Final Report- Estuary 2100-2 “San Francisco Bay Water Quality

Improvement Fund”

San Francisco Bay Living Shorelines:

Near-shore Linkages Project Integrating Subtidal Habitat Restoration Projects to Increase Connectivity, Function, and

Resiliency across Multiple Habitats in San Francisco Bay.

July 10, 2015

Marilyn Latta, Project Manager, State Coastal Conservancy (510-286-4157, marilyn.latta@scc.ca.gov)

Contributors to this Report: San Francisco State University: Katharyn Boyer, Jen Miller, Cassie Pinnell, Julien Moderan, Stephanie Kiriakopolos and Kevin Stockmann University of California at Davis: Chela Zabin, Edwin Grosholz, Stephanie Kiriakopolos United States Geological Survey: Susan De La Cruz, Ashley Smith, Tanya Graham, and Laura Hollander ESA: Jeremy Lowe, Michelle Orr, Elena Vandebrook, Damien Kunz

II. Table of Contents Executive summary of project goals and results……………………………………2-6 Progress in Addressing the Project’s Objectives…………………………………...6-11

Description of Project Components (substantive tasks)……………………………11-13 Partnerships…………………………………………………………………………13 Project Evaluation - Summary of monitoring results……………………………….13-18 Summary of Expected Outputs and Outcomes/Accomplished Deliverables………..17-18 Key messages, lessons learned and project implications……………………………18-19 Conclusions………………………………………………………………………….20 Appendices…………………………………………………………………………..Attached

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II. Executive summary of project goals and results

Introduction and project description The San Francisco Bay Living Shorelines: Near-shore Linkages Project is a multi-objective habitat restoration pilot project managed by the State Coastal Conservancy, in collaboration with biological and physical scientists with San Francisco State University, University of California, Davis, USGS Western Ecological Research Center, and consultants at ESA. Critical initial grant funding has been provided by the Environmental Protection Agency in partnership with the San Francisco Estuary Partnership/Association of Bay Area Governments, which was then matched by California State Coastal Conservancy with additional project funds provided by the California Wildlife Conservation Board and NOAA Fisheries. Additional project partners include landowners The Nature Conservancy and the California Department of Fish and Wildlife, and construction support was provided by the California Wildlife Foundation, Reef Innovations, Drakes Bay Oyster Company, and Dixon Marine Services. Grant term: March, 2010 – June, 2015 Funding from this grant: $300,000. Match funding $100,000 from the State Coastal Conservancy. Additional leveraged funding $1,510,000 in funding from multiple partners including the State Coastal Conservancy, Wildlife Conservation Board, and NOAA Fisheries. While not a new concept nationally and globally, “living shorelines” projects are new to San Francisco Bay, where pilot restoration work on eelgrass and oyster reefs has led to recommendations for additional experimental testing of techniques and gradual scaling up to larger projects. The 2010 San Francisco Bay Subtidal Habitat Goals Report (see www.sfbaysubtidal.org) recommended that the next generation of projects consider the possibility of integrating multiple habitat types to improve linkages among habitats and promote potential synergistic effects of different habitat features on each other as well as associated fauna. Such habitat features, if scaled up slightly beyond previous projects would have the potential to positively influence physical processes (such as sediment erosion and accretion) that influence shoreline configuration. With this critical first seed grant from the Estuary 2100-2 project led by the San Francisco Estuary Partnership with funding from EPA, the State Coastal Conservancy assembled an interdisciplinary team to build on previous restoration lessons and begin to test integrating multiple habitats. The project further tests subtidal restoration techniques, restores critical eelgrass and oyster habitat, tests the individual and interactive effects of restoration techniques on habitat values, begins to evaluate and test soft shoreline alternatives to hard/structural stabilization. Due to limited historical information on distribution and abundance of native oysters and eelgrass, we use the term “restoration” in the sense of enhancing valuable functions and services promoted by these types of features in San Francisco Bay and elsewhere, rather than in the strict sense of replacing previously known distributions or extent.

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The project was designed in 2010-11, fully permitted in July 2012, and constructed over a three week window in July-August 2012. Eelgrass plantings and oyster treatments were installed at two sites: San Rafael Shoreline and the Eden Landing Ecological Reserve in Hayward. There is a larger project with both physical and biological goals at the San Rafael site, and a smaller project to test just oyster and eelgrass recruitment at both sites. The overarching goals of the project have remained consistent since the original project inception, but the final project constructed and monitored differs from the original grant proposal description, as approved by grant managers as the project design was finalized. This project is the first of its’ kind and scale in San Francisco Bay, testing an experimental “living shorelines approach” through construction of offshore native oyster and eelgrass reefs to achieve biological and habitat goals, and also test the ability of reefs to increase wave attenuation and protect the shoreline from erosion in the face of climate changes such as sea level rise. Existing subtidal areas are poorly understood and undermanaged, due to the limited research that has been done in submerged areas, but the connection between the subtidal bay and the shoreline edge is increasingly important with climate change. Subtidal environments in San Francisco Bay have harsh work conditions- with extremely cold temperatures and strong currents- that make conducting research, experiments, and restoration projects difficult in these areas. Developing complementary biological and physical goals in a sound restoration design has involved a lot of technical input and willingness to experiment by an interdisciplinary team and multiple regional land management and regulatory agencies. There were a wide variety of technical considerations ranging from land ownership and physical site selection considerations, permitting process and issues including current allowable beneficial fill amounts, and multiple special-status species considerations that were incorporated into the final design and construction timing. There have only been a few pilot subtidal restoration projects in the bay since 2002 and none at this one acre scale before. There are limited entities to lead the technical work and a need to better educate regional resource agency staff and key stakeholders on the goals, methods, and benefits of this type of multi-habitat and multi-objective approach. This truly is a pioneering and experimental project, particularly at this stage of new science with both subtidal restoration and pilot climate adaptation methods in San Francisco Bay. The San Francisco Bay Subtidal Habitat Goals Report describes the many data gaps with subtidal habitats and restoration project methods, and therefore recommends a thoughtful and metered approach, starting with small-scale shoreline monitoring and slowly phasing up once key information has been gained on restoration methods and outcomes.

The project development involved substantial communications and developing new partnerships between different science and management disciplines, new restoration techniques and methods, and new contractor and vendor partnerships. Planning specific logistics with oyster shell material purchase and configuration into reef elements, and the creation and configuration of artificial reef elements (Reef balls, etc.), required establishing methods and entities locally who could do the work. The Bay Conservation and Development Commission currently has limits on the amount of fill that can be placed in the bay due to concerns about development and filling of habitat, and the use of beneficial fill such as oyster shell is a new concept in San Francisco Bay that requires

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discussion and experimental testing before permitting agencies will allow larger scale projects. BCDC is currently reviewing beneficial fill policies, particularly in light of climate change stressors and adaptation, and this project will provide new information that will help to guide fill policies moving forward.

Oyster and eelgrass habitats are typically located in fairly quiescent estuarine conditions, and we are testing the ability of these species to provide ecosystem services in areas of the shoreline that receive wind waves, ferry and boat wakes, extreme king tides, etc. Site selection criteria had to include not only appropriate conditions for oyster and eelgrass beds, which can be ephemeral species, but also willing landowners who would give permission for access to their shoreline and subtidal parcels and co-sign on permits. Given our objectives and these constraints, we began the process of identifying locations to conduct this pilot project. We found it quite challenging to achieve siting that could permit us to meet all our objectives. We decided to identify criteria most critical to conducting the project, and also secondary criteria to meet if possible:

Highest priority:

Appropriate region and depth for eelgrass and oysters (based on known distributions and/or evidence of success at proposed sites)

Appropriate substrate for oyster reefs (coarser can minimize sinking of and sedimentation on reef) and eelgrass (coarser can lead to increased light availability)

Willing landowners with expected reasonable time frame for permits/approvals

Very important, but not as critical:

Large enough shoreline, oriented so that treatment array can be placed in a line parallel to the shore and perpendicular to the direction of waves (an array that meets only the latter is less ideal)

Distance to shore amenable to shore access for ease of monitoring (e.g., a few hundred meters at most, not a mile)

To achieve if possible:

Multiple locations to provide replication and allow comparison of treatment effects in different regions

If multiple locations, then same experimental design and depth at all

Soft shoreline with paired comparison to hard shoreline nearby, if possible

We identified two locations within the Bay that would meet our most important site selection criteria, and thus should allow us to meet many of our objectives.

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The original project concept included a goal of constructing the project offshore from a tidal marsh edge at three different locations in the bay. We considered Corte Madera Bay adjacent to Muzzi Marsh/ Corte Madera Ecological Reserve. This area had multiple technical issues that required further study, including ferry wake impacts, mixed results from prior pilot eelgrass restoration projects, communications required with multiple private landowners; as well as a study being conducted at the time by BCDC and ESA that was evaluating shoreline erosion at the mouth of Corte Madera Creek and the preferred projects to mitigate and adapt. We decided the Corte Madera Bay area was not a good candidate for these reasons and selected a final preferred site about half mile north that is owned by The Nature Conservancy along the San Rafael shoreline. We continue to explore the future possibility of a living shorelines project in Corte Madera Bay, building on revegetation and high tide island construction enhancement work in progress by the Coastal Conservancy’s Invasive Spartina Project and additional work in the area by the Friends of Corte Madera Creek and others. Our project team evaluated and included the originally planned Eden Landing Ecological Reserve site within the South Bay Salt Pond Restoration Project. This site also has multiple technical issues and considerations we needed to further study such as the impacts of non-native Atlantic oyster drills and the evolution of newly breached tidal channels, before implementing a full-scale project at this site. For these reasons we only included our smaller study at this site to assess oyster and eelgrass response to reef elements. Last, our project team evaluated three locations within Eastshore State Park: Berkeley North Basin, Albany Beach, and Breuner Marsh. East Bay Regional Park District was already engaged in restoration planning for all three sites, and with our input was able to incorporate subtidal treatments as part of their own restoration design at the North Basin/Albany Beach area. The Breuner Marsh project was too early in planning for us to select the site for our adjacent offshore project in 2012, and also includes multiple offshore landowners that must be engaged. The Breuner Marsh project includes tidal and seasonal wetlands that are in the final stages of construction now in 2015-16, and our project team is continuing to explore a future living shorelines project offshore from Breuner Marsh and the adjacent Giant Marsh to the north. Design Summary- Large and Small Projects For more detail, please see Appendices A and B. Larger scale experiment to test both biological and physical effects: This experiment includes four 32 x 10m treatment plots situated parallel to the shore, approximately 200 m from shore. This design allows us to compare the effects of Pacific shell bag mounds, eelgrass, and both together, in comparison to a control of the same size. We designed this experiment to be at a large enough scale to compare effects on physical factors such as wave attenuation and accretion as well as effects on biological properties that operate at larger scales (e.g., bird and fish utilization, water quality interactions of oysters and eelgrass). The larger project is only implemented at the San Rafael Shoreline site.

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“Substrate element” experiment to examine small-scale biological effects: This experiment consists of replicate 1x1 m substrate elements of different substrate types, intended to compare native oyster recruitment and growth parameters to inform future restoration projects. At the San Rafael Shoreline site, this experiment is set up in the 30-m spaces between and on either side of the line of larger scale plots described above. Four oyster substrate types not tested in the large scale experiment (reef balls, mini reef ball stacks, oyster blocks, and layer cakes) are replicated 5 times, for a total of 20 elements. These elements are placed in groups (blocks) of four, with each of the four substrate types represented in each block. This substrate element experiment is the only project installed at Eden Landing Ecological Reserve. The large and small projects at the two final sites are functioning well and proving to be an innovative and successful pilot project to date that is being recognized as a model project that provides critical new data to a variety of science and management entities in the bay area. The project is advancing the state of the science of living shorelines, pioneering new ideas and methods, and engaging an interdisciplinary set of partners in designs and methods that can be applied to additional sites in San Francisco Bay. We have accomplished a lot with a little- the original $300,000 grant has been leveraged with $1.7M in additional state and local funds in a robust project that includes substantial annual scientific monitoring that involves long hours of field work during limited low tide windows, and associated lab work to conduct species counts and assess results. The 2012, 2013, and 2014 monitoring reports are the three annual reports for the EPA/SFEP grant (see Appendix A), and project monitoring is ongoing as part of a five year monitoring program through 2017.

Brief snapshot summary of progress on original objectives: Please see Appendix A for full data and progress to date. Restore native subtidal habitat for the benefit of multiple species including aquatic invertebrates, salmon, herring, diving ducks, and shorebirds. We have completed this objective and the reefs are providing habitat for a wide variety of species. Please see monitoring reports for specific species data. The only species we have not yet observed are Pacific herring, but we continue to monitor during the herring spawning window December- April each year. Generate new data on the functional relationships between subtidal habitats and adjacent tidal and riparian areas. As described in our modification to the grant agreement in February 2014, the final site selected for the larger project with multi-objective (physical and biological) goals was the San Rafael Shoreline. This area is offshore from a hardened riprap shoreline, and we are testing concepts that can be applied to future sites offshore from soft shorelines/tidal wetland edge. Improve water quality through a reduction in suspended sediments at the sites. The reefs are accreting sediment within the reef test elements, and inshore of the project area.

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Test the ability of these subtidal treatments to protect critical shoreline and wetland areas vulnerable to erosion, through increased three-dimensional subtidal structure that will stabilize sediment and increase wave attenuation. The reefs are stabilizing sediment and they increase wave attenuation by 30-50%, with the highest benefit at mean tide levels. The project will educate and involve the Bay Area public in these restoration projects so participants will have the opportunity to learn abou the importance of healthy subtidal habitat and its connection to healthy shorelines, wetlands, creeks, and San Francisco Bay. A total of 30 volunteers assisted with construction of oyster reef elements and recruitment tiles, outplanting of eelgrass, and project monitoring from April 2012- April 2013. Due to the extremely hard access that requires early morning hours and physical ability to wade through 200 meters of mudflats to get to the site, we discontinued the use of volunteers in the project area due to safety concerns. Instead we have focused our educational efforts on outreach and project information sharing via television, web, and print media; conference presentations; and presentations at local stakeholder meetings such as the San Francisco Bay Joint Venture. Please see list attached in Appendix B. Site summary

The Nature Conservancy Site- San Rafael

The San Rafael site is a coastal area owned by The Nature Conservancy (TNC), located along the western shoreline of San Rafael Bay in the City of San Rafael. San Rafael Bay is one of several embayments along the eastern margin of the Marin Peninsula in northern San Francisco Bay. San Rafael Bay has an average depth of less than 1.8 meters [m]) (6 feet [ft]) at mean lower low water (MLLW) and lies between Point San Quentin to the south and Point San Pedro to the north. The TNC site is subject to the mixed semi-diurnal tides typical to San Francisco Bay. Latitudinal cross-sections through the project site show minimal vertical changes across the mudflats until reaching the dredged shipping channel that runs southeast-northwest.

Eden Landing Ecological Reserve Site

The Eden Landing Ecological Reserve (ELER) site is owned and managed by the California Department of Fish and Wildlife (CDFW), and is part of the South Bay Salt Ponds Restoration Project managed by the Coastal Conservancy, US Fish and Wildlife Service, and CDFW. The site is near the eastern shore of South San Francisco Bay (South Bay) near the San Mateo Bridge. It is considered “sovereign land” and is held in public trust under the responsibility of the California Wildlife Conservation Board. The South Bay is a large shallow basin, containing an inundated, deep, relict river channel surrounded by broad shallow areas, mudflats, and fringing tidal marsh. The areas between mean high and low tide contain a network of small branching channels that effectively drain the South Bay at low water, leaving an expanse of exposed mudflats.

Summary of Project Goals and Results Overarching Goal:

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To create biologically rich and diverse subtidal and low intertidal habitats, including eelgrass and oyster reefs, as part of a self-sustaining estuary system that restores ecological function and is resilient to changing environmental conditions.

The State Coastal Conservancy (www.scc.ca.gov) and multiple state, federal, and non-profit partners constructed native oyster and eelgrass beds in summer 2012 as part of an innovative habitat restoration and climate change adaptation pilot project in San Francisco Bay. The project builds upon 50 year regional goals for the restoration and protection of subtidal habitats in the bay (www.sfbaysubtidal.org). It is the first time that restoration of oyster and eelgrass beds is occurring at this scale, and results will provide critical information about the potential benefits of using natural reefs along the shoreline to protect habitat in the face of sea level rise and climate change. This type of work is new to San Francisco Bay but is building on the lessons learned from other restoration efforts in the estuary and around the nation. As mentioned, the pilot project was constructed in two locations in summer 2012: in San Rafael Bay and along the Hayward shoreline. Through frequent monitoring, information is being generated about how the project can be scaled up to balance shoreline protection, environmental impacts, and habitat needs. More than two million native oysters have settled at the San Rafael site, along with juvenile Dungeness crabs, bay shrimp, white sturgeon, and a wide diversity of other fish, birds, and wildlife. We estimate that the reefs have increased the numbers of oysters in this region of the bay by 2 orders of magnitude. Initial data shows that the reefs reduce wave energy by 30-50% at certain water levels. Complete annual monitoring reports (2012, 2013, and 2014) and more information about the project and all of our partners is available at www.sfbaylivingshorelines.org.

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Figure 1. Total number of vegetative and flowering eelgrass shoots present, per donor and treatment plot at TNC site, quarterly through summer 2014. E = eelgrass plot, E+O = eelgrass and oyster plot, PM = plants from the Point Molate donor site and PSP = plants from the Point San Pablo donor site.

Figure 2. Number of vegetative and flowering shoots by donor at ELER site, Hayward, quarterly through fall 2013 (after which plants were essentially gone). BFI = plants from

Spring 2013: Repeat transplant

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the Bay Farm Island donor site and ELER = plants from the Eden Landing Ecological Reserve site. Potential factors affecting eelgrass survival at the site include 1) high densities of the non-native Atlantic mud snail, which smothers the plants and may be limiting sunlight for photosynthesis; and 2) shallower tidal height 1.0+ MLLW- where higher heat stress may affect the plants. We were aware of these two issues, which is why only the smaller project was planned for site as we needed to gather more information on these issues before planning a larger scale project.

Figure 3: Estimated total number of oysters at San Rafael site (TNC)

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Figure 4: North facing baycrete elements- mean oyster densities at San Rafael site (TNC)

Figure 5. TNC site at San Rafael showing change in elevation between May 2012 and June 2014. (green is accretion, orange and red is erosion)

Figure 6. Notable sedimentation over entire bottom level of shell bags.

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Figure 7 Sedimentation and oyster space for shell bags at TNC.

Figure 8. Increase in mean densities of wading, fish-eating birds (egrets, herons)

Progress in Addressing the Project’s Objectives

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Objective 1: Use a pilot-scale, experimental approach to establish native oysters and eelgrass at multiple locations in San Francisco Bay. As this project is the first Living Shorelines concept design carried out in San Francisco Bay and is one of the first on the US west coast, it was important to start small to gain acceptance for such projects among regulators and the public. However, the project team recognized the need for the project to be large enough to allow assessment of physical effects along shorelines and to attract species that require a larger habitat area for food or refuge services. Thus, at the San Rafael site we chose a size deemed large enough to meet our science goals but small enough to still be a reasonable pilot project to install and permit. An experimental approach was important to the project team, as we wished to understand the successes and shortcomings of the pilot restoration project in a rigorous way. However, we settled on only one replicate of each treatment type at the San Rafael site due to space limitation on the TNC parcel and our need to limit the overall size of the installation as we learned to construct the largest reefs in San Francisco Bay to date and gained permitting approval. From the standpoint of statistical analysis, having only one plot per treatment type means that replicate samples within a plot are not true replicates, as they are not interspersed with other treatment types across the space of the TNC property. The risk in interpreting data with only the four large plots spread across the site is that there could be other differences across that space that are not related to the treatments, thus confounding interpretation of differences by treatment. The Quality Assurance Project Plan finalized March 26, 2012 includes information on monitoring methods to assess functionality of the restored habitats. The original 2010 grant proposal project description differs from the final project designed and constructed, which was communicated and approved at the time to San Francisco Estuary Partnership staff, and memorialized in a grant amendment in March 2014. While we originally wanted to have more sites and more replicated plots for the large-scale project, we settled on one site at San Rafael with one plot per treatment due to the amount of funding, landowner support, and permitting considerations to minimize fill. Still, with care in interpretation, we can say quite a bit about how the treatments evolve habitat and physical functioning characteristics over time and relative to each other. The results are good and we are still able to say a lot about the functionality of our project at San Rafael, but limited sites and replicated makes us qualify our statements about the application of our results to other locations and how we represent the bay as a whole. We are working on additional phases of living shoreline projects at additional sites with additional replicates, so that we can say more about how different sites perform. For the smaller scale comparison of oyster substrates, we were able to achieve true replication at both the San Rafael and Hayward sites, making a rigorous comparison of treatments possible statistically. We intended to repeat the same design in multiple locations around the bay so that we could determine how environmental context influenced our results; however, we found it difficult to identify locations that met our site selection criteria (e.g., with shorelines roughly parallel to waves, relative ease of access, appropriate depths for eelgrass and

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oysters, willing landowners, etc.) and thus began with just one larger-scale project in this first phase of the work. At Hayward, many of our site selection criteria were met; however, we felt we did not have enough information about the site to be confident that we could establish both oysters and eelgrass, and were unwilling to scale up to a larger project until that was achieved. Objective 2: Compare the effectiveness of different restoration treatments in establishing these habitat-forming species. Approaches We have used five approaches to address the effectiveness of different restoration treatments in establishing native oysters and eelgrass.

1. Our project explicitly aimed to test whether restoring oysters and eelgrass together vs. each habitat alone would improve outcomes for either species. This test entails evaluating eelgrass growth patterns (densities, heights, etc.) when eelgrass is grown alone versus in proximity to oyster shell reef, and similarly by assessing oyster growth patterns (densities, sizes) when oyster shell reef is restored alone versus in proximity to eelgrass.

2. We tested five types of oyster settlement substrates to determine which would perform the best. In the ideal, a substrate would promote native oyster recruitment, growth, and survival, while discouraging the growth of non-native species, would not be prone to sinking into soft sediment substrates, and would not cause significant scour, or accumulate large amounts of sediment. Obviously, restoration substrates also need to maintain their structural integrity over time.

The five treatments included: Pacific shell bag mounds, large reef balls, mini reef ball stacks, oyster blocks, and layer cakes. See pictures below.

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Pacific shell bag mound

Construction of large and small reef balls

Construction of oyster blocks

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Completed oyster blocks

Completed mini reef balls and oyster blocks

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Completed large reef balls and oyster blocks

3. We tested transplants versus seeding of eelgrass at the San Rafael site.

4. We tested whether the donor (the natural bed collected from) mattered to the outcomes achieved for eelgrass establishment and development of functional attributes of the restored eelgrass.

5. We assessed whether the position on oyster elements or the placement of whole oyster settlement substrates at different elevations would influence the effectiveness of native oyster success.

Effectiveness Our findings on the effectiveness of each of the restoration treatment approaches:

1. Several lines of evidence suggest that there is a benefit to restoring native oysters and eelgrass together. Although trapping has caught a limited number of individuals, there were a few species of fish which were found among oyster reefs at San Rafael only when eelgrass was also present. In addition, community similarity analysis showed that the oyster reef + eelgrass plots at San Rafael are intermediate in epibenthic invertebrate assemblages between the oyster only and eelgrass only plots. On the other hand, we have not found benefits of oyster reef presence to eelgrass growth characteristics (and in fact eelgrass spread is likely to be limited by the surrounding oyster reefs in our checkerboard design), nor have we seen oyster abundance or size increase in the presence of eelgrass. At Hayward, eelgrass was present for a limited time, so we are unable to assess this effect there. We have not finished analyzing stable isotope data yet, but these may provide a useful indication of how nutrition to eelgrass or oysters differs with the other species present, and more broadly if other aspects of the food web are enhanced in either habitat with the presence of the other species and associated species in that habitat. In order to adequately test for effects of dual restoration,

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we need additional sites where oysters and eelgrass are restored both together and separately.

2. For our second approach, we found that oysters performed equally well across the

various types of baycrete structures at San Rafael, with one exception – there were far fewer oysters on layer cakes. This was because oysters generally did better on vertical vs. horizontal surfaces, and layer cake surface area is primarily horizontal. Shell bag mounds outperformed all baycrete structures in terms of number of oysters on a per-element basis. Two element types appear to have less structural integrity than the others: layer cakes and small reef ball stacks, both of which are beginning to shift and/or break down.

At Hayward, oysters recruited initially to shell bags only, but currently longer-term survival appears to be best on the oyster blocks, with the other baycrete structures doing less well (layer cakes were not included at this site due to the expectation that they would not hold up under high wave action).

3. For our third approach, we were only able to use buoy deployed seeding at the

San Rafael site and only with flowering shoots from the Point San Pablo donor, as flowering shoots were not available at the time of our late summer project start for the other three populations used as donors for transplant material. We did not plan to implement seeding at Hayward, where we installed whole shoot transplants only. At San Rafael, we did not detect seedling recruitment in the spring of 2013 following buoy-deployed seeding, and we did not repeat seeding after we conducted the second transplant that April; we would not have had flowering shoots available until summer and did not want to risk damaging transplants by adding the seed buoys into the plots afterwards. Thus, in comparing the two methods of eelgrass establishment, we conclude that transplanting whole shoots was the more effective technique overall, both in terms of availability of propagules and success of establishment. However, we still recommend seeding when possible due to the fact that sexual reproduction can increase the genetic diversity of restored stock and may therefore increase the resiliency of eelgrass to perturbations at restoration sites over time.

4. In our fourth approach, the Point Molate donor bed initially showed a trend of

greater transplant success at San Rafael, with higher overall densities than the Point San Pablo donor. This trend continued and became magnified over time, especially in the eelgrass only plot. We suggest that Point Molate eelgrass may be better adapted to the type of sediment conditions found at San Rafael, as both have a higher amount of clay present than at Point San Pablo (Boyer and Wyllie-Echeverria 2010). Although we found no difference in growth characteristics between the two donors used at the Hayward site in the limited time we had to assess the eelgrass, the trend of differential success among donors at San Rafael, and similar evidence from previous projects (Boyer et al. 2008; Lewis and Boyer 2014), lends support to our hypothesis that donor choice can matter to restoration success.

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5. In our fifth and final approach to assessing restoration techniques, we found tidal

height, surface orientation, and direction to have strong effects on oyster density at the San Rafael site. Across all element types at San Rafael, more oysters were present at the lower and mid-level elevations than at the high elevation. More oysters were present on the north side than the south side and on vertical vs. horizontal faces. While longer immersion times could explain greater abundance on at lower tidal elevations, the north-south and surface orientation differences strongly suggest that heat and/or desiccation stress is a factor in determining oyster abundance at San Rafael. At Hayward, while oysters recruited initially to shell bags and then to the interior surfaces of the large oyster balls, two structure types that ought to be the best in mitigating heat and desiccation stress, more oysters are currently found on the higher elevations of castle blocks and large reef balls. This is likely due to predation by the Atlantic oyster drill Urosalpinx cinerea, which is more abundant at the lower elevations. Further experimental work at this site indicates greater drill abundance and greater mortality of oysters due to predation by drills at lower vs. higher elevations. Eden Landing has proven itself a challenging site for oyster recruitment, due at least in part to the non-native predatory snail, the Atlantic mud snail (Urosalpinx cinerea). However, at one year post reef construction (July 2013) we observed a sudden increase in oyster recruitment. This recruitment occurred at higher elevations, a zone where we also observe higher surface temperatures. Data over the last year also indicates that drill densities are potentially lower at higher elevations. We hypothesize that oysters are surviving at higher elevations because it is a potential refuge zone from drill predation. We conducted an experiment in 2014 to to test if elevation and surface direction influences oyster survival when Urosalpinx cinerea is present. Recruitment tiles were placed at two heights from the bottom (10cm and 40 cm), and in three orientations (horizontal facing up, horizontal facing down, and vertical facing north). All tiles were pre-seeded with oysters, and follow up monitoring was done every ten days for 3 months (June-August 2014) to assess initial oyster mortality rates. Oyster survival, size, and recruitment is monitored along with drill damage, drill densities, and establishment of other sessile organisms. Please see Appendix 2 for more information on the study results.

Objective 3: Determine the extent to which restoration treatments enhance habitat

for invertebrates, fish, and birds, relative to areas lacking structure and pre-treatment conditions.

We have accumulated evidence that providing the physical structure of our project design attracted mobile invertebrates that benefit from such structure. Preliminary data suggest that several fish species of concern including white and green sturgeon and steelhead lingered at the project site at San Rafael, although additional analysis is necessary to evaluate these patterns. At both San Rafael and Hayward, wading bird presence increased after the placement of reef structures, and at San Rafael, black oystercatchers are utilizing

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the reefs for foraging. Additional monitoring over several more years is necessary to determine the how the strengths of these relationships develop over time. Objective 4: Determine if the type of treatment (e.g., oyster reefs, eelgrass plantings,

or combinations of oyster reefs and eelgrass) influences habitat values differently.

Preliminarily, we can conclude from the San Rafael experiment that certain species are benefitted more by one substrate than the other. Black oystercatchers and wading birds increased in the presence of the reef structures. Black surfperch and bay pipefish were shown to have a greater association with eelgrass habitat, and epibenthic invertebrates assemblages are beginning to differentiate between the eelgrass and oyster reef habitats. Eelgrass presence increased the occurrence of certain fish species among oyster reef structures (bay pipefish, shiner surfperch, and saddleback gunnel), suggesting that restoring the two habitats in proximity to each other can increase the richness of species present. Objective 5: Begin to evaluate potential for subtidal restoration to enhance

functioning of nearby intertidal mudflat, creek, and marsh habitats, e.g., by providing food resources to species that move among habitats.

As we do not have marsh or creek habitat in close proximity to the San Rafael site, we are not able to determine the degree to which our added structures influence functioning or subsidies from our project to these habitats. This was confirmed with San Francisco Estuary Partnership staff as planning progressed between 2011-2013, and in the February 2014 modification to the grant agreement. The changes were due to difficulties in finding sites with 1) willing landowners and 2) that also had the appropriate conditions to support oysters and eelgrass. This was a minor component of the project rather than the main focus, and it will be addressed in a future phase as part of the recently funded San Francisco Bay Multi-Habitat Enhancement Project (see Future Work section page 25). We are able to say that increasing physical structure enhances functions relative to mudflats, at least for species that benefit from the refuge and food resources that are provided by our project. An increase in wading birds and in black oystercatchers through the addition of our project is a good indication that certain guilds of birds are benefiting. Objective 6: Evaluate potential for living subtidal features to reduce water flow

velocities, attenuate waves, and increase sedimentation, and assess whether different restoration treatments influence physical processes differently.

Our reefs achieved a reduction in wave energy (30%-50% depending on the tide level, with the greatest effect at mean tides) more so than the broad mudflat alone accomplished at mean tide level; however, we are cautious in our interpretation of this result considering we had limited measurements. Ideally, we would have similar reefs located in multiple locations with different slopes and wave environments to permit further assessment of such structures in attenuating wave energy along San Francisco Bay shorelines.

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Our measurements of physical processes have shown accumulation of sediment around the reefs, but a small impact on accretion across the area of the project; additional measurements are needed over time to assess this trend. We expected greater subsidence of the reefs and over a longer period of time; our data showing only a 10 cm subsidence into the sediments ending after 5 months suggest that even in the very soft sediments of the San Rafael site, sinking of our reef structures is not a great concern. Sediment accumulating around the oyster shell bags is unlikely to support oyster survival at the lower elevations, leading us to include only the upper portions of the reefs in our estimates of oyster abundance and size, and also suggesting that future projects should consider this issue when predicting habitat availability on the reefs. Since the different element types appear to perform similarly in terms of stability, the choice for the construction of future reefs should be made based on their performance in oyster habitat terms which may point to the use of shell bags, or perhaps oyster blocks based on the Hayward results. Future deployments should allow for the loss of available space for oysters due to subsidence and sedimentation. Larger elements, if used in the future, will tend to subside more.

Objective 7: Determine if position in the Bay, and the specific environmental context

at that location, influences foundational species establishment, habitat provision, and physical processes conferred by restoration treatments.

Although we currently have just two project sites to compare, and only the small substrate comparison that can be made at the Hayward site, there are a number of preliminary conclusions we can draw about the effects of environmental context. For example, eelgrass persistence and spread has been far superior at San Rafael, perhaps due to much less exposure on the low tides, or due to the Atlantic mud snails at Hayward (not present at San Rafael) weighing down the plants or blocking light to the leaves with their egg masses. In addition, oyster shell bags easily outperformed other substrates in terms of oyster recruitment at San Rafael, but at Hayward, oyster blocks currently appear to be the best. A shell bag element offers more surface area than any of the baycrete elements and greater protection from heat and/or desiccation stress due to more shading and water retention and the generally lower tidal elevation relative to the baycrete structures; this is the most likely explanation for their high performance at San Rafael. However, at Hayward, where predation pressure is strong and greater at lower elevations, taller structures with more exposed surfaces have ultimately outperformed shell bags. Thus it appears that selection of optimal substrate needs to be guided by an understanding of the key stressors for eelgrass and oysters at each site. Having additional sites at which to deploy test substrates and measure potential stressors would be useful to further refine site-specific design criteria. Objective 8: Where possible, compare the ability to establish restoration treatments,

habitat functions, and physical changes along mudflats/wetlands versus armored shores.

At this point our project does not include a comparison of soft shoreline versus hardened shoreline environment. A future project at Hayward could accomplish this by comparing

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areas north (riprap) and south (marsh) of Mount Eden Creek. In January 2015, the Coastal Conservancy successfully secured a new grant through the USFWS North American Wetland Conservation Act, to build upon the information and lessons learned from this project and construct an additional set of Living Shoreline reefs at an additional site in San Francisco Bay. This “Phase Two” effort will include additional tidal marsh habitat (Pacific cordgrass, marsh gumplant), linking a more diverse set of habitat types up the slope that can have cumulative benefits with further integration of habitat linkages and increased wave attenuation potential. Description of Project Components (substantive tasks) Tasks included:

1) Project Management and Reporting- Project Manager Marilyn Latta (SCC) and Science Lead Katharyn Boyer (SFSU) successfully completed all project management and reporting. This included management of the draft and final designs, permitting documents, coordination between all project team members, and final annual monitoring reports and reporting for the EPA grant.

2) Develop Monitoring Protocols, including QAPP- Katharyn Boyer (SFSU) successfully managed the development and finalization of monitoring protocols for eelgrass, fish and invertebrates, and the final approved QAPP for the project.

3) Final Design and Permitting- Marilyn Latta (SCC) worked closely with all

project team members to successfully submit and secure permit applications. Brief Permitting Review The Coastal Conservancy and consultants at AECOM (formerly URS) prepared all documentation for regulatory permits and approvals required for the project. Additional consultants on the project provided support for coordination with regulatory agencies and assisted in application for permits. The Coastal Conservancy coordinated early with the permit agencies, including review of draft design and an interagency meeting in Fall 2011 to discuss design modifications, regulatory permit mechanisms, project questions, and input regarding benefits and impacts to specific species. Permitting discussions focused in particular on the methods and resulting benefits and impacts to bay species, seasonal windows for the work, and issues regarding the placement of clean Pacific oyster shell as beneficial fill to create the habitat reefs. Permit applications were submitted in February 2012, and numerous follow-up meetings and correspondence occurred on particular aspects of each agencies requirements. Final permits were secured in July 2012 prior to construction. Permit applications and approvals include:

US Army Corps of Engineers: Nationwide Permit 27 (Aquatic Habitat Restoration, Establishment, and Enhancement Activities)

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NOAA Fisheries consultation with US Army Corps of Engineers: Section 7 consultation relative to the Endangered Species Act, Essential Fish Habitat consultation relative to the Magnuson Stevens Fishery Conservation and Management Act and Fish and Wildlife Conservation Act.

San Francisco Bay Conservation and Development Commission: Administrative permit.

California Department of Fish and Wildlife consultation with BCDC: Consultation to limit any impacts and maximize benefits to state-listed fish and wildlife; Scientific Collecting Permit for eelgrass donor collections; Letter of Authorization for transplanting eelgrass to restoration sites.

San Francisco Bay Regional Water Quality Control Board: Section 404 Water quality certification.

California State Lands Commission: Coordination to confirm that the project is not on state-leased lands, and to confirm CEQA compliance.

License Agreement with landowner The Nature Conservancy for the San Rafael site.

Letter of Permission with landowner California Department of Fish and Wildlife for permission to access the Eden Landing Ecological Reserve site.

Letter of Permission and support from City of San Rafael

4) Eelgrass Restoration Implementation and Monitoring- Katharyn Boyer (SFSU) successfully led all aspects of eelgrass design, construction, and monitoring.

5) Oyster Restoration Implementation and Monitoring (other funds)- Chela Zabin of UC Davis successfully led all aspects of native oyster design, construction, and monitoring.

6) Outreach and Public Involvement- Marilyn Latta successfully led all aspects of

public outreach and involvement for the project. We held a public informational meeting 5/24/12. We secured excellent media coverage of construction by multiple tv, radio, and print outlets on 7/22/12. Kathy Boyer and Marilyn Latta made multiple presentations on the project, including Oct 2011 and 2013 State of the Estuary Conferences, Coastal and Estuarine Research Federation in November 2013, Society for Ecological Restoration Northern California May 2014, CALFED conferences October 2012 and October 2014, SF Bay Joint Venture presentations 2013-14, Bay Area Ecosystem Climate Change Collaborative 2013-14, San Francisco Exploratorium May 2014, Marin Conservation League May 2015. The San Francisco Chronicle ran a front page story on the project in November 2013, The Nature Conservancy highlighted the project in their Bay Nature Magazine included a feature story on the project in their April - July 2014 issue. The project website is www.sfbaylivingshorelines.org. A partial summary of all public outreach was posted to basecamp in March 2013.

Partnerships

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The project managed by the State Coastal Conservancy, in collaboration with biological and physical scientists with San Francisco State University, University of California, Davis, USGS Western Ecological Research Center, and consultants at ESA. Funding has been provided by the Environmental Protection Agency in partnership with the San Francisco Estuary Partnership/Association of Bay Area Governments, California State Coastal Conservancy, California Wildlife Conservation Board, and NOAA Fisheries. Additional project partners include landowners The Nature Conservancy and the California Department of Fish and Wildlife, and construction support was provided by the California Wildlife Foundation, Reef Innovations, Drakes Bay Oyster Company, and Dixon Marine Services.

III. Project Evaluation a. Summary of monitoring results

San Rafael and Hayward are the two sites for the project. San Rafael information is listed first, followed by a section on Hayward. San Rafael Site Eelgrass After replanting eelgrass in April 2013 (as the original late-summer planting in 2012 did not succeed), plants at the larger scale project at San Rafael performed well, reaching 50% of planted densities by July 2013 and 124% by July 2014. Plant heights were comparable to those in natural beds (tallest shoots 150-190 cm in spring and summer 2014). A trend appears to be developing of lower overall densities and heights in the eelgrass + oyster plot compared to the eelgrass-only plot, possibly due to abrasion of plants against the oyster shells. Plants originating from Point Molate tended to produce higher densities than those from Point San Pablo, perhaps due to better matching of site conditions between the Point Molate and San Rafael sites (finer sediments than Point San Pablo). The two donors have become difficult to distinguish due to overlapping clonal growth and we will discontinue tracking them separately on future sampling dates. Oysters Native oysters quickly recruited to the reef structures (by the first fall), with over 2 million present in the first year; to be conservative, the counts included only the top portions of the oyster shell mounds, as the lower portions have accumulated sediment and may not support living oysters. While estimates of the total population show some fluctuations over time, numbers have remained in the millions of oysters. We estimate that the reefs have increased the numbers of oysters in this region of the bay by 2 orders of magnitude. Oysters also recruited in high numbers to the small “baycrete” structures, with the exception of the layer cake configuration, which did not perform as well; overall, baycrete structures did not support as many oysters as the shell bag elements. The stacked oyster balls are also not holding up as well as the reef balls and oyster blocks. Measures of the baycrete structures in small quadrats (10 cm2) showed that more oysters were present at lower and mid-level elevations than at the high elevation, on the north side than the south side, and on vertical than horizontal faces.

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Interactions between eelgrass and oyster habitats In relation to eelgrass and oyster reef interactions, we are assessing whether there is an advantage to restoring both habitats in close proximity. We can address this question by evaluating the recruitment and growth characteristics of both eelgrass and oysters grown separately and together, determining if there is a benefit to either organism in the “combined” plots compared to each habitat taken singly. However, it is important to understand the mechanisms behind any such benefits. For example, eelgrass could benefit from reduced wave energy within the “combined” plots, or it could be receiving a supplement of nutrients excreted from oysters, or from other organisms that are growing on the shell bag units. Knowing the mechanisms involved is important to our understanding of these species interactions and also to our ability to make informed recommendations for future restoration designs. With other funds, the eelgrass group at SF State and the oyster group at UC Davis are measuring natural abundance stable isotopes in these organisms to evaluate whether exchange of nutrients is important to the success of both eelgrass and native oysters. In fall 2013, the SF State team has found that eelgrass is approximately 10 cm taller in plots where both eelgrass and oysters are present, and that densities are also higher, in comparison to eelgrass grown alone. We can assess whether the mechanism of benefit to eelgrass stems from the provision of nitrogen from oyster excretion by comparing the stable isotopic signatures of N in eelgrass with and without oyster reefs present. Similarly, native oysters may benefit from increased dissolved carbon availability through the presence of eelgrass, which sheds leaves, producing organic carbon in the vicinity of the oysters. Measuring stable isotopic signatures of nitrogen, carbon, and sulfur permits an assessment of the degree to which these two species are interacting. Further, we are evaluating these signatures from all of the most abundant species on the reefs in order to determine the degree to which they are interacting through nutrient exchange; this will help to provide a causal link between the habitat we have provided and the benefits to organisms that use the habitat. At the San Rafael site, in the eelgrass, sampling the eelgrass itself, the epiphytes growing on the eelgrass blades, gammarid amphipods, and caprellid amphipods. In the large plots with oyster shell reef present, sampling includes the oysters themselves, barnacles, sponges, crabs (two species; e.g., Dungeness and Hemigrapsus), and nudibranchs. Stable isotopic signatures of eelgrass (Fig. 5 please see above) appeared different with oyster reef present in an early comparison; a detailed collection of tissues to evaluate isotopic signatures that can indicate food web relationships was conducted in summer 2014 in collaboration with the project’s oyster team at UC Davis, and analysis is underway. Epibenthic invertebrate response Two sizes of traps were used to ensure that a size range of invertebrates and fish could be detected. Minnow Traps and Oval Traps are baited with a mixture of shrimp and fish. Minnow Traps have double entrance openings of 1 inch. The construction is ¼-inch galvanized mesh. The larger collapsible Oval Fish Traps have double entrances measuring 6 inches x 5 3/8 inches. The traps are 38 inches x 25 inches x 20 inches with a

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5/8-inch square mesh. When deployed, the Minnow Traps will be attached to the larger Oval Traps with 8 feet of line ensuring both traps sample the same area.

Trapping with minnow (small traps for and oval traps indicated an early response of species reliant on physical structure, including bay shrimp and Dungeness crab. Additional species that are attracted to physical structure have been trapped in plots with oyster reef and/or eelgrass present (e.g., red rock crabs and red crabs). Suction sampling of epibenthic invertebrates indicated that community composition was distinct in the structured habitats relative to the controls and pre-construction conditions, and eelgrass + oyster invertebrate communities were intermediate between those in the eelgrass-only and oyster-only plots. Similarly, eelgrass shoots are collected and dipped in freshwater to rinse off invertebrates and assess epifauna communities showed differences where oyster reef is present along with eelgrass. Epifauna assemblages on eelgrass at the San Rafael site have not converged with those at natural comparison sites Point Molate and Keller Beach (the closest two natural beds, just across the bay), with two native species known to remove epiphytes (Lewis and Boyer 2014) notably absent (the isopod Idotea resecata and the sea hare Phyllaplysia taylori) at the restored site. Fish response Trapping of fish (see Monitoring Reports, 2012, 2013, 2014 in Appendix A) showed much overlap in species composition among the treatments; however, a pattern has emerged of black surfperch and bay pipefish having a greater association with eelgrass habitat. Seining results indicated early recruitment to eelgrass by bay pipefish (within one month of the April 2013 replant), and that eelgrass presence increased the occurrence of certain fish species among oyster reef structures (bay pipefish, shiner surfperch, and saddleback gunnel). Acoustic monitoring (see Monitoring Reports, 2012, 2013, 2014 in Appendix A) to detect tagged fish showed that individuals of several species visited the site, including two white sturgeon, a green sturgeon (threatened species), a leopard shark, a steelhead smolt, and a striped bass. Positional analysis currently underway will help to determine the degree to which the fish were lingering at the site and whether they exhibited preferences among the treatments. Comparisons of visitation at our San Rafael project site with that at the Marin Rod and Gun Club (a site with restored oyster reefs and eelgrass) and Point Molate (on the pier and in the nearby eelgrass bed), should help to put our data in context relative to abundance and composition of acoustically tagged fish within the region. Bird and infaunal invertebrate response To evaluate bird and infaunal invertebrate responses, the treatment area at San Rafael was subdivided into zones encompassing eelgrass and oyster treatment plots (zone B) as well as 150-m zones immediately inshore (zone A) and offshore (zone C) of the plots, and a nearby control (un-manipulated) area was divided in the same way. Densities of Black Oystercatcher increased at treatment plots in comparison to pre- installation and control densities, and Forster’s terns and wading birds began using the treatment plots post-installation. The site was used primarily for foraging at low tide , and non-foraging (resting, preening, etc.) behaviors at high tide. Avian diversity and species richness were greater at the San Rafael site than at the Hayward site for nearly all years and tide heights in both control and treatment areas (Table 1). Preliminary analyses suggest that the

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treatments at San Rafael have positively influenced benthic invertebrate density, richness and biomass. Our results suggest that some avian and invertebrate species are responding to oyster and eelgrass habitat restoration; however, continued monitoring as these habitats will be important for understanding species responses to living shoreline restoration methodologies. Physical Effects Sedimentation has occurred adjacent to both the reefs and shell mound units, with the greatest accumulation occurring inside the latter. Using hydrographic survey methods to measure the mudflat surface around the reefs at San Rafael in May 2012 and then again in June 2014 showed sedimentation of roughly 0.07 m in the lee of the treatment plots and erosion of roughly 0.09 m to the north of the plots . The north-south difference may be related to the proximity of San Rafael Creek to the north. The east-west difference may be related to the treatment elements but the same pattern can be seen in relation to the control plot, which should not have an impact. From the two surveys it appears that the treatment plots have a small impact on the overall pattern of erosion and sedimentation in the area. This is the result of only one repeat survey and it would be necessary to undertake another survey in the future to see if the pattern of erosion and accretion was an ongoing trend. Roughly 0.04 m of sedimentation occurred around the oyster reefs each since year since construction with slightly less accumulation where eelgrass had been planted. The reefs subsided about 10 cm over 5 months but did not continue to sink after that. The combination of shell bag settling, sediment accumulation around the reefs and subsidence means that the space available for oysters on the individual elements decreased over time. Wave heights show different patterns between the lee of the oyster-eelgrass plot and the control plot. Wave heights ranged 0.06- 0.26 m for both although the waves behind the oyster-eelgrass plot tended to be smaller. The reefs dissipate approximately 30% more wave energy than the mudflat does alone at mean tide level (MTL), but the broad mudflat itself extracts substantial amounts of wave energy. Water Quality The original 2010 grant proposal project description differs from the final project designed and constructed, which was communicated and approved at the time to San Francisco Estuary Partnership staff, and memorialized in a grant amendment in March 2014. While we originally wanted to have more sites and more focus on monitoring of suspended sediments, we settled on one site at San Rafael with one plot per treatment due to the amount of funding, landowner support, and permitting considerations to minimize fill. We have data indicating that sediment accretion and deposition is occurring, but this is not a direct measurement of suspended sediment concentrations. Continuous sondes to collect this data are expensive- we were able to deploy one sonde and move it between the plots in the project area, as opposed to four sondes that would be needed to place one in each plot. In addition, we need larger plots to effectively measure suspended sediments, which is being pursued as part of next phases for this work. We have not detected substantial treatment effects on water quality measures that can be specifically attributed to the treatment plots, and it may be that even our relatively large treatment plots do not influence characteristics of flowing water in a detectable way. Onset

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temperature/conductivity loggers provided continuous data for temperature that should be useful for exploring seasonal patterns in response variables for multiple groups within the project team; however, defective conductivity sensors (recalled by the manufacturer) did not provide reliable salinity data. Hayward (ELER) Site Eelgrass Eelgrass at this smaller scale project site reached 75% of planted densities by July 2013 (after a May 2013 replant) and survived through the fall months; however, major declines occurred during the next winter and only two shoots remained by summer 2014 across the ten small plots. Eelgrass was always shorter at Hayward (~80 cm; Fig. 18) than San Rafael, perhaps due to shallower site conditions at the former. Plants at this site had high densities of the Atlantic mud snail, Ilyanassa obseleta (both adults and eggs) on their leaves and also appeared to experience substantial sediment movement and burial; either or both could have contributed to the observed eelgrass mortality. Oysters Oyster recruitment at Hayward did not occur until Spring 2013 and at a much lower rate than at San Rafael. However, we estimate ~2000 oysters on our test elements there; even this relatively modest effort increased the population of native oysters at that site by one order of magnitude. Oyster blocks and higher tidal elevations currently appear to be the best at supporting oyster recruitment at this site, in contrast to the oyster shell bags performing best at San Rafael. Epibenthic invertebrate response Trapping results at Hayward showed that shore crab abundances increased within the treatment area relative to controls and pre-project conditions. Atlantic mud snails (Ilyanassa obsoleta) were by far the most common invertebrates in traps, with hundreds found per trap in some seasons but no difference with reef/eelgrass structure. Suction sampling of epibenthic invertebrates indicates that the oyster shell reefs developed a distinct community relative to the eelgrass (when still present), control area and baseline conditions. Fish response Only trapping was conducted to assess fish use of this site, in the treatment area versus control (unmanipulated) area. Besides leopard sharks, which were commonly caught in both control and treatment areas, only 1-3 individuals of other species were caught (barred surfperch, Pacific staghorn sculpin, topsmelt, jacksmelt, sand dab, sevengill shark) over the course of the project to date, making it impossible to discern patterns relative to the addition of reef structure (and eelgrass before the end of 2013). Bird and infaunal invertebrate response Although the footprint of the treatment area was substantially smaller at Hayward than at San Rafael, the same zone arrangement was used to assess bird and infauna responses to

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treatments and for consistency between the two sites. While avian diversity and richness were higher at San Rafael, both pre- and post-installation avian densities were higher at the Hayward treatment and control sites where small shorebirds predominated. Even with the small project footprint, wader species increased significantly post-installation in the treatment area at Hayward. As at San Rafael, the Hayward site was used primarily for foraging at low tide, and non-foraging (resting, preening, etc.) behaviors at high tide. We observed a substantial increase in bivalves in the first post-treatment installation sampling period. Several years of monitoring at this site have established a baseline of avian and infaunal invertebrate characteristics that will be very useful if larger scale restoration projects go forward in the future. Physical effects Subsidence of the individual elements at Hayward was similar to San Rafael and was not found to differ by substrate type. Water Quality The Hayward project site was frequently warmer and more saline than the San Rafael site, although dissolved oxygen, chlorophyll-a, and light attenuation were generally similar. The small scale of this project does not permit comparison of water quality on a per treatment basis. Summary of Expected Outputs and Outcomes and Accomplished Deliverables Outputs included:

Amount of structural oyster enhancements (206 1Mx1M elements over one acre) Amount of eelgrass seed buoys installed (96 buoys over one acre) Number of oysters recruited/year (4.8M/3 years); number of adults persisting/year

(2M) Number of eelgrass shoots propagated/year (750), persisting/year (380) Presence/absence and diversity of species use (epifauna, fish, birds) at the

treatment sites and at control sites at each location- see full monitoring report Measurement of change in sedimentation rates between subtidal treatments at the

treatment sites and at control sites- accretion of 15-24cm of sediment Measurement of change in flow velocity rates between subtidal treatments at the

treatment sites and at control sites- 30-50% reduction in wave energy at mean tides

Community participation, including volunteer hours and public events- 25 volunteers donated 6 hours each to the project for a total of 150 volunteer hours. We discontinued the use of volunteers in 2014 as the site is difficult to access and it was more effective to focus on collecting data with trained staff.

Written products, including Summary Results Report, conference abstracts/proceedings, peer review publications, etc.- Three annual monitoring reports are available at www.sfbaylivingshorelines.org. Conference abstracts are available on request.

Workshops/conferences, including information sharing, coordination, training, etc. Marilyn Latta and Kathy Boyer made more than 15 public presentations about the project, and there are multiple media stories on the project.

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Final Project Outcomes:

Increased settlement, growth, and survivability of multiple age classes of oysters- We estimate that the reefs have increased the numbers of oysters in this region of the bay by 2 orders of magnitude. Increased settlement, growth, and survivability of eelgrass at restored site. Eelgrass is at 124% of planted densities as of Dec 2014, and is expanding clonally and by seed. The project has implemented one acre of direct restoration, and five acres of enhancement- reaching the 1 year goals for eelgrass and 5 year goal for oyster restoration in the 2010 Subtidal Habitat Goals Project, out of a 50 year goal of 8,000 acres for restoration for each habitat.

Demonstrated fish, epifaunal, wildlife, and vegetation presence and increased biodiversity at restored site. The San Rafael site provides habitat for juvenile Dungeness crabs, red rock crabs, shorecrabs, bay shrimp, bay pipefish, white sturgeon, American black oystercatchers, Great and white egrets, great blue herons, and a wide diversity of other fish, birds, and wildlife. Please see 2012, 2013, and 2014 monitoring reports in Appendix A for more detailed information and data on all species we’ve documented on the reefs.

Enhanced ecological services derived from oyster and eelgrass ecosystems (fish foraging, interstitial habitat niche space, diving duck and shorebird use, etc.) The San Rafael reefs provide substantial habitat structure in the four large project plots, providing food resources for fish and other species, interstitial habitat space has resulted in an increase of 10 taxa of invertebrates, birds and wildlife compared to the control plot of bare mudflat, and we have documented diving duck and shorebird use. Please see 2012, 2013, and 2014 monitoring reports in Appendix A for more detailed information and data ecological services we’ve documented on the reefs.

Enhanced shoreline protection and decreased shoreline erosion at restored site. As mentioned, the scale of the final project constructed in 2012 is testing shoreline protection concepts that we plan to apply to future larger-scale projects. The scale of the current project does not protect the shoreline, but we are observing sediment accretion and wave attenuation at the site.

Improved socio-economic conditions (fishing, bird-watching, open space, etc.) There is a diverse community in nearby neighborhoods of San Rafael, many of whom regularly use the Bay Trail adjacent to the site. These residents interact with project biologists during monitoring events several times per year. We’ve had more than 150 inquiries into the project goals and methods, and we regularly hear support and enthusiasm for the project from residents. Residents indicate bird watching has improved, and they are enthusiastic about a pilot climate adaptation project occurring on their local shoreline.

Increased data on subtidal restoration techniques that can be applied to other regional project locations. This project is directly implementing research and restoration recommendations in the 2010 San Francisco Bay Subtidal Habitat Goals Report, including the phase approach for oyster and eelgrass monitoring and restoration. We have developed an innovative design for multi-objective, multi-habitat approach to test climate adaptation methods. We have shared

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information on our process with design, permitting, construction, and monitoring with many entities interested in exploring the living shorelines approach in their jurisdictions, including US Coast Guard, Port of San Francisco, USWFWS Refuge lands, County of Marin, City of Tiburon, and many others. We’ve also shared the project goals and preliminary results with technical experts and resource agency staff via local and national conferences and additional regional presentations. Last, design ideas have been incorporated into the forthcoming 2015 climate change update to the San Francisco Baylands Habitat Goals Project and 2016 forthcoming update to the Comprehensive Conservation Management Plan led by the San Francisco Estuary Partnership. Please see list in Attachment B.

Increased stewardship of estuarine ecosystems, and awareness of the multiple benefits of eelgrass and oyster restoration, and Living Shorelines. The project has involved direct volunteers in the project, and conducted extensive outreach to share information about the value of subtidal habitats, restoration, and climate adaptation planning. Project Manager Marilyn Latta and Science Lead Kathy Boyer have given multiple community presentations, including to the Bay Area Chapter of the Sierra Club, the Exploratorium Speaker Series, the Marin Conservation League, and others. People often tell us they knew nothing about these submerged hidden habitats, and come away with increased awareness and understanding for this part of the bay. We consistently receive good feedback and positive support for the restoration efforts, such as this email after a recent presentation “Thank you so much for your presentation to the Marin Conservation League group last Thursday. The subject was timely, interesting and presented in terms a non-scientist audience could understand. You made some fans. We look forward to following the project's progress and use of the findings to improve bay habitat and help adapt our shoreline to sea level rise.”

We measured these outcomes by conducting monitoring (funded by EPA and other partners) of native oyster settlement density and timing at the treatment sites and control sites; monitoring eelgrass seedling establishment density and timing at the treatment sites and control sites; monitoring of fish, epifauna, birds, and other species use in the treatment site and at control site; monitoring sedimentation rates at the treatment sites and control sites; and tracking the volunteer participation number and number of presentations that give information about the project. Please see 2012, 2013, and 2014 monitoring reports in Appendix A for more detailed information. The project met all expected outputs and outcomes described above. Key messages, lessons learned and project implications: Key Messages for the project include:

Oyster and eelgrass habitats are important features of the San Francisco Bay ecosystem and provide critical habitat for a wide variety of fish, invertebrates, and wildlife.

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Constructed Living Shorelines with oyster and eelgrass reefs are providing valuable benefits, including increased ecosystem functions (such as nesting, breeding, food resources) and increased ecosystem services (such as wave attenuation, sediment accretion, shoreline protection).

As referenced in the recently released report “Living Shorelines: From Barriers to Opportunities” by Restore America’s Estuaries, these recommendations also hold apply to San Francisco Bay. Please see full report at https://www.estuaries.org/first-national-report-on-living-shorelines-institutional-barriers-released

There is a regional need to develop a broad and common understanding of the efficacy, impacts, and benefits of living shorelines as well as hardened structures. Collecting reliable information, making it generally available, and providing education and training to the various constituencies affected by shoreline management decisions is necessary to overcoming each of the identified barriers and promoting the wider use of living shorelines.

To successfully implement comprehensive regulatory reform and wider use of living shorelines, the capacity of the major constituencies must be improved and expanded. The current availability of designers, engineers, builders, and regulators sufficiently knowledgeable of living shoreline techniques is not adequate and must be increased, primarily through specialized training.

Lessons Learned and Future Design Criteria: To date, we are able to draw the following conclusions toward future designs:

This project and several others (Boyer, unpublished data) suggest that eelgrass should be restored early in the growing season; we did not have success in establishing eelgrass at either site in late July and early August 2012. Our second planting in April and early May 2013 led to successful establishment at both sites (although the Hayward site ultimately failed to support eelgrass by fall/winter 2013).

We can eliminate two of the baycrete element designs: layer cakes and small reef ball stacks. Neither stand up well over time, and layer cakes have fewer oysters compared with other configurations.

Key stressors for oysters vary with location within San Francisco Bay. Shell bags potentially offer protection from heat and desiccation stress and provide a lot of complex surface area for oysters and other organisms to attach to and live in, but surfaces that are at higher tidal elevations and more stressful in terms of exposure may provide oysters with some measure of protection from marine predators and non-native fouling species.

Additional protection from oyster predators and cover of fouling species might be gained by encouraging larger mobile predators (such as crabs) and mesograzers to settle on restoration substrates. Future designs might include developing substrate types and/or configurations that attract large crabs and fish.

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We tentatively suggest that restoration projects incorporating both oyster reef and eelgrass together should be considered; although neither species appears to be benefiting from the other so far, the preliminary evidence that differences in the two habitats lead to distinct invertebrate and fish communities suggests that their co-location will maximize habitat value.

Oyster reef designs should consider the fact that the lower portion of substrates will experience sediment burial. Future designs could be elevated on materials that are less difficult to source than bags of oyster shells, which will be less available in the future.

Wave energy reduction measured in our San Rafael project is encouraging, but we recommend many additional sites should be used for similar projects and measurements in order to determine optimal design and the need for site-specific differences in reef configuration.

Future work: In January 2015, the Coastal Conservancy successfully secured a new grant through the USFWS North American Wetland Conservation Act, to build upon the information and lessons learned from this project and construct an additional set of Living Shoreline reefs at an additional site in San Francisco Bay. This “Phase Two” effort titled the San Francisco Bay Multi-Habitat Enhancement Project will include additional tidal marsh habitat (Pacific cordgrass, marsh gumplant), linking a more diverse set of habitat types up the slope that can have cumulative benefits with further integration of habitat linkages and increased wave attenuation potential. Conclusions: Funding from the EPA/ SFEP Estuary 2100-2 grant was critical initial seed funding that started this project. All grant goals and objectives were met, resulting in a highly successful one acre subtidal restoration project that is now being replicated in other climate adaptation pilot project designs. The project has helped to advance specific recommendations in the 2010 San Francisco Bay Subtidal Habitat Goals Report, and is noted as a successful example demonstration project recommended in the forthcoming Baylands Ecosystem Goals Climate Change Update (2015 in prep). The project has helped to raise both resource agency and local environmental consulting awareness of Living Shoreline techniques, and public awareness of subtidal habitats in general. Attachments

a. Annual Monitoring Reports (2012, 2013, 2014) b. Supporting documents/data- Summary of Outreach and Presentations

Photos (see Appendix A) d. Media articles

Tables and Figures (See Appendix A)