Keeping the Bay Blue

Sep 15, 2022
Sejal Choksi-Chugh
by Sejal Choksi-Chugh

A few years ago, during a strategic planning session, our legal and science teams brainstormed a list of 82 different threats to San Francisco Bay. As we evaluated where to focus Baykeeper’s resources, our staff scientist told us he believed the biggest threat to the Bay was nutrient pollution.

He described high levels of nitrogen and phosphorus in the Bay—due mainly to discharges from the 40 Bay Area sewage treatment plants—and he predicted the possibility of a devastating algal bloom turning the Bay red or green and completely destroying the Bay’s ecological balance. It was not a question of if, but when.

So Keeping the Bay Blue rose to the top of our priorities.

Over the following years, we dedicated staff time and energy to working with regional agencies to create a nutrient management strategy and a related nutrient pollution permit for the Bay. It made our fundraising team sigh, because while they understood the importance of the work, wonky nutrient issues do not make for sexy donation appeals.

But even though we had been preparing for the possibility, there are still some things you never want to see.

In July of this year, recreational users in the Alameda/Oakland estuary began reporting to our pollution hotline that the water looked reddish brown. People were concerned, asking what it was and whether it was safe to go in the water.

Baykeeper’s field investigators started sampling the discolored water, assessing the extent of the plume by drone, and updating the public. We alerted the agencies and waited for them to run the samples and diagnose the problem. But even before the test results were confirmed, our in-house science team knew we were facing a dreaded algal bloom.

The Bay has had algae blooms in the past. They’d mostly been concentrated in shallow waters, and the last one worth mentioning was way back in 2004. But the Bay had never seen anything like this. Within a week of those first hotline reports, the bloom rapidly spread to cover most of the Bay, turning the waters a murky brown.

Then, our pollution hotline began ringing again. Countless fish were washing up on the Bay’s shores: sharks and sturgeon, huge striped bass, stingrays, tiny minnows, and even mussels, crabs, and native oysters. It was a one-two punch. The algae were spreading and releasing toxins deadly to fish and, at the same time, dying off and sucking the oxygen out of the water, suffocating fish and other critters. The carnage reported by the local and national media was only the tip of the iceberg. Magnitudes more dead fish sank to the Bay’s floor and in places where no one could see.

The loss of so much life was sobering. And a wake-up call to do more.

While dry weather, bright sun, and warmer waters might have triggered this bloom event, excessive nutrient pollution from the Bay Area’s antiquated wastewater treatment practices fed the algae and helped it thrive. That’s why Baykeeper has doubled down to advocate for a significantly stronger permit that imposes stricter controls on nutrient discharges into the Bay.

We’re also urging Bay Area wastewater agencies to invest in upgrades on par with their Southern California counterparts that include wastewater recycling. This will cut down on the nutrients we flush into the Bay, make the Bay Area more drought resilient, and reduce the city’s dependence on fresh water from the Sierras. That’s a win-win-win for the Bay. And investing in treatment wetlands and natural marsh restoration will not only filter nutrient pollution out of wastewater discharges, but it will also increase shoreline resilience to sea level rise and protect local communities from toxic floods.

The solutions are out there to prevent another massive fish kill in the Bay. Let the Regional Water Board and the San Francisco Public Utilities Commission know that you don’t want the Bay to suffer through another toxic algal bloom. These agencies need to act now to protect our beautiful Bay and keep the waters blue and healthy for all.

In solidarity,



Sejal Choksi-Chugh, Executive Director

Join us to hold polluters accountable and defend the Bay DONATE NOW >