If player's head is slightly above water no breath bar will be displayed in the bottom bar, but the player will start to suffocate after a while.
I believe what's going wrong is that the player is rather A: slightly above the water causing the game to get confused and then decides to make you suffocate as if you were really underwater, or B: The player's head is slightly BELOW the water, but breath indicator doesn't display.
NOTE: The breath indicator will show at the right time, but in this case the position confused the game.
Duplicate of MC-816 - If you have not, please use the search function in the future, to see if your bug has already been submitted. If you could not find the original report, please comment with the keywords you searched for.