Yawning is an involuntary process of opening the mouth and breathing in deeply, filling the lungs with air. Why we yawn has puzzled scientist throughout the ages.
Your eyes water when you yawn, doctors have some theories as to why. As you know when you yawn your face becomes contorted and you close your eyes. This puts pressure on the lacrimal glands under your eyebrows. The lacrimal glands are paired exocrine glands found in most terrestrial vertebrates and some marine mammals that secrete the aqueous layer of the tear film that keeps the eye protected from irritants and infection causing pathogens.
Tears normally drain out through tiny little ducts in the corner of the eye but by squeezing the muscles in your face during a yawn closes up the ducts and the tears have no way to drain so they overflow. When the yawn is over and you open your eyes this fluid can drain normally again through the ducts.