The logjam, which spans about 500 yards, formed as debris flowed down river after last weekend's rain. The logs got caught up in the railroad trestle piers, stopping the flow of debris and logs.
The San Antonio River Authority, which manages the river, expressed concerns over the clean up.
"We told them to take more of an environmental approach," said Gloria Rodriguez, a spokeswoman for the San Antonio River Authority. She added the environmentally responsible thing to do would be to remove the trees.
Rodriguez said Union Pacific plans to break up the trees and allow for the stream to flow.
"Breaking up the trees would just give the problem to somebody else down the river," Rodriguez said.
Union Pacific would not say how it planned to clean up the jam, only that is was working with the landowner to clean up the area.
"We are trying to do this as fast as possible, hopefully a couple of days," Espinoza said.