Aquaculture, the most dynamic food sector, is continuously growing to meet the challenge of the increasing demand for animal protein and health benefits of fish consumption. Intensification of production, introduction of new farmed species, and other unpredicted factors may create animal welfare problems, resulting inevitably in higher risks of disease outbreaks and thus increasing use of antimicrobials mainly in top-producing countries. Residues of antimicrobials in farmed animals have received much attention in recent years because of growing food safety and public health concerns, especially in regions where imports of aquatic food are necessary to cover unmet local demand. Development of antimicrobial drug resistance, hypersensitivity reaction, possible carcinogenicity, and disruption of normal intestinal flora are the most crucial concerns for consumers. Several legislative directives and control systems have been implemented to regulate use of antimicrobials and protect consumers from unwanted side effects. Along with the encouragement for modern husbandry and biosecurity practices, increased prevention and prudent chemical use at a farm level, international organizations and national governments should enforce rigid monitoring of antimicrobials and promote further measures to reduce potential human health risks.