Using Science to Protect and Track Salmon and Steelhead


Juvenile Salmon are surgically implanted with with acoustic tracking tags by DWR scientists to track the fish migration along the Sacramento River in West Sacramento, California. Photo taken April 18, 2024.

Juvenile Salmon are surgically implanted with with acoustic tracking tags by DWR scientists to track the fish migration along the Sacramento River in West Sacramento, California. Photo taken April 18, 2024.

Department of Water Resources (DWR) scientists wanted to understand why high numbers of Chinook salmon and steelhead were migrating and collected at the State Water Project’s Skinner Fish Facility this season. Thanks to DWR’s use of the best available science in advanced fish tracking technology and genetic tools, they now have some answers.


The mystery started this spring, when higher than expected numbers of winter-run Chinook salmon and steelhead were being collected at DWR’s Skinner Fish Facility, resulting in significant water export reductions. Winter-run Chinook salmon and steelhead are both “listed species,” which are species classified as either threatened or endangered on federal or state Endangered Species Act lists.


The DWR team started by examining hatchery salmon marked with coded wire tags. Coded wire tags are the size of the tip of mechanical pencil lead and are each laser-etched with a code, which indicates the fish’s hatchery of origin and when they were released. Coded wire tags are inserted into the nasal cavity of approximately one quarter of hatchery-produced juvenile Chinook salmon in California.


Of the 3.4 million salmon tagged with coded wire tags between late December 2023 and early March 2024, the fish facilities at the State Water Project and federal Central Valley Project South Delta pumping operations collected less than 400 of these tagged fish at the fish screens. Meanwhile, DWR estimates over 1.5 million of the tagged salmon entered San Francisco Bay in good health by early April 2024. Together, these estimates point to high survival rates of tagged salmon through the Delta system and into the Bay, compared with estimates of previous years.


Next, DWR’s science team looked at the results of special studies designed to examine the effectiveness of DWR’s Georgiana Slough Bio-acoustic Fish Fence. This large barrier is installed where the Sacramento River meets Georgiana Slough and is sometimes called the “disco barrier” because it uses bubbles, lights, and sound to deter migrating salmon and steelhead from entering Georgiana Slough, which would lead fish into the predator-rich waters of the Central Delta and South Delta and to the south Delta State and federal pumping operations.


For these studies, scientists inserted acoustic tags into hatchery salmon and wild steelhead to see if the barrier was effective. Acoustic tags emit a unique frequency that gets recorded by nearby receivers, which can indicate the migration path of that fish. So far, studies this year with the acoustic tags are showing the disco barrier is exceeding expectations at keeping both Chinook salmon and steelhead in the Sacramento River and away from the State Water Project pumps. The disco barrier might also be contributing to the high survival rates estimated from the coded-wire-tagging studies.


And finally, DWR is using rapid genetic technology to determine which Chinook salmon runs are showing up at the fish screens. Since water exports are affected when listed species are found at the fish facility, DWR needed to be certain the “winter-run Chinook” being found were actually winter-run. This uncertainty comes from the fact that the four Central Valley Chinook run-types all look the same. While winter-run are “endangered” species and spring-run are “threatened” species under the Endangered Species Act; fall-run and late-fall-run are not listed species and their capture at the fish facilities does not trigger export reductions. With the aid of SHERLOCK, which stands for Specific High-sensitivity Enzymatic Reporter un-LOCKing, as well as other genetic tools, DWR was able to determine that the number of genetic-confirmed winter-run salmon collected at the State Water Project fish screens were a small fraction of what was initially identified. This is the second year of experimental work to test genetic tools to determine run-type of juvenile salmon collected at fish facilities, and it is proving extremely helpful for accurate identification and appropriate application of required export reductions.


Further inspection of the Chinook salmon collected at the fish screens showed most were non-listed runs and they were primarily coming from the San Joaquin River, not the Sacramento River as originally suspected. The river source matters, because permit regulations state that DWR is only responsible for Chinook salmon originating from the Sacramento River Basin. If a Chinook salmon comes from the San Joaquin River Basin, then operations are not affected.


Altogether, DWR’s team has used science-based technologies to determine that protected runs of Chinook salmon and steelhead from the Sacramento basin experienced high survival and low entrainment into the interior Delta and State Water Project fish screens. Although much of the story has yet to be explained, it appears that the San Joaquin basin salmon were driving fish collections this spring. During upcoming years, DWR will use science from genetic and barrier technologies to provide improved assessments of real-time risks so that water operations and environmental protections can be managed for the listed salmon and steelhead runs that need protection.


DWR remains committed to using and advancing the best available science, such as environmental DNA, and collaborating with partners at the Tribal, local, state, and federal levels so salmon can thrive.


Visit DWR’s Protecting California’s Salmon StoryMap to see more of the work being done to help salmon in California.