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Bay Delta Salmon, Part 1: Damming The Chinook to Near-Extinction

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Chinook salmon in the lower Tuolumne River | Photo: U.S. Fish and Wildlife Service/Flickr/Creative Commons License

An explanatory series focusing on one of the most complex issues facing California: water sharing. And at its core is the Sacramento-San Joaquin Bay Delta. Stay with for all the project's stories.

So much change has come to California in the last 150 years that it's sometimes hard to picture the state's previous natural landscape. Imagine, for instance, an unregulated, un-diked Bay and Delta, full of water from a dozen major undammed rivers.

Before 1860, all the rain and snow that fell in a watershed of 58,000 square miles -- more than a third of California -- would make its way to the Delta, and then the Bay, and then the Pacific, without so much as a concrete curb to slow it down. In wet years the waters would flood the Central Valley, creating vast inland seas where Sacramento and Stockton now sit. As they shrank under the summer sun, vast plains of riparian wetlands and wildflowers took their place.

The Sacramento-San Joaquin river system, in other words, was truly a thing to behold. It was the second-largest river entering the Pacific in the Lower 48, after the Columbia, and it was as fertile and productive as a huge, wild river system can be. And the foremost expression of that ecological fertility were the Central Valley's majestic salmon runs.

The folklore has it that early travelers used to be able to cross Sierra Nevada rivers by walking across on the backs of spawning salmon. That's obviously a tall tale. Less easy to dismiss are stories of early settlers harvesting nearly unlimited amounts of salmon, in the 50-pound range and larger, by the simple expedient of wading into rivers like the Feather and the Yuba and pitchforking the fish onto the bank like so many bales of hay.

The salmon runs in the Delta's tributary rivers, from the Pit River in the northwest to the San Joaquin itself, were nothing short of formidable. The fish supported entire societies in places like the Pit River watershed, where rough terrain made hunting difficult and game sparse. There wasn't really a salmon season: whether they were spawning adults or adults not yet ready to spawn, there were big salmon in the rivers pretty much year-round.

All five species of Pacific salmon were found in at least some of the rivers that fed the Delta, but the vast majority of the salmon in the Sacramento and San Joaquin and their tributaries were chinook salmon, also called king salmon, known to biologists as Oncorhynchus tshawytscha.

This monarch of fish made up around 99 percent of salmon migrating along the main stems of the Sacramento and San Joaquin. Unlike California's coastal coho, which seem to prefer short, steep coastal streams, chinook have a tendency to select large main-stem rivers to cruise hundreds of miles from the ocean before spawning. (In the Yukon River, chinook have been known to swim 2,000 miles upstream before reaching their spawning grounds.) (Chum and pink salmon tend to spawn in rivers' lower reaches, while sockeyes can cruise well inland like chinooks, but there just aren't that many in California other than planted kokanee, which is what sockeye are called when they live in lakes and can't swim downstream to the ocean.)

More than one kind of chinook

There were, and so far still are, four distinct "runs" of chinook salmon in Central Valley streams, each one named for when adults generally start swimming upstream. The valley as a whole has spring, fall, and late-fall runs, and there's an additional winter run that's restricted to the Sacramento and its tributaries. Spring run chinook enter the rivers starting in late March, then start a couple months of spawning in August. For the fall and late-fall runs that's July and October, and October and January, respectively. Sacramento winter run chinook enter the river starting in December, then spawn beginning in around mid-April. There are no other winter-run chinook anywhere else in the world.

And each of those four runs was, and is, made up of genetically distinct groups of chinook with specific tributary streams as home spawning grounds. At least 25 of the rivers and streams feeding into the Sacramento and San Joaquin, including both the Sierra Nevada's westside rivers and the smaller watercourses that flow into the Central Valley from the Coast Ranges to the west, supported at least one run of chinook salmon, and often more than one.

The spring run was once the largest by far; only a remnant now remains, and the run is listed as a Threatened species under the state and federal Endangered Species Acts. Before we began reengineering the state's waterways, spring-run chinook went as far into the mountains as they could to spawn. As we shall see, that made them especially vulnerable to our engineering projects. The Sacramento River winter run, which originally spawned mainly in spring-fed pools at the headwaters of the Pit, McCloud, and Upper Sacramento rivers, is in even worse shape. Winter-run chinook were listed as Endangered by the state in 1989. The feds followed suit in 1994. Fall-run chinook primarily spawned along the main stems of rivers below about 500 feet in elevation. They're currently the most abundant salmon in the watershed, with the late-fall run in second place, but their future is just as clouded.

Regardless of which run we're talking about, the chinook's life history is about the same. Eggs laid in gravel beds called "redds" hatch out, and young fish emerge with yolk sacs still attached. Called "alevin," these baby salmon generally stay in the crevices between bits of gravel where they can breathe the oxygenated water flowing through the redds, growing as they consume the contents of their yolk sacs. After about four months, their yolk sacs emptied, the alevin must emerge from the gravel to find more food. Now called "fry," the young chinooks are about an inch in length when they emerge.

Chinook fry in other parts of the world can stay in freshwater for several years, but in the Central Valley -- the species' southernmost population -- many young chinooks migrate to the ocean -- the "smolt" stage -- the same year they hatch. Others will wait a year or so before heading for saltwater. Once they're there, they grow to adulthood in the open Pacific, spending four years or so in the ocean. They then return to the Bay and Delta, hold for a period as their systems become reaccustomed to fresh water, and then head upstream to spawn.

It's not hard to imagine that trait of earlier return to the sea as being a good hedge against occasional drought. If a drought-stricken river dries up and the juvenile chinook holding in its pools die off, it's a lot better to have fry from just one or two years' spawning seasons affected, rather than three or four.

At the spawning grounds, a female chinook will hollow out a depression in a likely gravel bed with a few flicks of her massive tail. She lays her eggs in that depression, and then a suitable male will fertilize those eggs with a cloud of watery sperm called "milt."

Salmon runs in the Delta before the advent of western civilization must have been incredible to behold. In 1979, well after California's chinook runs had begun to fall apart in the face of our destruction of their habitat, angler O.H. Lindberg caught an 88-pound chinook -- the state's record. Fish of that size were likely much more common before we started depriving them of habitat, but even at a more currently typical 20 or 30 pounds? A stream full of spawning adult chinook might have been something between awe-inspiring and terrifying.

This would have been a common sight in the mountains above the Central Valley 200 years ago | Photo: Jitze Couperus/Flickr/Creative Commons License


What did we do to start mucking up their habitat? Just about everything, including adding tons of literal muck to their habitat.

Washing away whole hillsides

One of the first major threats came during the Gold Rush: the practice of hydraulic mining, in which whole hillsides were washed away with water jets in order to find gold in the buried sediment. Most of that sediment ended up in local streams, where it buried the gravel beds chinook might have laid their eggs in, suffocating untold millions of juvenile fish.In the Feather River, once one of the Lower Sacramento River's tributaries richest in salmon habitat, sludge washed into the streambed from hydraulic mining was so thick that one 19th Century observer said it and nearby rivers had been...

...completely ruined as spawning grounds, in consequence of the immense deposit of mud in them... Not a salmon ever enters these streams now. Except possibly at a time of very high water, these streams are so thick with mud that it would kill any fish attempting to ascend them."

A landmark environmental lawsuit resulted in most hydraulic mining being banned in California in 1884. By then, though, much of the spawning habitat downstream of the mines had been covered in as much as a hundred feet of gravel. In the canyons of smaller streams, such as the Feather tributary the Bear River, that gravel remains to this day. Bigger streams like the Yuba washed more of the debris out into the valley, where it filled in potholes and other wetlands young chinook relied on as freshwater habitat. Mud and silt from the mines regularly reached downstream as far as Vallejo on San Pablo Bay.

There's a dam in the way

Chinook also began to suffer from pollution, from water diversion of smaller streams, and from conversion of their downstream wetland habitat into farms and then towns. But the biggest single source of harm to California's chinook began in the last two decades of the 19th century, when Californians started damming the Bay and Delta's tributary streams. At first those dams went up on smaller feeder streams, like the Salt Springs Valley Dam, completed in 1882 on Rock Creek, a tributary of the Mokelumne River. Then dams started going up on the main stems of larger rivers, like 1894's La Grange Dam on the Tuolumne River. La Grange didn't create that big a reservoir, at about 500 acre-feet in capacity, but it did stop chinook from leaving the Central Valley stretches of the Tuolumne and heading into former prime spawning grounds in the foothills of the Sierra Nevada.

How far up into the Sierra Nevada did Tuolumne River chinook get before La Grange Dam was built? That's a matter of some conjecture. According to the paper "Historical and Present Distribution of Chinook Salmon in the Central Valley Drainage of California," a 2001 paper by fisheries biologists Ronald Yoshiyama, Eric Gerstung, Frank Fisher, and Peter Moyle, Clavey Falls, a set of 15-foot tall rapids at the confluence of the Clavey River and the Tuolumne, might well have been the upstream limit for fall run and late-fall run on the Tuolumne River. Spring run salmon, aided by abundant snowmelt runoff, likely leapt Clavey Falls with something approaching ease, to be stopped by Preston Falls. That meant that La Grange Dam might well have barred chinook access to more than 50 miles of suitable spring-run spawning habitat on the Tuolumne. By 1928, state fisheries officials were already calling the once-abundant Tuolumne spring-run chinook "scarce."

Dams started going in on one tributary after another in the Delta's watershed.

On the American River, the Old Folsom Dam and its associated Folsom Powerhouse generated electrical power transmitted by wire 27 miles to Sacramento. It was an engineering marvel; at the time the world's largest electrical power grid. The dam also blocked spawning access to at least 150 miles of spawning habitat on the South, Middle, and North forks of the American. The American's chinooks were already devastated by the effects of hydraulic mining, and the Old Folsom didn't do the surviving fish any favors. A fish ladder added to the Old Folsom Dam in 1931 allowed chinooks to use some of their historic upstream spawning grounds for a few decades, and the fall and spring runs recovered during the World War II era, but soon dwindled -- to be killed off entirely when the present-day Folsom and Nimbus dams were built in the mid-1950s.

The Merced River was throttled with the Exchequer Dam in 1926, cutting off salmonid access to the habitat upstream -- including, if some historical accounts are to be believed, the Merced's course through Yosemite Valley. Those reports aren't universally accepted, but chinook are reasonably well documented to have made it to within a few miles of El Portal.

The Pardee Dam went up on the Mokelumne in 1929, providing a reliable source of drinking water for the cities in the East San Francisco Bay Area, and cutting off spring-run spawning grounds between the dam site and 30-foot Bald Rock Falls, 19 miles upstream. (Fall-run salmon likely didn't make it past a large waterfall just downstream of the Pardee Dam site, that fall later submerged when the East Bay Municipal Utility District built Camanche Dam downstream of Pardee in 1963.

And so on, and so on, and so fewer salmon. There were at least 6,000 miles of excellent chinook spawning habitat in pre-Gold-Rush California, according to one estimate. In the 1990s, the California Department of Fish and Game estimated remaining chinook spawning habitat at about 300 miles.

Shasta Dam under construction in 1942, before the last door slammed shut on the winter-run's habitat. | Photo: Russell Lee, U.S. Farm Security Administration


The biggest and baddest

Two single dams were especially devastating to the Central Valley's chinook. The Friant Dam on the San Joaquin River, begun during the 1930s and completed in 1942, may not have blocked access to very much upstream spawning habitat: one estimate has it that only about 16 miles of the San Joaquin above the town of Friant was accessible to salmon. But by diverting the entire flow of the San Joaquin for irrigation except in very wet years, the Friant Dam essentially dried up the river for 60 miles downstream of the dam.

That meant that the Merced River, by about 1945, became the world's southernmost limit of chinook salmon, and that the distinctive run of salmon that had inhabited the San Joaquin upstream from its confluence with the Merced had gone extinct. Nineteenth Century chinook ranged as far south in wet years as the Kings River. In essence, California water planners destroyed the southernmost 125 miles if the San Joaquin Chinook's range.That extinction may well have deprived the chinook salmon of genetic diversity that would have come in handy in this newly warming world. As Yoshiyama et al relate, an 1875 report by the state Board of Fish Commissioners -- now known as the California Fish and Game Commission -- flat out marveled at the San Joaquin fall-run chinook's ability to withstand water temperatures that could prove disabling or even fatal to chinook elsewhere:

Large numbers pass up the San Joaquin River for the purpose of spawning in July and August, swimming for one hundred and fifty miles through the hottest valley in the State, where the temperature of the air at noon is rarely less than eighty degrees, and often as high as one hundred and five degrees Fahrenheit, and where the average temperature of the river at the bottom is seventy-nine degrees and at the surface eighty degrees.

Current best practices by California fisheries managers recommend keeping water at or below 55 degrees Fahrenheit when spawning chinook are present. Chinook that could tolerate water 25 degrees warmer than that might well have come in handy in years like this. Building the Friant Dam, and dewatering the San Joaquin for more than 60 years so that the descendants of those heat-tolerant chinook died out, may prove a devastating handicap to the fish as they struggle to adapt to a warming world.

But for real salmon run devastation it's hard to top the Shasta Dam, completed in 1945 on the main stem of the Sacramento River about three miles before its confluence with the Pit River. When its gates were closed in 1943, the 602-foot dam completely closed off salmon access to both the Pit and the Upper Sacramento, along with the McCloud River, which flowed into the Pit about two miles before the Pit joined the Upper Sacramento.

It's estimated that the closing of the Shasta Dam deprived chinook of half of the really good spawning habitat in the Sacramento Basin. In the 19th Century and earlier, native Californians caught salmon in the streams flowing off Mount Shasta that fed into the Upper Sacramento. Chinook were known to have swum up the Pit River at least as far as the site of the present-day town of Fall River Mills north of Mount Lassen. From there, the salmon apparently headed into snowmelt-fed Fall River, which was significantly cooler than the Pit upstream of the confluence.

And then there was the McCloud, which rises from the melting snow on the southern slopes of Mount Shasta, flowing 77 miles to its confluence with the Pit. A series of pretty falls on the Upper McCloud blocked salmon access to spots farther upstream, and it seems that most chinook stayed well below the falls, using only the bottom 32 or so miles of the river for spawning.

But that 32 miles of the McCloud River was described in 1890 by the Board of Fish Commissioners as the "best salmon-breeding river in the world," and reasonably reliable accounts from the late 19th Century mentioned hundreds of thousands of chinook using those 32 miles of the McCloud, along with a few tributary streams.

When Shasta Dam went up, in other words, several hundred miles of the best chinook habitat in the state was irretrievably lost. But it wasn't just any good chinook habitat upstream of the dam: it was almost all of the spawning habitat of the Sacramento winter-run chinook. Aside from 16-mile Battle Creek, which flows into the Sacramento below the Shasta Dam near Anderson, every last bit of the Sacramento River's winter run chinook spawning habitat was above the dam. The run went from hundreds of miles of spawning habitat to 16 the day the Shasta Dam's gates closed.

It's thus no surprise that the Valley's winter-run chinook are faring more poorly than their cousins in the spring, fall, and late-fall runs, and it's likely that those state and federal Endangered listings are all that's kept the winter run from blinking out of existence.

Imagine a snapshot of California chinook spawning habitat in 1700 compared with one taken just before the current drought hit. What had been a network of dozens of major rivers, hundreds of feeder streams was systematically amputated, dams eventually going up on every major watercourse aside from the Cosumnes River, which didn't contribute significantly to historic chinook numbers. The most convenient locations for dams just happened to cut off the majority of preferred spawning habitat for spring- and winter-run chinook, which is the main reason those runs are in more trouble than their fall and late-fall colleagues.

And that's just the spawning habitat. But chinook do a lot more than spawn. In part two of our look at chinook salmon in the Bay-Delta watershed we'll discuss how the main reason the dams went up -- to provide water for an increasingly populated, increasingly thirsty California -- affects salmon even if they spawn successfully, as different human constituencies battle over water in the beating heart of the state to which all the Chinook's rivers flow: The Delta.

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