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The hydrodynamic interaction between two vessels in a side-by-side configuration attracted research attentions in recent years. However, because the conventional potential flow theory does not consider the fluid viscosity, in the hydrodynamic results, the wave elevations were overestimated in the narrow gap under resonance conditions. To overcome this limitation and investigate the complex fluid flow around multiple bodies in detail, this study examines the fluid resonance between two identical floating barges using a viscous flow analysis program FLOW-3D. The volume of fluid method is implemented for tracking the free surface, and a porous media model is used near the outflow boundary to enhance the wave absorption. A three-dimensional numerical wave basin is established and validated by comparison with the waves generated using theoretical values. On this basis, a computational fluid dynamics (CFD) simulation of the two barges in a resonance wave period is performed, and the wave elevations, the fluid flow around the barges, and the motions of the barges are discussed. The numerical simulation is verified by comparison with results of corresponding experimental data.