Nautical imagery occasionally appears as a symbol for – well, we're not quite sure what, but going from everything else in the story, it probably has to do with confusion and lack of knowledge. The Governess first alludes to ships when she arrives at Bly and comments on how strange it is that she should be metaphorically steering the household, which she compares to a "great drifting ship" (1.9) full of lost passengers.
Boats make an appearance in both of the scenes at the lake with Flora, and possibly symbolize her deception of the Governess. First, the little girl attempts to build a little toy boat out of wood while the Governess, horrified, sees the ghost of Miss Jessel for the first time. In the return to the lake, Flora somehow manages to abscond with the rowboat that's usually docked at the lake and move it to a more hidden location; there's never any explanation of how or why she does this by herself, but the Governess takes it to be another sign of her dishonesty.
Creepy, unnatural silence is a sign of Peter Quint's presence in both his first appearance and when he shows up inside the house on the staircase. In the first of these scenes, the Governess, who is strolling happily outside, notices that everything goes quiet when the mysterious figure appears, even the peaceful sounds of birdsong. This is a signal that something abnormal and certainly unnatural is happening – even though she doesn't yet know that he's a ghost yet, she can already tell that he's not meant to be there.
Inside the house, the silence is even more marked; though this close encounter seems more "human and hideous" (9.6), the lack of conversation between the Governess and her nemesis is what really makes it freaky. Finally, when the Governess actually tries to speak to one of the ghosts (Miss Jessel in the schoolroom, 15.5), the ghost does not – or cannot – answer.
"Depths" and the Unknown
OK, you've got us – this isn't exactly an image, symbol, or allegory. However, it is a hugely significant word, so bear with us. "Depth" is probably the most notable recurring word that shows up in the story; the Governess is always going on about how she has greater depths, or the children have depths, or how the situation as a whole has depths that are as yet unexplained. We can read this word as a stand-in for the concept of the unknown – or things that are known and hidden, which are even more dangerous.
Mrs. Grose also uses the word to describe her fear of Quint – she's afraid of him, she says, because he "was so clever – he was so deep" (6.10). We're not quite sure what lies in these depths in people, which is what makes them so scary. As you can probably tell, the Governess really loves to know things, so, naturally, things that are unknowable or undiscoverable are menacing to her, and in turn to us, as readers.