For open-water swimmers like me, autumn in San Francisco Bay is a halcyon moment between the punishing winds of summer and the frigid swells of winter. It’s the one season when both water and air are calm and warm.
Early fall is also the saltiest time of year. To me, the autumn Bay tastes like very briny chicken soup. In winter and spring when rain and snowmelt from the Sierra Nevada dilute the seawater, it’s more palatable—only a third as saline.
For a human, swings in salinity in this range are not a problem. But when I have been immersed in extremely salty seas—for example, the Sea of Cortez—my throat and nasal passages and eyes burned. My mucous membranes were reaching the limits of their osmoregulation—their ability to maintain a healthy electrolyte balance. Regular ocean water is more than three times saltier than the fluids in the human body.
This made me wonder what extreme salinity shifts feel like for creatures that are continuously immersed. Most marine invertebrates are osmoconformers. Water flows in and out of them, and, unable to adapt, they die when it’s too salty or fresh. In fall, the underparts of docks in the Bay are covered with bryozoans and sea squirts. Many of these tiny, mostly exotic, salt-loving animals almost disappear from the Bay in winter when fresh water pours in.
Swimming in the Bay
A series by Susan Kuramoto Moffat on what you can learn about our local waters from diving in. See her Summer 2025 Issue column for resources on how to get started swimming outside.
And continue the journey with her seasonal columns on Bay waters:
Spring 2026: Swimming with the Fish
Other animals, the osmoregulators—which include mammals and most fish—maintain a specific internal balance of electrolytes. As Chinook salmon swim upstream from the Bay into rivers, their kidneys discharge excess fresh water through urine as their gills keep their bodily salts in balance.
It is biologically challenging to be euryhaline—amenable to a wide range of salinities—and the vast majority of aquatic organisms are not. But many of the organisms of the Bay are masters of this form of adaptability. Foundational species including eelgrass and native Olympia oysters can thrive in a wide range of salinities, although they prefer near-oceanic conditions. Some native mussels can handle more salinity variation than exotic ones, notes environmental scientist Daniel Killam from the San Francisco Estuary Institute.
Remarkably, many Bay creatures acclimate to salinity that fluctuates dramatically not just by season, but throughout each day. In response, some mussels clamp open and shut, Taylor’s sea hares adjust their respiration, and fish swim toward their preferred salinities as hormones change the way their gills filter water.
Salinity in San Francisco Bay varies dramatically by the season. In this plot for September 2 (left), salty water (shown in red) reached all the way up to the Delta, while on February 2 (right), fresh water reached down to Treasure Island. Credit: Plots generated from NOAA/NOS’ San Francisco Bay Operational Forecast System by NOAA/NOS/CO-OPS Modeling Team. See a live animation of current salinity forecasts here.
Nearly a quarter of the Bay sloshes in and out of the Golden Gate twice each day with the tide, mixing salt and fresh water on a staggering scale. The surface of the Bay reveals this flux in subtle shades—fresher, browner, more sediment-laden water floats next to, and in some places on top of, denser, clearer salt water, with turbulent churning and stratification happening below. The daily salinity forecast on the National Oceanic and Atmospheric Administration website makes the surface flows vividly clear: It features a mesmerizing animation in colors from deep blue (fresh) to yellow (brackish) to red (salt).
In early fall, the animation looks a bit alarming. The central Bay is a seething sea of red (salty) water. The round basin of San Pablo Bay pulses like a crimson heart pumping ocean water up into the Delta. The salty water extends well upstream of the Carquinez Bridge to Antioch and beyond.
As late fall rains bring fresh water into the Bay, the red shifts downstream toward the ocean and the pattern becomes more complex. Soon, winter water from the Sacramento and San Joaquin Rivers pushes west and south in a blue-coded tongue of fresh water under the Richmond Bridge. It then squeezes between Angel Island and Tiburon on its way to getting sucked out the Golden Gate into the Pacific with the ebbing tide. But a couple of seconds later in the animation (and a few hours later in real life), the ocean pushes back against the river water, sending a flood of yellow-coded brackish water toward Alcatraz Island. The flows are not always continuous streams but detach and float in ragged blobs—variations that swimmers can taste and feel.
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In the current dry season, though, the complexity is reduced to a simple line between blue and green sliding up and down in a narrow stretch of river some 50 miles upstream from the Pacific Ocean.
This constantly shifting line between salt and fresh, known to scientists and policymakers as the X2 line, is literally the front line of California’s water wars. The salty territory of the Bay has been subject to change as dams and diversions sluice more than half of the fresh river water from the Sierras away from the Bay and toward Central Valley agriculture and to Southern California cities. This salinity threatens not only to wipe out certain fish species, but to invade agricultural and urban water supplies.
The Bay water on my tongue is saltier than it’s been for most of the past millennium. That’s a big problem for some organisms, including humans, and climate change is making it worse. By immersing myself in the Bay, I’m getting a taste of things to come.
