PERMIT Act

The bill expanded from a single-issue navigable waters definition bill to a 26-section comprehensive water permitting reform act covering NPDES permits, Section 404 dredge and fill permits, water quality standards, certifications, compensatory mitigation, and state-federal cooperation.

Section 13 requires the Army Corps to maintain nationwide general permits for linear infrastructure projects (communications, electricity, transportation) discharging into less than 3 acres of navigable waters per single and complete project, and for linear pipeline projects with less than 0.5 acres of navigable water loss. Reissuance of these permits is exempt from Endangered Species Act consultation and NEPA requires only an environmental assessment rather than a full EIS.

Section 16 ratifies the Section 404 permit programs of Michigan, New Jersey, and Florida as 'of full force and effect' and prohibits EPA from withdrawing approval without a new Act of Congress. A 90-day transition period allows both the Corps and Florida to issue permits. The Administrator must approve any state program determined to be comparable to these three.

Section 8 clarifies that compliance with NPDES permit conditions constitutes compliance with the Clean Water Act for pollutants covered by the permit (including those controlled through indicator parameters or identified during the application process). It also requires water quality-based limitations to be expressed as numerical limits or clear narrative descriptions.

Section 25 establishes a voluntary pilot program for state-led water quality improvements in waters impaired for nitrogen or phosphorus, with an explicit savings clause stating it does not authorize regulation of nonpoint sources or expand federal jurisdiction.

Section 10 exempts agricultural stormwater discharges (including subsurface drainage) in direct response to precipitation from NPDES permitting. 'Agricultural land' is broadly defined to include land where animals, crops, or vegetation are present for farming/ranching, plus immediately adjacent functionally related land.

Section 11 exempts discharges of EPA-registered pesticides from NPDES permitting, with exceptions only for discharges resulting from violations of FIFRA, stormwater subject to existing rules, manufacturing/industrial effluent, treatment works effluent, and vessel-related discharges.

Section 9 exempts discharges resulting from aerial application of fire retardant products on the Forest Service Qualified Products List from NPDES permitting requirements.

Section 5 overhauls the Section 401 water quality certification process: states must publish certification requirements within 30 days of enactment, identify all needed information within 90 days of a request, and decisions may only be based on specific enumerated Clean Water Act provisions. A new subsection (h) creates expedited judicial review with a 30-day filing deadline, limited standing (only the applicant or those with direct irreparable economic harm), and a 120-day decision deadline.

Section 18 requires the Army Corps to publish a proposed rule within 180 days revising the 2008 compensatory mitigation regulations. Required changes include promoting flexibility among mitigation options, supporting regional watershed approaches, recognizing temporary impacts from mining and energy projects with approved reclamation plans, allowing surplus credit generation from reclamation activities, and encouraging off-site and out-of-kind mitigation.

Section 3 requires EPA to issue new or revised water quality criteria by rule, making them subject to the Administrative Procedure Act and judicial review under Section 509(b)(1) of the Clean Water Act.

Sections 2 and 4 require that cost and commercial availability of treatment technologies (including whether demonstrated at applicable scale) be considered when reviewing state water quality standards, developing water quality criteria, and setting technology-based effluent limitations.

Section 5(e) provides that conditions imposed on federal licenses/permits via Section 401 certification may be enforced only by the licensing or permitting agency, not by EPA or private parties.

Section 15 establishes a 60-day statute of limitations for challenging Section 404 permit approvals, individual permits, or general permit verifications. Challengers must have submitted a sufficiently detailed comment during the public comment period. Courts may only remand (not vacate) unless there is an imminent and substantial danger to health or environment. Agencies get 180 days to comply with court orders.

Section 7 extends NPDES individual permit terms from 5 years to 10 years. Section 13 extends Section 404 general permit terms from 5 years to 10 years.

Section 19 requires the Army Corps to eliminate any backlog of Section 404 permit applications and jurisdictional determination requests existing as of June 5, 2025, within 60 days of enactment.

The navigable waters exclusion for prior converted cropland was significantly expanded. It now includes any area that was drained or manipulated before December 23, 1985 for agricultural production AND has been used for agricultural purposes (including grazing, haying, conservation idling, irrigation tailwater storage, farm-raised fish, cranberry production, nutrient retention, and post-disaster soil recovery) at least once in the preceding 10 years and has not reverted to wetlands.

The waste treatment systems exclusion from navigable waters was expanded to include any lagoon or treatment pond (such as settling or cooling ponds) designed to actively or passively convey, retain, concentrate, settle, reduce, or remove pollutants from wastewater.

Section 26 authorizes the International Boundary and Water Commission to accept funds from federal or non-federal entities for wastewater treatment, water conservation, or flood control projects, with a $5 million annual reimbursement limit and restrictions on accepting funds from entities connected to foreign countries of concern.

Section 21 raises SPCC rule applicability thresholds: aboveground storage capacity threshold increased from 20,000 to 42,000 gallons; other thresholds raised from 1,000 to 1,320 and 2,500 to 3,000 gallons.