Guide to Nature-Based Infrastructure Around the Bay Area

Any talk of infrastructure usually brings to mind roads, bridges, pipelines, and potholes. It suggests big, bulky, costly, and grey. Visions of storm drains and culverts, cement mixers and backhoes, seawalls and tide gates, dance before our eyes.

But in the San Francisco Bay Area, as the region confronts rising sea levels and wetter storms, this infrastructure is being reinvented. Engineers and scientists are using different materials and different designs to make grey infrastructure bluer and greener. To soften the hard edges with plants and more absorbent and moveable materials. To use oyster reefs and gravel beaches and humpbacked levees to make our shores more resilient to flooding. 

This “nature-based” infrastructure isn’t a new thing, but it’s trending. It focuses on working with nature, not against it. “The real value of nature-based solutions is not that they replace traditional infrastructure, but that they make it work better, last longer, and provide benefits concrete never will,” says San Francisco Estuary Institute environmental scientist Jeremy Lowe. 

If you want to get an idea of the variety of resilience projects around the Bay, the region maintains several databases (BCDC Inventory 2050, Plan Bay Area 2050+, and the EcoAtlas). 

In this love-fest for nature-based infrastructure, however, there has always been a key warning: one size does not fit all. Local conditions change everything. Projects must take into account the local microtopography and microclimate, not to mention the needs and vulnerabilities of the adjacent communities and ecosystems. That’s why there are as many project types as there are spots that need them.

The following offers a representative guide.

Horizontal Levees

A horizontal levee is a wedge-shaped levee, planted on one side with hardy native species and irrigated with wastewater. As a “levee,” it’s still basically a wall between the shore and the water designed to prevent flooding, but the resemblance to a more conventional riprapped levee or dirt berm stops there. Rather than a mound, it’s a wedge; rather than hard, it’s soft; rather than bare, or covered in broken rock, it’s vegetated. Often they are sited just inland of an older, weaker levee. 

Horizontal levees — also variously known also as ecotone slopes or habitat levees (see next section) — are fast becoming a popular transitional object in the fight to adapt to a rising Bay. Some will help sewage plants better “polish” and remove nutrients from their wastewater; some will offer flood protection to critical infrastructure; some will provide high ground for marsh mice and birds to escape high tides; and some will grow native species favored by Indigenous tribes for cultural use. Many will try to do more than one of these things, all at once. 

As of 2022, there were already half a dozen of different sizes and shapes planned around the Bay Area. As of 2026, two have actually been built (Palo Alto and a pilot at Oro Loma). Other projects include: The First Mile-Hayward; North Richmond-West Contra Costa Sanitary District; Emeryville Crescent; and more (see map above).  

Ecotones & Transition Zones

An ecotone is a transition zone between two ecosystems. In the Bay region, shoreline managers most often use the term to describe the slope or border zone between terrestrial and aquatic systems, like tidal wetlands and the Bay. With sea level rise, more attention is being paid to bulking up and widening these zones, and planting them with hardy native species, so they can better serve as on-ramps for wetland or habitat to “migrate” inland. But ecotones are not just being deployed in the uplands around wetlands. They are also creeping into designs for managed retreat of parks, trails, beaches, and other shoreline features away from the water. Imagine something like a levee but not so crisp, blending into the existing landscape rather than serving as a divider. 

Almost every new wetland restoration project in the Bay Area now includes elements called transition zones. Examples can be found in Menlo Park, the Coyote Hills, Pacheco Marsh in Walnut Creek, and Point Pinole’s Giant Marsh (see map above). The ongoing restoration of the South Bay Salt Ponds includes numerous ecotone levees, Pond A8, Pond A2W, Ponds A12, A13, and A18, and Pond R4, for example. 

Oyster Reefs

Oysters are often called ecosystem engineers: once they attach themselves to rocks or other hard structures on our shores, dozens of other species join them. But the soft muddy shallows of San Francisco Bay don’t offer much for them to attach to, so local scientists have been creating structures in the shape of blocks or balls and placing them in the subtidal zone. These structures are like a miniature apartment complex for marine life, and are made of local “baycrete,” a mix of concrete, native sand, and gravel, and crushed oyster shell to attract, or “recruit,” oyster larvae.

In San Francisco Bay, there have been three major experiments with creating oyster reefs in the shallows to date: San Rafael, Giant Marsh, and Heron’s Head (see map above). Many other projects seek to foster wild oysters in one way or another, but these three offer more direct examples of local “nature-based engineering.” Numerous other oyster restoration efforts are underway between San Diego and Seattle. 

Eelgrass Beds

Eelgrass is subtidal seagrass (Zostera marina) that grows in shallow water meadows. It stabilizes sediment with its deep, dense root systems, filters nutrients and pollutants, and provides habitat for a whole cast of juvenile fish and invertebrates. It grows naturally in San Francisco Bay, but recently shoreline managers have been planting eelgrass near oyster reefs. In association with each other and as part of nature-based infrastructure, these two ecosystem engineers produce more ecological benefits than they do in isolation. Eelgrass can also buffer wave energy, absorbing the force of waves with the back-and-forth sway of its long, skinny leaves.

Currently, there are about 3,000-4,000 acres of eelgrass meadows on the bottom of San Francisco Bay; restoration projects in the last decade added about 5-10 acres per year. Major projects include: Giant Marsh, Middle Harbor in the Port of Oakland, and Richardson Bay in Marin County (2023 eelgrass restoration plan), among others (see map above).

Coarse Gravel Beaches

Beaches — the small and gravelly kind, rather than the fine, sandy, and expansive kind — are fast becoming an important component of nature-based infrastructure around the Bay. Adding pockets and peninsulas (also called tombolos) of coarse gravel around eroding or drowning wetlands can help buffer them from waves. Gravel pockets or beaches can be positioned so that tides and prevailing waves or currents move the gravel to places where it’s needed to bulk up eroding edges, or to deflect waves from vulnerable shores. Traditional “groins” or hard infrastructure can be used to guide where the sediment goes. 

Examples of built Bay beaches include Heron’s Head in San Francisco, Arambaru Island in Marin, and Bay Farm Island in Alameda (see map above). Many other projects are in the design, planning, or construction phase, adding shores that can either shape shift or stay put as sea levels rise, storm surge intensifies, and erosion worsens. 

Living Shorelines

Living shorelines protect the coast with organic materials — plants, sand, stone, shell — strategically placed to attenuate wave energy, keep sediment on the beach, and filter runoff moving from land to sea. “Living shoreline” is a sort of umbrella term that can include many of the other elements in this guide, often combined — eelgrass and oyster beds are both recurring cast members in living shoreline projects. 

Unlike seawalls or levees, living shorelines can move. As seas rise, oysters, eelgrass, and other biological elements have the potential to migrate inland (as long as there’s space), mobile coastal protection infrastructure that doesn’t have to be demolished and rebuilt when the tide line shifts. 

The strategic placement of stone, sand fill, and other structural materials can all play a role in living shoreline projects to create “hybrids of traditional shoreline armoring and the softer approaches to shore protection,” as described by Restore America’s Estuaries.

The Bay region now hosts a variety of living shoreline projects, including Giant Marsh near Point Pinole in the East Bay, as mentioned above. There’s a plan to regionally advance living shorelines projects now underway that aims to design and permit 10 more projects (see map above and inside sidebar). 

Living Seawalls

The smooth concrete of most seawalls offers little habitat for marine life, but it doesn’t have to be that way. Texturing seawalls to give native species a slimy foothold is a growing priority worldwide: both Australia’s Sydney Harbor and Seattle have species-facing seawalls in the water already. 

In San Francisco, those working to protect the waterfront have been experimenting with adding grooved, ribbed, and dimpled pieces of the seawall so they can attract and support herring, oysters, rockweed, hermit crabs, and other native species of the Bay’s natural rocky shore. In an ongoing experiment, the Port of San Francisco deployed more than 288 experimental tiles ranging in size from large to small, and from bumpy to smooth. Not only do these tiles have texture, an “admixture” of bumps, ridges, and pockets, but also a special chemical signature marine species find attractive. They were molded and cast by an international company called Econcrete. The Port is also exploring the idea of a gray-green, rocky-intertidal engineered bluff as one option for creating more vertical habitats along San Francisco’s aging seawall, as well as other nature-based waterfront resilience options. 

Creek & Wetland Links

Humans building new infrastructure with natural processes in mind often consider creating links across existing wetlands, rivers, creeks, upland habitats, and corridors to open space. A more connected ecosystem is a healthier one, with more bandwidth to shift, swell, and contract with rising tides and variable water years. 

In the Bay region, one of our most critical flood protection buffers, for example, is tidal wetlands. An SFEI report found that the Bay Area has 53,700 acres of tidal wetlands as of 2020, an increase of 16% since 2009. Regular tracking of the region’s wetland extent and health is now undertaken by a collaborative monitoring program. 

In addition, more than a hundred creeks drain into the Bay, bringing important building blocks for elevation rise, such as eroded sediment and fresh water, to the Estuary. They in turn also serve as natural and engineered flood control channels, and water storage and conveyance systems. If designed, engineered, or restored with current precipitation extremes and natural processes in mind, creeks can become powerful pieces of nature-based infrastructure.  

Wetland and creek restoration projects are nothing new to the region, and recent climate forward examples include the shoreline at Mountain View and shallow water sediment placement to support Eden Landing. Creek projects include: Colgan Creek near Santa Rosa, Adobe Creek and Tolay Creek in the North Bay, Rheem Creek and Pacheco Marsh in the East Bay, and Calabazas and San Tomas Aquino Creeks in the South Bay (see map above).

Nature-Based Mentality

Every project in this guide is shaped by the history of the piece of coast it sits on: the mud, the tides, the dikes and drains, the agricultural plots, the marsh mice and waterfowl. Nature-based infrastructure is a negotiation between engineered structures and living systems, working with what the water and sediment and oyster larvae want to do instead of straitjacketing the shoreline in concrete. It’s an attempt to find a compromise between the Bay as it was, and the shoreline the region now needs. 

In the Bay Area, we already have some amazing tools for deciding which nature-based solution is going to work best where, including the Adaptation Atlas. This atlas breaks the bayshore down into 30 operational landscape units, “geographic areas that share common physical characteristics….and adhere to the boundaries of natural processes like tides, waves, and sediment movement.” Within these units, only certain kinds of nature-based infrastructure will work. Another tool offers a mapbook of resilience metrics.

A few words to the wise from leaders in this field:

“Geography is fate. You have to adapt to the local setting,”
— Peter Baye, ecologist

“There are no solutions, there are only choices.”
— Kate Orff, founding principal, SCAPE Studio

“You can’t always stick to the plan, you need to build and try things,”
— Roger Leventhal, engineer, San Rafael Public Works