Just so you know, I'm looking into these, though I haven't found any cause for them yet (or been able to reproduce the problem on my iPads, for that matter). I'll update the thread if I find anything.
In the meantime, if you run into this problem again, any details you can provide about what was happening at the time would be helpful -- for example: where did it happen, were you swimming / singing / fighting / etc., how long were you playing before it happened, anything else that comes to mind.
(As a side note, Aquaria follows Apple's requirements and disables its own sound if you have any other apps playing sound, like the built-in Music app, when you first start the game. In this case, Aquaria's sound may start playing when the other app goes silent, only to disappear again if another app plays an alert or other sound. To fix this, you'll need to force-quit Aquaria from the Recent Apps bar on the Home screen -- see
http://www.apple.com/support/iphone/assistant/phone/#section_3 -- and then make sure all other sound-playing apps are closed before restarting Aquaria.)
