Well, that would be a realistic scenario if you titled it "Oh S---!" Because if said airplane is caught in the explosion of the depth charge, it's going to be joining the sub in a nice long dive to the bottom.
That said, fluffing up white cotton is probably your best material for a water column, in that scale. You could mount the plane on a clear acrylic rod and then "hide" the rod with the cotton. But in that scale, isn't the U-boat going to be about 3 feet long? Unless you're only showing part of it. I recall a pic of such a diorama in FSM some time ago, but it was just the conning tower and deck gun of a U-boat, and the builder "forced" the perspective by using a 1/144 scale PBY as the attacking aircraft.