Structured Light Systems (SLS) are widely used for various purposes. Recently, a strong demand to apply SLS to underwater applications has emerged. When SLS is used in an air medium, the stereo correspondence problem can be solved efficiently by epipolar geometry due to the co-planarity of the 3D point and its corresponding 2D points on camera/projector planes. However, in underwater environments, the camera and projector are usually set in special housings and refraction occurs at the interfaces between water/glass and glass/air, resulting in invalid conditions for epipolar geometry which strongly affect the correspondence search process. In this paper, we tackle the problem of underwater 3D shape acquisition with SLS. In this paper, we propose a method to perform 3D reconstruction by calibrating the system as if they are in the air at multiple depth. Since refraction cannot be completely described by a polynomial approximation of distortion model, grid based SLS method solve the problem. Finally, we propose a bundle adjustment method to refine the final result. We tested our method with an underwater SLS prototype, consisting of custom-made diffractive optical element (DOE) laser and underwater housings, showing the validity of the proposed approach.