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Bay Primed for Pea Soup?

by Robin Meadows
Nutrients could be the next big problem for San Francisco Bay — or make that in the Bay, because they’re already here at levels high enough to have caused trouble elsewhere. But despite its excess nitrogen and phosphorus, the Bay has been free of harmful algal blooms and oxygen-depleted dead zones for decades. Indeed, we’ve been so sure of this immunity to nutrients that most wastewater treatment plants don’t even have to remove them before discharging into the Bay. Recent chinks in the Bay’s resistance to nutrients are now alerting us, however, to get ready in case there’s worse to come.

RMP water quality sensor playing host to animals called hydroids. Photo by Emily Novick, SFEI.
RMP water quality sensor playing host to animals called hydroids. Photo by Emily Novick, SFEI.

“The tricky part is the Bay’s response to nutrients is changing, but it’s not yet clear how best to manage them,” says David Senn, a scientist at the San Francisco Estuary Institute (SFEI). Another challenge is that because nutrients haven’t been troublesome here, we have a lot to learn about them in the Bay. “It will take a regional collaborative effort to understand how the Bay is changing and what regulatory actions to take,” says Naomi Feger, Planning Chief of the S.F. Bay Regional Water Quality Control Board. To accomplish this, the Board drafted a Regional Nutrient Management Strategy in 2012 in collaboration with SFEI, the Regional Monitoring Program, wastewater dischargers and other stakeholders. The goal is to develop monitoring and regulations that proactively protect the Bay from nutrient pollution, backed by solid science. Within this major initiative, Senn is coordinating an expert team to outline monitoring and research needs. “It’s a first step toward identifying the scientific issues we need to tackle,” he says.

The financial stakes for getting a handle on nutrients in the Bay are high. “It’s being called the most costly wastewater issue reorder in the Bay the since 1970s,” Senn says. Most of the nutrients come from the 41 wastewater treatment plants which discharge into the Bay, and retrofitting them could cost billions of dollars. In the North Bay, nutrients also come from agriculture and wastewater in the Central Valley and the Delta.

Why haven’t all those nutrients pouring into the Bay caused problems? The answer — based on nearly four decades of US Geological Survey work on the Bay’s large swings in phytoplankton abundance — is a combination of three things: suspended sediment, tidal mixing, and clams.

Algae needs light to grow but Bay water contains so much sediment that it’s murky. “It’s like overfertilizing a garden and then covering it with a tarp,” Senn says. “The nutrients are there but the other key ingredient, sunlight, is missing.” In addition, algae often grows best in estuaries where the entering fresh water floats across the surface. This creates a top layer that concentrates phytoplankton and keeps them near the light. But here, the Bay’s strong tides usually break up fresh water layers before algae can bloom. The third factor is large populations of clams and other bottom-dwelling filter feeders that can eat phytoplankton as fast as it can grow.

So what’s changed? “At least two of the three factors that increase resistance to algal growth,” Senn says. Suspended sediment is down by half since the 1990s in the North Bay and South Bay, letting the algae-boosting light shine twice as deep into the water. This trend toward clearer water is expected to continue because excess sediment from the Gold Rush is thought to have finally washed away.

Another change is that clam populations are down sharply in the South Bay, coinciding with a three-fold algae hike in those waters since the 1990s. The drop in clams and other bottom-dwelling algae eaters may be due to a rise in predators like fish and Dungeness crab, which in turn is linked to a shift in large-scale, long-term ocean patterns called the Pacific Decadal Oscillation.

So far there’s less concern about the amount of algae than about the pace of change. “Algae levels were low before so it’s not like the Bay is pea green now,” Senn says. “But it changed at a fast rate.”

Monthly-average estimated dissolved inorganic nitrogen and phosphorous (DIN & DIP) loads to San Francisco Bay subembayments in kilograms per day based on data from 2006-2011. Colors indicate source (POTWs = publicly owned treatment works, i.e., wastewater treatment plants; storm water; refinery, or upstream inputs), and with loads specified in terms of NO3 (nitrate) and NH3 (ammonia/ammonium), or as DIN (NO3+NH3), depending on source. Loads to San Pablo Bay include estimates of loads entering from Suisun Bay (labeled “Upstream” in the San Pablo panel). Loads to Suisun Bay include loads entering from the Delta (labeled “Upstream” in the Suisun panel). See Novick and Senn 2014 for more details (link at page bottom).
Monthly-average estimated dissolved inorganic nitrogen and phosphorous (DIN & DIP) loads to San Francisco Bay subembayments in kilograms per day based on data from 2006-2011. Colors indicate source (POTWs = publicly owned treatment works, i.e., wastewater treatment plants; storm water; refinery, or upstream inputs), and with loads specified in terms of NO3 (nitrate) and NH3 (ammonia/ammonium), or as DIN (NO3+NH3), depending on source. Loads to San Pablo Bay include estimates of loads entering from Suisun Bay (labeled “Upstream” in the San Pablo panel). Loads to Suisun Bay include loads entering from the Delta (labeled “Upstream” in the Suisun panel). See Novick and Senn 2014 for more details (link at page bottom).

Other signs of cracks in the Bay’s resilience to nutrients include less dissolved oxygen in places where algae is highest. Microbes that eat dead algae also use oxygen, so algal blooms can lead to dead zones in the water. Also troubling was a rare red tide or undesirable algal bloom in the fall of 2004. In addition, small amounts of algae that cause toxic blooms elsewhere are beginning to pop up here too, and recent monitoring has also detected toxins from harmful algae in the Bay. However, Senn stresses that we can’t tell if this is related to nutrients — or if it’s even a change — because this monitoring has only been underway for a few years.

Besides affecting the quantity of algae, nutrients may also affect their quality. While low algae levels are thought to contribute to the dearth of small fish that larger animals eat in Suisun Bay and the Delta, now a new idea implicating high nutrient levels is being floated. For example, recent studies suggest that high levels of nutrients could dampen the growth of ‘good’ algae or encourage the growth of ‘junk’ algae not favored by small fish in Suisun Bay. More research is needed to test this hypothesis, however.

Indeed, more research is needed on just about all aspects of nutrients in the Bay. Right now, we don’t know much beyond the facts that algae are rising in parts of the Bay, low levels of potentially harmful algae are common, and algal toxins are detectable. In fact, we don’t even know if nutrients are behind what we see. “We need to understand the problem better to help identify the most effective fix,” says Senn.

That’s where the expert team he coordinates comes in. Their report, due out this month, outlines what we know, what we need to find out, and what a range of plausible scenarios might mean for algae in the Bay. Questions include: Will suspended sediments keep dropping? Do high nutrients really tip the phytoplankton balance toward kinds not favored by small fish? Will clam populations rise again after the next shift of the Pacific Decadal Oscillation? How will the changing climate and changing shoreline affect the nutrient balance? And can we keep nutrients out of the Bay in the first place?
The first step to finding answers is a Bay-wide monitoring program aimed at nutrient pollution. Current monitoring is spotty for key measures like nutrients, kinds of algae, algal toxins, dissolved oxygen, and clams, and also lacks sustainable funding.

Besides being costly, stemming the flow of nutrients into the Bay could take decades. Says Senn, “If problems are on the horizon, starting before they are widely entrenched will give us more flexibility.”

“We’re taking this seriously,” adds Feger, whose agency already has a draft regional permit addressing nutrients in wastewater discharges throughout the watershed out for public review. “We don’t want to experience the problems we see elsewhere in the country.”

CONTACT: Naomi Feger, David Senn

USGS Plankton & Water Quality Monitoring
SFEI Documents & New Reports
RMP Report Novick and Senn 2014

About the author

Robin Meadows is an independent science journalist in the San Francisco Bay Area. She covers water and climate change adaptation for Estuary News, is the water reporter for the Bay Area Monitor, and contributes to Bay Nature, Frontiers in Ecology and the Environment, PLOS Research News and Water Deeply. Robin also enjoys hiking and photography.