Clean Cruise Ship Act of 2009

Clean Cruise Ship Act of 2009 - Declares the purpose of this Act to be the establishment of national standards and prohibitions for discharges from cruise vessels. Defines "cruise vessel" as a passenger vessel that is authorized to carry at least 250 passengers and has onboard sleeping facilities for each passenger. Excludes vessels owned or operated by federal, state, or local governments.

Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to prohibit cruise vessels departing from, or calling on, a U.S. port from discharging effluents, including sewage or sewage sludge, incinerator ash, hazardous waste, graywater, or bilge water, into navigable waters. Allows an exception for discharges made solely to secure the safety of a cruise vessel or to save a human life at sea.

Requires the Administrator of the Environmental Protection Agency (EPA) to: (1) promulgate effluent limits for sewage, graywater, and bilge water discharges from cruise vessels; (2) establish dates for compliance with such limits; (3) require sampling, monitoring, and reporting to ensure compliance with such limits and other applicable requirements; and (4) establish an inspection program to ensure the compliance of cruise vessels with the requirements of this Act.

Requires the Commandant of the Coast Guard, in consultation with the Administrator, to establish and carry out a program for hiring and placing trained, independent, observers on cruise vessels to monitor and inspect vessel operations, equipment, and discharges.

Establishes in the Treasury the Cruise Vessel Pollution Control Fund. Requires the Commandant and the Administrator to collect fees from cruise vessels and deposit such fees in the Fund for use in carrying out this Act.