Toronto City (Island) Airport has the Toronto Harbour on the approach path to runway 26, the most commonly used runway. In years past, it was common to have to spot and dodge leisure sailboat masts off the end of the runway. I've adjusted my approach a few times for these. Since Porter Airlines started operating , a boat exclusion zone is bouyed off the approach end of 26. Google Earth tells me that the exclusion zone extends 1380 feet back from the threshold to 26, and this seems to do the trick. Though large, lake freighters also use the harbour, they seem to stay only on the east end, a few miles from the airport, so it's only the recreational boaters which have the potential to cause conflict - though recreational boaters can also be the most unaware too!
I recall while on a family cruise of the Caribbean, we spent a day in San Juan. The maneuvering area for cruise ships is quite close to the approach end of runway 09. I recall having a really close view of a landing Cessna Caravan!