Scientific research into fish wellness is critical, and the concerns about crowding-related stress due to 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 0.5 g/L (T1), 1 g/L (T2), 1.5 g/L (T3), and 2 g/L (T4) and fed a 35% protein diet. After the 90-day trial, the physio-biochemical, molecular, and tissue-level changes were assessed. An integrated biomarker response (IBR) analysis for the key stress indicators aided us in better understanding them. There was a significant difference in blood count between T1 and T4 (total erythrocyte count, hemoglobin, and packed cell volume). 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 stocking 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 pronounced 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 cultured 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.