After years of searching high and low for a culprit in the collapse of Delta fish populations, scientists are learning the problem may lie right under their noses.

The likely fish killer is ammonia, a common byproduct of human urine and feces.

Sacramento's regional sewage treatment plant is the largest single source of ammonia in the Delta. It discharges treated wastewater from nearly 1.4 million people into the Sacramento River near Freeport – without removing ammonia.

Two recent studies by Richard Dugdale, an oceanographer at San Francisco State University, show that ammonia disrupts the food chain in the Sacramento-San Joaquin Delta.

The discovery, if it holds up to further scientific review, reveals how just one factor can tilt the Delta's complex ecological balance. It also illustrates how fixing the Delta will be a costly task for many California residents who mistakenly assume their lives are not connected to the estuary.

Boaters cast their fishing lines last week on the Sacramento River,
just south of the Freeport Bridge. Two recent studies suggest that
ammonia, a byproduct of wastewater released from the regional sewage
treatment plant, harms the food chain in the Sacramento-San Joaquin Delta.
(Photo by José Luis Villegas)

The Sacramento Regional County Sanitation District estimates it needs as much as $1 billion to remove ammonia from the metro area's wastewater. Monthly sewer bills would have to triple throughout the region.

"We're not going out on the edge to say this is the whole answer," said Dugdale, co-author of the studies along with others at the university's Romberg Tiburon marine lab. "But we think it's part of the reason for the decline in (ecological) productivity."

Ammonia in the river does not make fish unsafe to eat, nor does it pose a threat to recreation. It does, however, seem to interrupt a natural food production line that would otherwise yield abundant blooms of tiny aquatic animals to feed salmon, smelt and bass, Dugdale said.

Those species have been in steady decline.

The ammonia threat was dramatically illustrated last May when dozens of chinook salmon showed up dead in the San Joaquin River near Stockton's sewage outfall. Anke Mueller-Solger, an environmental scientist at the state Department of Water Resources, said the fish may have been killed by high levels of ammonia in the wastewater.

Sacramento's effluent problem is slightly different. Rather than high concentrations of ammonia, the threat is the enormous volume of ammonia-laced wastewater. The regional sewer agency treats human waste from Sacramento, West Sacramento, Folsom, Carmichael, Rancho Cordova, Elk Grove and other unincorporated communities.

The plant near Freeport each day releases about 146 million gallons of treated wastewater into the Sacramento River. That's enough to fill about 225 Olympic-size swimming pools daily.

Despite this volume, Mueller-Solger said, the Sacramento River is traditionally considered the Delta's lifeblood, because it provides the vast majority of fresh water entering the estuary.

"But there is this big urban area called Sacramento and it's been growing like gangbusters," she said. "Obviously, sewage is produced proportionally to the number of people, so the water's perhaps not quite as nice and clean as we thought."

The ammonia load in Sacramento's wastewater has more than doubled since 1985 due to rapid urbanization, and is now more than 125,000 gallons per month. That's 10 times more than the Stockton sewage plant.

To handle more growth, the regional sewer agency is planning a major expansion that would allow total discharge volume to grow 30 percent. The plan includes no ammonia controls.

"This is a cost of growth that is too often externalized onto a degraded environment," said Bill Jennings, executive director of the California Sportfishing Protection Alliance and longtime Delta water-quality watchdog.

Jennings called it "simply reprehensible" that the sewer agency hasn't already improved its systems to remove ammonia and other contaminants.

Sewage officials counter that they have a responsibility to ratepayers. They estimate upgrading the wastewater treatment plant to filter out ammonia would cost $740 million. To remove excessive nitrates produced as a byproduct of that treatment would raise the cost to $1 billion.

District engineers estimate these steps together would boost sewage rates in the region from $19.75 per month to $62.17.

"If it's causing a problem, I think we have to recommend going to that," said Mary Snyder, district engineer. "But on the other hand, we don't want to leap into anything precipitously simply because of the effect on ratepayers. The average person is going to object to paying that much."

Dugdale's research suggests the volume of human wastewater may be starving Delta fish by shutting down food production.

It works like this:

• Young fish eat small animals in the aquatic food chain, called zooplankton. The zooplankton, in turn, feed on diatoms and other phytoplankton.
  
  
• Phytoplankton require nutrients in the water and enough sunlight to bloom in sufficient numbers. Nitrates are the favored nutrient. Ammonia is another.
  
  
• For reasons that remain unclear, phytoplankton can't feed on nitrates when there is too much ammonia in the water, Dugdale said. They must eat the ammonia first, and by the time that's gone, the phytoplankton bloom dies out before it gets big enough to feed fish.

In addition, ammonia is preferred by a bad breed of phytoplankton, called mycrocystis. A toxic type of algae, it has begun to replace more nutritious phytoplankton that normally dominate the food chain. So ammonia may also encourage the rise of harmful foods.

The phenomenon is especially important in Suisun Bay, Dugdale said. The shallow bay near Pittsburg is a vital feeding area for young fish in spring.

New studies are under way to explore the problem further and confirm whether Sacramento's sewage is the true cause.

"If it's part of the problem, it's big because there's so much of it," Dugdale said. "The river just could never handle that amount and reduce it by the time it gets to Suisun. It just can't absorb that."

Sacramento's regional sewage plant uses a so-called "secondary" treatment process that has become outdated. Most other urban areas have upgraded to "tertiary" systems that add rigorous filtration steps.

Sacramento has been able to avoid this expense so far, Snyder said, because its wastewater is quickly diluted to legally acceptable levels by the strong flow of the Sacramento River.

"We are a very large discharger," Snyder acknowledged. "But when you look at the Sacramento River, we have a small impact on the river."

Sacramento may not be able to rely on this free dilution as urban growth continues.

In November a Sacramento Superior Court judge ruled against the district on a number of points in a lawsuit against the environmental impact report prepared for the planned sewer expansion. The suit was filed by many of the water agencies that divert drinking water from the Delta to serve more than 20 million people throughout California.

Importantly, the court ruled that the Sacramento district "ignored a significant component of the environment" by failing to fully assess the additional nutrients pumped into the Delta in the region's wastewater.

Ammonia is one of those nutrients. The sewer district appealed the ruling.

"We had long discussions with them, before we got to the point of a lawsuit, on ways they might be able to offset their discharges," said Greg Gartrell, assistant general manager at the Contra Costa Water District, the lead plaintiff in the case. "They just weren't willing to entertain any of those issues yet."

Mueller-Solger at DWR noted that, compared with other problems in the Delta, the ammonia threat can be fixed if further research confirms it to be a danger.

There is no ready fix for the predicted sea level rise that could overwhelm Delta levees, nor any practical way to remove foreign species invading the estuary. But technology exists to remove ammonia from wastewater.

"It's expensive and it's sometimes hard to push through, so it needs the political will. But it's possible," she said. "To me as a scientist, it's not about finger pointing. We are all in this together."