Accelerating Ecological Restoration in the Sacramento-San Joaquin Delta and the Suisun Marsh

A central issue is the uneven application of existing restoration tools. Survey respondents noted inadequate staff training, staff turnover, perceived risk, and ambiguity within agencies about when newer tools like the CEQA Statutory Exemption for Restoration Projects (SERP) and Restoration Management Permit (RMP) apply. The result is that projects that do qualify for restoration-specific pathways sometimes are subject to traditional permitting, and those that do use restoration-specific pathways can still take as long and cost as much as if they had gone the traditional route due to additive requirements or inconsistent application.

Applicants pointed to a need for established systems of institutional learning that incorporate lessons learned, which can consolidate what has worked across completed projects so agencies can scale the practices rather than relying on knowledge that leaves with departing staff. Restoration-focused teams like CDFW’s CGT team and the NOAA Restoration Center were widely valued for exactly this reason, but equivalent teams do not exist at every permitting agency, leaving proponents without a consistent point of technical support across the full set of approvals a project requires. Risk aversion by agency staff and the need to get more expedient decisions on complex policy questions from agency leadership are also a factor.

Because a project needs approval from every agency involved, one agency without a restoration pathway can stall implementation and erase efficiency gained elsewhere. For example, the Central Valley Flood Protection Board (Flood Board), which as the non-federal sponsor, typically must receive Section 408 permission before issuing their encroachment permit, faces review demands and reported staff shortages. The Flood Board is currently undertaking a rulemaking process to better align regulations with restoration and that process is expected to conclude in 2027.

In Suisun Marsh, the San Francisco Bay Conservation and Development Commission (BCDC) has some streamlined processes for small projects, however most restoration projects have to undertake the more involved process to obtain a “major permit.” BCDC is also actively analyzing and developing approaches for a programmatic restoration permit to expedite project approval.

Avoiding and minimizing impacts to special-status species is an important part of responsible habitat restoration; however, in some Delta and Suisun settings, fully addressing those impacts at the individual project level can be exceptionally difficult or costly, even where the project is expected to provide substantial overall ecological benefits. This can create conflicts between natural resource objectives and varied agency application of regulations that can result in delayed permits, difficulties in demonstrating net-benefit to biodiversity, and uncertain mitigation requirements that may be hard to satisfy given limited suitable land and willing landowners.

Another complicating factor is that restoring wetlands on reclaimed agricultural land is central to addressing subsidence and carbon emissions, but those lands are foraging habitat for birds like the CESA-listed Swainson’s hawk and mitigation may be required for conversion of those lands. In addition to convening a broader interagency working group, DWR’s in-progress Regional Conservation Investment Strategy offers a potential route to address some of these conflicts at a landscape-scale rather than project by project.

Mitigation projects sometimes struggle to demonstrate eligibility for restoration-specific permitting processes. The RMP requires projects to have a substantial net benefit above a baseline that includes required mitigation activities, and because the permit took effect in January 2025, neither CDFW nor applicants have extensive experience applying it to mitigation projects.

Habitat requirements tied to Delta Levees Program funding add another layer, with AB 360’s net long-term habitat improvement standard interpreted by some respondents as excessive and difficult to reconcile with restoration permitting tools. Marketplace constraints are another issue, with scarce available credits for species like giant garter snake where the demand is high, and finding land to create mitigation banks is getting harder.

One-third of project proponents named cost as one of the major challenges of planning, permitting, and implementing restoration in the Delta and Suisun Marsh, with species mitigation, biological monitoring, and lengthy competitive grant cycles all contributing. The Delta Conservancy estimates a $2 billion need ($1 billion for restoration and $1 billion for levee work) against which recent Proposition 4 allocations of $29 million to the Conservancy and $150 million to DWR fall well short. General obligation bonds, the primary vehicle for this work, can cost the state close to double the principal.

Few grants cover long-term operations and maintenance, and while agencies want longer-term monitoring to quantify restoration’s benefits Delta-wide, applicants view monitoring beyond demonstrating their own project’s success as cost-prohibitive without an alternative funding source.

Delta governance reflects a shared priority around agricultural protection across DWR, CDFW, the Delta Stewardship Council, the Delta Protection Commission, and the counties, and restoration proponents must engage with all of it. Taking land out of production may reduce county tax revenue, impact agricultural jobs, and strain reclamation districts funded by assessments on farmed land, with additional landowner concerns about seepage, flooding, invasive species, and crop damage from increased wildlife.

Subsidence and flooding will require some land to come out of production or be replaced with alternative practices. Options like growing rice and other forms of paludiculture or the rewetting of subsided peat while keeping land in production and generating revenue for levee maintenance offer a partial answer, as exemplified by the Staten Island and Webb Tract whole-island demonstration projects. Early engagement remains the most reliable indicator of durable projects, yet consideration of the Good Neighbor Checklist used for engaging local interests was documented in only about one quarter of relevant Delta Plan certifications since 2023, and local frameworks like the Delta Protection Commission’s LURMP require updating to meet the pace of restoration and climate change now underway.

Restoration projects can offer Tribes opportunities for cultural resource protection and revitalization, access to gather culturally important plants, and potentially greater co-management of Delta lands. These opportunities are best realized when engagement begins in early planning and, where feasible, before land is acquired.

Metropolitan Water District’s Webb Tract project showcases what that can look like: an Ecocultural Working Group co-led by Tribal cultural bearers, where participants were paid for time and travel, and were able to propose a design change that enabled protection of cultural resources produced.

Following Sackett v. EPA, fewer projects will require a Clean Water Act 404 permit from the Army Corps, which historically served as the gateway to interagency consultation under Section 7 of the federal Endangered Species Act. Without it, projects not receiving federal funding or significant federal involvement will require proponents to pursue compliance through Section 10, a substantially longer and more complex process.

Thirty-eight percent of survey respondents expect the changed WOTUS definition to negatively affect their projects, and most have no alternative plan for establishing a federal nexus. Without one, the efficient and much less expensive USFWS’ Statewide Restoration Programmatic Consultation cannot be used, regardless of how well it fits the project.