National Estuary Protection Act - Amends the Federal Water Pollution Control Act to: (1) prohibit as a matter of national policy the construction or use of a floating storage regasification unit in an estuary of national significance; and (2) require national estuary grant program applicants to certify to the Administrator of the Environmental Protection Agency that they will not construct or use a floating storage regasification unit on an estuary of national significance, unless ordered to do so by a federal agency or court.