December 23, 2020

California’s evolving regulation of wetlands: Will new rules bring clarity?

Keith Garner

California is often seen as a precursor for setting new environmental standards in a variety of fields, including wetlands. The state recently adopted new regulations that define wetlands and permit discharges of dredged or fill material to waters of the state. The objectives of the new rules, which went into effect on May 28, 2020, are to bring clarity and uniformity to the regulation of wetlands by the state and to minimize conflicts with related federal requirements.


In California, wetlands are regulated through a combination of federal and state law. Under section 404 of the federal Clean Water Act (33 U.S.C. § 1251 et seq., the CWA), the discharge of dredged or fill material into “waters of the United States,” including wetlands, requires the issuance of a permit (Section 404 Permit) from the U.S. Army Corps of Engineers (Corps). 33 U.S.C. § 1344. Before the Corps can issue a Section 404 Permit, CWA section 401 requires that the applicable state issue a water quality certification (Section 401 Certification) verifying compliance with existing water quality requirements. 33 U.S.C. § 1341.

The Porter-Cologne Water Quality Control Act, which is codified in the California Water Code (Water Code), regulates discharges of waste into “waters of the state.” Cal. Water Code § 13050(c).The Water Code requires dischargers to obtain Waste Discharge Requirements (WDRs), from either the State Water Resources Control Board or one of the nine Regional Water Quality Control Boards (collectively, the Water Boards) before commencing discharge activities. The Water Code does not define or even use the term “wetland.”

Thus, the Water Boards can regulate aquatic impacts either under federal law by issuing Section 401 Certifications pursuant to the CWA, or under state law by issuing WDRs pursuant to the Water Code.

Historically, almost all surface waters of the state were also waters of the United States, and the Section 401 Certification program was California’s de facto regulatory program. When someone needed to fill wetlands or other waters, the applicant obtained a Section 404 Permit from the Corps and a Section 401 Certification from the Water Boards. Separate WDRs under California law were seldom sought or obtained.

In the early 2000s, the scope of “waters of the United States” was narrowed by two U.S. Supreme Court decisions. In 2001, the Court held that “isolated” wetlands, which might otherwise include vernal pool features in California, were not waters of the United States and thus no longer subject to the CWA. Solid Waste Agency of N. Cook County v. U.S. Army Corps of Eng’rs, 531 U.S. 159 (2001). Five years later, a fractured Court further limited CWA jurisdiction by excluding “waters lacking a significant nexus” to traditional navigable waters—at least under a test proposed by Justice Kennedy in his concurring opinion. Rapanos v. United States, 547 U.S. 715 (2006).

The Water Boards’ jurisdiction was not directly affected by these rulings, but the actual regulation under state law of “isolated” waters or those lacking a “significant nexus” was uneven. The regulated community was not widely familiar with the WDR process, and the procedural and substantive requirements for issuance of WDRs often varied from region to region.

In response to these issues, the State Water Resources Control Board adopted a resolution in 2008 directing staff to develop a new program that would ensure that all “waters of the state” were protected and that would provide uniform requirements that would apply throughout the state. Development of the new program took several years, with extensive and often contradictory input from environmental groups, regulated entities, and the relevant regional Water Board. The new rules, officially entitled “Amendment to the Water Quality Control Plan for Ocean Waters of California and the Water Quality Control Plan for Inland Surface Water, Enclosed Bays, and Estuaries of California to Establish a State Wetland Definition and Procedures for Discharges of Dredged or Fill Material to Waters of the State” (Procedures), became effective May 28, 2020. State Water Res. Control Bd., Res. No.2019-0015.

The new Procedures

The Procedures regulate discharges of waste, including dredged or fill material, that may affect the quality of “waters of the state.” The Procedures include provisions that define and delineate wetlands and establish a framework for identifying which wetlands are subject to the Procedures. They also contain detailed application and permitting requirements for activities that would result in a discharge of regulated materials into state waters.

Defining and regulating jurisdictional wetlands

The Procedures define the term “wetland” in a manner that is similar but not identical to the three-parameter federal definition under the 1987 U.S. Army Corps of Engineers Wetland Delineation Manual (as supplemented, the “1987 Corps Manual”). An area is a wetland and, thus, a regulated water of the state (subject to certain exceptions described in more detail below) if, under normal circumstances, (1) the area has continuous or recurrent saturation of the upper substrate caused by groundwater or shallow surface water, or both, (2) the duration of such saturation is sufficient to cause anaerobic conditions in the upper substrate, and (3) the area’s vegetation is dominated by hydrophytes or the area lacks vegetation. Procedures § II.

The similarity in definitions was deliberate and intended to minimize conflicting determinations by the Corps and Water Boards. The definition of “wetland” in the Procedures differs from the federal definition in two important ways. First, to be a wetland, the area’s vegetation must be dominated by hydrophytes or the area must lack vegetation. The federal definition requires that the subject area support hydrophytic vegetation such that areas that lack vegetation would not be considered a wetland under normal circumstances. Second, the area must have continuous saturation of the upper substrate, while the federal definition requires saturated soil conditions. Playas (an ephemeral water located in desert basins) and mudflats are areas that are wetlands in California but not under the CWA.

The Water Board’s Procedures also include guidance on mapping and delineating the extent of wetlands and, as with defining the term “wetland,” attempt to minimize conflict with how wetlands are delineated by the Corps. If a wetland is a water of the United States, the Water Boards should accept the Corps’ delineation. Procedures § III. If the area is not a water of the United States, the Water Boards are directed to utilize the 1987 Corps Manual except that, if an area lacks vegetation, it may still be a wetland. Procedures § III.

Importantly, not all areas that meet the “wetland” definition are regulated under the Procedures. Instead, the Water Boards listed the type of wetlands that are subject to the new requirements, including: (1) natural wetlands; (2) wetlands created by modification of a surface water; and (3) artificial wetlands, including (i) compensatory mitigation, (ii) wetlands identified as waters of the state in a basin plan, (iii) wetlands resulting from historical human activity but that are not regularly maintained and that have become a relatively permanent part of the landscape, and (iv) artificial wetlands greater than one acre. Procedures § II. Certain artificial wetlands over one acre in size are excluded from regulation, including treatment and storage facilities, agricultural crop irrigation, industrial cooling ponds, and fields flooded for rice growing, among others. Procedures § II.3.d.

Permitting Procedures and the alternatives analysis requirement

As implied by the name, the Procedures include provisions for submitting and processing applications for discharges of dredged or fill material under the Section 401 Certification and WDR programs. But, the new procedural steps incorporate new substantive requirements, the most noteworthy of which is the requirement for an alternatives analysis.

An alternatives analysis is not a new concept in wetland permitting. As required under CWA section 404(b)(1), the Corps must issue permits in accordance with rules developed by the U.S. Environmental Protection Agency, and these rules require the Corps to make a finding that the permitted activity is the least environmentally damaging practicable alternative (LEDPA). An alternative is practicable if it is available and capable of being done after taking into consideration cost, existing technology, and logistics in light of overall project purposes. These concepts have been further developed over years of practice. The LEDPA finding, which has been referred to as the “steepest hurdle” in the Section 404 Permit process, is supported by an analysis of alternative locations and site designs. J. Schutz, The Steepest Hurdle in Obtaining A Clean Water Act Section 404 Permit, 24 UCLA J. of Envtl. L. & Pol’y 235 (2006). The alternatives analysis often requires input from a team of experts, including biologists, civil engineers, land planners, and attorneys.

The Water Board incorporates the alternatives analysis requirement by including State Guidelines that are almost a verbatim copy of the 404(b)(1) Guidelines). Procedures § IV.B.3; Appendix A, § 230.10(a). To reduce the chances that the two agencies could reach different LEDPA determinations, the Procedures direct the Water Boards to defer to the Corps’ LEDPA finding when considering permits dealing with waters of the United States, unless the Water Boards were not afforded an opportunity to provide input on the alternatives or that input was not sufficiently considered by the Corps. For impacts to waters of the state that are not federally jurisdictional “water of the United States,” the State Guidelines apply.

One key difference between the state and federal processes are impact limits that trigger the preparation of an alternatives analysis. The Corps issues general permits such as nationwide permits (NWPs) for certain activities that have limited impacts to waters of the United States, generally up to one-half acre. Under federal practice, a project-specific alternatives analysis is not required for most activities that qualify for one or more of the 52 NWPs issued by the Corps. The Procedures require an alternatives analysis for all impacts to waters of the state unless the discharge meets certain exemptions. NWPs are Section 404 Permits and, thus, must be certified. The State Water Boards have certified only 14 of the 52 NWPs in advance, requiring projects that qualify for one or more of the remaining uncertified NWPs to obtain a project-specific Section 401 Certification. Under the Procedures, there are exemptions to the alternatives analysis requirement for projects that impact nonfederal waters of the state but would have qualified for a certified NWP had the waters been subject to CWA jurisdiction. Projects that qualify for the 38 uncertified NWPs may also be exempt from the alternatives analysis requirement, but only if they impact less than 0.2 acre (less than half the federal limit) and do not impact any wetlands, habitat for listed species, or other sensitive aquatic areas. The numerical impact limits are lower than those that apply to most NWPs, which also do not have the other criteria that would trigger the need for an alternatives analysis. Thus, many projects that would be exempt from the alternatives analysis under federal law will require one under the new Procedures. The Water Boards attempt to limit this burden through tiering, so that smaller projects that do not affect high-value resources require less-detailed (and less costly) reports.


Because many applicants rushed to file their applications before the effective date of the Procedures and because permitting activity has slowed due to the COVID-19 pandemic, relatively few applications have been subject to the new requirements and even fewer have made it all the way through the permitting process. At this point, the effect of the new rules is unclear, but that will change with time. In adopting the Procedures, the State Water Board directed staff to prepare annual progress reports on implementation, including application processing timelines and environmental performance measures. These annual progress reports will provide real information on the actual implementation of California’s new regulation of wetlands, assuming the Procedures survive pending litigation.

Editors’ Note: At the time of publication, the author advised that a California trial court has tentatively indicated that it will likely enjoin the application of the Procedures to waters (and wetlands) of the state that were not federally regulated “navigable waters.” It is likely that any final trial court ruling will be appealed or the subject of further administrative action on remand. In the interim, however, the application of the new California Procedures for evaluating wetlands is likely to remain confined to the same waters as regulated under the federal Clean Water Act.


Keith Garner


Keith Garner is a partner at the San Francisco office of Sheppard, Mullin, Richter & Hampton LLP, where he focuses on state and federal environmental laws, land use planning, and natural resources permitting issues.