Accurately estimating the 3D position of underwater objects is of great interest when doing research on marine animals. An inherent problem of 3D reconstruction of underwater positions is the presence of refraction which invalidates the assumption of a single viewpoint. Three ways of performing 3D reconstruction on underwater objects are compared in this work: an approach relying solely on in-air camera calibration, an approach with the camera calibration performed under water and an approach based on ray tracing with Snell's law. As expected, the in-air camera calibration showed to be the most inaccurate as it does not take refraction into account. The precision of the estimated 3D positions based on the underwater camera calibration and the ray tracing based approach were, on the other hand, almost identical. However, the ray tracing based approach is found to be advantageous as it is far more flexible in terms of the calibration procedure due to the decoupling of the intrinsic and extrinsic camera parameters.