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.