Batgirl (Comics)

Title: Batgirl Issue #7
Description: Batgirl is held underwater.

Thanks Foolinthewater!

Injustice (Comic)

Title: Injustice Issues 18, 20
Description: Brief underwater shots.

Thank you Foolinthewater!

Richie Rich (Comic)

Title: Richie Rich Millions Issue 34 (545)
Description: Dry breath-holding with underwater in the end.

Pokemon Adventures (Manga)

Title: Pokemon Adventures Chapter 58
Description: Yellow gets dragged underwater by the tentacool.

Thank you Foolinthewater!

Azumi (Manga)

Title: Azumi Chapters 126-127
Description: The girl gets dragged underwater and faints.

Thank you SGD (SecretGameDeveloper)!

Pokemon Adventures (Manga)

Title: Pokemon Adventures Volume 17, Chapters 212-213
Description: Sapphire and Flannery are trapped in a car underwater.

Special thanks to ~emi for bringing this up!

The Powerpuff Girls (Comic)

Title: The Powerpuff Girls Issues #46 and #66
Description: It's nice to see these girls underwater although briefly!

Thank you lordmmx (Dave)!

Champions (Comic)

Title: Champions 2016 Issue 4
Description: A brief scene of underwater breath-holding.

Thank you Foolinthewater!

Hagure Idol Jigokuhen (Manga)

Title: Hagure Idol Jigokuhen Volume 4 Chapter 28

Description: A one-frame-long breath holding contest. I guess there's still not a translated version of this manga but if anyone speaks Japanese out there; feel free to explain what is said here.