The Empire Builder, which runs from Chicago to Seattle and Portland, Ore., carries more passengers than any of Amtrak's long-distance trains, 543,000 in 2012.
But it also recorded the worst on-time performance in Amtrak's nationwide network in November, at 44.5 percent. Any number below 80 percent is considered substandard under a law Congress passed in 2008.
Amtrak took the drastic step this month of canceling five Empire Builder trains in one week, three eastbound and two westbound, between St. Paul, Minn., and Spokane. Delays in North Dakota and Montana were causing an imbalance of equipment and personnel at each end of the scenic, 2,000-mile run across the country's northern tier.
"Crews have to go off-shift. Equipment has to be serviced," said Marc Magliari, an Amtrak spokesman. "We thought it best to stand down."
He added that the move was largely because of congestion on the lines of the BNSF Railway Co., the 32,500-mile freight railroad bought by billionaire investor Warren Buffett in 2009.
BNSF, based in Fort Worth, Texas, is a major hauler of coal from Wyoming's Powder River Basin and of crude oil from the booming Bakken region in North Dakota. The railroad and energy companies are working to develop terminals in Washington state to handle more of both.
Opponents, including environmentalists and community groups, fear the increased traffic could choke the Northwest's rail network and harm the industries and people in the region that depend on it. An unusually robust fall harvest doubled the number of grain trains on the BNSF network, on top of a growing volume of crude oil.
Amtrak's Cascade trains operate on the BNSF route between Portland, Ore., and Vancouver, B.C., which also is the path of fossil fuel shipments.
BNSF already hauls coal through Washington state to an export terminal in Canada and crude oil to a refinery in Anacortes. These long, heavy trains share the rails with the Empire Builder along much of its journey.
Roxanne Butler, a BNSF spokeswoman, attributed the congestion to an increase in the number of grain trains from 60 a day to 122. She said the crude oil shipments account for 85 trains a day, "one-half of 1 percent of the total daily train volume."
Still, that's 85 trains BNSF was not operating before the Bakken boom, and many observers have questioned whether the railroad has enough track space to handle the increased shipments without delaying other trains.
"What the long-term implications are is hard to say," said Russ Capon, president of the National Association of Railroad Passengers, an advocacy group. "It depends on how fast the railroad's able to add track capacity."
Butler said the railroad's system-wide traffic levels remain below their pre-recession peak. But the railroad anticipates growth, as reflected in its capital spending plans.
BNSF said in August that it would spend $335 million this year to add capacity to its lines in Montana and North Dakota, and an additional $125 million to improve its network in Washington state, all part of a $4.1 billion system-wide investment.
Washington received nearly $800 million in economic stimulus funds from the Obama administration to pay for passenger rail improvements in the Cascade Corridor, including more double track and longer passing sidings on the BNSF line. Though that investment was intended to expand passenger service, it could also boost freight.
Crude oil production in North Dakota is setting records every month and is predicted to surpass 1 million barrels a day next year, from next to nothing five years ago. In October, almost 70 percent of the oil was shipped by rail, and much of that by BNSF. In the absence of new pipelines, including the controversial Keystone XL pipeline, rail has become the alternative.
The Bakken boom has increased ridership on the Empire Builder, which stops at two North Dakota towns, Minot and Williston, that have become home base for thousands of workers. Many arrive by train.
But increasing delays have put a dent in those gains. In 2013, the passenger count fell 1.2 percent.
Magliari said Amtrak has a good relationship with BNSF, and it's working to get the trains back on schedule.
"Our passengers aren't concerned with what freight shipments are impeding our traffic," he said. "They are concerned about trains being delayed hours and hours and hours."