Fish Kill on Weems Creek in Annapolis, MD; Taken 9/10/07
Algal blooms deplete oxygen levels in water and can result in “dead zones” such as this one in Annapolis, Maryland along the Chesapeake Bay, an estuary like the San Francisco Bay. Photo courtesy of John Surrick/Chesapeake Bay Foundation (

Nutrients — such as nitrogen — are essential to life, but an overabundance can mean trouble for waterways. Take Chesapeake Bay and the Gulf of Mexico, which are infamous for “dead zones” where closely-packed bodies of fish float to the surface or wash ashore by the thousands. These dead zones are caused by nutrient pollution, which makes algae grow too fast. The resulting algal blooms ultimately kill fish and other aquatic creatures by using up the oxygen they breathe.

Nitrogen is high in the San Francisco Bay as well, but so far it has escaped the catastrophic effects of nutrient pollution. That may be about to change, however.

“Nutrients are one of the more substantial problems the San Francisco Bay may face over the long-term,” said the San Francisco Estuary Institute’s David Senn, lead scientist for the Bay Area Nutrient Management Program.

Besides causing dead zones, some algae produce toxins that kill fish and other aquatic life directly. These harmful algal blooms can also cause health problems in people — including rashes, respiratory issues, and liver illness — who swim in or accidentally swallow the water.

Why has the Bay been immune to nutrient pollution? “There’s inherent protection in the system,” Senn said, explaining that “one of the things keeping a lid on algae is sediment suspended in the water.” Algae need both nutrients and sunlight to grow, and sediment makes water cloudy, blocking the light.

But this protection may not last much longer. “The Bay is changing,” Senn said. Notably, sediment has decreased by as much as half in recent decades. Since the Gold Rush, sediment from pulverized rock has come down from the Sierra Nevada foothills and into the Bay. And now the last of that sediment is washing away. As the water in the Bay becomes clearer, algae get more light and can use the extra nitrogen in the water to grow more.

Most of this excess nitrogen comes from the 37 major wastewater treatment plants that discharge into the Bay. Sewage is full of ammonia — which contains nitrogen — and it goes straight through most treatment plants here. “The plants are treating waste from more than seven million people, and most do not treat nutrients,” Senn said, adding that “nutrient concentrations here can be two or more times higher than in areas where they are a problem.”

Nutrients are challenging to regulate, however. This is partly because, unlike toxicants, nutrients are needed and too little is as dangerous as too much. “They fuel the base of the food web,” said Naomi Feger, a planner with the San Francisco Bay Regional Water Quality Control Board. Another complication is that the impact of nutrients varies with environmental factors such as water depth and tidal mixing, which in turn vary across the Bay. “It’s not just the concentration, it’s also the conditions — the science will identify the parts of the Bay that are more vulnerable,” she said.

For now, rather than setting a cap on nitrogen, the Water Board wants to help keep anthropogenic sources out of the Bay. Some wastewater treatment plants are using or testing natural approaches for removing nitrogen. “Marshes process nutrients,” Feger explained, adding that “the Petaluma treatment plant has a created wetland and gets good nitrogen reduction.” Another example is the Oro Loma wastewater treatment plant in San Lorenzo, where effluent irrigates a “living levee” that slopes gradually from wetlands to uplands and is planted with native vegetation. Baykeeper, a nonprofit dedicated to stopping pollution in the Bay, is looking to see where else these approaches could be implemented, said Feger.

In addition, under a nutrient permit established by the Water Board in 2014, water agencies are required to explore ways of reducing the nitrogen in wastewater treatment plant effluent. The Bay Area Clean Water Agencies (BACWA) expects to submit a report detailing options and costs in the fall, said BACWA Executive Director David Williams.

According to the upcoming report, nitrogen could be reduced about 10 percent by optimizing current wastewater treatment plants. “They can use existing tanks to convert ammonia to nitrate, which is a form of lesser concern,” said Williams, who formerly was the director of wastewater of the East Bay Municipal Utility District. Then bacteria would convert nitrate to nitrogen gas, which would go “back into the atmosphere where it belongs,” he said, noting that the air we breathe is 80 percent nitrogen. Altogether, this would cost upwards of $220 million total.

Alternatively, nitrogen could be reduced about 17 percent by concentrating the nitrogen-containing organic material — such as feces and food scraps — and then treating this sidestream separately from the rest of the wastewater. The first step would be coarse screening to remove things like diapers, rags, and two-by-fours, Williams said, adding, “You’d be surprised what gets into wastewater.” The resulting organic sludge would then go into a tank with microbes, yielding methane that would be burned for energy, as well as biosolids that could be used as fertilizer. The sidestream approach would cost about $660 million total.

The most effective nitrogen reduction method is also the most expensive. Upgrading wastewater treatment plants would lower nitrogen 65 percent to 85 percent, depending on the type of upgrade, at a cost of $8 to $10 billion total, respectively. As in the first option, microbes would convert ammonia into nitrate, which would then be converted to nitrogen gas. The difference is that the upgrades would treat the nitrogen in organic sludge more completely.

Williams likes the local, collaborative approach to keeping nutrient pollution at bay. “The rest of the country has reverted to litigation to solve these issues, but we have a good process here,” he said. He also recognizes the need to regulate nutrients in the Bay: “It’s common sense — we can’t continue to have ever-increasing nitrogen. We will need to limit it.”

Robin Meadows covers water for the Monitor.