The university has six major Departments/ Divisions including Aquaculture; Fisheries Resources, Harvest and Post Harvest; Fish Genetics and Biotechnology; Aquatic Environment and Health Management; Fish Nutrition and Biochemistry and Fisheries Economics, Extension and Statistics.

Its four Centres at Rohtak (Haryana), Kolkata (West Bengal), Kakinada (Andhra Pradesh) and Powarkheda (Madhya Pradesh) are spread over different agro-climatic zones and have inland-saline, freshwater and marine farm facilities for on-farm education and extension. Two training-cum-research fishing vessels M.F.V. Saraswati (36 m OAL) and M.F.V. Narmada (11 m OAL) greatly contribute to the learning and research experience of our students and other institutions.