Clean Water Compliance and Affordability Act - Requires the Environmental Protection Agency (EPA) to carry out a pilot program to work with and facilitate the efforts of eligible municipalities to develop and implement integrated plans to meet 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 EPA to select at least 15 municipalities to participate in the program. Sets forth eligibility and selection factors. Prescribes standards for approval of a municipality's integrated plan under the pilot program. Allows priority to be given to municipalities seeking to develop and implement approaches that adapt to changed or future uncertain circumstances.

Authorizes the EPA to: (1) extend the allowable national pollutant discharge elimination system permit term to a maximum of 25 years, (2) modify the implementation terms of a consent decree, and (3) provide additional regulatory flexibility in approving and implementing an integrated plan that includes adaptive approaches.