Taking this sucker out before you get in the water is possible, but like Santadog points out - it takes an awful lot of ammo. Kaiser's strategy of just jumping in and out as fast as possible is the one that i always use. Essentially you have 2 options:

Use up a load of ammo (that you may not have); or wait for the beastie to move more towards one of the sides and discharge electricity before running straight to the object and getting out as quick as possible (but lose a bit of health).

I usually enter the pool from the middle of the farside (as you enter the room) and exit via one of the sides - that way you don't have to waste time turning around. Always line up on the object so you can run straight to it without turning when you enter the pool and pretty much forget about the beastie when you're in the water (don't try to dodge etc), just concentrate on getting out as quickly as possible. Don't panic and use some herbs / spray as soon as you have been hit and you shouldn't have a problem with this (there's even some herbs in the bit of tunnel just before this room i seem to recall).