Commercial production of catfish is the leading aquaculture industry in the United States. Production in Mississippi, Louisiana, Alabama, and Arkansas representing 96% of the total catfish sales in the USA. In 2017, the USDA-FSIS added testing of generic Escherichia coli and Enterococcus to the sampling of Siluriformes. The incidence of Escherichia coli in fish and seafood has been associated with possible fecal matter contamination. However, this indicator bacteria could also be a part of the natural microflora of catfish ponds where processing plants collect hybrid catfish. Aerobes, Psychrotrophs, Coliforms, Escherichia coli, and Enterobacteriaceae counts among environmental, liquid and fish samples were tested every season and periodically during one day of operation. Generic Escherichia coli counts were greater in late Summer (P ≤ 0.05) for liquid samples (1 log CFU/g) . During the day, Escherichia coli appeared to be more recurrent in the afternoon at the skinning step (P ≤ 0.05).