This study aims to evaluate the influence of different carbohydrate sources on water quality, growth performance and immunomodulation in pacific white shrimp and to find an alternate for molasses in biofloc system. The experiment consists of 8 biofloc treatments with different carbon sources, C1 (maida flour), C2 (wheat flour), C3 (gram flour), C4 (millet flour), C5 (rice flour), C6 (corn flour), C7 (molasses), C8 (multigrain flour) and un-supplemented control C0 was conducted in 200 L tank system for 120 days. Shrimp juveniles of average weight 1 g were stocked at the rate of 300 nos/m3. Shrimp reared in C8, C7 and C4 treatments had similar growth, survival rate, and disease resistance and were significantly higher (P < 0.05) than other treatments including control. Immune parameters like total hemocyte count (THC) and prophenoloxidase (ProPO) activity showed significantly higher (P < 0.05) levels in biofloc treatment groups. The genes targeting the proPO cascade (PX, BGBP) and antioxidant defense systems (SOD, MnSOD, CAT) revealed significant upregulation in the transcript levels indicating an enhancement in the immune-regulatory functions in the BFT groups. The results suggest that millets and multigrain flour can effectively replace molasses as the carbohydrate source for biofloc system and the biofloc system offers higher growth, survival, and immunomodulation than control.