The derailment happened just before 7 am on Monday, closing a 10-mile stretch of the highway in Goshen for hours.
Crews worked through the night to repair the wreckage left behind after the Union Pacific train derailed, spilling toxic chemicals near Goshen.
Union Pacific officials said six tank cars derailed. One carrying hydrochloric acid, a chemical that can be harmful to humans, leaked as the train came to a crashing halt.
Early Tuesday morning, officials had removed all the overturned cars, and were working to repair the rails.
NB lanes on Hwy 99 remain closed after freight train derails near Goshen
On Monday night, all three southbound lanes and one northbound lane had reopened to drivers. Travelers inched their way along Highway 99 in Tulare County more than 12 hours after the accident.
By Tuesday morning, a second northbound lane was opened.
The California Highway Patrol had more people on patrol as part of the heavily used freeway heading north is still closed off, and dozens of local and state agencies remain at the crash site.
CHP officials said there were no longer any leaks, and the air quality was good and stable.
More road closures expected after train derailment on Highway 99
Railroad officials said they hope to have the highway fully reopen by the end of Tuesday.
The cause of the derailment is still under investigation.
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