A.01.13_California_Eelgrass_Mitigation_Policy_and_Implementing_Guidelines.pdf

West Coast Region

California Eelgrass Mitigation Policy and Implementing Guidelines

October 2014

Photo credit: www.Lorenz-Avelar.com http://www.lorenz-avelar.com/ i

Table of Contents

I. NATIONAL MARINE FISHERIES SERVICE’S (NMFS) CALIFORNIA EELGRASS MITIGATION

POLICY

A. POLICY STATEMENT

B. EELGRASS BACKGROUND AND INFORMATION

C. PURPOSE AND NEED FOR EELGRASS MITIGATION POLICY

D. RELEVANCE TO OTHER FEDERAL AND STATE POLICIES

1. Corps/EPA Mitigation Rule and supporting guidance

2. State of California Wetland Conservation Policies

3. NOAA Aquaculture Policy and National Shellfish Initiative

4. NOAA Seagrass Conservation Guidelines

5. Southern California Eelgrass Mitigation Policy

II. IMPLEMENTING GUIDELINES FOR CALIFORNIA

A. EELGRASS HABITAT DEFINITION

B. SURVEYING EELGRASS

1. Survey Parameters

2. Eelgrass Mapping

3. Survey Period

4. Reference Site Selection

C. AVOIDING AND MINIMIZING IMPACTS TO EELGRASS

1. Turbidity

2. Shading

3. Circulation patterns

4. Nutrient loading

5. Sediment loading

D. ASSESSING IMPACTS TO EELGRASS HABITAT

1. Direct Effects

2. Indirect Effects

E. MITIGATION OPTIONS

1. Comprehensive management plans

2. In-kind mitigation

3. Mitigation banks and in-lieu-fee programs

4. Out-of-kind mitigation

F. IN-KIND MITIGATION FOR IMPACTS TO EELGRASS

1. Mitigation Site Selection

2. Mitigation Area Needs

3. Mitigation Technique

4. Mitigation Plan

5. Mitigation Timing

6. Mitigation Monitoring and Performance Milestones

7. Mitigation Reporting

8. Supplemental Mitigation

G. SPECIAL CIRCUMSTANCES

1. Localized Temporary Impacts

2. Localized Permanent Impacts

III. GLOSSARY OF TERMS

IV. LITERATURE CITED

ii

ATTACHMENT 1. Graphic depiction of eelgrass habitat definition including spatial distribution and aerial coverage of vegetated cover and unvegetated eelgrass habitat.

ATTACHMENT 2. Example Eelgrass Habitat Percent Vegetated Cover.

ATTACHMENT 3. Flow chart depicting timing of surveys and monitoring.

ATTACHMENT 4. Eelgrass transplant monitoring report.

ATTACHMENT 5. Wetlands mitigation calculator formula and parameters.

ATTACHMENT 6. Example calculations for application of starting and final mitigation ratios for impacts to eelgrass habitat in southern California.

ATTACHMENT 7. Example mitigation area multipliers for delay in initiation of mitigation activities.

ATTACHMENT 8. Summary of Eelgrass Transplant Actions in California

I. National Marine Fisheries Service’s (NMFS) California Eelgrass Mitigation Policy

A. Policy Statement

It is NMFS’ policy to recommend no net loss of eelgrass habitat function in California.

For all of California, compensatory mitigation should be recommended for the loss of existing eelgrass habitat function, but only after avoidance and minimization of effects to eelgrass have been pursued to the maximum extent practicable. Our approach is congruous with the approach taken in the federal Clean Water Act guidelines under section 404(b)(1) (40 CFR 230). In absence of a complete functional assessment, eelgrass distribution and density should serve as a proxy for eelgrass habitat function. Compensatory mitigation options include comprehensive management plans, in-kind mitigation, mitigation banks and in-lieu-fee programs, and out-of-kind mitigation. While in-kind mitigation is preferred, the most appropriate form of compensatory mitigation should be determined on a case-by-case basis.

Further, it is the intent of this policy to ensure that there is no loss associated with delays in establishing compensatory mitigation. This should be accomplished by creating a greater amount of eelgrass than is lost, if the mitigation is performed contemporaneously or after the impacts occur. To achieve this, NMFS, in most instances, should recommend compensatory mitigation for vegetated and unvegetated eelgrass habitat be successfully completed at a ratio of at least 1.2:1 mitigation area to impact area. This ratio is based on present value calculation1 using a discount rate of 0.03 (NOAA-DARP 1999). This ratio assumes that restored eelgrass habitat achieves habitat function comparable to existing eelgrass habitat within a period of three years or less (Hoffman 1986, Evans & Short 2005, Fonseca et al. 1990).

For ongoing projects, once mitigation has been successfully implemented to compensate for the loss of eelgrass habitat function within a specified footprint, NMFS should not recommend additional mitigation for subsequent loss of eelgrass habitat if 1) ongoing project activities result in subsequent loss of eelgrass habitat function within the same footprint for which mitigation was completed and 2) the project applicant can document that no new area of eelgrass habitat is impacted by project activities.

This policy does not address mitigation for potential eelgrass habitat. NMFS recognizes impacts to potential eelgrass habitat may preclude eelgrass movement or expansion to suitable unvegetated areas in the future, potentially resulting in declines in eelgrass abundance over time.

In addition, it does not address other shallow water habitats. Regulatory protections in the estuarine/marine realm typically focus on wetlands and submerged aquatic vegetation. Mudflats, sandflats, and other superficially bare habitats do not garner the same degree of recognition and

1 Present Value (PV) is a calculation used in finance to determine the present day value of an amount that is received at a future date. The premise of the equation is that receiving something today is worth more than receiving the same item at a future date; PV = C1/(1+r)n where C1= resource at period 1, r= interest or discount rate, n=number of periods.

concern, even though these are some of the most productive and fragile ecosystems (Reilly et al.

1999). NMFS will continue to collaborate with federal and state partners on these issues.

B. Eelgrass Background and Information

Eelgrass species (Zostera marina L. and Z. pacifica) are seagrasses that occur in the temperate unconsolidated substrate of shallow coastal environments, enclosed bays, and estuaries. Eelgrass is a highly productive species and is considered to be a "foundation" or habitat forming species.

Eelgrass contributes to ecosystem functions at multiple levels as a primary and secondary producer, as a habitat structuring element, as a substrate for epiphytes and epifauna, and as sediment stabilizer and nutrient cycling facilitator. Eelgrass provides important foraging areas and shelter to young fish and invertebrates, food for migratory waterfowl and sea turtles, and spawning surfaces for invertebrates and fish such as the Pacific herring. Eelgrass also provides a significant source of carbon to the detrital pool which provides important organic matter in sometimes food-limited environments (e.g., submarine canyons). In addition, eelgrass has the capacity to sequester carbon in the underlying sediments and may help offset carbon emissions.

Given the significance and diversity of the functions and services provided by seagrass, Costanza et al. (2007) determined seagrass ecosystems to be one of Earth’s most valuable.

California supports dynamic eelgrass habitats that range in extent from less than 11,000 acres to possibly as much as 15,000 acres statewide. This is inclusive of estimates for poorly documented beds in smaller coastal systems as well as open coastal and insular areas. While among the most productive of habitats, the overall low statewide abundance makes eelgrass one of the rarest habitats in California. Collectively just five systems, Humboldt Bay, San Francisco Bay, San Diego Bay, Mission Bay and Tomales Bay support over 80 percent of the known eelgrass in the state. The uneven distribution of eelgrass resources increases the risk to this habitat and also contributes to its dynamic nature. Further, the narrow depth range within which eelgrass can occur further places this habitat at risk in the face of global climate change and sea level rise predictions.

Seagrass habitat has been lost from temperate estuaries worldwide (Duarte 2002, Lotze et al.

2006, Orth et al. 2006). While both natural and human-induced mechanisms have contributed to these losses, impacts from human population expansion and associated pollution and upland development is the primary cause (Short and Wyllie-Echeverria 1996). Human activities that affect eelgrass habitat distribution and abundance, including, but not limited to, urban development, harbor development, aquaculture, agricultural runoff, effluent discharges, and upland land use associated sediment discharge (Duarte 2008) occur throughout California. For example, dredging and filling; shading and alteration of circulation patterns; and watershed inputs of sediment, nutrients, and unnaturally concentrated or directed freshwater flows can directly and indirectly destroy eelgrass habitats. Conversely, in many areas great strides have been made at restoring water quality and expanding eelgrass resources through directed efforts at environmental improvements and resource enhancement. While improvements in eelgrass management have occurred overall, the importance of eelgrass both ecologically and economically, coupled with ongoing human pressure and potentially increasing degradation and losses associated with climate change, highlight the need to protect, maintain, and where feasible, enhance eelgrass habitat.

C. Purpose and Need for Eelgrass Mitigation Policy

Eelgrass warrants a strong protection strategy because of the important biological, physical, and economic values it provides, as well as its importance to managed species under the Magnuson- Stevens Fishery Conservation and Management Act (MSA). Vegetated shallows that support eelgrass are also considered special aquatic sites under the 404(b)(1) guidelines of the Clean Water Act (40 C.F.R. § 230.43). The National Oceanic and Atmospheric Administration’s (NOAA) National Marine Fisheries Service (NMFS) developed this policy to establish and support a goal of protecting this resource and its habitat functions, including spatial coverage and density of eelgrass habitats. This NMFS policy and implementing guidelines are being shared with agencies and the public to ensure there is a clear and transparent process for developing eelgrass mitigation recommendations.

Pursuant to the MSA, eelgrass is designated as an essential fish habitat (EFH) habitat area of particular concern (HAPC) for various federally-managed fish species within the Pacific Coast Groundfish Fishery Management Plan (FMP) (PFMC 2008). An HAPC is a subset of EFH that is rare, particularly susceptible to human-induced degradation, especially ecologically important, and/or located in an environmentally stressed area. HAPC designations are used to provide additional focus for conservation efforts.

This policy and guidelines support but do not expand upon existing NMFS authorities under the MSA, the Fish and Wildlife Coordination Act (FWCA), and the National Environmental Policy Act (NEPA). Pursuant to the EFH provisions of the MSA, FWCA, and obligations under the NEPA as a responsible agency, NMFS annually reviews and provides recommendations on numerous actions that may affect eelgrass resources throughout California. Section 305(b)(1)(D) of the MSA requires NMFS to coordinate with, and provide information to, other federal agencies regarding the conservation and enhancement of EFH. Section 305(b)(2) requires all federal agencies to consult with NMFS on all actions or proposed actions authorized, funded, or undertaken by the agency that may adversely affect EFH. Under section 305(b)(4) of the MSA, NMFS is required to provide EFH Conservation Recommendations to federal and state agencies for actions that would adversely affect EFH (50 C.F.R. § 600.925). NMFS makes its recommendations with the goal of avoiding, minimizing, or otherwise compensating for adverse effects to EFH. When impacts to NMFS trust resources are unavoidable, NMFS may recommend compensatory mitigation to offset those impacts. In order to fulfill its consultative role, NMFS may also recommend, among other things, the development of mitigation plans, habitat distribution maps, surveys and survey reports, progress milestones, monitoring programs, and reports verifying the completion of mitigation activities.

Eelgrass impact management and mitigation throughout California has historically been undertaken without a statewide strategy. Federal actions with impacts to eelgrass require considerable NMFS staff time for project review, coordination and development of conservation recommendations. As federal staff resources vary with budgets, and threats to aquatic resources remain steady or increase, regulatory streamlining and increased efficiency are crucial for continued protection of important coastal habitats, including eelgrass. The California Eelgrass Mitigation Policy (CEMP) is meant to increase efficiency of existing regulatory authorities in a programmatic manner, provide transparency to federal agencies and action proponents, and ensure that unavoidable impacts to eelgrass habitat are fully and appropriately mitigated. It is the intent of NMFS to collaborate with other federal, state, and local agencies charged with the protection of marine resources to seek a unified approach to actions affecting eelgrass such that consistency across agencies with respect to this resource may be enhanced.

D. Relevance to Other Federal and State Policies

Based on our understanding of existing federal and state policies regarding aquatic resource conservation, the CEMP does not conflict with existing policies and complements the federal and state wetland policies as described below. NMFS does not intend to make any recommendations, which, if adopted by the action agency and carried out, would violate other federal, state, or local laws. The CEMP also complements the NOAA Aquaculture Policy and National Shellfish Initiative and builds upon the NOAA Seagrass Conservation Guidelines and the Southern California Eelgrass Mitigation Policy.

1. Corps/EPA Mitigation Rule and supporting guidance

In 2008, the Environmental Protection Agency (EPA) and the U.S. Army Corps of Engineers (Corps) issued revised regulations governing compensatory mitigation for authorized impacts to wetlands, streams, and other waters of the U.S. under Section 404 of the Clean Water Act. The regulations emphasize avoiding impacts to wetlands and other water resources. For unavoidable impacts, the rule incorporates Natural Resource Council recommendations to improve planning, implementing and managing wetland replacement projects, including: science-based assessment of impacts and compensation measures, watershed assessments to drive mitigation sites and plans, measurable and enforceable ecological performance standards for evaluating mitigation projects, mitigation monitoring to document whether the mitigation employed meets ecological performance standards, and complete compensation plans. The regulations also encourage the expansion of mitigation banking and in lieu fee agreements to improve the quality and success of compensatory mitigation projects.

The NMFS policy to recommend no net loss of eelgrass function and the eelgrass mitigation guidelines offered herein align with the provisions of the EPA and Corps mitigation rule, but provide more specific recommendations on how to avoid and minimize impacts to eelgrass and how to implement eelgrass surveys, assessments, mitigation, and monitoring.

2. State of California Wetland Conservation Policies

The 1993 State of California Wetlands Conservation Policy established a framework and strategy to ensure no overall net loss and long-term gain in the quantity, quality, and permanence of wetlands acreage and values in California in a manner that fosters creativity, stewardship, and respect for private property, reduce procedural complexity in administration of state and federal wetlands conservation programs, and encourage partnerships to make landowner incentive programs and cooperative planning efforts the primary focus of wetlands conservation and restoration.

The State of California is also developing a Wetland and Riparian Area Protection Policy. The first phase of this effort was published as the “Preliminary Draft Wetland Area Protection Policy” with the purpose of protecting all waters of the State, including wetlands, from dredge and fill discharges. It includes a wetland definition and associated delineation methods, an assessment framework for collecting and reporting aquatic resource information, and requirements applicable to discharges of dredged or fill material. The draft specifies that dredge or fill projects will provide for replacement of existing beneficial uses through compensatory mitigation. The preliminary policy includes a determination that compensatory mitigation will sustain and improve the overall abundance, diversity and condition of aquatic resources in a project watershed area.

Based on the definition of wetlands included in these state wetland policies, the policies do not directly apply to subtidal eelgrass habitat, but may apply to intertidal eelgrass habitat. The NMFS policy of recommending no net loss to eelgrass habitat function and recommendations for compensatory mitigation for eelgrass impacts complement the state protection policies for wetlands.

3. NOAA Aquaculture Policy and National Shellfish Initiative

In 2011, NOAA released the National Marine Aquaculture Policy and the National Shellfish Initiative. The Policy encourages and fosters sustainable aquaculture development that provides domestic jobs, products, and services and that is in harmony with healthy, productive, and resilient marine ecosystems, compatible with other uses of the marine environment, and consistent with the National Policy for the Stewardship of the Ocean, our Coasts, and the Great Lakes (National Ocean Policy). The goal of the Initiative is to increase populations of bivalve shellfish in our nation’s coastal waters—including oysters, clams, abalone, and mussels— through both sustainable commercial production and restoration activities. The Initiative supports shellfish industry jobs and business opportunities to meet the growing demand for seafood, while protecting and enhancing habitat for important commercial, recreational, and endangered and threatened species and species recovery. The Initiative also highlights improved water quality, nutrient removal, and shoreline protection as benefits from shellfish production and restoration. Both the Policy and the Initiative seek to improve interagency coordination for permitting commercial and restoration shellfish projects, as well as support research and other data collection to assess and refine conservation strategies and priorities.

The regulatory efficiencies, transparency, and compensation for impacts to eelgrass promoted by the CEMP directly support the National Aquaculture Policy statements and National Shellfish Initiative through: (1) protection of eelgrass, an important component of productive and resilient coastal ecosystems in California and habitat for wild species, and (2) improved coordination with federal partners regarding planning and permitting for commercial shellfish projects.

Furthermore, research conducted under the direction of the National Shellfish Initiative could be informed by and also inform NMFS consultations regarding eelgrass impacts and mitigation in California.

4. NOAA Seagrass Conservation Guidelines

The NOAA publication, “Guidelines for the Conservation and Restoration of Seagrasses in the United States and Adjacent Waters” (1998) was developed by Mark Fonseca of NOAA’s Beaufort Laboratory along with Jud Kenworthy and Gordon Thayer and was funded by NOAA’s Coastal Ocean Program. The document presents an overview of seagrass conservation and restoration in the United States, discusses important issues that should be addressed in planning seagrass restoration projects, describes different planting methodologies, proposes monitoring criteria and means for evaluation success, and discusses issues faced by resource managers. The CEMP considers information presented in the Fonseca et al. document, but deviates in some cases in order to provide reasonable and practicable guidelines for eelgrass conservation in California.

5. Southern California Eelgrass Mitigation Policy

In southern and central California, eelgrass mitigation has been addressed in accordance with the Southern California Eelgrass Mitigation Policy applied by NMFS, US Fish & Wildlife Service, California Department of Fish and Wildlife, California Coastal Commission, US Army Corps of Engineers, and other resource and regulatory agencies since 1991, and which has generally been effective at ensuring eelgrass impacts are mitigated in most circumstances. Given the success of the Southern California Eelgrass Mitigation Policy over its 20-year history, this policy reflects an expansion of the application of the Southern California policy with minor modifications to ensure a high standard of statewide eelgrass management and protection. This policy will supersede the Southern California Eelgrass Mitigation Policy for all areas of California upon its adoption.

II. Implementing Guidelines for California

This policy and guidelines will serve as the guidance for staff and managers within NMFS for developing recommendations concerning eelgrass issues through EFH and FWCA consultations and NEPA reviews throughout California. This policy will inform NMFS’s position on eelgrass issues for California in other roles as a responsible, advisory, or funding agency or trustee. In addition, this document provides guidance to assist NMFS in performing its consultative role under the statutes described above. Finally, pursuant to NMFS obligation to provide information to federal agencies under Section 305(b)(1)(D) of the MSA, this policy serves that role by providing information intended to further the conservation and enhancement of EFH. Should this policy or guidelines be inconsistent with any formally-promulgated NMFS regulations, those formally-promulgated regulations will take precedence over any inconsistent provisions of this policy.

While many of the activities impacting eelgrass are similar across California, eelgrass stressors and growth characteristics differ between southern California (U.S./Mexico border to Pt.

Conception), central California (Point Conception to San Francisco Bay entrance), San Francisco Bay, and northern California (San Francisco Bay to the California/Oregon border). The amount of scientific information available to base management decisions on also differs among areas within California, with considerably more information and history with eelgrass habitat management in southern California than the other regions. Gaps in region-specific scientific information do not override the need to be protective of eelgrass habitat while relying on the best information currently available from areas within and outside of California. Although the primary orientation of this policy is toward statewide use, where indicated below, specific elements of this policy may differ between southern California, central California, northern California and San Francisco Bay.

NMFS will continue to explore the science of eelgrass habitat and improve our understanding of eelgrass habitat function, impacts, assessment techniques, and mitigation efficacy.

Approximately every 5 years, NMFS intends to evaluate monitoring and survey data collected by federal agencies and action proponents per the recommendations of these guidelines. NMFS managers will determine if updates to these guidelines are appropriate based on information evaluated during the 5-year review. Updates to these guidelines and supporting technical information will be available on the NMFS website.

The information below serves as a common starting place for NMFS recommendations to achieve no net loss of eelgrass habitat function. NMFS employees should not depart from the guidelines provided herein without appropriate justification and supervisory concurrence.

However, the recommendations that NMFS ultimately makes should be provided on a case-by-case basis to provide flexibility when site specific conditions dictate. In the EFH context, NMFS recommendations are provided to the action agency, which has final approval of the action; in accordance with the MSA, the action agency may take up NMFS recommendations or articulate its reasons for not following the recommendations. In the FWCA context, NMFS makes recommendations which must be considered, but the action agency is ultimately responsible for the wildlife protective measures it adopts (if any). For these reasons, neither this policy nor its implementing guidelines are to be interpreted as binding on the public.

A. Eelgrass Habitat Definition

Eelgrass distribution fluctuates and can expand, contract, disappear, and recolonize areas within suitable environments. Vegetated eelgrass areas can expand by as much as 5 meters (m) and contract by as much as 4 m annually (Donoghue 2011). Within eelgrass habitat, eelgrass is expected to fluctuate in density and patch extent based on prevailing environmental factors (e.g., turbidity, freshwater flows, wave and current energy, bioturbation, temperature, etc.). To account for seagrass fluctuation, Fonseca et al. (1998) recommends that seagrass habitat include the vegetated areas as well as presently unvegetated spaces between seagrass patches.

In addition, there is an area of functional influence, where the habitat function provided by the vegetated cover extends out into adjacent unvegetated areas. Those functions include detrital enrichment, energy dampening and sediment trapping, primary productivity, alteration of current or wave patterns, and fish and invertebrate use, among other functions. The influence of eelgrass on the local environment can extend up to 10 m from individual eelgrass patches, with the distance being a function of the extent and density of eelgrass comprising the bed as well as local biologic, hydrographic, and bathymetric conditions (Bostrom and Bonsdorff 2000, Bostrom et al.

2001, Ferrell and Bell 1991, Peterson et al. 2004, Smith et al. 2008, van Houte-Howes et al.

2004, Webster et al. 1998). Detrital enrichment will generally extend laterally as well as down slope from the beds, while fish and invertebrates that utilize eelgrass beds may move away from the eelgrass core to areas around the bed margins for foraging and in response to tides or diurnal cycles (Smith et al. 2008).

To encompass fluctuating eelgrass distribution and functional influence around eelgrass cover, for the purposes of this policy and guidelines, eelgrass habitat is defined as areas of vegetated eelgrass cover (any eelgrass within 1 m2 quadrat and within 1 m of another shoot) bounded by a 5 m wide perimeter of unvegetated area (See Attachment 1 for a graphical depiction of this definition). Unvegetated areas may have eelgrass shoots a distance greater than 1 m from another shoot, and may be internal as well as external to areas of vegetated cover. For isolated patches and on a case-by-case basis, it may be acceptable to include an unvegetated area boundary less than or greater than 5 m wide. The definition excludes areas of unsuitable environmental conditions such as hard bottom substrates, shaded locations, or areas that extend to depths below those supporting eelgrass. Suitable depths can vary substantially depending upon site-specific conditions. In general, eelgrass does not extend deeper than 12 feet mean lower low water (MLLW) in most protected bays and harbors in Southern California, and is more limited in Central and Northern California embayments. However, eelgrass can grow much deeper in entrance channels and offshore areas

B. Surveying Eelgrass

NMFS may recommend action agencies conduct surveys of eelgrass habitat to evaluate effects of a proposed action. Eelgrass habitat should be surveyed using visual or acoustic methods and mapping technologies and scales appropriate to the action, scale, and area of work. Surveys should document both vegetated eelgrass cover as well as unvegetated areas within eelgrass habitat (See section II.A. for definition). Assessing impacts to eelgrass habitat relies on the completion of quality surveys and mapping. As such, inferior quality of surveys and mapping (e.g., completed at an inappropriate scale or using inappropriate methods) may make proper evaluation of impacts impossible, and may result in a recommendation from NMFS to re-survey and re-map project areas. Also, to account for fluctuations in eelgrass habitat due to environmental variations, a reference site(s) should be incorporated into the survey (See section V.B.4 below for more details).

1. Survey Parameters

Because eelgrass growth conditions in California vary, eelgrass mapping techniques will also vary. Diver transects or boundary mapping may be suited to very small scale mapping efforts, while aerial and/or acoustic survey with ground-truthing may be more suited to larger survey areas. Aerial and above-water visual survey methods should be employed only where the lower limit of eelgrass is clearly visible or in combination with methods that adequately inventory eelgrass in deeper waters.

The survey area should be scaled as appropriate to the size of the potential action and the potential extent and distribution of eelgrass impacts, including both direct and indirect effects.

The resolution of mapping should be adequate to address the scale of effects reasonably expected to occur. For small projects, such as individual boat docks, higher mapping resolution is appropriate in order to detect actual effects to eelgrass at a scale meaningful to the project size.

At larger scales, the mapping resolution may be less refined over a larger area, assuming that minor errors in mapping will balance out over the larger scale. Survey reports should provide a detailed description of the survey coverage (e.g., number, location, and type of samples) and any interpolation methods used in the mapping.

While many parameters may be useful to describe eelgrass habitat condition (e.g., plant biomass, leaf length, shoot:root ratios, epiphytic loading), many are labor intensive and may be impractical for resource management applications on a day-to-day basis. For this reason, four parameters have been identified for use in eelgrass habitat surveys and assessment of effects of an action on eelgrass. These parameters that should be articulated in eelgrass surveys are: 1) spatial distribution, 2) areal extent, 3) percentage of vegetated cover, and 4) the turion (shoot) density.

a) Spatial Distribution

The spatial distribution of eelgrass habitat should be delineated by a contiguous boundary around all areas of vegetated eelgrass cover extending outward a distance of 5 m, excluding gaps within the vegetated cover that have individual plants greater than 10 m from neighboring plants.

Where such separations occur, either a separate area should be defined, or a gap in the area should be defined by extending a line around the void along a boundary defined by adjacent plants and including the 5 meter perimeter. The boundary of the eelgrass habitat should not extend into areas where depth, substrate, or existing structures are unsuited to supporting eelgrass habitat.

b) Aerial Extent

The eelgrass habitat aerial extent is the quantitative area (e.g., square meters) of the spatial distribution boundary polygon of the eelgrass habitat. The total aerial extent should be broken down into extent of vegetated cover and extent of unvegetated habitat. Areal extent should be determined using commercially available geo-spatial analysis software. For small projects, coordinate data for polygon vertices could be entered into a spreadsheet format, and area could be calculated using simple geometry.

c) Percent Vegetated Cover

Eelgrass vegetated cover exists when one or more leaf shoots (turions) per square meter is present. The percent bottom cover within eelgrass habitat should be determined by totaling the area of vegetated eelgrass cover and dividing this by the total eelgrass habitat area. Where substantial differences in bottom cover occur across portions of the eelgrass habitat, the habitat could be subdivided into cover classes (e.g., 20% cover, 50% cover, 75% cover).

d) Turion (Shoot) Density

Turion density is the mean number of eelgrass leaf shoots per square meter within mapped eelgrass vegetated cover. Turion density should be reported as a mean ± the standard deviation of replicate measurements. The number of replicate measurements (n) should be reported along with the mean and deviation. Turion densities are determined only within vegetated areas of eelgrass habitat and therefore, it is not possible to measure a turion density equal to zero. If different cover classes are used, a turion density should be determined for each cover class.

2. Eelgrass Mapping

For all actions that may directly or indirectly affect eelgrass habitat, an eelgrass habitat distribution map should be prepared on an accurate bathymetric chart with contour intervals of not greater than 1 foot (local vertical datum of MLLW). Exceptions to the detailed bathymetry could be made for small projects or for projects where detailed bathymetry may be infeasible.

Unless region-specific mapping format and protocols are developed by NMFS (in which case such region-specific mapping guidance should be used), the mapping should utilize the following format and protocols:

a) Bounding Coordinates

Horizontal datum - Universal Transverse Mercator (UTM), NAD 83 meters, Zone 11 (for southern California) or Zone 10 (for central, San Francisco Bay, and northern California) is the preferred projection and datum. Another projection or datum may be used; however, the map and spatial data should include metadata that accurately defines the projection and datum.

Vertical datum - Mean Lower Low Water (MLLW), depth in feet.

b) Units

Transects, grids, or scale bars should be expressed in meters. Area measurements should be in square meters.

c) File Format

A spatial data layer compatible with readily available commercial geographic information system software producing file formats compatible with ESRI® ArcGIS software should be sent to NMFS when the area mapped supports at least 10 square meters of eelgrass. For those areas supporting less than 10 square meters of eelgrass, a table may alternatively be provided giving the vertices bounding x, y coordinates of the eelgrass areas in a spreadsheet or an ASCII file format. In addition to a spatial layer and/or table, a hard-copy map should be included with the survey report. The projection and datum should be clearly defined in the metadata and/or an associated text file.

Eelgrass maps should, at a minimum, include the following:

- A graphic scale bar, north arrow, legend, horizontal datum and vertical datum;

- A boundary illustrating the limits of the area surveyed;

- Bathymetric contours for the survey area, including both the action area(s) and reference site(s) in increments of not more than 1 foot;

- An overlay of proposed action improvements and construction limits;

- The boundary of the defined eelgrass habitat including an identification of area exclusions based on physical unsuitability to support eelgrass habitat; and

- The existing eelgrass cover within the defined eelgrass habitat at the time of the survey.

3. Survey Period

All mapping efforts should be completed during the active growth period for eelgrass (typically March through October for southern California, April through October for central California, April through October for San Francisco Bay, and May through September for northern California) and should be considered valid for a period of 60 days to ensure significant changes in eelgrass distribution and density do not occur between survey date and the project start date.

The 60 day period is particularly important for eelgrass habitat survey conducted at the very beginning of the growing season, if eelgrass habitat expansion occurs as the growing season progresses. A period other than 60 days could be warranted and should be evaluated on a case-by-case basis, particularly for surveys completed in the middle of the growing season. However, when the end of the 60-day validity period falls outside of the region-specific active growth period, the survey could be considered valid until the beginning of the next active growth period.

For example, a survey completed in southern California in the August-October time frame would be valid until the resumption of the active growth phase (i.e., in most instances, March 1). In some cases, NMFS and the action agency may agree to surveys being completed outside of the active growth period. For surveys completed during or after unusual climatic events (e.g., high fluvial discharge periods, El Niño conditions), NMFS staff should be contacted to determine if any modifications to the common survey period are warranted.

4. Reference Site Selection

Eelgrass habitat spatial extent, aerial extent, percent cover and turion density are expected to naturally fluctuate through time in response to natural environmental variables. As a result, it is necessary to correct for natural variability when conducting surveys for the purpose of evaluating action effects on eelgrass or performance of mitigation areas. This is generally accomplished through the use of a reference site(s), which is expected to respond similarly to the action area in response to natural environmental variability. It is beneficial to select and monitor multiple reference sites rather than a single site and to utilize the average reference site condition as a metric for environmental fluctuations. This is especially true when a mitigation site is located within an area of known environmental gradients, and reference sites may be selected on both sides of the mitigation site along the gradient. Environmental conditions (e.g., sediment, currents, proximity to action area, shoot density, light availability, depth, onshore and watershed influences) at the reference site(s) should be representative of the environmental conditions at the impact area (Fonseca et al. 1998). Where practical, the reference site(s) should be at least the size of the anticipated impact and/or mitigation area to limit the potential for minor changes in a reference site (e.g., propeller scarring or ray foraging damage) overly affecting mitigation needs.

The logic for site(s) selection should be documented in the eelgrass mitigation planning documents.

C. Avoiding and Minimizing Impacts to Eelgrass

This section describes measures to avoid and minimize impacts to eelgrass caused by turbidity, shading, nutrient loading, sedimentation and alteration of circulation patterns. Not all measures are equally suited to a particular project or condition. Measures to avoid or minimize impacts should be focused on stressors where the source and control are within the purview of the permittee and action agency. Action agencies in coordination with NMFS should evaluate and establish impact avoidance and minimization measures on a case-by-case basis depending on the action and site-specific information, including prevailing current patterns, sediment source, characteristics, and quantity, as well as the nature and duration of work.

1. Turbidity

To avoid and minimize potential turbidity-related impacts to eelgrass:

- Where practical, actions should be located as far as possible from existing eelgrass; and

- In-water work should occur as quickly as possible such that the duration of impacts is minimized.

Where proposed turbidity generating activities must occur in proximity to eelgrass and increased turbidity will occur at a magnitude and duration that may affect eelgrass habitat, measures to control turbidity levels should be employed when practical considering physical and biological constraints and impacts. Measures may include:

- Use of turbidity curtains where appropriate and feasible;

- Use of low impact equipment and methods (e.g., environmental buckets, or a hydraulic suction dredge instead of clamshell or hopper dredge, provided the discharge may be located away from the eelgrass habitat and appropriate turbidity controls can be provided at the discharge point);

- Limiting activities by tide or day-night windows to limit light degradation within eelgrass habitat;

- Utilizing 24-hour dredging to reduce the overall duration of work and to take advantage of dredging during dark periods when photosynthesis is not occurring; or

- Other measures that an action party may propose and be able to employ to minimize potential for adverse turbidity effects to eelgrass.

NMFS developed a flowchart for a stepwise decision making process as guidance for action agencies to determine when to implement best management practices (BMPs) for minimizing turbidity from dredging actions as part of a programmatic EFH consultation in San Francisco Bay. The parameters considered in the flow chart are relevant to all marine areas of California.

This document is posted on the NMFS West Coast Region web page (http://www.westcoast.fisheries.noaa.gov/habitat/habitat_types/seagrass_info/california_eelgrass.

html) and may be used to evaluate avoidance and minimization measures for any project that generates increased turbidity.

2. Shading

A number of potential design modifications may be used to minimize effects of shading on eelgrass. Boat docks, ramps, gangways, and similar structures should avoid eelgrass habitat to the maximum extent feasible. If avoidance of eelgrass or habitat is infeasible, impacts should be minimized by utilizing, to the maximum extent feasible, design modifications and construction materials that allow for greater light penetration. Action modifications should include, but are not limited to:

- Avoid siting over-water or landside structures in areas where shading of eelgrass habitat would occur;

- Maximizing the north-south orientation of the structure;

- Maximizing the height of the structure above the water;

- Minimizing the width and supporting structure mass to decrease shade effects;

- Relocating the structure in deeper water and limiting the placement of structures in shallow areas where eelgrass occurs to the extent feasible; and

- Utilizing light transmitting materials in structure design.

Construction materials used to increase light passage beneath the structures may include, but are not limited to, open grating or adequate spacing between deck boards to allow for effective illumination to support eelgrass habitat. The use of these shade reducing options may be appropriate where they do not conflict with safety, ADA compliance, or structure utility objectives.

NMFS developed a stepwise key as guidance for action agencies to determine which combination of modifications are best suited for minimizing shading effects from overwater structures on eelgrass as part of a programmatic EFH consultation in San Francisco Bay. The parameters considered in the flow chart are relevant to all marine areas of California. This document is posted on the West Coast Region web page (http://www.westcoast.fisheries.noaa.gov/habitat/habitat_types/seagrass_info/california_eelgrass.htm

l) and may be used to evaluate avoidance and minimization measures for any project that results in shading.

3. Circulation patterns

Where appropriate to the scale and nature of potential eelgrass impacts, action parties should evaluate if and how the action may alter the hydrodynamics of the action area such that eelgrass habitat within or in proximity to the action area may be adversely affected. To maintain good water flow and low residence time of water within eelgrass habitat, action agencies should ensure actions:

- Minimize scouring velocities near or within eelgrass beds;

- Maintain wind and tidal circulation to the extent practical by considering orientation of piers and docks to maintain predominant wind effects;

- Incorporate setbacks on the order of 15 to 50 meters from eelgrass habitat where practical to allow for greater circulation and reduced impact from boat maneuvering, grounding, and propeller damage, and to address shading impacts; and

- Minimize the number of piles and maximize pile spacing to the extent practical, where piles are needed to support structures.

For large-scale actions in the proximity of eelgrass habitats, NMFS may request specific modeling and/or field hydrodynamic assessments of the potential effects of work on characteristics of circulation within eelgrass habitat.

4. Nutrient loading

Where appropriate to the scale and nature of potential eelgrass impacts, the following measures should be considered for implementation to reduce the potential for excessive nutrient loading to eelgrass habitat:

- diverting site runoff from landscaped areas away from discharges around eelgrass habitat;

- implementation of fertilizer reduction program;

- reduction of watershed nutrient loading;

- controlling local sources of nutrients such as animal wastes and leach fields; and

- maintaining good circulation and flushing conditions within the water body.

Reducing nutrient loading may also provide opportunities for establishing eelgrass as mitigation for project impacts.

5. Sediment loading

Watershed development and changes in land use may increase soil erosion and increase sedimentation to downstream embayments and lagoons.

- To the extent practicable, maintain riparian vegetation buffers along all streams in the watershed.

- Incorporate watershed analysis into agricultural, ranching, and residential/commercial development projects.

- Increase resistance to soil erosion and runoff. Sediment basins, contour farming, and grazing management are examples of key practices.

- Implement best management practices for sediment control during construction and maintenance operations (e.g., Caltrans 2003).

Reducing sediment loading may also provide opportunities for establishing eelgrass as mitigation for project impacts in systems for which sedimentation is a demonstrable limiting factor to eelgrass.

D. Assessing Impacts to Eelgrass Habitat

If appropriate to the statute under which the consultation occurs, NMFS should consider both direct and indirect effects of the project in order to assess whether a project may impact eelgrass.

NMFS is aware that many of the statutes and regulations it administers may have more specific meanings for certain terms, including “direct effect” and “indirect effect”, and will use the statutory or regulatory meaning of those terms when conducting consultations under those statutes.2 Nevertheless, it is useful for NMFS to consider effects experienced

2 In the EFH context, adverse effects include any impact that reduces quality and/or quantity of EFH, including direct or indirect physical, chemical, or biological alterations of the waters or substrate (50 CFR 600.910). The Council of Environmental Quality (CEQ) regulations regarding NEPA implementation (40 CFR 1508.8(a)) define direct and indirect impacts of an action for the purposes of NEPA. Other NMFS statutes provide their own definitions regarding effects.

contemporaneously with project actions (both at the project site and away from the project site) and which might occur later in time.

Generally, effects to eelgrass habitat should be assessed using pre- and post-project surveys of the impact area and appropriate reference site(s) conducted during the time period of maximum eelgrass growth (typically March through October for southern California, April through October for central California, April through October for San Francisco Bay, and May through September for northern California). NMFS should consider the likelihood that the effects would occur before recommending pre- and post-project eelgrass surveys. The pre-construction survey of the eelgrass habitat in the action area and an appropriate reference site(s) should be completed within 60 days before start of construction. After construction, a post-action survey of the eelgrass habitat in the action area and at an appropriate reference site(s) should be completed within 30 days of completion of construction, or within the first 30 days of the next active growth period following completion of construction that occurs outside of the active growth period. Copies of all surveys should be provided to the lead federal agency, NMFS, and other interested regulatory and/or resource agencies within 30 days of completing the survey. The recommended timing of surveys is intended to minimize changes in eelgrass habitat distribution and abundance during the period between survey completion and construction initiation and completion. For example, a post-action survey completed beyond 30 days following construction or outside of the active growing season may show declines in eelgrass habitat as a result of natural senescence rather than the action.

The lead federal agency and NMFS should consider reference area eelgrass performance, physical evidence of impact, turbidity and construction activities monitoring data, as well as other documentation in the determination of the impacts of the action undertaken. Impact analyses should document whether the impacts are anticipated to be complete at the time of the assessment, or whether there is an anticipation of continuing eelgrass impacts due to chronic or intermittent effects. Where eelgrass at the impact site declines coincident with and similarly to decline at the reference site(s), the percentage of decline at the reference site should be deducted from the decline at the impact site. However, if eelgrass expands within the reference site(s), the impact site should only be evaluated against the pre-construction condition of the reference site and not the expanded condition.