In a mine, I drowned while floating in running water. The cave roof was directly overhead, but there appeared to be space to breathe. The 'oxygen left' indicator was not present, but I took damage and died. The game reported that I had drowned.
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The oxygen meter hasn't reset. When I bob below the surface, I immediately start taking damage again.
I can reproduce--I was coming to file this ticket myself. Possibly duplicated by MC-1093.
You don't even need the block above in all circumstances. Here's a shot of a setup that can drown you without a block above (and no meter visible). You must stand in the lowest block (the last block of flowing water).
Confirmed in 13w25c! I was trying underwater viewing station(http://imgur.com/a/8laXp) and I drowned. Video : http://youtu.be/8DNGDYiTjsw
Reproduced it in a partially flooded tunnel. Oxygen meter doesn't reset when in air, when there is a block directly overhead.