We propose a method that corrects effects of refractions and absorptions for underwater scan data obtained by general-purpose laser range finders (LRFs) using HOKUYO UTM-30LX (Top-URG). For measurements by LRFs in water, it is known that refractions make measurement distances longer and absorptions make reflection intensities weaker. In order to confirm those characteristics of measurements in water, we first conduct two basic experiments that Top-URG measures a target in the environment with the assumed turbid deep-sea and evaluate an accuracy and a performance of Top-URG in water. The first basic experiment is that Top-URG measures surroundings in a sink filled with water by changing the turbidity of the water. The second basic experiment is conducted by changing a location and an angle of a target. Next, we develop a method that (1) corrects scan data of Top-URG by considering a refractive index of water and (2) eliminates scan data with low reliabilities based on reflection intensities obtained by Top-URG using automatically calculated thresholds. We evaluate those two methods by using two types of target objects and seven situations. Our developed methods can correct distorted scan points by refractions in water and can eliminate ghost scan points which are not existent. We confirm that their performances for underwater scan data are effective enough to use Top-URG in water.