It depends somewhat on the thing that is hanging over your shoulders, and how it is affecting you.
If you feel that you are being observed constantly, then someone or something is looking over your shoulder:
I can't concentrate with you looking over my shoulder all the time!
If you are uneasy because of some pressure or responsibility being placed upon you, there are a few phrases that would work:
I'm always stressed because of all the work that's been put on my shoulders.
I'd like to go out tonight, but I have an important deadline hanging over my head.
If something is irritating you because of its constant presence, you could say that it's on my back:
My boss is always on my back about getting these reports done.
If you can just barely sense the presence of something or someone, they might be lurking.
There were ghosts lurking in every corner, just out of sight.