State Waters Partnership Act of 2012 - Expresses the sense of Congress that the Administrator of the Environmental Protection Agency (EPA): (1) should take into account the effect of numeric nutrient criteria for nitrogen or phosphorus developed to meet the water quality requirements of the Federal Water Pollution Control Act (commonly known as the Clean Water Act) on the economy, job creation, consumers, municipalities, agriculture, small business, and other affected sectors; and (2) should not promulgate or enforce nutrient criteria that would result in a negative economic impact of at least 15% on any such sector.
Prohibits the Administrator from proposing, promulgating, or enforcing numeric nutrient criteria for any stream, lake, spring, canal, estuary, or marine water of Florida until the Administrator makes a final determination in accordance with such Act regarding the Florida amended rule approved for adoption by the Environmental Regulation Commission on December 8, 2011. Provides that if the Administrator determines that such rule meets the requirements of such Act: (1) the Adminstrator shall withdraw specified regulations concerning site-specific alternative criteria, and (2) the Administrator shall be prohibited from proposing or promulgating numeric nutrient criteria for streams, lakes, springs, canals, estuaries, or marine waters of Florida based on EPA's January 14, 2009, determination regarding numeric nutrient criteria.