Causes of ear discharge may be from the ear canal, the middle ear, or the brain. the most common causes of ear discharge are otitis media with perforation of the eardrum and cholesteatoma. Otitis externa The most serious causes are malignant otitis externa and cancer of the ear. Causes of Earache Ear infections. there may be watery or pus-like discharge coming out of the ear.... Glue ear. injury to the ear. fungus and swimmer's ear. Earwax or a foreign body in the ear. Throat infections. jaw diseases dental abscess.