SNOHOMISH — A much-anticipated purchase of a nearly 12-mile stretch of rail corridor between the city of Snohomish and Woodinville won’t be happening for now.

Snohomish County is preparing to back away from a $5 million sale agreement with the landowner, the Port of Seattle, which has been under discussion since late 2013. The County Council is expected to formally end negotiations on Wednesday.

“We just agreed with the port that maybe we need to start fresh,” county public works director Steve Thomsen said. “And we’re not sure what that looks like right now.”

Complications have included how to accommodate both train tracks and a pedestrian-bicycle trail over some bridges and trestles, Thomsen said. There are also potential ownership questions on portions of the trail.

The purchase has been talked up as a way to connect Snohomish County’s popular Centennial Trail to an extensive network of recreation trails in King County. The addition would have supplied a missing link to downtown Woodinville and King County’s Sammamish River Trail.

The corridor also sees some freight use.

The county’s plan has always been to use the corridor for both recreation and train traffic.

Snohomish city leaders have long eyed the rail segment’s potential to ferry trains full of tourists and — some day — even commuters. Mayor Karen Guzak called the setback “a short-term disappointment,” though she still harbors “a long-term hope.”

“We are still really excited about the potential for both rail and trail, but we understand the complexities of this purchase,” Guzak said. “We just need to be patient.”

No city projects are directly affected by the disintegration of the county deal. That includes the city’s plans to turn 20 acres of land recently purchased from the Stocker family into a park along the Snohomish River.

The Snohomish-to-Woodinville corridor is part of an old rail line the Port of Seattle bought in 2009. The East Side Rail Corridor originated in the 1880s, but had dwindled to minimal freight use by the time BNSF sold it.

The port paid BNSF Railway $81 million for 42 miles of track and right of way extending from Snohomish south to Renton. The property included a spur line to Redmond. The Port sold off sections to King County, Redmond, Kirkland and Sound Transit.

Woodinville hopes to finalize the purchase of a two-mile segment of the corridor later this year, leaving the Snohomish County portion the only stretch still under port ownership.

Grants from the county’s property-tax funded Conservation Futures program would have supplied $3.5 million of the Snohomish County purchase. Other county funds would have covered the remaining $1.5 million.

The property runs from the city of Snohomish to the north end of King County’s Brightwater treatment plant in Maltby. It measures about 100 feet wide in most places, but reaches up to 200 feet in some areas, Thomsen said. In spots, it’s more of a rail easement than solid real estate.

Any plans on those stretches need to accommodate the business of freight operator Eastside Community Rail. The Snohomish-based company stands ready to work with the county and the port to make the deal materialize, director Doug Engle said.

“The railroad continues to support rail and trail together,” Engle said. “We believe there are things we can do to help the county get the trail it’s looking for.”

In the near future, Engle wants to increase the number of freight cars it runs a couple of times per week to serve industrial properties in Maltby. The company still envisions excursion trains between Snohomish’s antique district and downtown Woodinville. Commuter trains, he said, could be running “within a decade.”

Noah Haglund: 425-339-3465; nhaglund@heraldnet.com. Twitter: @NWhaglund