The increased incidence of diseases in aquaculture will lead to reduced profits, affecting economic viability, and there is a concern that climate change may further increase this risk. The specific impacts of climate change on animal diseases are not clearly understood, and it is important to comprehend the disease risks of farmed aquatic animals in the face of future climate change for the success and sustainability of aquaculture. The climatic scenarios revealed that India could experience increasing trends in annual mean temperature, an increase in the frequency of hot days and multiple-day heatwaves, variation in rainfall above and below the averages, and an increase in intensity and frequency of extreme weather events such as cyclones, torrential rains, and floods. These seasonal variations and extreme weather events have enormous negative consequences on potentially stress-farmed fish and shellfish species through deterioration in the water quality, suppression of their immune system, and increasing the incidence of disease outbreaks through alterations in the distribution, prevalence, and virulence of pathogens, resulting in crop losses and yield reduction. The present chapter throws light on the climate change scenarios and their impact on the physiology and immunity of cultured aquatic animals and their health, virulence of pathogens, host–pathogen interaction, and mitigation and adaptation measures to improve environmental and animal health to prevent the outbreak of diseases.