The latest in a string of rush-hour disasters to hit San Francisco commuters occurred Thursday morning, after a flood at Embarcadero Station halted Muni service for hours and briefly stopped East Bay-bound BART trains.

Video posted by BART showed a waterfall cascading onto the tracks and splashing onto the marble floor. The culprit, a failed fire suppression test, sent water gushing onto trackways and platforms at 5:32 a.m. Crews set up traffic cones around the stairwells and escalators as workers in yellow vests mopped up.

“Watch your step,” a BART train operator warned passengers who gingerly stepped off a San Francisco-bound BART train.

The agency was testing the fire suppression system overnight when the drainage system malfunctioned and caused water to build up, said Paul Rose, a spokesman for the San Francisco Municipal Transportation Agency.

By 6:30 a.m., water had seeped from Muni tracks down to BART, located in the basement of the station. It continued to leak from pipes in the drainage system after work crews shut off the valve, Rose said.

Here is the situation right now. pic.twitter.com/6blqm09tbc — SFBART (@SFBART) July 18, 2019

For hours, the L-Taraval, M-Ocean View and J-Church lines stopped at Montgomery Station. Backups stretched throughout downtown San Francisco, making many commuters late to work. N-Judah and T-Third trains were passing through Embarcadero Station to Third Street but not stopping, according to Muni.

The subway was so congested by mid-morning that transit officials began switching back at Church Station to relieve the bottleneck.

Mark Miller, a retail manager who takes the Metro from Civic Center to Powell Street, said his normally quick commute took more than 20 minutes Thursday morning.

Many riders were stoic, shrugging off the delay as just another rush-hour hassle for San Francisco’s beleaguered rail system. Others ran out of the gates with agitated expressions.

Finance worker Aleksey Lakhchakov got so tired of waiting for the trains to move that he got off at Powell Station and walked to work, instead of exiting the train at Montgomery.

“It usually takes about 20 to 25 minutes,” he said of his daily commute from Cole Valley. “Today it was 40 minutes.”

“I might catch a bus or walk,” said Robyn Nason, a software engineer who got off the train at Powell several blocks from her normal stop at Embarcadero. She was also 20 minutes late.

Gwendolyn Wu and Rachel Swan are San Francisco Chronicle staff writers. Email: gwendolyn.wu@sfchronicle.com, rswan@sfchronicle.com Twitter: @gwendolynawu @rachelswan