This study investigates the bioactive potential of secondary metabolites produced by endophytic bacteria isolated from Enhydra fluctuans Lour., a medicinal plant known for its antioxidant and antimicrobial properties. Fresh leaves were collected, surface-sterilized, and used to isolate bacterial endophytes. The isolates were identified morphologically and confirmed by 16S rRNA gene sequencing. Metabolites were extracted using ethyl acetate and assessed for antibacterial activity via the disc diffusion method and antioxidant capacity by DPPH radical scavenging assay. GC-MS was used to identify volatile bioactive substances. The isolate showed 91.75% similarity with Pseudomonas campi (NR_181172.1), indicating a distant relationship and suggesting it may represent a novel or uncharacterized taxon. The isolate was mostly sensitive to Ciprofloxacin (5 µg). Its ethyl acetate crude extract showed moderate antibacterial activity against Staphylococcus aureus with a 13.4 ± 0.21 mm inhibition zone at 500 µg/disc, compared to kanamycin (30 µg/disc). Antioxidant activity showed an IC of 61.66 ± 0.33 µg/mL, versus 17.38 ± 0.63 µg/mL for ascorbic acid. GC-MS identified 19 bioactive compounds, with Phenol, 3,5-bis(1,1-dimethylethyl)-, 1,9-Diazaspiro (4,4 )nonane-2,8-dione, and Octacosanol as major constituents. In silico analyses showed that 9,10-anthracenedione, 2-[(tert-butylamino)methylcarbamoyl] exhibited strong antibacterial and antioxidant potential, with high binding affinities to MurD ligase (-9.8 kcal/mol) and myeloperoxidase (-9.6 kcal/mol), respectively. Molecular dynamics (MD) simulations over 100 ns confirmed the stability of these complexes, supported by analyses of RMSD, RMSF, hydrogen bonds, and MMGBSA free energy. Most molecules were predicted to be non-toxic. These findings suggest that 9,10-Anthracenedione exhibits promising binding characteristics, driven by non-covalent interactions, making it a potential candidate for further drug development studies. Our results provide preliminary evidence that endophytic bacteria harbor chemically diverse secondary metabolites, reinforcing their role in natural product-based drug discovery pipelines. While initial findings are promising, Pure compound isolation comprehensive in vivo studies, compound purification, and pharmacokinetic profiling are essential.