Sea Level Rise Threatens the Bay's Remaining Wetlands

A salt marsh harvest mouse feeds on pickleweed at low tide. These endangered animals are only found in salt marshes in Northern California. Source: USFWS.
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San Francisco Bay’s waterfront natural areas are on the frontlines of sea level rise. The National Academy of Science (2012) estimates that sea level rise will raise San Francisco Bay’s water levels by at least 1 meter (3 feet) by 2100. In addition to wreaking havoc on the Bay Area’s built environment, rising water levels will directly impact the Bay’s urban estuary ecosystem and its diverse community of plant and animal species.

Although a 1-meter rise in water level will affect the Bay as a whole, regional factors like landscape, flood control measures, available sediment, and shoreline development can influence how sea level rise affects local habitats (Stralberg et al., 2011). Habitats in close proximity to the current shoreline will be some of the first areas affected by sea level rise, including wetlands, mudflats, and subtidal areas (BCDC, 2002).

San Francisco Baykeeper advocates for taking preventative action to protect the Bay’s interconnected natural areas from sea level rise. Actions taken by agencies and local governments today can build future ecosystem resilience to rising water levels in San Francisco Bay. These include imposing responsible requirements for development projects along the Bay, minimizing sand mining and maximizing the beneficial reuse of dredged sediment, and restoring damaged ecosystems at the edges of our urban landscape to allow the landward migration of wetlands as seas rise.

Tidal Marshes and Wetlands

The Bay’s tidal marshes are extremely productive habitats, creating nutrients and organic material that support the Bay’s food web. Marsh plants give hundreds of Bay animals protected areas for foraging, breeding, and nesting, including endangered species, native animals, and over one million birds following the Pacific Flyway migration path (Takekawa et al., 2006).

Submerged marsh areas also shelter juvenile fish, including commercially and recreationally fished species (Herbold et al., 2014). Marshes also have benefits for cities and people by mitigating waves, protecting urban areas from flooding, filtering pollutants from water, reducing erosion, stabilizing shore areas, and sequestering carbon (Stralberg et al., 2011). Unfortunately, Bay marshes are extremely vulnerable to flooding caused by sea level rise because they are often in low-lying areas.

Sadly, the Bay has already lost much of its marsh habitat. Our shores were historically lined with 200,000 hectares, or approximately 770 square miles, of salt marshes, but urban development, land filling, and the construction of dikes, levees, and dams caused a 90% loss of these areas over the 20th century (Stralberg et al., 2011). Although 5,000 hectares of these lost marshes have been restored, projected rates of sea level rise threaten the Bay’s remaining 13,209 hectares of marshes. Agencies, lawmakers, and urban planners must take preventative steps to protect the Bay’s vulnerable tidal marshes from sea level rise.

To survive rising water levels, marshes need sustained flows of fresh water, a steady sediment supply, and nearby undeveloped higher ground to move into (Stralberg et al., 2011). Healthy tidal marsh systems are regularly flooded with a mix of freshwater and saltwater from streams, rivers, and the Bay. Marsh plants trap floating sediment, allowing the marsh to build up vertically or slowly move into new areas. Sea level rise can lead to increased erosion of marsh sediment, preventing the marsh from vertically building above the water level or moving to higher ground (Stralberg et al., 2011).

Model scenarios by Stralberg et al. (2011) show that with high sea level rise (1.65 m/100 years) and limited available suspended sediment (less than 200 mg/L), Bay marshes will not be able to build vertically or move inland quickly enough to escape permanent flooding. In this scenario, the majority of marshes wash away by 2110. In model scenarios with high sea level rise (1.65 m/100 years) but with more available suspended sediment (200-300 mg/L), more marshes recover from initial flooding and ultimately survive rising water levels. Sediment is therefore key to the survival of tidal marshes.

According to Stralberg et al. (2011), sea level rise will impact marshes differently depending on their location in the Bay. Marshes in areas with more suspended sediment (300 mg/L) will have a better chance of building above the water level, including the South Bay and the mouths of the Petaluma and Sonoma Rivers. Areas like the San Francisco Peninsula may not have enough suspended sediment (less than 100 mg/L) to support successful marsh retreat to higher elevations. Low suspended sediment in the Bay is a result of water redirection infrastructure like dikes, levees, and dams that disrupt sediment circulation before it has the chance to reach Bay habitats.

SLR High/Sed High

SLR High/Sed Low

SLR Low/Sed High

SLR Low/Sed Low



Currently Tidal





Habitat Type


Potential Restoration



Low Marsh

Mid Marsh

High Marsh


No Data































Area of potential future habitats within areas of high (North Bay) and low (Central Bay) sediment availability under different SLR and sediment ("Sed") scenarios. Projected survival of marsh areas depend on rates of sea level rise and available suspended sediment. The upper row shows future impacts on current marsh habitat. The lower row includes potentially restorable marsh habitat—note different scales. More marsh areas persisted in scenarios with more available sediment. Source: Stralberg et al., 2011

Shoreline development limits the potential for marsh survival in high sea level rise scenarios. The Bay’s urban areas are often developed right up to the water line, leaving no open land for retreating marshes to move into (Stralberg et al., 2011). Some waterfront areas can be restored or redeveloped into areas that could become future marsh areas.

Saltwater inundation and flooding from sea level rise will expose marsh plants throughout the Bay to more saltwater, potentially changing the structure of the habitat. If dikes, levees, and flood control infrastructure prevent fresh water from reaching marshes, plants that are adapted to survive in extremely salty conditions will dominate the landscape (Takekawa et al., 2006). Opportunistic invasive plant species often thrive in these conditions, including the invasive Spartina species, a mid-marsh plant that easily outcompetes native plants by forming dense and uninhabitable mats (Takekawa et al., 2006). Changes in plant communities can affect how much sediment the marsh traps, nutrient production, and the animals that can survive in the marsh.

Impacts of Sea Level Rise on Marsh Wildlife

As water levels rise in the Bay, marshes are projected to shrink into smaller, more isolated habitat fragments (Stralberg et al., 2011). Small habitat areas cannot support large animal populations, which could force some Bay animal species to move to new areas with better conditions (Takekawa et al., 2006). Many bird species, such as the common moorhen, have already shifted their winter nesting and breeding sites from Bay marshes to the Sacramento-San Joaquin River Delta freshwater marshes. Animals that use marshland on a temporary basis, including harbor seals that use marshes to haul out, rest and raise pups, will also need to seek out new areas.

Regular marsh flooding will drive resident marsh animals from the safety of the vegetated middle marsh into sparse upland areas. This crowding effect will create more competition among animals for food, space, and shelter from predators (Stralberg et al. 2011). For example, the endangered salt marsh harvest mouse relies on the low-lying pickleweed plant as its only food source. Flooding will force these thumb-sized mice to seek refuge in upland areas, further from their only food source and putting them at a greater risk of predation. Increased competition for food in marshes may drive other animal species to eat pickleweed. These added stressors may threaten the reproductive fitness and survival of these endangered mice.

Sea level rise also threatens birds that use marshes as nesting grounds. Increased saltwater flooding can cause higher rates of egg death and young bird mortality in some species (Takekawa et al., 2006). The California Ridgway’s rail, an endangered native bird species, is especially vulnerable to flooding caused by sea level rise. Ridgway’s rails have a significantly higher hatchling mortality rate when eggs are exposed to predators, salt water, and waterborne contaminants (Schwarzbach et al., 2005).

We can support future preservation of Bay marshes and wildlife by preserving freshwater flows, regional sediment supply, and restoring habitat (Stralberg et al. 2011). Plans to construct additional flood control infrastructure should consider potential impacts on sediment supply and marshes. Baykeeper advocates for reusing dredged sediment to restore wetlands through the process of beneficial reuse.

Tidal Mudflats

Mudflats, tidally exposed expanses of mud, connect the Bay’s marshes to submerged habitats. Mudflat habitat is a valuable part of the greater San Francisco Bay ecosystem, cycling nutrients, supplying sediment to marshes, and supporting animals above and below the water’s surface (Subtidal Habitat Goals Project). Marsh birds regularly forage on mudflats at low tide, searching for burrowing invertebrate animals like worms, amphipods, clams, snails, and crabs. At high tide, fish, diving ducks, bat rays, skates, and sharks also hunt for food on the surface of submerged mudflats. As water levels rise in the Bay, many lowland marsh areas will gradually lose their vegetation and transform into intertidal mudflats (Stralberg et al. 2011). Despite predictions that Bay mudflat areas will increase in size over the next century, the effects of sea level rise in the Bay threaten this crucial habitat (Stralberg et al. 2011).

Palo Alto Baylands at low tide. The expansive margin areas of the South Bay are considered the nursery of the Bay. Inundation of these flats will have unknown consequences on the ecology of the Bay. Source: Ingrid Taylar

As marshes disappear beneath rising water levels, mudflats may gradually decline. Many mudflat habitats rely on marshes to produce nutrients and organic material (Subtidal Habitat Goals Project). Mudflat animals and microbes break this material down, releasing it to the greater Bay ecosystem. Smaller marsh areas will release less organic material to mudflat areas, potentially limiting mudflat productivity and nutrient circulation. This shift could impact the entire Bay food web.

Like marshes, mudflats depend on a reliable sediment supply (Subtidal Habitat Goals Project). Commercial sediment mining, dredging, water flow redirection, and flood prevention infrastructure may change sediment distribution dynamics in the Bay. Interruptions in sediment supply may prevent mudflat habitats from accumulating enough sediment to remain close to shore. If mudflat habitats cannot accumulate enough sediment to move inland, these areas will be submerged in deeper water for longer periods of time, making them less accessible to many species of foraging marsh and shore birds (Subtidal Habitat Goals Project). Stronger waves and tides associated with sea level rise may also increase erosion of mudflat sediment, shrinking the habitat area and potentially dispersing buried contaminants (Subtidal Habitat Goals Project).

A long-billed curlew forages for a mudflat crab at low tide. Source: Pam and Richard Winegar.
Impacts of Sea Level Rise on Mudflat Wildlife

Flooding caused by sea level rise could wash toxic contaminants from 1,100 contaminated sites into the Bay. Tidal mudflat animals are especially vulnerable to accumulating toxic material, PCBs, selenium, mercury, arsenic, and other heavy metals, as well as other pollutants (Takekawa et al., 2006). Contaminants bind to sediment grains in the mud and remain in the Bay even after the initial pollution source is stopped (Subtidal Habitat Goals Project). Mud-dwelling animals then absorb contaminants from the sediment they live in, sometimes at lethal concentrations. For example, the invasive Asian clam can concentrate higher levels of selenium than any other aquatic invertebrate (Takekawa et al., 2006). Foraging animals, both native and nonnative, that eat contaminated mudflat animals like the Asian clam absorb toxins into their body tissue. This can lead to limited growth, reproductive failure, and death in fish and birds (Subtidal Habitat Goals Project). Toxic contaminants can travel further up the food web to sicken sharks, seals, and humans.

Sea level rise may also impact which species can survive in Bay mudflats. Immobile, burrowing animals that cannot tolerate higher salt content in the water may struggle to survive increased saltwater flooding (Subtidal Habitat Goals Project). Invasive benthic animals that are better adapted to survive in deeper water with higher salinity may outcompete native species, changing the dynamics of the food web. Higher salinity may also support oceanic animals moving into the Bay.

Although tidal mudflats are predicted to expand as a result of sea level rise, there are steps we can take to protect these habitats from erosion, contamination, and invasive species. Baykeeper advocates for protecting mudflat habitat by maintaining the Bay’s sediment supply and reusing dredged sediment to build up existing mudflats. Strengthening laws regarding contaminant discharge and cleaning up contaminated sites will also prevent additional toxic pollution from entering the Bay. Baykeeper also advocates for regulations that prevent accidental introductions of new invasive species that could permanently change the Bay’s food web dynamics.

Subtidal Habitat

Subtidal habitat—which refers to all of the Bay’s submerged habitat —connect the entire San Francisco Bay Estuary. The Bay’s waters are filled with diverse marine wildlife, including over 130 fish species (Subtidal Habitat Goals Project). Our Bay supports several commercial fisheries, including California halibut and Pacific herring. Rising water levels in the Bay will create saltier conditions, deeper water, stronger tide currents, higher wave energy, and increased rates of erosion (Subtidal Habitat Goals Project). These changes in water conditions will affect the Bay’s mosaic of subtidal habitats, including eelgrass beds, oyster reefs, sand and rock beds, and the open water column. Agencies must consider the impacts of sea level rise on these habitats to effectively manage the Bay’s marine resources and wildlife.

Eelgrass beds provide refuge for Bay animals. Source: Subtidal Habitats Goals Project.

Sea level rise will increase the amount of submerged habitat in the Bay. Rising water levels will create more open water habitat and increase the depth of the water column. The impact of rising water levels on bottom habitat is somewhat unpredictable. Higher concentrations of salt in the water may favor habitat types that thrive in high salinities, like eelgrass and oyster beds (Subtidal Habitat Goals Project). On the other hand, deeper water will prevent some light from reaching the bottom of the Bay, which could reduce the productivity and size of plant-based habitats like eelgrass beds. If these habitats are submerged too deep, they may disappear.

Many of the Bay’s underwater habitats depend on sediment to migrate to shallower depths and areas near shore (Subtidal Habitat Goals Project). Stronger tidal currents and wave activity may increase rates of erosion in the Bay, reducing the Bay’s sediment supply over time and altering the distribution of sediment throughout the Bay. Higher energy water will erode the smaller sand particles of soft-bottom habitats, stripping them to down to rocky substrate and pebbles (Subtidal Habitat Goals Project).

Submerged habitats like eelgrass beds and oyster reefs can buffer marshes and urban areas from the flooding and high wave activity caused by sea level rise (Subtidal Habitat Goals Project). Supporting restoration of these areas throughout the Bay may decrease erosion and protect Bay shorelines from rising waters.

Impacts of Sea Level Rise on Subtidal Wildlife

Increased saltwater flooding from sea level rise will favor the Bay’s salt-tolerant marine species (Subtidal Habitat Goals Project). Animals that prefer brackish and fresh water, including the endangered Delta smelt, will have to migrate further inland towards the Sacramento-San Joaquin River Delta to escape high salinity waters in the Bay. Rising water levels may also prevent diving birds from foraging in deeper habitats, forcing these animals to seek out new subtidal feeding areas. Changing geographic distributions of animals in the Bay will impact animals throughout the food web, especially predators like leopard sharks, harbor seals, sea lions, and porpoises.

Increased urban flooding may cause storm drains and municipal sanitary sewers to overflow on a regular basis. These overflows will introduce unwanted pollutants, sewage, and nutrients directly into the Bay (Takekawa et al., 2006). Increased pollution could trigger harmful plankton and algal blooms in the Bay that could have catastrophic impacts on the food web (Takekawa et al., 2006).

As rising water levels flood urban areas, the Bay’s marine animals will be exposed to higher levels of harmful contaminants from runoff pollution. Increased exposure could impact fish functioning and reproduction (Takekawa et al., 2006). For example, the endangered Chinook salmon lose their sense of smell when they are exposed to heavy metals, permanently preventing them from finding their way upstream to breeding grounds.

Changes in marsh and mudflat habitats will also impact subtidal animals. Shallow intertidal areas near marshes provide crucial nursery grounds for young fish. These fish will later move into other regions of the open Bay or out to the open ocean. Shrinking areas of sheltered tidal marsh or mudflat habitats may affect the survival of juvenile fish, altering food web dynamics in the Bay and beyond.

Protecting the Bay’s subtidal habitats from sea level rise can begin with preventing pollutants from entering the Bay, protecting the Bay’s sediment supply, and cleaning up low-lying sites that are at risk of flooding over the next century.


Herbold et al., The Role of Tidal Marsh Restoration in Fish Management in the San Francisco Estuary. 2014. San Francisco Estuary and Watershed Science, 12 (1).

Kimmerer, W., et al. San Francisco Bay Subtidal Habitat Goals Report. 2010.

Moyle, P. et al., Habitat Variability and Complexity in the Upper San Francisco Estuary. 2010. San Francisco Estuary & Watershed Science, 8(3).

San Francisco Bay Conservation and Development Commission (BCDC), San Francisco Bay Ecology and Related Habitats. 2002.

Stralberg et al., Evaluating Tidal Marsh Sustainability in the Face of Sea-Level Rise: A Hybrid Modeling Approach Applied to San Francisco Bay. 2011. PloS ONE, 6 (11).

Schwarzbach et al., Effects of Predation, Flooding, and Contamination on Reproductive Success of California Clapper Rails in San Francisco Bay. 2005. The Auk, 123(1):45-60.

Takekawa et al., Environmental Threats to Tidal-Marsh Vertebrates of the San Francisco Bay Estuary. 2006. Studies in Avian Biology 32:176-197.