Lyric discussion by GoRedSox 

Cover art for Sad Waters lyrics by Nick Cave and the Bad Seeds

If you want to go with what armagezon said, there's some stuff to support it. "Turning these waters into wine" could be the water changing color from blood. Running his hands across "the prison of her ribs" could be CPR. He needs to start her heart, but it's locked in a prison he can't penetrate without killing her. Her death certainly would cast a new and different shadow across the waters. Also, he says he's "forever a hostage of your child's world." That could be because all he knows of her is her child world-she never grew up to change into something else.

Just a theory. Nick is kinda dark, so it wouldn't be surprising if this is what he meant. And Your Funeral...My Trial has some of the creepiest songs I've ever heard (except for Murder Ballads, of course.) It just makes a little sense if you listen to it from this point of view.