New Life for Eroding Shorelines: Beach and Marsh Edge Change in the San Francisco Estuary

San Francisco Estuary Institute (SFEI) | April 1st, 2020

Wind, waves, storms, and changing water levels have reshaped shorelines for millennia and continue to do so today. The current shape of the San Francisco (SF) Estuary sho

Wind, waves, storms, and changing water levels have reshaped shorelines for millennia and continue to do so today. The current shape of the San Francisco (SF) Estuary shoreline is relatively new; 15,000 years ago, the California shoreline was west of the Farallon Islands and 140 meters below its current level (Cohen and Laws 1992, Malamud-Roam et al. 2007). By approximately 6,000 years ago (the end of the last glacial epoch), the sea had risen to nearly its present level and filled what is now San Francisco Bay, allowing marshes to form and maintain themselves (Atwater 1979). More recently, humans have changed the shape of the shoreline. During the 1850s, many marshes expanded extensively due to increased sediment supply from hydraulic mining in the Sierra Nevada (Gilbert 1917, Goals Project 1999). Diking, dredging, and filling of marshes for agricultural and urban development began in the late 19th century and continued through the first half of the 20th century.  Today, humans continue to reshape the shoreline through continued diking, dredging and filling as well as restoration projects, urbanization of watersheds, ferry wakes, and many other means. The most wide-ranging impact of human activity on the shape of shorelines is global climate change caused by greenhouse gas emissions, which is accelerating the rate of sea level rise worldwide (OPC 2018). Sea level rise is likely to cause much more dramatic changes in the shape of shorelines than have been seen in recent centuries. The magnitude and pace of change will depend on the rate of sea level rise, existing shoreline conditions, and the ability of shorelines to adapt. 

Novato Creek Baylands Historical Ecology Study

San Francisco Estuary Institute (SFEI) | July 31st, 2015

Over the past century and a half, lower Novato Creek and the surrounding tidal wetlands have been heavily modified for flood control and land reclamation purposes. Levees

Over the past century and a half, lower Novato Creek and the surrounding tidal wetlands have been heavily modified for flood control and land reclamation purposes. Levees were built in the tidal portion of the mainstem channel beginning in the late 1800s to convey flood flows out to San Pablo Bay more rapidly and to remove surrounding areas from inundation. Following levee construction, the wetlands surrounding the channel were drained and converted to agricultural, residential, and industrial areas. These changes have resulted in a considerable loss of wetland habitat, reduced sediment transport to marshes and the Bay, and an overall decreased resilience of the system to sea level rise. In addition to tidal wetland modification, land use changes upstream in the Novato Creek watershed have resulted in several challenges for flood control management. Dam construction and increased runoff in the upper watershed have resulted in elevated rates of channel incision, which have increased transport of fine sediment from the upper watershed to lower Novato Creek. Channelization of tributaries and construction of irrigation ditches have likely increased drainage density in the upper watershed, also potentially contributing to increased rates of channel incision and fine sediment production (Collins 1998). Downstream, sediment transport capacity has been reduced by construction of a railroad crossing and loss of tidal prism and channel capacity associated with the diking of the surrounding marsh. As a result of the increased fine sediment supply from the watershed and the loss of sediment transport capacity in lower Novato Creek, sediment aggradation occurs within the channel, which in turn reduces the flood capacity of the channel, necessitating periodic dredging (fig. 1; Collins 1998, PWA 2002).

Novato Creek Baylands Vision

San Francisco Estuary Institute (SFEI) | November 1st, 2015

As we rethink land management along the San Francisco Bay shoreline in the face of climate change, we know well-functioning resilient tidal landscapes can protect develop

As we rethink land management along the San Francisco Bay shoreline in the face of climate change, we know well-functioning resilient tidal landscapes can protect development and sustain native ecosystems. Here, we present a possible future vision for lower Novato Creek and adjacent baylands that includes several components that would restore and support natural processes, and, in turn, benefit aspects of flood risk management and ecosystem functioning. The Novato Creek Baylands Vision is an element of an EPA-funded project called Flood Control 2.0, which is aimed at advancing new approaches for flood risk management and habitat enhancement along the San Francisco Bay shoreline for the 21st century and beyond.

Pesticide Concentrations of Surface Water and Suspended Sediment in Yolo By-Pass and Cache Slough Complex, California, 2019–2021

U.S. Geological Survey (USGS) | July 9th, 2024

Managed flow pulses in the north Sacramento-San Joaquin Delta are an adaptive management tool used in efforts to enhance food availability in delta smelt (Hypomesus trans

Managed flow pulses in the north Sacramento-San Joaquin Delta are an adaptive management tool used in efforts to enhance food availability in delta smelt (Hypomesus transpacificus) habitat as part of the North Delta Food Subsidies Action. The California Department of Water Resources (DWR) monitors non-managed seasonal and local flow pulses and managed flow pulses from agricultural drainage or main stem Sacramento River water redirected through Yolo By-Pass. Augmented flow pulses are hypothesized to improve net positive flow during summer and fall in Yolo By-Pass and enhance plankton availability in delta smelt habitat in Cache Slough complex. However, flow pulses may also result in unintended negative effects of increased pesticides that are transported through Yolo By-Pass. Here, we evaluate pesticides in surface water and suspended sediment correlated with flow pulses in Yolo By-Pass during the 2019–21 calendar years. Surface-water and suspended-sediment samples were collected by DWR personnel. Water samples were analyzed at the U.S. Geological Survey Organic Chemistry Research Laboratory in Sacramento, California, for a suite of as many as 178 current-use pesticides and pesticide degradates using gas chromatography with mass spectrometry (GC/MS), gas chromatography with tandem mass spectrometry, and liquid chromatography with tandem mass spectrometry. Suspended sediments filtered from water samples were analyzed for a suite of as many as 173 current-use pesticides and pesticide degradates. There were 52 different current-use pesticides and pesticide degradates detected in water samples collected throughout the study. Concentrations ranged from below method detection limits to 4,070 nanograms per liter. Five different compounds in water samples were detected with concentrations above U.S. Environmental Protection Agency aquatic life benchmarks. In suspended-sediment samples collected throughout the study, eight different current-use pesticides and pesticide degradates were detected. Total pesticide concentrations were highest at surface-water sites in the northern end of Yolo By-Pass and decreased farther downstream during the same sampling events. Total pesticide concentrations generally were higher for most surface-water sites immediately before or during the managed flow pulse in 2019 versus after the flow pulse. Finally, mean total pesticide concentrations for each surface-water site generally were higher during all of 2019 than 2021, regardless of sampling period.

Potential impacts of increased coastal flooding in California due to sea-level rise

Climatic Change (Springer) | November 24th, 2011

California is likely to experience increased coastal flooding and erosion caused by sea-level rise over the next century, affecting the state’s population, infrastructu

California is likely to experience increased coastal flooding and erosion caused by sea-level rise over the next century, affecting the state’s population, infrastructure, and environment. As part of a set of studies on climate change impacts to California, this paper analyzes the potential impacts from projected sea-level rise if no actions are taken to protect the coast (a “no-adaptation scenario”), focusing on impacts to the state’s population and infrastructure. Heberger et al. (2009) also covered effects on wetlands, costs of coastal defenses, and social and environmental justice related to sea-level rise. We analyzed the effect of a medium-high greenhouse gas emissions scenario (Special Report on Emissions Scenarios A2 in IPCC 2000) and included updated projections of sea-level rise based on work by Rahmstorf (Science 315(5810): 368, 2007). Under this scenario, sea levels rise by 1.4 m by the year 2100, far exceeding historical observed water level increases. By the end of this century, coastal flooding would, under this scenario, threaten regions that currently are home to approximately 480,000 people and $100 billion worth of property. Among those especially vulnerable are large numbers of low-income people and communities of color. A wide range of critical infrastructure, such as roads, hospitals, schools, emergency facilities, wastewater treatment plants, and power plants will also be at risk. Sea-level rise will inevitably change the character of California’s coast; practices and policies should be put in place to mitigate the potentially costly and life-threatening impacts of sea-level rise.

Productive wetlands restored for carbon sequestration quickly become net CO2 sinks with site-level factors driving uptake variability

PLOS | March 25th, 2021

Inundated wetlands can potentially sequester substantial amounts of soil carbon (C) over the long-term because of slow decomposition and high primary productivity, partic

Inundated wetlands can potentially sequester substantial amounts of soil carbon (C) over the long-term because of slow decomposition and high primary productivity, particularly in climates with long growing seasons. Restoring such wetlands may provide one of several effective negative emission technologies to remove atmospheric CO2 and mitigate climate change. However, there remains considerable uncertainty whether these heterogeneous ecotones are consistent net C sinks and to what degree restoration and management methods affect C sequestration. Since wetland C dynamics are largely driven by climate, it is difficult to draw comparisons across regions. With many restored wetlands having different functional outcomes, we need to better understand the importance of site-specific conditions and how they change over time. We report on 21 site-years of C fluxes using eddy covariance measurements from five restored fresh to brackish wetlands in a Mediterranean climate. The wetlands ranged from 3 to 23 years after restoration and showed that several factors related to restoration methods and site conditions altered the magnitude of C sequestration by affecting vegetation cover and structure. Vegetation established within two years of re-flooding but followed different trajectories depending on design aspects, such as bathymetry-determined water levels, planting methods, and soil nutrients. A minimum of 55% vegetation cover was needed to become a net C sink, which most wetlands achieved once vegetation was established. Established wetlands had a high C sequestration efficiency (i.e. the ratio of net to gross ecosystem productivity) comparable to upland ecosystems but varied between years undergoing boom-bust growth cycles and C uptake strength was susceptible to disturbance events. We highlight the large C sequestration potential of productive inundated marshes, aided by restoration design and management targeted to maximise vegetation extent and minimise disturbance. These findings have important implications for wetland restoration, policy, and management practitioners.

Puzzling Over the Shallows

CALFED | December 1st, 2001

Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California

U.S. Fish and Wildlife Service (FWS) | September 23rd, 2013

The Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California features five endangered species: two endangered animals, California clapper rail (Rallus

The Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California features five endangered species: two endangered animals, California clapper rail (Rallus longirostris obsoletus) and salt marsh harvest mouse (Reithrodontomys raviventris) and three endangered plants, Cirsium hydrophilum var. hydrophilum (Suisun thistle), Chloropyron molle ssp. molle (soft bird’s-beak), and Suaeda californica (California sea-blite). The biology of these species is at the core of the recovery plan, but the goal of this effort is the comprehensive restoration and management of tidal marsh1 ecosystems. This recovery plan is an expansion and revision of The California Clapper Rail and Salt Marsh Harvest Mouse Recovery Plan (U.S. Fish and Wildlife Service 1984). The historic distribution of the California clapper rail encompasses major tidal marshes between Humboldt Bay and Morro Bay, defining the approximate geographic scope of this recovery plan. In addition to the California clapper rail and the salt marsh harvest mouse, the plan also covers three focal listed plant species that were listed as federally endangered in the 1990s and the northernmost population of an additional plant species. Two of the species, Cirsium hydrophilum var. hydrophilum and Chloropyron molle ssp. molle (this species’ former name is Cordylanthus mollis ssp. mollis which is how it appears on the List of Threatened and Endangered Species, but we use the currently accepted name here), are restricted to the northern reaches of the San Francisco Bay Estuary. The other endangered tidal marsh plant, Suaeda californica, historically occurred in both San Francisco Bay and Morro Bay but, except for three reintroductions to San Francisco Bay, is now restricted to Morro Bay. Another federally listed plant, Chloropyron maritimum ssp. maritimum (salt marsh bird’s-beak; formerly Cordylanthus maritimus ssp. maritimus), has its northern range limit in Morro Bay. Morro Bay was omitted from the Salt Marsh Bird’s-beak Recovery Plan (U.S. Fish and Wildlife Service 1985a) because the taxonomic interpretation at the time classified this population in another subspecies that is not federally listed. Current taxonomic interpretation considers the Morro Bay population as Chloropyron maritimum ssp. maritimum. It is included in this recovery plan due to its co-location with Suaeda californica in Morro Bay. Though recovery strategies and actions are provided for the Morro Bay population of C. maritimum ssp. maritimum, recovery criteria are not, therefore, the species should not be considered covered by the recovery portion of the document. In addition, this recovery plan addresses 11 species or subspecies of concern. These include the salt marsh wandering shrew (Sorex vagrans halicoetes), Suisun shrew (Sorex ornatus sinuosus), San Pablo vole (Microtus californicus sanpabloensis), California black rail (Laterallus jamaicensis coturniculus), three song sparrow subspecies of the San Francisco Bay Estuary (Alameda song sparrow [Melospiza melodia ssp. pusillula], Suisun song sparrow [M.m. maxillaris] and San Pablo song sparrow [M.m. samuelis]), saltmarsh common yellowthroat (Geothlypis trichas sinuosa), old man tiger beetle (Cicindela senilis senilis), Lathryrus jepsonii ssp. jepsonii (delta tule pea), and Spartina foliosa (Pacific cordgrass). These species occur in a variety of tidal marsh habitats where they are limited by the requirements of moisture, salinity, topography, soil types, and climatic conditions. Adjacent uplands and ecotone areas are also crucial habitats for many of these species. Primary threats to all the listed species include historical and current habitat loss and fragmentation due to urban development, agriculture, and diking related to duck hunting; altered hydrology and salinity; non-native invasive species; inadequate regulatory mechanisms; disturbance; contamination; risk of extinction due to small population size; and the most central threat, sea level rise due to climate change.

Reference Guide to On-Farm Groundwater Recharge on Annual Cropland | Recommendations for Creating Waterbird Habitat Benefits

Nature Conservancy | May 1st, 2019

With the Sustainable Groundwater Management Act (SGMA) requiring basins to balance water budgets and manage groundwater sustainably, there is an opportunity to demonstr

With the Sustainable Groundwater Management Act (SGMA) requiring basins to balance water budgets and manage groundwater sustainably, there is an opportunity to demonstrate groundwater recharge with benefits to birds and people. A multiple-benefit approach brings together water managers, farmers, agencies and conservation groups to stabilize groundwater in a manner that provides greater water reliability for farms and communities while protecting ecosystems, including migratory bird habitat.

Regional Supplement to the Corps of Engineers Wetland Delineation Manual: Arid West Region (Version 2.0)

U.S. Army Corps of Engineers (USACE) | September 9th, 2008

This document is one of a series of Regional Supplements to the Corps of Engineers Wetland Delineation Manual, which provides technical guidance and procedures for identi

This document is one of a series of Regional Supplements to the Corps of Engineers Wetland Delineation Manual, which provides technical guidance and procedures for identifying and delineating wetlands that may be subject to regulatory jurisdiction under Section 404 of the Clean Water Act or Section 10 of the Rivers and Harbors Act. The development of Regional Supplements is part of a nationwide effort to address regional wetland characteristics and improve the accuracy and efficiency of wetland-delineation procedures. This supplement is applicable to the Arid West Region, which consists of all or portions of 12 states: Arizona, California, Colorado, Idaho, Montana, Nevada, New Mexico, Oregon, Texas, Utah, Washington, and Wyoming.