But now, several environmental groups are demanding action on a similar challenge, miles upstream from the Bay. They're focused on a toxic bloom that's become almost a yearly occurrence in and around the Delta.
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"And it produces a toxin that's acutely poisonous to people and their pets. So this, this will kill your dog if it gets exposed to enough of it and can make people very sick if they come in contact with a water. But also, the toxins and the cyanobacterial cells get aerosolized in a heavy wind. So it makes it sort of a hazard, even if you're walking near the waterway," said Jon Rosenfield, senior scientist with San Francisco Baykeeper.
VIDEO: Improvements eyed for San Francisco Bay in wake of algae bloom
Improvements eyed for San Francisco Bay in wake of algae bloom
The group has captured images of the bright green bloom near Stockton and Discovery Bay. While the exact causes are still being studied, Baykeeper and other groups have filed an emergency petition with the State Water Resources Control Board. The petition asks the board to increase the seasonal flow of water into the Delta from the San Joaquin River to a 40% level. They say this was laid out in an amended Bay-Delta plan. It's a move that some researchers believe could help fish and wildlife and potentially flush out the organisms causing the bloom.
"If we had those flow standards operational by next February, and then 40% of the river made it to the delta, through June of next year, it's possible that it could ameliorate the bloom that will happen next summer," adds Rosenfield.
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VIDEO: Harmful algae bloom spreading across San Francisco Bay, turning water brown
Harmful algae bloom turning water brown across SF Bay
The petition comes as the state of California wrestles with the future of water allocations divided between residential, agricultural and other users. Groups like Restore the Delta are helping to conduct a pilot survey to monitor and better understand the bloom cycles, and fill in gaps in the data. But they believe the flow issue is critical to any overall solution.
"If you're able to increase flow, it prevents water from being stagnant, obviously the first one. And if water is not stagnant, the water doesn't sit there and absorb heat energy, which is what helps drive harmful algal blooms. And then also, if the water isn't sitting, if it isn't stagnant, it's also making sure that nutrients aren't compounding at a single spot," says Spencer Fern, science coordinator with Restore the Delta.
VIDEO: Is it still safe to swim in Bay Area waters amid toxic algae bloom? Experts weigh in
Experts weigh in on safety of Bay Area waters amid toxic algae bloom
Baykeeper has also filed a lawsuit questioning whether the 40% flow standard is even enough. But in the meantime, they're hoping the petition process will spark movement towards increasing flows to that level.
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"And those potentially could be beneficial to ameliorate this harmful algal bloom problem. So we would want those, the current, adopted standard to be implemented, while we get a better standard, that will actually protect fish and wildlife to the level the board has said needs to occur," says Rosenfield.
Representatives from the State Water Resources Control Board say they can't comment on the flow level request yet, but could have more to say as the review process on the petition moves forward.