Bivalve molluscs, such as oysters, mussels, and clams, are economically vital organisms that serve as major protein sources and support fisheries, particularly in coastal regions. Driven by rising consumer demand, the bivalve aquaculture industry is rapidly expanding, significantly contributing to global food security and coastal economies. However, bivalves are susceptible to diseases caused by various pathogens including bacteria, fungi, viruses, and parasites. Intensified aquaculture practices and environmental changes have increased the risk of disease outbreaks. Disease diagnosis in bivalves is challenging owing to the limited visible symptoms and their enclosed shell structure, which conceals clinical signs. Bacterial diseases, particularly those caused by Vibrio species, are common and often lead to mass mortality in hatcheries and wild populations. Herpesvirus and iridovirus infections have repeatedly devastated bivalve aquaculture, causing substantial economic losses. Parasitic diseases significantly threaten wild and farmed bivalves, and protozoans play a major role in causing severe mortality. Five of the seven diseases listed by the World Organisation for Animal Health (WOAH) in bivalves have parasitic etiologies. Protozoan parasites, especially Perkinsus, Bonamia, Marteilia, and Haplosporidium, have caused major disease outbreaks and have contributed to the global decline in bivalve populations. Perkinsus infections have been linked to mass mortality in farmed green mussels in India. Several other protozoan and metazoan parasites also impact bivalve health with varying degrees of pathogenicity. Many of these pathogens spread via passive or horizontal transmission in high-density aquaculture environments, complicating disease management. This review focuses on the major pathogens affecting bivalves in Indian waters. Effective disease management in bivalves requires a comprehensive understanding of the causative agents, their biology, transmission dynamics, and the host immune response. Early detection using specific and rapid diagnostic methods, implementation of suitable biosecurity measures, and maintaining good husbandry practices are crucial for the timely intervention and control of diseases in bivalves.