Redesignates existing paragraph (3) of subsection (g) as paragraph (4); inserts a new paragraph (3) in subsection (g) requiring the Administrator to send a written request for additional information to a State not later than 45 days after receipt of the State's program and statement when the Administrator determines additional information is necessary; and amends subsection (h)(1) by replacing the phrase 'paragraph (1) of this subsection' with 'subsection (g)(1)'.

Adds a new paragraph (4) to subsection (l) entitled 'Agricultural stormwater discharge' that prohibits the Administrator from requiring an NPDES permit (or requiring any State to require a permit) for discharges of stormwater, including from subsurface drainage, from agricultural land that occur in direct response to a precipitation event, and that defines the term 'agricultural land' with three clauses including adjacent/functionally related land.

Amends multiple subsections of 33 U.S.C. 1341: revises wording in subsection (a) (e.g., 'may result' -> 'may directly result'; 'activity' -> 'discharge'; pluralizes 'requests'); changes the process and wording for acting on certification requests to have the licensing or permitting agency grant, deny, or waive requests within a reasonable period determined by that agency not to exceed one year; modifies subsection (b) to add an exception reference to new subsection (e); revises subsection (d) to require that discharges comply with the applicable provisions of sections 301, 302, 303, 306, and 307 and that such limitations be imposed by the licensing or permitting agency as conditions on federal licenses or permits; and adds new subsections (e) (limiting enforcement of conditions to the licensing or permitting agency), (f) (defining the applicable provisions of sections 301, 302, 303, 306, and 307), and (g) (specifying the required contents of a complete request for certification, including detailed elements for individual and general permits).

Amends section 304(b) of the Federal Water Pollution Control Act (33 U.S.C. 1314(b)) by inserting additional text into paragraph (1)(B), paragraph (2)(B), and paragraph (4)(B) immediately before the existing semicolons.

Amends subsection (b)(1) by striking the phrase "section 402, and" and replacing it with "section 402,"; the amendment text also indicates an additional insertion after an unspecified point (inserted text not provided in the section).

Amends section 303(c) to revise paragraph (1) review provisions to require reviews to include assessment of cost-effectiveness of combined sewer overflow controls for water quality standards applicable to waters receiving discharges from municipal combined storm and sanitary sewers, and to require that results of each review be made available to the Administrator; also makes additional insertions in paragraph (1) and paragraph (2)(A).

Modifies thresholds and classification language in subsection (b), updates numeric thresholds in subsection (c)(2)(A), removes paragraph (4) of subsection (b), and strikes subsection (d).

Revises paragraph (7) (definition of 'navigable waters') to replace the existing text and add a new exclusions subsection listing specific features not included as 'navigable waters', including components of waste treatment systems, ephemeral features that flow only in response to precipitation, certain areas drained or manipulated prior to December 23, 1985 (consistent with designations of prior converted cropland by the Secretary of Agriculture) as determined by the Administrator and the Secretary of the Army acting through the Chief of Engineers, groundwater, and any other features those officials determine to be excluded.

Revises the statutory definition of "navigable waters" by replacing subsection (7) and adding a new subsection (B) that lists specific exclusions from the term.