Malocclusion (teeth problems) also can cause watering eyes
Your bunny may have a corneal ulcer, conjunctivitis, a foreign body in the eye, or other eye infection. He may also have an ear infection in the corresponding ear. If he has an ear infection which is painful or itchy, he could have accidently scratched his eye while trying to scratch his ear. Or, if the infection is just in the eye (with no ear involvement) the eye could have been itchy or painful and scratching could make it worse by introducing additional bacteria or irritants.
Rabbits can get ear mites, or mange around the eyes too.
Rabbits have extremely sensitive eyes. Rabbits eyes are used by the research community to test cosmetics and other chemicals due to their sensitivity. The reason rabbits eyes are used is due to the belief that if the chemical does not create a problem in the rabbit eye than it should be safe for human eyes. I personally find the use of rabbits to test cosmetics to be very sad for the rabbit. These tests are gradually being replaced with more humane tests. But for a long time it was a necessary evil.
But getting back to your little guy, I recommend that you take him to a vet and have diagnostics performed, because conjunctivitis and corneal ulcers can be painful, and if an ear infection is possible it can spread to the middle ear and cause neurological problems.