The current study investigated the combined effects of carbon sources and commercial probiotics on common carp welfare in a biofloc‐based system. Three hundred fingerlings (initial weight 43.2 ± 3.1 g) were distributed in 12 tanks including control, PR + BFT (rice bran + probiotics), PM + BFT (molasses + probiotics), and PC + BFT (corn starch + probiotics). After 12 weeks, the results showed that NNH3, NNO2, pH, and dissolved oxygen decreased in the PC + BFT and PR + BFT treatments when compared with the others. Unlike the control treatment, the fish reared in the biofloc treatments had significantly higher growth performances (p < 0.05). The highest protein and lipid content in microbial flocs, protease, and lipase activity followed by protein and lipid muscle content was observed in PR + BFT when compared with PM + BFT and control (p < 0.05). The sero‐immunological and antioxidant indices improved in the PC + BFT and PR + BFT treatments, and a significant difference was found than the control (p < 0.05). The higher ductal dilatation was seen in PM + BFT treatment which is worth more investigation. Overall, the results revealed that adding probiotics to complex carbon resources improves the water quality and common carp fingerlings welfare in the biofloc system.