Large offshore net cages have been rather successful in reducing coastal contamination and developing aquacultural technology for raising large body-size species such as bluefin tuna. Deformation and shrinkage of net cages due to severe current and waves is one of the main causes of mortality of cultivated fish, and is thus of great concern for marine cage aquaculture. Even though the cage depth can be determined by pressure sensors at several locations on the cage, this is generally insufficient to measure the deformation and shrinkage. In this study, the dynamic shape and volume of a net cage under the influence of current and waves was analyzed using a numerical net geometry simulator previously validated by tank tests. The dynamic behavior of finite mass points distributed on the net cage under various wave and current conditions was simulated in detail, and reduction coefficients of the volume were calculated by the positions of these mass points on the cage. A drastic reduction of the cage volume occurred for a current velocity of 0.28–0.39 m/s. As the current velocity increased, the deepest point of the cage changed position, moving toward the downstream direction. The effective reduction of cage volume for a wave height of 3 m and a current velocity of 0.26 m/s was the same as that for a wave height of 5 m without any current. These results suggest that the volume deformation must be based on the actual measured depth of each part of the net cage, that the combination of wave levels and current velocities may have synergistic effects on the reduction of cage volume, and that our computational method is valid for estimating the volume reduction of a net cage under the influence of a concurrent wave and current field.