A King County Superior Court judge sent the city back to the drawing board in its nearly three-decade quest to complete the last missing link of the Burke-Gilman Trail, which runs from Bothell through Fremont before abruptly shunting cyclists and pedestrians onto Ballard streets.

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The city of Seattle spent five years and $2.75 million to evaluate the environmental impacts of building a 1.4-mile stretch of bike trail through Ballard. It wasn’t enough.

King County Superior Court Judge Samuel Chung has sent the city back to the drawing board in its nearly three-decade quest to complete the last missing link of the Burke-Gilman Trail, which runs for 18 miles from Bothell through Fremont before abruptly shunting cyclists and pedestrians onto trafficked Ballard streets veined with railroad tracks.

The judge’s order effectively blocks construction on the project, which has become a long-running saga pitting trail users against industrialists. The city had planned on beginning construction of the trail early next year.

In an oral ruling Thursday, Chung said that although the city’s 300-page environmental impact statement adequately assessed the traffic, parking and environmental effects of the proposed bike path along Shilshole Avenue Northwest, it failed to fully account for the economic impacts of the path.

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Chung overruled a Seattle hearing examiner, who earlier this year said the city’s environmental study was sufficient.

A coalition of maritime and industrial businesses, led by the King County Labor Council, has been challenging the city’s proposed route for the path, in a dispute that stretches back to the late 1980s and has been in various stages of litigation for more than a decade.

“It vindicates what we’ve been saying for nearly 20 years, which is that this trail will put these maritime and industrial businesses out of business,” Josh Brower, a lawyer for the coalition, said of the judge’s ruling. “So they have to go back and redo it and tell the truth about the economic impacts that this trail will have.”

Of more than 4,400 public comments on the draft environmental impact statement, nearly 80 percent favored the route along Shilshole Avenue Northwest.

The businesses argue that putting the path on Shilshole, where it will cross dozens of driveways used by heavy trucks, is a safety hazard and would disrupt long-standing maritime businesses. They propose an alternate route along parallel Leary Way Northwest.

The city, and bicycling and pedestrian advocates, argue that Shilshole is the fastest, most direct route and that the Leary option passes through many more intersections.

The Cascade Bicycle Club stressed that Chung ruled that most of the environmental impact statement (EIS) was sufficient.

“Judge Chung identified the analysis of economic interests — specifically the potential for increased costs of insurance — as the single basis for ruling the EIS deficient,” said Claire Martini, Cascade’s policy manager. “We believe this can be resolved and that the city can move forward with getting construction back on track.”

The Shilshole route is already something of a compromise, as bike groups had wanted the trail to go along Northwest 54th Street between 24th Avenue Northwest and the Ballard Locks. Instead, the city’s proposed route has the trail swinging up to Northwest Market Street, as industry preferred.

Dan Nolte, a spokesman for Seattle City Attorney Pete Holmes, said the city disagrees with the judge’s decision and plans to appeal it.

In addition to the money spent on the environmental impact statement, the city has spent an additional $4.8 million on design work for now-scrapped routes.

The project is expected to cost more than $26 million to build, but the city says only about $7 million of that is for the trail itself; the remainder is for street paving, sidewalks and traffic lights that got folded into the project. The city has also spent hundreds of thousands of dollars on outside legal counsel to argue its case.