Biofloc (BFT) based nursery rearing system help provide additional food source, healthy juvenile production with better survival and an avenue for nitrogen removal through eco-friendly approach. It should be cost and energy effective with quick turn over. However, many questions remain unanswered regarding mechanisms of action and induced antibacterial/antiviral immune responses in penaeid shrimp especially during nursery phase. The present experiment was designed to evaluate the effects of biofloc treatments generated and maintained through three approaches on growth performances, physico-chemical parameters, microbial dynamics, feed utilization and immunological assessments in P. vannamei nursery rearing. The experiment was conducted in 500L FRP tanks stocked with PL-III stage of pacific white shrimp for 30 days at a stocking density of 6000 nos/m3. The heterotrophic bacteria level of 1 X107 CFU/ml was maintained through three approaches differing in their generation 1) biofloc lyophilized powder BFP 2) biofloc matured water (BFW) and 3) biofloc consortium (BFC) and compared with that of the conventional nursery rearing without biofloc treatment (Control). BFT treatments showed significantly higher growth as observed in average body weight (ABW) (BFP - 0.357 g, BFW - 0.363 g & BFC - 0.391 g) compared to control (0.188 g). BFT groups showed significantly (P < 0.01) higher survival (BFP (80%), BFW (79%), and BFC (90%), than control groups. The population of heterotrophic bacteria was (P < 0.05) significantly increased in treatments when compared to control. But higher vibrio load was recorded in the control than BFT reared water samples. BFT based nursery rearing system improves the water quality parameters when compared to control. Cumulative mortality rate of biofloc reared juveniles was significantly lowered when challenge with vibrio whereas control was higher. Further, certain immune genes like the prophenoloxidase, crustin, mas, serine protease, alpha2M, antiviral genes and Ran were upregulated in these groups. All these findings indicate that BFT nursery rearing system gives optimal and better culture condition displaying better survival, growth, disease tolerance, immune activity during the nursery phase and can be managed with minimal water exchange.