Clean Water Compliance and Ratepayer Affordability Act of 2013 - Requires the Administrator of the Environmental Protection Agency (EPA) to carry out a pilot program to work cooperatively with and facilitate the efforts of municipalities to develop and implement integrated plans to meet their wastewater and stormwater obligations under the Federal Water Pollution Control Act (commonly known as the Clean Water Act) in a cost-effective and flexible manner and consistent with the Integrated Municipal Stormwater and Wastewater Approach Framework issued by EPA in May 2012.

Directs the Administrator, in consultation with states that have approved National Pollutant Discharge Elimination System programs, to select at least 15 municipalities to participate in the program. Sets forth selection factors, including by giving a priority to those with a history of knowledgeable, detailed, and comprehensive efforts to develop integrated and adaptive clean water management practices, without regard to the municipality's status in the process of planning or implementing them.

Provides standards for approval of a municipality's integrated plan under the pilot program, including concerning financial capability, prioritization of obligations under the Clean Water Act, and the use of innovative and flexible approaches to meet obligations.

Allows priority to be given to municipalities seeking to develop and implement approaches that adapt to changed or future uncertain circumstances.

Provides additional authorities regarding selected municipalities concerning: (1) extension of the allowable national pollutant discharge elimination system permit term, (2) modification of implementation terms of a consent decree, and (3) additional regulatory flexibility in approving and implementing an integrated plan that includes adaptive approaches.