Of Mice and Marshes: Surveying Salties to Save Them

Of Mice and Marshes: Surveying Salties to Save Them

It’s five in the morning, and Don Edwards San Francisco Bay National Wildlife Refuge remains in the tight velvet grip of night. All is peaceful and quiet, despite the fact that the toll plaza of the Dumbarton Bridge is less than a quarter-mile away. By 5:15, car dome lights and slamming doors have transformed this lonely spot at the watery edge of Newark into a hub of activity. People are taking last sips of coffee, strapping headlamps to their foreheads,...
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Over time, the median actual flow to San Francisco Bay in the ecologically critical winter and spring months has declined to less than half of the unimpaired runoff. This bar chart divides actual inflow (the amount that actually made it to the Bay) and unimpaired runoff (the inflow to the Bay that would occur if there were no dams or diversions) into quintiles from wettest to dry, and marks years drier than 2015 (roughly, the driest 2% of years) as “super-critically dry” years. Over the last 54 years, “super-critically dry” runoff conditions in the Bay’s watershed occurred naturally only once, in 1977, but the Estuary received runoff volumes in the super-critical range in 22 years, or 40% of the time. Overall, flow volumes characteristic of the driest 20% of years now occur more than half the time as a result of storage and diversion of runoff for consumptive uses. Source: The Bay Institute, based on data from California Department of Water Resources.

Defining Unimpaired Flows

For the second time in four years, a proposal for a voluntary agreement between agencies and water contractors on flows into and through the Delta from the San Joaquin and Sacramento rivers and their tributaries is wending its way through the State Water Resources Control Board. The proposal, which would replace the regime outlined in the Board’s most recent update to the Bay-Delta Plan, calls for substantially less water remaining in the system than the update, but comparing the two...
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Bagman for Bay Mussels

Martin Trinh practically bounces along the dock at the Coyote Point Yacht Club on a breezy, sunny spring morning. He’s carrying a case full of instruments and scopes out an open slip at the end of the pier. Soon he’s lowering a probe into the water, alongside kelp clinging to the underside of the dock. Another trip back to his Prius, still sporting South Carolina license plates, and he’s got a white plastic dish pan and a scrub brush. He...
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Eyeballing the Fish

Longfin smelt were what hooked Jim Ervin when he first learned about the UC Davis South Bay Fish Survey through a presentation at the 2012 Bay-Delta Science Conference. “They were catching them right there in our effluent channel!” recalls Ervin, a self-trained naturalist and former compliance manager for the San Jose-Santa Clara Regional Wastewater Facility. Intrigued, he contacted the researchers, rode with them on their next survey, and has been part of the project ever since, devoting more time to...
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Gone Fishing

As the weekend dawns and California slumbers, the sportfishers descend, like clockwork, on the banks and waves of the San Francisco Bay and Sacramento-San Joaquin Delta. They carry nets for herring or poles for sturgeon, heavy and light tackle, bloodworms or anchovy or any number of delectable morsels to attract the desired target. They tread industrialized East Bay shorelines and marshy Delta banks, hop aboard sporty six-pack boats for more ambitious trips or humbler craft for a leisurely solo excursion....
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South Bay Trawls Show Fish Like Restored Shores

Twelve years ago, scientists at UC Davis began a survey of the southern end of San Francisco Bay — the Lower South Bay — to see how fish responded to the South Bay Salt Ponds Restoration Project. They discovered an unexpectedly diverse and robust aquatic community and a previously unknown spawning ground for the longfin smelt (Spirinchus thaleichthys), listed as endangered in California and a candidate for federal protection because of its declining numbers. The team, led first by Jim...
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Murky Future for Herring

This winter, herring spawns in San Francisco Bay – visible from land as frenzies of birds and pinnipeds and even water discolored by herring milt – have been few and far between, according to recreational fishers who pursue the fish each year using hand-thrown cast nets. With few other eyes on the resource, it seems reasonable to assume that the downward trend in biomass documented through the 2019-2020 winter has continued. But nobody knows for sure. For decades, the California...
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Natives Who Can Rough It

Name a native fish. One that spends lots of time in the Delta. One that’s not a salmon, smelt, or sturgeon. One whose population isn’t plummeting, and in fact seems to be doing just fine. By now the list of possibilities has been shortened severely — though not exhausted. A number of native fish still ply Delta waters in stable numbers, but precisely because there are no restoration projects, monitoring programs, or conservation efforts designed to save them — or...
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Let’s Not Forget Suisun Marsh

I started sampling the fishes of Suisun Marsh in 1979 because one of my UC Davis graduate students was looking for a place to study tule perch, a live-bearing native fish. We found not only a lot of tule perch in the marsh, but also an abundance of other native fishes. Clearly, this was a good place to study species for which we had little information at that time. Two things helped with our new project. First, sampling boats could...
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Sturdy Sturgeon

A 90-year-old Australian lungfish at San Francisco’s Academy of Sciences has received a lot of press lately, but there is a wild fish species living in the San Francisco Bay that has the potential to live that long or longer — or so we think. While one white sturgeon caught in the Columbia River Basin was estimated to be 104 years old, the life expectancy of white sturgeon, Acipenser transmontanus, which includes the Central Valley population endemic to the San...
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Bay Fish Still Not Good Eating

After decades of efforts to clean up San Francisco Bay, its fish still carry a toxic load that makes them unfit for human consumption. A new Regional Monitoring Program (RMP) report on its 2019 sport fish survey contains some positive news: an overall decline in polybrominated diphenyl ethers (PBDE), hopeful trends in polychlorinated biphenyls (PCBs) and dioxin, and continued low selenium levels. But no downward trend was found for mercury. Then there are per- and polyfluoroalkyl substances (PFAS), which the...
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sunset delta climate map

MEGA-PEARLS Part 4-Climate, Bay-Delta Science Conference, April 2021

A Stream of Science Takeaways. ESTUARY News sent reporters to the biennial Bay-Delta Science Conference in September. This special edition of Pearls shares more than 20 takeaways.
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Science-in-Short ~ Podcast

Drift, Drop or Floc? Tailing Sediment as it Moves Through Marsh Margins This June two USGS scientists will be trying to get as close as they can to the edge of the South Bay’s Whale’s Tail Marsh to lay out their tools: tiles, filter paper, current profilers, and other sediment accretion measuring instruments. Estuary Reporter Ariel Rubissow Okamoto interviews reseachers Jessie Lacy and Karen Thorne about what they’re looking for at the marsh edge, and how it may help us...
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pesticide resistance delta map

MEGA-PEARLS Part 3-HABs & More, Bay-Delta Science Conference, April 2021

A Stream of Science Takeaways. ESTUARY News sent reporters to the biennial Bay-Delta Science Conference in September. This special edition of Pearls shares more than 20 takeaways.
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photo of salmon injection USFWS

MEGA-PEARLS Part 2-Fish-Birds, Bay-Delta Science Conference, April 2021

A Stream of Science Takeaways. ESTUARY News sent reporters to the biennial Bay-Delta Science Conference in September. This special edition of Pearls shares more than 20 takeaways.
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Above: Lewis holding white sturgeon in Delta. Photo: Jim Ervin

MEGA-PEARLS-Part 1-Diversity, April 2021

A Stream of Science Takeaways. ESTUARY News sent reporters to the biennial Bay-Delta Science Conference in September. This special edition of Pearls shares more than 20 takeaways.
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As agencies wrangle over how best to protect the Delta’s dwindling native fish species, researchers want to see more consideration to the needs of the estuary’s birds.

 “If we want to restore the ecology of the Delta, we can’t just be looking in the water,” says Kristen E. Dybala of Point Blue Conservation Science. In a paper published in San Francisco Estuary and Watershed Science, Dybala and two co-authors make the case that “birds and their habitat needs are often not addressed in science syntheses, conservation planning, and large-scale restoration initiatives in the Delta.” While some birds use the same sloughs and channels that support such high-profile...
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Human activity could undermine the success of efforts to reintroduce sea otters to San Francisco Bay.

 Although past studies have found that the Bay could support 1.5 times the entire current southern sea otter population, a new study from the Estuary & Ocean Science Center at San Francisco State University and published by PeerJ last November indicates that anthropogenic risks like contaminants, vessel traffic, and oil spills may constrain the otter’s ability to gain a foothold. The study, led by Jane Rudebusch, at the time graduate student at SFSU, looked at the types of human stressors...
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The increasing flow of microplastics entering San Francisco Bay from trash, fleece clothing, car tires, and myriad other sources is likely being trapped by a surprising filter: native eelgrass (Zostera marina).

Miniscule polymer pieces the size of a sesame seed or tinier, microplastics pose a growing pollution threat to marine environments worldwide. To understand how microplastics accumulate in nearshore, urbanized environments, researchers quantified the prevalence of microplastics in and around the Zostera marina meadows of Deerness Sound, in the Orkney Islands of Scotland. Mark Hartl and colleagues at Heriot-Watt University found that microplastic flakes, fibers, and fragments were twice as concentrated in the water above eelgrass meadows as in adjacent control...
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Spawning and rearing habitat for important forage-fish species in San Francisco Bay apparently shifts geographically by many miles depending on how much freshwater is flowing into the Estuary.

In a recent study, a team of scientists found that in a dry year, Pacific herring and longfin smelt larvae occurred farther up the Estuary than in a wet year, when spawning and recruitment was pushed seaward. The results suggest that the fish have broader geographic ranges than previously believed, a finding that could inform efforts to manage and protect their habitat. Biologists have long assumed that longfin smelt, a protected species in steep decline for decades, spawn strictly in...
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