The good news comes with a downside, though. Scientists say the clearer water lets in more sunlight, which is causing more algae to grow in the bay.
Scientists monitoring the situation are concerned that new regulations may need to be imposed on the 42 sewage treatment plants around the bay if the algae growth isn't slowed significantly. The regulations would force the treatment plants to reduce the amount of nitrogen and phosphorous they pour into the bay. Nitrogen and phosphorous fertilize the algae.
The regulations could cost the sewage plants $10 billion, an expense that could lead to high sewage bills.
"It's a high-priority issue," said Naomi Feger, planning division chief of the San Francisco Bay Regional Water Quality Control Board in Oakland. "Our goal is to avoid serious water quality problems."
Feger said the water board will work to set limits for nitrogen and phosphorus. Scientists will also start computer modeling to determine if sewage plant operations can be changed to reduce algae growth before introducing regulations.
Feger said any new rules are at least five years away.
Starting in 1853, many gold miners used water cannons to blast away entire hills in the Sierra Nevada. The resulting sludge flowed into nearby rivers and slowly flowed into the bay. A judge halted the practice in 1884 as a "public and private nuisance," but the damage was done and the bay was clouded over for more than a century.
"If you applied a bunch of fertilizer to your garden but put a net over it that kept out the sun, that would prevent your plants from growing," said David Senn, a senior scientist at the San Francisco Estuary Institute. "If you removed that shade, your plants would grow more rapidly."