Using synthetic antibiotics/chemicals for infectious bacterial pathogens and parasitic disease control causes beneficial microbial killing, produces multi-drug resistant pathogens, and residual antibiotic impacts in humans are the major threats to aquaculture sustainability. Applications of herbal products to combat microbial and parasitic diseases are considered as alternative approaches for sustainable aquaculture. Essential oils (EOs) are the secondary metabolites of medicinal plants that possess bioactive compounds like terpens, terpenoids, phenylpropenes, and isothiocyanates with synergistic relationship among these compounds. The hydrophobic compounds of EOs can penetrate the bacterial and parasitic cells and cause cell deformities and organelles dysfunctions. Dietary supplementation of EOs also modulate growth, immunity, and infectious disease resistance in aquatic organisms. Published research reports also demonstrated EOs effectiveness against Ichthyophthirius multifiliis, Gyrodactylus sp., Euclinostomum heterostomum, and other parasites both in vivo and in vitro. Moreover, different infectious fish pathogenic bacteria like Aeromonas salmonicida, Vibrio harveyi, and Streptococcus agalactiae destruction was confirmed by plant originated EOs. However, no research was conducted to confirm the mechanism of action or pathway identification of EOs to combat aquatic parasites and disease-causing microbes. This review aims to explore the effectiveness of EOs against fish parasites and pathogenic bacteria as an environment-friendly phytotherapeutic in the aquaculture industry. Moreover, research gaps and future approaches to use EOs for sustainable aquaculture practice are also postulated.