This paper presents an underwater active stereo system that realizes 3D capture of dynamic objects in water such as swimming fish. The key idea on realizing a practical underwater 3D sensing is to model the refraction process by our pixel-wise varifocal camera model that provides efficient forward (3D to 2D) projections as well as an underwater projector–camera calibration. Evaluations demonstrate that our method achieves reasonable calibration accuracy using off-the-shelf cameras and projectors, and provides a 3D capture of real swimming fish in water.