Historically, the Delta was a vast network of tidal wetlands interwoven with meandering channels. However, widespread land use changes beginning in the late 1800s have resulted in the loss of approximately 95% of this habitat. To address this significant loss, the 2022 update to the Delta Plan established ambitious targets for large-scale wetland restoration throughout the region.
Wetland restoration serves multiple purposes, including reducing greenhouse gas emissions, mitigating flood risks, enhancing habitats, and supporting recreational opportunities. Another critical goal is to restore the health of the Delta’s food webs—the intricate networks of interactions between plants and animals that sustain the ecosystem.
At the November meeting of the Delta Stewardship Council, Delta Lead Scientist Dr. Lisamarie Windham-Myers highlighted a study focused on restoring Delta ecosystems, particularly tidal marshes and their associated food webs, in her monthly report.
The study, led by former Delta science fellow Megan Pagliaro and colleagues at the USGS, examined the extent to which tidal marsh restoration in the Delta can recover lost ecosystem functions. This question is particularly pressing given the loss of 95% of the Delta’s tidal wetlands.
The recent paper, ” Does tidal marsh restoration lead to the recovery of trophic pathways that support estuarine fishes?,” (Pagliaro et al., 2025), investigates the effects of tidal marsh restoration on food web health. Food webs, which are essentially interconnected food chains, describe how plants and animals interact, consume one another, and coexist within specific habitats. The research compared food web pathways in three restored tidal marshes of varying ages within the Delta to one another and to nearby historic, undisturbed marshes used as reference sites.
The maps shown below, created by the San Francisco Estuary Institute in 2012, illustrates how the Delta has been transformed since the 1800s. On the left, it shows the Delta as it once was: an expansive, intricate freshwater wetland intertwined with rivers and tides, featuring a maze of branching, meandering channels. In contrast, the modern Delta, shown on the right, is heavily altered. Levees now isolate water from the land, and much of the area has been converted for agricultural use.
In the historical Delta, the wetlands played a crucial role in the ecosystem by producing abundant food that was carried into the estuary as algae and detritus. Detritus, which consists of particulate organic carbon from decaying plant material, was especially important because fish generally relied more on food webs derived from detritus rather than algae, especially in the historic “natural” marshes.
“So we basically shifted the system of food being channeled to fish to a system where food is channeled to humans,” said Dr. Windham-Myers. “It’s really well documented by Dr Jim Cloern in a 2021 paper. It’s an epic paper that people cite a lot, but since we lost Jim earlier this month, I feel it’s important to call out his contributions. He was a former member of the Delta Independent Science Board and an icon of estuary science here and then around the world, and his long-term data here collected with the USGS really tells a story about this evolving Delta.”
The Delta Plan calls for 60-80,000 acres of restoration, which represents about 10% of the overall Delta acreage. Specifically, 52,000 acres of restoration are targeted for floodplains and seasonal wetlands.
The map highlights the three restoration sites chosen for the study in yellow. These include the Tule Red Project in Grizzly Bay, reconnected to tidal flows in 2019; Wheeler Island, restored in 2008; and Sherman Lake, which originated from an accidental levee breach in the 1800s. Historic natural marshes, used as reference sites for the study, are marked in orange.
Drawing from over 1,000 samples of plants, algae, and fish collected during the wet year of 2020 and the dry year of 2021, researchers uncovered some fascinating patterns.
Food chains were shorter in restored marshes. The shorter food chains indicate that these restored marsh ecosystems, regardless of age, are not operating at the same level as the historic natural marshes—the restored ecosystems produce less energy and are less balanced. There is a more complex food web in the older sites, which basically means more interaction.
“So the point is it’s good to be redundant because it gives resilience to those communities,” said Dr. Windham-Myers. “There are more choices for how fish get their energy. More choices and pathways really give more resilience to the food web.”
Fish generally relied more on food webs derived from detritus (decomposing plant matter from tidal wetlands) rather than algae (found in open waters), especially in the historic “natural” marshes.
This is especially true in the historic marshes, and it’s especially true for the native and the resident fish, as compared to the non native and the transient ones that are coming in and out.
“It’s not necessarily just the number of the fish and the number of the algae and so on; it’s the interactions. And it really points towards this slow recovery and the dominant role of decaying plant matter as an energy source in the tidal marsh.”
Management implications
The key takeaway for Delta management is that restoring tidal marsh habitat does not immediately equate to restoring a healthy tidal wetland food web.
It’s not about the number of acres, even though the number of acres of restored wetland to tidal flow is frequently used as a performance metric. There are important ecological dynamics, like robust and diverse feeding opportunities, that are not showing up in data focused solely on acres.
To restore resilient fish communities, restoration project designs could consider a marsh revegetation strategy, especially given how important the detritus-based food web is to resident fish.
“That means getting the right plants in the right place with the right hydrology to produce and export that food to the food web,” said Dr. Windham-Myers. “This is essential. You’ve heard it over and over again; getting the hydrology right is really important.”
Further targeted research is essential to understand how tidal wetland restoration influences food webs throughout the Delta. Long-term monitoring with a specific focus on food webs is critical for assessing the recovery of ecosystem functions and habitats over time. This approach allows us to consistently track progress and better understand responses to key stressors, including sea level rise, drought, species invasions, and the decline or loss of native species.
“There are a lot of changes going on. We need to understand how the metabolism of the system is working, who’s moving, and how the energy is moving through.”
She concluded by emphasizing that Delta science is a collaborative effort that requires sharing and maximizing the use of limited data. A substantial dataset has been developed through this work, which will support future studies, promising more insights to come on tidal wetland food web restoration.
Does tidal marsh restoration lead to the recovery of trophic pathways that support estuarine fishes?
By: Pagliaro, M. D., De La Cruz, S. E. W., Woo, I., Sousa, J., Rich, N., Grimaldo, L., Colombano, D., & Ruhí, A. (2025). https://doi.org/10.1002/eap.70110
Abstract: Evaluation of tidal marsh restoration success is typically based on the recovery of habitat size and target species. However, food-web structure may provide valuable insight into ecosystem functioning trajectories. Here, we studied restored tidal marshes of different ages (new, young, old; spanning 1–150 years) in comparison with nearby reference sites along the San Francisco Estuary. We asked: (1) How does restoration help recover energy pathways that support fishes? (2) Do fishes rely more on algal versus detrital pathways in restored sites?; and (3) How does food-web structure vary as a function of species origin and life history? To answer these questions, we sampled fish (n = 806) and basal resources (emergent vegetation and phytoplankton; n = 109) seasonally over two hydrologically contrasting years. Using stable isotopes (δ13C, δ15N, and δ34S), we calculated fish isotopic niche volumes, food chain lengths, and the relative importance of algal versus detrital energy pathways. We found that food chains in restored sites were 8% shorter than in their paired reference sites. Additionally, the young and old restored sites had 37% smaller niche volumes than their references, but the opposite was true for the new restored site (11% larger), illustrating the characteristic trophic surge of early succession. Fishes found in restored sites relied significantly less on detrital energy (7% less) than fishes found in reference sites, and resident fishes showed 12% higher reliance on the detrital pathway than transient species. Finally, most of the native niche volume overlapped with that of introduced fish, which was in turn 38% larger, and a similar pattern was observed when comparing resident to transient fish. Our findings demonstrate that food-web structure does not immediately recover with tidal marsh restoration, even if fish assemblages are species-rich; and show that transient trophic surges may complicate restoration success assessments of newly restored marshes. We contend that incorporating recovery of energy pathways as an indicator of performance may help strengthen monitoring and design of wetland ecosystem restoration projects.
