Bathymetry and Digital Elevation Models of Coyote Creek and Alviso Slough, South San Francisco Bay, California

U.S. Geological Survey (USGS) | March 15th, 2018

In 2010 the U.S. Geological Survey (USGS), Pacific Coastal and Marine Science Center completed three cruises to map the bathymetry of the main channel and shall

In 2010 the U.S. Geological Survey (USGS), Pacific Coastal and Marine Science Center completed three cruises to map the bathymetry of the main channel and shallow intertidal mudflats in the southern most part of south San Francisco Bay. The three surveys were merged to generate comprehensive maps of Coyote Creek (from Calaveras Point east to the railroad bridge) and Alviso Slough (from the bay to the town of Alviso) to establish baseline bathymetry prior to the breaching of levees adjacent to Alviso and Guadalupe Sloughs as part of the South Bay Salt Pond Restoration Project. Since 2010 the USGS has conducted twelve additional surveys to monitor bathymetric change in this region as restoration progresses.

Bringing Back Native Grasses

CALFED | June 1st, 2005

California Salmonid Stream Habitat Restoration Manual

California Department of Fish and Wildlife (CDFW) | August 6th, 2010

The first edition of this manual, written by Gary Flosi and Forrest Reynolds, and published in 1991, formally synthesized and described the Department of Fish and Game's

The first edition of this manual, written by Gary Flosi and Forrest Reynolds, and published in 1991, formally synthesized and described the Department of Fish and Game's approach and technical methods for anadromous salmonid habitat restoration. From 1991 through 1994 the first edition was broadly distributed and used as a "standard methods" text by many habitat restoration and resource inventory workers. As a result, many suggestions for improvement of the manual were received by the authors. The second edition, by Flosi and Reynolds was supported by a team that included the authors of this third edition, and was published in October of 1994. The second edition included a number of revisions: 1) a reorganization of sections for project planning and project implementation; 2) the just then recently revised stream channel classification system developed by David Rosgen; 3) a new monitoring and evaluation section; 4) a listing of all databases used for resource inventory and analysis as presented in the manual; 5) a protocol for a large woody debris inventory; 6) a description of required environmental review processes and permits; 7) an expanded and updated listing of sensitive species; and 8) numerous editorial changes to text and data forms. The third edition, like the second, incorporates changes recently developed in the practice of stream habitat inventory and restoration. The authorship list has changed with this edition to more accurately reflect the contributions of the writing team members. The manual is presented in binder form in this edition to more easily and economically incorporate future additions and developments as they evolve. This fourth edition incorporates all changes, corrections, and revisions of this manual up to July 2010. The manual continues in binder form in this edition to easily and economically incorporate future additions and developments as they evolve. The authors anticipate the continued widespread distribution and use of this manual will promote the implementation of the restoration techniques. Readers should also be aware that computer data entry and data summary programs are available upon request for all data collection protocols presented in this manual. Updates to this manual are available on line at http://www.dfg.ca.gov/fish/Resources/HabitatManual.asp.

California State Wildlife Action Plan 2015 Update, Volume II: Appendices

California Department of Fish and Wildlife (CDFW) | September 28th, 2015

Appendices A Required Report Elements and Compliance B California State Wildlife Action Plan 2015 Revision Summary C Species of Greatest Conservation Need D Ranked Li

Appendices A Required Report Elements and Compliance B California State Wildlife Action Plan 2015 Revision Summary C Species of Greatest Conservation Need D Ranked Lists of Vegetation Communities (Macrogroups) by Ecoregion E Conservation Strategies for All Macrogroups in California, Freshwater Aquatic Species Assemblages, Marine Ecosystems, and Anadromous Fishes F Invasive Species in California G Climate Adaptation Strategies Cross-Reference Guide H Offshore Islands I California State Wildlife Action Plan Implementation Evaluation Report 2005 – 2014 J Public Scoping Meeting Materials

Carbon accumulation and vertical accretion in a restored versus historic salt marsh in southern Puget Sound, Washington, United States

Society for Ecological Restoration | March 4th, 2019

Few comparisons exist between vertical accretion (VA) and carbon accumulation rates (CARs) in restored versus historic (i.e. reference) marshes. Here, we compare these pr

Few comparisons exist between vertical accretion (VA) and carbon accumulation rates (CARs) in restored versus historic (i.e. reference) marshes. Here, we compare these processes in a formerly diked, sparsely vegetated, restored salt marsh (Six Gill Slough, SG), whose surface is subsided relative to the tidal frame, to an adjacent, relatively pristine, historic salt marsh (Animal Slough, AS). Six sediment cores were collected at both AS and SG approximately 6 years after restoration. Cores were analyzed for bulk density (BD), % loss of ignition, % organic carbon, and 210Pb. We found that sharp changes in BD in surface layers of SG cores were highly reliable markers for the onset of restoration. The mean VA since restoration at SG (0.79 [SD = 0.29] cm/year) was approximately twice that of AS (0.41 [SD = 0.16] cm/year). In comparison, the VA at AS over 50 years was 0.30 (SD = 0.09) cm/year. VA consisted almost entirely of inorganic sediment at SG whereas at AS it was approximately 55%. Mean CARs at SG were somewhat greater than at AS, but the difference was not significant due to high variability (SG: 81–210 g C m−2 year−1; AS: 115–168 g C m−2 year−1). The mean CAR at AS over the past 50 years was 118 (SD = 23) g C m−2 year−1. This study demonstrates that a sparsely vegetated, restored salt marsh can quickly begin to accumulate carbon and that historic and restored marshes can have similar CARs despite highly divergent formation processes.

Colusa County | Managed Aquifer Recharge: benefitting aquifers, farmers, and migratory birds

Nature Conservancy | September 3rd, 2018

In partnership with growers and the Colusa Groundwater Authority (CGA), The Nature Conservancy (TNC) is implementing a pilot multiple-benefit managed aquifer r

In partnership with growers and the Colusa Groundwater Authority (CGA), The Nature Conservancy (TNC) is implementing a pilot multiple-benefit managed aquifer recharge (MAR) program on farmland in California’s Central Valley, Colusa County. This program will benefit local groundwater users by replenishing critical domestic and agricultural groundwater supplies in a Severely Disadvanateged Community (SDAC). Participating farmers will benefit economically through incentive payments, and migratory shorebirds will benefit through the creation of critical winter habitat on farms through our specific field and water depth specificiations. MAR sites will be selected where and when it is appropriate and cost-effective to do so based on farming practices, soil suitability, water availability, basin water balances, and migratory/shorebird habitat requirements. The relevance and success of this program for Groundwater Sustainability Agencies (GSAs), Severely Disadvantaged Communities (SDACs), and Groundwater Sustainability Plans (GSPs) will require all of these stakeholders and project participants to collaborate on its design. Thus, TNC will engage growers, water managers, and other stakeholders in a variety of formal and informal ways to ensure that this program will meet the needs of all parties involved in GSP development. This program serves as a model for other GSAs and stakeholders seeking to deliver multiple benefits through on-farm recharge in the Central Valley where such a program is appropriate.

Considerations for Management of the Mouth State of California’s Bar-built Estuaries

Southern California Wetlands Recovery Project | January 10th, 2019

Bar-built estuaries are the dominant estuary type in California, and many of these small estuaries are subject to closure with a sand barrier separating a lagoon

Bar-built estuaries are the dominant estuary type in California, and many of these small estuaries are subject to closure with a sand barrier separating a lagoon estuary from the ocean for days, months or even years. In the lagoon impounded behind the sand barrier, water levels may rise or fall depending on net water budget and water quality extremes may develop. These conditions and the obstruction of fish passage motivate managed breaching of the sand barrier in many systems statewide – an intervention that alleviates or preempts environmental problems, but which also can result in undesirable secondary impacts due to the acute effect of a single breach or the chronic effect of repeated breaching over years. Management decisions are based on an implicit trade-off between anticipated benefits and costs that depend on the values and priorities of stakeholders. This report was written to provide an overview of considerations for managed breaching in California. It presents a synthesis of processes and phenomena related to mouth closure and breaching in general and uses this to identify potential impacts of breaching, without intending any judgment of which impacts are more or less desirable. Three specific systems are reviewed in detail: Los Peñasquitos Lagoon in San Diego County, Scott Creek Estuary in San Mateo County and Russian River Estuary in Sonoma County. While there are fundamental similarities in the closure and breaching cycle across all bar-built estuaries statewide, there is also an immense diversity between these systems due to differences in size, in hydrology (wet north to dry south), and in development (rural, urban, agricultural, road/rail). The local community is likely to develop the best management strategy where there is significant effort and experience in local monitoring, science, and stakeholder consultation. However, where there is limited monitoring, science or consultation, the considerations outlined in this report provide preliminary guidance – and comparison with one of the study systems can provide more specific insight to the potential impacts of breaching management decisions. We synthesize current understanding related to how mouth state influences estuary functions and conditions, which in turn affect ecological services. While both natural and managed breaching affect many processes and phenomena in the estuary, breaching events and managed breaching regimes do not occur in isolation and many other factors affect the estuary functions and conditions, including freshwater inputs, the adjacent landscape, and stressors in the watershed. However, managed breaching is one of very few short-term management options and therefore a valuable adaptive management tool, specifically in systems that are already perturbed or impacted by human encroachment. Although emergency breaches may be required in rare occasions, our recommendation is to develop a breaching strategy for specific systems in which breaching has been used or in which it is likely to be used as a management tool. In this context, we recommend ways in which science can provide improved support for management decisions and identify a few systems in California in which there is already a well-developed, science-based management plan. Associated document: "Wetlands on the Edge: The Future of Southern California's Wetlands - Regional Strategy 2018"

Costs of Ecosystem Management Actions for the Sacramento-San Joaquin Delta

Public Policy Institute of California (PPIC) | April 22nd, 2013

California is at a critical juncture on policy for the Sacramento–San Joaquin Delta. This report summarizes the results of a wide-ranging study of cost-effective wa

California is at a critical juncture on policy for the Sacramento–San Joaquin Delta. This report summarizes the results of a wide-ranging study of cost-effective ways to improve the health of the Delta ecosystem. It highlights the need for science-based, integrated management of the many sources of ecosystem stress. The report also recommends improvements to the highly fragmented system of oversight that now involves dozens of federal, state, and local agencies. Several companion reports contain related findings: Aquatic Ecosystem Stressors in the Sacramento–San Joaquin Delta (Mount et al. 2012) summarizes the science of Delta ecosystem stressors for a policymaking audience. Integrated Management of Delta Stressors: Institutional and Legal Options (Gray et al. 2013) lays out proposals for institutional reform of science, management, and regulation. Scientist and Stakeholder Views on the Delta Ecosystem (Hanak et al. 2013) presents detailed results of the two surveys conducted by the report’s authors. Stress Relief: Prescriptions for a Healthier Delta Ecosystem (Hanak et al. 2013) summarizes the overall research project and the recommendations it generated. Where the Wild Things Aren’t: Making the Delta a Better Place for Native Species (Moyle et al. 2012) outlines a realistic long-term vision for achieving a healthier ecosystem.

CVFPP Conservation Strategy Appendix B. Advance Mitigation

California Department of Water Resources (DWR) | July 14th, 2016

Section 7.0 of the Conservation Strategy presents methods for coordinating the acquisition of permits for implementation of the Central Valley Flood Protection Plan (CVFP

Section 7.0 of the Conservation Strategy presents methods for coordinating the acquisition of permits for implementation of the Central Valley Flood Protection Plan (CVFPP). These approaches have been initiated and are expected to be used in the future to mitigate impacts on species and habitats that result from CVFPP actions. As explained in Section 7.0, one regional permitting tool used by the California Department of Water Resources (DWR) is the development of advance mitigation projects.  This appendix further describes the purpose and benefits of advance mitigation, DWR’s efforts to date, and the process for selecting the first set of advance mitigation projects that will support the CVFPP. Each advance mitigation project has been, or will be, carefully selected in collaboration with permitting agencies to mitigate the effects of activities that will be implemented by DWR and Local Maintaining Agencies in the Systemwide Planning Area (SPA). DWR and the resource agencies are continuing to develop the mechanisms for crediting and a process for tracking the credits. Future advance mitigation projects are likely to follow the same process described herein. 

CVFPP Conservation Strategy Appendix E. Invasive Plant Management Plan

California Department of Water Resources (DWR) | July 14th, 2016

The California Department of Water Resources (DWR) developed this Invasive Plant Management Plan (or Plan) as part of the Conservation Strategy of the Central Valley Floo

The California Department of Water Resources (DWR) developed this Invasive Plant Management Plan (or Plan) as part of the Conservation Strategy of the Central Valley Flood Protection Plan (CVFPP). The Conservation Strategy tiers from the Conservation Framework, which was an integral part of the State’s preferred SSIA, identified in the 2012 CVFPP. The Conservation Strategy describes how to make progress toward meeting the environmental objectives of the Central Valley Flood Protection Act of 2008 (Act) and related legislation throughout the flood management system in the Systemwide Planning Area (SPA). The SPA comprises five Conservation Planning Areas (CPAs) in California’s Central Valley: the Feather River CPA, the Upper and Lower Sacramento River CPAs, and the Upper and Lower San Joaquin River CPAs (Figure 1-1). The SSIA includes developing and implementing multipurpose projects, and this Plan will guide the invasive plant management approaches undertaken as part of these projects.  The Conservation Strategy recognizes invasive plants as a primary stressor on the habitats, species, and ecosystem processes that are the focus of conservation planning. As of 2014, at least 68 plant species considered to be invasive by the California Invasive Plant Council (Cal-IPC) potentially occur in upland, riparian, wetland, and open water habitats in the Sacramento and San Joaquin Valleys (Cal-IPC 2013a). Many are widespread and abundant in vegetation managed as part of State Plan of Flood Control (SPFC) operation and maintenance (O&M). These species degrade riverine and floodplain habitats by altering ecosystem processes and displacing native plants. In addition, some of these invasive species, such as tamarisk (or saltcedar) (Tamarix spp.), giant reed (Arundo donax), and red sesbania (Sesbania punicea), are stressors that increase the cost and difficulty of operating and maintaining the SPFC.  These species can alter hydrology and sedimentation rates in riparian and aquatic systems (Cal-IPC 2011a) and can degrade flood system effectiveness. Importantly, recent studies have shown that certain invasive plant species have greater impacts on channel conveyance than native species adapted to the same areas (Stone et al. 2013). Dense stands of certain invasive species can alter channel morphology by retaining sediments and increasing the hydraulic roughness of the channel, which restricts flows and reduces flood conveyance (Bossard et al. 2000). For example, saltcedar traps and stabilizes alluvial sediments, narrowing stream channels and contributing to more frequent flooding (Bossard et al. 2000). Species with shallow root systems, such as giant reed and red sesbania, promote bank undercutting, collapse, and erosion (Bossard et al. 2000; Cal-IPC 2011b). Invasive terrestrial plants can reduce groundwater availability by transpiring large amounts of water, leaving less water available for native riparian vegetation (Bossard et al. 2000).  Invasive plants can also reduce the integrity of native riparian plant communities by outcompeting native plants, reducing habitat quality and food supply for wildlife, and interfering with wildlife management (Bossard et al. 2000; Cal-IPC 2011a). Nationally, invasive species are the second greatest threat to endangered species, after habitat destruction (Cal-IPC 2011a), and approximately 42 percent of the species listed as threatened or endangered by the federal Endangered Species Act (ESA) are at risk primarily because of the adverse effects of invasive species (Pimentel et al. 2005). Aquatic invasive plants can degrade aquatic habitat by reducing areas of open water used by waterfowl for resting, by shading out algae in the water column and thereby diminishing the basis of the aquatic food web, and by displacing native aquatic plants that are used for food or shelter by wildlife (Bossard et al. 2000). In addition, invasive aquatic plants often form dense mats that kill fish by lowering pH, dissolved oxygen, and light levels and by increasing carbon dioxide and turbidity (Bossard et al. 2000).  Because of these adverse effects and the threats they pose to achieving the goals of the Conservation Strategy, this Plan is driven by the following vision: to reduce the impact of invasive plants as a stressor on conservation targets and as an impediment to the operation and maintenance of the State Plan of Flood Control.  This Plan seeks to increase DWR institutional support for an SPA-wide invasive plant treatment program, and facilitate consistent invasive vegetation treatment actions by levee maintaining agencies and other partners such as the California Department of Fish and Wildlife and the United States Fish and Wildlife Service who are also conducting invasive plant control efforts. SPA-wide implementation of invasive plant treatment faces challenges that include ever-decreasing O&M budgets, regulatory requirements to protect sensitive resources, and the need to meet multiple and sometimes conflicting management objectives. This Plan recognizes those challenges, but it is beyond the scope of a single plan to resolve them all. Instead, the Plan provides first steps toward addressing the challenges through a series of goals, objectives, and implementation actions. The Plan includes measurable objectives for the treatment of four target species (Initial Priority Species) in Channel Maintenance Areas within the SPA (Channel Maintenance Areas; Figure 1-2) and identified in the DWR State Plan of Flood Control Descriptive Document (DWR 2010). It is the intent of this Plan to increase the resources available for invasive plant treatment actions by fashioning an approach that meets multiple needs and, therefore, may take advantage of funding sources not previously available for these actions.