The overall operation and administration of BFAR-NIFTC focuses on supporting scientific research related to fish breeding, aquatic health, and sustainable farming techniques. This research helps inform practices and policies while ensuring efficient resource allocation for training, research, and production activities. The center is dedicated to maintaining various facilities, including hatcheries, pond systems, broodcages, laboratories, administrative buildings, pump systems, generators, and farm equipment.

Additionally, BFAR-NIFTC is involved in the production and distribution of fish species through open water stocking, targeting male and female fish farmers as well as NGOs, government organizations (GOs), and government agencies (GAs) involved in food fish production. The center also provides technical assistance and training to fishermen, fish farmers, and fisherfolks in both open water and upland/landlocked rural areas. These efforts aim to promote the adoption of low-cost farming technologies while ensuring sustainability and resource conservation. Lastly, BFAR-NIFTC is responsible for producing and packaging information, education, and communication (IEC) materials, as well as developing commodity-based aquaculture technologies for replication and distribution to the freshwater aquaculture sector.