The role of hatcheries in the Columbia River Basin is far more intricate than I knew when I arrived at the Leavenworth Fisheries Complex in 2015. Most people understand that hatcheries raise fish for release, usually to support fishing. But beyond that, goals can be lofty — like saving the unique genetic diversity of Chinook salmon in the Methow River, for instance. That’s part of what Winthrop National Fish Hatchery (NFH) does.

Winthrop NFH opened in 1942 to mitigate for the impact of Grand Coulee Dam on migrating fish, and to support tribal, sport and commercial fisheries. The hatchery aims now also to minimize domestication of the fish they raise. In partnership with Methow Fish Hatchery (FH) — funded and operated by Douglas County PUD — Winthrop NFH raises spring Chinook that are genetically linked to the wild population.

Why do genes matter? Salmon raised for generations in a hatchery behave differently from those in the wild, much like dogs behave differently from wolves. When domesticated hatchery fish breed with wild fish, the traits inherited by the offspring may not be useful in a wild setting, and could harm survival.

Diversity also matters. Salmon juveniles, for instance, might not all migrate at the same time or in the same way. Changing habitat or climate conditions might favor one migration strategy one year, another the next. A diverse population means flexibility in the face of change.

In operation of a conservation program for Methow spring Chinook, Methow FH collects wild, native spring Chinook each year and spawns them at their site. The resulting young fish are tagged internally and released to supplement the naturally-spawning population. Winthrop NFH takes some of the returning adults from this program for spawning. Biologists at each hatchery use internal tags and analyze scale patterns to tell wild fish apart from fish returning from the Methow FH.

Spring Chinook released from Winthrop NFH are tagged internally, and also fin-clipped so they can be harvested by anglers and commercial fishers. In most years, these returning adults are given to tribes in the region for food and are only rarely spawned. This means fish at the hatchery are seldom more than two generations away from their wild ancestors, reducing the risks of domestication. In years of low abundance, returns from Winthrop NFH provide the population a genetically linked safety net.

Some of the eggs from Winthrop NFH are provided each year to the Chief Joseph Hatchery (operated by the Confederated Tribes of the Colville Reservation) to support its reintroduction program for spring Chinook into the Okanogan River, where native runs were lost. Fish from the Methow Composite population (made up of the Methow’s wild population and fish produced by both hatcheries) were selected for the reintroduction effort because they remain the most closely-linked population to the ancestral Okanogan population. They likely have the best chance to survive and adapt to conditions in the Okanogan River.

Built into this whole process are state, federal, and tribal agreements, federal laws and permits, and reams of carefully recorded data and research.

Pacific Region Fish Health Program staff regularly visit Winthrop NFH to stay ahead of any health problems in the fish population. Winthrop NFH staff feeds by hand, keeping a close eye on the fish and reporting issues promptly. Mid-Columbia Fish and Wildlife Conservation Office (MCFWCO) staff do the research needed to track results of the Winthrop NFH programs.

Is it working? It looks like the answer may be yes. The proportion of natural genetics in the Methow River population appears to be slowly increasing since more concerted, collaborative efforts to manage adults have been made in the last 5-6 years (visit our website to read recent monitoring reports: and That’s encouraging. As the MCFWCO biologist Michael Humling says, “Some changes don’t occur for multiple generations, so we may just be beginning to see the benefit of decisions made five or 10 years ago now.”

I got the chance to help during one of the spawning events in August. A team of hatchery, MCFWCO and Fish Health staff, along with volunteers, collected eggs and milt and took samples for testing health and genetics. My coworkers and I washed fertilized eggs and put them into trays where the eggs slowly develop into tiny fish over the course of the winter. Each one of us held the future of the Methow River’s spring Chinook salmon in our hands. It is an amazing responsibility.

Julia Pinnix is visitor services manager for Leavenworth Fisheries Complex.