Recently, the infection with Shewanella spp. Results in health disorders and mortalities in Nile tilapia (Oreochromis niloticus). The present trial is proposed to look into the impact of Shewanella spp. Infection on the immune responses, antioxidant capacity, target genes expression of autophagy, endoplasmic reticulum stress (ER), and antimicrobial peptides in spleen tissue. As well as the antagonistic effects of chitosan nanogel composite (CNC; 75 μg/L) as a water application against Shewanella spp. Infection were studied. One hundred and sixty fish (27.55 ± 1.50 g) were assigned to four groups; each had four replicates for 14 days. The first (CONT) and second (CNC) groups were non-challenged and treated with 0 and 75 μg/L CNC, respectively, where the first was the control. The third (SH) and fourth (CNC + SH) groups were intraperitoneally challenged with 0.20 mL (containing 0.14 × 105 CFU) of Shewanella spp. The outcomes clarified that Shewanella spp. Infection induced oxidative stress by lowering the activity of superoxide dismutase and reduced glutathione and increasing the malondialdehyde level. Increases in the serum levels of C-reactive protein, complement-3, and immunoglobulin M were noticed in the Shewanella–infected fish comparable to the CONT. Shewanella infection down-regulated the expression of Beclin-1 and microtubule-associated protein light chain kinase 3 in the spleen, while up-regulated the expression of the mechanistic target of rapamycin and ubiquitin-binding protein. In addition, up-regulation of the ER stress-related genes (CCAAT/enhancer-binding protein homologous protein, c-Jun N-terminal kinase, activating transcription factor 6, X box-binding protein-1, and binding protein for immunoglobulins) and antimicrobial peptides genes (Piscidin 4 and hepcidin antimicrobial peptide 1) were consequences of Shewanella Spp. Infection compared to the CONT. On the contrary, CNC water treatment improved the survival of the Shewanella-infected fish (90 %) compared to the CONT (77.50 %). Moreover, an improvement in the antioxidant capacity and immune responses was noticed when the Shewanella-infected fish were treated with CNC. Modulation of the autophagy, ER stress, and antimicrobial peptide-related genes was noticed by treating the Shewanella-infected fish with CNC. Notably, CNC could be used as a water treatment for controlling the Shewanella challenge in Nile tilapia.