Clean Water Cooperative Federalism Act of 2013

Clean Water Cooperative Federalism Act of 2013 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to prohibit the Administrator of the Environmental Protection Agency (EPA) from:

• promulgating a revised or new water quality standard for a pollutant when the Administrator has approved a state water quality standard for such pollutant unless the state concurs with the Administrator's determination that the revised or new standard is necessary to meet the requirements of such Act;
• taking action to supersede a state's determination that a discharge will comply with effluent limitations, water quality standards, controls on the discharge of pollutants, and toxic and pretreatment effluent standards under such Act;
• withdrawing approval of a state program under the National Pollution Discharge Elimination System (NPDES), limiting federal financial assistance for a state NPDES program, or objecting to the issuance of a NPDES permit by a state on the basis that the Administrator disagrees with the state regarding the implementation of an approved water quality standard or the implementation of any federal guidance that directs the interpretation of such standard; or
• denying or restricting the use of an area as a disposal site for the discharge of dredged or fill material into navigable waters in a permit if the state where the discharge originates does not concur with the Administrator's determination that the discharge will result in an unacceptable adverse effect on municipal water supplies, shellfish beds, and fishery areas.

Shortens the period in which the Director of the United States Fish and Wildlife Service must submit comments with respect to a general dredge and fill permit application. Requires the Administrator and other agencies to submit comments on an application for a general permit or a permit to discharge into navigable waters at specified disposal sites within 30 days (or 60 days if additional time is requested) after the date of receipt of such application.

Applies this Act to actions taken on or after this Act's date of enactment, including actions taken with respect to permit applications that are pending or revised or new standards that are being promulgated.

Requires the Administrator, before issuing a regulation, policy statement, guidance, response to a petition, or other requirement or implementing a new or substantially altered program under this Act, to analyze the impact, disaggregated by state, of such action on employment levels and economic activity. Directs the Administrator to: (1) post such analysis on EPA's website; (2) request that the governor of any state experiencing more than a de minimis negative impact on employment levels or economic activity (a loss of more than 100 jobs or a decrease in economic activity of more than $1 million) post such analysis in the state's capitol; (3) hold a public hearing in each state where such action will have more than a de minimis negative impact; and (4) give notice of such impact to states' congressional delegations, governors, and legislatures.