In recent times, pollution and climate change have increased the risk of climate penalties particularly in aquatic ecosystems. Rising the temperature, metal pollution and ammonia contaminant are interlinked and have impact on aquatic life. This study investigates dietary zinc (Zn) for mitigation of arsenic, ammonia and high temperature stress on Pangasianodon hypophthalmus. The fish were exposed to different combination of arsenic (2.68 mg L−1), ammonia (NH3, 2.0 mg L−1) pollution and high temperature (34 °C) stress for 105 days. The average fish weight was 5.44 ± 0.17 g with length of 6.23 cm. The experiment involved 12 treatment groups, each with 18 fish in triplicates, totaling six hundred forty-eight fish (648). The treatments include control, As, NH3, As+NH3, NH3 + T, As+NH3 + T, Zn-5 mg kg−1, Zn-10 mg kg−1, Zn-15 mg kg−1, Zn-5 mg kg1As + NH3 + T, Zn-10 mg kg−1As + NH3 + T and Zn-15 mg kg−1As + NH3 + T. The gene related to apoptosis, cytokines, chemokines, immunity and growth particularly nuclear factor kappa B (NFkB), were studied in liver and gill tissues. Diets containing zinc were prepared with graded levels of 0, 5, 10 and 15 mg kg−1 diet. Cortisol, inducible nitric oxide synthase (iNOS), heat shock protein (HSP70), and metallothionine (MT), catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GPx), were upregulated by arsenic (As), ammonia (NH3) and high temperature (34 °C) stress, but downregulated with dietary Zn at 10 mg kg−1 diet. The NFkB pathway genes, including caspase 3a (CAS 3a), tumour necrosis factor (TNFα), interleukin (IL), and toll-like receptors (TLR), were noticeably upregulated due to stressors. However, Zn supplementation downregulated these genes and mitigated stress in the fish exposed to As+NH3 + T. Genes related to growth hormone (GH), growth hormone regulator 1 and β (GHR1 and GHRβ), were noticeably downregulated in response to stressors. Conversely, Zn-containing diets significantly upregulated GH, GHR1, and GHRβ, while myostatin (MYST) and somatostatin (SMT) results differed from other growth-related genes. The liver and kidney tissues showed the highest arsenic bioaccumulation. Notably, Zn-containing diet was observed to protect fish from Aeromonas hydrophila infection. Overall, the results indicate that Zn-containing diet at 10 mg kg−1 diet improved the regulation of the stress-related genes, enhancing the mitigating ability of fish against multiple stressors.