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National Pollutant Discharge Elimination System (NPDES)

Stormwater Discharges from Industrial Activities-Threatened and Endangered Species

Remember to throw your gloves in the trash

Multi-Sector General Permit (MSGP) Threatened and Endangered Species Eligibility

Part of the 2015 MSGP requires you to determine your eligibility with regard to protection of threatened and endangered species and critical habitat. You must make the determination before you submit a notice of intent (NOI) for permit coverage.

Determining your Endangered Species Act (ESA) eligibility

Appendix E - Procedures Relating to Endangered Species Protection - follow these procedures to assess the effects of your discharges and discharge-related activities on threatened and endangered species and critical habitat. Include all documentation supporting your eligibility in your stormwater pollution prevention plan (SWPPP).

Review this summary of the required steps in Appendix E:

Step 1. Determine if you can meet the eligibility requirements of criterion B, D, or E.

  • Criterion B: Your industrial discharges and discharge-related activities were already addressed in another operator’s valid certification of eligibility for your action area under the 2015 MSGP, and there is no reason to believe that federally listed species or designated critical habitat not considered in the prior certification may be present in your “action area” (e.g., due to a new threatened or endangered species listing or critical habitat designation).

    “Action area” is defined as “all areas to be affected directly or indirectly by the federal action and not merely the immediate area involved in the action.”

Note: You cannot select this eligibility criterion based upon a determination under an earlier version of the MSGP because revisions have been made to the eligibility requirements.

  • Criterion D: A separate Endangered Species Act (ESA) section seven consultation was completed that addresses the effects of your facility’s discharges and discharge-related activities.
  • Criterion E: Your facility’s activities are the subject of a permit under section 10 of the ESA that addresses the effects of your facility’s discharges and discharge-related activities.

If you meet criteria B, D, or E, skip to document eligibility on NOI and SWPPP.

If you do not meet criteria B, D, or E, continue to step 2.

Step 2. Determine the extent of your facility’s action area. Consider the following in determining the action area:

  • Include all receiving waterbodies that could receive pollutants from your facility. Discharges of pollutants into downstream areas can expand the action area well beyond the footprint of your facility and the discharge point(s). Account for controls you will implement to minimize pollutants and characteristics of the receiving waterbody (e.g., perennial, intermittent, ephemeral) in determining the extent of physical, chemical and biotic effects of the discharges.
  • Account for discharge-related activities, which include the siting, construction and operation of stormwater controls to control, reduce or prevent pollutants from being discharged. For example, any new or modified stormwater controls that will create noise—and any disturbances associated with construction of controls—are part of your action area.

Step 3. Determine if threatened species, endangered species, or critical habitat are present in your facility’s action area.

You must refer to National Marine Fisheries Service (NMFS) and U.S. Fish and Wildlife Service (FWS) listed species information:

  1. Refer to the following maps to determine if NMFS-listed species are potentially present:
  2. IPaC, Information for Planning and Conservation - access the FWS’s online mapping tool and follow these steps to determine if FWS-listed species are potentially present:
    1. Select get started.
    2. Select enter project location.
    3. Use an address, city name or other location to zoom into your action area.
    4. Use the zoom feature to see the entire extent of your action area on the screen.
    5. Use one of the mapping features (e.g., polygon or line feature) to draw your action area.
      • For the aquatic portion of your action area, trace the waterbody(ies) with the tool to characterize your action area.
      • If there will be any discharge-related activities associated with your 2015 MSGP coverage, or if there is some aspect of your discharge that would potentially result in effects to terrestrial species, include the corresponding upland areas within your action area.
      • When you are finished, press continue.
    6. Select request an official species list.
    7. Complete the fields on the official species list request page, and include “(MSGP)” at the end of the project description.
      1. For classification, select “water quality modification”.
      2. Select the appropriate requesting agency/organization type. (For most operators, this should be “other”.)
    8. Submit the request to acquire an official species list, which should show listed species as well as any designated critical habitat that are present in your action area. If a link to an official species list is not available on the page:
      • follow the Web link of the office(s) indicated; or
      • contact the office directly if a Web link is not shown.

FWS New England Field Office’s guidance - facilities located in EPA region 1 may alternatively follow this guidance for determining the presence of FWS species in your action area.

Note: If, after following NMFS and FWS guidance, the only listed species potentially present is the northern long-eared bat, and your facility will not be conducting discharge-related activities under your 2015 MSGP coverage, you are eligible for MSGP coverage under Criterion A and a Criterion C Eligibility Form is not required.

  • If you determine that no threatened or endangered species and no critical habitat are present in your facility’s action area, you are eligible for MSGP coverage under criterion A. Skip to Document eligibility on NOI and SWPPP.
  • If you determine that threatened or endangered species and no critical habitat are present in your facility’s action area, continue to completing the criterion C eligibility form.

Completing the Criterion C Eligibility Form

If you determined that threatened or endangered species or critical habitat are present in your facility’s action area, you must submit a Criterion C eligibility form from MSGP Appendix E to EPA to You must submit the form at least 30 days before submitting your NOI for permit coverage. The form must document:

  • threatened and endangered species in the action area,
  • potential stressors to species from pollutants in stormwater discharges, and
  • controls that will be implemented to avoid adverse effects.

After you submit this form, EPA may contact you with additional measures necessary to ensure your discharges and discharge-related activities are unlikely to cause adverse effects on threatened or endangered species or critical habitat. If you do not hear anything from EPA, you are eligible to submit your NOI under Criterion C 30 days after submitting your completed form.

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Document Eligibility on NOI and SWPPP

For all eligibility criteria (criteria A, B, C, D, and E):

  • identify the eligibility criterion you selected on your NOI for permit coverage and
  • include documentation supporting your eligibility determination in your SWPPP.

Go to NetMSGP to complete your NOI for permit coverage.

Contact Information

For questions about meeting the MSGP requirements in part and Appendix E, contact or your EPA regional permitting authority.

Legal Background

EPA revised the requirements for threatened and endangered species and critical habitat protection eligibility under the 2015 MSGP as a result of its consultation with FWS and NMFS under section 7 of the ESA.

U.S. Fish and Wildlife Service

FWS Regional Contact List

National Marine Fisheries Service

NMFS Alaska Region Contacts
NMFS Northwest Region Contacts
NMFS Pacific Islands Region Contacts
NMFS Southwest Region Contacts
NMFS Southeast and Caribbean Region Contacts
NMFS Northeast Region Contacts


Under section 9 (a)(1)(B) of the Endangered Species Act, with respect to any endangered species of fish or wildlife listed pursuant to section 4 of this Act, it is unlawful for any person subject to the jurisdiction of the United States to take any such species within the United States or the territorial sea of the United States. To ensure consistency with the conditional take exemption associated with the MSGP, MSGP-authorized dischargers shall notify the nearest National Marine Fisheries Service (NMFS) Regional Office within three days upon finding any dead, injured, or sick, specimen, nest, and/or egg(s) of endangered or threatened species under NMFS jurisdiction that appears to have been harmed by MSGP-authorized discharges into Waters of the United States. In addition, notify the National Marine Fisheries Service, Office of Protected Resources at (301) 427-8400 and EPA at Include the date, time, and precise location of the injured animal, carcass, nest, and/or egg and any other pertinent information in your notification. Leave the plant or animal alone, make note of any circumstances likely causing the death or injury, note the location and number of individuals involved and, if possible, take photographs. The finder may be asked to carry out instructions provided by NMFS to collect specimens or take other measures to ensure that evidence intrinsic to the specimen is preserved. Care should be taken in handling sick or injured specimens to preserve biological materials in the best possible state for later analysis of cause of death, if that occurs.

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