Bay Delta Salmon, Part 2: Making Rivers Flow Uphill

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 kcet.org/baydelta for all the project's stories.

Read Part 1, Damming The Chinook to Near-Extinction.

If you wanted an indication of how well the Bay Delta's Chinook salmon population is faring in the last few years of drought, here's one: the Sacramento River has been so low that Northern California Fish hatcheries are trucking their young fish hundreds of miles away from the hatcheries to release them way downstream.

Here's another: about 95 percent of the eggs laid by the last batch of Endangered Sacramento River winter-run Chinook salmon failed to become viable young fish heading downstream, and it looks like we've had a similar failure in the subsequent Fall run.

As we discussed in the first part of this series on Chinook salmon in the San Francisco Bay Delta and its tributary rivers, a century of dam building has devastated the fish's historic numbers. Over the subsequent decades, Chinook have had to contend with our increasing tinkering with their home streams. Whether we're polluting the water or diverting it into aqueducts, the Central Valley's Chinook salmon have come out the poorer. And the drought is just making everything a whole lot worse.

Like we said in Part One, two of the dozens of dams in the Sacramento San-Joaquin watershed stand out as especially damaging to the Valley's Chinook: Shasta Dam on the Sacramento River north of Redding, and the Friant Dam on the San Joaquin River a bit east of Fresno. The Shasta Dam (along with its companion Keswick Dam a couple miles downstrean) cut off access to hundreds of miles of spawning habitat in the Upper Sacramento, McCloud, and Pit Rivers, driving the Sacramento River's Winter-run Chinook near extinction. And while the Friant Dam didn't block that much spawning habitat upstream, it allowed irrigators to divert enough of the San Joaquin that the river actually dried up for about 60 miles below the dam.

But the context in which both dams were built may have been even more damaging than the dams themselves. Friant and Shasta dams are part of the Central Valley Project, a gigantic system of dams, aqueducts, pumps, and other infrastructure built for the state by the federal Bureau of Reclamation in the 1930s to provide water for farmers in the San Joaquin Valley.

The Central Valley Project was originally proposed by the state of California, but the feds took it over during the Depression when the state didn't have enough funding to build it. California was a bit more flush during the 1960s, and that's when the state built the Central Valley Project's sister, the State Water Project, primarily to deliver water to southern cities. (About 30 percent of the State Water Project's average deliveries go to agriculture.)

Together, the two massive projects include 42 dams -- most of them in the Sacramento and San Joaquin watershed -- and hundreds of miles of canals, gigantic pumping stations, and other infrastructure designed to move water away from its natural course, and into farm fields and faucets.

Trouble in the nursery

When the dams were built, salmon populations began to collapse. As a result, and a bit of an afterthought, the federal and state governments established hatcheries at the site of many of the major dams to boost the populations of the affected salmon runs. Though not necessarily the most-affected: of six hatcheries growing Chinook for release into the Sacramento-San Joaquin watershed, four only rear fish for the Sacramento's Fall and Late-Fall runs, which are much larger than the Endangered Sacramento Winter run and the Threatened Central Valley Spring run. The Feather River Hatchery, operated by the California Department of Fish and Wildlife below the Oroville Dam, does raise a few Spring run Chinook, and U.S. Fish and Wildlife's Livingston Stone hatchery at the foot of the Shasta Dam raises Winter run fry, which it usually releases a few miles downstream at Redding.

Hatchery programs are a mixed blessing for salmon runs. Hatchery operators have to be very careful that their charges' confined quarters don't contribute to contagious diseases, which could then be transmitted to wild stock once the hatchery fish are released. And a bigger problem, at least in the longer term, is hatcheries' effect on the wild salmon gene pool. Hatcheries necessarily produce salmon fry from fewer parents than would a wild stretch of spawning habitat with comparable productivity. That means a shallower gene pool for hatchery salmon than for wild, with potential problems resulting when the hatchery salmon are released to mingle and perhaps mate with their wild cousins.

In essence, though hatchery operators likely do sincerely want to help wild salmon, hatchery programs are mostly managed to benefit industry rather than the salmon themselves. Millions of Chinook fry are released each year mainly as support for the commercial salmon fishery, which is a $1.4 billion industry in California. And the fact that the hatcheries exist in the first place is an indirect subsidy for the customers of the water projects that built the dams in the first place.

Trouble for the salmon didn't end after the dams were built. Dams do more than block access to historic spawning grounds.

They can change the temperature of water downstream, for one thing. For the first 46 years of its operation, for instance, the Shasta Dam discharged water from the top of Shasta Lake into the lower Sacramento. That water, warmed by the sun as it sat atop the reservoir, raised downstream temperatures significantly enough that the salmon below the dam suffered. (In 1991, the Bureau of Reclamation installed a device allowing dam operators to release water from various depths within the reservoir, which helped matters somewhat.)

Dams also trap sediment and keep it from flowing farther downstream, including the gravel and cobbles that salmon prefer as spawning beds, and the nutrient-laden silt that provides juvenile salmon with cover -- both directly by muddying the water and by promoting growth of streamside plants.

Sucked into the pumps

But Chinook also face threats from the valley's water projects other than dams. Chief among them: the giant pumps that pull water from the Sacramento River across the delta and into the aqueduct, literally causing some rivers in the Delta to reverse their course.

Two pumps cause the biggest problems. The State Water Project's Harvey Banks Pumping Plant near Byron takes water from the Delta's Clifton Court Forebay, lifting it 240 feet into the California Aqueduct. The Central Valley Project's Bill Jones Pumping Plant just a few miles east takes water from the Sacramento River via a complex series of channels, then pumps it into the 117-mile Delta-Mendota Canal, from which it flows to the San Joaquin Valley to be used both for irrigation and to replace water removed from the San Joaquin River by the Friant-Kern Canal.

(If that makes your eyes glaze over, well, that's normal. Delta water engineering is mind-bogglingly complex.)

Pumps cause damage to salmon in a couple ways. The first is the one you're probably imagining: "entrainment," a jargon term for fish getting sucked into the vicinity of the pumps, is a serious problem. And you can't just slap up a screen smaller than the fish to keep them out: the fish would be injured and die, and they'd clog the pumps.

Instead, both the Banks and Jones pumps have "fish screens" that aren't actually screens at all, but racks of angled louvers across the pump inflow pipes that create water turbulence that fish avoid. The Skinner Fish Facility at the Banks Pumping Plant, along with the Tracy Fish Collection Facility at the Jones Pumping Plant, divert millions of fish annually from the pumps, including juvenile salmon along with green sturgeon, delta smelt, and other species.

Those fish are collected in separate holding tanks, then trucked farther north in the Delta and released. But not all of them make it. Some fish, including many Chinook smolts, are smaller than the louver gaps and can easily be sucked into the pump mechanisms. Even if they don't make it to the pump screening facilities, fish drawn into the Clifton Court Forebay, or the San Joaquin near the Jones Pumping Plant, are easy pickings for predators from striped bass to great blue herons.

There's another peril from pumping even if a salmon fry never makes it to the pumps. Let's consider that complex network of waterways that leads from the Sacramento River to the Jones Pumping Plant and the Delta Mendota Canal. Water leaves the Sacramento near Walnut Grove and enters the Delta Cross Channel, a 6,000-foot long canal that ends at Snodgrass Slough. That slough connects to the Mokelumne River, and the diverted water flows from there into the San Joaquin, where it then flows uphill to the pumps.

That causes two distinct problems for Chinook, even if they don't get turned into fish meal by pump machinery.

Salmon fry are not strong swimmers: they tend to drift downstream more than head there on purpose, and it's far too easy for fry drifting by the Delta Cross Channel gates on the Sacramento to get swept into the system. From there, they can easily get lost in the bewildering labyrinth of Delta channels, never making it out to sea.

And then there's the matter of Mokelumne River's fall-run chinook. A California Fish and Wildlife hatchery operates on the Mokelumne, and each year that hatchery's alumni attempt to return to the Mokelumne to spawn. The homing process by which salmon return to their natal streams to spawn is incompletely understood, but scent seems to play an important role: fish imprint on the odor of the water in their birth streams and head home by following those odors.

But when the Delta Cross Channel gates are open, the Mokelumne River gets filled with water from a hundred other streams from the Pit River in the far northeast of the state to Putah Creek, which drains the slopes of Napa County. That much "noise" drowns out the chinook's homing signal, it's suspected, and having those gates open when Mokelumne River Chinook are attempting to spawn has lead to disastrous spawning failures.

Those gates across the opening to the Delta Cross Channel are closed during winter when the majority of salmon are passing by in the Sacramento, as well as when Sacramento River flows are high to avoid causing floods in the San Joaquin basin. But there's constant disagreement over the timing of those closures, because with the gates shut, the Central Valley Project's pumps can't pull as much water into the Delta-Mendota Canal.

The many, many different ways in which both the State Water Project and the Central Valley Project cause harm to salmon have been the topic of legislation, agency wrangling, and protracted and confusing lawsuits. In 1992, in reaction to mounting concern over damage to the Central Valley's Salmon and other wildlife, Congress passed a bill -- the Central Valley Project Improvement Act - that required the Bureau of Reclamation to manage dam releases and diversions in order to maintain water in the rivers for the fish. The law ordered the Bureau to at least double Sacramento River salmon populations by 2002 over what they had been from the 1960s through the 1990s, and also required releases from Friant Dam to get the San Joaquin River flowing again.

That law did result in increased "instream flows," as the jargon has it, though controversy still swirls over re-watering the San Joaquin.

Both the Sacramento River winter run Chinook and the Central Valley spring run are protected under the federal Endangered Species Act (the Winter run as Endangered, and the spring run as Threatened), and that fact prompted the National Marine Fisheries Service -- a.k.a NMFS, the federal agency that administers ESA protection for most anadromous fish -- to issue a finding as to whether continued operations of the State Water Project and the Central Valley Project threatened the continued existence of those two runs. That finding, called a Biological Opinion or BiOp, came out in 2009. In the BiOp, NMFS held that continued operations of the Harvey Banks and Bill Jones pumping plants posed a threat to a number of protected species, including the winter and spring Chinook runs, along with Central Valley steelhead, green sturgeons, and southern resident orcas, which eat salmon.

NMFS's BiOp said that in order to avoid violating the Endangered Species Act, the Bureau of Reclamation would need to change the way it operated those projects: most importantly including pumping less water from the Delta and leaving more water in reservoirs for release when the fish needed it. That meant less water going to the state and federal water projects' customers, and so farm industry groups challenged the BiOp in court. District Court Judge Oliver Wanger held that the BiOp took too many liberties to protect wildlife and ordered NMFS to write a new BiOp. NMFS started that process, as environmental groups and fishing groups appealed the decision to the Ninth Circuit.

In 2014, a panel of the Ninth Circuit unanimously overruled most of Wanger's decision, essentially reinstating the main findings of the 2009 BiOp.

By then, both the Central Valley Project and State Water Project had cut water deliveries for a different reason: the state was in the throes of a multi-year drought, which continues to this day. Cutting those deliveries to water customers hasn't helped maintain instream flows as much as salmon advocates would prefer. As mentioned earlier, slack flows and consequent high water temperatures in the Sacramento River caused the loss of 95 percent of winter-run Chinook eggs laid in the 2014 "brood year." A typical success rate is more like 75 percent or less; which means that in a normal year, five times as many winter-run fry, or more, would be heading out to sea from the 2014 spawn right now. And that means far fewer winter-ruin Chinook coming back in 2017.

And according to recent data on the Sacramento River fall run's most recent spawn, we're probably looking at a similarly catastrophic failure of that brood.

Hatcheries are taking measures to make sure their fry, at least, have as good a chance of surviving to adulthood as possible. The federal Coleman hatchery in Anderson istrucking their fry to the Delta this year for the second year in a row; normally, they release their fry into Battle Creek right near the hatchery. But trucking them to Rio Vista to release them means the fry won't have to contend with a shrinking, warming Sacramento River -- or with the Delta Cross Channel gates, well upstream of the Rio Vista release site.

With any luck, this drought won't be the end for the Chinook runs of the Sacramento and San Joaquin rivers. True, they face a lot of perils, some of which are still on the drawing board, like the state's plan to divert Sacramento River water around the Delta in a pair of huge, expensive tunnels. Facing threats that haven't been built yet and those that already exist, Central Valley Chinook face an uphill battle if they're going to survive into the 22nd Century.

It's just a good thing Chinook salmon are really good at uphill battles.