Experiencing a blocked, full, or “underwater” sensation in one or both ears after recovering from the flu is a common and frustrating complaint. While the acute symptoms of fever, cough, and body aches may have resolved, the ear congestion can linger for days or even weeks. Understanding why this happens is the first step toward effective relief. Why Does the Flu Block Your Ears? The primary reason for post-flu ear blockage is not earwax, but dysfunction of the Eustachian tube . This small canal connects the middle ear (the space behind your eardrum) to the back of your throat (nasopharynx). Its job is to equalize air pressure and drain normal fluids from the middle ear.