For some reason, I run out of breath too fast. I can only get the Pokeball and the scuba mask, then I can't get to the next chest. I've watch lots of videos playing it, and they all run out of breath slower than me.
You need to find the scuba tank, that's what lets you hold your breath longer. I don't remember what chest it's in, but it was the second thing I found (after the scuba mask) so it shouldn't be too difficult to get to