So I've got a water bottle (a misc object) that fills up if the player is in water. Or, it should, but I can't seem to get any event involving that to fire to fire.

RegisterForAnimationEvent(Game.GetPlayer(), "SoundPlay.FSTSwimSwim") doesn't work, nor does RegisterForAnimationEvent(Game.GetPlayer(), "MTState"), nor does Game.GetPlayer()GetAnimationVariableInt("iState") == 63.

Any reasons why these wouldn't work, or are there any non-SKSE ways to make this work?

Have a look at http://www.gamesas.com/topic/1499115-detect-if-player-is-truly-swimming-underwater/?hl=%2Bisswimming#entry23752198