USGS Western Ecological Research Center

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Coastal Ecosystem Response to Sea-Level Rise

Kyle Spragens conducting elevation surveys with RTK in a salt marsh. Photo by Karen Thorne.

Coastal marshes and estuaries are currently being reshaped by changing ocean and atmospheric conditions through sea-level rise and increased extreme storm events. Many projected increases in sea level are expected to result in loss of tidal wetlands and their component species. In addition, changing sediment loads, extreme tide and storm events, and shifting salinity levels will affect tidal marshes by altering the plant community and structure that provide critical habitat for endangered species. Efforts to anticipate coastal ecosystem change have largely relied on global or regional data, and therefore it remains unknown how sea-level rise will impact nearshore habitat at local scales. Researchers at WERC and their partners are currently taking a local site network approach to describe current and future conditions and projected responses of coastal ecosystems to climate change. In partnership with the University of California at Los Angeles, and Oregon State University, USGS WERC leads a multidisciplinary Coastal Ecosystem Response to Climate Change (CERCC) program. The focus of CERCC is to engage natural resource managers at coastal sites and provide them with “bottom-up” climate change understanding and adaptation at local and regional scales. Through on-the-ground data collection, experiments, and modeling, this program examines how changing ocean and atmospheric conditions will influence these estuaries. Our goal for this ongoing research is to provide scientific support and information to resource and land managers for future planning and conservation of coastal ecosystems and their natural resources as our climate changes.

Project Details

Modeling Wetland Response to Sea-Level Rise on the Pacific Coast

To gather reliable estimates of climate change impacts at regional scales, scientists at WERC and partners are using local physical and biological data to assess change to nearshore ecosystems. WERC members and University partners have collected information from 18 coastal wetland sites in Washington, Oregon, and California. Our study is focused on collecting high-quality data at local site scales, and then using that data to provide information that may be interpreted across the entire latitudinal gradient of the Pacific Coast.

In addition to our extensive network of sites, three estuaries in California have been intensely surveyed and metered to represent Mediterranean and northern Oceanic climate regimes (San Diego, San Francisco Bay, and Humboldt Bay respectively). At all sites we examine potential climate change effects and vulnerability of nearshore habitats and their dependent wildlife. Using local habitat information, we develop approaches for investigating the complexity of climate-induced physical and biological changes to wetland ecosystems, both at scales relevant to land managers, as well as a broader Pacific coast perspective.

Elevation mapping (left) and CERCC site map
Map of CERCC sites along the Pacific Coast  divided into northern and southern regions.

concept map of coastal ecosystem
Conceptual model of elevation, tidal range, vegetation, and wildlife over the continuum of nearshore habitat.


1.      Downscale physical processes and climate projections to local scales


We are using climate models, such as the Weather Research and Forecasting Model (WRF) and the Coastal Storm Modeling System (CoSMoS), to assess impacts to tidal marsh and nearshore ecosystems at local scales and to provide information for future wave impacts and inundation (including frequency and depth of inundation) under a range of sea-level rise and storm scenarios.


2.      Measure morphological and ecological characteristics across the habitat continuum of tidal marsh, intertidal mud flat, and subtidal shoals

We use a variety of survey methods to capture marsh and nearshore characteristics which will then be used to model impacts from different sea-level rise and storm scenarios.

Information collected includes:

-          Fine-scale marsh elevation using a Real Time Kinematic GPS (RTK GPS)

-          Plant composition and diversity

-          Bird abundance and habitat use

-          Bathymetric surveys to map mud flats and shallow subtidal zones

-          Bed sediment flux (suspended sediment concentrations)

-          Water level, salinity, and temperatures

-          Weather characteristics

-          Marsh sediment cores to measure accretion rates and stability

-          Surface Elevation Tables (SETs) to measure marsh elevation changes

 Base station(left); current profiler deployment(top middle); low tide(bottom middle); RTK mapping(right)

3.      Model wildlife habitats and native species response


We are correlating vegetation data with elevation, inundation patters, soil salinity, and spatial location to model habitat and vegetation change in relation to climate change and sea-level rise. We are also creating endangered species distribution models to forecast wildlife species losses with sea-level rise scenarios in California estuaries.


4.      Examine spatial variability of sea-level rise vulnerability along a coastal latitudinal gradient

                        Results from modeling are synthesized to examine variation in ecological response to climate change at different latitudes and tidal ranges along the Pacific coast.
                        We determine relative risk of nearshore habitats to climate change and sea-level rise, and have identified areas of specific concern.

high tide and vegetation survey       sunset over salt marsh wetland

Modeling Wetland Response to Sea Level Rise: San Francisco Bay Estuary

Over 80% of wetlands in San Francisco Bay (SFB) Estuary have been lost to urban development and landscape modification. Though severely fragmented and modified, SFB Estuary represents the largest extent of tidal marsh in the western United States and contains important remaining habitat for federal and state listed species. USGS WERC is currently conducting studies at 13 salt marsh parcels throughout the San Francisco Bay Estuary. Remaining tidal marsh fragments surrounding the shorelines of San Francisco Bay are at further risk from projected sea level rise ranging from 0.3-1.9 m. Changes in sediment loads and depth and duration of extreme tide events will alter tidal marsh plant and animal composition and distribution. In addition, effects of sea level rise on San Francisco Bay endemic tidal marsh species will have consequences for both large-scale habitat restoration and urban-infrastructure protection projects. To date, work being done has shown variable impacts from projected sea level rise at our 13 study sites within the Bay. We have been able to identify “critical thresholds” in which a salt marsh parcel will transition to a new tidal dominance and when wildlife population viability may be affected. 
Link to project webpage  


Wetland Sustainability Modeling, WARMER 2.0    

Figure 6. WARMER 1-D conceptual model


We have been working to improve the performance of WARMER (Wetland Accretion Rate Model for Ecosystem Resilience) in Pacific coast estuaries.  We have added mechanisms to allow close calibration to soil core characteristics and added greater flexibility in the organic matter accumulation subroutine.  We have also added the capacity to allow input of suspended sediment concentrations.  WARMER 2.0 runs as an R script, a much needed update from the original Fortran code, allowing us to quickly analyze the results and produce figures. 





Science Delivery and Needs Assessment Workshops

To facilitate communication and outreach of climate change research results and implications, members of USGS WERC are hosting in-person workshops along the Pacific coast at 8 different sites in Washington, Oregon, and California. We will convene managers, biologists, Tribes, and other decision makers and partners at these regional workshops.  Our team proposes to bring results to the field to facilitate interactions that can help climate change adaptation planning at multiple scales. 


    1.      Disseminate site-specific baseline data and modeling results, reveal coast-wide trends, and identify data  
          gaps.  Inform local managers and decision makers about the Landscape Conservation Cooperatives and  
          their objectives and goals.

    2.      Identify science needs and how local climate science results may be incorporated into habitat
          conservation, planning, and adaptation strategies.


Scenario Planning for Climate Change Adaptation

The purpose of this project is to help USFWS Seal Beach National Wildlife Refuge and the U. S. Navy envision the range of possible natural resource scenarios given climatic change, and use this information to generate optimal climate adaptation strategies. 


  1. Identify biological and non-biological targets of concern in the project area through consultation with the Refuge and the U. S. Navy.
  2. Assemble and summarize current and potential climate change projections, impacts and other relevant information. 
  3. Assess vulnerability of targets and develop plausible scenarios of natural resource states as a result of climate change to develop and prioritize future management strategies.



Map of CERCC sites and workshop sites (yellow)
Map of CERCC study sites and workshop sites. 


Tidal Marsh Processes

Our coastal monitoring network is focused on involving managers in collecting tidal marsh data at several local sites along the Pacific coast. We use this data for both site-specific climate change and sea-level rise ecosystem response projections, and for interpreting across the entire latitudinal gradient of the Pacific coast. Methods we use to collect this information are outlined below.
Reading SETs  

-Sediment Elevation Tables (SETs)

Coastal wetlands normally accrete sediment at a rate similar to the rate at which they lose sediment to erosion. However with sea-level rise, coastal wetlands are in danger of being inundated or eroded before they can refill. SETs are being used to determine changes in marsh surface elevation due to either accretion (sediment input) or erosion. SETs also measure contributions of surface and subsurface processes (i.e. root growth, decomposition, compaction, water flux) and influence of these processes on overall marsh elevation.
Marsh organs installed at different elevations  

-Flooding effects on plant productivity

We are currently examining site-specific vegetation community response to inundation using experiments referred to as ‘marsh organs’. We are determining tidal inundation effects on plant growth, fecundity, root-shoot rations, and organic matter decomposition. We have installed these marsh platforms in three different estuaries with 4 different plant species at different elevations in the marsh to simulate the response of plant growth to different flooding regimes. We are measuring belowground plant production, decomposition rates, and soil salinity, as well as aboveground biomass. This approach facilitates a relatively quick assessment of how marsh plant species may fair in relation to sea-level rise.

Measuring suspended sediment  

-Suspended Sediment Flux Modeling

We measure suspended sediment concentrations at marsh interfaces (shallow intertidal to mud flat, and mud flat to tidal marsh) to determine how suspended sediment is contributing to the sediment budget and marsh stability (total terrestrial and marine sediment input) during months and seasons.
Sediment coring


-Marsh Coring

We measure marsh accretion rates and vegetation stability by analyzing sediment cores for basic sedimentology, and organic matter contributions. We use a Cesium 137 marker, which was left by the atomic bomb, along with radiocarbon data from macrofossils to date sediment cores, and thus calculate long-term deposition and accretion rates for marshes. Using this historic data, we are aiming to develop models for marsh sediment accreting rates and elevation adjustments to sea level changes, as well as changing sea level impacts on dominant vegetation and nesting habitat within coastal wetlands. 

Water Level Monitoring: Storm impacts

Members of WERC study the impact of extreme storm events on marsh wildlife and on sediment accumulation in coastal marsh habitat.  Water level loggers are deployed at 13 wetland sites in San Francisco Bay and at 16 additional sites along the Pacific coast.  Inundation and salinity patterns help inform flooding trends during tidal cycles, seasons and extreme storm events. For a time lapse video of inundation during a king tide: 

Storm Impacts and Marsh Wildlife

An objective for large-scale wetland restoration efforts in the San Francisco Bay Estuary is to be successful in ensuring the persistence of endangered species. In order to accomplish this goal, land managers will need to understand how habitat availability and quality for these wildlife species will be affected by changing climate conditions, particularly in relation to storm events. We projected the effects of increased storm frequency and intensity on breeding habitat availability and reproductive success for endangered California Black Rails in San Francisco Bay marshes. Our results suggested instead of focusing only on marshes with suitable habitat structure, restoration efforts should also be focused on high-elevation marshes, as they provide greater protection from nest flooding during high tides than low-elevation marshes.

California Black Rail

Storm Impacts on Sediment and Accretion

Tidal marsh ecosystems are dynamic systems that respond to changes in oceanic and freshwater processes and sea level. Therefore, how climate change will impact these coastal and estuarine systems is dependent on local conditions within each site. Projected sea-level rise and changes in storm frequency and intensity will affect tidal marshes by altering the supply of suspended sediment, the length of inundation of the marsh platform, and plant and wildlife communities. Lower energy storms that coincide with high tides can create extreme sea levels and cause extended periods of flooding which can substantially reduce habitat availability for wildlife, but can also increase the potential for marsh sediment accumulation, which is essential for marsh stability and persistence. The objective of this research is to evaluate how regional weather conditions resulting in low-pressure storms change local tidal conditions. Using site-level measurements of elevation, plant communities, and water levels, we study the impacts these storms and projected sea-level rise will have on the structure and function of tidal marshes, and how they may affect hydro-geomorphic processes and marsh biotic communities.
marsh during a storm

Inundation Patterns

To understand current tidal flooding patterns and cycles at local salt marsh locations, we deployed water-level loggers at large channel networks throughout our estuary study sites. The loggers measured water depth and duration, temperature, and conductivity at 6-minute intervals. This type of water level monitoring provides detailed information on salt marsh flooding and drainage patterns, including depth during tidal cycles, inundation periods for the salt marsh plain, and characteristics of flooding during storm events. Site-specific tidal data will be tied to established tide gauges to allow understanding of historic patterns of extreme tidal events.

USGS technician deploying water level logger

Predator Prey Relationships

Numerous publications have suggested that high tides can potentially negatively impact prey populations in tidal salt marshes through increased predation risk, primarily by forcing prey species to temporarily emigrate from flooded habitat. However, few studies have explicitly examined this hypothesis. During the winter of 2010-2011, we conducted surveys for avian predators at four tidal salt marshes throughout the San Francisco Bay at both monthly high and low tide levels. The study sites chosen contained water-level loggers, allowing us to compare observed predator densities and behavior with tide levels. We hypothesized that predator effort and efficiency would increase with increasing water level.

Vivian Bui surveying for avian predators. Photo by Nichola Hill.


  • Development of sea level rise impact models for the Pacific estuarine tidal gradient.
  • Monitor the effects of storms on availability of tidal salt marsh habitat to wildlife.
  • Incorporate wildlife movements and population monitoring into sea level rise modeling.
  • Inventory and monitor current species presence and develop a better understanding of species requirements.
  • Model sedimentation accretion processes on the marsh platform.

USGS Contact For This Project
Karen Thorne
(916) 502-2996
San Francisco Bay Estuary Field Station
505 Azuar Dr.
Vallejo, CA 94562
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