This is part of the immune response. Your cells, which are now in "attack mode" and are essentially trying to get rid of whatever pathogen is in the body, release a chemical called histamine. This causes your vessels to open up, causing more blood flow to the area. It will also stimulate more mucus to be produced by the membranes that line your sinuses, which can also affect your throat and eyes. Extra mucus can build up in your paranasal sinuses, causing the stuffy feeling, or it can run out of the nose, causing a runny nose.