a. underwater:
stop and wait till you catch your breathe
b. at the surface:
inflate your BCD and float
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The enchantment, Respiration, will help you breathe underwater. Not only that, but it makes your vision clearer while swimming underwater.
If you're refering to Twillight Princess, you can't swim underwater while in you're wolf form. You can swim underwater as a human while wearing the Zora Tunic.
Abandoned ship, Rm. 2, while trying to get the Scanner after diving.
Simply wear the helmet (or other armor piece, if you somehow have that) with the enchantment while underwater. It will be applied automatically.
use dive in dark colored water and "walk" around in the underwater grass if there is any and thats where it is but it might take a while for you to find it