VA Agreement Highlights Habitat Questions

Restoring marsh and wetland habitat can have significant benefits for dozens of species throughout the Bay and Delta—that’s beyond dispute. But when it comes to saving the Estuary’s most imperiled fish, how much habitat improvements can help in the absence of dramatically increased freshwater flows is a question that has dogged and divided scientists and […]

Lookout Slough Restoration will be the Delta’s Largest Yet

When the restoration of Lookout Slough is complete, Lookout Slough will be no more. Created to provide water for a century-old duck-hunting club, the human-made canal will be filled in as part of a $119 million, 3,400-acre tidal wetlands restoration, the largest ever in the Sacramento-San Joaquin Delta. “Drought and climate change have elevated the […]
Vogel Island after breaching during first filling. Photo: EIP/Bill Arnerich

The Long Haul to Restore San Joaquin Spring-Run Chinook

When a team of fish biologists was tasked with restoring spring-run Chinook salmon in the San Joaquin River in 2006, none of them quite knew where to begin. The thirsty farms that crowd the river on both sides had taken almost all the water out of it most years since the mid-1900s, leaving a nearly […]

Rocky Road to a Fresh Enough Delta

Nothing reveals just how much the upper Estuary's seesaw of tides and freshwater flows is micro-managed than prolonged drought, and the resulting fiddling with barriers, gates, and water quality standards to prevent the ocean tides and salinity from intruding too far upstream. Come summer, managers begin to talk fearfully of "losing control of the Delta" […]

The Tunnel Plan: Thoughts a Month Later

It’s now five weeks since Governor Newsom’s Delta tunnel plan was unveiled in a Draft Environmental Impact Statement. Time enough for the main ideas to sink in; time enough for familiar players to strike their familiar positions; and time enough for some of us to burrow deep into its tables, figures, and appendices. To recap […]

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 […]
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.

Reorienting to Salmon Recovery

The days when salmon and steelhead teemed in California’s coastal watersheds faded away last century. Today, many populations of the fish are gone or dwindling, the river systems where they spawn drained by diversions or too warm for native fish to survive. Warming trends and drought are squeezing water resources tighter. Nearly all efforts to […]

Living with a Novel Landscape: Suisun Evolves

Morning at Suisun Marsh is a living watercolor with a soundtrack. Miles of tule and pickleweed populate the foreground, split by canals glinting silver from the sun. In May, the hills undulate across the northern boundary in classic California gold. A red-tailed hawk’s iconic hoarse screech punctuates the insectine buzz as it takes off from […]
Adrienne Ernst among the Phragmites. Photo: Michael Adamson

West Coast Salmonids All Tired Out?

West Coast salmon and steelhead populations have declined steeply in the past century – a plight that biologists have primarily blamed on habitat loss. Dams, for instance, block adult fish’s access to historic spawning grounds, and juvenile survival is impacted by streamside development and water diversions. Now, it turns out, microplastic pollution may be a […]

Will Salmon Simmer Again?

After two critically dry years that coincided with Trump-era rollbacks to environmental protections, some iconic Delta fish are closer than ever to the point of no return. Last fall, for the second year in a row, the fall midwater trawl found zero wild Delta smelt, while a coalition of environmentalists and fishermen is asking a […]

Hatchery Delta Smelt Released to Wild

On a mild day between rainstorms in mid-December, wildlife biologists outfitted in rubber boots and orange lifejackets load drum after drum of precious cargo onto a small boat docked in Rio Vista, a town on the Sacramento River in the Sacramento-San Joaquin Delta. There is little fanfare but the occasion is nonetheless momentous. The shiny […]

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) […]

The Coast Whisperer

Sam Schuchat, outgoing chief of the California State Coastal Conservancy, is perhaps one of the most dapper state officials I’ve ever met. He often wears an elegant hat with a brim and band, no Giants bill cap or REI wooly for the leader of a powerful state agency, one that has done more to ensure […]

Invasive Mussels Hide in Aquarium Moss Balls

A few weeks ago, someone working in a big-box pet store in the Seattle area informed the U.S. Geological Survey that they had seen suspicious mollusks in ornamental aquarium plants that were being offered for sale. Federal scientists confirmed the presence of zebra mussels tucked away in a clump of Aegagropila linnaei, a green alga […]

Flow Rules Stalled As Tunnel Advances

As California stares down the barrel of yet another dry year, alarm bells are already ringing over conditions in the Delta. Environmental groups, fishermen, tribes, and a host of others are calling on the State Water Resources Control Board to complete and implement a long-delayed update to the Water Quality Control Plan for the Bay […]

Bay Oil Spills: Never Again, and Again

Oil spills in San Francisco Bay are frequent news, but for those old enough to remember there is only one Great Oil Spill, the disaster of January 18, 1971. In a predawn darkness thickened by heavy fog, two small Chevron tankers were maneuvering through the strait. At San Francisco’s Pier 45, Coast Guard technicians were […]

Science-in-Short ~ Sea Level Rise Podcast

In this podcast, Julie Beagle, a former lead scientist at the SF Estuary Institute now the Army Corps, tells what she calls "wicked scary" sea level rise stories. Beagle also describes several kinds of “nature-based” treatments that can delay and soften the onslaught and also addresses the problem of scale.

Science-in-Short ~ Aquatic Weeds Podcast

Wall-to-Wall Sampling of the Delta’s Aquatic Weeds Via Remote Sensing, an interview with Shruti Khanna.  In this episode of the podcast, Estuary News reporter Daniel McGlynn talks to Dr. Shruti Khanna, a senior environmental scientist at the California Department of Fish and Wildlife. Their conversation focuses on Khanna’s use of remote sensing technology to study […]

Nursing Salmon on Flooded Farms

In 2012 a team of salmon researchers tried a wild idea: putting pinky-sized Chinook on a rice field in the Yolo Bypass, a vast engineered floodplain designed to protect the city of Sacramento from inundation. The team found that rearing fish on farms works better than they had ever dreamed. Salmon in this managed floodplain […]

The Delta’s Blooming Problem

Bright-green blotches of algae have been popping up all over the Delta since early summer, from Discovery Bay to the Stockton waterfront, befouling the air and poisoning the water with toxins that can sicken or even kill humans and animals. Veteran Delta watchers believe that this year’s harmful algal blooms may be the worst ever, […]

Match Points in Stormwater Soup

Effluent from wastewater treatment plants is often seen as the primary source of emerging contaminants in San Francisco Bay. But a report published in July by the Regional Monitoring Program challenges that assumption by highlighting the importance of urban stormwater runoff as another major source.

Makeover for Delta Weed Patch & Salt Trap?

What began as a project to convert a submerged Delta island into habitat for endangered native fish has morphed into a multi-benefit package with additional payoffs for water quality and recreation. The collaborative design process for the Franks Tract Futures project brought initially skeptical local stakeholders on board and is being hailed as a model […]

Forty Miles of Creek, Six Adaptation Projects

In 2017, a perfect storm hit the City of San Jose in Santa Clara County. Coyote Creek, which winds through the heart of the city, overtopped its banks, flooding businesses and hundreds of homes up to depths of six feet. Thousands of people were evacuated and property damages exceeded $70 million. “If I’ve learned anything […]

Kinky Fish Spines Linked to Selenium

Scientists with the U.S. Geological Survey and the National Oceanic and Atmospheric Administration are using new tools to track selenium, with the Sacramento splittail, a California-endemic fish, as an indicator species. In some sampled splittail, selenium levels exceeded the proposed EPA protective criteria for fish ovaries.

Network Listens for Passing Salmon

It’s a cold morning in early February, and Chris Vallee of the U.S. Geological Survey is motoring upriver along Steamboat Slough. His two-man crew is hunched in the bow with backs to the wind, wrapped to the ears in water-resistant jackets above warm layers. Vallee pilots the vessel in relative comfort behind the shelter of […]

State Plan Doubles Down on Alignment

The California Water Plan Update 2018—released by the Department of Water Resources in July—is meant to guide state policy and investment over the next 50 years to maximize the benefits squeezed out of every drop of the water supply. The timing of Update 2018 is fortuitous. In April, Governor Newsom ordered the California Natural Resources […]

Just Shy of Splendor in the Grass

Tobias Rohmer and Ben Chen’s careful work in Hayward’s Cogswell Marsh represents one small moment in the massive, nearly 20-year-old Invasive Spartina Project. Treatment of the southern section of Cogswell marsh was halted in 2011, however, due to concerns about Ridgway’s rails who’d made homes in the invader. “Complete eradication has been and still is […]

True to the Trail

A small group of friends are walking the entire San Francisco Bay Trail by tackling one segment at a time, in order, once a month. After two years, they have covered more than half the trail, both the finished, and as best they can, the unfinished portions.

Next Day Delivery: PCBs, Plastics, and Mercury All in One Package

The slow, downstream chemical migration of legacy contaminants like mercury and PCBs into the Bay is something that Lester McKee and his colleagues at the San Francisco Estuary Institute hope to cut short. “The sooner we can stop the inputs of these contaminants,” says SFEI’s Alicia Gilbreath, “the sooner the Bay can have a chance […]

Needed Now: A Big Blue-Green Push

From rain gardens to green streets to permeable parking lots and pebble dunes, landscape architects and resource managers are working to soften up shorelines and sidewalks, all to sponge up and filter stormwater runoff before it reaches the Estuary. This article details projects in the South Bay Salt Pond Project’s Eden Landing, Hayward’s Turner Court, […]

Brinkmanship for Frail Smelt

Delta smelt had a bad year in 2017. Although scientists are still analyzing the data, the message seems to be that strong freshwater flows alone are not sufficient to allow the population to increase. The resulting sense of urgency has led fish biologists to consider how cultured smelt, raised in hatcheries, could be used to […]

Wildlife and Way of Life in the North Delta?

There may not be a way to give everyone what they want from the Delta. But there are ways to restore ecosystems while preserving local communities. This is true even along State Route 160, which traverses the most populated and most intensively farmed part of the region. The highway follows the Sacramento River into the […]
Sandhill crane

Choppy Waters for Flow Rules

By Cariad Hayes Thronson The winter kicked off with the State Water Resources Control Board’s December vote to adopt increased flow objectives for the southern Delta. The vote provoked an immediate volley of lawsuits, both from water users and from environmental organizations. The water users claim that the required flows would be an unconstitutional waste, […]

Putah Creek Pipeline for Salmon

By Robin Meadows “The dream is to reestablish a natural run of salmon in Putah Creek,” says UC Davis professor emeritus Peter Moyle. In 1972 Putah creek was a trickle of water between heavy machinery mining gravel for the campus roads. Moyle and others urged the university to cease mining and by the end of […]

Greening Dickson’s Heights

Looking east from the levee-top trail, a silvery swath of bay is dotted with low islands. This is low tide at the nearly 1,000-acre Sears Point wetland restoration project on the western side of San Pablo Bay. “Without the mounds, you would just have a big area of open water,” says Julian Meisler with Sonoma […]

River Flows on the Brink

It was a rare decisive moment in California water. On December 12, the State Water Resources Control Board resolved, at the close of a marathon meeting, to require more water to be left in the Tuolumne, Merced, Stanislaus, and lower San Joaquin Rivers.

Spring-run Salmon Need More Than Simple Answers

Salmon once flourished in California despite huge swings in climate that were far more extreme than those today. But then people re-engineered the state’s waterways to meet their own needs. “Complexity is what salmon thrive on, and we’ve been making their habitat simpler and simpler,” says biologist Bruce Herbold.  “We haven’t been playing to their […]

Recent Milestones for the Twin Tunnels and WaterFix

Spring and summer 2018 saw frenzied activity around California WaterFix, the latest iteration of a decades-long, on-again-of-again effort to convey fresh water from the Sacramento River to the South Delta while bypassing the Delta itself. Governor Jerry Brown has made WaterFix a top priority, but the project – including twin tunnels comprising the largest infrastructure […]

Kitchen Sink Update on Every Last Invader

On multiple fronts, with multiple forces and weapons, California’s battle against invasive aquatic organisms continues. Notoriously, San Francisco Bay is the world’s most invaded estuary. The state’s lakes, rivers, and other freshwater wetlands have their own problematic exotics. Keeping them out, and preventing their spread once established, requires coordination among agencies and levels of government.

Locals Trade Vines for Resilient Rivers

In 2002, when stretches of the Napa River running through Rutherford area vineyards breached levees and flooded yet again, Michael Honig did something remarkable: rather than call the authorities to complain, his neighbors and he banded together to restore their riverbanks. “It had became a kind of competition,” Honig says.

Non-Sticks Stick Around

Common coatings and repellants used in textiles for clothing and furniture are sticking around in San Francisco Bay. “The reason for the lack of declines is not clear,” says researcher Meg Sedlak of the San Francisco Estuary Institute. Some early environmental offenders in this line of fluorinated chemicals (PFASs) have been banned, including one used […]

Cold Curtain

Cold water, essential for the life cycle of Chinook salmon, is all too often in short supply along the Sacramento River. Two clever innovations have been implemented to conserve cold water into the autumn. First: A 300 foot tall, 250 foot wide “adjustable straw” possessing a series of intake gates enables power plant operators to […]

Indecision Point

The Delta Stewardship Council was created in 2009 but given no say over a pending dual tunnels plan. The state was pushing a grand program called the Bay-Delta Conservation Plan. However, the BDCP was abandoned in 2015 in favor of two new, independent programs: EcoRestore and California WaterFix (popularly known as the twin tunnels). Rather […]

Back to the Bones of the Delta

Anyone who’s been around debates about the Delta’s highest and best
 uses for decades has seen a long train of plans touting this or that kind of restoration to save salmon, smelt, mice, birds and other endangereds. What’s different about the San Francisco Estuary Institute’s recently released Delta Renewed guide is that it finally puts […]

Options for Orphan Species

Off a bustling Delta highway, next door to a branch of the California Aqueduct, sprawls a tidy collection of shipping containers, humming pumps, and cylindrical tanks. This resolutely artificial site is devoted to preserving a disappearing piece of natural California: the Delta smelt. “Our fish are a refuge population,” says Tien-Chieh Hung...

Bay Belle Retires; Catamaran Carries On

Side by side at a Redwood City marina, two vessels await their very different destinies. The Research Vessel Polaris, a classy 96-foot yacht, spent decades as the workhorse of the US Geological Survey’s San Francisco Bay science program. Her successor floats next to her in the Redwood City marina, a 67-foot aluminum catamaran named RV […]

Keeping the Salt Field at Bay II

After four of California’s driest years on record, our “wet” season was so dry that state water officials panicked.Major reservoirs were drawn way down, and record-low snowpack would limit replenishment to a trickle. Water managers worried about the hot, dry months. Would reservoirs still hold enough for freshwater releases to keep saltwater from pushing deep […]

The Most Under-Regulated Facility

The Kaiser Permanente Cement Plant (named after nearby Permanente Creek) produced six million barrels of cement to build Shasta Dam, and countless roads, buildings, and bridges. Now known as Lehigh Southwest Cement Company, the quarry and plant still supplies 50% of the Bay Area’s Portland cement, and recently earned some intense scrutiny from local regulators.

No Scapefish in Drought Wars

According to the Biblical book of Leviticus, the ancient Israelites designated a goat to bear the weight of their sins. Nowadays, the scapegoat is not required to be a goat. When it comes to assessing blame for the worsening California drought, a scapefish will suffice. Some media outlets, notably the Wall Street Journal in a […]

Freeing Fish While Locking Up Mercury

Restoration planners were worried that connecting a former salt evaporation pond with the Bay could introduce long-dormant mercury to the wider ecosystem, and initial studies of levels in water bird eggs and fish reinforced that concern. A set of adjustable gates between the pond and the river allows seasonal closure of the pond and the […]

Bay Primed for Pea Soup?

Nutrients could be the next big problem for San Francisco Bay — or make that in the Bay, because they’re already here at levels high enough to have caused trouble elsewhere. But despite its excess nitrogen and phosphorus, the Bay has been free of harmful algal blooms and oxygen-depleted dead zones for decades. Indeed, we’ve […]

The Island That Came in from the Cold

For years, Skaggs Island was a tantalizing blank in the map of San Pablo Bay wetlands restoration. Renee Spenst of Ducks Unlimited says it was “one of those places in a strange limbo.” Two-thirds of it was owned by the US Navy; the rest was privately-owned farmland. Converting any of the 4,400 acres back to […]

Estuary News
October 2022

This issue takes a deep dive into rivers, exploring promising restoration programs on two of them, as well as an effort to increase flows for fish in South Bay creeks. We also tag along on a first-of-its-kind species survey, and examine the challenges climate change is creating for monitoring. To see the magazine in its […]

Estuary News
June 2022

This issue explores the outer limits of Delta science and research: Can we recover salmon, capture carbon, live with the Russian thistle? It also profiles three young scientists, visits Delta drawbridges in action, and reviews state efforts to come to a voluntary agreement on flows, as well as to fastrack restoration projects.
Estuary News June 2022

Estuary News
February 2022

In this special issue on fish, Estuary shares both the heroics of saving a fish near extinction as well as the secrets of some sturdier, healthier natives. Stories detail how South Bay fish are faring now that so much fish-food-producing marsh habitat has been restored; reveal how shreds of rubber from our car tires are […]