Commercial Vessel Discharges Reform Act of 2013 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to prohibit a permit from being required under such Act for a discharge incidental to the normal operation of a covered vessel.

Defines a "covered vessel" to mean every description of watercraft, or other artificial contrivance used or capable of being used as a means of transportation on water, that is engaged in commercial service and that is: (1) less than 79 feet in length; or (2) a fishing vessel, regardless of length.

Directs the Administrator of the Environmental Protection Agency (EPA) to: (1) determine, within one year, the discharges incidental to the normal operation of a covered vessel for which it is reasonable and practicable to develop best management practices to mitigate adverse impacts on the waters of the United States; and (2) review such determination every five years.

Requires the Secretary of the department in which the Coast Guard is operating, in consultation with the Administrator, to promulgate regulations on the use of best management practices for discharges incidental to the normal operation of a covered vessel that the Administrator determines are reasonable and practicable.

Prohibits, upon the promulgation of such regulation, the owner or operator of a covered vessel from operating in, or discharging such discharge into, navigable waters, if the owner or operator of the vessel is not using such practices.