Defines a "recreational vessel" as any vessel that is leased, rented, or chartered to a person for that person's pleasure or that is manufactured or used primarily for pleasure, excluding vessels that are subject to Coast Guard inspection and that are engaged in commercial use or that carry paying passengers.

Requires the Administrator to: (1) develop management practices for recreational vessels to mitigate the adverse impacts on U.S. waters of discharges incidental to normal vessel operation (excluding sewage) in any case in which the Administrator determines that the use of those practices is reasonable and practicable; and (2) promulgate federal standards of performance (which may distinguish among vessel types) for each discharge for which such a management practice is developed.

Requires the Secretary of the department in which the Coast Guard is operating to promulgate regulations governing the design, construction, installation, and use of management practices for recreational vessels as necessary to meet such standards. Prohibits the owner or operator of a recreational vessel from operating in U.S. waters if such owner or operator is not using applicable management practices in compliance with such regulations.

Clean Boating Act of 2008 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to provide that no permit shall be required by the Administrator of the Environmental Protection Agency (EPA) under the national pollutant discharge elimination system for the discharge from a recreational vessel of graywater, bilge water, cooling water, weather deck runoff, oil water separator effluent, or effluent from properly functioning marine engines or for any other discharge that is incidental to the normal operation of such vessel.

Defines a "recreational vessel" as any vessel that is leased, rented, or chartered to a person for that person's pleasure or that is manufactured or used primarily for pleasure, excluding vessels that are subject to Coast Guard inspection and that are engaged in commercial use or that carry paying passengers.

Requires the Administrator to: (1) determine the discharges that are incidental to the normal operation (excluding sewage) of a recreational vessel for which it is reasonable and practicable to develop management practices to mitigate adverse impacts on U.S. waters within a year of this Act's enactment and to review such determinations every five years; and (2) develop management practices for recreational vessels to mitigate the adverse impacts of such discharges on U.S. waters. Directs the Administrator, in determining what discharges are incidental to normal operations, to consider: (1) the nature of the discharge; (2) its environmental effects; (3) the practicability of using a management practice; (4) the effect that such practice would have on the operation, operational capability, or safety of the vessel; (5) applicable federal and state law and international standards; and (6) the economic costs of the use of the management practice.

Requires the Administrator to: (1) promulgate federal standards of performance (which may distinguish among vessel types) for each discharge for which such a management practice is developed; and (2) review them every five years. Requires the Secretary of the department in which the Coast Guard is operating to promulgate regulations governing the design, construction, installation, and use of management practices for recreational vessels as necessary to meet such standards. Prohibits a recreational vessel from operating in or discharging in U.S. waters if such owner or operator is not using applicable management practices in compliance with such regulations.