"Stuffy nose" is a term often used to refer to obstruction to the flow of air in and out of the nose, while "runny nose" refers to a discharge (fluid) coming from the nasal passages. Both of these conditions are associated with inflammation and swelling (congestion) of the inner lining of the nasal passages and sinuses. A viral infection (the common cold) is the most common cause of a stuffy and/or runny nose, but allergies, influenza, and sinus infections also may cause these symptoms.

Less commonly, anatomical obstructions (e.g. a deviated nasal septum, foreign bodies) may lead to nasal congestion. Other causes of a stuffy or runny nose include environmental factors, hormonal changes, and some medications. Rarely, tumors of the nasal passages or chronic medical conditions may be the cause of a stuffy or runny nose.

Source: http://www.rxlist.com