In this paper, a new method for 3-D measurement of objects in water is proposed. When observing objects in water through a camera contained in a waterproof housing or observing objects in an aquarium tank filled with preserving liquid, we should solve a problem of light refraction at the boundary surfaces of refractive index discontinuity which gives image distortion. The proposed method uses a space encoding method which does not have a problem of corresponding point detection as a stereo vision system has, and is faster than spot light projection or slit light projection methods. A ray tracing technique solves the problem of image distortion caused by refractive index discontinuity. It should be noted that monochromatic light projection onto objects gives more accurate measurement than white light projection because the refractive index depends on the wavelength of the light. Then, in order to measure colored objects, we should project red, green and blue light patterns onto them separately. Experimental results show the validity of the proposed method.