The resistance of fish to microorganisms challenge depends mainly on the efficacy of the immune response. Most studies on the natural immune response of fish have focused on the effect of diets and immunostimulants. Few studies correlated the presence of commonly used agrichemical and susceptibility to infection by aquatic microorganism. Thus, this study aimed to investigate the effect of glyphosate and atrazine-based herbicides on immune cell phagocytosis and susceptibility of silver catfish to Aeromonas hydrophila infection. Following exposure to sublethal concentrations of glyphosate or atrazine (10% of the LC 50–96 h), a significant decrease in the number of intracelomatic cells and phagocytic index could be observed. In addition, silver catfish fingerlings exposed to glyphosate or atrazine were more susceptible to intracelomatic challenge with pathogenic A. hydrophila. Thus, the presence of these herbicides on the water alters the natural immune response to bacterial and possibly to other aquatic microorganism.