I had this problem too and just figured it out. I was trying to build my pond in a fenced off area that I had deleted the ground tiles on. I moved the tiles and built the pond and it filled up as it should. Hope that helps!
It worked! I just deleted one section of fence to make it not a room anymore and the pond tool works! Thank you so much!
As a work around if you want to have a fence enclosing your back yard but still have a pond. I used the same trick people use to add tiles to tiny houses without the game counting them. You delete one section of fence, recreate that piece with the same angle somewhere where it is not connected to anything. Then using the select tool move that freestanding section of fence to the open space, completing your desired fence without the game turning it into a "room".
