Spring-run Chinook salmon have long played second fiddle to winter-run Chinook salmon when it comes to conservation planning for the Central Valley salmonids protected under the California and federal Endangered Species Acts. But earlier this year, the California Department of Fish and Wildlife issued an Incidental Take Permit (ITP) that promises increased attention for spring-run Chinook. The ITP calls for the aggressive development of a spring-run Juvenile Production Estimate (JPE). The purpose of the JPE is to better track the abundance of juvenile spring-run Chinook and, ostensibly, to provide a basis for setting the number of juvenile spring-run Chinook that the State Water Project is allowed to entrain at the water-export facilities in the south Delta. 


While adult spring-run Chinook migrate into the Central Valley rivers between March and June, they wait to spawn until autumn, thus their spawning window overlaps with that of the much more abundant fall-run Chinook salmon. The overlap in spawning between spring-run and fall-run Chinook has significant implications.

  • Where spring-run and fall-run Chinook co-occur, individuals from the separate run-types cannot be reliably distinguished on the spawning grounds. As a result, our understanding of the abundance of true spring-run salmon is often uncertain.
  • Where spring-run and fall-run Chinook co-occur, they are likely to interbreed. Predictably, this hybridization creates ambiguities in run-specific abundance estimates and how fish are treated under the ESA.
  • Fish size on a specific date – referred to as “length-at-date” – can be used to reliably identify winter-run Chinook in certain months, however the approach is wholly ineffective for distinguishing spring-run Chinook from fall-run Chinook. This challenges the accuracy juvenile-monitoring programs (including the JPE). 

The spring-run Chinook JPE produced under the ITP should attempt to resolve those uncertainties by applying genetic-identification methods. However, to date genetic techniques have not been consistently adopted by the regulatory agencies dealing with listed fishes, at least not for the purpose of setting ESA “take” limits.  For example, annual take limits for juvenile winter-run Chinook at the export facilities are still based on a length-at-date classification, despite the fact that genetic methods available since 1996 have shown length-at-date measures can yield false-positive error rates approaching 80 percent. 

In contrast to winter-run Chinook, spring-run Chinook are broadly distributed and relatively abundant. The National Marine Fisheries Service considers any Chinook salmon exhibiting spring-run-like adult migration behavior (considered a phenotypic characteristic of the run) to be part of the protected spring-run Chinook Evolutionary Significant Unit (ESU). Therefore, all phenotypic spring-run Chinook are listed under the federal ESA and protected from “take.”  By this standard, NMFS has identified eleven Sacramento River basin tributaries hosting fish considered to be part of the Central Valley spring-run Chinook ESU; from 2000-2018, spawning abundance for spring-run Chinook salmon included in the ESU annually averaged 13,800 fish (ranging from 1,750 to 30,697).

Phenotypic spring-run Chinook in eleven tributaries (and one hatchery program) are protected by the ESA, but only fish occurring in Deer, Mill, and Butte Creeks are considered by NMFS to contribute to viability of the ESU.  Accordingly, while the Feather and Yuba rivers host some of the largest spring-run Chinook populations in the Central Valley, hatchery influence and possible fall/spring hybridization have led NMFS to conclude those populations pose a threat to spring-run Chinook viability rather than contributing to its survival and recovery.  Exemplifying the point, Feather River Hatchery spring-run Chinook are identified as a key threat to the ESU, yet the same fish are fully protected from “take” under the federal ESA. 

These contradictions and ambiguities in the application of the ESA are illogical. But of greater concern, they are major impediments to improved monitoring efforts, directed management actions, and species recovery. Monitoring programs designed to sample adult spring-run Chinook could be implemented to provide more reliable abundance estimates and allow critical genetic data to be collected. In some tributaries, temporary weirs could be operated to collect data, also to experiment with strategies to minimize interbreeding between fall-run Chinook and hatchery-produced Chinook salmon. Producing a reliable Juvenile Production Estimate, as the ITP requires, will require the capture of up to 100,000 juvenile spring-run Chinook. Such efforts could contribute to recovery of the ESU, but are nearly impossible to imagine being implemented under prevailing federal ESA “take” regulations that apply to the species.

Current policies have created a Catch-22 for spring-run Chinook that is inhibiting and disincentivizing actions that otherwise could contribute to its viability and recovery. The problem could be corrected with sensible revisions to listing determinations or to “take” standards. Until such reforms are realized, the most effective strategies to understand and recover Central Valley spring-run Chinook salmon will remain out of reach.

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