ACE train service from Stockton to San Jose was canceled Monday and won't be back to operating until Thursday.
Approximately 5,000 to 7,000 commuters had to find other ways to get to work.
ACE service has four westbound and four eastbound trains on the tracks each weekday with stops in Manteca, Tracy, Livermore, and Fremont.
The trains travel on Union Pacific rail lines, but weather disruptions on other Union Pacific freight lines in Northern California have closed some routes.
ACE Marketing Manager Chris Kay says, as a result, the ACE trains have to give way to the freight train traffic.
“There’s been some flooding and there was a derailment in Elk Grove," says Kay. "With the weather affecting their other routes, the only available route they had to move the trains is through the Altamont.”
Kay says the rail lines along the Altamont Pass are in good condition and expects regular service will resume on Thursday.
He adds that commuters in San Joaquin County can take the RTD bus to the Dublin Bart Station, and Fremont commuters can use their ACE ticket to ride the Capitol Corridor train.