The Central Valley Regional Water Quality Control Board said on Thursday it fined Tracy, Calif.-based Henry Tosta Dairy for the violations.
Officials said the dairy has a history of violations that negatively impact water quality.
In May 2012, inspectors found that wastewater lagoons had not been regularly cleaned, settling basins for manure wastewater were full, and manure slurry encroached on the cows' corrals.
The dairy's waste management plan was also not up to par.
Water authorities said the dairy ignored repeated orders to remove the manure piles.
A call to the dairy was not immediately returned.