Regional San's new Biological Nutrient Removal facility uses bacteria to remove nearly all the ammonia from wastewater in the Sacramento region. Photo by Regional San.

NOTEBOOK FEATURE: Sacramento’s New Wastewater Treatment Upgrade Will Help Recharge Groundwater—Will It Also Help the Delta?

by Robin Meadows

Two decades ago, scientists were alarmed by sudden declines in at-risk fish and their tiny prey, called zooplankton, in California’s Sacramento-San Joaquin River Delta.

“No one knew why,” says Dylan Stern, a Program Manager at the Delta Stewardship Council, a state agency. “Everyone was kind of freaking out.”

After a flurry of investigation, a potential cause emerged: nutrient pollution in the form of excess ammonia, a nitrogen compound, from Sacramento’s wastewater treatment plant. Operated by the Sacramento Regional County Sanitation District (Regional San), the treatment plant is the largest discharger to an inland body of water west of the Mississippi River.

In 2010 the State Water Resources Control Board required reducing nutrients in this effluent, which necessitated a significant upgrade to the treatment plant. This month marks completion of the $1.7 billion, decade-long upgrade, and nutrients in the effluent are way down.

“The new treatment process now removes 99 percent of ammonia, and 89 percent of nitrogen from the wastewater,” says Terrie Mitchell, Regional San’s Legislative and Regulatory Affairs Manager.

Will this nutrient reduction actually benefit the food web and fish—notably the endangered Delta smelt and the threatened longfin smelt—in the Delta? Researchers are conducting before and after studies of the upgrade to find out.

Either way, the modernized treatment plant will have environmental benefits. Regional San will soon supply recycled water to farms south of the city of Sacramento. This will reduce pumping from depleted groundwater basins and give farmers a reliable water supply as the state cracks down on overdrafting.

Cleaner water

Regional San’s new Biological Nutrient Removal facility uses bacteria to remove nearly all the ammonia from wastewater in the Sacramento region. Photo by Regional San.

Regional San’s wastewater treatment now includes three main steps. The first is screening out debris and separating solids from the water. The new upgrade adds additional steps, starting with biological nutrient removal (BNR) to reduce ammonia and other organic compounds.

Operational in 2021, the new BNR facility covers 39 acres and has eight enormous basins. Each basin is lined with thousands of tubes that bubble in oxygen, which supports bacteria that eat nutrients in the wastewater.

The BNR facility treats an average of 135 million gallons of wastewater per day, and the final step is running this effluent through the just-completed Tertiary Treatment Facility. This last  treatment includes finer filtration to remove additional particulates to meet requirements for non-potable water reuse.

Delta impacts

The hypothesis that excess nutrients were behind the food web and fish crash in the Delta was based on laboratory and field studies. Preliminary research suggested that concentrations of ammonium, which is derived from ammonia, in Delta waterways were high enough to kill zooplankton.

Other research suggested that ammonium concentrations were high enough to suppress the growth of phytoplankton, tiny plant-like organisms that are eaten by the zooplankton that in turn are eaten by fish. The logic behind the wastewater treatment plant upgrade was that reducing ammonium would restore phytoplankton and zooplankton, thus giving fish enough to eat.

This conclusion was not unanimous, however. “There were many conflicting ideas,” says the Delta Stewardship Council’s Stern, adding that other contenders included phytoplankton grazing by invasive clams, lack of light for phytoplankton in deep river channels, and native fish predation by non-native fish.

Lowering the “Sediment Roomba” to measure nutrient flows between the sediment and water. Photo by USGS.

So the Council decided to test the impact of the wastewater treatment plant upgrade on the Delta. Called Operation Baseline, this effort entails monitoring a host of environmental quality indicators throughout the Delta, from nutrients and phytoplankton to dissolved oxygen, salinity, temperature and turbidity.

Gathering comprehensive data required re-imagining the existing monitoring program, which sampled at fixed points. “The Delta is gigantic,” Stern says. “There’s a huge data gap between fixed stations.”

A $4-plus million revamp of the Delta monitoring program, which is led by the U.S. Geological Survey, resulted in thrice yearly boat-based surveys. Water is pumped continuously through on-board instrumentation and then back into the Delta via hoses.  The team has also tested hoovering sediment up for analysis via a suction cup dubbed the Sediment Roomba.

“The surveys give a detailed snapshot of the whole Delta,” Stern says. “It’s been revolutionary.”

Preliminary boat-based measurements of ammonium across the Delta in different seasons and years. Figure by USGS.

Operation Baseline began collecting data several years before the wastewater treatment plant’s BNR Facility became operational in 2021. “It’s important to have a baseline—you can’t manage what you’re not measuring,” Stern says. “Now we have a way to see what the new, expensive upgrade does for the Delta.” The findings will inform decisions about similar upgrades for other wastewater treatment plants that discharge into the Delta.

So far, it’s too early to tell. Nutrients can still be high in the Delta and sediment is a likely source. “There could be a giant pool of nutrients in the sediment that is released when it’s stirred up,” says Stern, who has a background in environmental science and management. “That could be muddying the picture.”

A definitive answer on the wastewater treatment plant upgrade’s impact on the Delta’s aquatic ecosystem could take decades.

Groundwater recharge

The Harvest Water Program service area includes farms and ranches, and is edged by rivers and reserves. Credit Regional San.

In the meantime, Regional San’s upgraded wastewater treatment plant has the immediate benefit of producing water clean enough for irrigating pastures and crops. Under the agency’s  Harvest Water Program, up to 50,000 acre-feet—about 16 billion gallons—of recycled water per year will be delivered to about 16,000 acres of land between the town of Elk Grove, the Stone Lakes National Wildlife Refuge, and the Cosumnes River Preserve.

This new recycled water will help replenish groundwater in the service area. “Everybody’s pumping water out of the ground,” says Walt Hardesty, one of 62 ranchers and farmers who’ve signed up for the Harvest Water Program. He raises up to 250 head of Angus cattle annually with his daughter and son. He doesn’t need water in the winter but in the summer he irrigates the pastures.

As 1st Vice President of the Sacramento County Farm Bureau, Hardesty sat on the Harvest Water Program steering committee. “They asked what they could do for us and we told them the recycled water needed to cost the same, or less, as the electricity for the wells,” says Hardesty, who grew up on a dairy farm and whose neighbors grow row crops, orchards, and vineyards.

“Farming margins have tightened up so much over the last 10 years that there’s no wiggle room anymore,” he adds. “If it’s the same amount of money, I can feel good about using recycled water and saving the environment.”

Regional San has received conditional approval from the California Water Commission for a $291 million Water Storage Investment Program grant, which is from Proposition 1, to fund constructing a pump station, laying the pipes, and developing ways of enhancing habitats in the service area. Regional San hopes to get the funding OK by the summer and to start construction in the fall. Recycled water could be delivered as soon as the end of 2025.

“In 15 years, there could be an up to a 30 foot increase in groundwater elevations in certain areas,” Regional San’s Mitchell says. The basin could ultimately store more than 370,000 acre-feet or about one-third the capacity of Folsom Lake, which provides drinking water to the greater Sacramento area.

Ecosystem benefits

A higher water table will support ecosystems such as riparian forests. This impact could extend to the Cosumnes River, which runs 52 miles from the Sierra Nevada to the Delta and borders the Harvest Water Program service area.

Sandhill Cranes congregate near Woodbridge Rd. in Acampo, CA, on December 14, 2012.

Thick forests that included valley oaks, Northern California walnut, and box elder once flourished all along the Cosumnes’ banks in the Delta. But these trees depend on summer water. The further upstream from the river’s confluence in the Delta, where groundwater is on the high side, the sparser the forest.

“There are fewer native tree species, and the trees are farther apart, and their mortality increases,” says Sara Sweet, a restoration ecologist at Cosumnes River Preserve, more than 50,000 acres of wildlife habitat and agricultural land managed by partners including The Nature Conservancy.

Besides revitalizing riparian forests, groundwater replenishment in the area may also help restore flows in the Cosumnes River. “It goes dry sometime in the summer and may not reconnect until January, depending on the rains,” Sweet says. “It’s dry when adult salmon are coming back in the fall.”

In the wet season, Regional San hopes to use recycled water to flood fields for sandhill cranes that overwinter in the region. These threatened birds, which stand as tall as four feet, roost in water as deep as one foot for protection against predators. The Harvest Water Program could flood 3,500 acres, enough for 700 cranes.

The triple win of benefiting farmers, the groundwater basin, and ecosystems drew widespread support for the Harvest Water Program. “It had no opposition whatsoever,” Mitchell says with a smile.

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