You're using RMXP, right? The only way I can think of to surround all bodies of water with clear events that you can't walk on without an item. In other words, a blank page 1, no preconditions, with a blank tile set to unpassable - then on page 2, the precondition is that some switch is activated (can't base it on the item itself - RMXP removed that ability), and the picture is a blank tile that you CAN walk over.

As for transparency, I'd say to just set that in the Terrain tab - but RMXP removed that functionality. Oh boy. Best thing is indeed to have a faux-transparent blue "filter" tile on top of all bodies of water (on the highest layer) - have it set to be above the hero, and don't "filter" the southernmost tiles of any bodies of water so you can walk on the shore below it without having your head look like it's underwater.