By Jenner Junghans, California Sea Grant
For millennia, the Kumeyaay people have maintained a mutually beneficial relationship with the salt marsh of Northern Mission Bay in San Diego. Through stewardship and responsible harvesting of plants, fish and shellfish and placing rocks to guide water flow, they have supported a healthy ecosystem since time immemorial.
But in 1769, Spanish settlers colonized the land, introducing cattle and invasive grasses that began reshaping the marsh. Over time, urban development followed. Natural waterways were altered and the bay was dredged. Surrounding land was transformed by various human uses. The region became a popular vacation destination and watercraft traffic increased.
Today, the UC San Diego Kendall-Frost Marsh Reserve and the Northern Wildlife Preserve protect what remains of the tidal salt marshes that once covered much of Mission Bay in San Diego. One-third its original size and hemmed in by development and infrastructure, the marsh’s natural flow of water has been significantly disrupted.
“The marsh in Northern Mission Bay has transitioned from an expansive fringe wetland fed predominantly by what was once the wide and meandering Rose Creek into a small corner wetland dotted with storm drains,” says Carrie Shuster, a California Sea Grant graduate research fellow.
Yet little is known about how long-term land use and weather pattern changes affect the marsh’s size, shape and elevation — the physical characteristics that determine how its ecosystem functions.
To close the knowledge gap, Shuster examined 150 years of changes in the marsh for her master’s thesis in the University of San Diego’s Environmental and Ocean Sciences program.
San Diego is planning to restore the marsh as part of De Anza Natural, an amendment to the Mission Bay Park master plan, the City of San Diego’s land use and development blueprint for the park along the waterfront. Shuster’s research could inform restoration efforts.
“We can’t manage and restore what we don’t understand,” she says.
A fundamentally new system
Marshes are some of the most productive ecosystems on Earth. Sitting at the edge of land and water, creeks and rivers supply freshwater, nutrients and sediment, while tides deliver those from the sea. Plants use this rich mix to grow. When they die and decompose, they feed the microbes, insects and small aquatic animals that feed fish and birds, whose waste returns nutrients to the ecosystem, explains Shuster.
To reconstruct how the marsh has changed over the past 150 years, she analyzed historical topographic maps, known as T-sheets, dating back to 1857; aerial photographs from the mid- to late 20th century; and modern digital elevation models. Then she calculated changes in the marsh’s vegetated land, creeks and salt pannes, as well as its edges, elevation zones and nearby ecosystems.
Between 1857 and 2023, the marsh lost 66% of its vegetated marshland. Storm drains increased the total length of creeks by 76%. All but 2% of salt panne habitat — sandy, shallow areas where salt concentrates as water ebbs and flows with the tides — has been lost. And nearly 100% of the marsh’s upland elevation is dominated by infrastructure and development — leaving the marsh nowhere to migrate inland as the sea rises, a phenomenon known as coastal squeeze.
“This isn’t a degraded version of a past system — it’s fundamentally a new system,” says Shuster.
Rose Creek, the principal freshwater tributary that fed the marsh once meandered through the wetland. But in 1953, it was diverted away from the marsh and channelized to control urban flooding.
“When a creek flows into a salt marsh, sediments from upstream get trapped by the plants, building up the elevation and contributing to a lush marsh that is able to keep pace with rising seas,” explains Theresa Talley, California Sea Grant extension specialist and Shuster’s academic advisor. “When the creek is diverted, all those inputs are lost and the marsh vegetation begins to disappear.”
Cordgrass is one of the common plants in California’s tidal marshes. A tall grass that grows in the low intertidal zone, trapping the sediment with its roots to build and stabilize the marsh, it creates critical habitat for fish, invertebrates and birds, such as the endangered light-footed Ridgway’s rail. Rails weave dried cordgrass shoots — which are hollow, so they float — among swaths of tall cordgrass tethering the edges of the nest to rigid living stalks. This allows the nests to move up and down with the tides to avoid flooding. But today, inadequate stands of cordgrass can’t support the nests. Each year, conservationists install artificial wooden platforms for rails to nest on instead, says Talley.
Beyond the marsh’s boundaries, roads and buildings replaced soil and vegetation that once slowed and regulated the flow of water and sediment. The storm drain system collects runoff from the adjacent neighborhood and funnels it directly into the marsh. Changing weather patterns increase the effect. “We go through bouts of drought followed by torrential storms. So now we’ve got these really intense pulses of freshwater, sediment and often trash and debris entering the marsh through storm drains,” says Talley.
The diversion of Rose Creek also contributed to the loss of most of the marsh’s salt pannes. That eliminated natural seasonal erosion, which continuously redistributed sediment and shaped the sandy flats. Along with fill for development, the salt pannes became overgrown with vegetation, which shrank and fragmented the distinctive Southern California habitat.
Although they may look lifeless, salt pannes are surprisingly productive, says Shuster. They support dwarf plants, algae and cyanobacteria, which attract bugs, beetles and flies, which in turn attract birds, she explains.
A blueprint for marsh restoration
Proposed restoration plans include adding sediment to raise lower-elevation mudflat areas — a common restoration practice — and branching the channelized Rose Creek to create more shoreline. But Shuster argues those approaches run counter to 150 years of data. The plans would do little to reconnect Rose Creek to the marsh and would fill a functioning mudflat to create marshland with an exposed shoreline vulnerable to erosion and elevations subject to flooding by 2100, she explains.
To restore the marsh, Shuster says plans need to design around how the marsh’s water flow, sediment, elevation and ecology all work together. Restoration also needs to give the marsh room to adapt to urban runoff, as well as changes in weather patterns and sediment deposits.
She recommends several approaches: reconnect Rose Creek to the marsh, and let storm drain channels meander instead of running straight to slow fast-moving urban runoff and reduce erosion. Preserve the remaining upland marsh from development. Rebuild the natural slope from water to land, so plants can trap more sediment and build up the marsh to keep pace with a rising sea. And use movable infrastructure like trailers for future buildings, such as the proposed interpretive nature center, to protect what’s left of the marsh’s unfragmented core.
Shuster also believes restoration has to account for how the community interacts with the marsh and the attitudes that shape how it’s managed. She sees cultural stewardship — education and public engagement — as one way to build that relationship. “We have to have an educated community that understands the marshland to have a true, scientific restoration,” she says.
“It’s a very different place, but there’s still salt marsh there. It can still function in many ways — we just need to come together as a society and agree on what it is we want out of this area, knowing it’s one of the last remnants of salt marsh in Mission Bay — and come up with a plan together,” says Talley.
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