Cage aquaculture in inland waters is being regarded as an opportunity to utilize prevailing reservoirs with great production potential to augment fish production. Indian reservoirs with a water spread area of 3.51 million ha offer an enormous opportunity to enhance productivity through enclosure culture. This untapped potential can be utilized in a well-planned manner to increase aquaculture production. Intensification of aquaculture production results in an increased level of stress in fishes, which ultimately increases the disease susceptibility of fishes. Diseases are the major constraint to the aquaculture industry, as they lead to huge losses to farmers. Two broad categories of diseases affect fish: infectious and non-infectious diseases. Bacterial, fungal, viral, and parasitic diseases are of an infectious origin and are widespread among freshwater fish populations; if not controlled early on, they may significantly reduce fish production. Aquatic animal diseases also depend on abiotic stress factors such as adverse environmental conditions and management practices. Cage environments are rich in nutrients that are a good substrate for heterotrophic bacterial and fungal growth, especially when hygiene practices are not carried out adequately. High stocking density, limited fish movement, and poor water quality parameters are the major stressors that fish encounter in the cage culture system. A comprehensive summary of the infectious and non-infectious diseases commonly encountered in cage-farmed freshwater fishes is provided here.