If you are attempting to remove mycelium or grass by flooding it, and you are using optifine, make sure that the 'Clear Water' feature is turned OFF.

It's not simply a visual feature, it actually allows more light to go through water which means grass and mycelium will not die underwater.

Figured I'd post this here in case anyone else was banging their heads against the wall, wondering "WHY WON'T THIS PURPLE S**T DIE ALREADY?!!?" c: