Ever had straw in your shirt (or, worse yet, your pants)? Pretty uncomfortable. It's scratchy, irritating stuff. Rubbing your cheek against it isn't going to feel very good at all.
This line gives us a physical sense of Jane's painful psychological state. Why would someone stir up nice clear water? Well, maybe they don't want to see themselves reflected in that crystal clear water—kind of like when someone can't look at themselves in the mirror. Stir up the water in a pond or lake, and all the mucky stuff that has settled down to the bottom comes up to the top and makes the water murky, the way sadness can cloud the way we see things.