Diseases are the major bottleneck causing low- to high-impact economic losses to farmers. Among the different aetiological agents, bacterial pathogens pose a severe threat to the aquaculture industry. With the increasing intensity of culture practices, the complexity of diseases has also increased manyfold. Although both Gram-positive and Gram-negative bacteria are responsible for causing diseases in fish, most of the bacterial infections in fish are of the Gram-negative origin. The genera Aeromonas, Edwardsiella, and Flavobacteria are mostly predominant in freshwater aquaculture and responsible for causing diseases. Several culture-dependent and culture-independent techniques for bacterial identification and characterization are well-established, aiding in timely diagnosis. Treatment of bacterial infections greatly depends on the use of antibiotics and other water sanitisers. In recent times, the increasing resistance commonly observed against a wide variety of antibiotics by several bacteria has rendered most treatments ineffective. Development of new-generation alternative eco-friendly means of bacterial disease management will be of immense help to the sustainable growth of the aquaculture sector.