Clean Water Affordability Act of 2012

Clean Water Affordability Act of 2012- Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to authorize the Administrator of the Environmental Protection Agency (EPA) to: (1) make grants to states for the purpose of providing grants to local or regional authorities or municipalities for use in planning, designing, and constructing treatment works to intercept, transport, control, or treat municipal combined sewer overflows (CSOs) and sanitary sewer overflows; and (2) make grants directly to local or regional authorities or municipalities for such purposes.

Requires the Administrator to establish a comprehensive and integrated planning approach to the obligations under the national pollutant discharge elimination system of a publicly owned treatment work (POTW) or a municipal separate storm sewer system. Authorizes states to approve a permit to discharge into navigable waters with a term of more than 5 years but fewer than 25 years if a permittee has an approved interrelated plan.

Requires the Administrator to: (1) amend the CSO control policy to allow a POTW that has an approved long-term control plan to modify the plan to incorporate green infrastructure and energy-efficient technologies on a showing that the use of such technologies can cost-effectively help to meet the terms of the POTW's CSO compliance obligations, and (2) allow for 30 years to meet compliance obligations under such modified plans.

Requires the Administrator to: (1) ensure that EPA's Office of Water, Office of Enforcement and Compliance Assurance, Office of Research and Development, and Office of Policy promote the use of green infrastructure in, and coordinate the integration of green infrastructure into, permitting programs, planning efforts, research, technical assistance, and funding guidance; (2) direct EPA's regional offices to promote and integrate the use of green infrastructure within the region; (3) promote sharing of green infrastructure information and provide technical assistance regarding green infrastructure approaches for reducing water pollution, protecting water resources, complying with regulatory requirements, and achieving other environmental, public health, and community goals; and (4) establish a voluntary green infrastructure portfolio standard to increase the percentage of annual water managed by eligible entities that use green infrastructure.

Allows loans from a state water pollution control revolving fund to have a term of the lesser of 30 years or the design life of the project to be financed with the proceeds of the loan. (Currently the term of the loan is capped at 20 years.)

Requires the Administrator, no later than December 31, 2010 (currently, 2003) and periodically thereafter, to report to Congress on recommended funding levels for sewer overflow control grants.

Requires the Administrator to update the guidance entitled "Combined Sewer Overflows -- Guidance for Financial Capability Assessment and Schedule Development," dated February 1997, to ensure that the evaluations by the Administrator of financial capability assessment and schedule development meet specified criteria, including criteria used in assessing financial capability of a community to make investments necessary to make water quality-related improvements and in implementing water quality-related improvements.

Requires such updated guidance to indicate that it is appropriate for the reconsideration and modification of financial capability determinations and implementation schedules to be based on such criteria.