The expanded emergence of drug‐resistant microbes remains a concern to the scientific community in developing effective therapeutics. Approach of green chemistry based nanomaterials fabrication is in high demand, due to biocompatibility, non‐toxic, and high surface area that adheres more biomolecules on surface. Green fabricated silver nanoparticles (AgNPs), copper oxide nanoparticles (CuONPs), and silver–copper oxide nanocomposites (Ag‐CuO NCs) were characterized by fluorescence and Raman spectroscopy, field emission scanning electron microscopy (FE‐SEM) with energy‐dispersive X‐ray spectroscopy (EDX), and thermogravimetric (TG)/differential scanning calorimetry (DSC) analysis. Antibiofilm potential of green fabricated AgNPs, CuONPs, and Ag‐CuO NCs was tested against aquatic pathogenic microorganisms such as Aeromonas hydrophila, Pseudomonas aeruginosa, and Staphylococcus aureus. This present study deals with bacterial growth rate, biofilm inhibition, and antibiofilm architecture of AgNPs, CuONPs, and Ag‐CuO NCs under the visualization of confocal laser scanning electron microscopy (CLSM). The FE‐SEM technique was used to observe dense and compact structure (control without NPs treatment) with treatment of NPs that showed reduced amount of cell population in A. hydrophila, P. aeruginosa, and S. aureus. The effective antibiofilm inhibition of Ag‐CuO NCs was achieved by reducing micro‐colonies compared with AgNPs and CuONPs. The AgNPs, CuONPs, and Ag‐CuO NCs demonstrated antibiofilm properties against Gram‐negative and Gram‐positive bacteria, indicating a combinatorial effect of green fabricated NPs in combination with plant metabolites against pathogenic bacteria. As a result, aforementioned nano‐product merits further investigation in order to be used as a potent adjuvant therapy as antagonistic toward various bacterial diseases in aquaculture.