At least five cars derailed into the water near East Penn Street around 8:15 a.m. in Huntingdon Borough.
The Norfolk Southern cargo train spilled non-hazardous materials into the water including peas, dried potatoes, pulp board and plastic pellets. Fire crews have set up a system to contain the plastic pellets before they get into the Juniata River.
The train was traveling from Altoona to Harrisburg when it derailed. It consisted of two locomotives, 75 rail cars and 10 empty cars.
Crews are expected to work around the clock on clean up weather permitting. Clean up is expected to last at least several days.
The cause of the crash is under investigation.