Locally in Oceanside harbor there are some large birds that make quite a mess; these include black crown night herons, great blue herons and snowy egrets. A few years ago an attempt was made to minimize the problem... http://www.nctimes.com/news/local/oceanside/article_9dc10de4-fee4-5dfa-b36a-b05315ab7f99.html

The birds of course just chose the next tall thing to nest in.

Elsewhere, such as Newport Beach harbor, they have a different issue that some boat owners are trying to resolve with nails... harbor seals.
http://newportbeach.patch.com/articles/newport-beach-man-aims-to-keep-seals-off-boats-humanely

Here is a great illustration of the problem.
http://www.youtube.com/watch?v=tt8stETtQ9Y

Boats with wide flat decks or swim steps have been sunk by seals in that harbor.