With $369M in upgrades, Palo Alto’s regional wastewater plant will help prevent algal bloom

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The concrete tank that overlooks the Palo Alto Baylands from Embarcadero Way resembles an industrial-sized Jacuzzi where ducks float through murky, bubbly water, seemingly oblivious to the lightly pungent, industrial scent of the processed sewage.

It is one of four aeration basins that are arranged in a giant square at the city’s Regional Quality Control Plant, a sprawling industrial complex that receives and treats sewage from Palo Alto and its partner agencies of Mountain View, East Palo Alto Sanitary District, Los Altos, Los Altos Hills and Stanford University. Three tanks are currently filled, while the fourth basin sits empty as construction workers fortify its concrete base as part of $369-million upgrade to the treatment plant on Embarcadero Road — the city’s most expensive and most complex ongoing infrastructure project.

The effort, which the city kicked off in 2022 and which it plans to complete in 2028, is the biggest upgrade that the plant has seen since 1972, when these basins were initially installed, said plant manager James Allen. Its largest component is a $193-million upgrade to the secondary treatment system, an industrial process that removes chemicals such as ammonia and nitrogen from sewage. Other ongoing components of the project include a new power distribution system and the rehabilitation of the primary sedimentary tanks, which are located just west of the aeration basins and which separate the sludge from the liquid.

When the city kicked off the project, its primary goal was to replace aged equipment, Allen said during a March 21 site tour. A long-term plan that the city approved for the wastewater plant in 2012 noted that much of the equipment at the plant is between 35 and 51 years old and shows significant signs of wear and tear.

But just as construction began, the project took on a second mission: preventing another red tide.

The clarion call for this new effort came in the summer of 2022, when an algal bloom killed more than 10,000 fish and turned water bodies connected to the bay a shade of reddish brown. The bloom, which first appeared near Alameda and then spread to South San Francisco Bay and San Pablo Bay, was the largest in recorded history, according to the California Ocean Protection Council.

State regulators have taken notice. The San Francisco Regional Water Quality Control Board, which regulates the region’s 37 wastewater treatment plants, is scheduled to adopt this summer an updated watershed permit that will set targets for reducing nutrients in wastewater. The current permit, which the board adopted in 2019, required wastewater plants to track and report their nutrient discharge into the bay.

The next permit is still under development, but it is expected to give agencies 10 years to meet new thresholds for reducing nutrient loads in the region, said Lorien Fono, executive director of the Bay Area Clean Water Agencies, an association that helps coordinate the efforts of the Bay Area’s dozens of water control plants.

Fono, whose group has been discussing the new requirements with the water board, said the forthcoming watershed permit will create a nutrient limit that would be 50% lower than what the region experienced in the mid-2010’s, when the nutrient levels were at their peak. They have since been reduced by about 10%, she said.

The effort will be neither easy nor cheap, she said. BACWA estimates that it will cost about $11 billion to implement the needed improvements. This works out to about $4,000 per household using the entire system, the agency estimated.

With the upgrade effort, the Palo Alto plant is methodically preparing for this new, nutrient-light world order. The Embarcadero Way facility has already been treating sewage for ammonia since 1980, Allen said. Once the plant upgrade is completed, the plant would also remove between 50% and 60% of the nitrogen in local wastewater, helping to meet the new standards.

“Ammonia is toxic to fish so we’ve been removing ammonia but we don’t break down the nitrate — that goes out to the bay and it’s converted to nitrogen gas out there,” Allen said. “Now we have to take the nitrogen gas out here.”

Fono said that meeting the requirements of the new permit would require Bay Area plants to make the largest investment in wastewater infrastructure since the 1970s, when cities across the country were upgrading their plants to comply with the Clean Water Act. But unlike at that time, when the federal government made billions of dollars available in grant funding, the agencies don’t have any such funding sources.

Her agency is trying to coordinate the regional response. Its members include the five “principal members”: Central Contra Costa Sanitary District, East Bay Dischargers Authority, East Bay Municipal Utility District, the City and County of San Francisco, and the City of San Jose. Palo Alto, which is the sixth-largest water control district, is one of 12 “associate members,” while dozens of other cities and agencies, including the City of Mountain View, are affiliated members.

“This isn’t going to be a contentious permit, but we want to see a thoughtful and strategic approach because this is going to be extremely costly,” Fono said.

Local ratepayers will soon experience this firsthand. When the Palo Alto City Council adopts its new budget in July, it plans to raise wastewater rates by 15% to pay for the various capital improvements at the wastewater plant, which will add about $7.30 to the average monthly bill, according to utilities department staff.

Ratepayers should also expect rate hikes of 9% in each of the next two years followed by 8% and 7% increases in each of the following two, according to a rate forecast from the department. The main drivers are the need to replace aged sewer lines, to refill depleted financial reserves and to pay for debt services on the capital projects at the wastewater plant, according to staff.

Palo Alto isn’t the only agency that is investing in upgrades that aim to reduce nitrogen. The Oro Lomo Sanitary District in Alameda County, for example, recently completed an upgrade to its nutrient treatment process by installing a “sidestream treatment system” on its San Lorenzo plant. The process focuses on the nutrient-rich liquid that results from dewatering anaerobically digested biosolids, which involves microbes breaking down organic matter in the absence of air. Meanwhile, the Union Sanitary District is adding a process for biological nutrient removal at a cost of $509 million, according to a letter that Fono submitted to the water board in January year.

Both the San Francisco Public Utilities Commission and Silicon Valley Clean Water, which is based in Redwood City, are also pursuing sidestream treatment improvements, which are slated to be completed in 2026 and 2029, respectively.

Some districts, like East Bay Municipal Utility District, are trying to meet the nutrient mandate by updating existing infrastructure to maximize nutrient reduction, Fono said. Others are pursuing nutrient-reduction measures through projects that bring other benefits such as water purification. In these cases, the nutrient-reduction component is a happy byproduct that may be valuable but that isn’t as conspicuous as the other benefits.

“Frankly, the advantages of these expenditures aren’t going to be visible on a dayto-day basis by the community,” Fono said of the nutrient-reduction measures. “Assuming we don’t have perpetual algal blooms.”

Palo Alto is in the third category of agencies: those that are already upgrading aged infrastructure and are including nutrient reduction as part of those projects. As part of the pending upgrade, the aeration basins will be divided with concrete walls to create different zones. Some of these would operate without oxygen and will treat nitrogen, allowing the wastewater plant to reduce the nitrogen that gets emitted into the Bay by about half, according to the city.

The plant upgrade, which is being funded by Palo Alto and its partner cities and agencies, is the city’s first major foray into removing nitrogen, a nutrient that serves as food for the algal species Heterosigma akashiwo. Historically, the Bay region has seen relatively cloudy weather, which helps reduce algal blooms because plants need light to grow, Fono said. But thanks to a confluence of factors that include upstream dams and climate change, conditions have become clearer and more favorable to algal blooms, she said.

It’s not entirely clear what exactly the “safe” threshold is for nutrients in wastewater, she noted. But the algal bloom events in 2022 and 2023 are a sign that the region needs to do more.

“For 10 years we have been studying the science to understand the impacts of nutrients in the Bay,” Fono said. “This project is not complete. We know we want to start reducing nutrients but we don’t know what the safe levels are now.”

The aeration basin from which Allen describes the ongoing improvements represents the middle step in wastewater’s journey from the household to the Bay. After getting flushed down the toilet into the sewer system, the wastewater moves through “bar screens” where bars act like filters to remove roots, rags and other solid items. Pumps then send the wastewater into sedimentation tanks where smaller solids like hair and grease get skimmed off while thick sludge settles at the bottom.

As bottom-feeding sludge thickens into cakes and gets trucked out, the wastewater moves through the plant’s two “fixed film reactors,” rusty two-story towers that would be instantly recognizable to anyone walking near Byxbee Park. Inside are films of microorganisms that feast on the organic matter in the wastewater before it moves on to the bubbly aeration basins. Once the renovation is complete, the city hopes to decommission the fixed film reactors and transfer the entire process to the aeration basin area.

The wastewater then goes through further filtering, where layers of anthracite coal and sand remove small particles, before getting disinfected by ultraviolet light and discharging into the San Francisco Bay.

The sheer amount of processes and equipment that is packed into the plant makes the upgrade particularly complex, said Karin North, assistant director of the Department of Public Works. She and Allen likened the upgrade to keeping a patient alive during an open-heart surgery. Every time one aeration basin gets upgraded, the city has to move the pumps and shift the effluent into the other three tanks — a process that will take about five years to complete.

“Other treatment plants that have lots of open land may be able to do it more efficiently than faster than we can, but a lot of the plants in the Peninsula are constrained and it’s one of the complexity aspects of removing a new pollutant,” Allen said.

Allen called the $193-million upgrade of the secondary-treatment process the “largest project in the city’s history.” North noted that it will have taken about 15 years from the point when the city began designing these improvements to their actual completion.

“We’re in the middle of upgrading our facility while we’re running and operating it at the same time,” North said.

Critical to the process are the bubbles in the water, caused by pressurized air blowers about 15 feet below the surface and which prevent sludge from settling at the bottom of this tank. The air, according to the city, supports the microorganisms that remove ammonia and other dissolved solids.

In the future, Allen said, the basin will be equipped with a serpentine path, with some sections with the air off (anoxic zone) and others with the air on.

“We’ll be selecting for the different microorganisms in the different sections of the serpentine paths, in one section to break down ammonia … and in the next section break down the nitrogen,” Allen said.

Once the improvements are complete and the secondary treatment system is enhanced, the city expects nitrogen levels to drop by 50% to 60%. According to Allen, the plant discharged an average of just under 2,000 kilograms per day of total inorganic nitrogen between 2019 and 2023 during dry seasons, which go from May to November. That number has been rising, first to 2,181 kg in 2022 and then 2,277 kg per day in 2023, indicating nitrogen levels are currently rising.

Allen estimates that once the improvements are complete, the nitrogen levels are expected to go down to about 800 kg per day, well within the proposed threshold of the new permit.

“If we do our part, other agencies do their part, all the nitrogen in the Bay will drop and we won’t be at a tipping point causing algae blooms,” Allen said.