The region’s wastewater agencies just got a little breathing room, but not everyone is thrilled about it.
This week, the San Francisco Bay Regional Water Quality Control Board opened the door for certain wastewater upgrade projects to take extra time to meet tough new nitrogen-reduction rules. That move could push compliance for a limited group of nature-based and recycled-water projects past 2034, out as far as 2039. The board’s logic is that horizontal levees, open treatment wetlands and complicated multi-agency builds simply take longer to find land for, permit and construct than the standard ten-year schedule allows.
Under the 2024 NPDES “Nutrients Watershed Permit,” publicly owned treatment works across the region are on the hook for a bay-wide 40 percent cut in total inorganic nitrogen, with a ten-year compliance schedule that runs through Oct. 1, 2034, according to the San Francisco Bay Regional Water Quality Control Board. In a staff notice on a related Basin Plan amendment, the board signaled that a narrow set of “Qualifying Special Projects” could qualify for up to a five-year extension, effectively sliding their deadline to Oct. 1, 2039. That group would include horizontal levees, open treatment wetlands, recycled-water plants and vetted pilot technologies.
Nature-Based Fixes Get a Real-World Test
One of those experimental approaches is already in the ground on the Peninsula. Palo Alto is piloting a horizontal levee next to its Regional Water Quality Control Plant, which the city says treats about 20 million gallons of wastewater per day. The pilot levee is built to capture and polish roughly 0.1 million gallons of that daily flow, according to recent reporting by SFGATE.
Launched in 2018 with federal, state and local backing, the roughly $7 million project is designed to do double duty: strip nutrients from treated wastewater and create new wetland habitat at the Bay’s edge.
Billions on the Line for Bay Plants
The broader buildout will not be cheap. The Bay’s 37 treatment plants face a complicated and expensive lift to hit the new nutrient limits. At San Francisco’s Southeast Treatment Plant alone, nutrient reduction work carries a price tag of about $1.47 billion, according to the San Francisco Public Utilities Commission. A separate Treasure Island Water Resource Recovery Facility, a next-generation plant designed with nutrient removal in mind, is pegged at roughly $165 million.
Those projects sit inside a multiyear regional capital program that runs into the billions for wastewater upgrades across the Bay Area.
Environmental Advocates Split on Extra Time
The idea of stretching deadlines for select projects has split local observers. Some environmental advocates warned the board that carving out too many exceptions could weaken the 2034 target and let a flood of projects slip into longer schedules, a concern highlighted by Palo Alto Online.
Supporters, on the other hand, argue that nature-based systems and recycled-water plants are worth the wait. They point out that these efforts are slower to site, permit and finance, but can deliver broader environmental benefits once built. They also note that the nitrogen limits themselves were a response to the 2022–23 Heterosigma algal blooms and associated fish kills in the Bay, as reported by High Country News, and say those events show why strict rules are non-negotiable.
Lengthy Approval Gauntlet Still Ahead
For now, the clock is ticking on public input. Water Board staff kicked off a CEQA scoping process in late July and are taking written comments through Aug. 6 as they work up draft Basin Plan amendment documents, according to the staff notice. Those drafts are expected to go out for a 45-day public review period this winter, with a Regional Board adoption hearing tentatively slated for spring or summer 2027.
Even if the Regional Board signs off, the Basin Plan amendment would still need approvals from the State Water Board, the Office of Administrative Law and the U.S. EPA before any extended compliance schedules could actually show up in NPDES permits, according to the San Francisco Bay Water Board.
