The aquaculture industry is suffering from significant financial setbacks due to an increasing frequency of disease outbreaks, posing a threat to the sector’s sustainability. Various bacterial, viral, parasitic, and fungal pathogens have led to massive mortalities in farmed fish worldwide. Throughout the years, the management of fish diseases has predominantly centered around the utilization of conventional antibiotics and chemicals. Nevertheless, their indiscriminate use has given rise to serious implications, including an increase in resistant pathogens, disruptions in the metabolic processes of fish, degradation of the aquatic environment, the presence of drug residues in aquatic products, and a potential threat to human health. Various effective bio-based and immunoprophylaxis alternative therapies have been developed to overcome these impediments. Recent alternative therapeutic approaches to fish diseases encompass a range of strategies, including phytotherapeutics, nanotherapeutics, probiotics, prebiotics, synbiotics, phage therapy, vaccination, quorum quenching, antimicrobial peptides, biosurfactants, bacteriocins, stem cells, and diagnostic-based therapy. Advancements in biotechnology have significantly enhanced the efficacy of these therapies. However, additional research is essential to refine the utilization of these therapeutic approaches. Critical concerns, such as efficacy, cost, risks, availability, and adverse effects on fish and the ecosystem, need to be addressed to establish guidelines for their sustainable application in aquaculture. This review will increase aquaculturists’ awareness of recent therapies used in fish farming, their mechanisms, challenges, and impacts while promoting the sustainability of commercial aquaculture.