The failure of pumps in a tunnel along the Blue and Yellow lines caused major delays for Metro riders Monday morning.

The transit authority suspended rail service between Braddock Road and Reagan National Airport stations, bridging the gap with shuttle bus service that more than doubled the commute time for some passengers.

Workers discovered flooding in the tunnel, which runs under Route 1, about 5 a.m., said Metro spokesman Dan Stessel. They were unsure why pumps in the tunnel lost power, he said.

Heavy rains soaked portions of the region Sunday, with more than an inch of rain recorded at National Airport and almost three inches in some portions of Montgomery and Prince George’s counties, according to The Washington Post’s Capital Weather Gang.

Stessel said crews brought in auxiliary pumps to move water out of the tunnel. The power problem was resolved by 9:30 a.m., and both tracks reopened to train traffic.

The “root cause” is under investigation, he said. “We honestly don’t know what the root cause is.” To bring them back up involved “rewiring.”

Metro officials said Monday afternoon that they would have “personnel monitoring the tunnel for flooding” through the night and that they are installing a “temporary backup pump in the event the main ones fail.”

Many riders reported confusion at the stations and complained about the long lines as they waited for shuttle buses.

Ashley Ackerley, 26, said her normal one-hour commute from her home in Alexandria to her job at American University, near the Tenleytown station, took 2 hours and 15 minutes.

She said that about 6:30 a.m., when she boarded at the Huntington station, Metro was “good at telling people” that the Blue and Yellow lines between Braddock Road and National were closed and directing riders that they would have to take a shuttle bus. At the Braddock Road station, she encountered disorganized crowds trying to board shuttles.

“It was truly chaos,” she said, noting that the train platform was crowded and riders were standing “body to body” waiting for buses.

“The entire sidewalk was packed,” she said. “I walked into a sea of people.”

Ackerley waited 47 minutes for a shuttle bus from Braddock Road to National. She then took the Yellow Line to Chinatown and boarded the Red Line to Tenleytown. Because of the delay, she canceled her plans to work out at the gym before work.

“I try to stay pretty calm with what goes with Metro,” she said. “But they need to have plans for when train lines do shut down. . . . It is frustrating. They need to get Metro employees to the station and help to direct people and the buses.”

At National, Matthew Hurtt, 24, of Arlington County said he saw “a few police officers directing hordes of people” as they tried to board shuttle buses just before 9 a.m. He was headed to his office in Alexandria. “It was pretty wild,” he said.

His normal 20-minute commute from the Pentagon City station to the King Street stop turned into an hour and made him 30 minutes late to his job as a copy writer for political fundraisers.

Stessel said “there’s no question there were long lines for the buses” but noted that it is hard to replace the capacity of riders a train can carry in a short amount of time with no warning. Long lines, he said, “are sort of expected” in this type of situation.

MARC service was also suspended temporarily Monday on the Penn Line between Washington and Baltimore.

A spokesman said that 18 inches of water was reportedly covering the rails in the Baltimore and Potomac Tunnel but that the impact on commuters was minimal because the shutdown occurred well after the morning rush.

Flooding delayed Amtrak trains, too.