Roger Castillo drives his dented Ram pickup truck on a steep-sided levee. We are only a few miles from downtown San Jose, California, in a landscape of warehouses and small bungalows. Below, a silty creek flows through heaps of garbage, concrete debris, and countless plastic bags. Along the opposite bank stands a makeshift structure built of cast-off wood and tattered tarps. 

Castillo, a former mechanic, is a self-trained naturalist. He grew up in San Jose and has lived here all his life, studying the bounteous life amid the nooks and crannies of the South Bay’s urban terrain. His best-known discovery came back in 2005, when he found a fully intact wooly mammoth fossil in an embankment on the Guadalupe River, minutes from downtown. (A statue of “Lupe” the mammoth commemorates the find.) On this cloudy late-November day, Castillo is scanning the murky water for something seemingly as improbable as a mammoth. He is looking for Chinook salmon.

It’s not long before he spots one, stranded on its side in a section of the riverbed covered in concrete. When Castillo sees the fish, he slams the gear shifter into park and leaps from the car nearly before the vehicle has stopped. My son, Owen, 16, seated in the pickup bed atop a large cooler, braces himself on the sidewalls to keep from being thrown asunder. For a man in his early sixties, Castillo moves with great speed, wriggling into his waders and shimmying down the steep hillside before we’ve even had time to slip a toe into our own waterproof gear. 

By the time we reach the water’s edge, Castillo already has his hands on the Chinook. He lifts it from the water. The fish is large, easily more than 20 pounds. Its size is completely out of keeping with the diminutive creek. Castillo carries it gingerly to a deeper section of the stream where the water churns over boulders. He holds the fish delicately, one hand wrapped about the tail and the other under its belly. Each pulse of water over its gills causes the fish’s languid muscles to tighten as its skin changes in color from an ashen gray to an iridescent silver. It is indeed surreal to witness a 40-inch fish in a creek that on most days outside of the rainy season is scarcely more than a few inches deep. Beside Castillo, in a section of still water near the bank, are the graying carcasses of four or five salmon. Several of them are females packed with eggs. 

“Just in time,” he says, rousing the fish with gentle undulations. “A few more minutes and this guy would have been a goner.” This section of Silver Creek, like dozens of others across the Bay Area, was modified into a box culvert to move water rapidly beneath the Highway 101 overpass, which carries a torrent of vehicle traffic. The water flows like a transparent glaze—fast, smooth, and featureless—too shallow even for a powerful mature fish like this to pass. As we scout the reaches of the culvert under the highway, we come across two more carcasses, both large females distended with eggs. 

“This is what we call the ‘kill zone,’” says Castillo. 

*

The scene at Silver Creek is a small tragedy unfolding within a larger, improbable ecological renaissance. Despite the urban and industrial alterations, over the past three years, as large winter storms have swelled the creeks, the numbers of salmon returning to the southern reaches of San Francisco Bay have risen sharply. According to the South Bay Clean Creeks Coalition, a local citizen science and watchdog group, as of early December, more than 180 fish were counted in creeks across the region (by the time of publication, that number had grown to more than 600 with more storms on the way). In one section of San Tomas Aquino Creek, near Levi Stadium, Castillo counted dozens of salmon congregating beneath a pedestrian bridge. “They were in a huge school just hanging out under the bridge,” he said. “Pedestrians and people on their bikes were stopping to watch.” But for every fish he sees, Castillo said he believes eight to 10 go uncounted.

An emerging beaver dam on Los Gatos Creek.

Though there is no doubt that salmon numbers are surging across San Jose and other parts of California, exactly where they are coming from is not entirely clear. One hypothesis is that the majority are wayward hatchery salmon. Over recent years, millions of juvenile Chinook salmon raised in hatcheries have been released at the mouth of the Golden Gate. These fish can be identified by their missing adipose fin, a small fan of skin between the fish’s dorsal and tail fins, which is clipped before their release. But some of the salmon showing up in the South Bay still have adipose fins—a telltale sign of a wild birth.

According to Clayton Leal, a biologist at the Santa Clara Valley Water Agency, they are not native to the region. Valley Water, as it is better known, delivers water to 2 million residents in the South Bay. The agency also oversees management of most of the waterways across the region. “Salmon get a lot of attention because they're big, and because they're coming in during these times of lower flow,” he told me. “But the real star of the show that we have in Santa Clara County is the federally threatened steelhead.” Leal’s contention—and by extension, his agency’s—is that the fall-run Chinook seen in the streams are not native to the area but are wayward strays from hatcheries in central California. “This is our driest time of year, in the September, October, November timeframe, and that's when we would expect these fish to migrate.” According to Leal, it wasn’t until the dams were built in the early and mid-20th century that the creeks carried enough water at that time of year to support a fall Chinook salmon run. “Having Chinook in our systems down here doesn't make a lot of ecological sense when you look at the natural hydrology.”

Others vehemently disagree with that interpretation. Rick Lanman, a Los Altos–based ecologist and natural historian, has led several studies to determine their origins. In 2021, he published a study that evaluated fish bones unearthed at Mission Santa Clara and found that Chinook salmon were caught and consumed in the South Bay as far back as the early 1800s. 

Lanman and his colleagues have also used molecular techniques to determine where the fish are coming from. Turns out that rivers and streams leave their own unique chemical imprint on the fish that inhabit them. That imprint can be read by analyzing different ratios of isotopes of sulfur and strontium contained in the ear bones and eyeballs. These chemical signatures give scientists an idea of not only what river a salmon came from but also whether it was born in a hatchery or in the wild. Of the 26 Chinook salmon sampled in their most recent study, Lanman said, 22 were born in hatcheries and four in the wild. Those fish, he added, were found to have strontium and sulfur ratio signatures from various rivers across the state. One showed the molecular signature of the Russian River, in the North Bay, which harbors a federally threatened population. “The problem is that all of these hatchery fish are swamping the native populations,” Lanman said. 

Lanman believes that Valley Water doesn’t want to accept these findings because it would mean having to relinquish adequate flows from upstream reservoirs to protect them. “They don't like to even admit that they could be native, because California coastal Chinook salmon are federally threatened,” he said. “If they acknowledge the fish are here at all, they will say they are all hatchery fish. But if you look at the genetic studies, there's always some coastal fish.” 

For now, salmon are back in the South Bay. But are they successfully spawning? One waterway, Los Gatos Creek, may offer a clue. A week after my visit with Castillo, I met with Steve Holmes, executive director of the South Bay Clean Creeks Coalition, in the city of Campbell, a few minutes southwest of downtown San Jose. He wanted to show me a short section of Los Gatos Creek where dozens of fish were spawning. This reach, flowing in a concealed ravine below tall office buildings, provides some of the best spawning habitat in the sprawl of San Jose.   

Holmes and I put our waders on and squeezed between a section of metal railing, descending a trash-strewn embankment into the streambed. Florid bursts of graffiti covered a concrete wall. Here, Los Gatos Creek is shallow and flows slowly. Beneath the surface were mounds of tidy-looking gravel—the characteristic nests, or redds, excavated by Chinook salmon. Holmes pointed out that a large salmon had been spotted here a few days earlier. We plodded farther upstream, through ankle-deep water, and soon arrived at a section of faster-flowing water, passing by the putrefying carcass of a large salmon. “The racoons have already been at it,” said Holmes as he hooked it with a rake and tossed it on the bank. A little farther on, in a shallow gravel-filled riffle, two large Chinooks, a male and female, swam side by side. Occasionally, the female skittered on her side, excavating pebbles in the creek bed in preparation for laying her eggs.

The differences between Los Gatos and Silver Creek were immediately apparent. Los Gatos Creek is slightly larger than Silver Creek, but unlike its counterpart, which is hemmed into a narrow streambed resembling a massive gutter, Los Gatos Creek flows in a wider, more natural floodplain filled with grasses and tall sycamores and cottonwoods. Those wider margins mean that Los Gatos Creek retains some of its natural characteristics, allowing the creek to widen during heavy winter and early spring flows. As Holmes and I negotiated tangles of brush along the banks, we came upon the leavings of another denizen of the riparian zone. Chewed sticks and logs lay strewn about the banks—unmistakable signs of beaver. The slow, flooded sections created by beaver dams provide important refuge for juvenile salmon. Holmes also points out that this area, with its wide, flat floodplain, was once the site of a large homeless encampment. “It’s a constant battle,” said Holmes. “Keeping this area free of tents.”

Just upstream from this section of Los Gatos Creek, a restoration project will improve habitat and eliminate yet another obstacle for spawning Chinook, a large flood-control structure resembling a dam that creates an almost impassable waterfall. According to Holmes, the project will cost $3 million to $4 million, much of which will be funded with a grant from the Knight Foundation. The goal is to improve streambed conditions by augmenting the amount of gravel available to fish for creating redds, as well as enhancing stream habitat. Additionally, the streambed will be graded, creating more riffles and slow sections to create more spawning zones for fish. It will also eliminate the waterfall structure, which, according to Holmes, “will give the fish a better chance of moving up into the next leg.” “These fish are giving it their all, so we should give it our all, too, to help them out,” said Scott McBain, a fluvial geomorphologist heading up the restoration project. “It’s definitely inspirational when you see a 30-pound Chinook salmon spawning next to Google headquarters. You want to do everything you can to help support having a semi-healthy river and healthy fish in a downtown setting.”

*

Back in the concrete channel of Silver Creek, Castillo, Owen and I walk deeper into the “kill zone.” In the shadows under Highway 101, we encounter another female, easily more than 30 inches long and heavy with eggs. She is on her side, barely alive. Castillo grabs the fish by the tail and attempts to resuscitate it as Owen and I slosh through the shallow water to retrieve the large cooler from the bed of his pickup. When we return, Castillo carefully lays the fish inside the cooler and begins to fill it with water from a plastic shopping bag plucked from the current. Once the fish is covered in water and partially revived, Owen and I haul the heavy container up the steep hillside, our feet struggling for traction on the slick, muddy slope. 

Castillo quickly hooks up an aerator and drives the egg-laden female to a more natural section of the creek a few hundred yards upstream. After a few seconds, it bolts from his hands with surprising ferocity. In his decades of stewardship, Castillo has rescued hundreds of salmon. How many of the fish we saw, I wondered, are the progeny of fish Castillo has carried to safety? And how many more could be saved here on Silver Creek if water managers made simple fixes to allow them passage across this flat, deadly swath of concrete? 

“It wouldn’t take much, just a little trench to get them through,” says Castillo as he hauls himself from the stream, wiping his hands on his waders. “But the water managers have to admit that these fish belong here in the first place.”