This paper reports an investigation of a flow over and through offshore fish cages using Computational Fluid Dynamics (CFD). As the cages are working in open seas, exposed to bio-fouling phenomena which can block the flow, and possibly to violent current/wave conditions, it is therefore important to investigate the water exchange between the inside and the outside of the cages and the hydrodynamic load on them. Different scenarios involving either a single cage or multiple cages in a certain arrangement are analyzed. In this work, the cage is of a spherical type, submersible, and assumed to be working under the water surface, totally submerged. It is modeled as a hollow sphere with its wall being a thin porous layer representing the net and the mechanical frame. The characteristic parameters of the porous medium are determined by fitting the numerical results with data available in the literature. Various flow characteristics are presented and discussed. It is found that the bio-fouling phenomena can drastically reduce the exchange of well-oxygenated water, and the staggered arrangement of four identical cages is superior than the square one.