The grand jury returned a total of 18 indictments against Columbia Packing and two officials, Joseph Carl Ondrusek and Donny Russell Ondrusek.
Prosecutors say investigators from several agencies saw blood and other waste from the processing of pigs being dumped into Cedar Creek, which feeds into the Trinity.
Columbia officials have admitted the plant spilled contaminants, but said it was by accident.
Columbia Packing and Joseph Ondrusek are charged with water pollution with water pollution. Both Ondruseks and the company are charged with tampering with evidence.
An attorney for Columbia Packing did not immediately return a phone message.