A trial was performed to investigate how carbon sources can affect the welfare status of African catfish (3.8±0.2g and 8±0.11 cm) juveniles in biofloc systems. Inocula was prepared in glass tanks (5L) by adding 20g of pond bottom soil in well aerated water (1L) containing 10mg L-1 ammonium sulphate (NH)4SO4 and 400mg L-1 of four different carbon sources (tapioca, wheat offal, brewery and cassava peel) for 24 hours. Each treatment group (carbon sources and control) were replicated and each tank contained 1000 Clarias gariepinus juvenile, fed with commercial feed (Crude protein 42%) at 5% of their body weight 72 days. The water quality showed that all water parameters remained at concentrations suitable for Clarias gariepinus culture in the studied systems. The enzymes activities were noticed to be different across the biofloc and the selected organs. There were significant differences in serological content in fish between the treatment’s groups (P<0.05). The significant difference was found between the treatments in case of enzymes activity (P<0.05). The study shows that the welfare status with reference to digestive enzymes activity, oxidative status and extent of the immune system stimulation in BFT system is carbon source dependent.