Abstract The emergence and prevalence of bacterial pathogens in freshwater aquaculture systems is a growing concern as the economic losses associated with diseases are mounting and impacting the fishery sector. One way of controlling fish mortality and morbidity is using bacteriocin‐secreting probiotics, which are generally considered safe without any adverse effects that usually accompany other treatment strategies. Understanding the mode of action of bacteriocin on pathogens is vital for considering them suitable for application as a prophylactic in aquaculture. Although several measures such as antibiotic treatment, chemotherapy, vaccination, etc., are available, though not without concerns, these methods have limitations for field‐level applications since they result in several adverse effects both for the animals and the aquatic environment affecting several species in the food chain. In this situation, the use of bacteriocin can be an excellent alternative to minimize the disease burden in freshwater aquaculture if delivered appropriately. Here, we provide an update on the various bacteriocins and their mode of action against important pathogens encountered in aquaculture.