BIOLOGICAL OPINION

FOR THE

NATIONAL POLLUTANT DISCHARGE ELIMINATION SYSTEM

MULTI-SECTOR GENERAL PERMIT

FOR STORMWATER DISCHARGES

ASSOCIATED WITH INDUSTRIAL ACTIVITY

(MSGP)

May 2015

U.S. Fish and Wildlife Service

Endangered Species Program

Division of Environmental Review

Falls Church, Virginia
2015 MSGP Biological Opinion i

TABLE OF CONTENTS

Abbreviations.................................................................................................................................. ii

INTRODUCTION ........................................................................................................................ 1

CONSULTATION HISTORY.................................................................................................... 1

BIOLOGICAL OPINION............................................................................................................ 2

DESCRIPTION OF THE PROPOSED ACTION ...................................................................... 2

OVERVIEW OF THE ASSESSMENT FRAMEWORK......................................................... 29

Approach to the Assessment......................................................................................................... 29

ANALYTICAL FRAMEWORK FOR THE JEOPARDY AND ADVERSE MODIFICATION 

DETERMINATIONS................................................................................................................ 33

Jeopardy Determination................................................................................................................ 33

Adverse Modification Determination ........................................................................................... 33

ACTION AREA........................................................................................................................ 34

STATUS OF THE SPECIES AND CRITICAL HABITAT..................................................... 35

Water Quality................................................................................................................................ 51

EFFECTS OF THE ACTION ................................................................................................... 51

CUMULATIVE EFFECTS....................................................................................................... 93

INTEGRATION AND SYNTHESIS OF EFFECTS................................................................ 94

CONCLUSION......................................................................................................................... 99

INCIDENTAL TAKE STATEMENT .................................................................................... 100

AMOUNT OR EXTENT OF TAKE ...................................................................................... 100

TERMS AND CONDITIONS ................................................................................................ 102

CONSERVATION RECOMMENDATIONS ........................................................................ 104

REINITIATION NOTICE....................................................................................................... 106

LITERATURE CITED ............................................................................................................ 107
2015 MSGP Biological Opinion ii

Abbreviations

BE – Biological Evaluation

BMP – Best Management Practices

Cu - Copper

CWA – Clean Water Act (33 USC 1342 et seq.)

EPA – Environmental Protection Agency

ELG – Effluent Limitation Guidelines

ESA – Endangered Species Act of 1973, as amended (16 U.S.C. 1531 et seq.)

MSGP – Multi-Sector General Permit for Stormwater Discharges Associated with Industrial 

Activity, or “the permit”

NOI – Notice of Intent to seek coverage under the permit

NPDES – National Pollutant Discharge Elimination System

NTU - Nephelometric Turbidity Units 

OMB – Office of Management and Budget

Opinion – Biological Opinion

PAH – Polyaromatic hydrocarbons

PBFs – essential physical and biological features of designated critical habitat.

Permit – Multi-Sector General Permit for Stormwater Discharges Associated with Industrial 

Activity

Service – U.S. Fish and Wildlife Service

Services – U. S. Fish and Wildlife Service and National Marine Fisheries Service 

TSS – Total Suspended Solids

Zn - Zinc
2015 MSGP Biological Opinion 1

INTRODUCTION

This document represents the U. S. Fish and Wildlife Service's (Service) Biological Opinion 

(Opinion) based on our review of the proposed reissuance of the Environmental Protection 

Agency’s (EPA) National Pollutant Discharge Elimination System Multi-Sector General Permit 

for Stormwater Discharges Associated with Industrial Activity (hereafter MSGP or “permit”), 

and its effects on listed species and designated critical habitat in accordance with section 7 of the 

Endangered Species Act of 1973, as amended (16 U.S.C. 1531 et seq.) (ESA). 

Your request for formal consultation was received on January 27, 2014. This Opinion is based 

on information provided in the January 27, 2014, Biological Evaluation (BE), additional 

information received February 26, and March 4, 6, and 12, 2014, and other sources of 

information as described below. A complete record of this consultation is on file at this 

Service’s headquarters office in Falls Church, Virginia. 

CONSULTATION HISTORY

In the fall of 2012, EPA staff requested early coordination with the U.S. Fish and Wildlife 

Service and National Marine Fisheries Service (Services) prior to drafting a BE for the 

reissuance of the MSGP. Subsequent meetings and conference calls were also used to assist 

EPA in identifying any issues related to listed species and critical habitat that were likely to be 

raised with permit language and implementation prior to the submission of a draft permit to the 

Office of Management and Budget (OMB). The following timeline describes early coordination 

and informal consultation between EPA and the Services and identifies key points in the 

consultation process:

• September 2011. Initial meeting between EPA and the Services to discuss the proposed 

reissuance of the MSGP.

• November 20, 2011. Follow-up meeting between EPA and the Services. Initial 

discussion of previous permit cycle and preliminary criterion selection data represented 

by geographic area.

• January 2012 through July 22, 2012. Frequent meetings between EPA and the Services 

to discuss refinements to the permit language and issues to be addressed in the BE to 

reduce the potential for adverse effects to listed species and critical habitat. Examples of 

issues that were discussed include, but are not limited to the following:

o Use of conservation measures, best management practices, and other measures to 

reduce potential adverse effects

o Use of monitoring efforts to reduce potential adverse effects

o Consideration of criterion selection errors from past permit cycles that may 

underestimate adverse effects

o Consideration of monitoring data from past permit cycles that may provide insight 

on likelihood of anticipated future compliance with the proposed permit

o Additional tools that EPA could implement to assist the MSGP applicants with

their efforts to avoid criterion selection errors
2015 MSGP Biological Opinion 2

o EPA’s oversight of the permit

• July 24, 2012. The EPA submitted the draft BE to the Services for review and comment.

• July 24, 2012. The EPA requested the Services provide supporting information regarding 

monitoring needs for their coordination with OMB during review of the draft permit.

• July 31, 2012. The Services submitted the requested supporting information to the EPA 

for demonstrating monitoring needs to OMB.

• September 30, 2012. Submission of Services’ combined comments on the BE to EPA for 

consideration in finalizing the BE.

• January 27, 2014. The EPA submitted the final BE to the Services and requested

initiation of formal consultation.

• February 26, 2014. The Service sent a letter to the EPA requesting additional 

information including: 1) a list of critical habitat designations covered under the permit;

2) determinations for listed species and critical habitat anticipated to be affected by the 

proposed action and descriptions of how the effects would be anticipated to occur; and 3) 

monitoring data for the last permit cycle.

• March 4, 2014. The EPA submitted their monitoring database.

• March 6, 2014. The EPA submitted a supplemental monitoring database file.

• March 12, 2014. The Service received a letter from the EPA clarifying critical habitat 

designations and determinations for listed species and critical habitat under the proposed 

action. 

• April 11, 2014. The Service sent a letter to the EPA confirming all requested information 

had been received and formal consultation had been initiated as of March 12, 2014.

• June 19, 2014. The EPA submitted a revised draft of Appendix E (Procedures Relating 

to Endangered Species Protection and attached E4 Criterion Selection Worksheet) of the 

permit to the Services.

• July 28, 2014. The EPA amended the BE to include a representative compliance check 

on Criterion A facility proposals to reduce Criterion A selection errors in an email to the 

Services.

• December 22, 2014. The EPA emailed the Service to clarify coordination procedures 

with the Service during review of Criterion C facilities where the Service has indicated in 

writing that the coverage proposal does not appear to support rationale for coverage 

under Criterion C.

BIOLOGICAL OPINION

DESCRIPTION OF THE PROPOSED ACTION

Under reissuance of MSGP or “permit”, EPA proposes to authorize stormwater discharges 

associated with industrial activity from 30 sectors into waters of the United States over the 

permit period from 2015 to 2020. The EPA estimates the 2015 MSGP will reauthorize 

discharges from approximately 2,365 existing facilities and that an average of approximately 52 

additional facilities will seek coverage under the MSGP each year totaling approximately 250 

new facilities over the life of the 5-year permit. 
2015 MSGP Biological Opinion 3

The statutory authority for the proposed action is the National Pollution Discharge Elimination 

System (NPDES) of the Clean Water Act (33 USC §§ 1342 et seq.; CWA). The purpose of the 

proposed general permit is to provide an efficient manner for industrial facilities discharging 

stormwater (and specified non-stormwater) to waters of the United States to secure authorization 

for discharges. Requiring a CWA permit (either the MSGP or an individual permit) for these 

discharges provides EPA with the authority to enforce CWA requirements and provides the 

ability of citizens to sue for permit violations. In its permit, EPA reserved the right to modify or 

revoke and reissue this permit under 40 CFR 122.62. 

The MSGP would provide NPDES permit coverage for stormwater discharges, certain allowable 

non-stormwater discharges, and discharge-associated activities for facilities where EPA is the 

NPDES permitting authority. In addition, the MSGP provides coverage for facilities in four 

States (Idaho, Massachusetts, New Hampshire, and New Mexico), the District of Columbia, 

Puerto Rico, Puerto Rico and other Pacific Territories (except the U.S. Virgin Islands), 

designated areas in Oklahoma and Texas, Tribal lands in 19 states, and facilities operated by 

federal operators in Colorado, Delaware, Vermont, and Washington. To be authorized to 

discharge under the MSGP a facility must1

:

• Be located in a state, territory, or Indian country, or be a federal operator 

identified in Appendix C of the MSGP where EPA is the permitting authority;

• Meet the eligibility requirements described in permit;

• Select, design, install, and implement control measures in accordance with the permit to

meet numeric and non-numeric effluent limits;

• Develop a Stormwater Pollution Prevention Plan (SWPPP) according to the requirements

in Part 5 of the permit or update the existing SWPPP consistent with Part 5 prior to

submitting the Notice of Intent to seek coverage under the permit (NOI) for coverage under 

the MSGP; and

• Submit a complete and accurate NOI in accordance with permit.

The 2015 MSGP has been modified from previous permits in an effort to strengthen protections 

to listed species and designated critical habitat (hereafter, “listed resources”). These 

modifications include: 1) revisions to the ESA eligibility criteria; 2) revisions to the procedures 

operators are required to implement prior to obtaining coverage to address potential adverse 

effects to listed resources; and 3) more clearly articulated, transparent and enforceable nonnumeric and best management practice-based effluent limits. 

The following sections summarize the proposed permit and pertinent details embedded in the 

permit fact sheets and appendices. More detailed information on implementation of the proposed 

permit can be found in the BE, addenda, and in the permit and is in the administrative record for 

this Opinion. A copy of the draft permit submitted for consultation was provided as an 

attachment to the BE, and is appended to this Opinion (Appendix A). In some instances, the 

information from the sections below was taken directly from the permit language and/or the BE 

in the interest of clarity.

 

1 Section 1.2.1 of the permit.
2015 MSGP Biological Opinion 4

Types of Facilities Covered by the MSGP

EPA proposes to cover 10 broad categories of industrial activities under the MSGP, which have 

been categorized into 30 sectors (Table 1) and associated subsectors (Appendix B). The broad 

categories include:

• Category One (i): Facilities subject to federal stormwater effluent discharge standards in 

40 CFR Parts 405-471

• Category Two (ii): Heavy manufacturing (e.g., paper mills, chemical plants, petroleum 

refineries, and steel mills and foundries)

• Category Three (iii): Coal and mineral mining and oil and gas exploration and processing

• Category Four (iv): Hazardous waste treatment, storage, or disposal facilities

• Category Five (v): Landfills, land application sites, and open dumps with industrial 

wastes

• Category Six (vi): Metal scrapyards, salvage yards, automobile junkyards, and battery 

reclaimers

• Category Seven (vii): Steam electric power generating plants

• Category Eight (viii): Transportation facilities that have vehicle maintenance, equipment 

cleaning, or airport deicing operations

• Category Nine (ix): Treatment works treating domestic sewage with a design flow of 1

million gallons a day or more

• Category Eleven (xi): Light manufacturing (e.g., food processing, printing and 

publishing, electronic and other electrical equipment manufacturing, and public 

warehousing and storage).

EPA reserves discretion to designate other industrial activities as eligible for coverage under the 

MSGP under Sector AD2

. Some industrial facilities are covered under multiple sector or 

subsector categories, and these are identified by the facilities’ Standard Industrial Classification 

(SIC) code(s) referenced when facilities seek coverage under the MSGP. 

Types of Activities Covered by the MSGP

The MSGP covers three main categories of activities that could result in potential effects to 

species listed as threatened or endangered under the ESA and their designated critical habitats: 

stormwater discharges, certain allowable non-stormwater discharges, and discharge-related 

activities3. These activities are described in the following sections.

 

2 Section 1.1.1 of the permit.

3 Sections 1.1.2 and 1.1.3 of the Permit
2015 MSGP Biological Opinion 5

Table 1. Primary industrial sectors eligible for coverage under the MSGP.

Primary Industrial Sectora

Sector A: Timber products Sector P: Land transportation and warehousing

Sector B: Paper and allied products Sector Q: Water transportation

Sector C: Chemicals and allied products Sector R: Ship and boat building and repairing yards

Sector D: Asphalt paving and roofing materials and 

lubricants

Sector S: Air transportation facilities

Sector E: Glass, clay, cement, concrete, and gypsum 

products

Sector T: Treatment works

Sector F: Primary metals Sector U: Food and kindred products

Sector G: Metal mining (ore mining and dressing) Sector V: Textile mills, apparel, and other fabric 

product manufacturing; leather and leather products

Sector H: Coal mines and coal mining-related facilities Sector W: Furniture and fixtures

Sector I: Oil and gas extraction and refining Sector X: Printing and publishing

Sector J: Mineral mining and dressing Sector Y: Rubber, miscellaneous plastic products, and 

miscellaneous manufacturing industries

Sector K: Hazardous waste treatment, storage, or 

disposal facilities

Sector Z: Leather tanning and finishing

Sector L: Landfills, land application sites, and open 

dumps

Sector AA: Fabricated metal products

Sector M: Automobile salvage yards Sector AB: Transportation equipment, industrial or 

commercial machinery

Sector N: Scrap recycling facilities Sector AC: Electronic, electrical, photographic, and 

optical goods

Sector O: Steam electric generating facilities Sector AD: Non-classified facilities

a

Subsector activities are identified in Appendix D of the MSGP

Allowable Stormwater Discharges

The MSGP is primarily intended to cover stormwater discharges from the industrial sectors listed 

above into the Nation’s receiving waters in locations and for facilities where EPA has retained 

permitting jurisdiction and has made the MSGP available for coverage. The receiving waters are 

defined as the first waters of the United States that are discharged into, or, for discharges that 

enter a storm sewer system or other water body prior to discharge, the first waters of the United 

States discharged to by the storm sewer system or water body. The BE notes that typical 

industrial activities that may contribute to pollutants in stormwater include: loading and 

unloading operations, outdoor storage, outdoor process activities, dust or particulate generating 

processes, and waste management. To reduce the discharge of pollutants in stormwater from 
2015 MSGP Biological Opinion 6

industrial activity into receiving waters, there are certain requirements that apply to the 

discharges. The following stormwater discharges will be authorized under the permit:

• Stormwater discharges associated with industrial activity for any primary industrial 

activities and co-located industrial activities (as defined in the permit);

• Discharges designated by EPA as needing a stormwater permit as provided in sector AD 

of the MSGP;

• Discharges that are not otherwise required to obtain an NPDES permit but are comingled 

with MSGP-authorized discharges (e.g., condensate from air conditioners); and 

• Discharges subject to the national stormwater-specific effluent limitations guidelines4

(discussed later in this section).

Allowable Non-Stormwater Discharges

Certain non-stormwater discharges are authorized under the MSGP, provided that all discharges 

comply with the effluent limitations as described at Part 2 of the MSGP, Control Measures and 

Effluent Limits. The allowable non-stormwater discharges are:

• discharges from fire-fighting activities;

• fire hydrant flushings;

• potable water, including water line flushings;

• uncontaminated condensate from air conditioners, coolers, and other compressors and 

from the outside storage of refrigerated gases or liquids;

• irrigation drainage;

• landscape watering provided all pesticides, herbicides, and fertilizers have been applied 

in accordance with the approved labeling;

• pavement wash waters where no detergents or hazardous cleaning products are used (e.g., 

bleach, hydrofluoric acid, muriatic acid, sodium hydroxide, nonylphenols), and the wash 

waters do not come into contact with oil and grease deposits or any other toxic or 

hazardous materials (unless cleaned up using dry clean-up methods);

• routine external building washdown / power washwater that does not use detergents or 

hazardous cleaning products, (such as those containing bleach, hydrofluoric acid, 

muriatic acid, sodium hydroxide, nonylphenols);

• uncontaminated ground water or spring water;

• foundation or footing drains where flows are not contaminated with process materials;

 

4 Table 1-1 in the Permit
2015 MSGP Biological Opinion 7

• incidental windblown mist from cooling towers that collects on rooftops or adjacent 

portions of the facility, but not intentional discharges from the cooling tower (e.g., 

“piped” cooling tower blowdown or drains); and

• discharges from the spray down of lumber and wood product storage yards where no 

chemical additives are used in the spray-down waters and no chemicals are applied to the 

wood during storage (applicable only to Sector A facilities provided the non- stormwater 

component of the discharge is in compliance with the non-numeric effluent limits 

requirements in the permit at Part 2.1.2 Non-Numeric Technology-Based Effluent Limits 

(BPT/BAT/BCT)).

Allowable discharges (both stormwater and non-stormwater discharges) commingled with a 

discharge authorized by a different NPDES permit and/or a discharge that does not require 

NPDES permit authorization are also authorized under the MSGP. 

Discharge-Related Activities5

Discharge-related activities are any activities that cause, contribute to, or result in stormwater 

and allowable non-stormwater point source discharges, and measures such as the siting, 

construction, and operation of stormwater controls to control, reduce, or prevent pollutants from 

being discharged. The majority of the facilities that are anticipated to seek coverage under the 

MSGP are not expected to propose discharge-related activities, as many of the facilities are 

existing facilities with ongoing discharges covered under previous permit cycles. However, new 

facilities, facilities seeking new or expanded coverage, or a limited number of existing facilities 

may plan to install new controls or engage in other discharge-related activities. Thus, this 

category of activities is also included in the MSGP.

Activities not Covered by the MSGP

Any discharges not expressly authorized as summarized above6 are not within the scope of the 

pollutants addressed by the MSGP and are not included as part of the proposed action. To 

provide greater clarity, the EPA has also defined activities and discharges that are explicitly not 

covered by the MSGP. Some of these activities may require an individual permit or other form 

of alternative permit, or, in some cases, no permit would be required. These activities are not 

part of the proposed action. 

Procedures for Addressing Listed Species and Critical Habitat in Permit Coverage 

Requests7

As noted above, coverage under the MSGP is available only for stormwater discharges, 

allowable non-stormwater discharges, and stormwater discharge-related activities. The MSGP 

specifies that facilities seeking coverage must ensure the effects of the discharges are not likely 

to adversely affect any species that are federally listed as endangered or threatened (“listed”) 

 

5 See Part 1.1.4.5 of the permit, 

6 Described in detail in parts 1.1.2 through 1.1.4 of the MSGP 7 Section 1.1.4.5 of the Permit
2015 MSGP Biological Opinion 8

under the ESA and are not likely to adversely affect habitat that is federally designated as critical 

habitat under the ESA. Alternatively, facilities can qualify for coverage under another operator’s 

permit coverage, or where effects of the allowable discharges and discharge-associated activities 

have previously been the subject of an ESA section 7 consultation or an ESA Section 10 permit. 

To demonstrate that the facility is eligible for coverage under the MSGP, a facility operator must 

determine which of five ESA eligibility criteria applies to the facility’s discharge(s), allowable 

non-stormwater discharge(s), and/or discharge-related activities. The facility operator must then 

submit an NOI to apply for coverage under the MSGP. The following sections describe the ESA 

eligibility criteria and the proposed process for facility operators to select an appropriate criterion 

while seeking coverage under the 2015 MSGP.

ESA Eligibility Criteria

The facility operators are directed to demonstrate their eligibility under one of the ESA criteria 

by following instructions outlined in Appendix E to the permit: Procedures Relating to 

Endangered Species Protection, which includes an “E4 Criterion Selection worksheet” 

(Appendix E of the permit and Appendix C of this Opinion). This form guides a permit 

applicant in selecting the most appropriate eligibility criterion their facility meets or will meet 

based on information such as existing documentation, facility location, and overlap of listed 

species/critical habitat with the area of potential effects (or “action area”) of their discharge(s) 

(and discharge-related activities, where proposed). The ESA eligibility criteria for Endangered 

Species Protection are shown in Table 2 below. 

Table 2. ESA eligibility criteria as defined in the MSGP (Note: The text below is reproduced 

from Appendix E of the draft permit (with minimal edits based on coordination with EPA), but 

reorganized into table format for clarity in the Opinion.

Criterion Additional Considerations

A: No federally-listed

threatened or endangered

species or their designated

critical habitat(s) are likely to 

occur in the “action area” as 

defined in Appendix A (of the 

MSGP).

To certify eligibility under this criterion, the permit applicant must use the E.4

Criterion Selection worksheet. The permit applicant must also provide a

description of the basis for the criterion the permit applicant selected on the NOI

form and provide documentation supporting the eligibility determination in the 

SWPPP.

B: The industrial activity’s

discharges and dischargerelated activities were already 

addressed in another operator’s

valid certification of eligibility

for the action area under this

permit and there is no reason to 

believe that federally-listed 

species or federally-designated

critical habitat not considered in

the prior certification may be 

present or located in the “action

area” (e.g., due to a new species

listing or critical habitat

designation).

To certify eligibility under this criterion, there must be no lapse of NPDES

permit coverage in the other operator’s certification. The permit applicant must 

also comply with any terms and conditions imposed under the other operator's

valid certification of eligibility to ensure that the discharges and dischargerelated activities are protective of listed species and/or critical habitat. 

To certify eligibility under this criterion, the permit applicant must use the E.4 

Criterion Selection worksheet. The NOI must include the NPDES ID from the 

other operator’s notification of authorization under this permit, and a description

of the basis for the criterion selected on the NOI form, including the eligibility

criterion selected by the other operator’s certification. The permit applicant 

must also provide any documentation in the SWPPP that supports the other

operator’s eligibility determination, as well as any terms and conditionsimposed

under the eligibility requirementsthat applied under the prior certification.
2015 MSGP Biological Opinion 9

C: Federally-listed threatened or

endangered species or their

designated critical habitat(s) are 

likely to occur in or near the 

facility’s “action area,” and the 

industrial activity’s discharges

and discharge-related activities

are not likely to adversely affect

listed threatened or endangered

species or critical habitat.

To certify eligibility under this criterion, the permit applicant must use the E.4 

Criterion Selection worksheet. At least 30 days prior to filing an NOI for permit

coverage, the permit applicant must submit to EPA a completed Criterion C 

Eligibility Form. After evaluation of this form, EPA may require additional

controls that the permit applicant must implement to avoid or eliminate adverse

effects on listed species and critical habitat from discharges and dischargerelated activities. The permit applicant may submit a NOI for permit coverage

30 days after submitting the form. The permit applicant must provide a

description of the basis for the criterion the permit applicant selected on the NOI

form and provide documentation supporting the applicant’s eligibility 

determination in the SWPPP.

D: Consultation between a 

federal agency and the U.S. 

Fish and Wildlife Service 

and/or the National Marine

Fisheries Service under section

7 of the ESA has been 

concluded.

Consultations can be either formal or informal, and would have occurred only as 

a result of a separate federal action (e.g., during application for an individual

wastewater discharge permit or the issuance of a wetlands dredge and fill

permit), and consultation must have addressed the effects of the industrial 

activity’s discharges and discharge-related activities on all federally-listed 

threatened or endangered species and all federally-designated critical habitat. 

The result of this consultation must be one of the following:

A biological opinion that concludesthat the action in question (taking into 

account the effects of the facility’s discharges and discharge-related activities) is

not likely to jeopardize the continued existence of listed species, nor result in 

the destruction or adverse modification of critical habitat; a biological opinion 

that concludes that the action is likely to jeopardize listed species or to result in 

the destruction or adverse modification of critical habitat with recommended 

reasonable and prudent alternatives that the facility is implementing; or written

concurrence from the applicable Service(s) with a finding that the facility’s

discharges and discharge-related activities are not likely to adversely affect

federally-listed species or federally-designated critical habitat.

To certify eligibility under this criterion, the permit applicant must use the E.4

Criterion Selection worksheet. The permit applicant must verify that the 

consultation remains valid, in accordance with 50 CFR §402.16. If reinitiation

of consultation is required, in order to be eligible under this Criterion the permit 

applicant must ensure the consultation is reinitiated and the result of the 

consultation must be consistent with (i), (ii), or (iii) above.

If eligible, the permit applicant must also provide supporting documentation for 

this determination in the NOI and SWPPP, including the Biological Opinion (or

PCTS tracking number) or concurrence letter.

E: Industrial activities are 

authorized through the issuance

of a permit under section 10 of

the ESA, and this authorization

addressesthe effects of the 

facility’s discharges and

discharge-related activities on

federally-listed species and 

federally-designated critical

habitat.

To certify eligibility under this criterion, the permit applicant must use the E.4

Criterion Selection worksheet. The permit applicant must also provide 

supporting documentation for the determination in the NOI and SWPPP, 

including a copy of the permit from the Services.

a Some of the criteria have been relabeled from previous permit cycles. Using this format: 2015 Criteria (2008 Criteria): 2015 B (2008 

F); 2015 C (2008 D & E); 2015 D (2008 B), and 2015 E (2008 C). Criterion A remains the same in both past and proposed permit 

cycles.
2015 MSGP Biological Opinion 10

Eligibility Criteria Selection Procedure 

As the facility operators prepare to seek coverage under the MSGP, they must use the E.4 

Criterion Selection worksheet to guide them in determining which ESA criterion most 

appropriately applies to their facility. The criterion selection process directs facility operators to 

consider first whether the facility is eligible for MSGP coverage under Criterion B, Criterion D, 

or Criterion E, as described above. When considering these criteria, the operator must ensure the 

facility’s stormwater discharges (and associated pollutants) were adequately addressed in the 

analyses associated with each of these criteria. For example, if a facility is selecting Criterion D 

based on an earlier, separate federal nexus with a completed ESA section 7 consultation for 

construction of a facility, the operator must confirm that effects of the stormwater discharge were 

considered during the section 7 consultation. If stormwater discharges were not considered in 

the suite of effects evaluated in the section 7 consultation, selection of Criterion D would not be 

appropriate. If an operator can demonstrate the facility is eligible for coverage under Criterion 

B, D, or E, the operator can proceed with submittal of an NOI.

Should the applicant be unable to meet either of Criteria B, D, or E, the operator must then 

determine whether Criteria A or C would apply to the facility. To do so, the applicant must first 

determine the extent of the action area of the facility to evaluate whether effects from the 

proposed activities overlap with endangered or threatened species or their designated critical 

habitats. The action area of the facility includes all areas potentially affected directly or 

indirectly by the stormwater discharges, allowable non-stormwater discharges, and any proposed 

discharge-related activities8 and not merely the immediate area (e.g., mixing zone) involved in 

the action. This area includes all waterbodies or downstream/down-current reaches within 

waterbodies that are reasonably expected to receive pollutants from these sources. Once the 

extent of the action area is determined for the facility, the applicant must request a species list of 

threatened and/or endangered species and designated critical habitat from the Service, as 

described by the permit. If the species and critical habitat list indicates no listed resources are 

present in the action area of the facility, the operator may select Criterion A, and proceed with 

submittal of an NOI.

If the applicant is unable to certify there is no overlap between their action area and any 

threatened or endangered species or their designated critical habitats (i.e., if facility discharges 

are not eligible under Criterion A), the applicant must complete the Criterion C Eligibility Form

(hereafter, “Eligibility Form”) and submit it to EPA. This Eligibility Form is a tool that is used 

to assist the operator in making a preliminary determination of whether listed species or critical 

habitat may be exposed to discharges and/or discharge-related activities, and whether such 

exposures would be likely to adversely affect listed threatened or endangered species or their 

designated critical habitats. If the applicant determines listed resources may be exposed to 

discharge pollutants, the form requires the applicant to evaluate discharge effects and verify that 

facility operators will implement controls and other measures to avoid adverse effects. 

If an operator determines the facility is likely to be eligible under Criterion C, the completed 

Eligibility Form must be submitted to EPA at least 30 days prior to the submission of a NOI. 

 

8 e.g., upland areas associated with installation of and operation of stormwater control measures
2015 MSGP Biological Opinion 11

Once the Eligibility Form has been received, EPA will review it for completeness and forward to 

the appropriate Service(s) Regional or Field Office9 (RO/FO) within 5 business days for 

consideration. If either of the Services requests additional time or information to complete 

review of the proposal, EPA will temporarily stop the clock and notify the operator of any 

additional information requests or requirements, as needed, when they are identified. For 

example, in some cases, a Service reviewer may request a SWPPP (or link to a SWPPP, as 

available) to supplement review of the Eligibility Form.

Once the Eligibility Form has been submitted to the Service RO/FOs, reviewers will be provided 

25 days (or a time extension, if requested) to respond if they have additional information needs, 

or if they have concerns that a proposal for coverage has not demonstrated sufficient measures in 

the Eligibility Form or SWPPP (if requested) to avoid adverse effects to listed species or their 

designated critical habitats. If no response or request for additional review time is received 

within the 25-day time period, EPA will assume that the Service has no objection to the use of 

Criterion C for coverage of the facility under the MSGP, and will proceed accordingly (although 

questions or concerns can be raised about listed resources or other Service trust resources until 

the end of the NOI review period, as described below). 

If, during review of a Eligibility Form, a Service reviewer responds in writing that the 

information submitted in the review package may not support the rationale for coverage under 

Criterion C for listed species under the Service’s jurisdiction, EPA will coordinate with the 

relevant Service field office to identify the appropriate controls or other additional measures in 

the facility’s SWPPP that are sufficient to support a “may affect, not likely to adversely affect” 

determination for the facility’s activities that would be covered by the permit. In deciding 

whether to provide authorization to discharge under the MSGP, EPA will ensure one of the 

following is met:

i. Additional information is provided that addresses the Service’s concerns and the 

Service subsequently agrees that coverage under Criterion C is appropriate;

ii. Additional measures are included in the SWPPP that would address the concerns 

raised during Service review;

iii. Changes to the facility’s proposal are made to address the Service’s concerns; or

iv. The Service subsequently determines no changes are necessary to support a “may 

affect, not likely to adversely affect” determination.

In making the eligibility determination, EPA will rely on the Services’ expertise.

Permittees must comply with any applicable terms, conditions, or other requirements developed

in the process of meeting these eligibility criteria to remain eligible for coverage under the 

 

9 Contact information for each Service Regional or Field Office has been forwarded to EPA to ensure timely 

electronic submission of the Criteria C Eligibility Forms.
2015 MSGP Biological Opinion 12

MSGP. The Eligibility Form and any additional documentation related to these requirements

must be kept onsite as part of the SWPPP. The operator may proceed with submittal of an NOI 

30 days after submitting the Eligibility Form. 

Submitting a Notice of Intent (NOI)10

As of the date of this Opinion, the EPA is currently in the process of transitioning their NOI 

submission system to a fully on-line system (the Integrated Compliance Information System, or 

ICIS) using electronic NOIs. EPA anticipates the use of this system for the MSGP will improve and 

streamline the coverage application process, as well as provide for better oversight capabilities for 

EPA. To be considered complete, the NOI must contain all the required information supporting the 

selected ESA criterion (as well as other non-ESA information required for the permit). A sample 

copy of the NOI form is included as Appendix D to this Opinion. The NOI serves as the facility 

operator’s certification that that the discharges are eligible for coverage according to the 

requirements of the MSGP. The NOI specifically describes:

• Industrial activities and associated discharges for the subject facility;

• Onsite industrial activities exposed to stormwater, including potential spill and leak 

areas;

• Pollutants or pollutant constituents associated with each industrial activity exposed

to stormwater that could be discharged in stormwater and/or any authorized nonstormwater;

• Stormwater control measures facility operators employ to comply with the nonnumeric technology- based effluent limits, and any other measures taken to comply

with the requirementsin MSGP Part 2.2 (Water Quality -Based Effluent

Limitations); and

• Schedule for good housekeeping and maintenance and schedule for all required

inspections.

Development of a SWPPP

Prior to submitting the NOI for coverage under the MSGP, the facility operators must develop a 

SWPPP11 or update their existing SWPPP. If facility operators choose to post the SWPPP on the 

Internet according to Part 5.4.1 of the permit, the URL must be included on the NOI form and 

this URL must directly link to the SWPPP (not just the corporate or facility homepage). If the 

SWPPP is not posted online, additional facility information from the SWPPP must be entered into 

the NOI. Once the SWPPP is complete and all other permit eligibility requirements are met, a 

complete and accurate NOI may be submitted to EPA. NOIs for coverage under the MSGP must 

be submitted by the appropriate deadline described below. Discharges are not authorized if the 

NOI is incomplete or inaccurate or if the facility was never eligible for permit coverage. 

 

10 Part 1.2.1.1 and 1.2.1.3 of the permit. 11 Detailed information on development of the SWPPP and all information to be included therein is described in the 

permit.
2015 MSGP Biological Opinion 13

Timelines for Seeking Coverage under the New Permit

All facilities seeking coverage under the 2015 permit are required to submit their NOIs according 

to an established timeframe, with separate deadlines for existing and new dischargers. Existing 

dischargers that were authorized for coverage under the 2008 MSGP must submit their NOIs no 

later than 90 days after the permit is issued (projected to be early summer 2015). New 

dischargers and existing dischargers that were not authorized for coverage under the 2008 MSGP 

must submit NOIs at least 30 days prior to commencing discharge. New owners/operators of an 

existing discharger where the discharge is authorized under the 2015 MSGP must submit an NOI

at least 30 days prior to the date of the transfer of ownership/operations. Finally, other eligible 

facilities (i.e., facilities that commenced discharging prior to the issuance of the 2015 MSGP but 

are/were not covered by any type of NPDES permit) must submit their NOIs immediately per 

EPA’s permit to minimize the time that unauthorized discharges would occur. In each of these 

cases, coverage would begin 30 days after EPA notifies the applicant that a complete NOI has 

been received (unless EPA notifies that applicant that authorization has been denied or delayed). 

A timeline integrating the ESA criterion certification process and the NOI submission process is 

provided in Figure 1 below.

Figure 1. Preparation, submittal, and approval sequence for documents required for coverage under the 

2015 MSGP

The majority of the facilities anticipated to seek coverage under the 2015 MSGP are existing 

dischargers; thus, most of the requests for coverage (i.e., via NOI submissions) are expected to 

occur within the first 3 months after issuance of the MSGP, and are administratively covered 

under the 2008 permit during this time in accordance with the Administrative Procedure Act and 

40 CFR 122.6. If a facility was authorized to discharge under the MSGP prior to its expiration 

date, any discharges authorized under this permit will automatically remain covered by this 

permit until the earliest of:
2015 MSGP Biological Opinion 14

• Authorization for coverage under a reissued permit or a replacement version of the 

MSGP following the timely submittal of a complete and accurate NOI requesting 

coverage under the new permit; or

• Submittal of a Notice Of Termination of coverage; or

• Issuance of an individual permit for the facility’s discharges; or

• A formal permit decision by EPA not to reissue this general permit, at which time 

EPA will identify a reasonable time period for covered dischargers to seek coverage 

under an alternative general permit or an individual permit. Coverage under the 

MSGP will cease at the end of this time period.

If facility operators fail to submit a timely NOI for coverage under a reissued or replacement 

permit, the coverage will terminate on the date that the NOI was due, and discharges from the 

industrial activities will continue to be unauthorized under the CWA until they are covered by 

this or a different NPDES permit. EPA may take enforcement action for any unpermitted 

discharges that occur between the commencement of discharging and discharge authorization. 

Enforcement actions are not part of the proposed action.

After submission of the NOI, the operator will receive notice their discharges are authorized 

unless EPA provides notice that coverage has been delayed or denied. EPA may choose to 

interrupt or postpone initiation of coverage during this timeframe for a number of reasons, 

including, but not limited to: requests to the operator for additional information, requirements 

for additional measures or controls, and suggested and/or recommended changes in permit type 

(e.g., to an individual or other alternative permit), as applicable. As noted above, the Services 

have the opportunity to provide input to the request for coverage until the end of the 30-day NOI

review period. As NOIs are submitted to EPA, notification of submittals will be automatically 

forwarded to Service’s ROs/FOs that have requested the opportunity to review the NOIs. This 

automated notification process will also allow Service’s ROs/FOs the opportunity to review 

NOIs that are seeking coverage under other criteria besides Criterion C.

Control Measures and Effluent Limits12

Facility operators must select, design, install, and implement control measures (including, but not 

limited to, best management practices) to minimize effects to water quality and adverse effects to 

listed species and critical habitat. In the technology-based limits included in the MSGP, the term 

“minimize” means reduce and/or eliminate to the extent achievable using control measures 

(including best management practices) that are technologically available and economically 

practicable and achievable in light of best industry practice.13

There are additional considerations for new dischargers under the MSGP. A new discharger is 

defined as a facility: 1) from which there is a discharge; 2) that did not commence the discharge 

 

12 Part 2.0 of the Permit 13 Part 2.0 of the permit
2015 MSGP Biological Opinion 15

at a particular site prior to August 13, 1979; 3) which is not a new source;and 4) which has never 

received a final effective NPDES permit for discharges at that site. The MSGP places additional 

limitations on new discharges to receiving waters that are identified as impaired or of high water 

quality. 

New dischargers are not eligible for coverage if EPA determines the discharges will not meet 

any applicable water quality standard prior to authorizing under this permit. In such cases, EPA 

may notify the facility that an individual permit application is necessary. However, EPA may 

authorize coverage under the MSGP if the facility includes appropriate controls and 

implementation procedures designed to ensure the discharge will meet water quality standards. 

In the absence of information demonstrating otherwise, EPA expects that compliance with the 

stormwater control requirements of this permit, including the requirements applicable to such 

discharges, will meet applicable water quality standards.

Water Quality Standards

Water Quality Standards define the goals for a waterbody by designating its uses, setting 

numeric and narrative criteria to protect those uses, and establishing provisions such as 

antidegradation policies to protect waterbodies from pollutants. EPA expects that if receiving 

waters continue to meet Water Quality Standards, exposures of listed species and critical habitat 

to hazardous concentrations of stormwater pollutants will have been avoided or limited. To this 

end, the MSGP employs effluent limit guidelines, water quality benchmarks, and SWPPPs to 

prevent stormwater and permitted non-stormwater discharges from creating conditions which do 

not meet Water Quality Standards. Effluent limit guidelines are sector-specific pollutant 

discharge concentrations based on the ability of technological controls (e.g., Best Management 

Practices [BMPs] and control measures described in SWPPPs) to control the amount of pollutant 

in stormwater discharges. Water quality benchmarks are based on national recommended water 

quality criteria, and are a level of concern at which a stormwater discharge could potentially 

cause or contribute to an impairment of water quality standards. 

A facility’s discharge must be controlled as necessary to meet applicable water quality standards. 

EPA expects that compliance with the conditions in this permit will control discharges as 

necessary to meet this goal. If, at any time, a facility operator becomes aware, or EPA 

determines, that the discharge does not meet applicable water quality standards, the facility 

operator must take corrective action (described in a subsequent section) and document the 

corrective actions taken. The facility must also comply with any additional requirements that the 

state or tribe requires (per Part 9 of the MSGP).

Control Measures14

The MSGP directs facilities to evaluate selection and design considerations when determining 

appropriate controls15 for the facility’s discharges, as well as to meet the specified limits 

 

14 Part 2.1 of the permit 15 Sector and pollutant source-specific control measures were developed by EPA for the 2008 MSGP. These are 

found at http://cfpub1.epa.gov/npdes/stormwater/swsectors.cfm.
2015 MSGP Biological Opinion 16

described in the permit (i.e., non-numeric effluent limits, applicable effluent limitations 

guidelines, and water quality-based effluent limitations). If control measures are not achieving 

their intended effect of minimizing pollutant discharges, facility operators must modify the 

control measures for their facilities in accordance with specified corrective action requirements 

described in the permit. In particular, facility operators are directed to consider a variety of 

measures, which include, but are not limited to:

• measures that prevent exposure to contaminants 

• combinations of controls

• minimization of impervious surfaces

• good housekeeping practices

• maintenance of control measures

• spill prevention and response measures

• erosion and sediment controls

Additionally, all employees who work in areas where industrial materials or activities are 

exposed to stormwater, or who are responsible for implementing activities necessary to meet the 

conditions of this permit must be provided appropriate training. (For additional measures, see 

Part 8 of the MSGP; EPA also provides facts sheets for the applicants that clarify sector-specific 

controls). Additional details related to consideration and implementation of controls is found in 

the permit.

Sector Specific Requirements

The MSGP outlines a number of sector-specific requirements with which facility operators must 

comply that are associated with the facility’s primary industrial activity and any co-located 

industrial activities. These requirements are in addition to any requirements specified elsewhere 

in the MSGP. Part 8 is organized by individual sectors to allow permit applicants to focus on 

only those requirements that apply to their facility. These measures are listed in the permit and 

are summarized in Appendex E of this Opinion. 

Numeric Effluent Limitations Based on Effluent Limitations Guidelines16

If a facility is in an industrial category subject to one of the effluent limitations guidelines 

identified in the permit, facility discharges must meet the corresponding effluent limits as 

described in the permit. These effluent limits apply to the following regulated activities:

 

16 Part 2.1.3 of the Permit
2015 MSGP Biological Opinion 17

• Discharges resulting from spray down or intentional wetting of logs at wet deck storage 

areas

• Runoff from phosphate fertilizer manufacturing facilities that comes into contact with 

any raw materials, finished product, by-products or waste products

• Runoff from asphalt emulsion facilities

• Runoff from material storage piles at cement manufacturing facilities

• Mine dewatering discharges at crushed stone, construction sand and gravel, or industrial 

sand mining facilities

• Runoff from hazardous waste landfills

• Runoff from non-hazardous waste landfills

• Runoff from coal storage piles at steam electric generating facilities

• Existing and new primary airports with 1,000 or more annual jet departures that discharge 

wastewater associated with airfield pavement deicing that contains urea commingled with 

stormwater

Water Quality-Based Effluent Limitations17

The MSGP includes a narrative water quality-based effluent limitation that discharges must be 

“controlled as necessary to meet applicable water quality standards.” EPA may also impose 

additional water quality-based limitations on a site-specific basis, or require the facility to obtain 

coverage under an individual permit, if information in the NOI, required reports, or from other 

sources indicates that the discharges are not controlled as necessary to meet applicable water 

quality standards. 

Discharges to Water Quality-Impaired Waters18

A facility will be considered to discharge to an impaired water if the first water of the United 

States discharged to is identified by a state, tribe, or EPA pursuant to Section 303(d) of the CWA 

as not meeting an applicable water quality standard, or is included in an EPA-approved or 

established total maximum daily load (TMDL). For discharges that enter a storm sewer system 

prior to discharge, the first water of the United States discharged to is the waterbody that 

receives the stormwater discharge from the storm sewer system.

If a facility discharges to an impaired water with an EPA approved or established TMDL, EPA 

will inform the facility operators if any additional limits or controls are necessary for the 

discharge to be consistent with the assumptions of any available wasteload allocation in the 

TMDL, or if coverage under an individual permit is necessary. If a facility discharges to an 

 

17 Section 2.2 18 Part 2.2.2 of the permit
2015 MSGP Biological Opinion 18

impaired water without an EPA approved or established TMDL, facility operators are still 

required to comply with Part 2.2.1 of the permit, and must comply with the corresponding 

monitoring requirements. This provision also applies to situations where EPA determines that 

the discharge is not controlled sufficiently to meet water quality standards in a downstream water 

segment, even if the discharge is to a receiving waterbody that is not specifically identified on a 

Section 303(d) list.

If the authorization to discharge under this permit relied on Part 1.1.4.8 for a new discharge to an 

impaired water, facility operators must implement and maintain any control measures or 

conditions on the site that enabled the facility to become eligible under Part 1.1.4.8, and modify 

such measures or conditions as necessary pursuant to any corresponding corrective actions. The

facility is also required to comply with Part 2.2.1 and the monitoring requirements of Parts 6.2.4.

The MSGP states that in some cases, a new discharger discharging to an impaired receiving 

waterbody19 is eligible for coverage under the permit. In these cases, the discharger must either: 

prevent all exposure to stormwater of the pollutant(s) for which the waterbody is impaired; 

demonstrate that the pollutant(s) for which the waterbody is impaired is not present at the site; or 

demonstrate to EPA that the facility’s discharge is expected to meet applicable water quality 

standards. A facility is eligible if the EPA Regional Office fails to respond within 30 days of 

data submission or provides an affirmative determination that the discharge will meet applicable 

water quality standards. Both the supporting documentation for the facility’s rationale and the 

EPA’s determination (if provided) must be maintained onsite with the SWPPP.

Discharges to Tier 2 or Tier 2.5 Waters

If the facility is a new discharger, or an existing discharger required to notify EPA of an 

increased discharge consistent with Part 7.7 (i.e., a “planned changes” report), and discharges 

directly to waters designated by a state or tribe as Tier 2 or Tier 2.5 for antidegradation purposes 

under 40 CFR 131.12(a), in the absence of information demonstrating otherwise, EPA expects 

that compliance with the stormwater control requirements of this permit will result in discharges 

that will not lower the water quality of the applicable water. However, EPA may notify facility 

operators that additional analyses, control measures, or other permit conditions are necessary to 

comply with the applicable antidegradation requirements, or that an individual permit application 

is necessary.

New dischargers are authorized to discharge to Tier 220 or Tier 2.5 waters provided the discharge 

does not lower the water quality of the receiving water. New dischargers are not eligible to 

 

19 A facility will be considered to discharge to an impaired water if the receiving water has been identified by a state, 

tribe, or EPA pursuant to Section 303(d) of the CWA as not meeting an applicable water quality standard, or is 

included in an EPA-approved or established total maximum daily load (TMDL). 20 Tier 2 waters are characterized as having water quality that exceeds the levels necessary to support propagation of 

fish, shellfish, and wildlife and recreation in and on the water. Tier 2.5 waters are those waters designated by states 

or tribes as requiring a level of protection equal to and above that given to Tier 2 waters, but less than that given Tier 

3 waters. States have special requirements for these waters. Tier 3 waters are identified by states as having high 
2015 MSGP Biological Opinion 19

discharge to Tier 3 waters. A list of Tier 2, Tier 2.5 and Tier 3 waters is provided in Appendix L 

of the MSGP. These waters are identified for antidegradation purposes, pursuant to 40 CFR 

131.12(a). 

Inspections and Monitoring Requirements

The MSGP outlines specific inspection and monitoring requirements that facilities must follow

once coverage has been granted. These requirements are specified in the permit, and are 

summarized below (see Appendix A for more detail).

Inspections

The MSGP requires facility operators to conduct quarterly inspections of the facility during 

normal facility operating hours by qualified personnel. Inspections are intended to ensure that 

exposure to pollutants is avoided or corrected, and focuses on locations of potential exposure 

(e.g., storage locations, discharge points) as well as areas where previous spills or leaks have 

been observed. Some facilities may be required to monitor more frequently based on the use of 

certain types of equipment, processes and/or stormwater control measures, or where areas of the 

facility may have significant activities and/or materials exposed to stormwater. 

The permit notes that at least one of the routine inspections must be conducted during a period 

when a stormwater discharge is occurring. Inspectors must consider the results of visual and 

analytical monitoring (if any) for the past year when planning and conducting inspections. 

Inspections should focus on and document instances where contaminants (e.g., industrial 

materials, residue or trash) may have or could come into contact with stormwater, leaks or spills 

have occurred, and offsite tracking of materials or sediment has occurred. Inspections should 

also document any control measures needing replacement, maintenance or repair. Control 

measures should also be inspected to determine whether the facility is complying with effluent 

limits. At least one inspection must be conducted during a stormwater discharge to ensure 

control measures are functioning correctly. Discharge points must also be observed during the 

inspection. If such discharge locations are inaccessible, the permit notes that nearby downstream 

locations must be inspected.

The MSGP allows for certain exceptions to routine inspections. For example, routine 

inspections are not required at facilities that are inactive and unstaffed as long as there are no 

industrial materials or activities exposed to stormwater. Such facilities are only required to 

conduct an annual site inspection. If the facility is already covered under the permit and the 

facility has changed from active to inactive and unstaffed, facility operators must modify the 

NOI to reflect the changed status, and the facility must maintain a statement to this effect in the 

SWPPP. If circumstances change and industrial materials or activities become exposed to 

stormwater or the facility becomes active and/or staffed, this exception no longer applies, and the 

permit requires that facility operators must immediately resume routine facility inspections. 

 

quality waters constituting an Outstanding Natural Resource Water (ONRW), such as waters of National Parks and 

State Parks, wildlife refuges, and waters of exceptional recreational or ecological significance.
2015 MSGP Biological Opinion 20

Additionally inactive and unstaffed facilities covered under Sectors G (Metal Mining), H (Coal 

Mines and Coal Mining-Related Facilities), and J (Non-Metallic Mineral Mining and Dressing), 

are not required to meet the “no industrial materials or activities exposed to stormwater” standard 

to be eligible for this exception from routine inspections.

Facility operators must document the findings of the facility inspections and maintain this report 

with the SWPPP. Facilities are not required to submit the routine facility inspection report to 

EPA, unless the facility is specifically requested to do so. However, findings must be 

documented and summarized in the annual report that is submitted to EPA.

Monitoring

All required monitoring must be performed in response to a storm event that results in an actual 

discharge from the site (“measurable storm event”) that follows the preceding measurable storm 

event by at least 72 hours (3 days). This storm interval does not apply if facility operators are 

able to document that a shorter interval is representative for local storm events during the 

sampling period. In the case of snowmelt, the monitoring must be performed at a time when a 

measurable discharge occurs at the site.

For each monitoring event (except snowmelt monitoring), facility operators must identify the 

date and duration of the rainfall event, rainfall total for that rainfall event, and time since the 

previous measurable storm event. For snowmelt monitoring, operators must identify the date of 

the sampling event.

Facility operators must take required samples from a discharge resulting from a measurable 

storm event as described above. Samples must be collected within the first 30 minutes of a 

measurable storm event. If it is not possible to collect the sample within the first 30 minutes of a 

measurable storm event, the sample must be collected as soon as practicable after the first 30 

minutes and documentation must be kept with the SWPPP explaining why it was not possible to 

take samples within the first 30 minutes. In the case of snowmelt, samples must be taken during 

a period with a measurable discharge. When adverse weather conditions21 prevent the collection 

of samples according to the relevant monitoring schedule, a substitute sample must be taken 

during the next qualifying storm event. Operators must report any failure to monitor indicating 

the basis for not sampling during the usual reporting period.

If the facility is located in areas where limited rainfall occurs during parts of the year (e.g., arid 

or semi-arid climates) or in areas where freezing conditions exist that prevent runoff from 

occurring for extended periods, required monitoring events may be distributed during seasons 

when precipitation occurs, or when snowmelt results in a measurable discharge from the site. 

Facility operators must still collect the required number of samples.

Monitoring requirements as specified in the MSGP begin in the first full quarter following either 

90 days after the permit issuance, or the date of discharge authorization, whichever date comes 

later. If the monitoring is required on a quarterly basis (e.g., benchmark monitoring), monitoring 

must at least once in each of the following 3-month intervals:

 

21 Adverse weather does not exempt facility operators from having to file a benchmark monitoring report in 

accordance with the sampling schedule.
2015 MSGP Biological Opinion 21

• January 1 – March 31;

• April 1 – June 30;

• July 1 – September 30; and

• October 1 – December 31.

This monitoring schedule may be modified by the facility if the revised schedule is documented 

with the SWPPP and provided to EPA with the first monitoring report.

Quarterly Visual Assessments

With a few exceptions, all facilities covered by the MSGP are required to conduct quarterly 

visual assessments of discharges covered under the permit22. A stormwater sample from each 

outfall must be collected and visually assessed once each quarter for the entire permit term. The 

MSGP notes that these samples should be collected in such a manner that the samples are

representative of the stormwater discharge, and on-line guidance on how to conduct monitoring 

is provided on EPA’s website (www.epa.gov/npdes/stormwater/msgp). The MSGP notes that 

samples should be taken within the first 30 minutes of an actual discharge from a storm event (or 

as soon as practicable), and should note any water quality characteristics indicative of 

stormwater pollution (e.g., color, odor, clarity, foam, oil sheen, and floating, settled, or 

suspended solids). Additional details on how the visual assessment should be conducted are 

available in the permit (Appendix A). Whenever the visual assessment shows obvious signs of 

stormwater pollution, facility operators must initiate the corrective action procedures described 

in the permit.

Facility operators must document the results of the visual assessments and maintain this 

documentation onsite with the SWPPP. Facility operators are not required to submit visual 

assessment findings to EPA, unless the facility is specifically requested to do so, although 

findings should be noted in the annual report.

The MSGP notes several exceptions to requirements for visual monitoring. In some cases, 

adverse weather conditions prevent the safe or practical collection of samples, and the MSGP 

requires substitute samples during the next qualifying storm event. In other cases, the MSGP 

allows for variation of the assessment schedule, such as in areas subject to longer-term snow 

accumulation or in arid/semi-arid areas where limited rainfall occurs. Other exceptions are 

provided for inactive and unstaffed sites, or where a facility has two or more outfalls that would 

most likely discharge substantially identical effluents (“substantially identical outfalls”). For 

each of these cases, the MSGP outlines appropriate procedures for inspections and reporting.

 

22 EPA considers the visual assessments to be part of the inspection process rather than categorized together with 

analytical monitoring; however for the purposes of the Opinion, we have included this discussion under monitoring 

to summarize the types of evaluations that will occur to evaluate the presence of pollutants in the discharge waters.
2015 MSGP Biological Opinion 22

Analytical Monitoring

Facility operators must collect and analyze stormwater samples23 and document all monitoring 

activities consistent with the procedures described in the MSGP including any additional sectorspecific or state/tribal-specific requirements that are applicable to their facility. Applicable 

monitoring requirements apply to each outfall authorized by this permit, except as otherwise 

exempt from monitoring (e.g., as with a substantially identical outfalls24). The permit includes 

five types of required analytical monitoring, one or more of which may apply to the discharge(s):

• Quarterly benchmark monitoring

• Annual effluent limitations guidelines monitoring

• State- or tribal-specific monitoring

• Impaired waters monitoring 

• Other monitoring as required by EPA 

When more than one type of monitoring for the same parameter at the same outfall applies (e.g., 

total suspended solids once per year for an effluent limit and once per quarter for benchmark 

monitoring at a given outfall), facility operators may use a single sample to satisfy both 

monitoring requirements (i.e., one sample satisfying both the annual effluent limit sample and 

one of the four quarterly benchmark monitoring samples). All required monitoring must be 

conducted in accordance with the procedures described in Appendix B, Subsection 10.D of the 

MSGP.

Benchmark Monitoring

The MSGP specifies pollutant benchmark concentrations that are applicable to certain 

sectors/subsectors. Benchmark monitoring data are primarily to determine the overall 

effectiveness of the control measures and to assist facility operators in knowing when additional 

corrective action(s) may be necessary to comply with the effluent limitations in Part 2 of the 

MSGP. The benchmark concentrations are not effluent limitations; a benchmark exceedance, 

therefore, is not a permit violation. However, if corrective action is required as a result of a 

benchmark exceedance, failure to conduct required corrective action is a permit violation. 

Facility operators must monitor for any benchmark parameters specified for the industrial 

sector(s), both primary industrial activity and any co-located industrial activities, applicable to 

the discharge. Industry-specific benchmark concentrations are listed in the sector-specific 

sections of Part 8 of the MSGP. If the facility is in one of the industrial sectors subject to 

benchmark concentrations that are hardness-dependent, facility operators are required to submit 

 

23 Facility operators are only required to monitor allowable non-stormwater discharges when they are commingled 

with stormwater discharges associated with industrial activity. 24 Facility operators are required to monitor each outfall covered by a numeric effluent limit
2015 MSGP Biological Opinion 23

to EPA with the NOI a hardness value established consistent with the procedures in Appendix J 

of the MSGP that is representative of the receiving water. Samples must be analyzed consistent 

with 40 CFR Part 136 analytical methods and using test procedures with quantitation limits at or 

below benchmark values for all benchmark parameters for which the facility is required to 

sample. 

Benchmark monitoring must be conducted quarterly for the first four full quarters of permit 

coverage commencing no earlier than 90 days after permit issuance. As noted earlier, facilities 

in climates with irregular stormwater runoff may modify this quarterly schedule provided that 

this revised schedule is reported to EPA when the first benchmark sample is collected and 

reported, and that this revised schedule is kept with the facility’s SWPPP. When conditions 

prevent obtaining four samples in four consecutive quarters, facility operators must continue 

monitoring until obtaining the four samples required for calculating the benchmark monitoring 

average. At the operator’s discretion, more than four samples may be taken during separate 

runoff events and used to determine the average benchmark parameter concentration for facility 

discharges.

After collection of four quarterly samples, if the average of the four monitoring values for any 

parameter does not exceed the benchmark, the facility has fulfilled the monitoring requirements 

for that parameter for the permit term. However, if the average of the four monitoring values for 

any parameter exceeds the benchmark, facility operators must review the selection, design, 

installation, and implementation of the control measures to determine if modifications are 

necessary to meet the effluent limits in this permit, and either:

• Make the necessary modifications and continue quarterly monitoring until four additional 

quarters of monitoring are completed for which the average does not exceed the 

benchmark; or

• Make a determination that no further pollutant reductions are technologically available 

and economically practicable and achievable in light of best industry practice to meet the 

technology-based effluent limits or are necessary to meet the water-quality-based effluent 

limitations in the MSGP, in which case monitoring must continue once per year. The 

facility operator must also document the rationale for concluding that no further pollutant 

reductions are achievable, and retain all records related to this documentation with the 

SWPPP.

Facility operators must review the control measures and perform any required corrective action 

immediately (or document why no corrective action is required), without waiting for the full four 

quarters of monitoring data, if an exceedance of the four-quarter average is mathematically 

certain. If after modifying the control measures and conducting four additional quarters of 

monitoring, the average still exceeds the benchmark (or if an exceedance of the benchmark by 

the four quarter average is mathematically certain prior to conducting the full four additional 

quarters of monitoring), operators must again review the control measures and take one of the 

two actions above.
2015 MSGP Biological Opinion 24

Following the first four quarters of benchmark monitoring (or sooner if the exceedance is 

triggered by less than four quarters of data, as noted above), if the average concentration of a 

pollutant exceeds a benchmark value, and the facility operator determines that exceedance of the 

benchmark is attributable solely to the presence of that pollutant in the natural background, the 

operator is not required to perform corrective action or additional benchmark monitoring 

provided that:

• The average concentration of the benchmark monitoring results is less than or equal to 

the concentration of that pollutant in the natural background;

• The operator documents and maintains with the SWPPP the supporting rationale for 

concluding that benchmark exceedances are in fact attributable solely to natural 

background pollutant levels. Any data previously collected by the facility and others 

must be included in the supporting rationale (including literature studies) that describe the 

levels of natural background pollutants in the stormwater discharge; and

• The operator notifies EPA on the final quarterly benchmark monitoring report that the 

benchmark exceedances are attributable solely to natural background pollutant levels.

Natural background pollutants include those substances that are naturally occurring in soils or 

ground water. Natural background pollutants do not include legacy pollutants from earlier 

activity on the site, or pollutants in run-on from neighboring sources that are not naturally 

occurring, such as other industrial sites or roadways. However, facilities may be eligible to 

discontinue monitoring for pollutants that occur solely from run-on sources, and operators are 

advised in the permit to consult the appropriate EPA Regional Office for related guidance.

The requirement for benchmark monitoring does not apply at a facility that is inactive and 

unstaffed, as long as there are no industrial materials or activities exposed to stormwater. This 

exception has different requirements for Sectors G, H, and J. To invoke this exception, a facility 

operator must maintain a statement with the SWPPP stating that the site is inactive and unstaffed, 

and that there are no industrial materials or activities exposed to stormwater in accordance with 

the substantive requirements in 40 CFR 122.26(g), and then sign and certify the corresponding 

statement as described in the MSGP. If circumstances change and industrial materials or 

activities become exposed to stormwater or the facility becomes active and/or staffed, this 

exception no longer applies and the facility must immediately begin complying with the 

applicable benchmark monitoring requirements as if the facility were in the first year of permit 

coverage. If the facility is not qualified for this exception at the time discharges are authorized 

under the MSGP, but during the permit term the facility becomes qualified because the facility is 

inactive and unstaffed, and there are no industrial materials or activities that are exposed to 

stormwater, then the facility operator must notify EPA of this change in the next benchmark 

monitoring report. The facility operator may discontinue benchmark monitoring once EPA has 

been notified, and has prepared and signed the certification statement described above 

concerning the facility’s qualification for this special exception. 
2015 MSGP Biological Opinion 25

Effluent Limitations Monitoring

As noted above, certain stormwater discharges subject to effluent limitation guidelines are 

authorized for coverage under the MSGP. Beginning in the first full quarter following 90 days 

after permit issuance or the date of discharge authorization, whichever date comes later, facility 

operators must monitor once per year at each outfall containing the discharges identified in the 

sector-specific section of Part 8 applicable to each regulated activity. 

Facility operators must monitor each outfall discharging runoff from any of the applicable 

regulated activities. The substantially identical outfall monitoring provisions are not available 

for numeric effluent limits monitoring. Facility operators must conduct follow- up monitoring 

within 30 calendar days (or during the next qualifying runoff event, should none occur within 30 

days) of implementing corrective action(s) taken in response to an exceedance of a numeric 

effluent limit contained in this permit. The MSGP also outlines specific monitoring 

requirements applicable to individual states or tribes. Monitoring must be performed for any 

pollutant(s) that exceeds the effluent limit. If this follow-up monitoring exceeds the applicable 

effluent limitation, facility operators must 1) submit an Exceedance Report no later than 30 days 

after receiving the lab result; and 2) continue to monitor, at least quarterly, until the discharge is 

in compliance with the effluent limit or until EPA waives the requirement for additional 

monitoring. Facility operators must comply with any state or tribal monitoring requirements 

applicable to the facility’s location. If a monitoring frequency is not specified for an applicable 

requirement, facility operators must monitor once per year for the entire permit term.

If a facility discharges to an impaired waterbody, facility operators must monitor all pollutants 

for which the waterbody is impaired and for which a standard analytical method exists. If the 

pollutant of concern for the impaired waterbody is suspended solids, turbidity or 

sediment/sedimentation, facility operators must monitor for Total Suspended Solids (TSS). If a 

pollutant of concern is expressed in the form of an indicator or surrogate pollutant, facility 

operators must monitor for that indicator or surrogate pollutant. No monitoring is required when 

a waterbody’s biological communities are impaired but no pollutant, including indicator or 

surrogate pollutants, is specified as causing the impairment, or when a waterbody’s impairment 

is related to hydrologic modifications, impaired hydrology, or other non-pollutant. Facility 

operators are directed to consult the appropriate EPA Regional Office for any available guidance 

regarding required monitoring parameters under this part. If the EPA’s Discharge Mapping Tool 

does not provide the needed information, facility operators may consult the appropriate EPA 

Regional Office for guidance regarding required monitoring parameters under this part.

Stormwater discharges to impaired waters without an applicable EPA-approved or established 

TMDL waste load allocation must be monitored once per year at each outfall (except 

substantially identical outfalls) beginning in the first full quarter following 90 days after permit 

issuance or the date of discharge authorization, whichever date comes later. This monitoring 

requirement no longer applies once the pollutant of concern is not detected above natural 

background levels in the stormwater monitoring results, and facility operators document this 

pollutant is not expected to be present above natural background levels in the discharge.

If the pollutant of concern is not present and not expected to be present in the discharge, or it is 

present but facility operators have determined that its presence is caused solely by natural 
2015 MSGP Biological Opinion 26

background sources, facility operators must include a notification to this effect in the first 

monitoring report, after which facility operators may discontinue monitoring. To support a 

determination that the pollutant’s presence is caused solely by natural background sources, 

facility operators must document and maintain with the SWPPP:

• An explanation of why facility operators believe that the presence of the pollutant of 

concern in the discharge is not related to the activities or materials at the facility; and

• Data and/or studies that tie the presence of the pollutant of concern in the discharge to 

natural background sources in the watershed.

Stormwater discharges to waters for which there is an EPA approved or established TMDL 

wasteload allocation are not required to be monitored for the pollutant for which the TMDL was 

written unless EPA informs facility operators, upon examination of the applicable TMDL and/or 

wasteload allocation, that facility operators are subject to such a requirement consistent with the 

assumptions of the applicable TMDL and/or wasteload allocation. EPA’s notice will include 

specifications on which pollutant to monitor and the required monitoring frequency. Facility 

operators must consult the appropriate EPA Regional Office for guidance regarding required 

monitoring under this part.

Additional Monitoring Required by EPA.

EPA may notify facility operators of additional discharge monitoring requirements. Any such 

notice will briefly state the reasons for the monitoring, locations, and parameters to be 

monitored, frequency and period of monitoring, sample types, and reporting requirements.

Corrective Actions

The MSGP outlines a number of corrective actions that may be required during the 5-year permit 

cycle and describes how and when these actions should be undertaken and reported to EPA. 

Although SWPPPs are intended to address anticipated conditions at covered facilities, EPA 

recognizes that unforeseen conditions or other factors may sometimes require the need for 

corrective actions at a facility. Where corrective actions are needed based on inspections, 

monitoring, or other observations, or when notified by the EPA, or local, state or tribal entity, 

operators are required to review their SWPPP to determine if and where revisions may need to be 

made to eliminate the condition, prevent its reoccurrence, and ensure that effluent limits are met. 

Corrective measures may be required to address the following:

• An unauthorized release or discharge (e.g., spill, leak, or discharge of non-stormwater not 

authorized by this or another NPDES permit) occurs at the facility.

• A discharge violates a numeric effluent limit.

• Control measures are not stringent enough for the discharge to meet applicable water 

quality standards or the non-numeric effluent limits in this permit.
2015 MSGP Biological Opinion 27

• A required control measure was never installed, was installed incorrectly, or not in 

accordance with Parts 2 and/or 8, or is not being properly operated or maintained.

• Visual assessments indicate obvious signs of stormwater pollution (e.g., color, odor, 

floating solids, settled solids, suspended solids, foam, sheen, etc.).

• The average of four quarterly sampling results exceeds an applicable benchmark. If less 

than four benchmark samples have been taken, but the results are such that an exceedance 

of the four quarter average is mathematically certain (i.e., if the sum of quarterly sample 

results to date is more than four times the benchmark level) this is considered a 

benchmark exceedance, triggering a review.

• Construction or a change in design, operation, or maintenance at the facility that 

significantly changes the nature of pollutants discharged in stormwater from the facility, 

or significantly increases the quantity of pollutants discharged.

The MSGP states that in all circumstances, facility operators must immediately take all 

reasonable steps necessary to minimize or prevent the discharge of pollutants until a permanent 

solution is installed and made operational, including cleaning up any contaminated surfaces so 

that the material will not discharge in subsequent storm events. In this context, the term 

“immediately” requires action on the same day it is discovered that a control measure needs to be 

replaced or repaired, and that all reasonable steps must be taken to minimize or prevent the 

discharge of pollutants until a permanent solution is installed and made operational. However, if 

a problem is identified at a time in the workday when it is too late to take action, the initiation of 

action must begin on the following workday.

If a facility operator determines that additional changes are necessary beyond those 

implemented, the operator must install a new or modified control and make it operational, or 

complete the repair, before the next storm event if possible, and within 14 calendar days from the 

time of discovery. If it is infeasible to complete the installation or repair within 14 calendar 

days, the operator must document why it is infeasible to complete the installation or repair within 

the 14-day timeframe. The facility operator must also identify the schedule for completing the 

work, which must be done as soon as practicable after the 14-day timeframe but no longer than 

45 days after discovery. Where the corrective actions result in changes to any of the controls or 

procedures documented in the SWPPP, the operator must modify the SWPPP accordingly within 

14 calendar days of completing corrective action work.

EPA does not consider these time intervals to be grace periods; they are instead schedules that 

are considered reasonable for documenting the findings and for making repairs and 

improvements. The time intervals are included in the permit to ensure that the conditions 

prompting the need for these repairs and improvements are not allowed to persist indefinitely.

If the event triggering corrective action is linked to an outfall that represents other substantially 

identical outfalls, the review must assess the need for corrective action for each outfall 

represented by the outfall that triggered the review. Any necessary changes to control measures 

that affect these other outfalls must also be made before the next storm event if possible, or as 

soon as practicable following that storm event. Any corrective actions must be conducted within 

the timeframes set forth in the permit.
2015 MSGP Biological Opinion 28

Facility operators must document the existence of any of the conditions listed requiring 

corrective action within 24 hours of becoming aware of such condition. Facility operators must 

also document the corrective actions taken that occurred as a result of the conditions within 14 

days from the time of discovery of any of those conditions. If applicable, facility operators must 

also document why it is infeasible to complete necessary installations or repairs within the 14-

day timeframe and document the schedule for installing the controls and making them 

operational as soon as practicable after the 14-day timeframe. Operators are required to submit 

to EPA a summary of any corrective action taken from the previous year of permit coverage in 

their Annual Report. 

If the event triggering the review is a permit violation (e.g., non-compliance with an effluent 

limit), correcting it does not remove the original violation. Additionally, failing to take 

corrective action in accordance with this section is an additional permit violation. EPA will 

consider the appropriateness and promptness of corrective action in determining enforcement 

responses to permit violations. 

Any noncompliance with any of the requirements of the MSGP constitutes a violation of the 

permit, issued under the CWA. The MSGP states that failure to take any required corrective 

actions constitutes an independent, additional violation of this permit, in addition to any original 

violation that triggered the need for corrective action. As such, any actions and time periods 

specified for remedying noncompliance do not absolve parties of the initial underlying 

noncompliance. However, where corrective action is triggered by an event that does not itself 

constitute permit noncompliance, such as an exceedance of an applicable benchmark, there is no 

permit violation provided the facility operators takes the required corrective action within the 

relevant deadlines established in Part 4.2. 

Reporting and Recordkeeping

The EPA requires that facility operators submit all NOIs, Notices of Termination, Annual 

Reports, Discharge Monitoring Reports, and other reporting information as appropriate 

electronically, unless a waiver was received from the relevant EPA Regional Office. Waivers 

are only granted for a one-time use for a single information submittal (i.e., an initial waiver does 

not apply for the entire term of the permit). All required information to be submitted under the 

permit will be submitted via EPA’s NOI system unless the permit states otherwise or unless a 

waiver has been granted. Thus, the NOI, discharge monitoring reports and annual reports, along 

with any no exposure certifications or Notices of Termination would be submitted electronically 

(or by hard copy if granted a waiver by EPA). 

Facility operators must submit an Annual Report to EPA electronically, per Part 7.2, by January 

30th for each year of permit coverage containing information generated from the past calendar 

year. The annual report must include the following information:

• The results or a summary of the past year’s routine facility inspection documentation 

required and quarterly visual assessment documentation;

• Information copied or summarized from the corrective action documentation required (if 

applicable). If corrective action is not yet completed at the time of submission of this 
2015 MSGP Biological Opinion 29

Annual Report, facility operators must describe the status of any outstanding corrective 

action(s);

• Regarding benchmark monitoring resulting in four quarter average exceedances, the 

rationale for why facility operators believe that no further pollutant reductions are 

achievable (i.e., technologically available and economically practicable and achievable in 

light of best industry practices); and

• Any incidents of noncompliance observed or, if there is no noncompliance, a signed 

certification signed stating the facility is in compliance with this permit.

For benchmark monitoring, note that facility operators are required to submit sampling results to 

EPA no later than 30 days after receiving laboratory results for each quarter that operators are 

required to collect benchmark samples, in accordance with Part 6.2.1.2. If operators collect 

multiple samples in a single quarter (e.g., due to adverse weather conditions, climates with 

irregular stormwater runoff, or areas subject to snow), facility operators are required to submit all 

sampling results to EPA within 30 days of receiving the laboratory results.

If follow-up monitoring exceeds a numeric effluent limit, facility operators must submit an 

Exceedance Report to the appropriate EPA Regional Office no later than 30 days after receiving 

the lab results. The report must include the following:

• NPDES ID;

• Facility name, physical address and location;

• Name of receiving water;

• Monitoring data from this and the preceding monitoring event(s);

• An explanation of the situation; what facility operators have done and intend to do (should 

the corrective actions not yet be complete) to correct the violation; and

• An appropriate contact name and phone number. 

In addition to the reporting requirements described above, facility operators are also subject to 

standard permit reporting provisions of the MSGP, as shown in the permit (see Appendix A of 

this Opinion). 

OVERVIEW OF THE ASSESSMENT FRAMEWORK

Approach to the Assessment

Section 7(a)(2) of the ESA of 1973, as amended, requires federal agencies, in consultation with 

and with the assistance of the Service, to ensure that any action they authorize, fund, or carry out 

is not likely to jeopardize the continued existence of endangered or threatened species, and is not 

likely to destroy or adversely modify critical habitat that has been designated for these species 

(16 U.S.C. 1539). During consultations on specific actions, the Service fulfills its obligations 
2015 MSGP Biological Opinion 30

using an assessment framework that begins by identifying the physical, chemical, or biotic 

components of proposed actions that are likely to have individual, interactive, or cumulative 

direct and indirect effects on the environment (we use the term “potential stressors” for these 

components of an action); we then determine whether ESA-listed species or designated critical 

habitat are likely to be exposed to those potential stressors; we estimate how ESA-listed species 

or designated critical habitat are likely to respond to any exposure; then we conclude by 

estimating the risks those responses pose to the individuals, populations, and species or 

designated critical habitat that are likely to be exposed.

General permits authorized by Federal agencies apply to activities over large geographic areas 

occurring over long periods of time, with substantial uncertainty about the number, location, 

timing, frequency, and intensity of specific activities those programs authorize, fund, or carry 

out. Our traditional approaches to section 7 consultations, which focus on the effects of a 

specific proposal, are not designed to address the spatial and temporal scales and level of 

uncertainty that is typical of consultations on general permits.

Instead of trying to adapt the traditional approach to programmatic consultations, we developed 

an assessment framework in recent years, in concert with NMFS, that allows the Services to help 

Federal agencies ensure that their programs comply with the requirements of section 7(a)(2) of 

the ESA as described in the Interagency Endangered Species Consultation Handbook (USFWS 

and NMFS 1998; Chapter 5). Our assessment framework for general permits, used in this 

consultation, first assesses whether the actions a general permit authorizes are likely to adversely 

affect ESA-listed species or designated critical habitats. We do this by estimating exposure and 

response to the stressors these actions contribute, just as described above for traditional 

consultations. If potential stressors are reasonably likely to measurably affect listed resources, 

we then examine the general permit’s structure and decision-making processes to determine 

whether they are likely to ensure that the actions the agency authorizes collectively comply with 

the requirements of section 7(a)(2). 

The steps followed in the assessment for this consultation are described in detail below.

The Proposed Action

In reviewing the proposed action and BE, the Service examined the activities that would be 

authorized by the proposed MSGP. This step of our analyses identified spatial and temporal 

patterns associated with each category of activity: specifically (a) the geographic distribution of 

the different activities; (b) the number of activities and/or covered facilities; (c) the types and 

amounts of pollutants that are likely to be discharged; and (d) the rate and other characteristics of 

discharges.

Our analysis evaluated the effects of all discharges of likely industrial stormwater pollutants and 

allowable non-stormwater discharges to waters of the United States incidental to the normal 

operation the facility sectors that would be covered by the MSGP. In addition, we will 

considered the discharge-related activities that are proposed as part of the action.

Action Area

We considered the degree of geographic and temporal overlap between: a) the activities that 

would be authorized by the proposed MSGP; and b) ESA-listed species and designated critical 

habitat. 
2015 MSGP Biological Opinion 31

Effects Analysis

Before assessing an agency’s decision-making process (in the approach as described above), the 

Service first established whether the proposed action could expose ESA-listed species and 

designated critical habitat to potentially harmful stressors and whether ESA-listed species and 

designated critical habitats are likely to be adversely affected. If exposure to stressors and 

adverse effects are not likely to occur, we do not assess the agency’s decision-making process. 

In this case, we determined that adverse effects were likely to occur, and the Opinion thus 

includes an assessment of the EPA’s decision-making process.

Our analysis of effects as presented in this Opinion will be divided into two sections. First, we 

will describe the potential stressors of the action, including both effects from the discharges and 

discharge-associated activities. Rather than discuss the literature for each species, we organize 

the data using categories of potential stressors. The anticipated effects to listed resources from 

the potential stressors will be discussed in general terms, using examples of effects to taxa as 

described in the relevant literature. These effects will be described in general terms, as would be 

anticipated to occur in the absence of protective BMPs and other measures. The second section 

of the effects analysis will consider whether EPA has structured the permit to provide sufficient 

avoidance and minimization of adverse effects to listed resources. Thus, we determine whether 

adverse effects are likely to occur though a review of the BE supplemented with additional 

information on the physical, physiological, behavioral, and ecological responses of endangered 

or threatened species or essential physical and biological features (hereafter, “PBFs”) of 

designated critical habitat. 

As we have already discussed, we treat the issuance of the proposed MSGP as a permitting 

“program” that would authorize discharges of pollutants over a five-year period. The specific 

questions we ask about the proposed MSGP as a permitting program are:

1. Scope

Has the general permit been structured to reliably estimate the probable number, location and 

timing of the discharges that would be authorized by the program?

2. Stressors 

Has the general permit been structured to reliably estimate the physical, chemical, or biotic 

stressors that are likely to be produced as a direct or indirect result of the discharges that would 

be authorized (e.g., the stressors produced by the actual discharges to waters of the United 

States)?

3. Overlap

Has the general permit been structured to reliably estimate whether or to what degree specific 

endangered or threatened species or designated critical habitat are likely to be exposed to 

potentially harmful impacts that the proposed permit would authorize?

4. Monitoring/Feedback

Has the general permit been structured to identify, collect, and analyze information about 

authorized actions that may have exposed endangered or threatened species or designated critical 

habitat to stressors at concentrations, intensities, durations, or frequencies that are known or 

suspected to produce physical, physiological, behavioral, or ecological responses that have 

potential individual or cumulative adverse consequences for individual organisms or constituent 
2015 MSGP Biological Opinion 32

elements of designated critical habitat?

5. Responses of Listed Resources

Does the general permit have an analytical methodology that considers: 

• Status and trends of endangered or threatened species or designated critical habitat; 

• Demographic and ecological status of populations and individuals of those species given 

their exposure to pre-existing stressors in different drainages and watersheds; 

• Direct and indirect pathways by which endangered or threatened species or designated 

critical habitat might be exposed to the discharges to waters of the United States; and 

• Physical, physiological, behavior, sociobiological, and ecological consequences of exposing 

endangered or threatened species or designated critical habitat to stressors from discharges at 

concentrations, intensities, durations, or frequencies that could produce physical, 

physiological, behavioral, or ecological responses, given their pre-existing demographic and 

ecological condition?

6. Compliance

Does the general permit have a mechanism to reliably determine whether or to what degree 

operators have complied with the conditions, restrictions or mitigation measures the proposed 

permit requires when they discharge to waters of the United States?

7. Adequacy of Controls

Does the general permit have a mechanism to prevent or minimize endangered or threatened 

species or designated critical habitat from being exposed to stressors from discharges: 

• At concentrations, durations, or frequencies that are potentially harmful to individual 

listed organisms, populations, or the species, or; 

• To ecological consequences that are potentially harmful to individual listed organisms, 

populations, the species or PBFs of designated critical habitat?

Additionally, we address the question of whether activities authorized by the proposed MSGP 

that may individually have minor direct and indirect effects on the environment but collectively 

may have large effects (i.e., aggregate effects). 

Integration and Synthesis

Our integration and sysnthesis section of the Opinion focuses on whether or to what degree an 

agency’s program is likely to ensure that the direct or indirect effects of actions the program 

would authorize are not likely to reduce the fitness of listed individuals to a degree that would be 

sufficient to reduce the viability of the population(s) those individuals represent and jeopardize 

the survival and recovery of the species. In particular, the programmatic assessment focuses on 

whether and to what degree the EPA structured the program in ways that would prevent or 

minimize endangered or threatened species or designated critical habitat from being exposed to 

harmful discharges of pollutants into waters of the United States and other harmful activities 

because such exposures commonly trigger responses that are difficult to prevent. Because it is so 

difficult to prevent free-ranging organisms from responding to anthropogenic stressors once they 

have been exposed, the most effective management measures are designed to influence the 
2015 MSGP Biological Opinion 33

exposure itself. For that reason, our assessment focuses on whether and to what degree the 

program prevents or minimizes endangered and threatened species and designated critical habitat

from being exposed to harmful discharges and other harmful activities that would be authorized 

by the proposed MSGP. 

ANALYTICAL FRAMEWORK FOR THE JEOPARDY AND ADVERSE 

MODIFICATION DETERMINATIONS

Jeopardy Determination

In accordance with policy and regulation, the jeopardy analysis in this Opinion relies on four 

components: (1) the Status of the Species, which evaluates the species’ range-wide condition, the 

factors responsible for that condition, and the survival and recovery needs of the species; (2) the 

Environmental Baseline, which evaluates the condition of the species in the Action Area, the 

factors responsible for that condition, and the relationship of the Action Area to the survival and 

recovery of the species; (3) the Effects of the Action, which determines the direct and indirect 

impacts of the proposed federal action and the effects of any interrelated or interdependent 

activities on the species; and (4) Cumulative Effects, which evaluates the effects of future, nonfederal activities that are reasonably certain to occur in the Action Area on the species.

In accordance with policy and regulation, the jeopardy determination is made by evaluating the 

effects of the proposed federal action in the context of the species’ current status, taking into 

account any cumulative effects, to determine if implementation of the proposed action is likely to 

cause an appreciable reduction in the likelihood of both the survival and recovery of the species 

in the wild.

The jeopardy analysis in this Opinion emphasizes consideration of the range-wide survival and 

recovery needs of the species and the role of the Action Area in the survival and recovery of the 

species. It is within this context that we evaluate the significance of the effects of the proposed 

federal action, taken together with cumulative effects, for purposes of making the jeopardy 

determination.

Adverse Modification Determination

This Opinion does not rely on the regulatory definition of “destruction or adverse modification” 

of critical habitat at 50 CFR 402.02. Instead, we have relied upon the statutory provisions of the 

ESA to complete the following analysis with respect to critical habitat.

In accordance with policy and regulation, the adverse modification analysis in this Opinion relies 

on four components: 1) the Status of Critical Habitat, which evaluates the range-wide condition 

of designated critical habitat for the species, the factors responsible for that condition, and the 

intended recovery function of the critical habitat overall; 2) the Environmental Baseline, which 

evaluates the condition of the critical habitat in the Action Area, the factors responsible for that 

condition, and the recovery role of the critical habitat in the Action Area; 3) the Effects of the 
2015 MSGP Biological Opinion 34

Action, which determines the direct and indirect impacts of the proposed federal action and the 

effects of any interrelated or interdependent activities on the PBFs and how that will influence 

the recovery role of affected critical habitat units; and 4) Cumulative Effects, which evaluates the 

effects of future, non-federal activities reasonably certain to occur in the Action Area on the 

PBFs and how that will influence the recovery role of affected critical habitat units.

For purposes of the adverse modification determination, the effects of the proposed federal 

action on the species’ critical habitat are evaluated in the context of the range-wide condition of 

the critical habitat, taking into account any cumulative effects, to determine if the critical habitat 

range-wide would remain functional (or would retain the current ability for the PBFs to be 

functionally established in areas of currently unsuitable but capable habitat) to serve its intended

recovery role for the species.

The analysis in this Opinion places an emphasis on using the intended range-wide recovery 

function of the species’ critical habitat and the role of the Action Area relative to that intended 

function as the context for evaluating the significance of the effects of the proposed federal 

action, taken together with cumulative effects, for purposes of making the adverse modification 

determination.

ACTION AREA

The 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 (50 CFR 402.02). In delineating the 

Action Area, we evaluated the farthest reaching physical, chemical, and biotic effects of the 

action on the environment.

The MSGP applies to states, territories, and other geographic areas where EPA retains permitting 

authority, as described above. The Action Area for the proposed action includes watersheds in 

the states and territories where facilities seeking coverage under the permit exist would discharge 

points to if granted coverage under the permit. Both current and future dischargers may request 

coverage under the MSGP in these geographic areas. Thus, the Action Area for the proposed 

action is not limited to existing discharge points and their associated areas of effect, but instead 

includes all waterbodies and watersheds in these geographic areas and the farthest downstream 

and/or down-current extent of the effects of the current and future discharges. The Action Area

also includes upland areas where new stormwater control features are installed or modified 

within the footprint of the industrial facilities’ boundaries. While not indicated in Figure 2 

(below), the Action Area would also include areas in adjacent states, as downstream movement 

of stressors are not fully contained within a state or territory where EPA retains full or partial 

permitting authority (e.g., for federal facilities or tribal lands).
2015 MSGP Biological Opinion 35

Figure 2. Action area of the proposed action (from the EPA’s BE), showing states, territories 

and other lands where EPA retain’s permitting jurisdiction. New and existing facilities located 

in the areas defined below may seek coverage under the MSGP.

STATUS OF THE SPECIES AND CRITICAL HABITAT 

In their BE, EPA identified numerous species that may be affected by the proposed permit, as 

well as a list of species for which they provided a “no effect” determination. Table 3 represents 

a refinement of EPA’s list of species to include only those species and designated critical habitat

under the jurisdiction of the Service that may be affected by the proposed action. This

conclusion is based on the overlap between the species’ ranges and designated critical habitats 

and the anticipated extent of effects from facility discharges and other activities authorized under 

the MSGP.

For more information regarding the individual species and critical habitats listed in Table 3, and 

the factors affecting their conservation status, please refer to proposed and final listing 

determinations, critical habitat designations, recovery plans, and 5-year reviews available at: 

http://ecos.fws.gov/ecos/home.action. The discussion that follows focuses on attributes of life 

history and distribution that influence the manner and likelihood that species may be exposed to 

the proposed action, as well as the species’ potential response and risk when exposure occurs.
2015 MSGP Biological Opinion 36

Table 3. List of threatened (T), endangered (E), and candidate (C) species addressed in the consultation, as compiled from the BE and 

its appendices. Species with designated critical habitat are indicated by an asterisk. (Species for which the EPA has made a “no 

effect” call are not included in this table, but are listed in an appendix to the BE for reference.)

Common Name Scientific Name Status State/Territory 

Range

BIVALVES

Hornshell, Texas Popenaias popei C NM, TX

Mucket, Neosho Lampsilis rafinesqueana E OK

Wedgemussel, dwarf Alasmidonta heterodon E MD, MA, NH, VT

CRUSTACEANS

Amphipod, Hay's Spring Stygobromus hayi E MA, MD

Amphipod, Noel's* Gammarus desperatus E NM

Crayfish, Shasta Pacifastacus fortis E CA

Fairy shrimp, Conservancy* Branchinecta conservatio E CA, NV

Fairy shrimp, longhorn* Branchinecta longiantenna E CA, NV

Fairy shrimp, Riverside* Streptocephalus woottoni E NM

Fairy shrimp, San Diego* Branchinecta sandiegonensis E CA

Fairy shrimp, vernal pool* Branchinecta lynchi T CA, OR

Isopod, Socorro Thermosphaeroma thermophilus E NM

Shrimp, California freshwater Syncaris pacifica E CA, NV

Tadpole shrimp, vernal pool Lepidurus packardi E CA

INSECTS

Tiger beetle, northeastern beach Cicindela dorsalis dorsalis T MD, MA

Tiger beetle, Puritan Cicindela puritana T MD, MA
2015 MSGP Biological Opinion 37

Common Name Scientific Name Status State/Territory 

Range

SNAILS

Ambersnail, Kanab Oxyloma haydeni kanabensis E AZ, UT

Limpet, Banbury Springs Lanx sp. E ID

Snail, Bliss Rapids Taylorconcha serpenticola T ID

Snail, Pecos assiminea* Assiminea pecos E NM, TX

Snail, Snake River physa Physa natricina E ID

Springsnail, Alamosa Tryonia alamosae E NM

Springsnail, Bruneau Hot Pyrgulopsis bruneauensis E ID

Springsnail, Chupadera Pyrgulopsis chupaderae E NM

Springsnail, Huachuca Pyrgulopsis thompsoni C AZ

Springsnail, Koster's* Juturnia kosteri E NM

Springsnail, Page Pyrgulopsis morrisoni C AZ

Springsnail, Roswell* Pyrgulopsis roswellensis E NM

Springsnail, San Bernadino* Pyrgulopsis bernardina T AZ

Springsnail, Socorro Pyrgulopsis neomexicana E NM

Springsnail, Three Forks* Pyrgulopsis trivialis E AZ

FISH

Catfish, Yaqui* Ictalurus pricei T AZ

Cavefish, Ozark Amblyopsis rosae T OK

Chub, bonytail* Gila elegans E AZ, CA, NV, UT

Chub, Chihuahua Gila nigrescens T NM

Chub, Gila* Gila intermedia E AZ, NM

Chub, headwater Gila nigra C AZ, NM

Chub, humpback* Gila cypha E AZ, UT

Chub, Mohave tui Gila bicolor mohavensis E CA
2015 MSGP Biological Opinion 38

Common Name Scientific Name Status State/Territory 

Range

Chub, Oregon* Oregonichthys crameri T OR

Chub, Virgin River* Gila seminuda (=robusta) E UT

Chub, Yaqui* Gila purpurea E AZ

Cui-ui Chasmistes cujus E NV

Gambusia, Pecos Gambusia nobilis E NM, TX

Gambusia, San Marcos* Gambusia georgei E TX

Goby, tidewater* Eucyclogobius newberryi E CA

Madtom, Neosho Noturus placidus T OK

Minnow, loach* Tiaroga cobitis E AZ, NM

Minnow, Rio Grande silvery* Hybognathus amarus E NM, TX

Pikeminnow (=squawfish), Colorado* Ptychocheilus lucius E AZ, CA, NM, UT

Pupfish, desert* Cyprinodon macularius E AZ, CA

Salmon, Atlantic Salmo salar E MA, NH, RI

Shiner, Arkansas River* Notropis girardi T NM, OK, TX

Shiner, beautiful* Cyprinella formosa T AZ, NM

Shiner, Pecos bluntnose* Notropis simus pecosensis T NM

Shiner, sharpnose Notropis oxyrhynchus E TX

Shiner, smalleye Notropis buccula E TX

Spikedace* Meda fulgida E AZ, NM

Spinedace, Little Colorado* Lepidomeda vittata T AZ

Stickleback, unarmored threespine Gasterosteus aculeatus williamsoni E CA

Sucker, June* Chasmistes liorus E UT

Sucker, Lost River Deltistes luxatus E CA, OR

Sucker, razorback* Xyrauchen texanus E AZ, CA, NV, NM, UT

Sucker, Santa Ana* Catostomus santaanae T CA

Sucker, shortnose Chasmistes brevirostris E CA, OR

Sucker, Warner* Catostomus warnerensis T NV, OR

Sucker, Zuni bluehead Catostomus discobolus yarrowi E AZ, NM

Topminnow, Gila (incl. Yaqui) Poeciliopsis occidentalis E AZ, NM

Trout, Apache Oncorhynchus apache T AZ
2015 MSGP Biological Opinion 39

Common Name Scientific Name Status State/Territory 

Range

Trout, bull* Salvelinus confluentus T ID, NV, OR, WA

Trout, Gila Oncorhynchus gilae T AZ, NM

Trout, greenback cutthroat Oncorhynchus clarki stomias T UT

Trout, Lahontan cutthroat Oncorhynchus clarki henshawi T CA, NV, OR

Woundfin* Plagopterus argentissimus E AZ, NV, NM, UT

AMPHIBIANS

Frog, mountain yellow-legged (northern California) Rana muscosa E CA, NV

Frog, mountain yellow-legged (southern California)* Rana muscosa E CA, NV

Frog, Oregon spotted Rana pretiosa T CA, NV, WA

Guajon* Eleutherodactylus cooki T PR

Salamander, California Tiger (Sonoma DPS)* Ambystoma californiense E CA, NV

Toad, arroyo (=arroyo southwestern)* Bufo californicus (=microscaphus) E CA

Toad, Houston* Bufo houstonensis E TX

Treefrog, Arizona Hyla wrightorum C AZ

REPTILES

Alligator, American Alligator mississippiensis SAT OK, TX

Plymouth Red-Bellied Turtle* Pseudemys rubriventris bangsi E MA

Sea turtle, green (All other areas) Chelonia mydas T 

(NMFS/FWS)

AS, CA, CT, DE, GU, MD, 

MA, NH, NMI, OR, PR, 

RI, TX, WA

Sea turtle, green (Florida & Mexico’s Pacific coast colonies) Chelonia mydas E 

(NMFS/FWS)

AS, CA, DE, GU, MD, 

MA, NH, NMI, OR, PR, 

RI, TX, WA, WK

Sea turtle, hawksbill Eretmochelys imbricate E 

(NMFS/FWS)

CA, DE, MD, MA, NH, 

PR, TX, WK
2015 MSGP Biological Opinion 40

Common Name Scientific Name Status State/Territory 

Range

Sea turtle, Kemp’s ridley Lepidochelys kempii E 

(NMFS/FWS) DE, MD, MA, RI, TX

Sea turtle, leatherback Dermochelys coriacea E 

(NMFS/FWS)

CA, DE, MD, MA, NH, 

OR, PR, RI, TX, WA, WK

Sea turtle, loggerhead, North Pacific Ocean Caretta caretta E 

(NMFS/FWS) CA, OR, WA

Sea turtle, loggerhead, Northwest Atlantic Ocean Caretta caretta T 

(NMFS/FWS)

DE, MD, MA, NH, RI, PR,

TX

Sea turtle, olive ridley (All other areas) Lepidochelys olivacea T 

(NMFS/FWS) PR

Sea turtle, olive ridley (Mexico’s Pacific coast

breeding colonies) Lepidochelys olivacea E 

(NMFS/FWS) CA

Snake, giant garter Thamnophis gigas T CA

Turtle, bog (=Muhlenberg) Clemmys muhlenbergii T DE, MD

Turtle, Sonoyta mud Kinosternon sonoriense longifemorale C AZ

BIRDS

Albatross, short-tailed Phoebastria (=Diomedea) albatrus E CA, OR, WA

Crake, spotless Porzana tabuensis C AS

Crane, whooping* Grus americana E OK, TX

Curlew, Eskimo Numenius borealis E OK, TX

Flycatcher, southwestern willow* Empidonax traillii extimus E AZ, CA, NV, NM, TX, UT

Knot, red Calidris canutus rufa T DE, LA, MD, MA, NH, TX

Moorhen, Mariana common Gallinula chloropus guami E GU, NMI, WK

Murrelet, marbled* Brachyramphus marmoratus T CA, OR, WA

Murrelet, Xantus's Synthliboramphus hypoleucus C CA, NV, OR

Plover, piping* Charadrius melodus T DE, MA, NH, OK, TX
2015 MSGP Biological Opinion 41

Common Name Scientific Name Status State/Territory 

Range

Plover, western snowy (Pacific Coast Population)* Charadrius alexandrinus nivosus T CA, OR, WA

Rail, light-footed clapper Rallus longirostris levipes E CA

Rail, Yuma clapper Rallus longirostris yumanensis E AZ, CA, NV

Shearwater, Newell's Townsend's Puffinus auricularis newelli T AS

Tern, California least Sterna antillarum browni E AZ, CA

Tern, least Sterna antillarum E NM, OK, TX

Tern, roseate Sterna dougallii dougallii E MA, NH, PR

Warbler, nightingale reed (old world warbler) Acrocephalus luscinia E GU, NMI, WK

MAMMALS

Manatee, West Indian* Trichechus manatus E TX

Mouse, salt marsh harvest Reithrodontomys raviventris E CA, NV, OR

Shrew, Buena Vista Lake ornate* Sorex ornatus relictus E CA, NV

PLANTS

Beaked-rush, Knieskern's Rhynchospora knieskernii T DE, MD

Bird's-beak, salt marsh Cordylanthus maritimus ssp. maritimus E CA

Bluecurls, Hidden Lake Trichostema austromontanum ssp.

compactum

T CA, NV

Brodiaea, Chinese Camp Brodiaea pallida T CA, NV

Brodiaea, thread-leaved* Brodiaea filifolia T CA

Bulrush, Northeastern Scirpus ancistrochaetus E MD, MA, NH, VT

Buttercup, autumn Ranunculus aestivalis (=acriformis) E UT

Button-celery, San Diego Eryngium aristulatum var. parishii E CA

Checker-mallow, Kenwood Marsh Sidalcea oregana ssp. valida E CA, NV, OR
2015 MSGP Biological Opinion 42

Common Name Scientific Name Status State/Territory 

Range

Checker-mallow, Nelson's Sidalcea nelsoniana T OR, WA

Cobana negra Stahlia monosperma T PR

Cress, Tahoe yellow Rorippa subumbellata C CA, NV

Crownscale, San Jacinto Valley* Atriplex coronata var. notatior E CA

Daisy, Willamette* Erigeron decumbens var. decumbens E OR

Desert-parsley, Bradshaw's Lomatium bradshawii E OR, WA

Grass, Colusa* Neostapfia colusana T CA, NV

Higuero de sierra Crescentia portoricensis E PR

Howellia, water Howellia aquatilis T CA, ID, OR, WA

Joint-vetch, sensitive Aeschynomene virginica T MD

Ladies'-tresses, Canelo Hills Spiranthes delitescens E AZ

Ladies'-tresses, Navasota Spiranthes parksii E TX

Ladies'-tresses, Ute Spiranthes diluvialis T ID, NV, WA, UT

Lily, Pitkin Marsh Lilium pardalinum ssp. Pitkinense E CA, OR, NV

Lily, Western Lilium occidentale E CA, OR

Meadowfoam, Butte County* Limnanthes floccosa ssp. Californica E CA, NV

Mesa-mint, Otay Pogogyne nudiuscula E CA

Navarretia, few-flowered Navarretia leucocephala ssp. pauciflora (=N. 

pauciflora) E CA, NV

Navarretia, many-flowered Navarretia leucocephala ssp. plieantha T CA, NV, OR

Navarretia, spreading* Navarretia fossalis E CA

No common name Gesneria pauciflora T PR

Orchid, eastern prairie fringed Platanthera leucophaea T OK

Orcutt grass, California Orcuttia californica E CA

Orcutt grass, hairy* Orcuttia pilosa E CA, NV

Orcutt grass, Sacramento* Orcuttia viscida E CA, NV, OR

Orcutt grass, San Joaquin* Orcuttia inaequalis T CA, NV, OR
2015 MSGP Biological Opinion 43

Common Name Scientific Name Status State/Territory 

Range

Orcutt grass, slender* Orcuttia tenuis T CA

Owl's-clover, fleshy* Castilleja campestris ssp. succulenta T CA, NV

Panic grass, Hirst Brothers' Dichanthelium (=Panicum) hirstii C MD, DE

Pink, swamp Helonias bullata T MD, DE

Primrose, Maguire Primula maguirei T UT

Rose-mallow, Neches River Hibiscus dasycalyx T TX

Seabeach Amaranth Amaranthus pumilus T DE

Sedge, Navajo* Carex specuicola T AZ, UT

Solano Grass Tuctoria mucronata E CA, NV, OR

Spurge, Hoover's* Chamaesyce hooveri T CA, NV

Stonecrop, Lake County Parvisedum leiocarpum E CA, NV

Sunflower, Pecos (=puzzle, =paradox)* Helianthus paradoxus T TX, NM

Sunshine, Sonoma Blennosperma bakeri E CA, NV

Thistle, Loch Lomond coyote Eryngium constancei E CA, NV, OR

Thistle, Sacramento Mountains Cirsium vinaceum T NM

Thistle, Suisun* Cirsium hydrophilum var. hydrophilum E CA, NV, OR

Vervain, Red Hills Verbena californica T CA, NV, OR

Watercress, Gambel's Rorippa gambellii E CA

Water-umbel, Huachuca* Lilaeopsis schaffneriana var. recurva E AZ
2015 MSGP Biological Opinion 44

ENVIRONMENTAL BASELINE 

Regulations implementing the Act (50 CFR 402.02) define the Environmental Baseline as the 

past and present impacts of all federal, state, or private actions and other human activities in the 

Action Area. Also included in the Environmental Baseline are the anticipated impacts of all 

proposed federal projects in the Action Area that have undergone section 7 consultation, and the 

impacts of state and private actions which are contemporaneous with the consultation in 

progress.

The key purpose of the Environmental Baseline is to describe the condition of the listed 

species/critical habitat that exist in the Action Area in the absence of the action subject to 

consultation. Due to the nationwide scope of the proposed action and the numerous listed 

species and critical habitat designations in the Action Area, this Opinion will consider the 

Environmental Baseline at a broad scale. Many of the listed species and their designated critical 

habitats are exposed to multiple stressors comprising the past and present impacts of actions and 

activities that are described below. Many of the ongoing stressors are also intensified by 

population growth and development pressures as well as variable effects of climate change and, 

for some species, ocean acidification. This Environmental Baseline focuses primarily on the 

status and trends of the aquatic ecosystems in the United States and the consequences of that 

status for listed resources.

All of the endangered and threatened species and designated critical habitat considered in this 

Opinion depend on the health of aquatic ecosystems for their survival. Many of these species 

were listed as endangered or threatened, at least in part, because of the consequences of human 

activities on aquatic ecosystems (including estuaries, rivers, lakes, streams, and associated 

wetlands, floodplains, and riparian ecosystems of the United States, its Territories and 

possessions). The status and trends of those aquatic ecosystems has a profound impact on the 

status and trends of these species and the critical habitat that has been designated for them. 

Habitat

Freshwater habitats are among the most threatened ecosystems in the world (Leidy and Moyle 

1998). Reviews of aquatic species’ conservation status over the past three decades have 

documented the cumulative effect of anthropogenic and natural stressors on freshwater aquatic 

ecosystems, resulting in a significant decline in the biodiversity and condition of indigenous fish, 

mussel and crayfish communities (Taylor et al. 2007; Jelks et al. 2008). Anthropogenic stressors 

are present to some degree in all water bodies of the United States, and are the result of many 

different impacts. These stressors often lead to long-term environmental degradation associated 

with lowered biodiversity, reduced primary and secondary production, and a lowered capacity or 

resiliency of the ecosystem to recover to its original state in response to natural perturbations 

(Rapport and Whitford 1999). 

Many of our nation’s rivers and streams have been altered by dams, stream channelization, and 

dredging to stabilize water levels in rivers or lakes. When examining the impacts of large dams 

alone, it is estimated that 75,000 large dams have modified at least 600,000 miles of rivers across 

the country (IWSRCC 2011). For example, more than 400 dams exist in the Columbia River 
2015 MSGP Biological Opinion 45

Basin alone (Columbia Basin Trust 2014). Habitat loss coupled with other stressors has led to 

impacts on fish communities as well. By the early 80’s, approximately 81 percent of the native 

fish communities in the United States had been adversely affected by human activities (Judy et 

al. 1984).

Wetland habitats have been drained to make land available for agriculture; they have been filled 

to make land available for residential housing, commerce, and industry; they have been diked to 

control mosquitoes; and they have been flooded for water supply. Efforts to create and restore 

wetlands and other aquatic habitats by agencies of federal, state, and local governments, nongovernmental organizations, and private individuals have dramatically reduced the rate at which 

these ecosystems have been destroyed or degraded, but many aquatic habitats continue to be lost 

each year. Between 2006 and 2009, approximately 13,800 acres of wetlands were lost per year 

(Dahl 2011). While this is significantly less than losses experienced in the previous decades 

(Figure 3), an estimated 72 percent of U.S wetlands have already been lost when compared to 

historical estimates (Dahl 2011). 

Estuaries are some of the most productive ecosystems in the world. Thousands of species of 

birds, mammals, fish, and other wildlife depend on estuarine habitats as places to live, feed, and 

reproduce. Many marine organisms, including most commercially-important species of fish, 

depend on estuaries at some point during their development. Estuaries are important nursery and 

rearing habitat for fishes such as salmon and sturgeon, sea turtles, and many other species. In 

estuaries that support salmon, changes in habitat and food-web dynamics have altered their 

capacity to support juvenile salmon (Bottom et al. 2005, Fresh et al. 2005, NMFS 2006d, 

LCFRB 2010). Diking and filling activities have reduced the tidal prism and eliminated 

emergent and forested wetlands and floodplain habitats. These changes likely have reduced 

these estuary’s’ salmon-rearing capacity. Restoration of estuarine habitats, particularly diked 

emergent and forested wetlands, reduction of avian predation by terns, and flow manipulations to 

restore historical flow patterns may have begun to enhance the estuary’s productive capacity for 

salmon, although historical changes in population structure and salmon life histories may prevent 

salmon from making full use of the productive capacity of estuarine habitats.
2015 MSGP Biological Opinion 46

Figure 3. Average annual net wetland acreage loss and gain estimates for the conterminous United States. (Taken 

from Dahl 2011)

Pollution

In addition to direct loss and alteration of aquatic habitat, many aquatic ecosystems have been 

impacted by various contaminants and pollutants. In 2008, the Heinz Center for Science, 

Economics and the Environment (Heinz Center) published a comprehensive report on the 

condition of our nation’s ecosystems. In their report, the Heinz Center noted the following:

• From 1992 to 2001, benchmarks for the protection of aquatic life were exceeded in 50 

percent of streams tested nationwide—83 percent of streams in urbanized areas—and 94 

percent of streambed sediments.

• Contaminants were detected in approximately 80 percent of sampled freshwater fish and 

most of these detected contaminants exceeded wildlife benchmarks (1992–2001 data) 

(Gilliom et al 2006)

• Nearly all saltwater fish tested had at least five contaminants at detectable levels, and 

concentrations exceeded benchmarks for the protection of human health in one-third of 

fish tissue samples—most commonly DDT, PCBs, PAHs, and mercury (USEPA 2007.)

Toxic contaminants, as noted above have, been documented in the Lower Columbia River and its 

tributaries (LCREP 2007). More than 41,000 waters are listed as impaired by pollutants that 

include mercury, pathogens, sediment, other metals, nutrient, and oxygen depletion, and other 

causes (USEPA 2013a). Pennsylvania reported the greatest number of impaired waters (6,957), 

followed by Washington (2,420), Michigan (2,352), and Florida (2,292). These figures likely 

underestimate the true number of impaired waterbodies in the United States. For example, 

EPA’s National Aquatic Resource Surveys (NARS) is a probability based survey that provides a 

national assessment of the nation’s waters and is used to track changes in water quality over 

-458,000

-290,000

-58,550

32,000

-13,800

-500,000

-400,000

-300,000

-200,000

-100,000

0

100,000

1950-1970 1970-1980 1980-1990 1998-2004 2004-2009

Acres of Wetlands
2015 MSGP Biological Opinion 47

time. Through this method, EPA estimates that 50 percent of the nation’s streams 

(approximately 300,000 miles) and 45 percent of the nation’s lakes (approximately seven million 

acres) are in fair to poor condition for nitrogen or phosphorus levels relative to reference 

condition waters (USEPA 2013b). However, data submitted by the states indicates that only 

about half of the NARS estimate (155,000 miles of rivers and streams and about four million 

acres of lakes) have been identified on EPA’s 303(d) impaired waters list for nutrient related 

causes (USEPA 2013b).

Water quality problems, particularly the problem of non-point sources of pollution, have resulted 

from changes humans have imposed on the landscapes of the United States over the past 100 to 

200 years. The mosaic or land uses associated with urban and suburban centers has been cited as 

the primary cause of declining environmental conditions in the United States (Flather et al. 1998) 

and other areas of the world (Houghton 1994). Most land areas covered by natural vegetation 

are highly porous and have very little sheet flow; precipitation falling on these landscapes 

infiltrates the soil, is transpired by the vegetative cover or evaporates. The increased 

transformation of the landscapes of the United States into a mosaic of urban and suburban land 

uses has increased the area of impervious surfaces such as roads, rooftops, parking lots, 

driveways, sidewalks, etc., in those landscapes. Precipitation that would normally infiltrate soils 

in forests, grasslands and wetlands falls on and flows over impervious surfaces. That runoff is 

then channeled into storm sewers and released directly into surface waters (rivers and streams), 

which changes the magnitude and variability of water velocity and volume in those receiving 

waters.

Increases in polluted runoff have been linked to a loss of aquatic species diversity and 

abundance, including many important commercial and recreational fish species. Nonpoint 

source pollution has also contributed to coral reef degradation, fish kills, seagrass bed declines 

and algal blooms (including toxic algae) (NOAA 2013). In addition, many shellfish bed and 

swimming beach closures can be attributed to polluted runoff. As discussed in EPA’s latest 

National Coastal Condition Report (NCCR), nonpoint sources have been identified as one of the 

stressors contributing to coastal water pollution (USEPA 2012). Since 2001, EPA has 

periodically released these reports detailing condition of the nation’s costal bays and estuaries 

and assessing trends in water quality in coastal areas. The latest NCCR report indicates that 

coastal water conditions have remained “fair” and the trend assessment demonstrates no 

significant change in the water quality of United States’ coastal waters since the publication of 

the NCCR II in 2004 (USEPA 2012).

In many estuaries, agricultural activities are major source of nutrients to the estuary and a 

contributor to the harmful algal blooms in summer, although according to McMahon and 

Woodside 1997 (EPA 2006a) nearly one-third of the total nitrogen inputs and one-fourth of the 

total phosphorus input to the estuary are from atmospheric sources. The National Estuary 

Program Condition Report found that nationally, 37% of national estuary program estuaries are 

in poor condition (http://water.epa.gov/type/oceb/nep/nepccr-factsheet.cfm).

Throughout the 20th century, mining, agriculture, paper and pulp mills, and municipalities 

contributed large quantities of pollutants to many estuaries. For example, the Roanoke River and 

the Albemarle-Pamlico Estuarine Complex which receives water from 43 counties in North 

Carolina and 38 counties and cities in Virginia. This estuarine system supports an array of 
2015 MSGP Biological Opinion 48

ecological and economic functions that are of regional and national importance. Both the lands 

and waters of the estuarine system support rich natural resources that are intertwined with 

regional industries including forestry, agriculture, commercial and recreational fishing, tourism, 

mining, energy development, and others. The critical importance of sustaining the estuarine 

system was reflected in its Congressional designation as an estuary of national significance in 

1987. Even so, today the Albemarle-Pamlico Estuarine Complex is rated in good to fair 

condition in the National Estuary Program Coastal Condition Report despite that over the past 

40-year period data indicate some noticeable changes in the estuary, including increased 

dissolved oxygen levels, increased pH, decreased levels of suspended solids, and increased 

chlorophyll a levels (EPA 2006b). 

Since 1993 EPA has compiled information on locally issued fish advisories and safe eating 

guidelines. This information is provided to the public to limit or avoid eating certain fish due to 

contamination of chemical pollutants. EPA’s 2010 National Listing of Fish Advisories database 

indicates that 98 percent of the advisories are due (in order of importance) to: mercury, PCBs, 

chlordane, dioxins, and DDT (USEPA 2010). Fish advisories have been issued for 36 percent of 

the total river miles (approximately 1.3 million river miles) and 100 percent of the Great Lakes 

and connecting waterways (USEPA 2010). Fish advisories have been steadily increasing over 

the National Listing of Fish Advisories period of record (1993-2010), but EPA interprets these 

increases to reflect the increase in the number of waterbodies being monitored by states and 

advances in analytical methods rather than an increase in levels of problematic chemicals 

(USEPA 2010).

Water-quality concerns related to urban development include providing adequate sewage 

treatment and disposal, transport of contaminants to streams by storm runoff, and preservation of 

stream corridors. Water availability has been and will continue to be a major, long- term issue in 

many areas. It is now widely recognized that ground-water withdrawals can deplete streamflows 

(Morgan and Jones 1999), and one of the increasing demands for surface water is the need to 

maintain instream flows for fish and other aquatic biota.

Climate Change

All species discussed in this Opinion are or will be impacted by the direct and indirect effects of 

global climatic change. Climate change is projected to have substantial direct and indirect 

effects on individuals, populations, species, and the structure and function of marine ecosystems 

in the near future (IPCC 2002). The Intergovernmental Panel on Climate Change (IPCC) 

estimated that average global land and sea surface temperature has increased by 0.85°C (± 0.2) 

since the late-1800s, with most of the change occurring since the mid-1900s (IPCC 2013). This 

temperature increase is greater than what would be expected given the range of natural climatic 

variability recorded over the past 1,000 years (Crowley and Berner 2001). The IPCC estimates 

that the last 30 years were likely the warmest 30-year period of the last 1,400 years, and that 

global mean surface temperature change will likely increase in the range of 0.3 to 0.7°C over the 

next 20 years.

Warming water temperatures attributed to climate change can have significant effects on 

survival, reproduction, and growth rates of aquatic organisms (Staudinger et al 2012). For 

example, warmer water temperatures have been identified as a factor in the decline and 
2015 MSGP Biological Opinion 49

disappearance of mussel and barnacle beds in the Northwest (Harley 2011). Shifts in migration 

timing of pink salmon (Oncorhynchus gorbuscha) which may lead to high pre-spawning 

mortality have also been tied to warmer water temperatures (Taylor 2008). Increasing 

atmospheric temperatures have already contributed to changes in the quality of freshwater, 

coastal, and marine ecosystems and have contributed to the decline of populations of endangered 

and threatened species (Karl et al. 2009; Littell et al. 2009; Mantua et al. 1997). Ocean 

acidification, as a result of increased atmospheric carbon dioxide, can interfere with numerous 

biological processes in corals including: fertilization, larval development, settlement success, 

and secretion of skeletons (Albright et al. 2010).

Climate change is also expected to impact the timing and intensity of stream seasonal flows 

(Staudinger et al 2012). Warmer temperatures are expected to reduce snow accumulation and 

increase stream flows during the winter, cause spring snowmelt to occur earlier in the year, and 

reduced summer stream flows in rivers that depend on snow melt. As a result, seasonal stream 

flow timing will likely shift significantly in sensitive watersheds (Littell et al. 2009). Warmer 

temperatures may also have the effect of increasing water use in agriculture, both for existing 

fields and the establishment of new ones in once unprofitable areas (ISAB 2007). This means 

that streams, rivers, and lakes will experience additional withdrawal of water for irrigation and 

increasing contaminant loads from returning effluent. Changes in stream flow due to use 

changes and seasonal run-off patterns may alter predator-prey interactions and change species 

assemblages in aquatic habitats. For example, a study conducted in an Arizona stream 

documented the complete loss of some macroinvertebrate species as the duration of low stream 

flows increased (Sponseller et al 2010). As it is likely that intensity and frequency of droughts 

will increase across the southwest (Karl et al. 2009), similar changes in aquatic species 

composition in the region is likely to occur. 

Warmer water also stimulates biological processes which can lead to environmental hypoxia. 

Oxygen depletion in aquatic ecosystems can result in anaerobic metabolism increasing, thus 

leading to an increase in metals and other pollutants being released into the water column 

(Staudinger et al 2012). In addition to these changes, climate change may affect agriculture and 

other land development as rainfall and temperature patterns shift. Aquatic nuisance species 

invasions are also likely to change over time, as oceans warm and ecosystems become less 

resilient to disturbances (USEPA 2008). If water temperatures warm in marine ecosystems, 

native species may shift poleward to cooler habitats, opening ecological niches that can be 

occupied by invasive species introduced via ships’ ballast water or other sources (Ruiz et al. 

1999, Philippart et al. 2011). Invasive species that are better adapted to warmer water 

temperatures would outcompete native species that are physiologically geared towards lower 

water temperatures; such a situation currently occurs along central and northern California 

(Lockwood and Somero 2011)

In summary, the direct effects of climate change include increases in atmospheric temperatures, 

decreases in sea ice, and changes in sea surface temperatures, patterns of precipitation, and sea 

level. Indirect effects of climate change include altered reproductive seasons/locations, shifts in 

migration patterns, reduced distribution and abundance of prey, and changes in the abundance of 

competitors and/or predators. Climate change is most likely to have its most pronounced effects 

on species whose populations are already in tenuous positions (Isaac 2008).
2015 MSGP Biological Opinion 50

Clean Water Act

Several laws and regulations have been put in place to help improve the state of our aquatic 

resources, the principal one being the CWA. The original 1948 statute was totally re-written in 

1972 to produce its current purpose: “to restore and maintain the chemical, physical, and 

biological integrity of the Nation's waters” (Federal Water Pollution Control Act, Public Law 92 

–500). Congress made substantial amendment to the CWA in the Water Quality Act of 1987 (P. 

L. 100-4) in response to the significant and persistent water quality problems.

To achieve its objectives, the CWA generally prohibits all point source discharges into the 

nation’s waters, unless otherwise authorized under the CWA. One of the main ways that point 

source discharges are regulated is through permits issued under the NPDES authorized under the 

CWA. For example, the NPDES program regulates discharges of pollutants like bacteria, 

oxygen-consuming materials, and toxic pollutants like heavy metals, pesticides, and other 

organic chemicals. EPA has also promulgated regulations setting effluent limitations guidelines 

and standards under sections 301, 304, and 306 of the CWA for more than 50 industries [40 CFR 

parts 405 through 471]. These effluent limitations guidelines and standards for categories of 

industrial dischargers are based on pollutants of concern discharged by industry; the degree of 

control that can be attained using pollution control technology; consideration of various 

economic tests appropriate to each level of control; and other factors identified in sections 304 

and 306 of the CWA (such as non-water quality environmental impacts including energy 

impacts) (F76 FR 22174-22288). These effluent limitations have been credited for helping 

reduce the amount of pollutants like toxic metals entering the aquatic environment (Smail et al

2012). While provisions of the CWA have helped significantly improve the quality of aquatic 

ecosystems, nonpoint sources of water pollution, which are believed to be responsible for the 

majority of modern water quality problems in the United States, are not subject to CWA permits 

or regulatory requirements. Instead, nonpoint sources of pollution are regulated by programs 

overseen by the states. 

Water quality is important to all of the listed resources identified above in Table 3. In some 

cases, the deterioration of water quality has led to the endangerment of aquatic species; in all 

cases, activities that threaten water quality also threaten these listed resources. Endangered and 

threatened species have experienced population declines that leave them vulnerable to a 

multitude of threats. Because of reduced abundance, low or highly variable growth capacity, and 

the loss of essential habitat, these species are less resilient to additional disturbances. In larger 

populations, stressors that affect only a limited number of individuals could once be tolerated by 

the species without resulting in population level impacts, whereas in smaller populations, the 

same stressors are more likely to reduce the likelihood of survival. It is with this understanding 

of the environmental baseline that we consider the effects of the proposed action, including the 

likely effect that CWIS’s will have on endangered and threatened species and their designated 

critical habitats.
2015 MSGP Biological Opinion 51

Water Quality

Changes in water temperature also affect water quality. Aquatic biota often require certain 

ranges of water temperatures for survival, growth, and reproduction; when water temperatures 

are modified beyond optimal ranges for species—or for their prey base or other species with 

which they share an obligate relationship, these life history functions can be significantly 

impacted. Human activities that can impact stream and other waterbody temperatures include 

removal of shading and insulating riparian vegetation, diversions of water for irrigation or other 

water supply needs, hypolimnetic releases of water from dams, and discharges of water (e.g., 

wastewater treatment plants, stormwater discharges, etc.). Carlisle et al. (2013) report that 17

percent of assessed streams in the United States had either cooler or warmer summer water 

temperatures than would be anticipated compared to natural conditions. 

Other contaminants that have been identified in various aquatic habitats in the United States. 

Elevated salinities have been observed due to road-deicing salts, wastewater effluent, aging 

septic systems, irrigation, and fertilizer applications (Carlisle et al 2013)

EFFECTS OF THE ACTION

An agency’s action is defined as activities or programs of any kind authorized, funded, or carried 

out, in whole or in part, by federal agencies. The Act regulations define “effects of the action” as 

“the direct and indirect effects of an action on the species or habitat together with the effects of 

other activities that are interrelated or interdependent with that action, that will be added to the 

environmental baseline” (50 C.F.R. 402.02). Indirect effects are those that are caused by the 

proposed action and are later in time, but still are reasonably certain to occur. Effects of the 

action also include the effects of other activities that are interrelated or interdependent with that 

action. Interrelated actions are those that are part of a larger action and depend on the larger 

action for their justification. Interdependent actions are those that have no independent utility 

apart from the action under consideration.

For this Opinion, our analysis of the probable effects of the proposed MSGP on listed resources 

under the Service’s purview is presented using the Approach to the Analysis described 

previously in this Opinion. The Effects of the Action section of this Opinion is divided into three 

parts. First, in the Stressors Overview section, we briefly summarize the anticipated stressors 

related to the proposed action and the anticipated pathways of exposure to listed species and their 

designated critical habitats. We also summarize the anticipated responses of listed species and 

critical habitat PBFs to these stressors, using examples from the literature. As BMPs and other 

controls will vary across facility subsectors and geographic areas, we do not include a detailed 

analysis of how such measures would avoid or reduce the effects of the stressors to listed 

resources in this section. In the next section of the Effects of the Action section, the Review of 

Permit Structure, we examine whether and to what degree EPA has structured the MSGP (as 

well as its monitoring and compliance components) to ensure discharges into waters of the 

United States and other stressors of the action are not likely to jeopardize the continued existence 

of endangered species or threatened species or result in the destruction or adverse modification 

of critical habitat. We follow this analysis with a review of any cumulative effects and 
2015 MSGP Biological Opinion 52

interrelated and interdependent activities identified for the proposed action. Finally, we 

summarize the analysis in the Integration and Synthesis section.

Section 1: Stressors Overview

The discharges and discharge-related activities authorized for coverage by the MSGP will 

introduce stressors into aquatic, riparian, and terrestrial habitats that support listed species and

provide critical habitat. We anticipate most of the direct effects to individuals of listed species 

and critical habitat from the proposed action are likely to be related to exposure to chemical and 

physical stressors such as pollutants or discharge flow characteristics (e.g., volume, rate, 

temperature, etc.) Indirect effects to listed species and critical habitat are also expected to occur, 

including degradation of habitat features and/or quality, reductions or alterations in their forage 

base, and/or effects to other species they depend upon to complete their life cycles (e.g., host 

species). 

Each of the main categories of stressors will be discussed in this section, roughly following the 

parameter divisions present in the BE. These include inorganic pollutants, organic pollutants, 

nutrients, and other pollutants. Due to the expansive number of contaminants and other stressors 

anticipated from the discharges and the wide variety of habitats within the Action Area, the 

Opinion will not include an exhaustive discussion of likely effects to all listed species from each 

stressor. Within each category, we will describe example constituents of specific stressor

categories and types of anticipated effects to various taxa groups and critical habitat PBFs. As 

noted previously, this section provides a general discussion of the effects of potential stressors on 

listed resources, in the absence of protective measures (such as BMPs and other conservation 

measures). Section 2 will discuss how the proposed implementation of the permit would address 

these effects.

Pollutants

We anticipate most, if not all, facilities are likely to have one or more pollutants in their 

respective discharges, based on the nature of stormwater discharges. Stormwater pollutants vary 

widely and affect the physiology and/or behavior of exposed biota in ways that disrupt normal 

behaviors (i.e., free movement, feeding, and sheltering), and reduce growth, migratory success, 

and reproduction. In sufficient concentrations, stormwater pollutants can also result in acute 

toxicity and death. Acute effects to aquatic life from activities covered under the proposed 

permit are influenced by the size and dilution capacity of the receiving waterbody. Other factors 

that influence exposure and response of listed resources include background water quality 

conditions, concurrent discharges and/or background levels of other contaminants, frequency and 

duration of exposure, concentration and relative toxicity of the pollutant(s), biological uptake and 

availability, and life stage of the organism. 

Upon entering the receiving waterbody, stormwater discharges will typically mix with and be 

diluted by flow and the ambient water quality conditions. In order to assess the potential for 

adverse effects stemming from acute exposures, it is necessary to know something of the 

physical and temporal extents of the pollutant mixing zone(s). Stormwater runoff is a complex 

chemical mixture. Even during the course of a single discharge event, physical and chemical 

properties (including pollutant concentrations) can vary by orders of magnitude (Glenn et al. 
2015 MSGP Biological Opinion 53

2002). Conditions in the receiving waterbody are also dynamic, and therefore estimates of the 

probable extent or duration of resulting mixing zones are imprecise and subject to uncertainty. 

Additional sources of uncertainty include the effect of intermittent, episodic, or transient 

exposures (Burton et al. 2000; Marsalek et al. 1999); variations in tolerance among exposed 

individuals and/or populations (Ellis 2000; Hodson 1988; Lloyd 1987); and the potential for 

synergistic or additive effects among pollutants with similar or the same modes of toxic action 

(Burton et al. 2000; Ellis 2000; Lloyd 1987). 

The main categories of pollutants addressed under the MSGP are presented below. Each 

category includes a discussion of selected parameters and describes the types of anticipated 

effects to aquatic biota. Due to the large numbers of parameters and listed resources that have 

the potential to be affected, the discussion does not include all possible effects to all listed 

resources that are likely to occur as a result of implementation of the MSGP. 

Inorganic Pollutants

In the BE, the EPA identified several types of inorganic pollutants that are most likely to be 

found in stormwater discharges covered under the permit. These pollutants include aluminum, 

ammonia, antimony, arsenic, beryllium, cadmium, chromium, copper, cyanide, fluoride, lead, 

magnesium, mercury, nickel, selenium, silver, and zinc. As the Opinion’s analysis will focus 

primarily on process, we will not evaluate the potential effects of all of the inorganic pollutants 

anticipated to be present in the discharges covered by the permit. To provide some context on 

the effects of the discharges, however, we will briefly discuss the effects of several examples of 

these chemicals, specifically: ammonia, selenium, and two metals (copper and zinc). 

Ammonia

Although ammonia is a common water pollutant, it is also produced endogenously (i.e. within 

organisms). Under normal conditions, physiological processes, such as passive diffusion through 

fish gills, enable ammonia to be excreted from the body. However, when concentrations in ambient 

water are elevated, ammonia may not be effectively removed, and toxic effects can result. Ammonia 

occurs in two forms, ionized (NH4+) and unionized (NH3), depending on the pH. The unionized 

form is toxic and the toxic action in aquatic organisms has been attributed to several causes (EPA 

2013) including; (1) proliferation of gill tissue, increased ventilation rates and damage to gill 

epithelium (Lang et al. 1987), (2) reduction in blood oxygen-carrying capacity due to progressive 

acidosis (Russo 1985), (3) uncoupling of oxidative phosphorlylation causing inhibition of production 

and depletion of adenosine triphosphate (ATP) in the brain (Camargo and Alonso 2006), and (4) the 

disruption of osmoregulatory and circulatory activity disrupting normal metabolic functioning of the 

liver and kidneys (Arillo et al. 1981, Tomasso et al. 1980). These pathways can lead to acute and 

chronic effects.

While much is known about the sensitivity of fish to ammonia, recent studies (Wang et al. 2007a; 

Wang et al. 2007b; Besser et al. 2009) have revealed that freshwater mollusks (mussels and snails) 

are also very sensitive. In fact, mollusks tend to be more sensitive than previously tested species, 

including fish. Mussel early life stages (glochidia and juveniles) are particularly sensitive to 

ammonia. Glochidia are the microscopic larval stage of mussels that live as temporary parasites on 
2015 MSGP Biological Opinion 54

the gills of host fish where they develop into juveniles. Toxicity tests have shown that lethal effects 

to glochidia can occur rapidly (within 6 hours) following exposure to ammonia (Black 2001, Wang et 

al. 2007a) indicating short term exposures may be sufficient to cause adverse effects.

In 2013, the EPA revised their CWA 304(a) aquatic life ambient water quality criteria for ammonia 

to include mollusk data so that freshwater mussels, snails and other mollusks receive greater 

protection. The acute and chronic criteria are formulaic, that is, their magnitude is a function of 

water temperature and pH. For example, the acute criterion (CMC or criterion maximum 

concentration) at pH 7 and 20C is 17 mg TAN(total ammonia nitrogen)/L, whereas, at pH 8.5 and 

25C the acute criterion is 0.98 mg TAN/L (EPA 2013; table 5a). This reflects the greater sensitivity 

of mollusks to ammonia in warmer, more alkaline waters. The ammonia benchmark in the MSGP, 

2.14 mg/L, falls within this range, however, there are no references or guidance regarding applicable 

temperature or pH values. Knowledge of the temperature and pH of receiving waters would be 

important for interpreting ammonia benchmark monitoring data. In addition, benchmark 

exceedences, even for a single sampling period, may be of sufficient magnitude and duration to cause 

adverse effects to sensitive aquatic species.

Selenium

Selenium is a naturally occurring trace element and is also an essential micronutrient for animals. 

The physiological range of selenium that supports normal function is quite narrow. In fish, 

selenium is required in the diet at concentrations of about 0.15 to 0.5 ug/g dry weight (Watenabe 

et al.1997). Lower dietary selenium levels can cause effects that are symptomatic of selenium 

deficiencies, whereas, at higher concentrations (>3 ug/g) selenium becomes a poison (Lemly 

1998).

Selenium can be acutely lethal at high concentrations, however, it is also a potent reproductive 

toxin at much lower levels. One of the more prominent outward manifestations of selenium 

toxicity in fish is teratogenic deformities (Lemly 1998). Selenium accumulated by adults is 

transferred to eggs and developing embryos. Because selenium is very similar to sulfur, 

selenium can replace sulfur in sulfur-containing amino acids. It is hypothesized that such 

substitutions can alter the tertiary structure of proteins and affect their function. This can result 

in deformities in both hard and soft structures in developing fish larvae and the prevalence of 

deformities increases when selenium concentrations in eggs exceed 10 ug/g (Lemly 1998). 

Typical examples of selenium-induced terata include: 1) lordosis – concave curvature of the 

spine; 2) scoliosis - lateral curvature of the spine; 3) kyphosis – convex curvature of the thorax 

region of the spine, resulting in “humpback” condition; 4) missing or deformed fins;5) missing 

or deformed gills or gill covers (opercle); 6) abnormally shaped head;7) missing or deformed 

eyes; and 8) deformed mouth (Lemly 1998). Mortality among deformed larvae can be high if the 

teratogenic effects are severe enough to impair critical body functions (Woock et al 1987). 

Similar teratogenic effects are also observed in birds that have been exposed to elevated 

concentrations of selenium in their diet.

There have been several incidents of fish and wildlife poisoning from selenium exposure in 

nature. Skorupa (1998) described 12 real-world examples. The source of selenium 

contamination in those cases ranged from coal and petroleum industrial activities, to agricultural 

drainage water in areas with selenium-rich soils, to mining. The affected waterbodies were 
2015 MSGP Biological Opinion 55

offstream aquatic systems, such as, reservoirs, impoundments, lakes, and wetlands. In some 

cases, these were terminal systems (e.g. Kesterson Reservoir and Salton Sea), where selenium 

concentrated in the water column due to evaporation. 

It is well known that selenium tends to bioaccumulate in the environment. In aquatic systems, 

selenium is bioconcentrated by living (primary producers such as algae) and non-living (detritus) 

particulate matter and then biomagnified in primary consumers and successively higher trophic 

levels. Aquatic and aquatic-dependent organisms that feed at the top of the food chain receive 

the highest dietary exposure to selenium. Presser and Luoma (2010) describe an ecosystem 

approach for modeling selenium dynamics in aquatic habitats that highlights the importance of 

food chain structure and composition in governing exposure to predator species. The EPA has 

adopted a similar approach in their recently updated draft aquatic life ambient water quality 

criterion for selenium (EPA 2014). The 2014 draft selenium criterion is comprised of fish-tissue 

based elements and water-based elements. The tissue-based elements include selenium 

concentrations in fish egg-ovary (15.2 mg/kg dry wt.), fish whole-body (8.1 mg/kg dry wt.), and 

fish muscle (11.8 mg/kg dry wt.). The water-based elements were extrapolated from the fish 

egg-ovary criterion element for both lentic aquatic systems (still waters), 1.3 ug/L, and lotic 

aquatic systems (flowing waters), 4.8 ug/L. The lentic and lotic water values reflect the apparent 

difference in enrichment from water into algae, detritus, and sediment in these two types of 

aquatic systems (EPA 2014). 

Based on the information described above, the stormwater exposure scenario that poses the 

greatest risk to listed species is likely where discharges flow into or will influence lentic habitats, 

such as reservoirs, impoundments, lakes, or wetlands. In those habitats, the selenium benchmark 

of 5 ug/L, if achieved, may not ensure that adverse effects to species will not occur considering 

that the proposed water-based criterion for lentic systems (1.3 ug/L) is substantially lower. 

Exceedence of the selenium benchmark values for discharges to lentic or lotic systems would 

likely pose greater risk and could potentially cause adverse effects.

Metals

We anticipate that exposure to metals in stormwater will result in adverse effects to aquatic biota, 

unless sufficient measures are incorporated to avoid or reduce exposure to listed resources. In 

this Opinion, we will consider the effects of copper (CU) and zinc (ZN) to fish (and primarily 

salmonids) as examples of types of likely effects that would be expected to result from 

discharges of stormwater. As with the previous pollutants, our discussion does not include all 

anticipated effects from these and other metals to salmonids and other types of fish and aquatic 

biota. However, this discussion represents reasonable worst-case scenarios that are applicable to 

the proposed action.

There are three pathways by which salmonids may be directly exposed to and/or may uptake 

metals: (1) uptake of ionic metals at the gill surfaces (Niyogi et al. 2004); (2) dietary uptake; and 

(3) olfaction (sense of smell) involving receptor neurons (Baldwin et al. 2003). Of these three 

pathways, the mechanism of dietary uptake is least understood. For dissolved metals, the most 

direct pathway is through the gill surfaces. Measurements of total recoverable metal 

concentration include a fraction that is bound to suspended solids and/or complexed with organic 
2015 MSGP Biological Opinion 56

matter or other ligands; this fraction is not available to bind to gill receptor sites. Most metal 

toxicity studies have examined the dissolved metal fraction which is more bioavailable and 

therefore of greater significance for acute exposure and toxicity.

The relative toxicity of a metal or metal species can be altered by hardness, water temperature, 

pH, organic content, phosphate concentration, suspended solid concentration, the presence of 

other metals or contaminants (i.e., synergistic effects), and other factors. Eisler (1998) and 

Playle (2004) found that some dissolved metal mixtures exhibit greater than additive toxicity. 

Water hardness affects the bio-available fraction of metals; as hardness increases, metals become 

less bio-available for uptake at the gill surfaces and therefore less toxic (Hansen et al. 2002; 

Niyogi et al. 2004). However, Baldwin et al. (2003) found water hardness did not influence the 

inhibiting effects of Cu on salmon olfactory functions. Additional analysis related to copper and 

zinc are presented below.

Copper

Even at low concentrations, Cu is acutely toxic to fish. Effects of Cu exposure include: 1) 

weakened immune function and impaired disease resistance; 2) impaired respiration; 3) 

disruptions to osmoregulation; 4) impaired function of olfactory organs and brain; 5) altered 

blood chemistry; 6) altered enzyme activity and function; and 7) pathology of the kidneys, liver, 

and gills (Eisler 1998). 

Sprague (1964) and Sprague and Ramsay (1965) reported incipient lethal levels for dissolved Cu 

of 48 μg/L and 32 μg/L at water hardnesses of 20 and 14 mg/L, respectively. The Incipient 

Lethal Level is that concentration which is required to kill half of the fish tested within 1 week of 

exposure. Sprague and Ramsay (1965) found higher concentrations of Cu killed juvenile salmon 

much more rapidly than did lower concentrations at 14 mg/L hardness. Baldwin et al. (2003) 

found short pulses of dissolved Cu, at concentrations as low as 2 μg/L, reduced olfactory sensory 

responsiveness by approximately 10 percent within 10 minutes, and by 25 percent within 30 

minutes. At 10 μg/L, responsiveness was reduced by 67 percent within 30 minutes. Baldwin et 

al. (2003) identified a Cu concentration neurotoxic threshold of an increase of 2.3 to 3.0 μg/L, 

when background levels are 3.0 μg/L or less. When exceeded, this threshold is associated with 

olfactory inhibition. The authors also reference three other studies examining long-duration Cu 

exposures (i.e., exceeding 4 hours); these studies found that long-duration exposures resulted in 

cell (olfactory receptor neuron) death in rainbow trout and Atlantic and Chinook salmon. 

Baldwin et al. (2003) found water hardness did not influence the toxicity of Cu to coho salmon 

sensory neurons.

More recently, Sandahl et al. (2007) documented sensory physiological impairment and related 

disruption to predator avoidance behaviors, in juvenile coho at concentrations as low as 2 μg/L 

dissolved Cu. The effects of short-term Cu exposure may persist for hours and possibly longer. 

Although salmonids may actively avoid surface waters containing an excess of dissolved Cu, 

those exposed individuals may experience olfactory function inhibition within minutes of 

exposure. Furthermore, avoidance of a chemical plume may cause fish to leave refugia or 

preferred habitats in favor of less suitable or less productive habitats. This, in turn, can make 
2015 MSGP Biological Opinion 57

fish more vulnerable to predation and can impair foraging success, feeding efficiency, and 

thereby growth.

Folmar (1976) observed avoidance responses in rainbow trout fry when exposed to a lowest 

observed effect concentration of 0.1 μg/L dissolved Cu (hardness of 90 mg/L). The EPA (1980a) 

also documented avoidance by rainbow trout fry of dissolved Cu concentrations as low as 0.1 

μg/L during a 1-hour exposure, as well as a LC10 for smolts exposed to 7.0 μg/L for 200 hours, 

and a LC10 for juveniles exposed to 9.0 μg/L for 200 hours.

Zinc (Zn)

Zn occurs naturally in the environment and is an essential trace element for most organisms. 

However, in sufficient concentrations and when bioavailable for uptake by aquatic organisms, 

excess Zn is toxic. Toxicity in the aquatic environment and for exposed aquatic organisms is 

influenced by water hardness, pH, organic matter content, levels of dissolved oxygen, phosphate, 

and suspended solids, the presence of mixtures (i.e., synergistic effects), trophic level, and 

exposure frequency and duration (Eisler 1993). Bioavailability of Zn increases under conditions 

of high dissolved oxygen, low salinity, low pH, and/or high levels of inorganic oxides and humic 

substances. Most of the Zn introduced into aquatic environments is eventually partitioned into 

sediments (Eisler 1993).

Effects of Zn exposure include: 1) weakened immune function and impaired disease resistance 

(Ghanmi et al. 1989); 2) impaired respiration, including potentially lethal destruction of gill 

epithelium (Eisler 1993); 3) altered blood and serum chemistry, and enzyme activity and 

function (Hilmy et al. 1987a; Hilmy et al. 1987b); 4) interference with gall bladder and gill 

metabolism (Eisler 1993); 5) hyperglycemia; and 6) jaw and branchial abnormalities (Eisler 

1993).

Hansen et al. (2002) determined 120-day lethal concentrations of Zn for test subjects that 

included bull trout and rainbow trout fry. Multiple pairs of tests were performed with a nominal 

pH of 7.5, hardness of 30 mg/L, and at a temperature of 8 °C. Bull trout LC50 values ranged 

from 35.6 to 80.0 μg/L, with an average of 56.1 μg/L. Hansen et al. (2002) found that rainbow 

trout fry are more sensitive to Zn (i.e., exhibit a lower LC50) than are bull trout fry. The authors 

also report that older, more active juvenile bull trout are more sensitive than younger, more 

docile juvenile bull trout based on observed changes in behavior at the juvenile life stage. The 

authors argue that the timing of Zn exposure and the activity level of the exposed fish are 

germane to predicting toxicity in the field.

The mode of action for Zn toxicity relates to net loss of calcium. Studies suggest that Zn 

exposure inhibits calcium uptake, although it appears this effect is reversible once fish return to 

clean water. The apparent difference in sensitivity between rainbow trout and bull trout may be 

due to the lesser susceptibility of bull trout to calcium loss. Hansen et al. (2002) state that 

differences in sensitivity between these two salmonids may reflect different physiological 

strategies for regulating calcium uptake. These strategies may include gills that differ 

structurally, differences in the mechanisms for calcium uptake, and/or variation in resistance to 

or tolerance for calcium loss.
2015 MSGP Biological Opinion 58

In addition to the physiological effects of Zn exposure, studies have also documented a variety of 

behavioral responses. Among these, Eisler (1993) includes altered avoidance behavior, 

decreased swimming ability, and hyperactivity. The author suggests these effects have

implications for growth, reproduction, and survival. Sub-lethal endpoints have been evaluated 

with test subjects that include both juvenile and adult rainbow trout (Eisler 1993; USEPA 1980b; 

USEPA 1987). Some of these test results clearly indicate that juvenile rainbow trout are more 

sensitive than adult rainbow trout. Using juvenile rainbow trout as test subjects, studies have 

found that sub-lethal effects occur at concentrations approximately 75 percent lower (5.6 μg/L) 

than the concentrations that result in lethal effects (24 μg/L) (Eisler 1993; Hansen et al. 2002). 

Sprague (1968) found that at concentrations as low as 5.6 μg/L juvenile rainbow trout exhibit 

avoidance behavior. 

Although salmonids may actively avoid surface waters containing an excess of dissolved Zn, it is 

likely that stormwater runoff contains a mixture of pollutants, including some known to affect 

the olfactory system, such as dissolved Cu. Bull trout exposed to these mixtures may not always 

be capable of detecting and avoiding elevated levels of dissolved Zn. Furthermore, avoidance of 

a chemical plume may cause fish to leave refugia or preferred habitats in favor of less suitable or 

less productive habitats. This can make fish more vulnerable to predation and can impair 

foraging success, feeding efficiency, and thereby growth. 

Organic Pollutants

The MSGP identifies the following seven organic pollutants as requiring effluent limit guidelines 

(ELGs) monitoring in stormwater discharges; alpha terpineol, benzoic acid, aniline, pyridine, 

naphthalene, p-cresol, and phenol. There are no benchmarks for organic pollutants in the permit

and therefore no benchmark monitoring is required for organic pollutants. 

As an example of an organic pollutant, we look briefly at polyaromatic hydrocarbons (PAH). 

Heintz et al. (2000) have reported findings that suggest a link between PAH exposure during egg 

incubation and subsequent rates of marine survival and growth for salmonids. The study found 

that statistically significant reductions in marine survival, or increases in delayed rates of 

mortality, resulted from exposure to concentrations as low as 5.4 ppb total PAH. The study also 

found that juvenile salmon surviving embryonic exposure exhibited reduced growth in response 

to doses as low as 18 ppb total PAH. The authors suggest that reductions in marine survival and 

growth are most likely attributable to biochemical impairment of gene and/or enzyme function, 

and that fish populations whose natal habitats are contaminated with PAHs “...can be expected 

to experience the compound effects of mortality during exposure, reduced survivorship 

afterwards, and reduced reproductive output at maturity.” (Heintz et al. 2000)

Although there are likely to be other organic pollutants in stormwater discharges from some 

facilities, we assume PAHs and other pollutants in this category will not cause adverse effects if 

appropriate BMPs are in place, are operational, and are maintained such that the discharges are 

controlled to avoid hazardous exposures to listed species. We also assume the EPA will provide 

the oversight needed as described in their permit to ensure the BMPs are effective and that listed 
2015 MSGP Biological Opinion 59

species are not exposed to hazardous concentrations of organic pollutants in stormwater 

discharges authorized under the MSGP.

Nutrients

Nutrient loadings in the form of nitrogen and phosphorus to waterbodies impact water quality by 

stimulating plant and algae growth which subsequently may result in depletion of dissolved 

oxygen, degradation of habitat, development of harmful algal blooms, impairment of the 

waterbody’s designated use, and impairment of drinking water sources. In general, nitrogen is 

most often the limiting nutrient in estuarine waters, and phosphorus is more often limiting in 

freshwater systems. This means that the growth of phytoplankton is substantially controlled by 

the concentration and availability of phosphorus in freshwater systems. Increased phosphorus 

concentrations can lead to changes in composition of flora and fauna present, increased 

eutrophication of a water body, rates of ecosystem functioning, nutrient uptake, recycling rates of 

the ecosystem, and decomposition rates (WERF, 2010). Determining risk to aquatic life from 

excess nutrients (e.g.,eutrophication) is complicated because nitrogen and phosphorus are 

essential for primary production in aquatic ecosystems, and over-enrichment problems involve 

multiple interrelated variables. The most visible symptom of eutrophication is the excessive 

algal growth that reduces water clarity. Eutrophication can also significantly affect 

phytoplankton community structure resulting in a greater abundance of less desirable taxa such 

as blue-green algae. These changes in the phytoplankton community can have cascading effects 

on higher trophic levels and the eventual transfer of organic carbon from the primary producers 

to less desired species – for example, the replacement of seagrasses with less desirable 

vegetation types (WERF, 2010) 

Suspended Sediments and Turbidity

We anticipate both discharges and certain discharge-associated activities are likely to result in 

elevated levels of suspended sediment and turbidity in the aquatic environment. Several 

facility subsectors are subject to either water quality benchmarks or ELGs (9 subsectors) 

associated with TSS, and one sector (metal mining) has a benchmark for both TSS and 

turbidity (Appendix E of this Opinion). We anticipate that inputs of sediment are likely to 

result in both direct and indirect effects to aquatic biota and aquatic critical habitat. 

Suspended sediment and turbidity may directly affect listed resources, their prey, hosts, or 

habitat, or may provide a future source of exposure from contaminants where these substances 

adsorb to sediments before and/or during discharges. As TSS and turbidity can result in direct 

effects to aquatic biota and can also serve as a substrate for adsorption or sink for other 

pollutants, we have selected it as an example to discuss in more detail in the following section. 

Examples related to fish (in the context of bull trout and other salmonids) and aquatic 

invertebrates are discussed briefly below.

The introduction of sediment in excess of natural amounts can have multiple adverse effects 

on fish and their habitat (Rhodes et al. 1994; Berry et al 2003), related to either suspended 

sediments or sediments that have settled into or onto the substrate. In either case, the effect of 

sediment beyond natural background conditions can be fatal at high levels. Several types of 

effects from sediments are described in Table 4 below. For example, embryo survival and 
2015 MSGP Biological Opinion 60

subsequent fry emergence success have been highly correlated to the percentage of fine 

material within the streambed (Shepard et al. 1984). Low levels of sediment may result in 

sublethal and behavioral effects such as increased activity, stress, and emigration rates; loss or 

reduction of foraging capability; reduced growth and resistance to disease; physical abrasion; 

clogging of gills; and interference with orientation in homing and migration (McLeay et al. 

1987; Newcombe and MacDonald 1991; Barrett et al 1992; Lake and Hinch 1999; Bash et al 

2001; Watts et al. 2003; Vondracek et al. 2003; Berry, Rubinstein, Melzian, and Hill 2003). 

The effects of increased suspended sediments can cause changes in the abundance and/or type 

of food organisms, alterations in fish habitat, and long-term impacts to fish populations 

(Anderson et al. 1996; Reid and Anderson 1999). No threshold has been determined at which 

the addition of fine sediment to a stream is harmless (Suttle et al. 2004). Even at low 

concentrations, fine sediment deposition can decrease growth and survival of juvenile 

salmonids. 

Table 4. Summary of adverse effects to fish resulting from elevated sediment levels.

Sediment Impacts to

Fish (Examples)

Summary of Adverse Effects

Related to Sediment Impacts

Gill trauma Clogs gills which impedes circulation of water over the gills and

interferes with respiration

Other Physiological 

Effects

Increases stress, resulting in decreased immunological competence,

growth and reproductive success

Behavioral Results in avoidance and abandonment of preferred habitat

Feeding efficiency Reduces visibility and impacts feeding rates and prey selection

Prey base Disrupts both habitat for and reproductive success of macroinvertebrates

and other salmonids (bull trout prey) that spawn and rear downstream of the 

Habitat Fills pools, simplifies and reduces suitable habitat

In the absence of detailed local information on population dynamics and habitat use, any increase 

in the proportion of fines in substrates should be considered a risk to the productivity of an 

environment and to the persistence of associated bull trout populations (Rieman and McIntyre 

1993). Specific effects of sediment on fish and their habitat can be put into three classes that 

include (Bash et al. 2001; Newcombe and MacDonald 1991; Waters 1995)

Lethal: Direct mortality to any life stage, reduction in egg-to-fry survival, and loss of 

spawning or rearing habitat. These effects damage the capacity of affected fish to 

produce fish and sustain populations.

Sublethal: Reduction in feeding and growth rates, decrease in habitat quality, reduced 

tolerance to disease and toxicants, respiratory impairment, and physiological stress. 

While not leading to immediate death, such effects and responses may produce 

mortalities and population decline over time.
2015 MSGP Biological Opinion 61

Behavioral: Avoidance and distribution, homing and migration, and foraging and 

predation. Behavioral effects change the activity patterns or alter the kinds of activity 

usually associated with an unperturbed environment. Behavior effects may lead to 

immediate death or population decline or mortality over time.

The following paragraphs provide more detailed discussion of the effects listed in Table 4

related to aquatic species using bull trout and other salmonids as exemplar species/taxa 

grouping. However, these effects are reasonably expected to manifest in other fish and 

invertebrate species (discussed below as prey for salmonids) as well. 

Gill Trauma

High levels of suspended sediment and turbidity can result in direct mortality of fish by 

damaging and clogging gills (Curry and MacNeill 2004). Fish gills are delicate and easily 

damaged by abrasive silt particles (Bash et al. 2001). As sediment begins to accumulate in 

the gill filaments, fish excessively open and close their gills to expunge the silt. If 

irritation continues, mucus is produced to protect the gill surface, which may impede the 

circulation of water over the gills and interfere with fish respiration (Bash et al. 2001). 

Gill flaring or coughing abruptly changes buccal cavity pressure and is a means of clearing 

the buccal cavity of sediment. Gill sediment accumulation may result when fish become 

too fatigued to continue clearing particles via the cough reflex (Servizi and Martens 1991).

Fish are more susceptible to increased suspended sediment concentrations at different times of 

the year or in watersheds with naturally high sediment such as glaciated streams. Fish secrete 

protective mucous to clean the gills (Erman and Ligon 1985). In glaciated systems or during 

winter and spring high flow conditions when sediment concentrations are naturally high, the 

secretion of mucous can keep gills clean of sediment. Protective mucous secretions are 

inadequate during the summer months, when natural sediment levels are low in a stream

system. Consequently, sediment introduction at this time may increase the vulnerability of fish 

to stress and disease (Bash et al. 2001).

Other Physiological Effects

Sublethal levels of suspended sediment may cause undue physiological stress on fish, which 

may reduce the ability of the fish to perform vital functions (Cederholm and Reid 1987). Stress 

is defined as a condition perceived by an organism that threatens a biological function of the 

organism, and a set of physiological and behavioral responses is mounted to counteract the 

condition (Overli 2001, p. 7). A stressor is any anthropogenic or natural environmental change 

severe enough to require a physiological response on the part of a fish, population, or ecosystem 

(Anderson et al. 1996; Jacobson et al. 2003; EPA 2001). At the individual level, stress may 

affect physiological systems, reduce growth, increase disease, and reduce the individual’s ability 

to tolerate additional stress (Anderson et al. 1996; Bash et al. 2001). At the population level, the 

effects of stress may include reduced spawning success, increased larval mortality, and reduced 
2015 MSGP Biological Opinion 62

recruitment to succeeding life stages and, therefore, overall population declines (Bash et al. 

2001).

Upon encountering a stressor, the fish responds through a series of chemical releases in its 

body. These primary chemical and hormonal releases include catecholamine (e.g. epinephrine, 

norepinehprine) in the circulatory system, corticosteroids (e.g. cortisol) from the interrenal 

tissue, and hypothalamic activation of the pituitary gland (Barton 2002; Davis 2006; Gregory 

and Wood 1999; Schreck et al. 2001). Primary chemical releases result in secondary releases or 

changes in plasma, glucose, tissue ion, metabolite levels, and hematological features. These 

secondary responses relate to physiological adjustments in metabolism, respiration, immune and 

cellular function (Barton 2002; Haukenes and Buck 2006; Mazeaud et al. 1977). After 

secondary responses, continued stress results in tertiary stress responses that affect wholeanimal performance such as changes in growth, condition, resistance to disease, metabolic 

scope for activity, behavior, and ultimately survival (Barton 2002; Pickering et al. 1982; Portz 

et al. 2006).

Stress in a fish occurs when the homeostatic or stabilizing process in the organism exceed 

the capability of the organism to compensate for the biotic or abiotic challenge (Anderson et 

al. 1996). The response to a stressor is an adaptive mechanism that allows the fish to cope 

with the real or perceived stressor in order to maintain its normal or homeostatic state 

(Barton 2002). Acclimation to a stressor can occur if compensatory physiological responses 

by the fish are able to re-establish a satisfactory relationship between the changed 

environment and the organism (Anderson et al. 1996). The ability of an individual fish to 

acclimate or tolerate the stress will depend on the severity of the stress and the physiological 

limits of the organism (Anderson et al. 1996). In a natural system, fish are exposed to 

multiple chemical and physical stressors that can combine to cause adverse effects (Berry et 

al. 2003). The chemical releases from each stressor results in a cumulative or additive 

response (Barton et al.1986; Cobleigh 2003; Milston et al. 2006; EPA 2001).

Stress in fish results in extra cost and energy demands. Elevated oxygen consumption and 

increased metabolic rate result from the reallocation of energy to cope with the stress (Barton 

and Schreck 1987; Contreras-Sanchez et al. 1998; McCormick et al. 1998). An approximate 

25 percent increase in metabolic cost, over standard metabolism requirements, is needed to 

compensate for a perceived stress (Barton and Schreck 1987; Davis 2006). Stressed fish 

would thus have less energy available for other life functions such as seawater adaptation, 

disease resistance, reproduction, or swimming stamina (Barton and Schreck 1987; ContrerasSanchez et al. 1998).

Tolerance to suspended sediment may be the net result of a combination of physical and 

physiological factors related to oxygen availability and uptake by fish (Servizi and 

Martens 1991). The energy needed to perform repeated coughing (see Gill trauma section) 

increases metabolic oxygen demand. Metabolic oxygen demand is related to water 

temperature. As temperatures increase, so does metabolic oxygen demand, but 

concentrations of oxygen available in the water decreases. Therefore, a fish’s tolerance to 

suspended sediment may be primarily related to the capacity of the fish to perform work 

associated with the cough reflex. However, as sediment increases, fish have less 
2015 MSGP Biological Opinion 63

capability to do work, and therefore less tolerance for suspended sediment (Servizi and 

Martens 1991).

Once exposed to a stressor, the primary chemical releases can take one-half to twenty-four hours 

to peak (Barton 2002; Quigley and Hinch 2006; Schreck 1981). Recovery or return of the 

primary chemical release to normal or resting levels can take two hours to two weeks (Mazeaud 

et al. 1977; Schreck et al. 2001). In a study of handling stress, chemical release of cortisol 

peaked at two hours and returned to normal in four hours. However, complete recovery took 2 

weeks (Pickering et al. 1982). Fish exposed to two or more stresses require longer recovery 

times than fish exposed only to one stressor indicating the cumulative effects of stress 

(Sigismondi and Weber 1988).

Redding el al. (1987) observed higher mortality in young steelhead trout exposed to a 

combination of suspended sediment (2500 mg/L) and a bacteria pathogen, than when exposed to 

the bacteria alone. Physiological stress in fishes may decrease immunological competence, 

growth, and reproductive success (Bash et al. 2001).

Behavioral effects

Increased turbidity and suspended sediment may result in behavior changes in salmonids. Such 

changes are often the first effects evoked from increased levels of turbidity and suspended 

sediment (Anderson et al. 1996). Behavioral changes include avoidance of habitat, reduction in 

feeding, increased activity, redistribution and migration to other habitats and locations, 

disruption of territoriality, and altered homing (Anderson et al. 1996; Bash et al. 2001; Suttle et 

al. 2004). Many behavioral effects result from changes in stream habitat (see Habitat effects 

section). As suspended sediment concentration increases, habitat may be lost which results in 

abandonment and avoidance of preferred habitat. Stream reach emigration can result in a 

bioenergetic demand that may affect the growth or reproductive success of the individual fish 

(Bash et al. 2001). Pulses of sediment result in downstream migration of fish, which disrupts 

social structures, causes downstream displacement of other fish and increases intraspecific 

aggression (Bash et al. 2001; McLeay et al. 1987; Suttle et al. 2004). Loss of territoriality and 

the breakdown of social structure can lead to secondary effects of decreased growth and feeding 

rates, which may lead to mortality (Bash et al. 2001; Berg and Northcote 1985).

Downstream migration by bull trout provides access to more prey, better protection from

avian and terrestrial predators, and alleviates potential intraspecific competition or 

cannibalism in rearing areas (MBTSG 1998). Benefits of migration from tributary rearing 

areas to larger rivers or estuaries may be increased growth potential. Increased sedimentation 

may result in premature or early migration of both juveniles and adults or avoidance of 

habitat and migration of nonmigratory resident bull trout. High turbidity may delay 

migration back to spawning sites, although turbidity alone does not seem to affect homing. 

Delays in spawning migration and associated energy expenditure may reduce spawning 

success and therefore population size (Bash et al. 2001). It is reasonable to assume that these 

effects would apply to other migratory species as well.
2015 MSGP Biological Opinion 64

Feeding Efficiency

Increased turbidity and suspended sediment can affect a number of factors related to feeding in 

salmonids, including feeding rates, reaction distance, prey selection, and prey abundance 

(Barrett et al. 1992; Bash et al. 2001; Henley et al. 2000). Changes in feeding behavior are 

primarily related to the reduction in visibility that occurs in turbid water. Effects on feeding 

ability are important as salmonids must meet energy demands to compete with other fishes for 

resources and to avoid predators. Reduced feeding efficiency would result in lower growth and 

fitness of bull trout and other salmonids (Barrett et al. 1992; Sweka and Hartman 2001).

Distance of prey capture and prey capture success both were found to decrease significantly 

when turbidity was increased (Berg and Northcote 1985; Sweka and Hartman 2001; Zamor 

and Grossman 2007). Waters (1995) states that loss of visual capability, leading to reduced 

feeding, is one of the major sublethal effects of high suspended sediment. Increases in 

turbidity were reported to decrease reactive distance and the percentage of prey captured 

(Bash et al. 2001; Klein 2003; Sweka and Hartman 2001). At 0 Nephelometric Turbidity 

Units (NTUs), 100 percent of the prey items were consumed; at 10 NTUs, fish frequently 

were unable to capture prey species; at 60 NTUs, only 35 percent of the prey items were 

captured. At 20 to 60 NTUs, significant delay in the response of fish to prey was observed 

(Bash et al. 2001). Loss of visual capability and capture of prey leads to depressed growth 

and reproductive capability.

To compensate for reduced encounter rates with prey under turbid conditions, prey density 

must increase substantially or salmonids must increase their active searches for prey (Sweka 

and Hartman 2001). Such an increase in activity and feeding rates under turbid conditions 

reduces net energy gain from each prey item consumed (Sweka and Hartman 2001).

Sigler et al. (1984) found that a reduction in growth occurred in steelhead and coho salmon 

when turbidity was as little as 25 NTUs. The slower growth was presumed to be from a 

reduced ability to feed; however, more complex mechanisms such as the quality of light may 

also affect feeding success rates. Redding et al. (1987) found that suspended sediment may 

inhibit normal feeding activity, as a result of a loss of visual ability or as an indirect 

consequence of increased stress.

Prey Base25

Sedimentation can have an indirect effect on fish populations through impacts or alterations to 

the macroinvertebrate communities or population (Anderson et al. 1996). Increased turbidity and 

suspended sediment can reduce primary productivity by decreasing light intensity and periphytic 

 

25 The following analysis applies both to the invertebrates in the context of the prey base for 

other species (including listed species such as salmonids and other fish), but is also applicable 

to some of the listed invertebrates addressed in this Opinion where appropriate. 
2015 MSGP Biological Opinion 65

(attached) algal and other plant communities (Anderson et al. 1996; Henley et al. 2000; Suren 

and Jowett 2001). This results in decreased macroinvertebrates that graze on the periphyton.

Sedimentation also alters the habitat for macroinvertebrates, changing the species density, 

diversity and structure of the area (Anderson et al. 1996; Reid and Anderson 1999; Shaw and 

Richardson 2001; Waters 1995). Certain groups of macroinvertebrates are favored by salmonids 

as food items. These include mayflies, caddisflies, and stoneflies. These species prefer large 

substrate particles in riffles and are negatively affected by fine sediment (Everest et al. 1987; 

Waters 1995). Increased sediment can affect macroinvertebrate habitat by filling of interstitial 

space and rendering attachment sites unsuitable. This may cause invertebrates to seek more 

favorable habitat (Rosenberg and Snow 1975). With increasing fine sediment, invertebrate 

composition and density changes from available, preferred species (i.e., mayflies, caddisflies, 

and stoneflies) to non-preferred, more unavailable species (i.e., aquatic worms and other 

burrowing species) (Henley et al. 2000; Reid and Anderson 1999; Shaw and Richardson 2001; 

Suren and Jowett 2001; Suttle et al. 2004). The degree to which substrate particles are 

surrounded by fine material was found to have a strong correlation with macroinvertebrate 

abundance and composition (Birtwell 1999). At higher levels of embeddednes, insect 

abundance can decline, especially for riffle-inhabiting taxa; one study in central Idaho, for 

example, noted an approximate 50 percent decline of insect abundance when embeddness was 

increased above natural conditions (Bjornn et al 1974 and 1977, as reported in Waters 1995). 

Increased turbidity and suspended solids can affect macroinvertebrates in multiple ways 

through increased invertebrate drift, respiratory problems, and feeding impacts (Berry et al. 

2003; Cederholm and Reid 1987; Shaw and Richardson 2001). For example, the effect of 

turbidity on light transmission has been well documented and results in increased invertebrate 

drift (Birtwell 1999; Waters 1995). This may be a behavioral response associated with the 

night-active diel drift patterns of macroinvertebrates. Some effects related to insect drift may 

result in impacts to habitat quality, where a temporary reduction in prey items may affect 

invertivores within a given reach of stream or other water body. However, drift can also help to 

improve prey availability in a previously disturbed stream. Invertebrate drift is an important 

mechanism in the repopulation, recolonization, or recovery of a macroinvertebrate community 

after a localized disturbance (Anderson et al. 1996; Reid and Anderson 1999). While increased 

turbidity results in increased macroinvertebrate drift, it is thought that the overall invertebrate 

populations would not fall below the point of severe depletion (Waters 1995).

Increased suspended sediment can affect macroinvertebrates by abrasion of respiratory 

surface and interference with food uptake for filter-feeders (Anderson et al. 1996; Berry et al. 

2003; Birtwell 1999; Shaw and Richardson 2001; Suren and Jowett 2001). Increased 

suspended sediment levels tend to clog feeding structures and reduce feeding efficiencies, 

which results in reduced growth rates, increased stress, or death of the invertebrates 

(Newcombe and MacDonald 1991). Invertebrates living in the substrate are also subject to 

scouring or abrasion, which can damage respiratory organs (Bash et al. 2001).
2015 MSGP Biological Opinion 66

Habitat Effects

Increases in sediment can alter fish habitat or the utilization of habitats by fish (Anderson et al. 

1996). The physical implications of sediment in streams include changes in water quality, 

degradation of spawning and rearing habitat, simplification and damage to habitat structure and 

complexity, loss of habitat, and decreased connectivity between habitats (Anderson et al. 1996; 

Bash et al. 2001). Biological implications of this habitat damage include underutilization of 

stream habitat, abandonment of traditional spawning habitat, displacement of fish from their 

preferred habitat, and avoidance of habitat (Newcombe and Jensen 1996). 

As sediment enters a stream it is transported downstream under normal fluvial processes and 

deposited in areas of low shear stress (MacDonald and Ritland 1989). These areas are usually 

behind obstructions, near banks (shallow water) or within interstitial spaces. This episodic filling 

of successive storage compartments continues in a cascading fashion downstream until the flow 

drops below the threshold required for movement or all pools have reached their storage 

capacities (MacDonald and Ritland 1989). As sediment load increases, the stream compensates 

by geomorphologic changes in increased slope, increased channel width, decreased depths, and 

decreased flows (Castro and Reckendorf 1995). These processes contribute to increased erosion 

and sediment deposition that further degrade salmonid habitat.

Loss of acceptable habitat and refugia, as well as decreased connectivity between habitats, 

reduces the carrying capacity of streams for salmonids (Bash et al. 2001). This loss of habitat or 

exclusion of fish from their habitat, if timed inappropriately, could impact a fish population if 

the habitat within the affected stream reach is critical to the population during the period of the 

sediment release (Anderson et al. 1996; Reid and Anderson 1999). For example, if summer 

pool habitat used by adults as holding habitat prior to spawning is a limiting factor within a 

stream, increased sediment and reduced pool habitat during the summer can decrease the 

carrying capacity of the stream reach and decrease the fish population. In systems lacking 

adequate connectivity of habitats, fish may travel longer distances or use less desirable habitats, 

increasing biological demands and reducing their fitness.

The addition of fine sediment (less than 6.4 mm) to natural streams during summer decreased 

abundance of juvenile Chinook salmon in almost direct proportion to the amount of pool 

volume lost to fine sediment (Bjornn et al. 1977). Similarly, the inverse relationship between 

fine sediment and densities of rearing Chinook salmon indicates the importance of winter 

habitat and high sediment loads (Bjornn et al. 1977). As fine sediments fill the interstitial 

spaces between the cobble substrate, juvenile Chinook salmon were forced to leave preferred 

habitat and to utilize cover that may be more susceptible to ice scouring, predation, and 

decreased food availability (Hillman et al. 1987). Deposition of sediment on substrate may 

lower winter carrying capacity for bull trout (Shepard et al. 1984). Food production in the form

of aquatic invertebrates may also be reduced.

For example, bull trout have more specific habitat requirements and many other salmonids 

species, and these requirements appear to influence their distribution and abundance (Rieman 

and McIntyre 1993). All life history stages are associated with complex forms of cover 

including large woody debris, undercut banks, boulders, and pools. Other habitat characteristics 
2015 MSGP Biological Opinion 67

important to bull trout include channel and hydrologic stability, substrate composition, 

temperature, and the presence of migration corridors (Rieman and McIntyre 1993).

Juvenile bull trout densities are highly influenced by substrate composition (MBTSG 1998; 

Rieman and McIntyre 1993; Shepard et al. 1984). During the summer, juvenile bull trout hold 

positions close to the stream bottom and often seek cover within the substrate itself. When 

streambed substrate contains more than 30 percent fine materials, juvenile bull trout densities 

drop off sharply (Shepard et al. 1984). Any loss of interstitial space or streambed complexity 

through the deposition of sediment would result in a loss of summer and winter habitats 

(MBTSG 1998). The reduction of rearing habitat will ultimately reduce the potential number of 

recruited juveniles and therefore reducing population numbers (Shepard et al. 1984). In fact, 

Johnston et al. (2007) found that density-dependent survival during the earliest of the juvenile 

stages (between egg and age-1) regulated recruitment of adult bull trout in the population.

Although an avoidance response by fish to increased sediment may be an initial 

adaptive survival strategy, displacement from cover could be detrimental. It is possible 

that the consequences of fish moving from preferred habitat, to avoid increasing levels 

of suspended sediment, may not be beneficial if displacement is to sub-optimal habitat, 

because they may be stressed and more vulnerable to predation (Birtwell 1999).

In addition to altering streambed composition, anthropogenic input of sediment into a stream can 

change channel hydrology and geometry (Owens et al. 2005). Sediment release can reduce the 

depth of pools and riffle areas (Anderson et al. 1996). This can reduce available fish habitat, 

decrease fish holding capacity, and decrease fish populations (Anderson et al. 1996).

Examples of Other Effects

Spawning, Redds, Eggs, and Alevins. The effects of suspended sediment, deposited in a redd 

and potentially reducing water flow and smothering eggs or alevins or impeding fry emergence, 

are related to sediment particle sizes of the spawning habitat (Bjornn and Reiser 1991). Sediment 

particle size determines the pore openings in the redd gravel. With small pore openings, more 

suspended sediments are deposited and water flow is reduced compared to large pore openings.

Survival of eggs is dependent on a continuous supply of well-oxygenated water through the 

streambed gravels (Anderson et al. 1996; Cederholm and Reid 1987). Eggs and alevins are 

generally more susceptible to stress by suspended solids than are adults. Accelerated 

sedimentation can reduce the flow of water and, therefore, oxygen to eggs and alevins. This can 

decrease egg survival, decrease fry emergence rates (Bash et al. 2001; Cederholm and Reid 

1987; Chapman 1988), delay development of alevins (Everest et al. 1987), reduce growth and 

cause premature hatching and emergence (Birtwell 1999). Fry delayed in their emergence are 

also less able to compete for environmental resources than fish that have undergone normal 

development and emergence (intra- or interspecific competition) (Everest et al. 1987). 

Sedimentation fills the interstitial spaces and can prevent alevins from emerging from the gravel 

(Anderson et al. 1996; Suttle et al. 2004).
2015 MSGP Biological Opinion 68

Several studies have documented that fine sediment can reduce the reproductive success of 

salmonids. Natural egg-to-fry survival of coho salmon, sockeye and kokanee has been 

measured at 23 percent, 23 percent and 12 percent, respectively (Slaney et al. 1977). Substrates 

containing 20 percent fines can reduce emergence success by 30-40 percent (MacDonald et al. 

1991). A decrease of 30 percent in mean egg-to-fry survival can be expected to reduce 

salmonid fry production to extremely low levels (Slaney et al. 1977).

Source for other Pollutants. Additionally, suspended sediment may serve as a pathway for 

exposure to other contaminants. Some pollutants and contaminants of concern have a strong 

affinity for suspended solids and the particulate-phase or fraction of treated and untreated 

runoff (Grant et al. 2003; Wong et al. 2000). As a result, a large fraction of the toxic 

(inorganic and non-polar organic) contaminant load in treated and untreated stormwater is in 

particulate form, either sorbed onto, or complexed with solids (Fan et al. 2001; Grant et al. 

2003; Marsalek et al. 1999; Muthukrishnan and Selvakumar 2006; Wong et al. 2000). The 

heavy metals, especially Cu, chromium (Cr), lead (Pb), and nickel (Ni) are closely associated 

with the particulate fraction (Grant et al. 2003; Wong et al. 2000); and Zn and cadmium (Cd) 

are to a somewhat lesser extent. PAHs, oils and petroleum hydrocarbons generally, and other 

non-polar organic contaminants are also closely associated with the particulate-phase or 

fraction. We anticipate that most of the PAH load in treated and untreated stormwater would 

be bound to solids. 

Particle size distribution exerts a strong influence on contaminant-particulate dynamics and 

association. Heavy metals, PAHs, and other non-polar organic contaminants are generally bound

in greatest concentration to the smallest of particles and colloids. For non-polar organic 

contaminants, particulate organic matter content also exerts a strong influence, but total 

particulate surface area is probably of greater significance. The smallest particles have the 

greatest “surface area to volume ratio,” and therefore provide a comparatively larger total surface 

area to which contaminants may bind, sorb, and complex (Fan et al. 2001; Herngren et al. 2005; 

John and Leventhal 1995; Pettersson 2002). 

Ambient conditions determine whether contaminated sediments will act as continuing sources or 

sinks for toxic metals and non-polar organic contaminants. Because ambient conditions are 

dynamic and can change over time and space, equilibrium levels of metals and organic 

contaminants in sediments, in interstitial/pore water, and the water column, are also variable. As 

noted in John and Leventhal (1995), “[b]ioavailability is a complex function of many factors ... 

Many of these factors vary seasonally and temporally, and most factors are interrelated”. 

Changes in ambient water and sediment chemistry, including redox state, dissolved oxygen 

concentration, pH, temperature, and buffering capacity/carbonate concentration/hardness, can 

release sequestered contamination to interstitial pore water or the water column (Chen et al.1996, 

p. ab; Marsalek et al. 2002; Muthukrishnan and Selvakumar 2006; Wong et al.2000). Bostick et 

al. (1998), Chen et al. (1996), and John and Leventhal (1995) each describe changes in Zn 

partitioning and bioavailability in response to altered chemical environments. Bostick et al. 

(1998) found that changes in redox state within a contaminated wetland influenced the size of 

fractions complexed to sorbents with varying properties. Chen et al. (1996) found that 74 

percent of Zn from bottom sediments of urban reservoirs was in easily remobilized fractions. 
2015 MSGP Biological Opinion 69

John and Leventhal (1995) found that contaminated sediments can release significant amounts of 

Zn to the dissolved phase when oxidized or exposed to acidic conditions.

In fluvial environments, hydrology and fine and coarse sediment dynamics also exert a strong 

influence on patterns of sediment contamination. Rhoads and Cahill (1999) describe variation in 

levels of sediment metal contamination reflecting distance from the source (outfalls), reach-scale 

variation in geomorphic conditions, and the degree of bed material sorting. Foster and 

Charlesworth (1996) and Marsalek et al. (2002) also emphasize the role of sediment deposition, 

accumulation, and remobilization. Baun et al. (2003) and Chen et al. (1996) suggest that 

hydraulic resuspension of contaminated sediments, and sporadic disturbance and release of 

contaminated interstitial pore water, influences bioavailability. Ellis (2000) has argued that 

understanding the “...probability of biotic uptake and ecosystem response ... requires 

incorporation of water quality effects with impacts on sediment and pore waters as well as 

habitat impairments resulting from flow hydraulics”.

Heavy metals do not degrade in the environment (Glenn et al. 2002; Muthukrishnan and 

Selvakumar 2006), and organic contaminants easily persist for durations that exceed the life 

spans of individual fish or multiple generations of fish (Heintz et al. 2000). Chronic effects to 

individuals stem from repeated exposures over time, through multiple exposure pathways, and 

from multiple stressors and combinations of stressors (Burton et al. 2000; Ellis 2000; Heintz et 

al. 2000). Ellis (2000) has argued that sediment-mediated exposures and effects have not yet 

been given adequate attention, and furthermore that “...procedures for the identification of 

chronic, sub-lethal no effects limits are still to be achieved.” Emphasizing the tendency for 

accumulation in sediments, both Hodson (1988) and Pettersson (2002) have argued that loads

and not simply water concentrations should be a focus for management where discharges of 

metals and persistent organic pollutants are concerned.

Summary of Effects to Listed Resources from Contaminants

In the absence of mitigation measures, the types of expected effects to individuals of listed 

species from the implementation of the permit would likely range from severe acute effects 

(lethal/sublethal), to behavioral and/or indirect effects (e.g., with effects to prey base or host 

species, or exposure to contaminants that are stored within the sediments but are resuspended 

and made available at a later time). At the scale of the Action Area, it is difficult to definitively 

determine the degree of likely effects and species responses related to chemical and sediment 

releases and bioavailability of contaminants stored in the sediments over the life of the permit. It 

is also difficult to predict the level of exposure and response to listed resources based on the 

frequency and duration of releases as a wide variety of flow and habitat conditions will 

complicate a site- or species-level analysis. Furthermore, it is difficult to separate the effects of 

individual discharges covered under the MSGP from other non-point sources of stormwater and 

inputs of contaminants and sediments into the receiving waters in the Action Area. The level of 

effects from exposure to and response of listed species is expected to be highly variable. We 

anticipate the magnitude of effects will vary among discharge events, watersheds, and species, 

and will be dependent on the conditions of the receiving waters, amount of contaminants and 

sediments released, and sensitivity of the life stages of listed species during exposure. 
2015 MSGP Biological Opinion 70

It is reasonable to assume the pollutants covered under the MSGP would, at minimum, contribute 

to the effect of the stressors affecting listed species during and after precipitation events. It is 

also reasonable to assume that contaminant and sediment-related effects to listed resources from 

the proposed Action would be more likely to occur and/or more pronounced where (1) multiple 

dischargers to a receiving waterbody occur in close proximity to each other, and/or (2) one or 

more dischargers release contaminants in concentrations that are not protective of listed species. 

We anticipate that the use of benchmarks and ELGs as guidelines may address some of the 

effects to listed species, although their use cannot be considered reliable for this purpose as the 

benchmarks and ELGs have not been previously undergone section 7 consultation for listed 

species or critical habitat. 

We anticipate the controls and other measures required under the permit are likely to reduce the 

amount of sediments and associated contaminants released from facilities covered under the 

MSGP. However, we do not anticipate that facilities covered under the permit will necessarily 

be able to completely avoid releases of sediments that would result in appreciable effects to 

listed species. In fact, past monitoring efforts have demonstrated that some facilities have 

exceeded benchmarks for aluminum, biological oxygen demand, chemical oxygen demand, 

copper, iron, lead, magnesium, nitrate + nitrite, pH, TSS, zinc during one or more sampling 

events, sometimes by orders of magnitude. The use of corrective measures (as needed) are

intended to prevent or reduce similar exceedences after the initial exceedence has occurred; 

however, it is reasonable to assume there will be adverse effects to listed species where exposure 

occurs (1) during the discharge where the exceedence is initially documented and potentially 

until the corrective measures are implemented; (2) during and after discharges where no 

monitoring occurs and thus stressors are not observed or recognized; and/or (3) during or after 

discharges where contaminants contained within the sediments are resuspended at a later time.

For critical habitat, we anticipate that the stressors described above would likely contribute to 

degradation of the overall conditions of critical habitat for listed aquatic species through 

incremental effects to the prey base and water quality components of critical habitat (as 

applicable). 

Physical Effects

In addition to effects from chemicals and other pollutants in the discharges, the proposed action 

is also expected to affect aquatic habitats of the receiving waters and the organisms they support 

through physical effects of the discharges. Physical effects may occur from the impacts of flow 

and other characteristics of the discharge waters as they enter the receiving waters such as the 

timing of releases of stormwater discharges or flow volumes. For example, erosion may occur as 

water passes over terrestrial portions of the site into stormwater controls, or through the erosion 

of shorelines or banks of receiving waters, particularly where controls or other measures have 

not been implemented to reduce or distribute energy from the inflows of the discharge into the 

receiving water. Other physical effects related to the characteristics and timing of the releases of 

stormwater discharges into receiving waters may also occur, such as differences in flow volumes 

related to the receiving waters during or after precipitation events. (Some of the potential 

consequences of erosive effects were described previously under Habitat Effects.)
2015 MSGP Biological Opinion 71

Another physical effect that is expected to result from some of the covered discharges is related 

to the differences in water temperatures between the discharges and the receiving waters. The 

temperature of the discharge waters may be of particular concern where: (1) the discharge water 

temperature is substantially different that the receiving water temperature and comprises a large 

proportion of the flow of the receiving water, and (2) the discharge water temperature is much 

warmer or much cooler than the requirements of listed species that reside in or migrate through 

the receiving water. Some aquatic species require optimal temperature ranges for survival, 

growth, and/or reproduction, and inputs of elevated or low temperatures (depending on the 

optimal range for a given species) may affect the species directly or degrade important critical 

habitat PBFs. For example, certain species are sensitive to water temperatures, with optimal or 

required temperatures specified for one or more life stages. Examples include, but are not 

limited to, the following species: 

• Apache trout (<25°C; USFWS 2009)

• Greenback cutthroat trout (5-8° C, during spawning; USFWS 1998)

• Gila trout (<25°C; USFWS 2003)

• Bull trout (<9°C, spawning; <15°C overall; USFWS 2005)

• Three forks springsnail26 (near 22°C)

• San Bernadino springsnail27 (14 to 22°C)

• Banbury springs lanx (15 to 16°C; USFWS 1995)

The volume of discharge flows compared to that of the receiving waters may also affect listed 

species and critical habitat. In some cases, flows from stormwater discharges may augment 

lower flows in the receiving waters, increasing the volume of water in the receiving body, which 

may have beneficial or negative impacts to biota, depending on their life history and habitat 

requirements. Where discharge flows constitute a large proportion of the receiving water flows, 

beneficial effects may be tempered (and negative effects exacerbated) by the reduced 

effectiveness of dilution and assimilative capacity of the receiving waters to address 

contaminants in the discharge. 

Riparian/Upland Effects

We anticipate that riparian and terrestrial effects would be most likely to occur as a result of 

discharge-related activities, where construction or modification of upland-sited controls or other 

features would directly or indirectly affect listed species and critical habitat if either is present in 

or near the activity area. The installation and use of controls are encouraged for use as part of 

the SWPPP to avoid or reduce introduction of contaminants into the aquatic and riparian 

environments, although unintentional impacts to terrestrial species may also occur where these 

activities overlap with listed resources. Under these conditions, we anticipate that a variety of 

effects could occur, depending on the nature of the activities conducted, types of equipment 

used, life history stage and behavior(s) of listed species present, and other site-specific 

 

26 Critical habitat designation (77 FR 23060 23092) 27 Critical habitat designation (77 FR 23060 23092)
2015 MSGP Biological Opinion 72

considerations. Some stressors related to discharge-related activities may be temporary (as in the 

case of brief noise or disturbance during construction) or longer-term (e.g., removal of habitat 

features). It is possible that pollutants from the discharges could affect listed species and 

designated critical habitats in the terrestrial environment (including riparian areas), such as 

through the creation of an attractive nuisance (e.g., infiltration pond holding water and pollutants 

may temporarily attract birds, amphibians, and other organisms) under certain conditions. The 

mechanisms by which stormwater pollutants affect listed species are described in previous 

sections and will not be repeated here. 

The following paragraphs will describe the types of effects that would most likely be expected 

from discharge-related activities and generalizations on the pathways of effect and likely 

responses from listed resources. Mechanisms in the permit structure that are expected to avoid 

or reduce the potential for adverse effects are described in a subsequent section of this Opinion 

and will not be addressed in this section.

The construction of new controls and modification of existing controls have the potential to 

result in a variety of effects. Construction-related effects to individuals may result from use of 

heavy equipment and vehicles, human presence and activity at the site, and temporary or 

permanent changes to habitat features that are used by listed species, their prey, hosts, 

pollinators, other species they depend upon. We anticipate that in some cases where overlap of 

listed species and/or critical habitat exists, the likely effects would include one or more of the 

following: potential injury or death of individuals, failed nesting or breeding attempts, and

significant disruption of normal behavior and/or use of the site during or after the construction or 

implementation of the discharge-related activities. In the absence of sufficient measures to 

address these impacts, the most acute direct effects that would be anticipated include direct 

injury or death of individuals of listed species due to: (1) interactions with heavy equipment or 

vehicles (e.g., crushing, collisions); (2) removal of vegetation or other habitat features are 

providing shelter for listed species (e.g., nests with eggs or young); or (3) temporary or 

permanent abandonment of eggs, nests, or juveniles leading to loss of offspring. These activities 

would likely be of most concern where individuals are attached (e.g., plant), or are in life stages 

that are sessile, less mobile, and/or cryptic (e.g., eggs, altricial young 28, hibernating or estivating 

individuals, etc.). Other effects include short-term or long-term disturbance or displacement of 

individuals of listed species due to human activities, and may result in abandonment of important 

foraging, nesting, roosting, or sheltering habitat that is necessary for survival, growth, and 

motionless reproduction.

Injurious and disturbance effects associated with human activities have been observed for some 

species, and we would anticipate similar effects to occur during activities associated with 

construction or modification of controls or other discharge-associated activities if sufficient 

BMPs are not followed to address these concerns. For example, the western snowy plover 

Recovery Plan lists a number of sources reporting loss or destruction of western snowy plover 

and piping plover nests, eggs, and chicks and disturbance to chicks and adults from a variety of 

anthropogenic sources, including pedestrians and motor vehicles (USFWS 2007). Both chicks 

 

28 Altricial young refers generally to offspring that require significant parental attention after hatching or birth, due 

to an inability or limited ability to move, forage, or otherwise survive without aid. 
2015 MSGP Biological Opinion 73

and adults have been observed using footprints and tire tracks for loafing (Powell and Collier 

1994 and U.S. District Court of Massachusetts 1998 in USFWS 2007); deeper tire tracks may be 

difficult for very young chicks in particular to escape, increasing their risk of accidental 

crushing, although both adults and juveniles may be crushed in tire tracks when vehicles reuse 

them. While some individuals may evade such effects by leaving the area if they are able, others 

may respond by remaining motionless as a natural defense mechanism (e.g., piping plovers as 

described in USFWS 2007). Where vehicles, heavy equipment, and/or workers’ activities are 

used or occur in the vicinity of nesting, rearing, foraging, or other important habitat for listed 

species and their critical habitat during the breeding season, we would anticipate similar effects 

to these listed resources in the absence of protective measures to avoid these effects.

Other effects related to construction and disturbance have also been reported in other actions. 

For example, construction activities can result in an attractive nuisance to native or non-native 

predators through generation of trash or debris disposal. Many listed species are particularly 

susceptible to predation or competition, and activities that attract native or non-native predators 

(e.g., rats, corvids, raccoons, etc.) can result in injury or mortality to individuals (e.g., predation 

of California red legged frogs by raccoons; USFWS 2002). Where these activities overlap with 

listed species that are unlikely to evade predators, we anticipate they would be similarly affected.

Summary of Stressors

The types of activities covered by the proposed action are generally expected to result in a 

number of effects to listed species and their critical habitat. In the absence of effective BMPs 

and control measures, we anticipate that contaminants and other pollutants in the facilities’ 

discharges, physical effects from the discharges related to flow characteristics, and disturbance 

and injurious effects from discharge-associated activities will affect listed resources where 

overlap occurs. However, the MSGP requires the use of controls and other measures to address 

the effects of discharges covered under the permit. The assumptions and uncertainties related to 

the implementation of the permit are discussed in the next section.

Section 2: Review of Permit Structure

In this evaluation, we specifically ask whether or to what degree EPA has structured its proposed 

permits so that the agency (1) understands the scope of its action; (2) reliably estimates the 

physical, chemical, or biotic stressors that are likely to be produced as a direct or indirect result 

of their action; (3) reliably estimates the exposure of ESA-listed resources (species and 

designated critical habitat) to these stressors; (4) collects and monitors information on authorized 

activities throughout the life of the permit; (5) evaluates the information to assess how its actions 

have affected listed resources; (6) monitors and enforces permit compliance; and (7) modifies its 

action if new information (including inadequate protection for species or low levels of 

compliance) becomes available. Where applicable and appropriate, we will use examples from 

previous permit cycles, relevant literature regarding species effects and/or specific contaminants, 

and reasonable worst-case scenarios (e.g., stream reaches with numerous aggregate discharges). 

In the following section, we also include a discussion of important provisions in the 2015 MSGP 

that are expected to reduce, and, in many cases, avoid or minimize the effects of the stressors 

described in Section 1.
2015 MSGP Biological Opinion 74

1. Scope

In this section, we ask whether EPA is aware of the scope of its Action. As described earlier, the 

scope of the Action includes all aspects of EPA’s issuance and implementation of the MSGP, 

including the monitoring of discharges authorized by the permits and enforcement of the permits. 

To reliably estimate the probable individual or accumulative effects to ESA listed species or 

designated critical habitat, the EPA would need to know or reliably estimate the probable 

number of facilities that it would authorize to discharge under the MSGP. Therefore, we also ask 

whether EPA has structured their permit accordingly. 

EPA requires an NOI for all facilities seeking coverage under the permit. The NOI must be 

submitted electronically no later than 90 days after issuance of the permit for existing facilities 

and 30 days prior to initiating discharges for new facilities or discharges. The NOI requires the 

submission of location information, including facility location, number and location of outfalls, 

receiving waters, and other site-specific information. The NOI also requires information on the 

types of contaminants expected in the discharges and controls and other measures that will be 

implemented to address these contaminants and other effects from the discharge and dischargerelated activities. The EPA used NOI and monitoring data from the 2008 MSGP to estimate the 

number of discharges that would be authorized under the 2015 MSGP. Based on this 

information, EPA was also able to estimate the location and relative timing of discharges (related 

to stormwater events). 

While EPA is able to estimate the approximate number of anticipated new dischargers/facilities 

over the life of the 2015 permit, they are unable to determine precisely where such new 

discharges will occur. However, facilities can only seek coverage under the MSGP in locations 

where EPA retains permitting jurisdiction. Thus, at a coarse scale, all facilities will be limited to 

these finite geographical areas as specified in the Description of the Action section of this 

Opinion, and thus EPA can reliably estimate the relative geographic limits of the locations of the 

facilities. It is reasonable to assume that the distribution of existing facilities is representative of 

the likely locations of most of the new facilities or discharges (comprising approximately 10% of 

the total facilities), and the coarser scale results in geographic bounds to the remaining facilities 

seeking coverage under the permit. While the numbers of existing and future dischargers may 

vary slightly under the new permit, no information has been provided that suggests there will be 

substantially greater (or fewer) numbers of facilities seeking coverage under the permit. 

The MSGP also includes several references to monitoring, compliance, and enforcement, all of 

which will be conducted by EPA as part of its Action. As summarized in the BE, EPA has broad 

inspection authority under the CWA §308(a)(B) to conduct compliance monitoring and access 

to the facilities’s records. In addition to this authority, EPA notes in the BE (p. 6-12):

Additionally, under CWA section 308, EPA may request other information from permittees 

(e.g., the SWPPP). In addition, permittees must certify under penalty of law that any 

information they submit to EPA is true, accurate, and complete, and signed by a 

responsible party. 40 CFR §122.22. Failure to comply with the information requirements 

is enforceable under CWA § 309. The proposed MSGP provides that noncompliance with 

any of the requirements of the permit constitutes a violation, issued under the CWA. CWA 

309 authorizes EPA to seek both civil penalties and injunctive relief to redress violations 
2015 MSGP Biological Opinion 75

of the Act. Violators are subject to civil penalties up to $37,500 per day for each violation. 

Once a violation is established, civil penalties are generally considered mandatory, 

though the amount is discretionary. EPA may seek injunctive relief to restrain violations 

or to require future compliance. The government’s injunctive authority has been 

interpreted broadly to enable it to require mitigation-type activities, such as sediment 

remediation, wetlands restoration, and other measures intended to “complement” permit 

requirements

EPA requires permit compliance under the MSGP and affirms its authority to determine 

enforcement responses to permit violations including fines, requirements, and schedules for 

taking corrective actions. In addition to their authorities, EPA has outlined specific monitoring 

and implementation requirements of the permit, including but not limited to the triggers for and 

reporting of corrective actions. Through the course of our consultation, EPA has also committed 

to several activities related to monitoring and compliance, discussed in the sections below (see 4, 

6, and 7). Therefore, we conclude that EPA is aware of the full scope of its action.

2. Stressors

Here we ask whether the EPA has reliably estimated the physical, chemical or biotic stressors 

that are likely to be produced as a direct or indirect result of the discharges and discharge-related 

activities that would be authorized by the MSGP. We also ask whether the EPA would know or 

be able to reliably estimate whether the discharges have occurred in concentrations, frequencies, 

or for durations that violate the terms of the proposed MSGP. As the MSGP does not limit the 

frequency or duration of stormwater discharges that are covered under the MSGP, based on their 

intermittent nature and relatively short durations, we focus primarily on reliable estimation of 

stressors and, in regards to chemical pollutants, their concentrations in discharges.

In their BE, EPA summarized the various categories of stressors that are likely to be associated 

with the proposed action and provided a brief description of some of the potential effects of most 

of the contaminants and other stressors within each category (some of which we discussed in 

more detail in the previous section). Thus, we anticipate that EPA will have the ability to 

reliably estimate the types of stressors associated with the MSGP. In some cases, we also 

assume that EPA will also be able to reliably estimate whether the discharges have occurred in 

concentrations that violate the terms of the proposed MSGP in regards to the CWA, although this 

is most likely to occur where timely and representative analytical monitoring is conducted as part 

of the facilities’ SWPPPs. There are several scenarios where we are less certain of EPA’s ability 

to estimate stressors and/or concentrations covered by the MSGP, and these are briefly described 

below. We describe these uncertainties in the paragraphs below.

Type of Anticipated Contaminants

The EPA has identified the list of contaminants that are most likely to be present in the 

stormwater discharges of various industry sectors and subsectors covered by the MSGP. The list 

was compiled based on observed stormwater discharge constituents for each of the industry 

sectors and is expected to reflect the most common and/or expected types of pollutants that 

would be discharged incidentally with stormwater from the facilities within a given sector or

subsector. Other contaminants may be present in the facilities’ discharges that have not been 
2015 MSGP Biological Opinion 76

identified as applicable to a given subsector. Such contaminants would most likely not be 

distinguished unless they were detected during inspections (e.g., in visual monitoring or 

samples), as all required analytical monitoring will focus on the benchmarks and ELGs of 

concern and is not expected to detect additional contaminants. 

While we acknowledge uncertainty associated with the possibility of additional contaminants in 

the covered discharges, we recognize the risk to listed resources may be relatively low, 

particularly since the covered discharges should not include exposure to process-related 

contaminants (in most cases) or other non-stormwater discharges that are not explicitly described 

in the permit. 

Analytical Monitoring

The 2015 MSGP permit outlines an analytical monitoring procedure for a number of facility 

types that can apply for coverage. For these facilities, EPA will be able to estimate 

concentrations discharged by these facilities, particularly where the monitoring results submitted 

are typical for each facility throughout the year. The EPA’s ability to estimate concentrations of 

discharged contaminants is less certain for facilities that: (1) are not required to perform 

analytical monitoring either at all or for one or more benchmarks; (2) are not required to perform 

analytical monitoring for one or more ELGs; (3) are allowed to suspend analytical monitoring 

during the permit term based on averaged quarterly results and anticipated compliance;and (4) 

are required to monitor but are unable to do so in a timely or effective manner and thus may 

under-report stressor presence or levels in their discharges. 

The MSGP defines the benchmarks and ELGs that must be met for certain pollutants according 

to industry sector and/or subsector that are expected in the discharge. Not all facilities have 

established benchmarks or ELGs, and are thus not required to perform analytical monitoring 

under the permit. It is reasonable to assume stormwater discharges from at least some of the 

facilities will include contaminants that are not included or addressed as benchmarks or ELGs. 

However, the BE states that EPA does not believe these other contaminants pose a risk to water 

quality concerns.

Facilities in industrial subsectors that have benchmarks and/or ELGs must monitor for the 

constituents associated with those values; however, these facilities are not required to perform 

analytical monitoring for other potential pollutants in their discharge. The MSGP stipulates that 

if the average of four quarterly sampling results exceeds an applicable benchmark, the operator 

must review the facility’s SWPPP to determine whether revisions are needed. If this occurs, 

operators may make the necessary modifications and continue monitoring until benchmarks are 

met, or they may make a determination that no further pollutant reductions are technologically

available and economically practicable. If the latter determination is made, no corrective actions 

will be implemented and pollutant concentrations in discharges may continue to exceed 

benchmark values for the duration of the permit, resulting in potentially harmful exposures to 

listed species. Alternatively, if after collection of four quarterly samples, the average of the 

values for any parameter does not exceed the benchmark, the facility is not required to monitor 

for that parameter for the remainder of the term. Relying on averages to assess benchmark 

attainment allows for the possibility that one or more of the quarterly samples exceeds 

benchmark values while the four-quarter average does not. Hazardous exposures to listed 
2015 MSGP Biological Opinion 77

species may have occurred, yet because the annual average did not exceed benchmarks, no 

SWPPP review or corrective actions will be required, so this uncertainty remains. 

There are also uncertainties regarding the protectiveness of ELGs and benchmarks. ELGs are 

developed by EPA on an industry-by-industry basis and are intended to represent the greatest 

reductions that are economically achievable for an industry. EPA identifies the best available 

technology that is economically achievable for a particular industry and sets the ELG based on 

the performance of that technology. Unlike water quality-based effluent limits, ELGs are not 

derived with the intent of achieving a particular level of environmental protection. Thus, the 

level of protection afforded listed species by ELGs is uncertain. For some pollutants, ELGs may 

meet water quality standards at the “end of pipe” while others may require mixing zones to dilute 

pollutant loads before water quality standards are met in the receiving water. The size of the 

mixing zone is dependent on a number of factors including the hydrologic characteristics of the 

discharge and receiving water, the mass loading of pollutants from the discharge, and the 

assimilative capacity of the receiving water. For receiving waters with low assimilative capacity,

large mixing zones may be necessary in order to dilute pollutant concentrations. The 

consequences for listed species would be a larger proportion of aquatic habitat where hazardous 

exposures are more likely to occur.

Most of the benchmark values included in the MSGP are based on EPAs aquatic life ambient 

water quality criteria. Some benchmarks are equivalent to acute criteria while others are equal to 

chronic criteria. Chronic criteria are typically lower than acute criteria and would therefore 

result in lower exposures, if attained. However, the process for deriving water quality criteria 

does not explicitly assess effects to listed species and among the criteria included as benchmarks 

in the MSGP, none have undergone ESA Section 7 consultation for all species that may be 

affected by MSGP-authorized discharges. Thus, the extent to which stormwater pollutants at 

benchmark concentrations affect listed species is uncertain.

Additionally, some of the reporting exceptions that are granted to certain categories of facilities 

may result in stressors that are not adequately evaluated. For example, the MSGP states that 

inactive and unstaffed sites are only required to conduct an annual site inspection (i.e., the 

quarterly monitoring requirement is waived) if the facility operator can demonstrate that no 

industrial materials or activities would be exposed to stormwater. We agree that the risk of 

exposure is likely to be relatively low as a single, annual site inspection in such cases may be 

adequate to determine site conditions and compliance with the MSGP’s water quality 

requirements. However, EPA specifically provides the following exception in the MSGP that is 

more problematic: “Operators of inactive and unstaffed mining sites may exercise this waiver 

without demonstrating their industrial materials or activities are not exposed to stormwater, due 

to the unique issues affecting such facilities (e.g., the remoteness of many mining sites).” We 

anticipate that inactive and unstaffed mining sites may be inactive for a variety of reasons and 

that cessation of operations may or may not have included implementation of measures to avoid 

or reduce contact of stormwater with contaminants. In cases where discharges overlap with 

listed species or critical habitat, we anticipate that the risk of exposure of listed resources to 

contaminants is likely to be higher where it cannot be demonstrated that industrial materials or 

activities are not exposed to stormwater. We recognize the remoteness of a facility may impede 

or affect opportunities for access, although the remoteness of a facility does not reduce the 
2015 MSGP Biological Opinion 78

likelihood that listed resources are present. Some listed species are found in remote geographic 

areas (e.g., bull trout in headwater streams). 

The timing and effectiveness of inspections and/or analytical monitoring may also affect EPA’s 

ability evaluate concentrations of discharge pollutants. The inspection and monitoring schedules 

allow for a degree of flexibility in scheduling routine facility inspections, evaluating controls, 

and collection of samples. For example, the permit requires samples to be representative of 

stormwater discharge and collected (1) within the first 30 minutes of an actual discharge (except 

for snowmelt) and (2) on discharges that occur at least 72 hours (3 days) from the previous 

discharge. However, if assessors determine it is not possible to collect a sample within the first 

30 minutes, they are directed to collect a sample as soon as practicable after the first 30 minutes 

and provide a rationale for the delay. Adverse weather conditions may also affect sampling, with 

contingencies in the permit stipulating sample collection during the next qualifying storm event 

if conditions are unsafe. While accessibility and safe sampling conditions are necessary and 

certainly advisable in the latter situation, there is inherent subjectivity related to what is 

“practicable.” For example, if facilities routinely do not find it practicable to collect samples 

within the first 30 minutes of an actual discharge, detection of water quality issues may go 

unnoticed. While this uncertainty exists, trends in timing of sample collection (and thus potential 

understated effects) should be determinable through the reporting process EPA has proposed.

While these uncertainties are difficult to analyze, the EPA nontheless requires that facilities 

seeking covereage under the MSGP do not have measurable impacts to listed species or critical 

habitat (except under Criterion D and E as previously described), and thus these facilities remain 

subject to the other requirements of the permit related to stressors and water quality. These 

considerations, coupled with the NOI submittal and review process, will promote transparency to 

reduce inappropriate coverage of facilities under the MSGP.

3. Overlap

In this section, we ask whether EPA has reliably estimated whether and to what degree listed 

resources are likely to be exposed to potentially harmful impacts of discharges authorized by the 

permit. Determination of overlap requires consideration of two things: 1) the action area of a 

given facility; and 2) the listed species and designated critical habitat within that facility’s action

area. By delineating a facility’s action area, the operator identifies where the farthest-reaching 

effects of the facility’s proposed activities are likely to extend. Facility action areas are 

anticipated to include the receiving waterbody(ies) for stormwater and allowable non-stormwater 

discharges as well as certain upland areas where terrestrially based discharge-related activities 

occur. When listed species, their prey, obligate hosts (e.g., as required by certain species of 

freshwater mussels and snails), habitat, and/or designated critical habitat are present within the 

aquatic or terrestrial (when applicable) portions of a facility’s action area, the effects of the 

proposed activities are considered to overlap with these listed resources, even where such 

overlap would not occur year-round (e.g., as with certain migratory species). If listed species 

and/or the resources they depend on for survival, growth, and reproduction overlap with effects 

from the proposed activities, these listed resources may be exposed to potentially harmful 

stressors authorized by the proposed permit. 
2015 MSGP Biological Opinion 79

Of particular concern for listed resources are instances where overlap occurs but is not 

recognized or identified as such by a facility. In these cases, the potential for adverse effects to 

listed resources would not be analyzed. While it is reasonable to assume that the measures 

required in the MSGP to protect water quality may also adequately protect listed resources, this 

may not be true for all facilities and/or listed resources. Thus, EPA’s ability to reliably estimate 

overlap of listed resources and the action areas of the various facilities is instrumental in the 

identification of facilities that may require additional measures to avoid adverse impacts to listed 

species or critical habitat impacts or that would require an alternative permit (e.g., an individual 

permit) where avoidance of adverse effects is not feasible or practicable.

The EPA has specifically designed the MSGP to address the question of overlap of listed 

resources with effects from discharges and discharge-related activities covered under the permit. 

Two of the ESA criteria selected by facility operators (Criteria A and C) directly address overlap. 

Any facilities that are unable to claim coverage under another operator (Criterion B), a previous 

ESA section 7 consultation (Criterion D), or an ESA section 10 permit (Criterion E)29 are 

required to determine whether their proposed activities overlap with listed species or designated 

critical habitat. Where facility operators accurately complete the criterion selection process, 

EPA will be able to determine the degree of overlap with listed species and designated critical 

habitat.

EPA has revised the MSGP significantly since the previous permit cycle to more clearly address 

concerns regarding listed resources, including concerns associated with improving accuracy in 

identification overlap. The following paragraphs describe some of the measures that EPA has 

included to address these uncertainties. Overall, we anticipate that the measures will greatly 

improve EPA’s ability to identify and coordinate with applicants to avoid potential errors in 

criterion selection related to overlap prior to the coverage of the facilities under the permit.

Use of the E4 Criterion Selection Worksheet

All applicants are required to use the process outlined in the MSGP’s E4 Criterion Selection 

worksheet to determine which criterion is applicable to their facilities’ proposed activities. 

Operators are required to retain the worksheet and associated documentation (including the 

species list) as part of their facilities’ SWPPPs. The permit further requires facilities to make 

their SWPPPs available to EPA and other reviewers either via a direct website link or provided 

upon request. Facility operators that request coverage under Criterion A (concluding no overlap) 

must provide the rationale for criterion selection as they complete the NOI, providing EPA an 

opportunity for review of their rationale prior to the start of coverage. Criteria C facilities must 

submit additional documentation prior to submitting their NOI, including a species list and 

description of their action area.

Guidance for Determining a Facility’s Action Area

The EPA has provided additional guidance for applicants in the 2015 MSGP to improve 

accuracy and consistency among facility operators in their efforts to determine overlap and non-

 

29 Where facilities claim coverage under Criteria B, D, or E, overlap is addressed through these other mechanisms. 
2015 MSGP Biological Opinion 80

overlap with listed resources when seeking coverage under the MSGP. In previous permit 

cycles, the basis and rationale for an operator’s selection of either Criterion A (no overlap) and 

Criterion C (overlap) appears to have varied in quality and consistency. Our review of 

preliminary data from the 2008 MSGP suggests that facilities have had difficulty selecting the 

appropriate criteria or evaluating the action area for their facility’s discharges. 

For example, most of the facilities shown in Figure 4 (below) discharge to the Rio Grande River 

near Albuquerque, New Mexico. This reach of the Rio Grande River contains both listed species 

and designated critical habitat. A large proportion of the facilities discharging to this reach of 

the stream selected Criterion A while other nearby facilities selected a criterion indicating 

overlap (Criterion D and E in 2008 MSGP). While it is possible that some of these facilities 

selected Criterion A appropriately in this instance (e.g., based on site-specific characteristics or 

locations of their discharge), it is unclear from the available data whether the action area for the 

facility was determined correctly, or what information was used to support their selection of no 

overlap with listed resources. Based on the available information, it is reasonable to assume in 

this example that at least some, if not most, of these facilities selecting Criterion A under the 

2008 MSGP did so in error, as the majority of the facilities discharge directly (or indirectly) to 

the Rio Grande River, and the reach contains both listed species and designated critical habitat.

Figure 4. Facility locations selecting Criterion A (no overlap with listed resources, light/yellow 

circles) and Criterion E (overlap with listed resources under the 2008 MSGP, dark/green circles) 

discharging to the Rio Grande River near Albuquerque, New Mexico. (Data points are from 

preliminary monitoring data provided from EPA. Circles indicate approximate facility 

locations, not discharge points.)

The EPA has included additional guidance in the 2015 MSGP to facility operators seeking 

coverage that is intended reduce the errors in determining overlap with listed resources under the 
2015 MSGP Biological Opinion 81

Service’s jurisdiction. The ESA procedures listed in Appendix E of the permit direct the facility 

operators seeking coverage under both Criteria A and C to obtain an official species list using the 

Service’s Information, Planning, and Conservation (IPaC) website30. The 2015 MSGP provides 

guidance to applicants when considering the extent of their respective action areas (which are 

required in IPaC to create a species list), and describes considerations that should be included in 

the delineation of an action area. The following statements are excerpted from the guidance in 

Appendix E of the MSGP:

• When evaluating the potential effects of your activities, you must consider effects to 

listed species or critical habitats within the “action area.” Action area is defined in 

Appendix A [of the MSGP] as all areas to be affected directly or indirectly by the federal 

action and not merely the immediate area involved in the action. This includes areas 

beyond the footprint of the facility that are likely to be affected by stormwater 

discharges, discharge-related activities, and allowable non-stormwater discharges. For 

example, discharges of pollutants into downstream areas can increase the “action area” 

beyond the footprint of the facility.

• Consider the following in determining the action area for your facility:

o Discharges of pollutants into downstream areas can expand the action area well 

beyond the footprint of your facility and the discharge point(s). Take into 

account the controls you will be implementing to minimize pollutants and the 

receiving waterbody characteristics (e.g., perennial, intermittent, ephemeral) in 

determining the extent of physical, chemical, and/or biotic effects of the 

discharges. All receiving waterbodies that could receive pollutants from your 

facility must be included in your action area. 

o Discharge-related activities must also be accounted for in determining your 

action area. Discharge-related activities are any activities that cause, contribute 

to, or result in stormwater and allowable non-stormwater point source 

discharges, and measures such as 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 

have noise or other similar effects, and any disturbances associated with vehicle 

access or construction of controls, are part of your action area. 

o If you have any questions about determining the extent of your action area, you 

may choose to contact EPA or the Services for assistance. 

o You must describe the action area of your facility in Attachment 1 of this 

Appendix [of the MSGP, i.e., the worksheet].

 

30 As of the date of this Opinion, official species lists are available for many states and counties directly on the 

website, and contact information is provided in IPaC for the remaining Service offices that have not yet made 

official species lists available. 
2015 MSGP Biological Opinion 82

Criterion C Eligibility Form Reviews

Facilities selecting Criterion C will submit their Eligibility Form to EPA for review at least 30 

days prior to submitting their NOI. The E4 Criterion Selection worksheet31 directs applicants to 

attach the official species list they received from the Service to the Eligibility Form so that is 

available for EPA and the Service’s respective reviews. In most cases32, the official species list 

would include the map drawn by the applicant indicating the action area for the facility. The 

Eligibility Form also requires a written description of the action area. The inclusion of these two 

components will allow EPA to quickly verify during their review whether the action area (and 

thus overlap with listed resources) was appropriately determined. Thus, EPA will have the 

ability to verify whether the applicant described a reasonable action area (e.g., a line or polygon 

extending an appropriate distance downstream from the outfall to characterize the action area), or 

simply listed a point location (such as an outfall or facility location) or a mixing zone estimation. 

After reviewing the Eligibility Form for completeness (estimated to be ≤5 days), EPA will 

forward the document and any attachments to the Service(s) for review. Once the Service has 

received the Eligibility Form, Service reviewers will have the opportunity to comment within 25 

days should they notice that the species list appears to be incomplete or if the action area does 

not appear to be drawn correctly, as well as any other concerns. In such a case, a reviewer can 

then contact the EPA (or with their concerns so that EPA can address them prior to finalization 

of coverage. 33

Evaluation of a Subsample of Criterion A Facilities 

The EPA has proposed an additional method of further reducing the likelihood of facility 

operators selecting Criterion A in error. According to additional information submitted via email 

July 28, 2014: 

After the permit is issued, EPA intends to do a “compliance check” on a subset of 

facilities who have selected Criterion A on their Notice of Intent (NOI) for coverage 

under the MSGP during the 30 day waiting period. EPA envisions that the compliance 

check would consist of a GIS analysis to determine if the facility’s action area is within 

designated critical habitat or within the range of a threatened or endangered species. 

For any incorrect Criterion A determinations, EPA would place the NOI on hold, and 

require the facility to submit a Criterion C worksheet [Eligibility Form] for coverage 

under Criterion C.

 

31 The E4 Criterion Selection Worksheet contains both guidance for selection of all the criteria as well as the 

Eligibility Form

32 Where an official species list is not available in IPaC and applicants contact the appropriate Service office, a map 

may not be included as part of an official species list; however, direct coordination with the Service in these 

instances should reduce the likelihood of an incorrectly estimated action area for the facility.

33 While the potential for the Service(s) to provide feedback to the EPA exists through this process, the Service 

considers its review of the Criterion C Eligibility Form to be advisory. The level of review will likely be affected by 

workload and priorities of the reviewing office. The Service’s review is expected to assist EPA, in some caes, but 

will not ensure that all errors in action area delineation would be detected by the Service reviewers. 
2015 MSGP Biological Opinion 83

EPA would like to work with the Services to identify the Criterion A sample, perhaps 

based on priority watersheds for threatened and endangered species and/or critical 

habitat protection. EPA envisions that this focused Criterion A compliance check would 

occur in the 6 months following the permit reissuance (when the majority of facilities will 

be submitting NOIs for permit coverage). EPA envisions that the focused Criterion A 

compliance check would look at no greater than 100 separate facility NOIs.

With these proposed changes to the 2015 MSGP, EPA will have an improved ability to detect 

errors in operators’ efforts to calculate the action area for their facilities and determine the degree 

of overlap with listed resources. Neither underestimating nor overestimating the action area and 

degree of overlap is preferable for implementation of the permit. Underestimating the action 

area and degree of overlap would be more problematic for listed resources than underestimating 

overlap, as the risk of adverse effects would not be considered where overlap is not assumed to 

occur. 

If the proposed measures described above are fully implemented by the facility operators, most 

overlap errors are likely to be avoided prior to the coverage decision by EPA. For example, 

based on the revised guidance for determining a facility’s action area, we do not anticipate that 

facilities are likely to assume overlap where none exists (i.e., erroneously selecting Criterion C 

instead of Criterion A). However, there is less certainty as to whether facilities erroneously 

selecting Criterion A will be consistently detected in the proposed process. We anticipate that 

EPA has the ability to assess the degree of overlap of facilities’ effects and the presence of listed 

resources using the tools and procedures described previously. EPA also has access to IPaC to 

assist them in evaluating action areas and associated species lists during the application for 

coverage process should a question arise. EPA has not indicated that they will review every 

proposal under the MSGP to determine whether the criteria were selected appropriately in every 

case. However, the proposed measures are anticipated to improve accuracy through spotchecking potential instances of erroneous selections of Criterion A facilities. 

Summary of Uncertainties

Potential uncertainties include the following:

• The likelihood of facility operators adequately following the new guidance for drawing 

action areas and acquiring species lists. Although EPA directs the operators to follow 

the guidance when delineating their action areas and determining overlap, EPA does not 

require the operators to submit the action area description or the species list unless they 

are requested to do so34, except where a facility operator selects Criterion C and submits 

an Eligibility Form with an attached species list and action area. Therefore, if applicants 

underestimate the action area and erroneously conclude Criterion A, EPA will be 

unlikely to detect such an error unless: 1) a facility denotes a receiving waterbody 

identified on the Service-generated list referenced above, 2) the facility is part of the 

 

34 While EPA requires each facility operator to post a facility’s SWPPP online or provide a copy if requested, this 

does not mean that EPA will review all of the SWPPPs. 
2015 MSGP Biological Opinion 84

subsample in the compliance check, or 3) another entity (e.g., the Service(s), general 

public, local government, or other entity) notifies EPA. 

• The permit timeline requires that all existing dischargers submit requests for coverage 

within 90 days of reissuance of the permit. The large number of applicants that are 

existing dischargers from the previous permit cycle (~2,400) facilities, and the large

percentage of facilities selecting Criterion A (76% per the BE, based on previous cycles) 

may affect the amount and/or level of oversight EPA conducts on this part of the review 

process.

• Based on preliminary review of 2008 MSGP data, it appears that a substantial number of 

facilities that previously selected Criterion A may instead be prompted to select Criterion 

C. At this time, it is unclear exactly how many facilities may be more likely to select 

Criterion C. However, if a large proportion of the facilities find discover Criterion C is 

more applicable than in previous permit cycles, the number of facilities selecting 

Criterion A may be reduced, and the measures proposed above may be more effective at 

addressing potential errors.

• If facility operators do not recognize that overlap occurs, they would not be expected to 

consider whether additional measures would be needed to avoid or minimize adverse 

effects to listed resources. In a reasonable worst case scenario for aquatic or aquaticdependent species, one or more facilities discharging to a receiving waterbody with 

listed species may use controls and other measures to meet water quality standards and 

support designated uses, but may not include measures that would be needed to avoid 

direct exposure of individuals of listed species that are present and exposed to the 

pollutants in the discharges. It is reasonable to assume that such effects may be 

accumulative or magnified where multiple facilities erroneously assume no overlap and 

discharge into the same receiving waters (such as those shown in the example in Figure 4

above) without sufficient controls to avoid exposure to pollutants.

The MSGP has been designed to allow for estimation and tracking of overlap, as defined above. 

We anticipate that errors related to facilities assuming overlap where none exists are unlikely to 

occur based on the new permit guidance for delineation of a facility’s action area. Additionally, 

EPA has committed to implementing certain measures that would allow the agency’s reviewers 

to determine whether a large proportion of the facilities have accurately determined their 

proposed activities would have no overlap with listed resources. We recognize the large number 

of facilities and streamlined permit coverage process as proposed is likely to inhibit the EPA’s 

ability to confirm the accuracy of facility-specific action areas and associated determination of 

overlap in a consistent manner for all Criterion A facilities. However, we assume that EPA will 

continue to endeavor to address this issue and the annual compilation of facility coverage and 

monitoring information will allow opportunities for review of process implementation.

4. Monitoring and Feedback

In this section, we ask whether EPA proposes to identify, collect, and analyze information about 

its authorized discharges that may expose listed resources to harmful stressors. The EPA 

requires facility operators to self-monitor their discharges as one means to identify, collect, and 

analyze information to determine whether discharges into waters of the United States expose 
2015 MSGP Biological Opinion 85

listed resources to pollutants at concentrations, durations, or frequencies that are known or 

suspected to produce adverse effects. 

The MSGP outlines monitoring requirements for the various industrial sectors. All facilities are 

required to perform quarterly visual monitoring and inspections. A relatively small proportion of 

facilities are also required to perform quarterly analytical testing for all or a portion of the permit 

cycle (with duration related in part to their results), based on the sector or subsector category and 

anticipated pollutants. In most cases, reporting is limited to annual monitoring reports submitted 

to EPA, although ELG exceedences or other serious conditions are to be reported in the facilities 

end of year reports. Annual reports will be uploaded into the EPA’s new tracking system by the 

facility operators, which will allow for improved availability of reports for review by EPA (and 

other interested entities such as other agencies, public, etc.). 

We conclude that EPA is likely to identify, collect, and analyze important information about its 

authorized discharges under its MSG, although, in most cases, the results would not provide a 

direct justification for insignificant or discountable effects to listed resources. We recognize that 

the benchmarks and ELGs are more directly relatable to water quality conditions and effects than 

to listed species and critical habitat, and most, if not all, of the benchmarks and ELGs have not 

undergone ESA section 7 consultation. Thus, while the benchmarks, ELGs, and visual 

inspections and monitoring may be helpful in suggesting the avoidance (or existence) of certain 

effects to listed resources from stressors from a given facility, we do not expect the reports alone 

will provide a complete rationale for the avoidance or minimization of adverse effects to listed 

resources. Nonetheless, the use of these tools will provide EPA with information that may help 

to indicate problem discharges that should be re-evaluated and addressed with corrective actions 

or other solutions. 

5. Responses of Listed Resources

Here we ask whether EPA has used analytical methodology that considers: 

a) the status and trends of endangered or threatened species or designated critical habitat; 

b) the demographic and ecological status of populations and individuals of those species 

given their exposure to pre-existing stressors in different drainages and watersheds; 

c) the direct and indirect pathways by which endangered or threatened species or

designated critical habitat might be exposed to the discharges to waters of the United 

States; and 

d) the physical, physiological, behavior, and ecological consequences of exposing 

endangered or threatened species or designated critical habitat to stressors from 

discharges at concentrations, intensities, durations, or frequencies that could produce 

physical, physiological, behavioral, or ecological responses, given their pre-existing 

demographic and ecological condition. 

Due to the large number of listed species and critical habitat designations in the Action Area of 

the permit, EPA elected to evaluate representative species and critical habitat as example taxa 
2015 MSGP Biological Opinion 86

that were then extrapolated to the remaining species and critical habitat covered under the 

consultation. While this method allows for discussion of types of stressors and related effects to 

listed resources, consideration of status and trends of listed resources to provide context for the 

analysis is less likely to be specifically captured. However, EPA addressed these issues by first 

discussing broad applicable habitat types in the Action Area and environmental baseline stressors 

affecting biota in the Action Area and discussed various factors in the context of a representative 

exemplar listed species. While this analysis strategy does not fully capture the subtleties 

associated with status and trends of all listed species and designated critical habitat addressed by 

the BE, or their demographic and ecological status in the context of an environmental baseline, it 

does nonetheless frame the analysis using habitat as a surrogate for more detailed speciesspecific information.

The BE does address the direct and indirect pathways of exposure of listed resources to the 

stressors of the proposed action. For each type of stressor and representative taxa/critical habitat, 

EPA describes the most likely effects and then compares benchmarks and ELGs to selected 

toxicity values for each stressor (BE Tables 6-5 and 6-7) to determine whether acute lethal 

effects are likely to occur. For a given taxa–stressor combination, if the toxicity value is above 

the benchmark and ELG, EPA concludes that the proposed permit terms are sufficiently 

protective to ensure no likely adverse effects to listed species with that taxa. If the toxicity value 

was lower than the benchmark or ELG, EPA acknowledged that the pollutant may affect the 

species, but that those effects are not likely to raise population-level concerns because of the 

numerous species/habitat safeguards in both obtaining permit coverage and complying with the 

permit terms (permitting structure) and considering the transitory nature of MSGP-authorized 

discharges.

From the Service’s perspective, situations where operators are able to control their discharge 

such that concentrations of pollutants in stormwater achieve no effect or acceptably low effect 

concentrations (for a listed species of concern), at “end-of-pipe,” provide the greatest assurance 

that individuals of the species occurring in receiving waters are not likely to be adversely 

affected. This scenario would be comparable to EPA’s effects assessment (described above) 

where, (1) toxicity values, used by EPA to represent the sensitivity of listed species, were 

equivalent to no effect or acceptably low effect concentrations (e.g., insignificant or discountable 

effects resulting in a “may affect, not likely to adversely affect” determination), (2) benchmarks 

are equal to or less than toxicity values, and (3) pollutant concentrations in stormwater 

discharges are less than or equal to benchmarks (i.e. no exceedences). Under these 

circumstances it would be reasonable to arrive at a “may affect, not likely to adversely affect”

determination without having to rely on, or make assumptions about, site-specific discharge 

and/or receiving water information. However, the toxicity values used by EPA to represent the 

sensitivity of taxa/species to individual pollutants (in Tables 6-5 and 6-7 of the BE) are not 

equivalent to no effect or acceptably low effect concentrations, rather, they are concentrations 

expected to kill 50% of exposed individuals, i.e. LC50s. We do not consider the LC50 to be an 

acceptably low effect concentration, and would expect some individuals to be adversely affected 

if exposed to pollutants at the LC50. If a given benchmark value is lower than the toxicity value 

(LC50) for a taxa/species, it may be possible to conclude effects would be insignificant or 

discountable, without additional site-specific information, if the benchmark is sufficiently lower 

than the toxicity value such that no or acceptably low levels of effect would be expected. If a 

benchmark is greater than the toxicity value for a given taxa/species, it would not be reasonable 
2015 MSGP Biological Opinion 87

to make a “may affect, not likely to adversely affect” determination without consideration of 

site-specific information about the discharge and/or receiving water. Similarly, if benchmark 

exceedences have occurred or are expected to occur it is not reasonable to conclude effects 

would be insignificant or discountable, without considering site-specific information about the 

discharge, receiving water, species location and species sensitivity. 

Site-specific factors may need to be considered to assess whether conditions are consistent with a 

not likely to be adversely affected determination, particularly where concentrations of 

stormwater pollutants at “end of pipe” suggest that effects to listed resources may be more than 

minimal (i.e., “insignificant”). This will be necessary when pollutant benchmarks are not 

adequately protective of listed species (described above), for example, when past performance 

indicates benchmarks are likely to be exceeded, and/or when exceedences are reported in the 

current permit cycle. Based on the EPA’s effects analysis in the BE, there are several taxa–

benchmark combinations where benchmark values are above toxicity values (Tables 6-5in the 

BE), indicating that, for those combinations, exposure of species at benchmark concentrations 

would cause adverse effects. Similarly, benchmark monitoring data reported by the EPA for the 

previous permit cycle (2008) show that a large number of responding facilities had at least one 

annual benchmark exceedance. In both cases, benchmark exceedance and underprotective 

benchmark values, the EPA assumed adverse effects to listed species were not likely because 

dilution of stormwater pollutants in receiving waters would reduce exposures below 

concentrations that affect listed species. While this may be true for some facilities, is not 

reasonable to assume that potential adverse effects will be ameliorated in all instances without 

knowledge of site-specific information. 

The EPA’s assumptions that adequate control (meeting benchmarks etc.) or adequate dilution (in 

cases where there are exceedences and/or permit conditions do not ensure protection, i.e. underprotective benchmarks) are sufficient to avoid adverse effects to listed species can be evaluated 

for specific facilities by individuals reviewing the facilities Eligibility Form and NOI. Sitespecific information regarding the discharge, receiving water, occurrence of other stormwater 

discharges in the vicinity, assimilative capacity of the receiving water, proximity of the species 

to stormwater discharges, lifestage likely to be exposed, and the SWPPP will help inform the 

assessment. If, after review, conditions are not consistent with a “not likely to adversely affect”

determination, the EPA will direct the facility to revise their SWPPP, improve their performance, 

or determine that the facility is not eligible for coverage under the MSGP and the operator needs 

to seek an alternative permit (i.e. an individual permit).

The EPA identified uncertainties in both their exposure and response analyses. In section 6.9 of 

the BE, the EPA provided a discussion of uncertainties associated with pollutant exposure 

concentrations, toxicity data, extrapolation of effects from representative species to other listed 

species, effects of mixtures, aggregate discharges (i.e., co-occurrences of discharges), chronic 

effects, sediment bound pollutants, and other discharge- and species-related issues. In order to 

address whether the EPA has demonstrated sufficient knowledge of the effects on listed species

resulting from exposures to discharges authorized by the MSGP, we must first review these 

uncertainties for the BE’s assessment and how EPA addressed them, then evaluate the additional 

uncertainties.
2015 MSGP Biological Opinion 88

Pollutant Exposure Concentrations

In an effort to ensure facilities comply with water quality standards, EPA outlines benchmarks 

and ELGs for some subsectors to be used as indicators of compliance with the permit and, in the 

case of benchmarks, as tools to help facility operators evaluate the effectiveness of their controls. 

However, we are not certain that the proposed benchmarks and ELG values are necessarily 

protective of listed species and critical habitat. The BE notes that the use of benchmark 

concentrations are considered to be a conservative method of measuring the effectiveness of the 

implementation of the SWPPPs. However, the proposed benchmarks and ELGs related to the 

contaminants listed in the BE have generally not undergone section 7 consultation, and thus an 

evaluation of the proposed levels has not been done for listed species or critical habitat. As the 

MSGP is intended to provide coverage to facilities that would not result in adverse effects to 

listed resources (or are covered under another nexus under Criteria B, D, or E), simply meeting 

these levels does not necessarily ensure that listed resources are sufficiently addressed. The BE 

notes these levels are to be met at end-of-pipe, before the discharge meets the receiving waters, 

and suggests that the intermittent and short-term nature of discharges considered along with 

anticipated dilution of pollutants is likely to further reduce the concentrations of the 

contaminants to levels that would not measurably affect listed resources. In some cases, this 

may be a reasonable assumption, particularly where the discharge comprises a very small 

proportion of the volume of flows in the receiving waters. However, there are several 

uncertainties that must be evaluated. We anticipate that conditions of both discharges and 

receiving waters will vary significantly across the Action Area of the MSGP. We also expect 

that facilities may not consistently meet benchmarks and ELGs based on the relatively large 

number of facilities that had at least one annual benchmark/ELG exceedance during the 2008 

permit cycle. Given these uncertainties it is not reasonable to assume there will always be 

adequate dilution and that listed species will not be adversely affected. As discussed in the 

previous section, site-specific information will be needed to determine whether hazardous 

concentrations of pollutants in stormwater, resulting from under-protective benchmarks or 

benchmark exceedances, are likely to affect listed species in receiving waters. Considering the 

hundreds of facilities that will seek coverage under Criterion C, there are likely to be reasonable 

worst-case situations at some facilities where dilution will not be adequate to avoid hazardous 

exposures. 

Other Sources of Uncertainty

Other important sources of uncertainty addressed by EPA in their BE include extrapolation of 

representative species effects information to other listed species, effects of mixtures and cooccurrences of discharges, chronic effects, and effects resulting from exposure to sedimentbound pollutants. Unfortunately, ESA section 7 consultations have not been completed for the 

water quality criteria on which most of the benchmark values were based. Those consultations 

and their species-specific analyses would have provided greater certainty as to the degree of 

protection afforded to listed species. The representative species approach adopted by EPA in 

their BE could not match the rigor of individual criteria consultations, but was a reasonable 

approach given the scope of the action. Nevertheless, data gaps identified by EPA along with 

variation in species sensitivity within taxa, contribute to the uncertainty in using such an 

approach.
2015 MSGP Biological Opinion 89

Stormwater discharges, by their very nature, typically contain a complex mixture of naturally 

occurring and anthropogenic pollutants. Predicting the toxicity of mixtures is challenging. For 

the MSGP BE, the EPA considered the toxicity of each pollutant in stormwater (which required 

monitoring) individually, not as a mixture. Because pollutants can act additively, synergistically 

(super additive), and/or antagonistically, the combined effects of multiple pollutants can be 

greater that the effect of any one pollutant in the mixture.

The EPA did not consider chronic effects in their effects analysis because of the episodic nature 

of stormwater discharges covered under the MSGP. This may be reasonable for nonbioacumulative pollutants when there are long intervals between discharges. However, 

bioaccumulative pollutants such as selenium and mercury will accumulate and persist in aquatic 

food chains, thereby providing and pathway for chronic dietary exposure to listed species that 

feed on aquatic organisms. Omitting chronic toxicity data/endpoints from the effects analysis for 

these pollutants would likely result in an underestimation of the effects of stormwater discharges 

that contain these pollutants. Similarly, exposure of listed species to sediment-associated 

pollutants was not consider in the effects analysis. Stormwater pollutants that sorb to suspended 

sediment will be transported downstream and settle in depositional zones. Benthic organisms 

may be directly exposed to sediment-bound pollutants and/or pollutants that partition into pore 

water. These chronic exposures may persist well beyond the stormwater event and potentially 

beyond the distance(s) were effects from water-born exposure would be expected. Species in 

higher trophic levels may also be affected if the sediment-bound pollutants are bioaccumulative.

Riparian/Terrestrial Effects

The MSGP coverage application process has been designed to address the riparian/terrestrial 

stressors described above. These stressors are most likely to be related to discharge-related 

activities. The installation of controls and other similar discharge-related activities are expected 

to serve an important role for the facilities’ ability to reduce pollutants in their discharges. 

Consequently, the installation and improvement of controls is encouraged, as are methods to 

avoid or reduce unintentional impacts from their construction and use. The Eligibility Form

includes a section that provides guidance to the facility operators that are proposing dischargerelated activities for coverage to help them determine whether they can avoid adverse effects to 

listed species in the terrestrial environment. In particular, facility operators must comply with all 

of the following measures if discharge-related activities are proposed and listed species and/or 

critical habitat is present in the facility’s action area: 

a) All discharge-related activities will occur on previously cleared/developed 

areas of the site where maintenance and operation of the facility are currently 

occurring or where existing conditions of the area(s) in which the dischargerelated activities will occur precludes its use by listed species (e.g., work on 

existing impervious surfaces, work occurring inside buildings, area is not used 

by species), and

b) if discharge-related activities will include establishment of structures 

(including but not limited to infiltration ponds and other controls)or any 

related disturbances, these structures and/or disturbances will be sited in areas 

that will not result in isolation or degradation of nesting, breeding, or foraging 

habitat or other habitat functions for listed animal species (or their designated 
2015 MSGP Biological Opinion 90

critical habitat), and will avoid the destruction of native vegetation (including 

listed plant species)

c) If vegetation removal (e.g., brush clearing) or other similar activities will 

occur, no terrestrial listed species that use these areas for habitat would be 

expected to be present during vegetation removal.

If the facility can comply with these measures, they must submit the Eligibility Form to EPA as 

certification of their compliance. EPA will review the Eligibility Form for completeness and 

submit it to the Service for review as described previously. If the facility is unable to comply 

with one or more of these measures, they can submit the Eligibility Form to EPA and request 

technical assistance to identify additional measures that would help to avoid or minimize adverse 

effects to listed species or critical habitat prior to submitting an NOI. 

The vast majority of the facilities are not expected to propose discharge-related activities, as 

relatively few facilities are anticipated to request coverage for new facility discharges (or 

additional discharge points) under the MSGP. Most existing facilities are anticipated to limit 

their requests for coverage to stormwater and allowable non-stormwater discharges, although 

contaminants and other discharge-associated effects have the potential to affect riparian habitats 

and food webs as well. While it is possible that no discharge-related activities would overlap 

with listed species, the exact locations of these facilities cannot be predicted or discerned until 

the applicant begins the coverage application process. If no proposed discharge-related activities 

are proposed in the vicinity of listed resources during the life of the permit, we would not expect 

exposure to occur. 

However, since EPA estimates that an average of 52 facilities will seek coverage for new 

discharges each year, we anticipate that some proportion of these facilities will seek coverage for 

discharge-related activities. It is also reasonable to assume that at least some of the existing 

facilities may decide to install new or modified controls and would thus request coverage for 

discharge-related activities. We must also assume that discharge-related activities could occur 

anywhere in the Action Area where EPA has retained permitting authority. 

In summary, it is reasonable to assume that exposure to aquatic and upland stressors and 

associated adverse effects may occur from time to time. However, it is difficult to predict the 

likelihood of exposure and level and frequency of adverse effects in every watershed for every 

precipitation and discharge event. The EPA may not be able to evaluate effects to individuals of 

a listed species related to discrete discharge events. However, by evaluating past information 

related to water quality conditions in the various watersheds, coupled with facility monitoring 

and inspection reporting, the EPA will be able generally evaluate physical, physiological, 

behavior, and ecological consequences of exposing endangered or threatened species or 

designated critical habitat to stressors from discharges at concentrations, intensities, durations, or 

frequencies that could produce physical, physiological, behavioral, or ecological responses, 

given their pre-existing demographic and ecological condition. 
2015 MSGP Biological Opinion 91

6. Compliance

Here we ask whether EPA has a mechanism to reliably determine whether and to what degree 

operators have complied with the conditions, restrictions, or mitigation measures required of the 

MSGP.

To know or be able to determine reliably estimate compliance for dischargers participating in 

general permits, EPA must have an effective means of oversight. EPA collects information on 

NPDES permit compliance through Integrated Compliance Information System - National 

Pollutant Discharge Elimination System (ICIS-NPDES) database. The ICIS-NPDES database 

track the number of inspections and enforcement actions over 5 years, along with the number of 

non-compliance and effluent exceedances over three years. The data are classified for major and 

minor dischargers. While we cannot know in advance the compliance rate for the MSGP, we 

agree that EPA has established a mechanism to reliably determine compliance with the permit.

7. Adequacy of Controls

Finally, we ask whether EPA has a mechanism to prevent or minimize listed resources’ exposure 

to stressors in discharges if (1) EPA finds that these stressors occur at concentrations, durations, 

or frequencies that are potentially harmful to individual listed organisms, populations, or species; 

or (2) EPA identifies that the discharges lead directly or indirectly to ecological consequences 

that are potentially harmful to individual listed organisms, populations, species, or PBFs of 

designated critical habitat.

The MSGP has been designed in part with the goal of avoiding adverse effects to listed species 

and designated critical habitat. With the exception of facilities that can demonstrate that their 

effects were addressed under a completed ESA section 7 consultation under a separate federal 

nexus or ESA section 10 permit (or conceivably under another operator with either of these 

outcomes), all facilities must provide rationale supporting the conclusion that there would be no 

overlap with listed resources, or that any effects would be limited to insignificant, discountable, 

or wholly beneficial effects. The mechanism used for addressing adequacy of controls at the 

permit implementation scale can be characterized as twofold: 1) application for coverage under 

the MSGP, and 2) compliance with the conditions and requirements of the permit after coverage 

begins. Each of these categories addresses the potential for addressing exposure to discharges at 

concentrations, durations or frequencies that are potential harmful to individuals, populations, or 

the species as a whole, as well as to ecological consequences that are potentially harmful to listed 

species and critical habitat.

Application for Coverage

The EPA limits coverage under the MSGP to facilities that meet the five ESA criteria previously. 

Facility operators must determine whether they can seek coverage under a previously completed 

process that satisfactorily addressed effects to listed species (i.e., Criteria B, D, or E). If not, 

operators must determine whether their proposed activities would have either no overlap with 

listed species (i.e., Criterion A), or would be expected to have only insignificant or discountable 

effects if overlap occurred (i.e., Criterion C). Facilities that could not meet these criteria would 

not be eligible for coverage under the MSGP. 
2015 MSGP Biological Opinion 92

The mechanism for determining whether the facilities would avoid adverse effects to listed 

species is outlined in the permit. Uncertainties remain regarding the level of oversight and 

review that EPA would be able to perform to determine whether adverse effects would be 

avoided by the coverage of each facility. EPA has worked with the Services to identify 

procedures for criterion selection to reduce some of the potential uncertainties as described in 

earlier parts of this Opinion. In particular, we anticipate improved descriptions of the action area 

for each facility and more accurate and consistent selection of Criteria A and C based on the 

improved guidance. 

Additionally, and as described earlier, the 2015 MSGP will include an opportunity for the 

Service to provide input on a site-by-site basis for facilities whose discharges overlap with listed 

species and their designated critical habitats. The additional step for facilities considering 

selection of Criterion C and the associated Eligibility Form review by the EPA and the Service is 

expected to assist the EPA in identifing discharges or other activities authorized by the permit for 

a subset of facilities where risk to listed resources would be most likely to occur. While the 

Service field offices’ reviews will be volitional based on their other workload, priorities, and 

deadlines, this approach is due in large part in response to the structure of the EPA’s permit, 

which has been designed with deadlines that do not easily accommodate the timelines of a 

traditional programmatic consultation process. Although the lack of a Service response to a 

request for Eligibility Form review under the 2015 MSGP would not constitute an official 

Service concurrence with a “may affect, not likely to adversely affect” determination by EPA for 

a given facility’s proposed activities, but we anticipate that this new step in the process will 

greatly reduce the frequency of instances in which coverage is extended to facilities that do not 

meet the terms of the permit (i.e., result in adverse effects).

Thus, while the stressors described above have the potential to result in measurable effects to 

listed species and designated critical habitat if not adequately mitigated, the 2015 permit has 

included key changes in implementation that are expected to 1) significantly reduce or eliminate 

errors in determining overlap with listed resources, and 2) reduce the likelihood of mistakenly 

providing coverage to facilities that cannot demonstrate adverse effects would be avoided or 

minimized.

Compliance with Permit Conditions and Requirements

Once coverage begins, facilities must abide by the MSGP’s requirements and conditions for 

inspections, monitoring, and reporting, and must implement corrective actions as needed.

As with application for coverage, the basic mechanism for addressing potential impacts to listed 

resources associated with permit compliance. Uncertainties remain with recognizing or detecting 

actual occurrence of adverse effects and ensuring implementation of appropriate measures to 

fully avoid or minimize adverse effects is less certain.

Based on these considerations, specifically, the coverage application process and permit 

compliance, the EPA has demonstrated that they have developed a reasonable mechanism to 

prevent or minimize listed resources’ exposure to stressors in discharges and other activities 

authorized for facilities applying for coverage under the permit.
2015 MSGP Biological Opinion 93

Summary of Effects

The MSGP requires the use of controls and BMPs in an effort to address many of concerns 

related to the potential stressors of the action to both listed resources and water quality. We 

anticipate that effects related to the various pollutants are less likely to occur if effective and 

well-designed controls and BMPs are in place and operational, and if facilities select the 

appropriate criteria that apply to their discharges and discharge-related activities. We expect 

implementation of the permit, including, but not limited to such measures, will likely reduce the 

amount and/or concentrations of pollutants that are discharged into receiving waters in the 

Action Area. However, we do not assume that all impacts will be avoided, particularly from 1) 

aggregate discharges in to a receiving waterbody; 2) one or more facilities are unable to reduce 

the stressors in their discharges to levels that harass or harm listed species, their prey, their host 

species, and/or their habitat; and/or (3) where facilities discharge chemical pollutants which 

adsorb to suspended sediments and are re-released into the aquatic environment at a later time

(as described in Section 2 of the Effects Section of the Opinion). Thus, the effects of the 

potential stressors described above are expected to apply to at least some of the facilities and 

listed resources within the Action Area, although the exact contaminant concentrations, 

frequency and degree of exposure, and responses of listed individuals and critical habitat to each 

exposure event is difficult, if not impossible, to predict at the Action Area scale in advance. 

CUMULATIVE EFFECTS

Cumulative effects include the effects of future state, tribal, local, or private actions that are 

reasonably certain to occur in the Action Area considered in this Opinion. Future Federal actions 

that are unrelated to the proposed action are not considered in this section because they require 

separate consultation pursuant to section 7 of the Act.

The biological evaluation that EPA submitted to support its request for formal consultation and 

which is required to discuss cumulative effects (as they are defined for the purposes of section 7 

of the ESA) did not identify future state, tribal, local, or private actions that were reasonably 

certain to occur in the Action Area. During this consultation, we searched for information on 

future State, Tribal, local or private actions that were reasonably certain to occur in the Action 

Area and we determined the following types of activities are likely to occur.

We anticipate that human population expansion and associated infrastructure development; 

construction and operation of dams along major waterways; water retention, diversion, or 

dewatering of springs, wetlands, or streams; recreation, including off-road vehicle activity; 

expansion of agricultural or grazing activities, including alteration or clearing of native habitats 

for domestic animals or crops; and introductions of non-native plant, wildlife, or fish or other 

aquatic species, which can alter native habitats or out-compete or prey upon native species will 

occur in the Action Area due to state, tribal, local or private actions. Given the Action Area has 

been identified as waters over which EPA has jurisdiction, from which existing facilities 

discharge stormwater and allowable non-stormwater releases, many of these activities are 

expected within the range of various federally protected wildlife, fish, and plant species, and 

could contribute to cumulative effects to the species within the Action Area. Species with small 

population sizes, endemic locations, or slow reproductive rates will generally be more 

susceptible to cumulative effects.
2015 MSGP Biological Opinion 94

INTEGRATION AND SYNTHESIS OF EFFECTS

EPA proposes to issue the MSGP to authorize stormwater discharges associated with industrial 

activity from 30 sectors into waters of the United States over the permit period from 2015 to

2020. EPA expects the permit to cover just under 3,000 facilities, based on previous permit 

cycles, with the majority of the facilities comprised of existing discharges covered under the 

2008 MSGP. The proposed action is likely to adversely affect the species and critical habitats 

listed previously. Here, we integrate information presented in this Opinion to summarize 

stressors and the likely consequences of exposing listed resources to these stressors.

A significant portion of the nation’s waters have been impacted by anthropogenic stressors 

described within this Opinion. In the Environmental Baseline, Status of the Species, Status of 

Critical Habitat, and Cumulative Effects sections of the Opinion, we established that the effects 

of past and ongoing activities in the Action Area would maintain the existing degraded habitat 

conditions that are prevalent. Listing documents and recovery plans for the listed species in the 

Action Area describe numerous causes of decline and threats to these species throughout their 

ranges. Species and the habitats that are needed for carrying out their various life history 

requirements have been impacted by development and other stressors. In the Effects of the 

Action section, we provided an overview of the types of effects that would typically be expected 

from the stressors associated with activities proposed by the facilities for coverage under the 

MSGP, and then described the how EPA has structured the MSGP to address their oversight of 

the permit as it relates to effects to listed resources. 

Review of Permit Structure

Our Effects Analysis assesses whether, and to what degree, EPA structured the MSGP to 

establish processes that require EPA and the applicant, and the Directors to collectively 

implement the permit in a manner that addresses adverse effects to listed resources, and ensures

the operation of facilities subject to the permit are not likely to jeopardize the continued 

existence of endangered or threatened species or destroy or adversely modify designated critical 

habitat. We addressed this by answering seven questions. 

First, we concluded that EPA understands that the scope of their action includes issuance and 

implementation of the MSGP, which addresses the coverage application process, monitoring, and 

compliance. Second, we expect EPA will understand the types of stressors from the action, 

although there are some gaps in EPA’s identification of stressors of the action on a site-specific 

or sector-specific basis. However, EPA has identified the most likely contaminant stressors 

associated with the facility subsectors and has focused on these contaminants for their analytical 

monitoring requirements and visual inspections as specified in the permit. Third, EPA was 

unable to reliably estimate exposure of ESA listed resources to these stressors; however, they 

will use monitoring programs to reduce the likelihood of exposure from individual facilities

through the life of the permit. EPA has also included additional completeness and consistency 

review measures during the coverage application process, which is expected to reduce errors and 

improve accuracy during this process. Fourth, EPA will collect and monitor information on 

authorized activities throughout the life of the permit, aided through the more efficient electronic 

submission of annual inspection and monitoring reports. Fifth, EPA concluded the proposed

discharges and discharge-related activities may affect listed resources. While direct observation 
2015 MSGP Biological Opinion 95

of adverse effects on listed species is not likely to occur based on the life history and 

distributions of listed species, types of behavioral and sublethal effects anticipated, and other 

factors, EPA will be able to use the results from the monitoring program and facility reports to 

determine the relative effectiveness of the SWPPPs and corrective measures employed by the 

facilities. Sixth, EPA has programs in place for the MSGP to monitor for compliance, and they 

have the authority to enforce the permit as needed. Finally, EPA has the ability to modify their 

action if new information (including inadequate protection for species or low levels of 

compliance) becomes available and coordinating with facility operator where corrective actions 

are needed or violations occur. Modifications may include additional actions or requirements, 

and reinitiation of section 7 consultation. This review of the permit structure gives us confidence 

in EPA’s ability to ensure that discharges into waters of the United States are not likely to 

jeopardize the continued existence of endangered species or threatened species or result in the 

destruction or adverse modification of critical habitat that has been designated for those species.

Types of Anticipated Effects and Exposure

EPA has worked to improve the language and implementation of the permit over previous cycles 

to better address potential effects to listed species, and reduce the amount of error during 

application for coverage under the permit. EPA has also provided improved guidance and 

clarification of permit language and expectations so that both facility operators and EPA staff are 

better able to ensure compliance with the permit. We expect these changes will help to address 

some of the uncertainties and reduce adverse effects resulting from the implementation of the 

permit, but will not avoid all adverse effects to listed species from stressors covered under the 

action. The measures proposed by EPA are expected to reduce the severity of effects and allow 

for site-specific flexibility to address targeted stressors through requirements for controls and 

other measures as well as appropriate corrective actions where inspections and/or monitoring 

indicates such actions are needed. The proposed action may result in both short-term and longterm effects to listed species and designated critical habitat through the permitting of the 

proposed activities. The proposed action is anticipated to generate primarily physical and 

chemical stressors to listed species and critical habitat due to the presence of chemical 

constituents and other characteristics of the discharges. We anticipate the most significant 

effects to listed species and critical habitat from the proposed action will result from:

• Direct exposure of listed individuals to pollutants within the stormwater discharges;

• Direct exposure to physical stressors from the discharges, and related habitat changes 

(e.g., erosion, scouring);

• Reduced or degraded forage base;

• Effects to other species on which listed species depend to complete their life cycle (e.g., 

fish host species in the case of mussels); and

• Direct effects to critical habitat through short-term and/or long-term effects to PBFs that 

give the designated area value for the conservation of listed species.

In the short-term, stormwater discharges and allowable non-stormwater discharges may directly 

affect listed individuals and critical habitat. The stormwater discharges and allowable nonstormwater discharges authorized by the MSGP are anticipated to contain a variety of chemicals 

or other pollutants, including organic and inorganic constituents, sediments, and nutrients. 
2015 MSGP Biological Opinion 96

Individuals may be exposed to pollutants associated with the discharges during and immediately 

after storm events. In some cases, listed species may also be exposed to significant water 

temperature differences between discharges and the receiving waters they inhabit. Other direct 

effects to listed species may occur from increased flow velocities downstream of the discharge 

point(s) of facilities that are covered by the MSGP. These stressors are also likely to affect the 

prey base and habitat for listed species, sometimes leading to long-term effects where the prey 

base and/or habitats are unable to recover sufficiently to adequately support individuals of a 

listed species. Additionally, certain long-lived pollutants and associated degradates may 

accumulate in prey items or habitat features (e.g., benthic sediments), extending the duration of 

exposure of listed species to contaminants. Where discharges are not adequately attenuated, 

erosion of banks, shorelines, substrates, and habitat features (e.g., in-water spawning habitat) can 

be degraded or eliminated. Where multiple discharges occur within the same reach of stream or 

other waterbody, aggregate effects from combinations of multiple stressors are likely to have a 

greater overall effect to listed species, their prey, and their habitat than single discharges, in some 

cases and/or watersheds. Critical habitat may also be affected through similar routes of 

exposure. 

Based on the life histories of many of the species, and types of habitat used, it is unlikely that 

EPA or the facilities will directly observe the expected adverse effects with the exception of very 

noticeable, unexpected events (such as a large fish kill, which is not anticipated to occur as a 

result of this proposed action). For example, listed species such as fish and aquatic invertebrates 

may not be easily observable in streams or aquatic habitat, or mobile species or life stages of 

species may move great distances from the exposure site after exposure occurs. However, the 

expected lack of likely observations of sublethal, behavioral, or other effects from the discharges 

(even in combination with discharges from other sources, does not confirm that they have not 

occurred. Because of the limited ability for direct observation of effects to listed resources, the 

components of the MSGP that address criterion selection, inspections, monitoring (both visual 

and analytical), use of corrective actions, and reporting will be most important in EPA’s ability 

to determine whether facilities are meeting the requirements of the MSGP, including avoidance 

and/or minimization of effects to listed resources. Each of these is discussed in the subsequent 

paragraphs:

Criterion Selection

We anticipate that accurate selection of Criteria A and C will be the most challenging to address. 

The EPA has included several measures within the permit that provide clarified guidance and 

requirements to reduce the instances of potential error in selection of these criteria. For example, 

EPA will not review the individual action area of every facility submitting an NOI under 

Criterion A (indicating no overlap with listed resources); however, they will selectively review a 

subset of NOIs (not to exceed 100 facilities), and have provided additional guidance to facilities 

for delineating an action area within IPaC to acquire an official species list from the Service. For 

Criterion C, EPA will review the submitted Eligibility Forms for completeness prior to sending 

them to the Service for a consistency review. These measures are expected to improve clarity, 

consistency, and accuracy among applicants as they determine which criterion applies to their 

facilities, and for EPA as they review the applications for coverage. 

While it is possible that erroneous selections of Criterion A could still occur, we expect the 

number of inappropriate selections will be appreciably reduced. However, the delineation of an 
2015 MSGP Biological Opinion 97

action area remains a subjective exercise, and without direct oversight of every facility, it is 

reasonable to assume that at least a portion of the applicants will underestimate their facilities’ 

action areas and erroneously select Criterion A, even with the measures that EPA has included in 

their proposed action. 

We do not anticipate that every facility that is erroneously covered under Criterion A of the 

MSGP would necessarily generate stressors that would rise to the level of adverse effects to 

listed resources. However, without recognition of the presence of listed species and/or critical 

habitat it is reasonable to assume that a subset of facilities selecting Criterion A in error would 

not be detected through EPA’s oversight process. It is also reasonable to assume that in some of 

those instances, the facilities’ SWPPPs may include measures that would avoid or reduce the 

potential for adverse effects to listed species and critical habitat related to stressors covered by 

the permit. 

We also assume that, in other instances, the proposed measures may not fully avoid or reduce 

adverse effects to listed resources to an insignificant or discountable level. We anticipate that 

there will be some degree of adverse effect to listed species albeit of a temporal nature or of short 

duration. 

There are several uncertainties that factor into the analysis of the likelihood of exposure and 

response for listed resources. The condition of the receiving waters, proportion of discharge 

flows to receiving water flows, and sensitivity of the listed resources to the MSGP’s stressors 

will all influence how individuals, populations, species, and critical habitat are affected by the 

proposed action. Additionally, other uncertainties exist related to the effects of mixtures in 

receiving waters (e.g., either related to background levels of pollutants or from coverage of 

multiple facilities). Finally, we are not certain whether facilities that have had difficulties 

meeting benchmarks or other requirements under previous permit cycles where no or insufficient 

corrective actions have been clearly implemented (or deemed feasible) would be provided 

coverage under the MSGP. 

Exposure and Response Scenarios 

Due to the often unpredictable nature and frequency of precipitation events resulting in 

stormwater discharges, it is not possible to predict every discharge event (including duration and 

volume) that would result in adverse effects to listed resources from discharge stressors. 

However, it is reasonable to assume that at least some of the discharges that occur during the 5-

year permit cycle will generate stressors that will measurably affect listed resources. We 

anticipate that measurable effects are most likely to occur in the following scenarios (either 

singly or in combination), where:

• Relatively large numbers of facilities discharge into the same reach of a receiving 

waterbody,

• Assimilative capacity of the waterbody during discharges is not sufficient for the 

pollutant concentrations from the facility(ies) discharging to the waterbody,

• Facilities are unable to meet their required benchmarks during one or more sampling 

events, 

• Facilities observe evidence of pollutants during visual inspections,
2015 MSGP Biological Opinion 98

• A need for corrective measures is triggered especially where there have been 

observations or suspected releases of pollutants as described in Part 4 of the permit, or 

where a required control measure was not installed or correctly installed, or

• Corrective measures for benchmark exceedences or other suspected or observed chemical 

or physical stressors are determined to be infeasible and are not implemented.

The frequency and duration of exposure will likely vary across habitats and species. Some 

highly mobile aquatic or aquatic-associated individuals may be able to avoid periodic and/or in 

frequent plumes of contaminants or the vicinity of a mixing zone if they are able to detect 

pollutants or other stressors, although the avoidance may result in other effects (e.g., increased 

energy use, increased risk of predation, delayed migration or reproduction), if they are unable to 

migrate through, forage or reproduce in a preferred area. In other cases, individuals will be 

unable to detect contaminants (e.g., copper, in the case of salmonids) and thus be unable to avoid 

exposure resulting in decreased ability to perform necessary life history functions (e.g., avoid 

predation or detect forage items, for example). Where species are highly mobile and multiple 

discharges exist in a receiving waterbody, they may encounter multiple discharges during the 

same event. Alternatively, attached and/or sessile individuals (or life history stages) or those that 

are confined to limited areas within or adjacent to waterbodies, will in most cases be unable to 

avoid exposure to stressors from the action, even if they are able to detect pollutants or other 

stressors. Thus, we anticipate that where discharges include constituents in concentrations that 

would result in sublethal effects to listed species (either mobile or sessile), exposure to these 

substances would impair essential behavior patterns of these individuals, including breeding, 

feeding, or sheltering. Where these and other stressors of the action result in avoidance or delay 

in accessing habitats important for foraging, migration, reproduction, or other critical life history 

functions, or where effects to prey base and/or host species occur, we anticipate these stressors 

will significantly disrupt normal behavioral patterns of listed species.

Uncertainties

Due to the nature of the proposed action (a national general permit for stormwater discharges), 

adverse effects from the discharges covered by the MSGP within a given watershed may be 

difficult to distinguish from effects of other point or non-point discharges during increased 

runoff and/or high flow levels following precipitation events, particularly in urban areas or other 

areas where high levels of impervious surfaces are present. The stressors from the covered 

discharges may result in adverse effects related to the discharge pollutants or physical 

characteristics, or may contribute to the overall short- or long-term degradation within the 

receiving waters from all sources. Direct effects to individuals of listed resources would include 

sublethal effects or induce behavioral responses that affect the fitness of individuals exposed to 

the discharges. Indirect effects would include, but are not limited to, reductions in and/or or 

changes to prey base and host species (e.g., for mussels), and degradation of habitat conditions in 

the receiving waters, and in certain cases may contribute to reductions in fitness of listed species. 

We do not necessarily assume that all discharges would result in measurable effects to listed 

resources. However, we acknowledge that variable precipitation events, receiving water 

conditions and individual and combined discharge events are expected to result in episodic 

adverse effects to listed species and designated critical habitat, even though the specific timing 

and duration of such effects are difficult to predict at the scale of the Action Area.
2015 MSGP Biological Opinion 99

Summary

As described in the BE and this Opinion, discharges and discharge-related activities may affect 

listed species and designated critical habitat. However, we expect that these effects will be 

mitigated in large part by the changes to the application and review process whereby EPA will 

have the ability to evaluate, monitor, and determine compliance of covered facilities under the 

permit. We are unable to describe the full extent of facility- or site-specific adverse effects and 

species responses, although we are able to describe the overall extent of anticipated effects 

related to the proposed action. We expect that the geographical extent of disturbance and 

injurious effects, where they occur, will be highly variable over the life of the permit, based on 

differences between precipitation/discharge events, seasonal changes in the receiving waters, and 

other site-specific conditions. Thus, we anticipate the geographical extent of disturbance and 

injurious effects will vary by location and event and may range from a few meters to many 

kilometers downstream of the discharge point, or in many cases, aggregated discharge points. 

While low levels of disturbance and sublethal effects may occur for individuals of species within 

the receiving waters in the Action Area, these effects are not expected to rise to the level of loss 

of individuals or population-level effects. 

It is our Opinion that issuance of the MSGP is not likely to result in an appreciable reduction in 

the likelihood of both the survival and recovery of any listed species by reducing the 

reproduction, numbers, or distribution of that species. It is also our Opinion that the MSGP is 

not likely to result in destruction or adverse modification of designated critical habitat. The 

process achieves this through a comprehensive suite of requirements, including, but not limited 

to:

• Improved guidance to facility operators to identify the presence of listed resources in 

their individual action areas;

• Additional evaluation of facilities that overlap with listed resources via the Eligibility 

Forms;

• Opportunities for technical assistance and consistency review from the Service field 

offices for facilities requesting coverage under Criterion C; and

• Limiting coverage to facilities that are not expected to have adverse effects on listed 

resources and requiring inspections, analytical monitoring and the use of corrective 

measures when needed.

CONCLUSION

After reviewing the current Status of Species, the Environmental Baseline for the Action Area, 

the effects of the proposed reissuance of the MSGP and the cumulative effects, it is the Service's 

Biological Opinion that the (action), as proposed, is not likely to jeopardize the continued 

existence of the species covered in this consultation, and is not likely to destroy or adversely 

modify designated critical habitat. 
2015 MSGP Biological Opinion 100

INCIDENTAL TAKE STATEMENT

Section 9 of the ESA and federal regulation pursuant to section 4(d) of the ESA prohibit the take 

of endangered and threatened species, respectively, without special exemption. Take is defined 

as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt to 

engage in any such conduct. Harm is defined by the Service as an act that actually kills or 

injures wildlife. Such act may include significant habitat modification or degradation where it 

actually kills or injures wildlife by significantly impairing essential behavior patterns, including 

breeding, feeding, or sheltering (50 CFR 17.3). Harass is defined by the Service as an 

intentional or negligent act or omission which creates the likelihood of injury to wildlife by 

annoying it to such an extent as to significantly disrupt normal behavioral patterns which 

include, but are not limited to, breeding, feeding, or sheltering (50 CFR 17.3). Incidental take is 

defined as take that is incidental to, and not the purpose of, the carrying out of an otherwise 

lawful activity. Under the terms of section 7(b)(4) and section 7(o)(2), taking that is incidental to 

and not intended as part of the agency action is not considered to be prohibited taking under the 

ESA provided that such taking is in compliance with the terms and conditions of this Incidental 

Take Statement.

AMOUNT OR EXTENT OF TAKE

This consultation has focused on whether the EPA has ensured that their issuance of the general 

permit is not likely to jeopardize the continued existence of any endangered or threatened species 

or result in the destruction or adverse modification of critical habitat of such species. It does not 

identify the individual facilities expected to be covered by the MSGP, nor does it describe details 

of the specific effects and conservation measures related to individual facilities, although the 

jeopardy analysis does, in fact, include the activities authorized under the 2015 permit. Because 

of the large scale and broad scope of the proposed action, however, even the best scientific and 

commercial data available are not sufficient to enable the Service to estimate the the exact 

amounts of anticipated incidental take35 associated with the action on a facility-by-facility (or 

species-by-species) basis related to discrete precipitation and discharge events; however, the 

incidental take described in the following paragraphs does apply to the activities authorized by 

the 2015 permit. We address types of incidental take associated with the proposed action that are 

reasonably certain to occur in the action area in the paragraphs below.

Harassment

The proposed action will result in appreciable disturbance of aquatic and semi-aquatic species 

during feeding, breeding, sheltering or other important behaviors. Such disturbance is also 

expected to occur via delays to migration to foraging, spawning, or rearing habitats, and/or 

impacts to their prey base, host species, and/or habitat. All aquatic listed individuals present in 

the receiving waterbodies downstream of the discharge points are expected to experience 

disturbance to some degree of over the course of the 5-year permit.

 

35 i.e., exact numbers of individuals of each species.
2015 MSGP Biological Opinion 101

Harm

The proposed action will result in harm of listed aquatic species through injurious sublethal (but 

not lethal) effects due to direct exposure to pollutants released during implementation of the 

proposed action. This take will include disruption of normal behavioral patterns for aquatic 

species such as feeding, breeding, or sheltering through delays to migration to foraging, 

spawning, or rearing habitats, and/or impacts to their prey base or habitat. We anticipate that all 

sessile individuals (or life history stages) and individuals that are unable to detect and thus avoid 

the relevant stressors will experience harm in conditions where the assimilative capacity of the 

receiving waters is insufficient to reduce concentrations to required levels to avoid injurious 

effects. The extent of this area is anticipated to be in the receiving waterbodies from the 

discharge point(s) of the facility(ies) to the furthermost area downstream of the discharge 

point(s) where the pollutants exceed levels that would result in sublethal harmful effects (e.g., 

injury) to listed species. The duration associated with each qualifying event will generally range 

from a few hours to a few days for most cases based on the anticipated decrease in contaminant 

load over time in response to a stormwater-generating event In rare cases, the duration may 

extend to 14 days for a given facility if corrective actions are needed to address unforeseen 

emergency situations.

For both categories, we anticipate that incidental take will most frequently occur when there are: 

(1) aggregate effects from multiple discharges within the same receiving waters; (2) one or more 

facilities are unable to reduce the stressors in their discharges to levels that harass or harm listed 

species, their prey, their host species, and/or their habitat; and (3) where facilities discharge 

chemical pollutants which adsorb to suspended sediments and are re-released into the aquatic 

environment at a later time.

The Service anticipates incidental take of all listed species as described above in the action area 

will be difficult to detect for the following reasons:

• finding an impaired specimen is unlikely;

• sublethal/delayed effects to growth and reproduction would not generally be 

observed;

• the species occurs in habitat (e.g., streams, wetlands, lakes, and other off-site 

locations) that makes detection difficult; and

• the relationship between habitat conditions and distribution and abundance of 

individuals is imprecise such that the number of specific individuals affected 

cannot be practicably obtained.

REASONABLE AND PRUDENT MEASURES

The following reasonable and prudent measure is necessary and appropriate to minimize impacts 

of incidental take to species identified in Table 3.

1. EPA will use its authorities under the CWA to minimize impacts to listed species 

pursuant to the MSGP and CWA.
2015 MSGP Biological Opinion 102

TERMS AND CONDITIONS

In order to be exempt from the prohibitions of section 9 of the Act, the EPA must comply with 

the following terms and conditions, which implement the reasonable and prudent measure 

described above and outline required reporting/monitoring requirements. These terms and 

conditions are non-discretionary. 

The following Terms and Conditions are required for the implementation of RPM 1:

1. If, during review of the Criterion C Eligibility Form, the reviewing Service field office 

requests future notification by and/or coordination with EPA regarding unexpected 

developments once a facility is provided coverage under the MSGP, EPA shall comply 

with the request. 

A. Such requests would generally be expected to relate to:

i. unexpected issues that arise after coverage has begun, for a 

given facility or group of facilities, especially where unexpected exceedences 

of benchmarks or ELGs occurred, 

ii. or where a proposed/required control or other measure was not installed or 

was not installed properly. 

B. Additional scenarios may be identified by the Service reviewer during the 

consistency reviews.

2. EPA shall compile and provide to the Service an annual report that is comprised of data 

from EPA’s Integrated Compliance Information System (ICIS) summarizing the covered 

facilities as well as reporting and monitoring data submitted by the facilities to EPA 

pursuant to the MSGP. (This annual report should not be confused with the annual 

reports provided to EPA from the covered facilities.)

A. The report shall include, at minimum, the following data:

i. Locations of facilities covered under the MSGP by selected criterion (these 

should be provided in an electronic spreadsheet including at minimum: 

facility sector/subsector, name, ESA criterion selection, state, and geographic 

point data for the facilities and their outfall locations).

ii. All instances of facilities covered under any ESA criteria that exceeded 

benchmarks and numeric ELGs for their subsector(s) during one or more 

quarterly monitoring efforts and data associated with these exceedences. 

iii. All instances where an operator (or EPA) determined there was a need to 

consider corrective actions at facilities covered under any criteria. This 

listing shall also include, if available, the trigger for corrective actions (e.g., 

spill, lack of required control, etc.) and the outcome (e.g., any actions taken 

or implemented to correct the problem).

iv. A brief description of any instances of coverage provided under the MSGP 

where the reviewing Service field office initially noted, in writing, that the 

facility's proposal did not appear to support coverage under the permit. The 
2015 MSGP Biological Opinion 103

description shall include how the Service's concerns were addressed, and 

shall specify whether the reviewing Service field office provided 

confirmation that any additional information and/or changes to the proposal 

(including but not limited to additional BMPs) were sufficient to address the 

Service's concerns.

v. Any observed/reported impacts to ESA-listed species or critical habitat as 

documented by facilities during or between the required inspection and/or 

monitoring efforts conducted at the facility36.

vi. All data in bullets 2(A)(2-3) above should be provided to the Service 

Headquarters office (see accompanying cover letter) along with a brief 

summary, and:

a) If possible, data should be submitted in a format that is sortable (such 

as an electronic spreadsheet that can be sorted by sector/subsector, 

state, county, receiving waters, and parameter measured/exceeded at 

minimum). 

b) The data should be clearly linked to sector type, geographic location 

(e.g., point data) to enable efficient review by the Service that can be 

linked to the data specified in 2(A)(1) above (e.g., to facility ID and 

location to allow for review by receiving water). 

B. The first annual report shall be submitted to the Service no later than 3 months 

after the deadline for submitting results from the fourth quarterly inspection after 

issuance of the permit, as described by the MSGP. 

i. Subsequent annual reports to the Service should be submitted at 12-month 

intervals after this date. 

ii. For the first monitoring report to the Service, EPA may request a 3-month 

extension to the report submission deadline to address unforeseen challenges 

with querying and compiling information from the new reporting system.

C. A preliminary report listing facility locations as described in Term and Condition 

3(A)(i) above should be submitted to the Service no later than 12 months after the 

issuance of the permit.

The reasonable and prudent measure, with its implementing terms and conditions, are designed 

to minimize the impact of incidental take that might otherwise result from the proposed action. 

If, during the course of the action and subsequent monitoring, this level of incidental take is 

exceeded, such incidental take represents new information requiring reinitiation of consultation 

and review of the reasonable and prudent measures provided. The Federal agency must 

immediately provide an explanation of the causes of the taking and review with the Service the 

need for possible modification of the reasonable and prudent measures.

 

36 While we recognize the ICIS system does not specifically request this information, if such information is provided 

in the narrative section of the report, EPA should forward this to the Service as part of their annual report of 

implementation of the MSGP.
2015 MSGP Biological Opinion 104

The Service is to be notified within three working days upon locating a dead, injured, or sick 

endangered or threatened species specimen, nest, and/or egg(s). Initial notification must be made 

to the nearest Service Law Enforcement Office. Notification must include the date, time, and 

precise location of the injured animal, carcass, nest, and/or egg and any other pertinent 

information. 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. In 

conjunction with the care of sick or injured endangered or threatened species or preservation of 

biological materials from a dead animal, the finder has the responsibility to ensure that evidence 

associated with the specimen is not unnecessarily disturbed. Contact the Service Law 

Enforcement Office at (425) 883-8122, the appropriate Service Regional Office or Field Office 

as provided to EPA during consultation, or the Service’s Headquarters Office at (703) 358-2171. 

All such instances should also be documented in the annual report described above.

CONSERVATION RECOMMENDATIONS

Section 7(a)(1) of the Act directs Federal agencies to utilize their authorities to further the 

purposes of the Act by carrying out conservation programs for the benefit of endangered and 

threatened species. Conservation recommendations are discretionary agency activities to 

minimize or avoid adverse effects of a proposed action on listed species or critical habitat, to 

help implement recovery plans, or to develop information. We make the following conservation 

recommendations:

1. We recommend that the EPA develop additional tools to assist facility operators with 

further measures and considerations that will improve both EPA’s and the facilities’ 

efforts to consistently avoid, reduce, or minimize effects to listed species and designated 

critical habitat associated with the MSGP. To assist EPA with this effort, we are 

providing some examples based on coordination with some of our Regions:

A. We have attached a list of measures to this Opinion that can be used for facilities 

in the Pacific Islands that will provide greater assurances to EPA that any 

terrestrial effects from discharge-related activities are truly insignificant or 

discountable for discharge-associated activities (Appendix F). We recommend 

that EPA encourage applicants to clearly communicate that they will implement 

the relevant measures when constructing controls or other measures in the 

geographic areas applicable to these activities. This will help avoid and minimize 

effects to listed resources and streamline the review of Criterion C Eligibility 

Forms during Service review.

B. For facilities in New Mexico, we recommend that EPA encourage applicants 

whose discharge points are within one mile of critical habitat for aquatic species 

to complete a Criterion C Eligibility Form instead of selecting Criterion A when 

seeking coverage under the MSGP. Of particular concern are facilities that 

discharge to the mainstem or tributaries of the following rivers, or are within one 

mile of these rivers in New Mexico:

• Pecos River
2015 MSGP Biological Opinion 105

• San Juan River

• Rio Grande River, from the reach north of Elephant Butte upstream to 

Cochiti

2. We recommend that EPA maintain a list of receiving waters where Criterion A has been 

selected in error in previous permit cycles and crosscheck requests for coverage under 

Criterion A against this list to avoid inadvertent errors in criterion selection as NOIs are 

submitted. As additional receiving waters are identified where listed species and/or 

critical habitat are likely to occur either through notification by the Service Headquarters 

Office, ROs, or FOs, or through other means (e.g., EPA’s proposed review of a 

subsample of Criterion A facilities), the list and crosscheck should be expanded 

accordingly. For example, facilities discharging to the following receiving waters should 

generally not be allowed to proceed with coverage under Criterion A:

• New Mexico: Pecos River; San Juan River; and Rio Grande River (from 

the reach north of Elephant Butte upstream to Cochiti)

• Washington: Puget Sound; tributaries to eastern Puget Sound, from the 

Puyallup River north; mainstem Columbia River; and certain tributaries to 

the Upper and Lower Yakima River

3. We recommend that the EPA encourage facilities to describe and ensure control 

maintenance schedules are clearly defined and adhered to as part of their SWPPP, and 

that these activities are addressed both in the NOIs, and, where applicable, in Criterion C 

Eligibility Forms. For example, facilities that include settling ponds or other controls that 

allow contaminants to settle out prior to discharge into the receiving waters should 

specify the maintenance schedule for removing contaminants and confirm such 

maintenance was performed in annual reporting. This would be of particular concern in 

dry areas (such as portions of the desert Southwest), where contaminants that are 

successfully filtered out during a storm event may be resuspended and discharged in 

future storm events occurring many months later. At minimum, we recommend that this 

particular control measure and associated maintenance be specifically addressed in the 

NOIs, Criterion C Eligibility Forms, and annual reporting for facilities in Arizona, New 

Mexico, and western Texas.

4. We recommend that the EPA, in coordination with states and other water quality 

regulating entities in the Action Area (as applicable), consider and develop monitoring 

plans or programs, or other assessment tools that enable the agency to better discern the

impacts of aggregate discharges of stormwater from facilities covered under general or 

individual permits, particularly in reaches of water bodies receiving stormwater 

discharges from multiple facilities and that also contain listed resources.

5. We recommend that the EPA review and update the contents of the Sector Specific Fact 

Sheets to ensure that the pollutants listed within the permit and recommended BMPs to 
2015 MSGP Biological Opinion 106

address the pollutants are up to date and ensure all relevant emerging issues are 

addressed. For example:

A. The fact sheets should systematically reviewed and revised as necessary to clearly 

identify measures with similar levels of detail. 

B. The analysis that was originally performed to establish the types of stormwater 

pollutants likely to be generated from the various facility subsectors should be 

periodically reanalyzed and peer-reviewed to ensure that the most updated 

information is being used for stormwater permits (i.e., for both general permits 

and individual permits).

C. Ensure the permit includes any additional measures necessary to address 

emerging issues related to stormwater contaminants that might not be measured or 

observed in quarterly sampling or inspections (e.g., PAHs in runoff after coal tar 

application to parking areas and other surfaces).

6. Finally, we recommend that the EPA begin informal ESA Section 7 consultation with the 

Service early in the development of the next draft MSGP permit and incorporate 

monitoring results and trends from the reporting generated during this permit cycle. Such 

informal consultation should also include a joint evaluation of the effectiveness of the 

consistency review process from the 2015 permit cycle, or whether a more formalized, 

programmatic consultation would be more appropriate for the next permit cycle.

In order for the Service to be kept informed of actions minimizing or avoiding adverse effects or 

benefitting listed species or their habitats, the Service requests notification of the implementation 

of any conservation recommendations by contacting the Service’s Headquarters Office at the 

address listed on the cover letter to this document.

REINITIATION NOTICE

This concludes formal consultation on the action(s) outlined in the reinitiation request. As 

provided in 50 CFR 402.16, reinitiation of formal consultation is required where discretionary 

Federal agency involvement or control over the action has been retained (or is authorized by law) 

and if: 1) the amount or extent of incidental take is exceeded; 2) new information reveals effects 

of the agency action that may affect listed species or critical habitat in a manner or to an extent 

not considered in this opinion; 3) the agency action is subsequently modified in a manner that 

causes an effect to the listed species or critical habitat not considered in this opinion; or 4) a new 

species is listed or critical habitat designated that may be affected by the action. For example, 

reinitiation may be warranted if EPA makes modifications to the permit that would result in 

changes to the coverage process related to consideration or analysis of effects to listed resources, 

including, but not limited to reductions or elimination of certain types of inspections, analytical 

monitoring, or reporting. Such modifications may occur prior to issuance of the permit or during 

the life of the MSGP. Additionally, in instances where the amount or extent of incidental take is 

exceeded, any operations causing such take must cease pending reinitiation.
2015 MSGP Biological Opinion 107

LITERATURE CITED

Anderson, P.G., B.R. Taylor, and G.C. Balch. 1996. Quantifying the effects of sediment release 

on fish and their habitats. Fisheries and Oceans, Canada, Canadian Manuscript Report of 

Fisheries and Aquatic Sciences 2346.

Arillo, A., C. Margiocco, F. Melodia, P. Mensi and G. Schenone. 1981. Ammonia toxicity 

mechanism in fish: Studies on rainbow trout (Salmo gairdneri Richardson.). 

Ecotoxicol. Environ. Saf. 5(3): 16-328.

Baldwin, D.H., J.F. Sandahl, J.S. Labenia, and N.L. Scholz. 2003. Sublethal effects of 

copper on coho salmon: impacts on nonoverlapping receptor pathways in the 

peripheral olfactory nervous system. Environmental Toxicology and Chemistry 

22(10):2266-2274.

Barrett, J.C., G.D. Grossman, and J. Rosenfeld. 1992. Turbidity-induced changes in reactive 

distance of rainbow trout. Transactions of the American Fisheries Society 121:437-

443.

Barton, B.A. 2002. Stress in fishes: a diversity of responses with particular reference to changes 

in circulating corticosteroids. Integrated and Comparative Biology 42:517-525.

Barton, B.A., and C.B. Schreck. 1987. Metabolic cost of acute physical stress in juvenile 

steelhead. Transactions of the American Fisheries Society 116:357-363.

Barton, B.A., C.B. Schreck, and L.D. Barton. 1986. Multiple acute disturbances evoke 

cumulative physiological stress responses in juvenile Chinook salmon. 

Transactions of the American Fisheries Society 115:245-251.

Bash, J., C.H. Berman, and S. Bolton. 2001. Effects of turbidity and suspended solids on 

salmonids. Center for Streamside Studies, University of Washington, Seattle, 

WA, November 2001. 72 pp.

Baun, A., A.M. Christensen, and F. Nakajima. 2003. Ecotoxic effects of wet weather discharges 

in an urban stream. Pages 4-1; 4-5 In Buren, M. (ed): Diffuse Pollution Conference: 

IWA Proceedings of the 7th international Specialised Conference on Diffuse Pollution 

and Basin Management and 36th Scientific Meeting of the Estuarine and Coastal Sciences 

Association, 17th-22nd August 2003, Vol. 1, Center for Water Resources Research, Civil 

Engineering Department, University College Dublin, Dublin.

Berg, L., and T.G. Northcote. 1985. Changes in territorial, gill-flaring, and feeding behavior in 

juvenile coho salmon (Oncorhynchus kisutch) following short-term pulses of suspended 

sediment. Canadian Journal of Fisheries and Aquatic Sciences 42:1410-1417.
2015 MSGP Biological Opinion 108

Berry, W., N.I. Rubinstein, B. Melzian, and B. Hill. 2003. The biological effects of suspended 

and bedded sediment in aquatic systems: a review. USEPA, Office of Research and 

Development, National Health and Environmental Effects Laboratory, Narragansett, 

Rhode Island.

Besser J, Hardesty D, Greer I, Ingersoll C. 2009. Sensitivity of freshwater snails to aquatic 

contaminants: Survival and growth of endangered snail species and surrogates in 28-day 

exposures to copper, ammonia and pentachlorophenol. U.S. Geological Survey, 

Columbia, MO.

Birtwell, I.K. 1999. The effects of sediment on fish and their habitat. Fisheries & Oceans 

Canada, Canadian Stock Assessment Secretariat Research Document 99/139, 

West Vancouver, British Columbia. 34 pp.

Bjornn, T.C., M.A. Brusven, M.P. Molnau, J.H. Milligan, R.A. Klamt, E. Chacho, and C. 

Schaye. 1977. Transport of granitic sediment in streams and its effects on insects and fish. 

University of Idaho, Idaho Cooperative Fisheries Research Unit, Research Technical 

Completion Project B-036-IDA, Bulletin 17, Moscow, Idaho. 43 pp. 

Bjornn, T.C., and D.W. Reiser. 1991. Habitat requirements of salmonids in streams. Pages 83-

138 In W.R. Meehan, ed. Influences of forest and rangeland management on salmonid 

fishes and their habitats, American Fisheries Society Special Publication 19.

Black, M.C. 2001. Water quality standards for North Carolina’s endangered mussels. Final 

Report. Department of Health Science, University of Georgia, Athens, GA, USA.

Bostick, B.C., A.J. Hansen, M.J. La Guardia, and S.E. Fendorf. 1998. Zinc local structure and 

partitioning within a contaminated wetland.1998 SSRL Activity Report. Dept of 

Geological and Environmental Science, Stanford University, Proposal 2519M, Stanford, 

CA. 8 pp.

Brommer, J.E. 2000. The evolution of fitness in life-history theory. Biological Reviews of the 

Cambridge Philosophical Society 75(3):377-404.

Brommer, J.E., Merila J. and H. Kokko. 2002. Reproductive timing and individual fitness. 

Ecology Letters 5:802-810. 

Brommer, J.E., Pietainen, H., and Kolunen, H. 1998. The effect of age at first breeding on Ural 

owl lifetime reproductive success and fitness under cyclic food conditions. The Journal of 

Animal Ecology 67:359-369. 

Burton, G.A., R. Pitt, and S. Clark. 2000. The role of traditional and novel toxicity test methods 

in assessing stormwater and sediment contamination. Critical Reviews in Environmental 

Science and Toxicology 30(4):413-447.
2015 MSGP Biological Opinion 109

Carlisle, D.M., Meador, M.R., Short, T.M., Tate, C.M., Gurtz, M.E., Bryant, W.L., Falcone, J.A., 

and Woodside, M.D. 2013, The quality of our Nation’s waters—Ecological health in the 

Nation’s streams, 1993–2005: U.S. Geological Survey Circular 1391, 120 p., 

http://pubs.usgs.gov/circ/1391.

Camargo J. and A. Alonso. 2006. Ecological and toxicological effects of inorganic nitrogen 

pollution in aquatic ecosystems: A global assessment. Environ. Internat. 32: 831-

849.

Castro, J., and F. Reckendorf. 1995. RCA III: Effects of sediment on the aquatic 

environment; potential NRCS actions to improve aquatic habitat. Natural Resources 

Conservation Service, Oregon State University, Department of Geosciences.

Cederholm, C.J., and L.M. Reid. 1987. Impact of forest management on coho salmon 

(Oncorhynchus kisutch) populations of the Clearwater River, Washington: A project 

summary. Pages 373-398 In E.O. Salo, and T.W. Cundy, eds. Streamside 

management: Forestry and fishery interactions. University of Washington Institute 

of Forest Resource Contribution 57.

Chapman, D.W. 1988. Critical-review of variables used to define effects of fines in redds 

of large salmonids. Transactions of the American Fisheries Society 117(1):1-21.

Chen, W., S.K. Tan, and J.H. Tay. 1996. Distribution, fractional composition and release of 

sediment-bound heavy metals in tropical reservoirs. Water, Air, & Soil Pollution 92(3-

4):273-287.

Clutton-Brock, T.H., Stevenson, I.R., Marrow, P., MacColl, A.D., Houston, A.I., and J.M. 

McNamara. 1996. Population fluctuations, reproductive costs and life-history tactics in 

female Soay sheep. The Journal of Animal Ecology 65:15. 

Cobleigh, M.M. 2003. Stress, growth, and survival of juvenile Chinook salmon. Master's Thesis. 

University of Washington, School of Aquatic and Fisheries Science, Seattle, WA.

Contreras-Sanchez, W., C.B. Schreck, M.S. Fitzpatrick, and C.B. Pereira. 1998. Effects of stress 

on the reproduction performance of rainbow trout (Oncorhynchus mykiss). Biology of 

reproduction 58:439-447.

Coulson, T., Benton, .TG., Lundberg, P., Dall, S.R.X., Kendall, B.E., and J.M. Gaillard. 2006. 

Estimating individual contributions to population growth: evolutionary fitness in 

ecological time. Proceedings of the Royal Society of London, Series B: Biological 

Sciences 273: 547- 55. 

Curry, R.A., and W.S. MacNeill. 2004. Population-level responses to sediment during early 

life in brook trout. Journal of the North American Benthological Society 23:140-150.
2015 MSGP Biological Opinion 110

Davis, K.B. 2006. Management of physiological stress in finfish aquaculture. North American 

Journal of Aquaculture 68:116-121.

Ellis, J.B. 2000. Risk assessment approaches for ecosystem responses to transient pollution 

events in urban receiving waters. Chemosphere 41(1-2):85-91.

Eisler, R. 1993. Zinc hazards to fish, wildlife, and invertebrates: a synoptic review. United 

States Fish and Wildlife Service, Patuxent Wildlfe Research Center, Biological Report 

10, Laurel, Maryland, April 1993. 106 pp.

Eisler, R. 1998. Copper hazards to fish, wildlife, and invertebrates: a synoptic review. 

Biological Resources Division, U.S. Geological Survey, Biological Science Report 

USGS/BRD/BSR--1997-0002, Laurel, MD, January 1998. 120 pp.

EPA. 1980a. Ambient water quality criteria for copper. Criteria and Standards Division, Office 

of Water Regulations and Standards, Publication 440/5-80-036, Washington, D.C. 162 

pp. 

EPA. 1980b. Ambient water quality criteria for zinc. The Division; Available to the public 

through the National Technical Information Service, Washington, D.C; Springfield, Va.

EPA. 1987. Ambient aquatic life water quality criteria document for zinc. U.S. Environmental 

Protection Agency, Office of Research and Development, Environmental Research 

Laboratories; Available from the National Technical Information Service, Washington, 

D.C; Springfield, Va.

EPA. 2001. Temperature interaction: Issue paper 4 prepared as part of EPA Region 10 

temperature and water quality criteria guidance development project. EPA-910-D-01-

004.

EPA 2013. Aquatic Life Ambient Water Quality Criteria for Ammonia - Freshwater 2013. 

EPA 822-R-13-001. April 2013.

EPA, 2014. External Peer Review Draft Aquatic Life Ambient Water Quality Criterion for 

Selenium – Freshwater. EPA 822-P-14-001. May 2104.

Erman, D.C., and F.K. Ligon. 1985. The response of algal communities in streams of the 

Jackson Demonstration State Forest to timber harvest activities. State of California, 

Department of Forestry. 49 pp.

Everest, F.H., R.L. Beschta, J.C. Scrivener, K.V. Koski, J.R. Sedell, and C.J. Cederholm. 1987. 

Fine sediment and salmonid production: A paradox. Pages 98-142 In E.O. Salo, and T.W. 

Cundy, eds. Streamside management: Forestry and fishery interactions, University of 

Washington Institute of Forest Resources Contribution 57.
2015 MSGP Biological Opinion 111

Fan, C., R. Field, W.C. Pisano, J. Barsanti, J.J. Joyce, and H. Sorenson. 2001. Sewer and tank 

flushing for sediment, corrosion, and pollution control; Mini-symposium on urban 

drainage. Journal of Water Resources Planning and Management 127(3):194-201.

Folmar, L.C. 1976. Overt avoidance reaction of rainbow trout fry to nine herbicides. Bulletin of 

Environmental Contamination and Toxicology 15(5):509-514.

Foster, I.D.L., and S.M. Charlesworth. 1996. Heavy metals in the hydrological cycle: Trends and 

explanation. Hydrological Processes 10(2):227-261

Ghanmi, Z., M. Rouabhia, O. Othmane, and P.A. Deschaux. 1989. Effects of metal ions on 

cyprinid fish immune response: invitro effects of Zn2+ and Mn2+ on the mitogenic 

response of carp pronephros lymphocytes. Ecotoxicology and Environmental Safety 

17(2):183-189.

Glenn, D., L. Dingfang, and J. Sansalone. 2002. Influence of chemistry, hydrology and 

suspended solids on partitioning of heavy metals to particles - considerations for in-situ 

control of urban stormwater quality, Louisiana State University.

Grant, S.B., N.V. Rekhi, N.R. Pise, R.L. Reeves, M. Matsumoto, A. Wistrom, L. Moussa, and S. 

Bay. 2003. A review of the contaminants and toxicity associated with particles in 

stormwater runoff. CALTRANS (California Department of Transportation), CTSW-RT03-059.73.15, Sacramento, CA 95826. 172 pp.

Gregory, T.R., and C.M. Wood. 1999. The effects of chronic plasma cortisol elevation on the 

feeding behaviour, growth, competitive ability, and swimming performance of juvenile 

rainbow trout. Physiological and Biochemical Zoology 72(3):286-295.

Hansen, J.A., P.G. Welsh, J. Lipton, D. Cacela, and A.D. Dailey. 2002. Relative sensitivity of 

bull trout (Salvelinus confluentus) and rainbow trout (Oncorhynchus mykiss) to acute 

exposures of cadmium and zinc. Environmental Toxicology and Chemistry 21(1):67-75.

Haukenes, A.H., and C.L. Buck. 2006. Time course of osmoregulatory, metabolic, and endocrine 

stress responses of Pacific halibut following a 30-min air exposure. Journal of Applied 

Ichthyology 22:382-387.

Heintz, R.A., S.D. Rice, A.C. Wertheimer, R.F. Bradshaw, F.P. Thrower, J.E. Joyce, and J.W. 

Short. 2000. Delayed effects on growth and marine survival of pink salmon 

Oncorhynchus gorbuscha after exposure to crude oil during embryonic development. US 

National Marine Fisheries Service, Auke Bay Laboratory, 205-216, Juneau, Alaska, 

December 08, 2000. 12 pp.

Herngren, L., A. Goonetilleke, and G.A. Ayoko. 2005. Understanding heavy metal and 

suspended solids relationships in urban stormwater using simulated rainfall. Journal of 

Environmental Management 76(2):149-158.
2015 MSGP Biological Opinion 112

Henley, W.F., M.A. Patterson, R.J. Neves, and A.D. Lemly. 2000. Effects of sedimentation and 

turbidity on lotic food webs: a concise review from natural resource managers. Reviews 

in Fisheries Science 8(2):125-139.

Hillman, T.W., J.S. Griffith, and W.S. Platts. 1987. Summer and winter habitat selection by 

juvenile Chinook salmon in a highly sedimented Idaho stream. Transactions of the 

American Fisheries Society 116:185-195.

Hilmy, A.M., N.A. Eldomiaty, A.Y. Daabees, and H.A.A. Latife. 1987a. Some physiological and 

biochemical indices of zinc toxicity in 2 fresh-water fishes, Clarias lazera and Tilapia 

zilli. Comparative Biochemistry and Physiology, C. 87C(2):297-301.

Hilmy, A.M., N.A. Eldomiaty, A.Y. Daabees, and H.A.A. Latife. 1987b. Toxicity in Tilapia zilli 

and Clarias lazera (Pisces) induced by zinc, seasonally. Comparative Biochemistry and 

Physiology, C. 86C(2):263-265.

Hodson, P.V. 1988. Effect of metal metabolism on uptake, disposition, and toxicity in fish. 

Aquatic Toxicology 11(1-2):3-18.

Jacobson, K.C., M.R. Arkoosh, A.N. Kagley, E.R. Clemons, T.K. Collier, and E. Casillas. 2003. 

Cumulative effects of natural and anthropogenic stress on immune function and disease 

resistance in juvenile Chinook salmon. Journal of Aquatic Animal Health 15:1-12.

John, D.A., and J.S. Leventhal. 1995. Bioavailability of metals; Preliminary compilation of 

descriptive geoenvironmental mineral deposit models. U. S. Geological Survey, Reston, 

VA, United States (USA), OF 95-0831, United States (USA).

Johnston, F.D., J.R. Post, C.J. Mushens, J.D. Stelfox, A.J. Paul, and B. Lajeuness. 2007. The 

demography of recovery of an overexploited bull trout, Salvelinus confluentus, 

population. Canadian Journal of Fish and Aquatic Science 64:113-126.

Klein, R. 2003. Duration of turbidity and suspended sediment transport in salmonid-bearing 

streams, north coastal California. U.S. Environmental Protection Agency, Region IX, San 

Francisco, CA, March 2003.

Kotiaho, J.S., Kaitala, V., Komonen, A., and P. Paivinen. 2005. Predicting the risk of 

extinction from shared ecological characteristics. Proceedings of the National 

Academy of Sciences of the United States of America 102(6):1963-1967. 

Lake, R.G., and S.G. Hinch. 1999. Acute effects of suspended sediment angularity on juvenile 

coho salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic 

Sciences 56:862-867.

Lang, T., G. Peters, R. Hoffmann and E. Meyer. 1987. Experimental investigations on the 

toxicity of ammonia: Effects on ventilation frequency, growth, epidermal mucous cells, 

and gill structure of rainbow trout Salmo gairdneri. Dis. Aquat. Org. 3: 159-165.
2015 MSGP Biological Opinion 113

Lemly, A.D. 1998. Pathology of Selenium Poisoning in Fish. Pages 281-296 In W.T. 

Frankenberger, Jr. and R.A. Engberg, eds. Environmental Chemistry of Selenium, Marcel 

Dekker, INC, New York. 

Lloyd, R. 1987. Special tests in aquatic toxicity for chemical mixtures: Interactions and 

modifications of response by variation of physicochemical conditions. Pages 491-507 In 

V.B. Vouk, G.C. Butler, A.C. Upton, D.V. Parke, and S.C. Asher, eds. Methods for 

assessing the effects of mixtures of chemicals, John Wiley & Sons, New York.

MacDonald, A., and K.W. Ritland. 1989. Sediment dynamics in type 4 and 5 waters: A review 

and synthesis. PTI Environmental Services, Timber Fish and Wildlife. TFW-012-89-002, 

Bellevue, Washington.

MacDonald, L.H., A.W. Smart, and R.C. Wissmar. 1991. Monitoring guidelines to evaluate 

effects of forestry activities on streams in the Pacific Northwest and Alaska. U.S. 

Environmental Protection Agency, Region 10. University of Washington, EPA 90/6-91-

001, Seattle, WA. 166 pp.

Marsalek, J., Q. Rochfort, B. Brownlee, T. Mayer, and M.R. Servos. 1999. An exploratory study 

of urban runoff toxicity. Water Science and Technology 39(12):33-39.

Mazeaud, M.M., F. Mazeaud, and E.M. Donaldson. 1977. Primary and secondary effects of 

stress in fish: some new data with a general review. Transactions of the American 

Fisheries Society 106(3):201-212.

McCormick, S.D., J.M. Shripton, J.B. Carey, M.F. O'Dea, K.E. Sloan, S. Moriyama, and B.T. 

Björnsson. 1998. Repeated acute stress reduces growth rate of Atlantic salmon parr and 

alters plasma levels of growth hormone, insulin-like growth factor I and cortisol. 

Aquaculture 168:221-235.

McGraw, J.B., and H. Caswell. 1996. Estimation of individual fitness from life-history data. 

The American Naturalist 147:47 – 64. 

McLeay, D.J., I.K. Birtwell, G.F. Hartman, and G.L. Ennis. 1987. Responses of arctic grayling 

(Thymallus arcticus) to acute and prolonged exposure to Yukon placer mining 

sediment. Canadian Journal of Fisheries and Aquatic Sciences 44(3):658-673.

Milston, R.H., M.W. Davis, S.J. Parker, B.L. Olla, S. Clements, and C.B. Schreck. 2006. 

Characterization of the physiological stress response in lingcod. Transactions of the 

American Fisheries Society 135:1165-1174.

MBTSG (The Montana Bull Trout Scientific Group). 1998. The relationship between land 

management activities and habitat requirements of bull trout. Montana Fish, Wildlife, 

and Parks, Helena, MT, May 1998. 77 pp.
2015 MSGP Biological Opinion 114

Muthukrishnan, S., and A. Selvakumar. 2006. Evaluation of retention pond and constructed 

wetland BMPs for treating particulate-bound heavy metals in urban stormwater runoff. 

In Muthukrishnan, S. and A. Selvakumar eds. 2006 World Environmental and Water 

Resources Congress 2006: Examining the Confluence of Environmental and Water 

Concerns, May 21 -25, 2006, World Environmental and Water Resources Congress, 

Omaha, Nebraska. 13 pp.pp.

(NMFS and USFWS) National Marine Fisheries Service and U.S. Fish and Wildlife Service. 

1998. Recovery Plan for U.S. Pacific Populations of the Hawksbill Turtle (Eretmochelys 

imbricata). National Marine Fisheries Service, Silver Spring, MD.

Newcombe, C.P., and J.O.T. Jensen. 1996. Channel suspended sediment and fisheries: synthesis 

for quantitative assessment of risk and impact. North American Journal of Fisheries 

Management 16(4):693-727.

Newcombe, C.P., and D.D. MacDonald. 1991. Effects of Suspended Sediments on Aquatic 

Ecosystems. North American Journal of Fisheries Management 11(1):72-82.

Newton I, and P. Rothery. 1997. Senescence and reproductive value in sparrowhawks. Ecology 

78:1000-1008.

Niyogi, S., P. Couture, G. Pyle, D.G. McDonald, and C.M. Wood. 2004. Acute cadmium biotic 

ligand model characteristics of laboratory-reared and wild yellow perch (Perca 

flavescens) relative to rainbow trout (Oncorhynchus mykiss). Canadian Journal of 

Fisheries and Aquatic Sciences 61:942-953.

NRC (National Research Council). 1986. The special problem of cumulative effects. Pages 93-

136 In: Ecological knowledge and environmental problem-solving. National Academy 

Press, Washington, D.C. 

Oli M.K., and F.S. Dobson. 2003. The relative importance of life-history variables to population 

growth rate in mammals: Cole's prediction revisited. The American Naturalist 

161(3):422-440. 

Overli, O. 2001. Behavioural and neuroendocrine effects of stress in salmonid fishes. Acta 

Universitatis Upsaliensis. Comprehensive Summaries of Uppsala. Dissertations from the 

Faculty of Science and Technology 623, ISBN 91-554-5007-5, Uppsala, Sweden. 79 pp.

Owens, P.N., R.J. Batalla, A.J. Collins, B. Gomez, D.M. Hicks, A.J. Horowitz, G.M. Konkolf, 

M. Marden, M.M. Page, D.H. Peacock, E.L. Petticrew, W. Salomons, and N.A. Trustrum. 

2005. Fine-grained sediment in river systems: environmental significance and 

management issues. River Research and Applications 21:693-717.

Pettersson, T.J.R. 2002. Characteristics of suspended particles in a small stormwater pond. Urban 

Drainage 2002, ASCE Publications 2004. 12 pp.
2015 MSGP Biological Opinion 115

Pickering, A.D., T.G. Pottinger, and P. Christie. 1982. Recovery of the brown trout, Salmo trutta 

L., from acute handling stress: a time-course study. Journal of Fish Biology 20:229-244.

Playle, R.C. 2004. Using multiple metal-gill binding models and the toxic unit concept to help 

reconcile multiple-metal toxicity results. Aquatic Toxicology 67(4):359-370.

Portz, D.E., C.M. Woodley, and J.J. Cech. 2006. Stress-associated impacts of short-term 

holdingon fishes. Reviews in Fish Biology and Fisheries 16:125-170.

Presser, T.S., and S.N Luoma. 2010. A method for Ecosystem-scale Modeling of Selenium. 

Integrated Environmental Assessment and Management. 6(4): 685-710.

Quigley, J.T., and S.G. Hinch. 2006. Effects of rapid experimental temperature increases on 

acute physiological stress and behaviour of stream dwelling juvenile Chinook salmon. 

Journal of Thermal Biology 31:429-441.

Redding, J.M., C.B. Schreck, and F.H. Everest. 1987. Physiological effects on coho salmon and 

steelhead of exposure to suspended solids. Transactions of the American Fisheries 

Society 116(5):737-744.

Reid, S., and P.G. Anderson. 1999. Effects of sediment released during open-cut pipeline water 

crossings. Canadian Water Resources Journal 24:23-39.

Rieman, B.E., and J.D. McIntyre. 1993. Demographic and habitat requirements for conservation 

of bull trout. U.S. Department of Agriculture, Forest Service, Intermountain Research 

Station, General Technical Report INT-302, Ogden, Utah. 38 pp.

Rhoads, B.L., and R.A. Cahill. 1999. Geomorphological assessment of sediment contamination 

in an urban stream system. Applied Geochemistry 14(4):459-483.

Rhodes, J.J., D.A. McCullough, and F.A. Espinosa Jr. 1994. A coarse screening process for 

potential application in ESA consultations. Columbia River Inter-Tribal Fish 

Commission, Technical Report 94-4, Portland, Oregon. 126 pp.

Roff, D.A.. 2002. Life history evolution. Sinauer Associates, Inc.; Sunderland, Massachusetts. 

Rosenberg, D.M., and N.B. Snow. 1975. A design for environmental impact studies with special 

reference to sedimentation in aquatic systems of the Mackenzie and Porcupine River 

drainages. Pages 65-78 In Proceedings of the circumpolar conference on northern 

ecology, September 15-18, 1975, National Research Council of Canada, Ottawa, 

Ontario. 12 pp.

Russo, R.C. 1985. Ammonia, nitrite, and nitrate. In: Fundamentals of aquatic toxicology and 

chemistry. Rand, G.M. and S.R. Petrocelli eds. Hemisphere Publishing Corp., 

Washington, D.C. pp. 455-471.
2015 MSGP Biological Opinion 116

Sandahl, J.F., D.H. Baldwin, J.J. Jenkins, and N.L. Scholz. 2007. A sensory system at the 

interface between urban stormwater runoff and salmon survival. Environmental Science 

& Technology 41(8):2998-3004.

Schreck, C.B. 1981. Stress and compensation in teleostean fishes: response to social and 

physical factors. Pages 295-321 In A.D. Pickering, ed. Stress and Fish, Academic Press, 

London; New York.

Schreck, C.B., W. Contreras-Sanchez, and M.S. Fitzpatrick. 2001. Effects of stress on fish 

reproduction, gamete quality, and progeny. Aquaculture 197:3-24.

Servizi, J.A., and D.W. Martens. 1991. Effect of temperature, season, and fish size on acute 

lethality of suspended sediments to coho salmon (Oncorhynchus kisutch). Canadian 

Journal of Fisheries and Aquatic Sciences 48(3):493-497.

Shaw, E.A., and J.S. Richardson. 2001. Direct and indirect effects of sediment pulse duration 

on stream invertebrate assemblages and rainbow trout (Oncorhynchus mykiss) growth 

and survival. Canadian Journal of Fisheries and Aquatic Sciences 58:2213-2221.

Shepard, B.B., S.A. Leathe, T.M. Weaver, and M.D. Enk. 1984. Monitoring levels of fine 

sediment within tributaries to Flathead Lake, and impacts of fine sediment on Bull 

trout recruitment. In Proceedings of the Wild Trout III Symposium, September 24 -

25, 1984, Mammoth Hot Springs, Yellowstone National Park, Wyoming. 11 pp.

Sigismondi, L.A., and L.J. Weber. 1988. Changes in avoidance response time of juvenile 

Chinook salmon exposed to multiple acute handling stresses. Transactions of the 

American Fisheries Society 117(2):196-201.

Sigler, J.W., T.C. Bjornn, and F.H. Everest. 1984. Effects of chronic turbidity on density and 

growth of steelheads and coho salmon. Transactions of the American Fisheries 

Society 113:142-150.

Skorupa, J.P. 1998.Selenium Poisoning of Fish and Wildlife in Nature: Lessons from twelve 

Real-World Examples. Pages 315-354 In W.T. Frankenberger, Jr. and R.A. Engberg, eds. 

Environmental Chemistry of Selenium, Marcel Dekker, INC, New York. 

Slaney, P.A., T.G. Halsey, and A.F. Tautz. 1977. Effects of forest harvesting practices on 

spawning habitat of stream salmonids in the Centennial Creek watershed, British 

Columbia. British Columbia Ministry of Recreation and Conservation, Fish and Wildlife 

Branch, Fisheries Management Report 73, Victoria, British Columbia.

Sprague, J.B. 1964. Avoidance of copper-zinc solutions by young salmon in the laboratory. 

Journal - Water Pollution Control Federation 36:990-1004.
2015 MSGP Biological Opinion 117

Sprague, J.B. 1968. Avoidance reactions of rainbow trout to zinc sulfate solutions. Water 

Research 2:367-372.

Sprague, J.B., and J.A. Ramsay. 1965. Lethal levels of mixed copper-zinc solutions for juvenile 

salmon. Journal of the Fisheries Research Board of Canada 22(2):425-432.

Stearns, S.C. 1992, The evolution of life histories. New York, New York, Oxford University 

Press. 

Suren, A.M., and I.G. Jowett. 2001. Effects of deposited sediment on invertebrate drift: an 

experimental study. New Zealand Journal of Marine and Freshwater Research 35:725-

537.

Suttle, K.B., M.E. Power, J.M. Levine, and C. McNeely. 2004. How fine sediment in riverbeds 

impairs growth and survival of juvenile salmonids. Ecological Applications 14(4):969-

974.

Sweka, J.A., and K.J. Hartman. 2001. Influence of turbidity on brook trout reactive distance and 

foraging success. Transactions of the American Fisheries Society 130:138-146.

Tomasso J.R., C.A. Goudie, B.A. Simco and K.B. Davis. 1980. Effects of environmental pH and 

calcium on ammonia toxicity in channel catfish. Trans. Am. Fish Soc. 109: 229-234.

Turchin, P. 2003. Complex population dynamics: a theoretical/empirical synthesis. Princeton 

University Press; Princeton, New Jersey. 

(USFWS) U.S. Fish and Wildlife Service. 1995. Snake River Aquatic Species Recovery Plan. 

Snake River Basin Office, Ecological Services, Boise, Idaho. 92 pp.

USFWS. 1998. Greenback cutthroat trout recovery plan. U.S. Fish and Wildlife Service, Denver, 

Colorado. 62 pp.

USFWS. 2002. Recovery Plan for the California Red-legged Frog (Rana aurora draytonii). 

U.S. Fish and Wildlife Service, Portland, Oregon. viii + 173 pp.

USFWS. 2003. Gila trout recovery plan (third revision). Albuquerque, New Mexico. i-vii + 78 

pp.

USFWS. 2005. Draft recovery plan for the Coastal-Puget Sound Distinct Population Segment 

of Bull Trout (Salvelinus confluentus). Volume I (of II): Puget Sound Management Unit. 

Portland, Oregon. 389+xvii pp.

USFWS. 2007. Recovery Plan for the Pacific coast population of the Western snowy plover 

(Charadrius alexandrinus nivosus). In 2 volumes. Sacramento, California. xiv + 751 

pages.

USFWS. 2009. Apache Trout Recovery Plan, Second Revision. Albuquerque, New Mexico. 76 

pp.
2015 MSGP Biological Opinion 118

USFWS and NMFS. 1998. Endangered Species Consultation Handbook: Procedures for 

conducting consultation and conference activities under section 7 of the Endangered 

Species Act. Washington D.C.

Vondracek, B., J.K.H. Zimmerman, and J.V. Westra. 2003. Setting an effective TMDL: 

sediment loading and effects of suspended sediment on fish. Journal of the American 

Association 39(5):1005-1015.

Wang N, Ingersoll CG, Hardesty DK, Ivey CD, Kunz JL, May TW, Dwyer FJ, Roberts AD, 

Augspurger T, Kane CM, Neves RJ, Barnhart MC. 2007a. Acute toxicity of copper, 

ammonia, and chlorine to glochidia and juveniles of freshwater mussels (Unionidae). 

Environmental Toxicolology and Chemistry 26: 2036-2047.

Wang N, Ingersoll CG, Greer IE, Hardesty DK, Ivey CD, Kunz JL, Brumbaugh WG, Dwyer FJ, 

Roberts AD, Augspurger T, Kane CM, Neves RJ, Barnhart MC. 2007b. Chronic toxicity 

testing of juvenile mussels with copper and ammonia. Environmental Toxicology and 

Chemistry 26: 2048-2056.

Watanabe, T., V. Kiron and S. Satoh. 1997. Trace minerals in fish nutrition. Aquaculture 151: 185-

207.

Waters, T.F. 1995. Sediment in streams: Sources, biological effects, and control. American 

Fisheries Society, Monograph 7, Bethesda, Maryland.

Watts, C.D., P.S. Naden, D. Cooper, and B. Gannon. 2003. Application of a regional 

procedure to assess the risk to fish from high sediment concentrations. The Science of 

the Total Environment 314-316:551-565.

WERF (Water Environment Research Foundation) 2010. Linking Receiving Water Impacts to 

Sources and to Water Quality Management Decisions: Using Nutrients As An Initial 

Case Study. WERF 3C10. IWA Publishing, London.

Wong, T., P. Breen, and S. Lloyd. 2000. Water sensitive road design - design options for 

improving stormwater quality of road runoff. Cooperative research centre for catchment 

hydrology, 00/1. 83 pp.

Woock, S.E., W.R. Garrett, W.R. Partin, and W.T. Bryson. 1987. Decreased survival and 

teratogenesis during laboratory selenium exposures to bluegill, Lipomis macrochirus. 

Bulletin of Environmental Contamination and Toxicology. 39:998-1005.

Zamor, R.M., and G.D. Grossman. 2007. Turbidity affects foraging success of drift-feeding 

rosyside dace. Transactions of the American Fisheries Society 136:167-176.