Water Quality Basics

Water quality management requirements for transportation agencies are related to implementation of the NPDES program along with the water quality certification program under the CWA.

Currently there are three areas related to water quality that are having a significant impact on transportation practice nationwide:

1. NPDES requirements for obtaining permits for operation and maintenance of Municipal Separate Storm Sewer Systems (MS4s).
2. NPDES requirements for permitting Stormwater Discharges Associated with Construction Activities.
3. NPDES requirements for compliance with effluent standards related to established Total Maximum Daily Loads or other effluent discharge standards that may be required by the state regulatory agency.

[Note: Water quality issues span a broad range of concerns that overlap into many areas of science and numerous environmental issues and concerns. This section deals only with the primary issues of stormwater quality and that impact the detailed design and construction of transportation facilities. Other water related issues, such as ground water, water supply, water and stormwater quantity, aquatic habitat, etc., are not addressed here.]

National Pollutant Discharge Elimination System (NPDES) Municipal Separate Storm Sewer Systems (MS4) Permitting Requirements under CWA Section 402

To achieve its objectives, CWA Section 402 considers all point source discharges into the nation’s waters unlawful, unless authorized by a permit. Thus industrial and municipal entities that discharge any type of water such as waste water or stormwater, must obtain permits from EPA or a designated state program, under the NPDES.

Stormwater runoff from transportation facilities and construction projects is considered by broad definition under the CWA to be a point source discharge and has been identified as a major source of pollutants discharged into the nation’s waters.

At this time all state departments of transportation are working on implementing their SWMPs to address the six minimum measures. Because there is such variety in the implementation strategy the individual states should be contacted for specific program information.

More information on the NPDES Stormwater Program is available here. 

NPDES Stormwater Management for Construction Sites

The rules implementing the NPDES required that eleven categories of industrial activity obtain permits to discharge stormwater. Because stormwater discharges from construction sites are significantly different than other types of industrial stormwater, EPA opted to permit construction activities separately from other industrial activities. The rules require stormwater discharge permits for sites of one acre or greater. Some states classify sites of one to five acres as “small sites.” Sites of five acres or more are classified “large sites,” and they have different permitting requirements from state to state.

The permitting requirements for construction projects should not be confused with other management requirements of the MS4 permits. Although construction is a temporary activity, the loss of surface cover exposes the soil and will result in accelerated erosion if not properly managed. By volume, soil particles are the number one pollutant in the nation’s waters. Sediment-bearing runoff from construction sites has been identified as a source of pollutants that can result in significant damage to water quality. As runoff moves over a construction site, it mobilizes all available pollutants, which may include: soil particles which may bond with other chemicals, surface debris, soluble chemicals, pathogens, grease and oil, etc. If this runoff is allowed to reach a water body or a conveyance that is connected to a water resource it can result in significant adverse impacts.

The NPDES stormwater program recognizes that construction site runoff represents a risk that is significantly different from other industrial stormwater discharges. Therefore the NPDES requires operators of constructions sites of one acre or larger (including smaller sites that are part of a larger common plan of development) to obtain authorization to discharge stormwater under a state or federal NPDES construction stormwater permit. The Construction General Permits (CGPs) issued by states and EPA require the filing of a Notice of Intent, the development of a Storm Water Pollution Prevention Plan (SWPPP) and filing a Notice of Termination once the construction site has been restabilized. The key document is the SWPPP which details how the site will be managed to prevent impacts of adjacent waters.

EPA has delegated the construction permitting authority to most of the state resource agencies; however, EPA remains the permitting authority in a few states, territories, and on most federal and Indian lands. For construction on EPA regulated lands, construction projects must seek coverage under the EPA Construction General Permit (CGP). State construction general permits have a similar structure to EPA’s CGP, but individual states may have additional requirements that are tailored to protect the unique characteristics of their water resources.

Coverage of NPDES general permits for construction stormwater discharges is limited to five years.

Total Maximum Daily Loads (TMDLs): Establishment of State-based Water Quality Standards under Clean Water Act Section 303

Under Section 303(d) of the Clean Water Act (CWA), all states, territories, and authorized tribes must develop a list of impaired water bodies—commonly referred to as the “303(d) list.” These are waters that do not meet applicable water quality standards, even after the implementation of minimum required pollution control technologies. For each water body on the list, jurisdictions must establish Total Maximum Daily Loads (TMDLs) to restore the water to a fishable and/or swimmable condition.

A TMDL defines the maximum amount of a pollutant—such as nutrients, sediments, pathogens, or other chemical contaminants—that a water body can receive while still meeting water quality standards. These pollutant loads are then allocated among point and non-point sources, including those regulated under the National Pollutant Discharge Elimination System (NPDES).

In addition to TMDL-based effluent standards, many states are incorporating stormwater-specific effluent limits into general permits for construction activities. These standards aim to protect high-quality waters and ensure that Best Management Practices (BMPs) used on construction sites are effective in safeguarding adjacent water bodies.

The 2026 EPA Integrated Reporting Guidance provides updated direction for preparing biennial reports under Sections 303(d), 305(b), and 314. Key updates include:

• Clarification on defining assessment units and segment boundaries.
• Use of fish consumption and swimming advisories in impairment decisions.
• Priority ranking methodologies for impaired waters.
• Integration of water quality data from Section 305(b) reports into Section 106 grant allocations.
• Continued support for adaptive management approaches and iterative BMP implementation for stormwater discharges.

The EPA emphasizes the use of its Assessment and TMDL Tracking System (ATTAINS) for submitting Integrated Reports and encourages consistency with both the 2026 guidance and prior memoranda.

EPA retains oversight authority and must approve or disapprove state-submitted lists and TMDLs. If a submission is inadequate, EPA is required to step in and establish the list or TMDL. This oversight has been reinforced through legal actions in multiple states, resulting in court orders and consent decrees mandating timely TMDL development.

For more information, including access to the full 2026 guidance memo, visit the EPA’s Integrated Reporting Guidance page.

Stormwater Provision in SAFETEA-LU

The Safe, Accountable, Flexible, Efficient Transportation Equity Act: A Legacy for Users (SAFETEA-LU) modified the eligibility of Federal-aid funds to participate in environmental restoration and stormwater impacts activities to minimize or mitigate the impacts of transportation projects. According to FHWA guidance, this section primarily deals with the impacts of transportation facilities that were built prior to the current, more stringent requirements for abatement of stormwater runoff. These transportation facilities may have been constructed with limited or no stormwater treatment controls.

The guidance specifies that SAFETEA-LU provides the means to fund retrofits and the construction of stormwater treatment systems to address water impacts and environmental degradation that is caused in whole or in part by a transportation facility. These measures may be implemented under two basic scenarios:

• • a stand-alone project, one that is developed solely to address stormwater concerns and is not associated with a transportation project that is being developed or is under construction; or
  • in conjunction with a project that is currently being developed for the reconstruction, rehabilitation, resurfacing, or restoration of a transportation facility. In this case, the costs for environmental restoration and stormwater runoff abatement may not exceed 20 percent of the total cost of the project.