When the nasal passages are irritated and become inflamed they produce excess mucus to flush away the irritant, and so it is the inflammation that causes congestion. Nasal congestion and sinus pressure have many causes, including colds, flu, allergies and sinus problems. A sinus headache is the result of a buildup of pressure in the sinuses of the skull, i.e. the cavities or spaces in the bones of the skull. These spaces contribute to the strength of the skull and its ability to resist trauma, and their mucous lining secretes mucus to humidify and filter air.