A system for the 3D tracking of underwater farmed fry using action cameras in multiple directions is presented. In a real environment, owing to light reflection and the small size of fry relative to the size of the tank, blind spots and unclear figures often appear in pictures taken by a camera. The proposed system continuously monitors the fry’s figure clearly and avoids blind spots by using multiple cameras. The proposed method changes the combination of multiple viewing points from frame to frame in a movie depending on the fry’s location to maintain clear fry figures and obtains the 3D coordinates of the location by the direct linear transformation. The regions of fry are sequentially obtained by taking the difference between the background image and each frame where fry appear. By taking movies of some farmed fry, we examined the tracking performance by comparing the 3D coordinates of the locations obtained by the proposed method with the correct coordinates. The mean and the standard deviation of the distance between the two points were 2.619 and 1.333 cm, respectively, i.e., it was confirmed that the proposed method can correctly capture the locations of fry because the distance was smaller than the body length of the fry.