aeris was thought to be a witch. long ago, when people believed if somebody was a witch, they would say "okay, we're gonna throw you in the lake, and if you float or swim, (something like that) you must be a witch, and if you die..... my bad!"
that's why cloud put her in the water at the ancient city. he wanted to see if she would float, cuz then she'd be a which, and then he would have to REALLLY kill her, not just weakly stab her in the back. and there was a hidden cutscene where it showed the conversation between aeris and cloud, so cloud was explaining, and tossed her in the lil lake. she didn't float. guess she wasn't a which. oops.