Juvenile Chinook salmon swim in a raceway at Iron Fish Gate Hatchery in Siskiyou County, Calif., before their relocation to the Fall Creek facility on July 7, 2021.

As many as hundreds of thousands of fall-run Chinook salmon died early last week in Siskiyou County, California, due to suspected gas bubble disease.

The fish were released into the 257-mile-long Klamath River near the California-Oregon border following November’s historic dam removal at the former Iron Gate Dam site. Removal was intended to help the stream flow freely again and bolster the habitat for the protected species.

Gas bubble disease is noninfectious, and it’s caused by environmental or physical trauma resulting from a change in pressure in spring or groundwater, per the National Library of Medicine. Officials with the California Department of Fish and Wildlife believe up to 830,000 salmon fry — the young that have just consumed their egg sac and emerged from the gravel where they are born — succumbed to the disease as they migrated through the 16-foot-wide Iron Gate Dam tunnel, where they may have encountered a “severe pressure change.” The tunnel and the dam itself are considered “old infrastructure” and are among the three others targeted for removal later this year.

“The problems associated with the Iron Gate Dam tunnel are temporary and yet another sad reminder of how the Klamath River dams have harmed salmon runs for generations,” a news release from the agency read. “CDFW will plan all future salmon releases below Iron Gate Dam until this infrastructure is removed. Poor habitat conditions caused by the dams and other circumstances such as this are reasons why CDFW conducts releases of hatchery fish at various life stages.”

Officials determined the likely culprit due to the visual appearance of the dead fry; typically, fish that are afflicted with the disease develop lesions and hemorrhaging of the gills and fins, and may exhibit violent head shaking and abnormal buoyancy that causes them to float to the water’s surface. Fish captured by the CDFW’s partners downstream from the dam had “popped eyes,” another telltale sign, Jordan Traverso, a spokesperson for the CDFW, told SFGATE in an email.

“It was discouraging and sad to learn of this issue,” Traverso said. “Our staff invest so much of their time and care into these fish, it is really tragic to have something like this happen.”

The 830,000 fish that passed through the river last Monday were the first to be released from the CDFW’s new hatchery in Siskiyou County. Officials have ruled out other issues in water quality conditions, including turbidity and dissolved oxygen, which were “at suitable levels” during the release and on the days prior to the “large mortality” event. They also noted that monitoring equipment “documented other healthy yearling coho and Chinook salmon that came from downstream of the dam.”

Last year’s deconstruction of Copco No. 2 — the first of four hydroelectric dam removals in total — is part of what is believed to be the largest project of its kind in U.S. history. It comes just over two decades after more than 30,000 fish were wiped out on the Klamath River due to low flow rates, warm water temperatures and other conditions related to the dams, which allowed for parasites and bacteria to develop and delayed migration for the fish.

The Klamath River was once home to the third-largest Chinook salmon population on the West Coast. The recent mortality event comes after three reservoirs behind the dams exposed thick sections of mud and sediment that turned the water into a murky, chocolate milk shade of brown, trapping deer that subsequently had to be euthanized. Large numbers of non-native fish species, like largemouth and smallmouth bass, catfish, bluegill and yellow perch, were also found dead in the drained lake beds.

Still, the CDFW said those conditions, while unfortunate, were anticipated, and that its hatchery has over three million more salmon it plans to release later this month, downstream from the dam and tunnel. Juvenile fish like salmon fry can have high mortality rates due to predators, lack of food or disease, and the CDFW’s planned release will include fish in later stages of the species’ life cycle, specifically smolts and yearlings.

“The additional stock of fall-run Chinook salmon remaining in the hatchery exceeds the annual production goal and will help offset losses experienced with the initial release of fry,” the CDFW said.