Aquaponics is an alternative method of food production that confers advantages of biological and economic resource preservations. Nonetheless, one of the main difficulties related to aquaponics systems could be the outbreak and dissemination of pathogens. Conventional treatments need to be administrated carefully because they could be harmful to human, fish, plants and beneficial microorganisms. Aquaponics practitioners are relatively helpless against plant diseases when they occur, especially in the case of root pathogens. Biological control agents (BCAs) may be an effective alternative to chemical inputs for dealing with pathogens of plants under aquaponics systems. Research of BCAs on aquaponics systems is limited, but there are numerous publications on the use of BCAs to control plant pathogens under soilless systems which confirm its potential use on aquaponics systems. The present review summarized the principal plant pathogens, the conventional and alternative BCA treatments on aquaponics systems, while considering related research on aquaculture and soilless systems (i.e., hydroponic) for its applicability to aquaponics and future perspectives related to biological control. Finally, we emphasized the case that aquaponics systems provide relatively untapped potential for research on plant biological control agents. Biological control has the potential to reduce the perturbation effects of conventional treatments on microbial communities, fish and plant physiology, and the whole function of the aquaponics system.