This article proposes a method of three-dimensional orientation of underwater leaking bubbles using a three-dimensional five-element hydrophone array. First, the orientation errors of the four-element planar array, five-element planar array, and the five-element stereo array are analyzed theoretically and simulated, and the relationships among the orientation errors, time delay, sound speed, and source position are compared. The results show that the five-element stereo hydrophone array is not affected by the sound speed error, has a smaller influence from the time delay error and source position, and has the best orientation effect. A hydrophone array with a radius of 20 cm is set up in a tank for experimentation. The four-element planar array and the five-element stereo array are used to collect sound signals from four positions of bubbles, and the first peak of the sound signal is used as the reference point for the first arrival time to calculate the delay. Ten direction estimates are made for each position. The experimental results show that the azimuth angle estimation accuracy of the two arrays is similar, the elevation angle estimation effect of the five-element stereo array is better than that of the four-element planar array, and the average orientation error of azimuth angle and elevation angle is less than 4°, which is consistent with the theoretical analysis. Therefore, the five-element stereo hydrophone array can estimate the azimuth angle and elevation angle of the leakage point at different positions, and can realize leakage point orientation based on bubble sound signals in the underwater environment.