Scientific research into fish wellness is critical, and concerns about crowding-related stress caused by increased stocking density are inevitable. Taking this into consideration, the study defines the physiological signature of Ompok bimaculatus (Butter catfish) in a biofloc system when subjected to varying levels of stocking density. Fish (mean weight = 1.21 g ± 0.08, n = 600) were randomly stocked in 40-L glass aquaria at stocking densities of 0.5g/L (T1), 1g/L (T2), 1.5g/L (T3), and 2g/L (T4) and fed a 35% protein feed. At the end of the 90-day period, the physio-biochemical, molecular, and tissue-level changes were assessed. An integrated biomarker response (IBR) study of the most important stress indicators aided us in better understanding them. There was a significant difference in total erythrocyte count between T1 and T4 (total erythrocyte count, haemoglobin, and packed cell volume), according to our findings. T1 had higher levels of globulin and total plasma protein, but T2 had higher levels of albumin. Only in T1 did the respiratory burst and lysozyme activity appear to be higher (p 0.05). Increased densities had a significant impact on the liver function enzymes GOT and GPT (p 0.05). In comparison to lower densities (T1 & T2), higher stocking density (T3 & T4) was found to raise glucose and cortisol levels (p 0.05). Antioxidant enzymes such as catalase, glutathione-S-transferase, and malondialdehyde were found to be more active in lower density tissues (T1). Furthermore, the IBR plots show that lower densities have better health than higher densities. At higher stocking densities, mRNA expression of HSP70, IL-1, and IL-20 increased (p 0.05) in kidney and liver tissues. The Nrf-2 and Tlr-9 genes were also upregulated. Also, when stocking density was increased, tissue-level histo-architectural changes were more pronounced than when stocking density was kept low. The findings of this study show that the welfare of Butter catfish cultivated at high density in biofloc systems suffers from severe stress and therefore draw more attention to the development of a species-specific standard rearing methodology in the pursuit of a profitable aqua-farming enterprise.