I've requested axis independent scaling several times before and it's said to come in the future, but you'll have to wait for the new WED. Until then you have to use a script.
As a workaround, you can scale the water uniformly until you have the correct size in x-dimension, then save or memorize the scale factor and do the same for its y-size.

@Uhrwerk: The passable flag does not work anymore since OBB and meshes/ mesh mode for levels have been introduced, you have to use map entities or models.