Breath (water) – The ability to breathe through water in lieu of a gaseous medium. Not to be confused with an ability to go without breathing or to be able to breathe an alternative air supply.
Namor (Marvel) learns how to breathe water again in Fantastic Four V1 #4.
Water breathing at the expense of breathing air was often used as a plot device during the Silver Age in the DC universe (Batman V1 #118, Action Comics V1 #244, House of Mystery V1 #37, House of Mystery V1 #122, House of Secrets V1 #10).
The Walkatrout (Ben 10) can breathe and live underwater.
Merfolk – D&D 3.5 – Monster Manual I
Pirana – Unearthly Spectaculars #2 (Harvey)
Did you know most fish can breathe in fresh water or salt water but not both? This principle is applied to aquatic aliens in Undersea Agent #5 (Tower). I guess both DC and Marvel c0mics Atlanteans are Euryhaline organisms that can handle freshwater and saltwater unlike most fish.
Water Breathing Trading Card