An 8 weeks trial was performed to evaluate the effects of crud protein (CP) levels (20 and 30%) each in three carbon sources in BFT (sugarcane molasses: M, rice bran: R, M + R and control) on water quality and performance of Common carp (cyprinus carpio) juveniles. Seven hundred twenty healthy juveniles (30.5 ± 3.1 g) were randomly distributed in 24 rectangle tanks (200 L) at a density of 4.5 kg m−3 (30 fish/tank). Juveniles in BFT treatments were fed at 75% of the daily feeding rate (DFI) of control. At the end of the experiment, the results showed that among the BFT treatments, M + R in both CP level had the lowest amount of total ammonia nitrogen (TAN) in comparison with other carbon sources in CP levels. The 30% CP level and rice bran contained treatments (R, R + M) significantly increased weight gain, specific growth rate (SGR) and survival and decreased feed conversion ratio (FCR) when compared the M and control treatments (P < 0.01). The highest activity of amylase, total protease and lipase was seen in the higher CP level and R + M treatment which was coincidental with growth performance data in this group. The CP levels did not changed white blood cell (WBC) and packed-cell volume (PCV) but in comparison to low level of CP and control, the 30% CP level and R + M significantly increased red blood cells (RBC) and (hemoglobin test) HB (P < 0.05). Glucose as a stress indicator was not affected by diet CP level however the fish reared in M treatment showed a significant increase in concentration when compared with others (P < 0.01). The higher CP level improved immune response in the fish reared in BFT treatments and the highest concentration for IgM, ACH50, total protein and globulin was seen in R + M treatment which significantly differed from the control (P < 0.05). The similar trend was observed for antioxidant enzymes and the fish fed higher CP level and reared in BFT treatments had significantly better antioxidant status than the control (P < 0.05). According to normal range of CP for Common carp juveniles (35–40%), the results of this experiment suggest that microbial flocs could not compensate 15% reduction of CP in juveniles diets but using R + M as carbon source improves growth performance, immune and antioxidant status in the fish when fed 30% CP.