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Refraction of light underwater is a major source of error for 3D reconstruction. Use of a physically correct camera model taking into account properties of the optical system is essential for understanding the reasons why errors occur and obtaining quantitative estimates of errors. It was proven that use of the single viewpoint model of the camera leads to significant distortions in reconstruction. This paper proposes a novel technique to determine the physical parameters that influence refractive effects. Relative importance of various parameters was investigated in simulations and experiments with real targets underwater. The results of 3D reconstructions are compared with known ground truth in case of numerical modeling and with models acquired by Kinect2 in case of experiments underwater.