Video showed train travelers stepping carefully and lifting suitcases as several inches of water flowed through the downtown Los Angeles station's indoor walkways.
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Cleanup crews were on scene, trying to redirect the streams and clear paths for people to walk.
"LA Union Station is an absolute mess right now," one traveler tweeted.
A Metro spokesman says the flooding in the passageway began around 6 a.m. Thursday. Metro and Amtrak provided carts to carry passengers and luggage through the flooded area.
Staff used sandbags, hoses and pumps to channel and collect the rainwater, and had the flooding stabilized by around noon. The passageway was clear of water by 1 p.m. he said.
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It did not appear train operations were affected.