Abstract Aquaculture intensification exposes fish to environmental stressors that can compromise growth, immunity, and welfare. We applied a multi-omics approach integrating physiology, targeted transcriptomics (qPCR), and proteomic profiling to investigate stress responses of Oreochromis niloticus reared for 8(weeks in plastic tanks, concrete ponds, and earthen ponds under standardized feeding. Water quality, growth, survival, cortisol and antioxidant biomarkers (SOD, CAT), relative expression of stress/immune genes (HSP70, CAT, IL-1β, TNF-α), and differentially expressed protein categories were evaluated. Earthen ponds yielded superior water quality, growth, FCR, and survival, along with lower cortisol and pro-inflammatory gene expression, and higher antioxidant capacity. Plastic tanks showed the inverse pattern; concrete ponds were intermediate. The multi-omics integration indicates that oxidative stress, heat-shock response, and pro-inflammatory signaling dominate in tanks, whereas immune homeostasis and efficient redox metabolism characterize ponds. Findings highlight system-dependent stress biology and practical levers for welfare-oriented, productive tilapia culture.