The scientists go out on the bay about 20 times a year to take careful measurements about what is happening to the water chemistry. Senior scientist Jim Cloern calls it "taking the pulse of the bay." He's been studying bay water since 1976.
Cloern's team travels on the Research Vessel Polaris, one of the oldest working federal boats on the water. It was built as a luxury yacht in 1927. Now, its elegant wood trimmed lounges have been repurposed as laboratories.
San Francisco Bay is constantly changing, according to Cloern. Right now, the drought has cut the flow of fresh water from rivers that feed the bay, so parts of the bay are unusually salty.
"We are seeing the highest salinities ever recorded in the 40 years we've been recording salinity in the bay," Cloern said.
The team usually samples water in specific spots over a 90 mile route, from the extreme South Bay all the way to the delta. It is a carefully choreographed routine, with elaborate high tech instruments, and each step is done exactly the same way each time.
"You have to move quickly," USGS biologist Charlie Martin said. "We collect a lot of samples at each station and there's not a lot of time between each station. Some of the samples are light sensitive, so we have to get them processed and preserved as quickly as possible."
Some of the changes being found in the bay are natural. Some are caused by humans. And it's not always obvious what's good and what's bad. For example, bay water has been getting clearer in recent years. It had been extremely murky for decades, mainly because of gold mining sediment that washed down rivers into the bay.
"There was something like a billion yards of sediment deposited in the bay in the 1860s, 70s and 80s," Cloern said.
Now all these decades later, the sediment is finally disappearing. That is good news, but it has a flip side too. As the water gets clearer, sunlight penetrates deeper. Jim said that has contributed to "a 3-fold increase in the amount of chlorophyll during the summer months." And that could eventually lead to a serious algae bloom, with dire consequences such as have occurred in the Chesapeake Bay on the East Coast.
Cloern said no one can predict yet what will happen, but "the worst case scenario would be recurrent fish kills and bird kills and public health problems." The USGS is part of a regional effort to make sure that worst case scenario does not happen here.
In the future that could mean long term changes in sewage treatment to keep the nutrients that fuel algae out of the water. But a change like that could cost billions of dollars. So, for now, Cloern's focus is to get local officials to commit to just monitoring the water "to develop a knowledge base so we can anticipate changes in the future."
Written and produced by Jennifer Olney