Why do allergies make my eyes water?

Immune reactions. The conjunctiva, the thin membrane on the inner surface of the eyelids and the white part of the eye, has lots of mast cells, which are the cells that react to allergens. So just as you get an allergic reaction in the nose, you get an allergic reaction in the eye as well. The eye is also connected to the nose through a small duct, and sometimes allergens can travel back and forth.
Histamine. Histamine acts directly on the eye to cause redness, swelling, itching, and tearing. There is also an effect through histamine causing nasal symptoms like itching which in turn can cause tearing in the eye through the naso-ocular reflex.