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Chinook Salmon in the San Joaquin Valley: Natural History and Current Conditions

By Stacy Small and Dan Efseaff

(Above) Inundated floodplains provide excellent habitat for juvenile salmon to forage and grow. This is an aerial photo of the San Joaquin River National Wildlife Refuge. Photo by Stephen Sheppard.

To many, springtime in the San Joaquin Valley means the brilliant bloom of almond orchards, the hum of irrigation pumps, and the rush of traffic along Highway 99. However, in the few remaining pockets of riparian habitat, cottonwoods and valley oaks are leafing out, Song sparrows are cranking up their singing along the riverbanks, and Wilson’s warblers are passing through on their way to montane nesting grounds. Less than a lifetime ago, you could add the churning splash of spring-run Chinook salmon migrating upstream to the sounds, sights, and cycles of spring.

Chinook salmon are anadromous, that is they spend most of their life cycle in the ocean and breed in freshwater. Adults spawn in the flowing, well-oxygenated, cold-water riffles of streams, and hollow out gravel nests called “redds.” After the young emerge from the nest, they feed and seek protection along river banks and in shallower, warmer nutrient-rich waters of side channels and inundated floodplains.

Pacific Chinook salmon grow to maturity in the ocean over several years, foraging on small fish and invertebrates and completing their life cycle by migrating back into freshwater streams to spawn a single time before dying. Pacific salmon populations have evolved several races or “runs” in Central Valley rivers over many generations. These runs are typically separated by the time of year that they enter the San Francisco Bay Delta and may differ in quite a few ways, including upstream migration timing, length of migration route, breeding elevations, body size, and length of juvenile rearing period.

Spring-run Chinook were historically the most abundant salmon run in the San Joaquin River system, which makes a lot of sense in terms of the historic patterns of water flow and physical conditions of this system. The melting snowpack of the southern Sierra Nevada once triggered the migration of spring-run adults in peak physical condition up the tributaries. These individuals sought the deep, coldwater pools where they would survive over long, hot, dry California summers and spawn in the early fall (Yoshiyama et al. 1996). It’s easy to see how abundant snowpack, ample gravel, clean water, and massive food sources would contribute to the success of spring-run Chinook.

While in many places these conditions still exist, major barriers to fish migration have gone up. Passage to these higher elevation reaches has long been blocked by a series of man-made obstacles, including early hydropower dams and, more recently, large dams on the mainstem and tributaries. Dams have tamed flood flows and provide hydroelectric power and more dependable water source for crops and cities, but they have come at a cost to salmon. Spring-run Chinook have disappeared from San Joaquin River tributaries, including the Stanislaus, Tuolumne, and Merced Rivers.

Fall-run Chinook are now the last remaining legacy of the great historic Pacific salmon runs in the San Joaquin River system. Throughout California, fallrun Chinook have become the mainstay of Pacific salmon fisheries. These runs have historically occupied lower reaches on the valley floor and foothills than spring-runs. With later upstream migration timing, they arrive in the rivers with eggs ripe and spawn soon after reaching lower elevation spawning beds, rather than holding over in cold pools. Fall-run Chinook have persisted through the large dam-building era largely because they could still gain access to portions of their historic breeding areas. However, numbers have declined over time, and this year, it has become undeniably clear that the Chinook fall-runs are in big trouble, too.

Preliminary data from California Department of Fish and Game indicate that the 2007 fall-runs in the San Joaquin river system were stunningly small, returning in the hundreds rather than thousands to the tributaries (Figure 1). 315 Chinook spawners returned to the Stanislaus River, compared to 8,498 in 2000. 115 returned to the Tuolumne River, compared to 17,873 in 2000. The total natural (nonhatchery) adult run was 1,450 for the San Joaquin River, compared to 39,474 in 2000. Initial reports from NOAA and the Pacific Fishery Management Council attribute the recent crash largely to a 2005 shift in ocean currents that delayed upwelling for the California Current, depleting spring food supplies at the time young salmon would have been arriving to the oceans, possibly resulting in high mortality.

Figure 1. Fall-run Chinook spawner numbers for this decade in the San Joaquin River system. Preliminary data from CA Department of Fish and Game.

By all accounts, though, Chinook numbers have been affected over time by a century and a half of historic events in Central Valley rivers related to mining, vegetation clearing, dambuilding, predation by non-native fish, water diversions and regulation. In general, smaller populations may be less resilient to sudden environmental shifts, and one major detrimental event can have catastrophic effects on a dwindling population. This may be what we are seeing with the recent crash, which would most appropriately be seen as a long-term culmination of alterations to river and delta environments, coupled with largescale shifts in ocean conditions likely related to climate change.

The greatest hope for Chinook runs in Central Valley rivers lies in the fact that some, if only few, individuals have survived in each tributary to breed this year. Although the origins of the problem may seem diffuse, it is incumbent upon every individual and institution to determine their immediate sphere of influence and take corrective action in that part of the system where they can be most effective. Although the most recent declines may strongly correlate to oceanic conditions, protection and improvement of riverine habitat becomes all the more critical in the face of dwindling populations. Conditions of freshwater breeding and rearing habitat must be closely examined and improved to maximize reproductive success and improve juvenile survival and condition.

Actions are being taken range-wide to protect and restore Chinook populations. The 2008 salmon fishing season is being limited in phases along the California coast. Planning for the San Joaquin River Restoration Program is underway, which aims to restore water flows and re-introduce spring-run Chinook to the San Joaquin River between the Merced River and Friant Dam by the year 2012. Throughout the state, water regulation and diversion patterns are being re-examined in light of the current salmon crisis.

While the issue of salmon declines is complex and multi-faceted, we know that many features of the freshwater environment are directly tied to salmonid reproduction and juvenile survival, and that these features can be improved. Essentially, a stream with vegetated banks and floodplain connectivity offers a more complex habitat structure and a higher quality aquatic environment. Riparian vegetation is a key component of healthy salmonid habitat, as it improves physical habitat structure and provides necessary organic inputs, benefiting salmonids throughout the life cycle by creating conditions that sustain reproduction, survival, and better overall physiological condition. We at River Partners believe that restoration and management of these key freshwater habitat features is one very important part of the solution to the current salmon crisis.


Yoshiyama, R. M., E.R. Gerstung, F.W. Fisher, P.B. Moyle. 1996. Historical and present distribution of chinook salmon in the Central Valley drainage of California. Pages 309-362.

Sierra Nevada Ecosystem Project: Final report to Congress, Vol. III, assessments, commissioned reports, and background information. University of California Centers for Water and Wildland Resources, Davis, CA.

Editor’s Note: This article is first in a series. See the next issue of the River Partners Journal to learn about the benefits to salmon in the San Joaquin Valley from riparian restoration.

The above article originally appeared in the Spring 2008 issue of the River Partners Journal.