016

23

VA

NAO-2001-03946

Oyster

2019

24

VA

NAO-2003-01984

Oyster

2014

25

VA

NAO-2010-02401

Oyster

2012

26

VA

NAO-2014-00463

Seagrass

2014

27

VA

NAO-2015-00310

Seagrass

2016

28

WA

NWS-2010-00968

Tidal flat

2010

29

WA

NWS-2011-00183

Shallow water

2014

30

WA

NWS-2011-00761

Shallow water

2017

31

WA

NWS-2012-00699

Shallow water

2013

32

WA

NWS-2012-00759

Shallow water

2013

33

WA

NWS-2012-01110

Seagrass

2014

34

WA

NWS-2012-01175

Shallow water

2014

35

WA

NWS-2013-00171

Shallow water

2014

36

WA

NWS-2013-00419

Shallow water

2013

37

WA

NWS-2013-01124

Shallow water

2013

38

WA

NWS-2014-00159

Shallow water

2015

39

WA

NWS-2014-00433

Shallow water

2015

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

Reference
#

State

DA NUMBER

Mitigation habitat

Year permit
issued

40

WA

NWS-2014-00804

Shallow water

2017

41

WA

NWS-2014-00890

Shallow water

2016

42

WA

NWS-2014-01177

Shallow water

2017

43

WA

NWS-2015-00291

Shallow water

2015

44

WA

NWS-2015-00601

Shallow water

2016

45

WA

NWS-2015-00696

Shallow water

2016

46

WA

NWS-2015-00971

Shallow water

2016

47

WA

NWS-2016-002 00

Shallow water

2016

48

WA

NWS-2016-003 20

Shallow water

2016

49

WA

NWS-2016-003 24

Shallow water

2016

50

WA

NWS-2016-00902

Shallow water

2017

51

WA

NWS-2017-00809

Shallow water

2018

52

WA

NWS-2012-01111

Shallow water

2013

53

WA

NWS-2013-00213

Shallow water

2013

54

WA

NWS-2013-00245

Shallow water

2015

55

WA

NWS-2014-00736

Shallow water

2015

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Compensatory Mitigation in Estuarine and Marine Habitats

Table 5- Ambient monitoring programs	

February 2023

Type	Program or Survey Name

Worldwide

SeagrassNet program

Zostera Experimental Network (ZEN) program

National

EPA NARS NCCA survey

EPA NARS NWCA survey

FWS Status and Trends/National Wetlands Inventory program

National Park Service Eutrophication Survey

NOAA NERRS program

EPA NEP program

Multi-State

VIMS Annual Aerial Seagrass Survey

10 Tributaries by 2025 NOAA Oyster Restoration

USGS Marshes to Mudflats project

State

Maryland DNR Fall Recruitment Survey

Florida DEP Aquatic Preserve Program

VIMS Long-Term Seagrass Transect Program

North Carolina DMF Sanctuary Survey

Seagrass restoration in Virginia's coastal bays

San Elijo Lagoon Restoration project, California

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Compensatory Mitigation in Estuarine and Marine Habitats	February 2023

Table 6- California Eelgrass Mitigation Policy Performance Standards

Month

Standard

0

Monitoring should confirm the full coverage distribution of planting units over the
initial mitigation site as appropriate to the geographic region.

6

Persistence and growth of eelgrass within the initial mitigation area should be
confirmed, and there should be a survival of at least 50 percent of the initial planting
units with well-distributed coverage over the initial mitigation site. For seed buoys,
there should be demonstrated recruitment of seedlings at a density of not less than
one seedling per four (4) square meters with a distribution over the extent of the
initial planting area. The timing of this monitoring event should be flexible to ensure
work is completed during the active growth period.

12

The mitigation site should achieve a minimum of 40 percent coverage of eelgrass and
20 percent density of reference site(s) over not less than 1.2 times the area of the

impact site.

24

The mitigation site should achieve a minimum of 85 percent coverage of eelgrass and
70 percent density of reference site(s) over not less than 1.2 times the area of the

impact site.

36

The mitigation site should achieve a minimum of 100 percent coverage of eelgrass
and 85 percent density of reference site(s) over not less than 1.2 times the area of the

impact site.

48

The mitigation site should achieve a minimum of 100 percent coverage of eelgrass
and 85 percent density of reference site(s) over not less than 1.2 times the area of the

impact site.

60

The mitigation site should achieve a minimum of 100 percent coverage of eelgrass
and 85 percent density of reference site(s) over not less than 1.2 times the area of the

impact site.

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Compensatory Mitigation in Estuarine and Marine Habitats

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Appendix B- Out-of-kind mitigation

Introduction- The 2008 Mitigation Rule upholds a preference for in-kind (of the same
type) mitigation to increase likelihood that the functions and services that are lost at the
impact site will be gained at a mitigation site.10 Out-of-kind compensatory mitigation,
however, can be considered if in-kind replacement is not possible, is unlikely to adequately
compensate for the impact, or out-of-kind mitigation is environmentally preferable. For
instance, out-of-kind mitigation can be proposed when a mitigation provider believes that
the habitat proposed to be used as mitigation will better serve the aquatic resource needs
of the watershed/ecoregion. Out-of-kind mitigation often results in a higher mitigation
ratio (amount of compensation to impact).

Methods- Records from DARTER were used for this analysis (see PRM section of the
Methods in the main report). The objective was to find projects that either impacted or
provided compensatory mitigation involving seagrass, oysters, tidal flats, and shallow
water (Table 1) to determine the proportion of in- and out-of-kind projects.

Results- Fifty-eight projects were used for the out-of-kind analysis; among them, 11
projects compensated out-of-kind. The majority of the projects (26 of 58) were from
Washington state and consisted of shallow water impacts that were compensated for in-
kind.

Seagrass impacts were mostly mitigated for in-kind; there was only one project (in
California) with seagrass impact that mitigated out-of-kind. The impact was to surf grass
[P. torreyi), a type of seagrass that grows in rocky intertidal habitats, and a contribution
was made to a local non-profit for kelp (macroalgae) restoration in its place. The 14 other
in-kind seagrass mitigation projects were from California, Virginia, Washington, and
Florida, with the most being from California and Florida.

Oyster compensation occurred equally between in-kind and out-of-kind projects. There
were three out-of-kind projects that took place in Virginia. In one project, tidal flat and
shallow water were impacted to stabilize a pier and build a bulkhead at a restaurant, and a
contribution was made to a non-profit to buy oyster shell for oyster restoration in return.
In another, tidal flat was dredged to build a multi-use facility (a dredged material transfer
station and canoe launch). A contribution was made to the same non-profit to buy oyster
shell for oyster restoration in return. Finally, an oyster restoration project was permitted
as compensatory mitigation for a shipping facility that was building new structures by
placing fill in unvegetated intertidal and shallow water areas. The three in-kind projects
were from Texas and Florida.

There were five projects that impacted tidal flats and compensated out-of-kind compared
to three that mitigated in-kind. One Texas project was permitted to impact sand tidal flats
to build a residential development and coastal prairie pothole construction was approved
as compensatory mitigation; another Texas project impacted tidal flats to build a recreation

10 33 CFR 332.3(e) / 40 CFR 230.93(e)

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

center and approved creation of a lagoon as mitigation. Of two Florida projects that
impacted tidal flats, one restored salt marsh and installed stormwater filtration systems,
and the other planted mangroves as compensation. In Virginia, a project that dredged a
mudflatto build a multi-use facility (mentioned above) purchased shell for oyster
restoration as compensatory mitigation. The three in-kind projects were from Washington
and California.

There were six out-of-kind projects that involved shallow water compared to 30 in-kind
projects. In Texas, two permits were issued for fill of shallow water areas, for modification
of a shipping channel and construction of a shipping facility, and salt marsh was created to
compensate for each one. A third Texas project used shallow water to compensate for an
out-of-kind impact; a tidal flat was impacted to build a recreation center, and mitigation
was creating a lagoon (mentioned above). In Virginia, there were three projects that
impacted shallow water and compensated out-of-kind (two have already been mentioned
above). The third permit impacted tidal flat and shallow water by placing fill for a
bulkhead. The permittee was approved to create on-site salt marsh as mitigation. In-kind
compensatory mitigation projects came from Florida, California, and Washington.

Discussion- The ratio of in-kind to out-of-kind compensation observed was roughly 4:1,
but this figure is based on limited data. These examples can inform mitigation work and
policy but do not completely represent the amount of out-of-kind compensatory mitigation
occurring in seagrass, oyster, tidal flat and shallow water areas nationwide. Other examples
of out-of-kind projects that involve these habitats exist. For instance, a recently permitted
(2020) large infrastructure project in Maryland is impacting wetlands but is compensating
via oyster restoration. Another Maryland project where streams were impacted used
estuarine shallow water mitigation (removal of crab pot debris) as compensation. The most
instances of out-of-kind projects in the dataset came from oyster and tidal flat habitats.
Oysters may be used as out-of-kind mitigation because they are a popular form of
restoration that receives public support.

For many projects, it was difficult to understand from the documentation available which
habitats were impacted and which habitats were used as mitigation. If it was not possible
to tell, the projects were excluded from this analysis. In some projects, a matrix of different
habitats was impacted, and a matrix of different habitats was used as compensation.

Project documentation did not always make it clear which mitigation habitat was intended
to compensate for which impact habitat (i.e., in- or out-of-kind), and thus those projects
were also excluded. Finally, there were situations where the impact or mitigation habitats
were simply not described. For instance, permit documentation for a bulkhead build does
not typically describe the habitat it is impacting, even though it could be a subaqueous area,
tidal flat, intertidal area, etc.

There were also several projects that withdrew credits from a PRM site that was
functioning as a bank, but because information about the PRM site was not within the
permit documentation, there was no way of knowing what habitats were present at the
site. This was the case with four permitted projects in Florida with seagrass impacts; all
withdrew credits from two different PRM sites, but those projects could not be included in
this analysis.

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Compensatory Mitigation in Estuarine and Marine Habitats

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The reasoning for using out-of-kind mitigation should be clearly explained in the
Memorandum for the Record (MFR) for PRM projects, along with a description of which
habitat is being exchanged for which habitat. For this research, the most important
document to obtain was the MFR, which described both impact and mitigation, and that
anyone undertaking this type of research in the future should request these documents.

Table 1- In-kind and out-of-kind mitigation

Reference

State

In kind/ out-

DA#

Impact

Mitigation

#

of-kind

habitat

habitat

1

CA

In kind

SPN-2016-00053

Shallow
water

Shallow water

2

CA

In kind

SPL-2010-00028

Shallow
water

Shallow water

3

CA

In kind

SPL-2010-01129

Seagrass

Seagrass

4

CA

In kind

SPL-2011-00463

Seagrass

Seagrass

5

CA

In kind

SPL-2012-00172

Tidal flat

Tidal flat

6

CA

In kind

SPL-2013-00146

Seagrass

Seagrass

7

CA

In kind

SPL-2015-00569

Seagrass

Seagrass

8

CA

In kind

SPL-2015-00651

Seagrass

Seagrass

9

CA

Out-of-kind

SPL-2011-00333

Seagrass

Macroalgae-
kelp

10

FL

In kind

SAJ-1999-03746

Shallow
water

Shallow water

11

FL

In kind

SAJ-2004-01945

Seagrass

Seagrass

12

FL

In kind

SAJ-2008-01022

SAV

SAV

13

FL

In kind

SAJ-2008-04801

Oyster,
seagrass

Oyster, seagrass

14

FL

In kind

SAJ-2010-00817

Seagrass

Seagrass

15

FL

In kind

SAJ-2013-00319

Oyster,
shallow
water

Oyster, shallow
water

16

FL

In kind

SAJ-2014-02406

Seagrass

Seagrass

17

FL

In kind

SAJ-2014-03521

Seagrass

Seagrass

18

FL

Out-of-kind

SAJ-2017-01640

Tidal flat

Mangrove

19









Oyster, salt



FL

Out-of-kind

SAJ-2004-03490

Oyster,
tidal flat

marsh,
stormwater
filtration
devices

20

TX

In kind

SWG-2014-00905

Oyster

Oyster

21

TX

Out-of-kind

SWG-2011-00303

Shallow
water

Salt marsh

22

TX

Out-of-kind

SWG-2011-00561

Tidal flat

Prarie pothole

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

Reference
#

State

In kind/ out-
of-kind

DA#

Impact
habitat

Mitigation
habitat

23

TX

Out-of-kind

SWG-2012-00602

Shallow
water

Salt marsh

24

TX

Out-of-kind

SWG-2012-00203

Tidal flat

Shallow water

25

VA

In kind

NAO-2 014-00463

Seagrass

Seagrass

26

VA

In kind

NAO-2015-00310

Seagrass

Seagrass

27

VA

Out-of-kind

NAO-1992-02651

T idal flat,
shallow
water

Salt marsh

28

VA

Out-of-kind

NAO-2001-03946

Tidal flat,
shallow
water

Oyster

29

VA

Out-of-kind

NAO-2003-01984

Shallow
water

Oyster

30

VA

Out-of-kind

NAO-2010-02401

Tidal flat

Oyster

31

WA

In kind

NWS-2 010-00968

Tidal flat

Tidal flat

32

WA

In kind

NWS-2011-00183

Shallow
water

Shallow water

33

WA

In kind

NWS-2011-00761

Shallow
water

Shallow water

34

WA

In kind

NWS-2 012-00699

Shallow
water

Shallow water

35

WA

In kind

NWS-2 012-00759

Shallow
water

Shallow water

36

WA

In kind

NWS-2012-01110

Seagrass

Seagrass

37

WA

In kind

NWS-2012-01175

Shallow
water

Shallow water

38

WA

In kind

NWS-2013-00171

Shallow
water

Shallow water

39

WA

In kind

NWS-2 013-00419

Shallow
water

Shallow water

40

WA

In kind

NWS-2013-01124

Shallow
water

Shallow water

41

WA

In kind

NWS-2 014-00159

Shallow
water

Shallow water

42

WA

In kind

NWS-2 014-00433

Shallow
water

Shallow water

43

WA

In kind

NWS-2 014-00804

Shallow
water

Shallow water

44

WA

In kind

NWS-2 014-00890

Shallow
water

Shallow water

45

WA

In kind

NWS-2 014-01177

Shallow
water

Shallow water

46

WA

In kind

NWS-2015-00291

Shallow
water

Shallow water

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Compensatory Mitigation in Estuarine and Marine Habitats

February 2023

Reference
#

State

In kind/ out-
of-kind

DA#

Impact
habitat

Mitigation
habitat

47

WA

In kind

NWS-2015-00601

Shallow
water

Shallow water

48

WA

In kind

NWS-2 015-00696

Shallow
water

Shallow water

49

WA

In kind

NWS-2 015-00971

Shallow
water

Shallow water

50

WA

In kind

NWS-2 016-00200

Shallow
water

Shallow water

51

WA

In kind

NWS-2 016-00320

Shallow
water

Shallow water

52

WA

In kind

NWS-2 016-00324

Shallow
water

Shallow water

53

WA

In kind

NWS-2 016-00902

Shallow
water

Shallow water

54

WA

In kind

NWS-2 017-00809

Shallow
water

Shallow water

55

WA

In kind

NWS-2012-01111

Shallow
water

Shallow water

56

WA

In kind

NWS-2013-00213

Shallow
water

Shallow water

57

WA

In kind

NWS-2 013-00245

Shallow
water

Shallow water

58

WA

In kind

NWS-2 014-00736

Shallow
water

Shallow water

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