India has vast and varied inland fisheries resources in the form of rivers, estuaries, reservoirs, floodplain wetlands, lakes, ponds, etc. These resources play an important role in fish production of the country, ensuring food and nutritional security as well as employment generation especially in rural areas. Besides, this sector is an important source of livelihood to a sizable section of the country's rural populace. Recognizing the role of inland fisheries, Government of India established a Central Inland Fisheries Research Station on 17 March 1947 at Kolkata under the Ministry of Food and Agriculture. Latter this research station was elevated to a full-fledged "Central Inland Fisheries Research Institute" in 1959 and it moved to its own building at Barrackpore, West Bengal. In 1967 the institute came under the administrative control of the Indian Council of Agricultural Research (ICAR), New Delhi.

In 1971 four All India Coordinated Research Projects, viz., "Composite Fish Culture", "Riverine Fish Seed Prospecting", "Air-breathing Fish Culture" and "Ecology and Fisheries Management of Reservoirs" were started by the institute. Another AICRP on "Brackishwater Fish Farming" was initiated in 1973. The first two projects were combined together as Composite Fish Culture and Fish Seed Production" in 1974. These AICRPs were turning points in the history of inland fisheries and aquaculture in India. The resounding success of these projects has given a firm support for the development of freshwater aquaculture in the country.

Over the years the institute has grown to a premier research organization in inland fisheries in the country. It carried out benchmark studies on the fish and fisheries of major rivers, estuaries, lakes and wetlands spread along the length and breadth of the country. During the pre seventh plan period, the Institute identified the potential zones in major rivers where riverine major carp seed can be collected and supplied to aquaculture farms. It also developed and standardized spawn collection nets for the purpose. Oxygen packing for long distance transportation of fish seeds was developed by the institute resulting in lower mortality of fish seeds, while transportation. The development of induced breeding technology for Indian and Chinese major carps, during the seventies coupled with the bundh breeding of Chinese carps, nursery management techniques and composite fish culture technology gave a fillip to freshwater aquaculture development in India. Development of seed production and culture technologies for air-breathing fishes, methods of aquatic weed control and integrated fish farming systems gave additional support to the growth of freshwater aquaculture. The Institute also developed eco-system oriented management guidelines for increasing fish production from large reservoirs (> 5000 ha area).

During the seventies, the institute focused its attention on aquaculture research in consonance with the plan priorities of Government of India and established the Freshwater Aquaculture Research and Training Centre (FARTC) at Dhauli, Orissa in 1977, which eventually became the Central Institute of Freshwater Aquaculture (CIFA) in 1987. Simultaneously, the Central Institute of Brackish-water Aquaculture (CIBA) and National Research Centre on Cold Water Fisheries (NRCCWF) were carved out from this Institute to provide added research thrust on brackish-water aquaculture and cold-water fisheries, respectively. The name of the Institute was changed to Central Inland Capture Fisheries Research Institute (CICFRI) in 1987, West Bengal and its mandate reoriented. The ICAR, however, restored its original name "Central Inland Fisheries Research Institute" (CIFRI) in 2002.