Sensing in aquatic environments is important to maintain underwater structures and research aquatic life. This paper proposes a 3D measurement method of objects in water using a fish-eye stereo camera. Aquatic sensing meets the difficulty of 3D measurement because of light refraction due to the difference of refractive indices of air and water. This problem is enhanced by distortion of fish-eye images. The proposed method removes distortion of fish-eye images by converting them to perspective projection images. The corrected images are searched for corresponding points and measurement points are located by triangulation. The effect of light refraction is considered by ray tracing to measure accurately in aquatic environments. Experimental results show the effectiveness of the proposed method.