The Institute has state of the art infrastructure and facilities at HQ. Barrackpore; Regional Centers, Allahabad, Guwahati, Bangalore and adequate facilities at its other centers and stations to carry out advanced research in various aspects of inland open waters under the given mandate. Based on the facilities available, ICAR-CIFRI has been identified as the Eastern Zonal Centre for Agricultural Research Information System of ICAR. The library at HQ. Barrackpore subscribes more than 20 international and 60 national Journals, 106 e-journals related to the fisheries and allied sciences. Presently, the library has a holding of 9849 books, 4278 reprints, 1252 maps, and 4222 miscellaneous publications. All the publications are digitized and most of these are available on-line.

The Institute has state of the art laboratories for water and soil chemistry, fisheries/ fish biology, limnology, microbiology/ Pathology, biochemistry/ nutrition, genetics/ biotechnology, biodiversity, aquarium and hatchery, GIS and computer application and a fish feed mill. The laboratories hold modern equipments like Particle Analyzer, HPLC, GLC, GCMS, Real Time PCR, Spectrophotometer, AAS, Biolog Systems, Microwave Digester, Portable water quality probes, GIS facilities, etc. are some of these. The Institute has well equipped conference room for 30 persons, state of the art meeting room for 60 persons and state of the art auditorium seating 120 parsons. The Institute maintains a trainee's hostel that can accommodate 35 persons; the Teestha hostel can accommodate 22 persons and has dining room, kitchen, gym, visiting doctor; the Bhagirathi guest house has a VVIP suit, VIP rooms and Standard rooms in all for 10 persons, with kitchen and dining hall.