One of the constraints in fish disease management in aquaponic systems is related to undesired effects of chemicals on fish, plants and beneficial bacteria. Plant-derived compounds with nontoxic features to fish, plants, and microflora provide an alternative treatment strategy against the harmful pathogens in the aquaponic system. The present study assessed the antiparasitic activity of garlic (Allium sativum) and onion (A. cepa) extracts against Gyrodactylus elegans (Monogenea) in vivo and in vitro, and physiological stress responses in carp, Cyprinus carpio, treated with these extracts in an aquaponics system. Garlic and onion extracts exhibited in vitro antiparasitic activity against G. elegans. The mean survival time of G. elegans in vitro ranged from 30 sec to 6 min depending on the concentration and exposure time both for garlic and onion extracts. For garlic extract EC50 (median effective concentration) was 8.37±4.75 mg/mL in 3 min exposure and for onion extract 4.72±7.10 mg/mL. These concentrations were in vivo tested in carp heavily infected with G. elegans as a single application for 3 min. In vivo treatment of carp with garlic and onion extracts reduced G. elegans found on the skin by 14.4% and 19.8%, respectively. In both treatment groups, the physiological stress response of carp was mild based on the alterations in the secondary stress indicators (hematocrit, plasma glucose, and lactate). The stress indicators of carp returned to normal levels after an hour recovery in freshwater. The antiparasitic potential of onion and garlic extracts may be considered as an alternative treatment to reduce Monogenean infections in aquaponic systems.