Isn't that a Skullfish?
Skullfish are small skeleton fish that appear in front of you and attempt to take a chomp at Link.
These things tend to appear one at a time when in open water. You can hear them coming by the crackling or clicking sound they make.
The best thing to do is really just avoid them, but if you feel like it, they can easily be killed with just about anything. The best way to take them out is to simply swim through them with your Electrical Barrier (Zora Mask + Swimming + R).
In Twilight Princess, Skullfish appear in the Lakebed Temple. Like in Majora's Mask, they will follow Link and try to attack him by biting him. They often appear in groups. Skullfish can be caught with the Fishing Rod, but they cannot be kept.