ELLENSBURG, Wash. — Twelve years ago this month, Manastash Creek became the epicenter of conflict over the future of fish runs in the Yakima River Basin.

An environmental group, the Washington Environmental Council, had issued a notice of intent to sue irrigators under the Endangered Species Act, contending that barriers erected to allow for irrigation harmed threatened fish by preventing them from reaching 25 miles of prime spawning and rearing habitat in the creek’s headwaters, west of here.

After some early, tense negotiations, the council, local irrigators, tribal, state and federal agencies decided that same year to work together to solve the two key goals — restoring historic fish runs and sustaining irrigated agriculture that began in Manastash Creek in 1871, just a few short years after the Civil War.

It took the groups six years, but they reached an important agreement in 2007 on how to restore the creek while assuring farmers they would have the water they need.

“I don’t know if anyone would have predicted 10 years ago this is where we would be,” said Anna Lael, manager of the Kittitas Conservation District, one of the organizations partnering in the project to restore the creek. “It has been an interesting process to watch and be part of.”

The 2007 agreement paved the way for $7 million to be spent to consolidate irrigation diversions and add fish ladders and screens in the lower six miles of the creek, where all the irrigation development has occurred. Additionally, some water rights have been purchased, leaving water in the creek to boost flows. A diversion is the spot along a river or creek where farmers take water to irrigate crops.

Manastash Creek drains a watershed of 97 square miles southwest of Ellensburg. The creek originates in the north and south fork branches where the 25 miles of stream habitat is located.

Another major milestone for this important Yakima River tributary is about to be realized. Those 25 miles of pristine habitat in the upper portions of Manastash Creek could be open to fish by the end of the year with the removal of the final old irrigation dam, more efficient use of water by farmers and additional flows in the creek.

All that is being made possible by a $5 million state-federal project sponsored by the U.S. Bureau of Reclamation to pipe a small open canal belonging to the Kittitas Reclamation District, a 57,000-acre district that is the largest irrigation water supplier in Kittitas County. The proposed route generally follows the creek.

The bureau project marries with a plan by the Kittitas conservation district headed by Lael and the stakeholder groups she is working with to pipe a delivery system for the remaining three independent farmers who draw water from the creek.

“This project will get three diversions out of the creek and provide them better service, and gives them the opportunity to conserve water,” said Walt Larrick, an activities manager for the agency’s basin enhancement program. “It gives us the ability to put water back in the creek.”

Pressurizing the district lateral will allow farmers to use less water and reduce the amount of seepage and evaporation losses that exists in an open lateral. The water saved will be placed in the creek, adding about 3 cubic feet per second of water to existing flows.

Additional flow in an unrestricted creek is expected to help threatened summer steelhead, as well as coho and other salmon species populate the creek. Steelhead have been listed as threatened under the Endangered Species Act since 1999.

“We are talking about a significant amount of water,” Larrick said. “Even now with the improvements we have seen, it still dries up in the summer. This will help with that situation.”

The bureau’s proposal must be submitted to Congress under a 1994 federal law that authorized water conservation projects in the Yakima River Basin. The plan also must be subjected to public review and comment. The comment period ends March 18.

While farmers and fish along Manastash Creek benefit, the project is seen as a template for improvements in other tributaries that can benefit the Yakima Valley and the entire Columbia River, said Urban Eberhart, a farmer and district director.

Eberhart, an enthusiastic supporter of the lateral piping project and the Manastash Creek restoration, said Manastash shows what can happen in a separate, sweeping $5 billion plan highlighted by additional storage and fish passage that is being pursued in the state Legislature and Congress.

“This project can have full Yakima River system benefits for steelhead,” he said. “This seems like a little project, but its benefits can be seen almost immediately in the rest of the Yakima River and the Columbia River.”

David Lester can be reached at 509-577-7674 or dlester@yakimaherald.com.