It happens and it happened to me at TJIG (Dominicci Airport) in San Juan, Puerto Rico when I was a student pilot. I was coming in to land on Rwy 9 which starts at one end of the San Juan Bay. Well, there was a sail boat navigating north near the shore line that was aligned with the center line as I was on final at about 300 ft.
I guess with a little more experience I could have done a short-field approach but all I could think was to go around. I told ATC and when asked for reason I said: ‘Uhh, there is a big boat here’. I can only imagine what they were saying afterwards. I was flying a heavy C-152. LOL.