Endangered Species Act Section 7 Consultation

Programmatic Biological and Conference Opinion on the 

U.S. Environmental Protection Agency’s 

Proposed Vessel General Permit and Small Vessel General Permit

U.S. Fish and Wildllife Service

Endangered Species Program

Arlington, Virginia
Consultation History................................................................................................................... 2

DESCRIPTION OF THE PROPOSED ACTION..................................................................... 3

Vessel General Permit (VGP)..................................................................................................... 4

Discharges to be Authorized by the VGP............................................................................... 5

VGP Vessel-Class-Specific Requirements........................................................................... 24

VGP Inspections, Recordkeeping, Reporting, Compliance, and Enforcement .................... 30

Small Vessel General Permit (sVGP)....................................................................................... 38

Discharges to be Authorized by the sVGP ........................................................................... 38

sVGP Recordkeeping, Inspections, Compliance, and Enforcement..................................... 45

Additional Specific Actions Taken by EPA to Conserve Listed Resources............................. 47

Reinitiation Clause................................................................................................................ 47

VGP Requirements ............................................................................................................... 47

sVGP Requirements.............................................................................................................. 48

VGP Compliance .................................................................................................................. 48

sVGP Compliance................................................................................................................. 49

Monitoring of Stressors (ANS and Pollutants)..................................................................... 50

APPROACH TO THE ASSESSMENT.................................................................................... 52

OVERVIEW OF FWS’ ASSESSMENT FRAMEWORK...................................................... 53

Application of this Approach in this Consultation ................................................................... 57

Evidence Available for the Consultation .................................................................................. 62

Treatment of “Cumulative Impacts” (in the sense of NEPA)..................................................... 63

ACTION AREA .......................................................................................................................... 64

STATUS OF THE SPECIES AND CRITICAL HABITAT AND ENVIRONMENTAL

BASELINE .................................................................................................................................. 65

Species and Critical Habitat Not Likely to be Adversely Affected by the Proposed Action ... 82

Species and Critical Habitat Likely to be Adversely Affected by the Proposed Action .......... 82

ENVIRONMENTAL BASELINE............................................................................................. 83

The Changing Landscapes of the United States ....................................................................... 84
Status and Trends of Waters of the United States..................................................................... 86

Aquatic Nuisance Species..................................................................................................... 87

Climate Change..................................................................................................................... 87

Clean Water Act.................................................................................................................... 90

San Francisco Bay as an Example of the Impact.................................................................. 91

Integration and Synthesis of the Environmental Baseline ........................................................ 92

EFFECTS OF THE PROPOSED ACTION, TRADITIONAL APPROACH ...................... 93

Vessel Populations Covered by the VGPs................................................................................ 94

VGP Vessels ......................................................................................................................... 94

sVGP Vessels........................................................................................................................ 98

Aquatic Nuisance Species....................................................................................................... 101

Exposure Analysis .............................................................................................................. 101

Stressors.............................................................................................................................. 111

Response Analysis.............................................................................................................. 112

Extinction and Endangerment as a Result of ANS Invasions............................................. 120

Traditional Pollutants.............................................................................................................. 122

Exposure Analysis .............................................................................................................. 122

Response Analysis.............................................................................................................. 157

EFFECTS OF THE PROPOSED ACTION, PROGRAMMATIC APPROACH .............. 183

(1) Scope ................................................................................................................................. 183

(2) Stressors ............................................................................................................................ 185

ANS..................................................................................................................................... 185

Pollutants............................................................................................................................. 186

(3) Exposure to potentially harmful impacts .......................................................................... 188

Uncertainties in Exposure Estimates Identified by EPA .................................................... 188

Services Assessment of Uncertainty in the Exposure Analysis.......................................... 189

ANS..................................................................................................................................... 190
(4) Monitoring/Feedback ........................................................................................................ 191

(5) Effects on Listed Resources.............................................................................................. 195

Uncertainty in Effects Analysis Identified by EPA ............................................................ 195

Services Assessment of Uncertainty in the Repose Analysis............................................. 197

ANS..................................................................................................................................... 198

(6) Compliance........................................................................................................................ 198

(7) Adequacy of Controls........................................................................................................ 204

CUMULATIVE EFFECTS...................................................................................................... 206

INTEGRATION AND SYNTHESIS....................................................................................... 206

CONCLUSION ......................................................................................................................... 210

INCIDENTAL TAKE STATEMENT..................................................................................... 211

Amount or Extent of Take ...................................................................................................... 211

Reasonable and Prudent Measures.......................................................................................... 212

Terms and Conditions............................................................................................................. 212

CONSERVATION RECOMMENDATIONS........................................................................ 213

REINITIATION NOTICE....................................................................................................... 213

LITERATURE CITED ............................................................................................................ 214
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LIST of TABLES

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and 

Proposed Critical Habitat in the Action Area. There are 45 Candidates for listing also included 

and treated herein as “Proposed.” ................................................................................................. 65

Table 2. Phenomena associated with projections of global climate change including levels of 

confidence associated with projections......................................................................................... 89

Table 3. Distribution of vessel service classes, equipment, and metrics among VGP covered 

vessels submitting NOIs and reporting vessel tonnage/ballast water capacity............................. 98

Table 4. Vessel metrics for sVGP eligible vessels with specified length less than 79.............. 100

Table 5. Vessel service class relative distribution of ballast water capacity reported in the NOI 

database....................................................................................................................................... 106

Table 6. Discharge classes authorized under the Vessels General Permit and small vessels 

general permit. ............................................................................................................................ 123

Table 7. Copper loading AFC of various vessel service classes................................................. 125

Table 8. Estimated Bilgewater Discharge Rates used in EPAs BE Analyses. .......................... 126

Table 9. Estimated Bilgewater Pollutant Concentrations used in EPAs Biological Evaluation 127

Table 10. Estimated Deck Washdown Discharge Rates used in EPAs BE Analysis. ............... 128

Table 11. Estimated Deckwash Pollutant Concentrations used in EPAs Biological Evaluation.

..................................................................................................................................................... 129

Table 12. Estimated Propulsion and Generator Engine Wet Exhaust Discharge Rates used in 

EPAs Analysis. ........................................................................................................................... 130

Table 13. Estimated Engine Wet Exhaust Pollutant Concentrations used in EPAs Biological 

Evaluation. .................................................................................................................................. 131

Table 14. Estimated Exhaust Gas Scrubber Washwater Discharge Rates used in EPAs Analysis

..................................................................................................................................................... 132

Table 15. Estimated Exhaust Gas Scrubber Washwater Pollutant Concentrations used in EPAs 

Biological Evaluation.................................................................................................................. 133

Table 16. Fish Hold Effluent and Cleaning Effluent Discharge Rates. ..................................... 133

Table 17. Estimated Fish Hold and Fish Hold Cleaning Effluent Pollutant Concentrations used 

in EPAs Biological Evaluation. .................................................................................................. 135

Table 18. Estimated Graywater Discharge Rates Used in EPAs BE......................................... 136

Table 19. Estimated Graywater Pollutant Concentrations used in EPAs Biological Evaluation.

..................................................................................................................................................... 137

Table 20. Estimated Stern Tube Packing Gland Effluent Discharge Rates used in EPAs BE. . 138

Table 21. Estimated Stern Tube Packing Gland Effluent Pollutant Concentrations used in EPAs 

Biological Evaluation.................................................................................................................. 138

Table 22. Dissolved Copper Release from Vessel AFSs During an Underwater Hull Cleaning 

“Event”........................................................................................................................................ 139
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Table 23. Decision Process for those Vessel Discharges Not Evaluated in EPA's BE. ............ 141

Table 24. RAAs Selected for Exposure Assessment Modeling to Represent Water Bodies and 

Ecosystems Inhabited by Listed Resources. ............................................................................... 147

Table 25. Receiving Water Model Scenarios Assessed by EPA. .............................................. 149

Table 26. Estimated Receiving Water Concentrations Resulting from Vessel Discharge Pollutant 

Loadings Under Estuary Mixing Conditions. ............................................................................. 151

Table 27. Estimated Receiving Water Concentrations Resulting from Vessel Discharge Pollutant 

Loadings Under River Mixing Conditions. ................................................................................ 153

Table 28. Average nutrient concentrations in vessel discharges at levels above screening level 

benchmarks. ................................................................................................................................ 159

Table 29. Generalized steps in ecosystem-scale methodology for translation of a tissue Se 

concentration to a water-column Se concentration for protection of fish and aquatic-dependent 

wildlife. ....................................................................................................................................... 170

Table 30. Equations used to calculate Fish and Bird ECT’s for the Biological Opinion. .......... 171

Table 31. Kd and TTF values used to calculate fish and bird ECT’s.......................................... 171

Table 32. Application of the Ecosystem-scale approach to: a) estimate tissue concentrations of 

selenium from water concentrations predicted from vessel discharges, and b) calculating risk 

quotients for sensitive fish and bird species. .............................................................................. 173
U.S. Fish and Wildlife Service

Endangered Species Act Section 7 Consultation

Biological and Conference Opinion 

Agency: United States Environmental Protection Agency

Activities Considered: Proposed issuance and implementation of the Vessel 

General Permit and the Small Vessel General Permit, 

which would authorize discharges incidental to the normal 

operation of vessels in waters of the United States from 

2013 through 2017

Consultation Conducted by: Branch of Consultation and HCPs, Endangered Species 

Program, U.S. Fish and Wildlife Service

Approved by:

__________________________________________________ 

Paul Souza, Deputy Assistant Director

 Endangered Species Program

Date: 

___________________________________________________

Section 7(a)(2) of the Endangered Species Act of 1973, as amended (ESA; 16 U.S.C. 1536(a)(2)) 

requires Federal agencies to insure that any action they authorize, fund, or carry out 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. When a Federal agency’s 

action “may affect” a protected species, that agency is required to consult formally with the 

National Marine Fisheries Service (NMFS) or the U.S. Fish and Wildlife Service (FWS; 

together, “the Services”), depending upon the endangered species, threatened species, or 

designated critical habitat that may be affected by the action (50 CFR 402.14(a)). Federal 

agencies are exempt from this general requirement if they determine that an action “may affect, 

but is not likely to adversely affect” endangered species, threatened species, or designated 

critical habitat, and if the Services concur with that determination (50 CFR 402.14(b)). 

The U.S. Environmental Protection Agency (EPA) initiated formal consultation with the 

Services on EPA’s proposal to authorize discharges incidental to the normal operation of vessels 

and small vessels into waters of the United States from 2013 through 2018 under the National 

Pollutant Discharge Elimination System (NPDES) permit program, as authorized by the Clean 

Water Act. This document represents FWS’ Biological Opinion (Opinion) on EPA’s issuance 

and implementation of its Vessel General Permit (VGP) and Small Vessel General Permit 

(sVGP; together the VGPs) and their effects on ESA listed and proposed species and critical 
2

habitat. This Opinion is based on our review of the EPA’s draft VGPs, EPA’s Biological 

Evaluation (BE), EPA’s fact sheets, reviews of the effectiveness of the NPDES program and 

compliance for existing general permits, Section 7 consultations on Clean Water Act actions, 

species status reviews, listing documents, recovery plans, reports on the status and trends of 

water quality, past and current research and population dynamics modeling, published and 

unpublished scientific information, and other sources of information gathered and evaluated 

during our consultation on the proposed VGPs. This Opinion has been prepared in accordance 

with section 7 of the ESA, associated implementing regulations, and agency policy and guidance 

(50 CFR 402; U.S. Fish and Wildlife Service and NMFS 1998a).

Consultation History

On March 30, 2005, the U.S. District Court for the Northern District of California (in Northwest 

Environmental Advocates et al. v. EPA) issued a ruling vacating a long-standing regulatory 

NPDES permitting exclusion for vessels. 

On May 7, 2008 EPA requested Sec. 7 consultation with FWS on its planned issuance of a 

Vessel General Permit for Discharges Incidental to the Normal Operation of Commercial Vessels 

and Large Recreational Vessels, and a General Permit for Discharges Associated with 

Recreational Vessels. On July 18, 2008, FWS delivered notice to EPA determining that its 

initiation package was insufficient to initiate consultation.

On July 23, 2008, the Ninth Circuit upheld the District Court’s decision after EPA appealed. On 

July 31, 2008, Public Law 110-299 was signed into law and provided a two-year moratorium for 

non-recreational vessels less than 79 feet in length and all commercial fishing vessels regardless 

of length, from the requirements of NPDES (with the exception of ballast water). This law also 

directed the EPA to study the impacts of discharges incidental to the normal operation of those 

vessels and evaluate potential impacts.

On December 18, 2008, EPA finalized the first Vessels General Permit.

On July 30, 2010, the Congressional moratorium initiated by Public Law 110-299 was extended 

by Public Law 111-215 until December 18, 2013. In August 2010, EPA published its final 

“Report to Congress: Study of Discharges Incidental to Normal Operation of Commercial 

Fishing Vessels and Other Non-Recreational Vessels Less than 79 Feet.” The report noted that 

many of the pollutants present in the vessel discharges were at end-of-pipe concentrations that 

exceeded an NRWQC; there is the potential for these discharges to contribute a water quality 

impact on a more localized scale. The study results indicate that total arsenic and dissolved 

copper were the most significant water quality concerns for the study vessels as a whole, as they 

are more likely than other pollutants to contribute to exceedances of water quality criteria. In 

2011, at the request of EPA the National Academies of Sciences published a report on 

“Assessing the Relationship Between Propagule Pressure and Invasion Risk in Ballast Water.” 

That report noted that data “are not sufficient in present form to characterize a biologically 

meaningful relationship, much less estimate the associated uncertainty, to be able to identify with 

confidence the invasion probabilities associated with particular discharge standards.”
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EPA published a draft VGP by on December 8, 2011 and plans to issue the final VGP by 

November 30, 2012, one year before the expiration of the current permit.

On November 29, 2011, EPA initiated informal Section 7 consultation on its proposed 2013 

VGPs. On July 3, 2012, EPA’s Office of Water requested formal Section 7 consultation on the 

draft VGPs. Their initiation package included the draft permits, fact sheets, a Biological

Evaluation (BE), and responses to the Service’s comments during informal consultation.

As described in a joint letter sent by the Services on August 6, 2012, we confirmed initiation of

formal consultation effective July 3, 2012. We also sent our analysis plan, including the 

Services’ joint “Approach to the Assessment,” which is included in this Opinion.

BIOLOGICAL AND CONFERENCE OPINION

Description of the Proposed Action

Under the Vessel General Permit (VGP) and the Small Vessel General Permit (sVGP, together 

the VGPs), EPA proposes to authorize discharges incidental to the normal operation of all nonrecreational and non-military vessels into waters of the U.S. The EPA expects that most vessels 

seeking coverage under the VGP will be greater than 79 feet in length, whereas vessels less than 

79 feet may be eligible for coverage under the sVGP, which has less stringent restrictions and 

fewer reporting requirements. The EPA estimates that approximately 72,000 vessels may be 

eligible for coverage under the VGP, and an additional 138,000 vessels under the sVGP 

(http://www.epa.gov/npdes/vessels). 

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 permits is to satisfy the goals and policies of the CWA (33 USC 1251). 

Requiring a CWA permit for these discharges provides EPA with the authority to enforce CWA 

requirements and provides the ability of citizens to sue for permit violations.

For both permits, EPA includes the follow clause for modification of the permits and reinitiation: 

Permit modification or revocation will be conducted according to 40 CFR §§ 122.62, 122.63, 

122.64, and 124.5.This permit is subject to modification in accordance with 40 CFR §§ 124.5 

and 122.62. Grounds for such modification include receipt of new information that was not 

available at the time of permit issuance (other than revised regulations, guidance, or test 

methods) and would have justified the application of different permit conditions at the time of 

permit issuance. This information would also allow EPA to determine whether to request 

reinitiation of formal ESA Section 7 consultation as provided in 50 CFR 402.16 and described in 

the VGPs Fact Sheets. 
4

For the VGP, with respect to ballast water discharges, new information that will be considered in 

determining whether to modify this permit includes, but is not limited to, data or information 

from permittees, the general public, states, academia, scientific or technical articles or studies, 

and results of monitoring conducted under this permit indicating that: 

• Treatment technology has improved such that these improved technologies would have 

justified the application of significantly more stringent effluent limitations or other permit 

conditions had they been known at the time of permit issuance; 

• Treatment technologies known of at the time of permit issuance perform better than 

understood at the time of permit issuance such that this improved performance would 

have justified the application of significantly more stringent effluent limitations or other 

permit conditions had this been understood at the time of permit issuance; 

• Scientific understanding of pollutant effects or of invasion biology has evolved such 

that this new information would have justified the application of significantly more 

stringent effluent limitations or other permit conditions had this been understood at the 

time of permit issuance; or 

• The cumulative effects of any discharge authorized by the VGP on the environment are 

unacceptable. 

Vessel General Permit (VGP)

The proposed VGP authorizes discharges incidental to the normal operation of a vessel into 

waters of the U.S. The following narrative describes the discharges that will be authorized or 

prohibited should the EPA issue the VGP. It also describes the activities that EPA will require of 

vessel owners/operators for vessels covered under the VGP, including reporting and compliance 

requirements. 

Unless expressly prohibited, all discharges of pollutants into waters of the U.S. incidental to the 

normal operation of all eligible vessels are eligible to be authorized by the proposed VGP. In 

this Opinion, we assess the effects of all authorized discharges, which EPA has grouped into the 

following broad discharge types:

 Deck Washdown and Runoff, and Above Water Line Hull Cleaning

 Bilgewater and Oily Water Separator Effluent

 Ballast Water

 Anti-fouling Hull Coatings/Hull Coating Leachate

 Aqueous Film Forming Foam (AFFF) 

 Boiler/Economizer Blowdown

 Cathodic Protection

 Chain Locker Effluent

 Controllable Pitch Propeller and Thruster Hydraulic Fluid and other Oil Sea Interfaces

 Distillation and Reverse Osmosis Brine

 Elevator Pit Effluent

 Firemain Systems
5

 Freshwater Layup

 Gas Turbine Washwater

 Graywater

 Motor Gasoline and Compensating Discharge

 Non-Oily Machinery Wastewater

 Refrigeration and Air Condensate Discharge

 Seawater Cooling Overboard Discharge

 Seawater Piping Biofouling Prevention

 Boat Engine Wet Exhaust

 Sonar Dome Discharge. 

 Underwater Ship Husbandry

 Welldeck Discharges

 Graywater Mixed with Sewage from Vessels

 Exhaust Gas Scrubber Washwater Discharge

 Fish Hold Effluent

The VGP also contains requirements to address hull foulding, which can result in the discharge 

of aquatic nuisance species into waters of the US. As vessels move from one area to another, 

they often carry fouling organisms on their hulls or other exposed surfaces. These organisms 

may release themselves or gametes into ports, harbors, or waterways. Hull fouling is considered 

to be one of the main sources of aquatic nuisance species.

Discharges not authorized by the VGP include: sewage, used or spent oil, garbage or trash, 

photo processing effluent, dry cleaning effluent, medical waste, noxious liquid substance 

residues, tetrachloroethylene (perchloroethylene) and trichloroethylene degreasers, discharges 

from vessels not operated as a means of transportation, and discharges covered by other permits.

Discharges to be Authorized by the VGP

For vessels covered under the VGP, EPA requires vessel owners and operators to minimize 

vessel discharges. They define minimize as to reduce and/or eliminate to the extent achievable 

using control methods, including best management practices, that are technologically available

and economically practicable and achievable in light of best marine practices. They require all 

vessel owner/operators to ensure adequate training for the master, operator, person-in-charge, 

and crew who manage or affect incidental discharges.

Water Quality-Based Effluent Limits

For vessels covered under the VGP, EPA requires vessel owners/operators to control their 

discharges as necessary to meet applicable water quality standards in the receiving water body or 

another water body impacted by a vessel’s discharges. The EPA requires corrective actions, as 

described below, if they or the vessel owner operators become aware that a vessel’s discharges 

are causing or contributing to an exceedance of applicable water quality standards. They also 
6

require that the vessel owners/operators report the exceedence to EPA. Vessel discharges must 

be consistent with the assumptions and requirements of a specified waste load allocation (WLA) 

if the owners/operators discharge to an impaired water with an EPA-approved or established 

total maximum daily load (TMDL) as indicated by EPA or state TMDL authorities. EPA will

inform vessel owners/operators if such a WLA exists and if any additional limits or controls are 

necessary for discharges to be consistent with the assumptions of any available WLA in the 

TMDL, or whether an individual permit application is necessary. The EPA and/or state TMDL 

agencies will inform vessel owners/operators if an applicable TMDL exists either individually or 

categorically for their vessel or vessel class (including disallowing discharges).

Technology-Based Effluent Limits

For vessels covered under the VGP, EPA will require all vessel owners and operators to meet the 

effluent limits as described below for each authorized discharge.

Material Storage. For vessels covered under the VGP, EPA requires vessel owners and operators 

to minimize the potential for cargoes or materials to blow overboard or dissolve in sea spray by 

minimizing exposure time and using covered storage areas. The EPA does not authorize the 

discharge of oil in quantities that may be harmful, which might otherwise be inconsistent with 

requirements found in Section 311 or the Clean Water Act or the Act to Prevent Pollution from 

Ships or under the International Convention for the Prevention of Pollution from Ships, 1973 as 

modified by the protocol of 1978 (MARPOL 73/78). If water draining from storage areas comes 

in contact with oily materials, the vessel owners and operators must: 

 Use dry cleanup methods or absorbents to clean up the wastewater; 

 Store the water for onshore disposal; or 

 Run water through oily water separator as required by Coast Guard regulations, or other 

effective method 

Toxic and Hazardous Materials. For vessels covered under the VGP, EPA requires vessel 

owners and operators to minimize the potential for discharge of toxic and hazardous materials as 

follows:

 Store toxic and hazardous materials in appropriate sealed containers constructed of a 

suitable material, labeled, and secured; the containers must not be overfilled; wastes 

should not be mixed

 Locate toxic and hazardous materials in protected areas 

 Report any dischanges 

Fuel Spills/Overflows. For vessels covered under the VGP, EPA prohibits the discharge of oil in 

harmful quantities (40 CFR Part 110). The VGP does not authorize large-scale fuel spills or 

overflows, which are not incidental to the normal operation of the vessel. They require vessel 

owners and operators to:
7

 Conduct fuel operations using control measures and practices designed to minimize spills 

and overflows and ensure prompt containment and cleanup. 

 Conduct fueling in a manner that prevents overfilling and release from the system to the 

environment. 

 For vessels with air vents from fuel tanks, use spill containment or other methods to 

prevent or contain any fuel or oil spills

 Owner/operators shall ensure that any crew members responsible for conducting fueling 

operations are trained in methods to minimize spills caused by human error and/or the 

improper use of equipment

 For fueling of auxiliary vessels, (e.g., lifeboats, tenders or rescue boats), vessel owners 

and operators must:

o While fueling, examine the surrounding water for the presence of a visible sheen. If a 

visible sheen is observed, as a result of your fueling, it must be cleaned up 

immediately. 

o Know the capacity of the fuel tanks before you begin fueling in order to prevent 

unintentionally overfilling the tank. 

o Prevent overfilling and do not top off your fuel tanks. 

o When possible, fill fuel tanks while boat is on shore or recovered from the water. 

o When possible, fill portable tanks on shore or on the host vessel, not on the auxiliary 

vessel. 

o Use an oil absorbent material or other appropriate device while fueling the auxiliary 

vessel to catch drips from the vent overflow and fuel intake. 

o Regularly inspect the fuel and hydraulic systems for any damage or leaks, for instance 

during fueling, when performing routine maintenance on the auxiliary vessel, and/or 

during deployments for testing.

Deck Washdown and Runoff/Above the Water Line Hull Cleaning. The proposed permit

authorizes the discharge of deck washdown and runoff from deck and bulkhead areas, associated 

equipment, areas of the hull, and exteriors of the vessel above the water line as a result of 

precipitation or from washing. Pollutant discharges may include residues and any soaps or 

detergents used for cleaning. 

For vessels covered under the VGP, EPA requires vessel owner/operators to minimize the 

introduction of on-deck debris, garbage, residue, and spill into deck washdown and runoff 

discharges. They require vessel owner/operators to broom clean exposed decks or use 

comparable managmenet measures to remove all existis debris prior to deck washdown. In 

addition, EPA requires vessel owner/operators to:

 Minimize the presence of floating solids, visible foam, halogenated phenol compounds, 

and dispersants, or surfactants in deck washdowns

 Minimize deck washdowns while in port

 Maintain their topside surface and other areas above water line portions of the vessel to 

minimize the discharge of rust (and other corrosion by-products), cleaning compounds, 
8

paint chips, non-skid material fragments, and other materials associated with exterior 

topside surface preservation

 Minimize residual paint droplets from entering waters subject to this permit whenever 

they are conducting maintenance painting. Minimization techniques include, but are not 

limited to: avoiding paint spraying in windy conditions or avoiding overapplication of 

paint. Disposal of unused paint into waters of the U.S. is not permitted under the VGP.

 Deck washdowns or above water line hull cleaning that will result in a discharge must be 

conducted with biodegradable, “non-toxic,” and “phosphate free” cleaners and detergents 

as defined in Appendix A of the VGP. EPA expects that soaps that are “minimally” or 

non-toxic will contain little to no nonylphenols

 Where necessary and feasible, machinery on deck must have coamings or drip pans to 

collect any oily discharge that may leak from machinery and prevent spills. The drip pans 

must be drained to a waste container for proper disposal and/or periodically wiped and 

cleaned. 

Bilgewater/Oily Water Separator Effluent. The proposed permit authorizes the discharge of 

bilgewater and the residues that accumulate therein. These residues may originate from 

machinery and from deck drainage etc. Pollutant discharges may include seawater, oil, grease, 

organic compounds, inorganic salts, and metals. 

All bilgewater discharges must be in compliance with the regulations in 40 CFR Parts 110 

(Discharge of Oil), 116 (Designation of Hazardous Substances), and 117 (Determination of 

Reportable Quantities for Hazardous Substances) and 33 CFR §151.10 (Control of Oil 

Discharges). Under the VGP, EPA prohibits:

 Use of dispersants, detergents, emulsifiers, chemicals, or other substances that remove 

the appearance of a visible sheen in their bilgewater discharges 

 Addition of substances that drain to the bilgewater and are not produced in the normal 

operation of a vessel 

 Use of oil solidifiers, flocculants, or other required additives, unless used as part of an oil 

water separation system during processing and provided they do not alter the chemical 

make-up of the oils being discharged. The EPA requires vessel owners/operators to 

minimize any discharge of such materials into waters of the U.S. 

 Vessel owners/operators must minimize the discharge of bilgewater by minimizing the 

production of bilgewater, disposing of bilgewater on shore where adequate facilities 

exist, or discharging into waters not subject to this permit (i.e., more than 3 nautical miles 

from shore) following regulations under Annex I of the International Convention for the 

Prevention of Pollution from Ships as implemented by the Act to Prevent Pollution from 

Ships and U.S. Coast Guard regulations found in 33 CFR part 151. 

 For vessels greater than 400 gross tons, the following will be prohibited: 

o Discharge of untreated oily bilgewater

o Discharge of treated bilgetwater within 1nm of shore, if technologically feasible (e.g., 

holding does not impact safety and stability, does not contaminate other holds or 
9

cargo, or does not interfere with essential operations of the vessel). Any discharge 

which is not technologically feasible to avoid must be documented and reported to 

EPA as part of the vessel’s annual report.

o Discharge of treated bilgewater into federally protected waters referenced in 

Appendix G of the VGP, unless the discharge is necessary to maintain the safety and 

stability of the ship. Any discharge of bilgewater into these waters must be 

documented and reported to EPA as part of the vessel’s annual report. 

o For vessels that regularly sail outside the territorial sea (at least once per month), if 

treated bilgewater is discharged into waters subject to this permit, it must be 

discharged when the vessel is underway (sailing at speeds greater than 6 knots), 

unless doing so threatens the safety and stability of the ship. EPA notes that vessel 

operators may also choose to dispose of bilgewater on shore where adequate facilities 

exist. Any discharge, which is made for safety reasons must be documented and 

reported to EPA as part of the vessel’s annual report. 

For new builds (on or before December 19, 2013), EPA requires electronic submittal of annual 

oil content monitoring. 

Ballast Water. Ballast water is water taken on to vessels to aid in buoyancy and stability and in 

increasing or decreasing the vessel’s draft. According to EPA, cruise ships have a typical ballast 

capacity of 1,000 cubic meters and cargo ships may contain up to 93,000 cubic meters. Pollutant 

discharges from ballast water may include contain rust inhibitors, flocculent compounds, epoxy 

coating materials and metals. Ballast water may also serve as a vector for biological pollutants 

including aquatic nuisance species (ANS) and pathogens.

For vessels covered under the VGP, EPA requires vessel owner/operators to ensure adequate, 

prompt training for the master, operator, person-in-charge, and crew who manage, take part in, or 

affect ballast water discharge. All vessel owners/operators are required to maintain a written 

training plan, including a description of the training, the date of the training, and the names of 

those that were trained. They are required to maintain a ballast water management plan 

developed specifically for their vessel that will ensure that those responsible for the plan’s 

implementation understand and follow the vessel’s ballast water management strategy (i.e., how 

the vessel will meet the requirements of the VGP). 

The EPA requires owner/operators of vessels with ballast water tanks to:

 Avoid the discharge or uptake of ballast water in Federally Protected Waters (listed in 

Appendix G of the VGP)

 Minimize or avoid uptake of water in 

o Critical habitat of ESA listed species

o Areas known to have infestations or populations of harmful organisms and pathogens 

(e.g., toxic algal blooms)

o Areas near sewage outfalls

o Areas near dredging operations
10

o Areas where tidal flushing is known to be poor or times when a tidal stream is known 

to be turbid

o In darkness, when bottom-dwelling organisms may rise up in the water column

o Where propellers may stir up the sediment

o Areas with pods of whales, convergence zones, and boundaries of major currents 

 Clean ballast tanks regularly to remove sediments in mid-ocean (when not otherwise 

prohibited by applicable law) or under controlled arrangements in port, or at dry dock

 No discharge of sediments from cleaning of ballast tanks is authorized in waters subject 

to this permit

 When discharging ballast water in port, if the vessel is equipped with high and low 

suction within ballast tanks, utilize the high suction for ballast tank discharge to minimize 

the discharge of entrained sediment. The low suction may be used to strip sediment from 

tanks when suitable disposal facilities are available

 Minimize the discharge of ballast water essential for vessel operations while in the waters 

subject to this permit

For vessels covered under the VGP, EPA requires certain vessel owner/operators to meet the 

following discharge limits: 

1. For organisms greater than or equal to 50 micrometers in minimum dimension: 

discharge must include fewer than 10 living organisms per cubic meter of ballast water. 

2. For organisms less than 50 micrometers and greater than or equal to 10 micrometers: 

discharge must include fewer than 10 living organisms per milliliter (mL) of ballast 

water. 

3. Indicator microorganisms must not exceed: 

(i) For Toxicogenic Vibrio cholerae (serotypes O1 and O139): a concentration of 

less than 1 colony forming unit (cfu) per 100 mL. 

(ii) For Escherichia coli: a concentration of fewer than 250 cfu per 100 mL. 

(iii) For intestinal enterococci: a concentration of fewer than 100 cfu per 100 mL. 

The EPA will continue to explore new technologies with industry and states, and when 

warranted, will make this numeric limit more stringent in the future. Additionally, EPA 

encourages and anticipates, as part of this process, that States will continue to work with industry 

to test and provide opportunities for new technologies. 

The EPA authorizes four methods for meeting the above ballast water discharge limits: ballast 

water treatment system; onshore treatment of ballast water; use of public water supply; or no 

discharge of ballast water. 

The EPA has established dates by which vessels, categorized by size and drydock date, are 

required to use ballast water treatment systems (BWTS) as the best available technology 

economically achievable. Under the VGP, EPA requires a BWTS which has been shown to be 

effective by testing in accordance with the EPA-ETV protocol for the verification of ballast 

water treatment technology conducted by an independent third party laboratory, test facility or 
11

test organization. Following installation of a BWTS, EPA requires the master, owner, operator, 

agent, or person in charge of the vessel to maintain the BWTS in accordance with all 

manufacturer specifications. Furthermore, EPA requires all treatment to be conducted in 

accordance with the BWTS manufacturer’s instructions. The BWTS must be used prior to any 

discharge of ballast water to waters of the U.S. Under the proposed VGP, EPA would require:

 Monthly monitoring of equipment performance to assure the system is fully functional

 Annual calibration of ballast water monitoring equipment

 Biannual monitoring from all ballast water systems for selected biological indicators (i.e., 

heterotrophic bacteria, E. coli, and Enterococci

 Biannual monitoring of the ballast water discharge itself for biocides and residuals (e.g. 

chlorine dioxide, chlorine, ozone, peracetic acid, hydrogen peroxide, etc.) to assure 

compliance with the effluent limitations 

 Annual electronic submittal of above listed testing results to the EPA

For those vessels whose design and construction safely allows for the transfer of ballast water to 

shore, EPA requires vessel owners/operators to ensure that all piping and supporting 

infrastructure up to the last manifold or valve immediately before the dock manifold connection 

of the receiving facility or similar appurtenance on a reception vessel must be fully free from any 

leaks or other avenues whereby untreated ballast may be discharged into waters subject to this 

permit. The EPA notes that transferring ballast water to a treatment barge for eventual treatment 

and discharge could constitute “on-shore treatment” for purposes of this subpart. The discharge 

of treated ballast water (transferred from other vessels) from a treatment barge is not eligible for 

coverage under the VGP as this is a discharge from an industrial operation, not a discharge 

incidental to the normal operation of a vessel. Instead, these vessels must apply for individual 

NPDES permit coverage from the appropriate NPDES permitting authority, generally the State 

in which they are operating. 

For vessels using water from a public water supply (PWS) as ballast, EPA requires that vessel 

owners/operators maintain a record of which PWS they received the water and a receipt, invoice, 

or other documentation from the PWS indicating that water came from that system. 

The EPA requires those vessels to use PWS water exclusively for all ballast water to avoid 

contamination of the ballast water tank. The EPA requires those vessels to have either: 

 Previously cleaned the ballast tanks (including removing all residual sediments) and not 

subsequently introduced ambient water; or 

 Never introduced ambient water to those tanks and supply lines. 

The EPA requires vessels utilizing water from a PWS as ballast water to certify in their 

recordkeeping documentation that they have met all the requirements of this section, including 

maintaining certification by the master or NOI certifier that one of the two above conditions are 

met regarding contamination. In the event a vessel that normally uses PWS water as ballast is 

forced for purposes of vessel safety to take on untreated ballast water from a sea, estuary, lake or 

river source, EPA prohibits the vessel from returning to using PWS water until the tanks and 
12

supply lines have been cleaned, including removal of all residual sediments. 

For certaiun vessels that are not required to meet the ballast water management measures (i.e., 

those that leave the US Exclusive Economic Zone and those engaged in Pacific nearshore 

voyages), EPA requires the vessel to exchange ballast water as follows:

 The exchange must occur in waters beyond the U.S. EEZ

 The exchange must occur in an area more than 200 nautical miles from any shore; 

 The exchange must be commenced as early in the vessel voyage as possible, as long as 

the vessel is more than 200 nm from any shore. 

 For vessels engaged in Pacific nearshore voyages

o Ballast water must occur in waters more than 50 nautical miles from any shore (US or 

otherwise), in waters more than 200 meters deep, prior to discharging ballast water 

into waters subject to this permit.

o Exchange should occur as far from the shore, major estuary and oceanic river plumes, 

subsurface physical features (e.g. seamounts), and known fishery habitats as 

practicable. 

For those tanks which are empty or contain unpumpable residual water, EPA requires vessel 

owners/operators to either seal the tank so that there is no discharge, or uptake and subsequent 

discharge of ballast water within waters subject to this permit or conduct saltwater flushing of 

such tanks in an area 50 nm from any shore and in waters at least 200 meters deep prior to the 

discharge or uptake and subsequent discharge of any ballast water to or from any waters subject 

to this permit. 

Anti-Fouling Hull Coatings/ Hull Coating Leachate. Vessel hull coatings can contain toxics and

may contain biocides designed to prohibit the growth of fouling organisms. These coatings 

discharge pollutants by leaching toxics into the water. Copper is a common biocide found in hull 

coatings. Discharges of the biocide tributyltin (TBT) and other organotin compounds are not 

permitted by the proposed permit due to their persistence in the environment and their high 

toxicity to marine life. 

For vessels covered under the VGP, EPA requires vessel owner/operators to give consideration, 

as appropriate for vessel class and vessel operations, to the use of hull coatings with the lowest 

effective biocide release rates, rapidly biodegradable components (once separated from the hull 

surface), or non-biocidal alternatives, such as silicone coatings, at the time of initial application 

or scheduled reapplication of anti-fouling coatings. EPA requires that all anti-fouling hull 

coatings subject to registration under FIFRA (see 40 CFR § 152.15) must be registered, sold or 

distributed, applied, maintained, and removed in a manner consistent with applicable 

requirements on the coatings’ FIFRA label. For anti-fouling hull coatings not subject to FIFRA 

registration (i.e., not produced for sale and distribution in the United States), EPA requires that 

hull coatings must not contain any biocides or toxic materials banned for use in the United States 

(including those on EPA’s List of Banned or Severely Restricted Pesticides). This requirement 
13

applies to all vessels, including those registered and painted outside the United States. 

Some ports and harbors are impaired by copper, a biocide used commonly in anti-foulant paints. 

A complete list of such waters may be found at www.epa.gov/npdes/vessels. When vessels spend 

considerable time in these waters (defined as spending more than 30 days per year), or use these 

waters as their home port (i.e., house boats, ferries or rescue vessels), EPA requires vessel 

owners/operators to consider using anti-fouling coatings that rely on a rapidly biodegradable 

biocide or another alternative rather than copper-based coatings. If after consideration of 

alternative biocides, vessel operators continue to use copper-based antifoulant paints, they must 

document in their recordkeeping documentation how this decision was reached. 

The discharge of Tributyltin (TBT) from any source (whether used as a biocide or not) or any 

other organotin compound used as a biocide is prohibited by this permit. Therefore, vessel 

owners/operators covered by this permit have a zero discharge standard for TBT (whether or not 

used as a biocide) or any other organotin compound used as a biocide. For vessels covered under 

the VGP, EPA prohibits the use an antifoulant coating containing TBT or any other organotin 

compound used as a biocide. If the vessel has previously been covered with a hull coating 

containing TBT (whether or not used as a biocide) or any other organotin compound used as a 

biocide, vessels must be effectively overcoated so that no TBT or other organotin leaches from 

the vessel hull or the TBT or other organotin coating must have been removed from the vessel’s 

hull. When used as a catalyst, an organotin compound other than TBT (e.g., dibutyltin) is not to 

be present above 2500 mg total tin per kilogram of dry paint. Furthermore, EPA requires that the 

coating shall not be designed to slough or otherwise peel from the vessel hull. Incidental amounts 

of coating discharged by abrasion during cleaning or after contact with other hard surfaces (e.g., 

moorings) are not prohibited by the VGP. 

Aqueous Film Forming Foam (AFFF). Fire fighting foams, known as AFFF, contain 

fluorosurfactants or fluoroproteins. When employed for this purpose, AFFFs are sprayed from 

hoses and may be discharged into waters of the U.S. Fluorosurfactants compounds are toxic, 

persistent in the environment and have been detected in the blood and tissues of humans and 

wildlife. Fluoroproteins are less toxic than fluorosurfactants and are biodegradable.

For vessels covered under the VGP, EPA authorizes the discharge of AFFF for emergency 

purposes only, when needed to ensure the safety and security of the vessel and crew. They 

prohibit maintenance and training discharge of fluorinated AFFF for vessels that sail outside of 

the territorial sea more than once per month (i.e., any such discharges should be collected and 

stored for onshore disposal or scheduled when the vessel is outside such waters). Vessel 

owners/operators must minimize discharge volumes associated with regulatory certification and 

inspection and a substitute foaming agent (i.e., non-fluorinated) must be used if possible within 

waters of the U.S. For vessels that do not leave the territorial sea more than once per month, 

maintenance and training discharges of AFFF must be collected and stored for onshore disposal, 

unless the vessel uses a non-fluorinated or alternative foaming agent. For all vessels, 

maintenance and training discharges are not allowed in port. For all vessels, AFFF discharges 

may not occur in or within 1 nm of Federally protected waters (Appendix G of the VGP) unless 
14

they are discharged:

 For emergency purposes;

 By rescue vessels such as fireboats for firefighting purposes; or 

 By vessels owned or under contract to do business exclusively in or within 1 nm of those 

protected areas by the United States government or state or local governments.

If AFFF discharges occur in waters referenced in Appendix G for emergency purposes, a written 

explanation must be kept in the ship’s log

Boiler/Economizer Blowdown. For vessels with steam generators or steam propulsion, boiler 

blowdown is employed to control corrosion and to remove sludge and residue by discharging 

boiler effluent into waters of the U.S. In addition to sludge and residue, discharges from 

boilers/economizers may contain chemicals used to reduce impurities or prevent scale formation.

For vessels covered under the VGP, EPA requires vessel owners/operators to minimize the 

discharge of boiler/economizer blowdown in port if chemicals or other additives are used to 

reduce impurities or prevent scale formation. They would prohibit the discharge of 

boiler/economizer in Federally protected waters listed in Appendix G of the VGP except for 

safety purposes. For vessels greater than 400 gross tons, which leave the territorial sea at least 

once per week, the EPA would prohibit the discharge of boiler/economizer blowdown in U.S. 

waters, unless: 

 The vessel remains within waters subject to this permit for a longer period than the 

necessary duration between blowdown cycles; 

 The vessel needs to conduct blowdown immediately before entering drydock; or 

 For safety purposes. 

Cathodic Protection. In order to prevent metal corrosion, two types of cathodic protection are 

employed: sacrificial anodes and Impressed Current Cathodic Protection (ICCP). Sacrificial 

anodes of zinc or aluminum create a flow of electrons to cathodic metals and prevent them from 

corroding. Residual zinc or aluminum is then released to the aquatic environment. ICCP 

employs a direct electrical current into the vessel hull to prevent corrosion.

For vessels covered under the VGP, EPA requires vessel owner/operators to maintain cathodic 

protection to prevent hull corrosion. They require vessel owner/operators to minimize the flaking 

of large, corroded portions of zinc, magnesium, and aluminum anodes. They require vessel 

owners to avoid using sacrificial anodes more than necessary to adequately prevent corrosion of 

the vessel’s hull, sea chest, rudder, and other exposed areas of the vessel. Vessel operators are 

required to appropriately clean and/or replace these anodes during periods of maintenance (such 

as drydocking), so that release of these metals to waters is minimized. If vessel operators use 

sacrificial electrodes, EPA requires that they select electrode devices with metals that are less 

toxic to the extent technologically feasible and economically practicable and achievable (i.e., 

magnesium is less toxic than aluminum and aluminum is less toxic than zinc). If a vessel 

owner/operator selects aluminum, they must document why they made this selection, and why 
15

use of magnesium is not appropriate. Likewise, if a vessel owner/operator selects zinc, they must 

document why they did not select magnesium or aluminum. If vessel owners/operators use 

Impressed Current Cathodic Protection (which is recommended by EPA), they are required to 

maintain dielectric shields to prevent flaking.

Chain Locker Effluent. Chain lockers are the storage areas that contain anchor chains. Water 

can collect in chain lockers and this effluent may be discharged. Chain locker discharges may 

contain toxics such as metals, paint and grease. These discharges may also serve as a vector for 

biological pollutants including aquatic nuisance species and pathogens.

For vessels covered under the VGP, EPA requires vessel owners/operators to carefully and 

thoroughly wash down (i.e., more than a cursory rinse) the anchor chain, as it is being hauled out 

of the water to remove sediment and marine organisms. They require vessel owners/operators to

clean chain lockers thoroughly during dry-docking to eliminate accumulated sediments and any 

potential accompanying pollutants. For vessels that regularly sail outside waters subject to this 

permit (at least once per month), vessel owners/operators are required to periodically clean, 

rinse, and/or pump out the space beneath the chain locker prior to entering waters subject to this 

permit (preferably mid-ocean) if the anchor has been lowered into any nearshore waters and if 

technically feasible. For vessels that leave waters subject to this permit at least once per month, 

EPA prohibits vessel owners/operators from rinsing or pumping out chain lockers in waters of 

the U.S., unless not emptying them would compromise safety, in which case the safety claim 

must be documented in the vessel’s recordkeeping documentation.

Controllable Pitch Propeller and Thruster Hydraulic Fluid and Other Oil-to-Sea Interfaces 

Oil to sea interfaces include any part of a vessel where seals or surfaces may discharge oil into 

waters of the U.S. These discharges include lubrication discharges from paddle wheel 

propulsion, stern tubes, thruster bearings, stabilizers, rudder bearings, azimuth thrusters, and 

propulsion pod lubrication, and wire rope and mechanical equipment subject to immersion in 

water. Examples include machinery that uses hydraulic oils or has parts that are lubricated with 

greases or oils. An additional example is the stern tube. Riggings and cables may also have 

surfaces that are lubricated with oils or greases and may cause discharges of these substances 

into waters of the U.S. As noted by EPA, these discharges can be substantial. 

The EPA does not authorize the discharge of any lubricant in a quantity that may be harmful as 

defined in 40 CFR Part 110. For vessels covered under the VGP, EPA requires vessel 

owners/operators to maintain protective seals on oil-to-sea interfaces in good operating order to 

minimize the leaking of hydraulic oil or other oils. Vessel owners/operators are prohibited from 

discharging oil in quantities that may be harmful as defined in 40 CFR Part 110 from any oil-tosea interface. Vessel owners/operators are required to minimize maintenance activities on stern 

tube seals when a vessel is outside of drydock. If maintenance or emergency repair must occur 

on stern tubes or other oil-to-sea interfaces which have a potential to release oil in quantities that 

may be harmful as defined in 40 CFR Part 110, appropriate spill response equipment (e.g., oil 

booms) must be used to contain any oil leakage. The EPA requires operators of the vessel to

have ready access to spill response resources to clean up any oil spills. After applying lubrication 
16

to wire rope and mechanical equipment subject to immersion, wire ropes, and other equipment 

must be thoroughly wiped down to remove excess lubricant. For vessels constructed on or after 

December 19, 2013, EPA requires the use of an environmentally acceptable lubricant in all oilto-sea interfaces. “Environmentally acceptable lubricants” means lubricants that are 

“biodegradable” and “non-toxic” and are not “bioaccumulative” as defined in Appendix A of the 

VGP. For vessels built before December 19, 2013, unless technically infeasible, EPA requires

owners/operators to use an environmentally acceptable lubricant in all oil to sea interfaces or 

document and report why they are unable to do so and which lubricant was used in their annual 

report (submitted electronically to EPA). 

Distillation and Reverse Osmosis Brine. Discharges of salt brine can result from seawater 

distillation and reverse osmosis activities used to generate freshwater from seawater. In addition 

to having high salinity, these discharges may cause thermal pollution as well as contain residual 

chemicals used in the various processes.

For vessels covered under the VGP, EPA prohibits brine from the distillation system and reverse 

osmosis reject water from containing or coming in contact with machinery or industrial 

equipment (other than that necessary for the production of potable water), toxic or hazardous 

materials, or wastes.

Elevator Pit Effluent. Liquids containing oils, hydraulic fluid and other materials may collect in 

elevator shaft pits aboard vessels. These liquids may enter waters of the U.S. from simple 

drainage off the vessel, transference to bilge followed by discharge, or by other means. 

For vessels covered under the VGP, EPA prohibits discharges of untreated elevator pit effluent 

within waters of the U.S., except in cases of emergency. They authorize elevator pit effluent to 

be discharged if it is managed with the vessel’s bilgewater and meets bilgewater discharge 

requirements. Otherwise, they require that it be treated with an oily-water separator and 

discharged with an oil-content below 15 ppm as measured by EPA Method 1664 or other 

appropriate method for determination of oil content as accepted by the IMO (e.g., ISO Method 

9377) or U.S. Coast Guard. Vessel owners/operators are required to document emergency 

discharges. 

Firemain Systems. Firemain systems take up ambient water to supply fire hoses, sprinklers and 

other fire suppression systems. These systems may also be used for other purposed such as 

washing the vessel and equipment, machinery cooling, ballast tank filling etc). 

For vessels covered under the VGP, EPA authorizes discharges from firemain systems for 

emergency purposes to ensure the safety and security of the vessel and her crew and other 

emergency situations. They authorize testing and inspections of the firemain systems in order to 

assure its operability in an emergency. They also authorize in port discharges from firemain 

systems for certification, maintenance, and training requirements if the intake comes directly 

from the surrounding waters or potable water supplies and there are no additions (e.g., AFFF) to 

the discharge. The EPA authorizes the use of firemain systems for deck washdown or other 
17

secondary uses if the intake comes directly from the surrounding waters or potable water 

supplies and the discharge meets all relevant effluent limitation associated with that activity. 

They prohibit the discharge of firemain systems in Federally protected waters listed in Appendix 

G of the VGP, except in emergency situations or when washing down the anchor chain to 

comply with anchor wash down requirements.

Freshwater Layup. When steam propulsion systems are shut down, biological growth can occur 

within the system. Freshwater layup replaces this water and may result in the discharge of 

metals and other contaminants into waters of the U.S.

For vessels covered under the VGP, EPA requires vessel owners/operators to minimize the 

amount of disinfection or biocidal agents used in freshwater layup (i.e., the minimum required to 

prevent aquatic growth).

Gas Turbine Washwater. Gas turbines must be cleaned to remove materials such as salts and 

spent lubricants. These materials may be discharged into waters of the U.S. and may also 

include cleaning agents. 

For vessels covered under the VGP, EPA prohibits the direct discharge of gas turbine washwater

within waters of the U.S. They require vessel owners/operators to prevent commingling of gas 

turbine washwater and bilgewater, where feasible. They prohibit the discharge of oils, including 

oily mixtures, from gas turbine washwater in quantities that may be harmful as determined in 

accordance with 40 CFR Part 110.

Graywater. Graywater is water that has been used for bathing, in sinks, laundry etc., and may 

contain pathogens, nutrients, soaps, detergents, and other organic pollutants. Some –usually 

large– vessels collect and store graywater for later treatment and discharge. Other vessels 

discharge untreated graywater directly into waters of the U.S.

For vessels covered under the VGP, EPA requires vessel owners/operators to minimize the 

discharge of graywater while in port. For those vessels that cannot store graywater, the owner or 

operator and their crews are required to minimize the production of graywater in port. Examples 

of ways to minimize production of graywater include delaying laundry, scullery activities, and 

restricting length of showers while in port, and using high efficiency faucets and showerheads. 

Vessel owner/operators are required to minimize the discharge of graywater when the vessel is 

not underway. Vessels that have the capacity to store graywater are prohibited from discharging 

graywater in Federally protected waters listed in Appendix G of the VGP. For vessels that cannot 

store graywater, vessel operators must minimize the production of graywater while in those 

waters. For vessels greater than 400 gross tons that regularly travel more than 1 nm from shore 

and have the capacity to store graywater for a sufficient period, treated graywater must be 

discharged greater than 1 nm from shore while the vessel is underway, unless the vessel meets 

the following treatment standards and requirements:
18

 The discharge must satisfy the minimum level of effluent quality specified in 40 CFR § 

133.102; 

 The geometric mean of the samples from the discharge during any 30-day period may not 

exceed 20 fecal coliform/100 milliliters (ml) and not more than 10 percent of the samples 

exceed 40 fecal coliform/100 ml; and 

 Concentrations of total residual chlorine may not exceed 10.0 micrograms per liter (μg/l). 

For vessels that do not travel more than 1 nm from shore, EPA requires vessel owners/operators 

to minimize the discharge of graywater and, provided the vessel has available graywater storage 

capacity, and dispose of graywater onshore, if appropriate facilities are available and such 

disposal is economically practicable and achievable, unless the vessel meets aboved listed 

treatment standards and requirements. The vessel owners/operators are required to minimize the 

introduction of kitchen oils to the graywater system if graywater will be discharged in waters of 

the U.S. They are required to remove as much food and oil residue as practicable before rinsing 

dishes. They are prohibited from adding excess oils used in cooking, including animal fats and 

vegetable oils, to the graywater system. They are prohibited from discharging galley and scullery 

oil in quantities that may be harmful as defined in 40 CFR Part 110. Under the VGP, EPA 

requires vessel owners/operators to use phosphate-free and non-toxic soaps and detergents for 

any purpose if graywater will be discharged into waters subject to this permit; EPA expects that 

non-toxic soaps will contain little to no nonylphenols. Soaps and detergents must be free from 

toxic or bioaccumulative compounds and not lead to extreme shifts in receiving water pH (i.e., 

fall below 6.0 or rise above 9.0 as a direct result of the discharge).

For vessels underway in a nutrient-impaired water, or a water that is impaired as a result of 

nutrient enrichment (such as waters listed as impaired for phosphorus, nitrogen, or for hypoxia or 

anoxia [low dissolved oxygen concentrations]), EPA prohibits discharge of graywater, if the 

vessel has adequate graywater storage capacity. If the vessel does not have adequate storage 

capacity, graywater production and discharge must be minimized and conducted while the vessel 

is underway and in areas with significant circulation and depth, to the extent feasible. For vessels 

constructed on or after December 19, 2013, EPA requires the vessel owners/operators to take two 

samples per year, at least 14 days apart, and analyze: Biochemical Oxygen Demand (BOD), 

fecal coliform, suspended solids, pH, and total residual chlorine. They require the sampling and 

testing to be conducted according to 40 CFR Part 136. They require annual reporting, including: 

 Date, exact place, and time of sampling or measurements; 

 Individual(s) who performed the sampling or measurements; 

 Date(s) analyses were performed; 

 Individual(s) who performed the analyses; 

 Analytical techniques or methods used and results of such analyses

 Whether the graywater effluent is treated or untreated

 Whether the effluent is graywater alone or if it is mixed with another effluent type (e.g., 

graywater mixed with sewage). 

Motor Gasoline and Compensating Discharge. Ambient water is taken up onto vessels to 
19

compensate for weight as motor gasoline is used. This water is later discharged into waters of 

the U.S. and may contain residual oils and other pollutants. 

For vessels covered under the VGP, EPA prohibits the discharge of motor gasoline and 

compensating effluent containing oil in quantities that may be harmful as defined in 40 CFR § 

110.3, which includes discharges resulting in a visible sheen, or an oil concentration that exceeds 

15 ppm. Determination of oil concentration may be measured by EPA Method 1664 or other 

appropriate method for determination of oil content as accepted by the IMO (e.g., ISO Method 

9377) or U.S. Coast Guard. The EPA authorizes compliance with the 15 ppm oil concentration 

limitation as established by visual monitoring for an oily sheen. They also require vessel 

owner/operators to minimize discharge of motor gasoline and compensating discharge in port. If 

an oily sheen were observed, the vessel operator is required to deploy appropriate oil 

containment practices. The EPA prohibits motor gasoline and compensating discharges in 

Federally protected waters (Appendix G, VGP).

Non-Oily Machinery Wastewater. Non-oily machinery wastewater systems contain water that 

does not come into contact with machinery that uses oil. Examples include distillers, condensate 

drains, pump drains, potable water tank overflows and leaks from propulsion shaft seals. These 

wastewater systems may result in discharges of various pollutants into waters of the U.S.

For vessels covered under the VGP, EPA requires non-oily machinery wastewater to be free 

from oils (in quantities that may be harmful pursuant to 40 CFR Part 110) and any additives that 

are toxic or bioaccumulative in nature, if discharged directly overboard. They permit non-oily 

machinery wastewater to be drained to the bilge. 

Refrigeration and Air Condensate Discharge. Condensation from refrigeration or air condition 

systems may discharge into waters of the U.S. and may contain detergents, metals and other 

pollutants.

For vessels covered under the VGP, EPA prohibits the discharge of refrigeration and air 

condensate, if it had come into contact with oily or toxic materials. They permit the discharge 

of refrigeration and air conditioning condensate that is collected and plumbed for internal 

recycling (e.g., recycled as “technical water”) which has commingled with oily water if the 

commingled discharge meets the discharge requirements for oily mixtures and oily water 

separator effluent. 

Seawater Cooling Overboard Discharge. Seawater cooling systems circulate ambient water 

through an enclosed system and may be discharged into waters of the US. These discharges may 

contain hydraulic fluid, lubricating oil and metals and may also be of higher than ambient 

temperature. These discharges include non-contact engine cooling water; hydraulic system 

cooling water, refrigeration cooling water.

For vessels covered under the VGP, EPA requires vessel owner/operators to maintain all piping 

and seawater cooling systems must meet the requirements as described below.
20

Seawater Piping Biofouling Prevention. Seawater cooling systems may contain anti-fouling 

compounds. These compounds may be discharged into waters of the U.S.

For vessels covered under the VGP, EPA requires vessel owner/operators to use seawater piping 

biofouling chemicals subject to FIFRA registration (see 40 CFR § 152.15) in accordance with 

their FIFRA label. They prohibit the discharge of pesticides or chemicals banned for use in the 

U.S. They require vessel owner/operators to use the minimum amount of biofouling chemicals 

needed to keep fouling under control and discharges containing active agents to contain as little 

chlorine as possible. Vessel owner/operators are required to remove fouling organisms from 

seawater piping on a regular basis (though regular is not defined) and dispose of removed 

substances in accordance with local, state, and federal regulations. The EPA prohibits the 

discharge of removed fouling organisms into waters of the U.S. 

Boat Engine Wet Exhaust. Boat engines use ambient water for cooling and noise reduction. 

This wet engine exhaust is discharged into waters of the U.S. and may contain various pollutants.

For vessels covered under the VGP, EPA requires vessel owner/operators to maintain vessel 

engines generating wet exhaust, ensuring that they are in good operating order, well tuned, and 

function according to manufacturer specifications to decrease pollutant contributions to wet 

exhaust. The EPA recommends that vessel owner/operators use four stroke engines instead of 

two stroke engines for vessels generating wet exhaust. For vessel owner/operators who use two 

stroke engines, EPA requires the use of environmentally acceptable lubricants (as defined in 

Appendix A of the VGP), unless technologically infeasible, in which case the vessel 

owner/operator must document why they are not using environmentally acceptable lubricants.

Sonar Dome Discharge. Sonar equipment may discharge water that contains metals and 

antifouling compounds.

For vessels covered under the VGP, EPA prohibits the discharge of water inside the sonar dome

for maintenance purposes. They prohibit the vessel owner/operators from using biofouling 

chemicals that are bioaccumulative for the exterior of sonar domes when non-bioaccumulative 

alternatives are available.

Underwater Ship Husbandry Discharges. Underwater ship husbandry is the maintenance and 

repair associated with vessel hulls while in water. This can result in the discharge of various 

pollutants used in repair and maintenance as well as the discharge of antifouling paints used on 

the hull. In addition, these activities may be a source of introduction of aquatic nuisance species.

Vessel hull coatings can contain toxics and may contain biocides designed to prohibit the growth 

of fouling organisms. These coatings discharge pollutants by leaching toxics into the water. 

Copper is a common biocide found in hull coatings. Discharges of the biocide tributyltin (TBT) 

and other organotin compounds are not permitted by the proposed permit due to their persistence 

in the environment and their high toxicity to marine life. 
21

For vessels covered under the VGP, EPA requires vessel owners/operators to minimize the 

transport of attached living organisms when traveling into U.S. waters from outside the U.S. 

economic zone or between Captain of the Port (COTP) zones. If vessel owners and operators use

water pressure-based systems to clean the hull and remove old paint, they must use facilities 

which treat the washwater prior to discharging to waters subject to this permit in order to remove 

the antifouling compound(s) and fouling growth from the washwater. If they use mechanical 

means (scraping, etc.) to clean the hull and remove old paint, the materials removed from the 

hull during that process must be collected, disposed of properly (e.g., onshore), and not be 

allowed to contaminate nearby waters. The EPA requires vessel owners/operators who remove 

fouling organisms from hulls while the vessel is waterborne to employ methods that minimize 

the discharge of fouling organisms and antifouling hull coatings, including:

 Use of appropriate cleaning brush or sponge rigidity to minimize removal of antifouling 

coatings and biocide releases into the water column; 

 Limiting use of hard brushes and surfaces to the removal of hard growth; and 

 When available and feasible, use of vacuum or other control technologies to minimize the 

release or dispersion of antifouling hull coatings and fouling organisms into the water 

column. 

The EPA requires vessel owners/operators to minimize the release of copper-based antifoulant 

paints during vessel cleaning operations. They require cleaning of hull surfaces coated with 

copper-based antifoulant paint that would not result in any visible cloud or plume of paint in the 

water; if a visible cloud or plume of paint develops, they require vessel owners/operators to shift 

to a softer brush or less abrasive cleaning technique. A plume or cloud of paint can be noted by 

the presence of discoloration or other visible indication that is distinguishable from hull growth 

or sediment removal. Production of a plume or cloud of sediment or hull growth is normal in 

some cases during vessel hull cleaning, but this plume or cloud must be substantially paint free 

(e.g., paint should not be clearly identifiable in the plume or cloud). The EPA requires 

owners/operators to minimize the release of fouling organisms and antifouling systems 

(including copper-based coatings) into surrounding waters. They require vessel owners/operators

to minimize hull husbandry in critical habitat for aquatic species. Vessels that use copper-based 

anti-fouling paint must not clean the hull in copper-impaired waters within the first 365 days 

after paint application unless there is a significant visible indication of hull fouling. EPA 

maintains a list of copper-impaired waters on its webpage at www.epa.gov/npdes/vessels. If 

vessel owners or operators clean before 365 days in copper-impaired waters, they must document 

in their recordkeeping documentation why this early cleaning was necessary.

Welldeck Discharges. The welldeck is a platform used for launching or loading boats and cargo. 

Discharges from welldecks may include pollutants from equipment washing, and oils and other 

materials associated with engines and machinery.

For vessels covered under the VGP, EPA prohibits welldeck discharges from washdown of gas 

turbine engines. Welldeck discharges from equipment and vehicle washdowns must be free from 
22

garbage and must not contain oil in quantities that may be harmful as defined in 40 CFR Part 

110. 

Graywater Mixed with Sewage from Vessels. Except for commercial vessels in the Great Lakes, 

discharges of graywater that contain sewage are eligible for coverage under the VGP and must 

meet additional effluent limits as described in the permit as well as any additional requirements 

applicable to sewage discharges outside of the VGP.

For vessels covered under the VGP, EPA requires that commingled discharge of graywater and 

sewage must comply with the effluent limits for graywater discharge and meet the requirements 

set forth in section 312 of the CWA. 

Exhaust Gas Scrubber Washwater Discharge. Exhaust Gas Scrubber washwater discharges 

(EGS washwater discharge) occur from exhaust gas cleaning systems on diesel engines. Some 

pollutants are transferred to the vessel’s sludge tank, but the remainder may be discharged into 

waters of the U.S. and may contain selenium, nutrients, oils, polycyclic aromatic hydrocarbons 

(PAHs) and metals, and may have a different pH than receiving waters.

For vessels covered under the VGP, EPA prohibits the discharge of exhaust gas scrubber 

washwater containing oil, including oily mixtures, in quantities that may be harmful as 

determined in accordance with 40 CFR Part 110. They prohibit the discharge of sludge or 

residues generated in treating exhaust gas scrubber washwater discharge and require these 

discharges to be delivered ashore to adequate reception facilities. In addition, vessel 

owners/operators with exhaust gas cleaning systems that result in washwater discharges must 

meet the numeric effluent limits and the monitoring requirements below: 

 The discharge washwater from the exhaust gas scrubber treatment system must have a pH 

of no less than 6.5 measured at the ship’s overboard discharge, with the exception that 

during maneuvering and transit, the maximum difference between inlet and outlet of 2.0 

pH units is allowed. 

 The maximum continuous PAH (Polycyclic Aromatic Hydrocarbons) concentration in 

the washwater must not be greater than 50 μg/L PAHphe (phenanthrene equivalence) 

above the inlet water PAH concentration for washwater flow rates normalized to 45 

t/MWh. MWh refers to the maximum continuous rating (MCR) or 80 percent of the 

power rating of the fuel oil combustion unit. For the purposes of this criterion, the PAH 

concentration in the washwater must be measured downstream of the water treatment 

equipment, but upstream of any washwater dilution or other reactant dosing unit, if used, 

prior to discharge. The 50-μg/L limit is adjusted upward for lower washwater flow rates 

per MWh, and vice-versa, and the specific permit limits are listed in the VGP. 

 The washwater treatment system must be designed to minimize suspended particulate 

matter, including heavy metals and ash. The maximum turbidity (monitored 

continuously) in washwater must not be greater than 25 FNU (formazin nephelometric 

units) or 25 NTU (nephelometric turbidity units) or equivalent units, above the inlet water 

turbidity. However, during periods of high inlet turbidity, the precision of the 
23

measurement device and the time lapse between inlet measurement and outlet 

measurement are such that the use of a difference limit is unreliable. Therefore, all 

turbidity difference readings must be a rolling average over a 15-minute period to a 

maximum of 25 FNU or NTU. For the purposes of this criterion, the turbidity in the 

washwater must be measured downstream of the water treatment equipment but upstream 

of washwater dilution (or other reactant dosing) prior to discharge. For a maximum of 

one 15-minute period within any 12-hour period, the continuous turbidity discharge limit 

may be exceeded by 20 percent. 

 The washwater treatment system must prevent the discharge of nitrates, plus nitrites 

beyond that associated with a 12 percent removal of NOx from the exhaust, or beyond 60 

mg/l normalized for washwater discharge rate of 45 tons/MWh, whichever is greater. 

MWh refers to the MCR or 80 percent of the power rating of the fuel oil combustion unit. 

For the purposes of this criterion, the nitrate concentration in the washwater must be 

measured downstream of the water treatment equipment, but upstream of any washwater 

dilution or other reactant dosing unit, if used, prior to discharge. The 60-mg/L limit is 

adjusted upward for lower washwater flow rates per MWh, and vice-versa, and the 

applicable permit limits are listed in the VGP. 

 The data recording system must comply with the guidelines in sections 7 and 8 of 

MEPC.184(59) and must continuously record pH, PAH, and turbidity.

 When the EGC system is operated in waters subject to this permit, the washwater 

monitoring and recording must be continuous. The values monitored and recorded must 

include pH, PAH, turbidity, and temperature.

 The pH electrode and pH meter must have a resolution of 0.1 pH units and temperature 

compensation. The electrode must comply with the requirements defined in BS 2586 or 

of equivalent or better performance and the meter should meet or exceed BS EN ISO 

60746-2:2003.

 The PAH monitoring equipment must be capable of monitoring PAH in water in a range 

of at least twice the discharge concentration limit given in the table above. A 

demonstration must be made that the equipment operates correctly and does not deviate 

more than 5 percent in washwater with turbidity within the working range of the 

application. For those applications discharging at lower flow rates and higher PAH 

concentrations, ultraviolet light monitoring technology or equivalent should be used due 

to its reliable operating range.

 The turbidity monitoring equipment must meet requirements defined in ISO 7027:1999 

or USEPA 180.1.

 All continuous monitoring equipment must be calibrated as recommended by probe 

manufacturers or Exhaust Gas scrubber manufacturers. At a minimum, all probes must be 

calibrated at least annually. 

 In addition to the continuous monitoring, vessel owner/operators must collect and analyze 

one sample per quarter for each of the following analytes to demonstrate treatment 

equipment maintenance, probe accuracy, and compliance with this permit. Records of the 

sampling and testing results must be retained onboard for a period of 3 years.
24

o Dissolved and Particulate Metals, including Aluminum, Antimony, Arsenic, 

Cadmium, Chromium, Copper, Lead, Manganese, Nickel, Selenium, Thallium, and 

Zinc

o Vessel owners/operators should have selenium analyzed using methods capable of 

accurately measuring selenium in saline samples (e.g., Octopole Reaction Cell ICPMS or Hydride generation AA methods or other methods which reduce matrix 

interference for selenium)

o PAHs including Acenaphthylene, Acenaphthene, Anthracene Benz[a]anthracene, 

Benzo[ghi]perylene, Benzo[a]pyrene, Benzo[b]fluoranthene +, benzo[k]fluoranthene, 

Chrysene, Dibenz[a,h]anthracene, Fluoranthene, Fluorene, Indeno[1,2,3,c,d]pyrene, 

Naphthalene, Phenanthrene, and Pyrene

o Nitrates 

o pH

o Turbidity

o Temperature

o Dissolved Oxygen 

 Vessel owners/operators are required to submit monitoring data to EPA annually; all 

monitoring data must be submitted electronically unless exempted

Fish Hold Effluent. Fish hold effluent is the seawater, ice-melt or ice slurry from fish hold tanks 

and may be discharged into waters of the US. These discharges may contain biological wastes, 

metals, nutrients, detergents and disinfectants.

For vessels covered under the VGP, EPA requires vessel owners/operators to minimize the 

discharge of fish hold water and/or ice while in port. They prohibit the discharge of unused bait 

overboard , unless that bait was caught in the same water body or watershed. The discharged of 

unused bait purchased from a bait shop or dealer is prohibited. The EPA requires all reasonable 

steps to be taken to prevent the discharge of excess fish hold water and ice while the vessel is 

stationary at the pier. If fish waste is contained in the fish hold effluent, they prohibit fish hold 

effluent from being discharged while in port, unless a physical separation method is used (e.g., 

filters or removal of residuals). They prohibit the discharge of fish hold effluent (including dirty 

ice) if unloading catch at a land-based seafood processing facility or pier. They prohibit the 

discharge of fish hold effluent (including dirty ice) if a shore-based discharge facility is available 

and meets the following standards:

 Its use is economically achievable, and

 The facility has a valid NPDES permit, or

 That facility discharges to an NPDES-permitted sewage treatment facility.

VGP Vessel-Class-Specific Requirements

Large and Medium Cruise Ships (100 people or more)
25

Graywater Management. The EPA requires vessel owners/operators to use appropriate onshore 

reception facilities for graywater while their vessel is pierside unless they meet stringent 

treatment requirements found in the VGP. If such facilities are not reasonably available and the 

vessel does not have the capacity to treat graywater, EPA requires the vessel to hold the 

graywater until the vessel is underway and not in waters subject to the sVGP. The EPA considers 

appropriate reception facilities those authorized for use by the port authority or local 

municipality and that treat the discharge in accordance with its NPDES permit. The EPA 

prohibits the discharges of untreated graywater from all large cruise ships and most medium 

cruise ships while operating within 3nm from shore. 

While operating in nutrient-impaired waters, EPA requires large cruise ship operators to:

 Not discharge any graywater in nutrient-impaired waters subject to this permit unless the 

length of voyage in that water exceeds the vessel’s holding capacity for graywater; and 

 Minimize the discharge of any graywater into nutrient-impaired waters subject to this 

permit, which may require minimizing the production of graywater; and 

 If a vessel’s holding capacity for graywater is exceeded, treat such excess graywater 

(above the vessel holding capacity) by a device to meet the standards prior to discharge 

into nutrient-impaired waters subject to the VGP; or 

 Dispose of the graywater at an onshore facility, which will discharge the effluent under a 

valid NPDES permit. 

Graywater Treatment Standards. For large cruise ships, EPA requires treated graywater 

discharges to meet the following standards:

1. The discharge must satisfy the minimum level of effluent quality specified in 40 CFR § 

133.102; 

2. The geometric mean of the samples from the discharge during any 30-day period may 

not exceed 20 fecal coliform/100 milliliters (ml) and not more than 10 percent of the 

samples may exceed 40 fecal coliform/100 ml; and 

3. Concentrations of total residual chlorine may not exceed 10.0 micrograms per liter 

(μg/l). 

The EPA requires quarterly monitoring of graywater (results to be submitted to EPA annually) 

for:

 BOD, fecal coliform, suspended solids, pH, and total residual chlorine

 E. coli, total phosphorus, ammonia, nitrate/nitrite, and total Kjeldahl nitrogen

Sculleries and Galleys. For large cruise ships, EPA requires the use soaps and detergents that are 

phosphate-free, non-toxic, and biodegradable; EPA expects that non-toxic will contain little to no 

nonylphenols. They require non-toxic degreasers if discharged as part of any waste stream. 

Other Materials. For large cruise ships, EPA requires that vessel owners/operators prevent
26

waste from mercury-containing products, dry cleaners or dry cleaner condensate, photo 

processing labs, medical sinks or floor drains, chemical storage areas, and print shops using 

traditional or non-soy-based inks and chlorinated solvents from entering the ship’s graywater, 

blackwater, or bilgewater systems if water from these systems will be discharged into waters of 

the U.S. The EPA recommends preventing these wastes from entering these systems by plugging 

all drains that flow to the graywater, blackwater, or bilge systems in areas where these wastes are 

produced and creating alternate waste receptacles or replumbing drains to appropriate holding 

tanks. The EPA prohibits vessel owners/operators from discharging any toxic materials, 

including products containing acetone, benzene, or formaldehyde into salon and day spa sinks or 

floor drains if those sinks or floor drains lead to any system which will be discharged into waters 

of the U.S. This includes using these materials on passengers (or crew) and rinsing residuals into 

these sinks. Alternate waste receptacles or holding tanks are required to be used for these 

materials. The EPA considers addition of these materials to any systems which will discharge 

into waters of the U.S. to be a permit violation. 

Pool and Spa Discharges. For large cruise ships, EPA prohibits discharges of pool or spa water 

to Federally protected waters (listed in Appendix G of the VGP). The EPA authorizes discharges 

from pools and spas are authorized into non-Appendix G waters, provided pool and spa water to 

be discharged is dechlorinated and/or debrominated, and discharge occurs while the vessel is 

underway. To be considered dechlorinated, the total residual chlorine in the pool or spa effluent 

must be less than 100 μg/l if the pool or spa water is discharged without going through an 

Advanced Wastewater Treatment System (AWTS). To be considered debrominated, the total 

residual oxidant in the pool or spa effluent must be below 25 μg/l if the pool or spa water is 

discharged without going through an AWTS. The EPA allows pool and spa water to be added to 

the graywater treatment systems; however, any resultant discharge must meet all standards and 

requirements found in the VGP and must be dechlorinated and/or debrominated as applicable. 

Monitoring Requirements. For large cruise ships, EPA requires that vessel owners/operators 

report the discharge of untreated graywater to waters of the U.S. For treated graywater, EPA 

requires the following of vessel owners/operators:

 Demonstrate an effective treatment system if discharging graywater within 3 nm of shore. 

 Take at least five (5) samples from the vessel on different days over a 30-day period that 

are representative of the treated effluent to be discharged. 

 For initial monitoring, take samples for BOD, fecal coliform, suspended solids, pH, total 

residual chlorine, E. coli, total phosphorus (TP), ammonia, nitrate/nitrite, and Total 

Kjeldahl Nitrogen (TKN). 

 Retain records onboard for three years

 For maintenance monitoring, collect and analyze one sample per quarter 

 Submit data showing that the graywater standards are achieved by their treatment system 

to EPA’s e-reporting system 

 Maintain records estimating the quantity and quality of all discharges of treated 

graywater into waters subject to this permit, including date, location and volume 

discharged, and pollutant concentrations monitored in their recordkeeping 
27

documentation. These records shall be maintained as part of or in combination with the 

vessel’s sewage and graywater discharge record book required under 33 CFR § 159.315. 

Even if owners/operators have demonstrated their systems meet the standards, EPA, its 

authorized representative, or the U.S. Coast Guard retains the right to sample their graywater 

effluent. If EPA finds that they are not meeting these standards, they will hold the cruise ship 

owners/operators liable for violating their effluent limits. 

For large cruise ships, EPA requires that vessel owners/operators monitor and record chlorine or 

bromine concentrations (as applicable) in pool or spa water before every discharge event using 

sufficiently sensitive 40 CFR Part 136 methods if they will discharge these streams directly into 

waters subject to this permit to ensure that the dechlorination/debromination process is complete. 

For large cruise ships, EPA requires that vessel owners/operators to provide the following 

educational and training requirements to ship personnel: 

 The ship’s crew members who actively take part in the management of a discharge or 

who may affect any discharge must receive training regarding shipboard environmental 

procedures and must be able to demonstrate proficiency in implementing these 

procedures; 

 Advanced training in shipboard environmental management procedures must be provided 

for those directly involved in managing specific discharge types or areas of the ship and 

these crew members must be able to demonstrate proficiency in implementing these 

procedures; and 

 Appropriate reprimand procedures must be developed for crew whose actions lead to 

violations of any effluent limit set forth in this permit or procedures established by the 

cruise ship operator to minimize the discharge of pollutants. 

The EPA also requires large cruise ships to educate passengers on their potential environmental 

impacts. The goals of these education efforts must include preventing trash from entering any 

waste stream, eliminating the addition of unused soaps, detergents, and pharmaceuticals to the 

graywater or blackwater systems, and minimizing production of graywater. This can be 

accomplished in a variety of ways including, but not limited to, posting signage and 

informational material in guestrooms and common areas, incorporating environmental 

information passenger orientation presentations or packages at the start of cruises, incorporating 

this information into additional lectures and seminars, or broadcasting information via 

loudspeakers. 

Large Ferries

Ferries are vessels for hire that are designed to carry passengers and/or vehicles between two 

ports, usually in inland, coastal, or near-shore waters. “Large Ferry” means a “ferry” that: a) has 

a capacity greater than or equal to 100 tons of cargo (e.g., for cars, trucks, trains, or other landbased transportation); or b) is authorized by the U.S. Coast Guard to carry 250 or more people. 
28

All large ferries authorized to carry 100 or more tons of cars, trucks, trains, or other land-based 

transportation must meet the deck water and education/training requirements. Large ferries 

authorized by the Coast Guard to carry 250 or more people must meet the graywater and 

education/training requirements. 

The EPA prohibits large ferries from discharging untreated below deck water from parking areas 

or other storage areas for motor vehicles or other motorized equipment into waters of the U.S.

without first treating the effluent with an oily water separator or other appropriate wastewater 

treatment system. The EPA requires large ferry operators to use oil absorbent cloths or other 

appropriate spill response resources to clean oily spills or substances from deck surfaces. Any 

effluent created by washing the decks may not be discharged into Federally protected waters 

listed in Appendix G of the VGP. 

The EPA requires pierside ferries to discharge graywater using appropriate onshore reception 

facilities, if available and their use is economically achievable, unless the vessel treats graywater 

to the limits found in the VGP. If such facilities are not available, they require the 

owners/operators to hold the graywater if the vessel has the holding capacity and discharge the 

effluent while the vessel is underway. Appropriate reception facilities are those authorized for 

use by the port authority or municipality and that treat the discharge in accordance with its 

NPDES permit. The EPA requires large ferries operating within 3 nm from shore to discharge 

graywater only while sailing at a speed of at least 6 knots if feasible. If not feasible, EPA 

requires documentation. 

The EPA requires ferry operators to do the following: 

 The ship’s crew members who actively take part in the management of the discharge or 

who may affect the discharge must receive training regarding shipboard environmental 

procedures and must be able to demonstrate proficiency in implementing these 

procedures; 

 Advanced training in shipboard environmental management procedures must be provided 

for those directly involved in managing specific discharge types or areas of the ship and 

these crew must be able to demonstrate proficiency in implementing these procedures; 

and 

 Appropriate reprimand procedures must be developed for crew whose actions lead to 

violations of any effluent limit set forth in this permit or procedures established by the 

ferry operator to minimize the discharge of pollutants. 

 Ferry operators must also educate passengers on their potential environmental impacts. 

The goals of these education efforts should include eliminating the discharge of trash 

overboard, minimizing the production of trash from parking areas or other storage areas, 

eliminating the addition of unused soaps, detergents, and pharmaceuticals to the 

graywater or blackwater systems, and minimizing production of graywater. This can be 

accomplished in a variety of ways including, but not limited to, posting signage and 

informational material in common areas, incorporating environmental information into 

orientation presentations, or broadcasting information via loudspeakers. 
29

Barges

For barges, EPA requires owners/operators to:

 Minimize the contact of below deck condensation with oily or toxic materials and any 

materials containing hydrocarbon. Whenever barges are pumping water from below deck, 

the discharge shall not contain oil in quantities that may be harmful as defined in 40 CFR 

Part 110. If a visible sheen is noted, vessel operators must initiate corrective action and 

meet the recordkeeping requirements in the VGP. 

 Have spill rails and must mechanically plug their scuppers before any cargo operations if 

required by vessel class society and/or 33 CFR Parts 155 and/or 156. Additionally, 

scuppers, when available, must be mechanically plugged during fueling of ancillary 

equipment (e.g., generators and compressors) located on the deck of the barge. If 

scuppers are unavailable, other types of secondary containment should be employed. If 

any spills result during loading or unloading of cargo, or other ancillary equipment 

fueling operations, vessel owners/operators must completely clean up spills or residue 

before scuppers are unplugged. 

 Clean out cargo residues (i.e., broom clean) such that any remaining residue is minimized 

before washing the cargo compartment or tank and discharging washwater overboard. 

 Conduct a visual sheen test after every instance of pumping water from areas below 

decks, or immediately following washing down the decks. The visual sheen test is used to 

detect free oil by observing the surface of the receiving water for the presence of an oily 

sheen. If a visible sheen is observed, EPA requires the owner/operator to initiate 

corrective actions and meet recordkeeping/reporting requirements of the VGP. 

Oil Tankers, Petroleum Tankers, and Bulk Chemical Carriers 

Under the VGP, the EPA authorizes the discharges of water from deck seals if the seals are 

installed as an integral part of an IGS system. For vessels which have an inert gas system, EPA 

authorizes the discharge of effluent produced from inert gas scrubbers (IGS) into waters of the 

U.S. They require owners/operators of oil tankers to plug scuppers during cargo loading and 

unloading operations to prevent the discharge of oil into waters subject to this permit. Any oil 

spilled must be cleaned with oil absorbent cloths or another appropriate approach. Additionally, 

owners/operators of oil tankers must comply with applicable requirements of 33 CFR § 155.310 

and 33 CFR Part 156, Subpart A. Vessel owners/operators must minimize the discharge of 

effluent produced from inert gas scrubbers if feasible for their vessel design. The EPA requires

operators to conduct a visual sheen test after every instance of pumping water from areas below 

decks, or immediately following washing down the decks. The visual sheen test is used to detect 

free oil by observing the surface of the receiving water for the presence of an oily sheen. If a 

visible sheen is observed, EPA requires the owner/operator to initiate corrective actions and meet 

recordkeeping/reporting requirements of the VGP. The EPA also requires tankers to do the 

following: 

 The ship’s crew members who actively take part in the management of the discharge or 

who may affect the discharge must receive training regarding shipboard environmental 

procedures and must be able to demonstrate proficiency in implementing these 

procedures; 
30

 Advanced training in shipboard environmental management procedures must be provided 

for those directly involved in managing specific discharge types or areas of the ship and 

these crew must be able to demonstrate proficiency in implementing these procedures; 

and 

 Appropriate reprimand procedures must be developed for crew whose actions lead to 

violations of any effluent limit set forth in this permit or procedures established by the 

ferry operator to minimize the discharge of pollutants. 

Research Vessels

Research vessels are those that are engaged in investigation or experimentation aimed at 

discovery and interpretation of facts, revision of accepted theories or laws in the light of new 

facts, or practical application of such new or revised theories or laws. For research vessels, EPA 

authorizes the discharge of tracers (dyes, fluorescent beads, SF6), drifters, tracking devices and 

the like, and expendable bathythermograph (XBT) probes, into waters subject to the VGP, 

provided such discharges are for the sole purpose of conducting research on the aquatic 

environment or its natural resources in accordance with generally recognized scientific methods, 

principles, or techniques. The EPA requires owners/operators of research vessels to discharge 

only the minimal amount of materials necessary to conduct research on the aquatic environment 

or its natural resources in accordance with generally recognized scientific methods, principles, or 

techniques. 

Emergency and Rescue Vessels

For emergency and rescue vessels, EPA authorizes owners/operators to discharge waste streams 

in conjunction with training, testing, and maintenance operations, provided that they comply 

with all additional requirements of the CWA (e.g., section 311) and the National Contingency 

Plan (40 CFR Part 300). This part does not relieve vessel operators of any additional 

responsibilities under the CWA and the National Contingency Plan which prohibits the discharge 

of oil for research or demonstration purposes without Administrator approval. The use of 

foaming agents for oil or chemical fire response must be implemented in accordance with the 

National Contingency Plan (40 CFR Part 300). 

VGP Inspections, Recordkeeping, Reporting, Compliance, and Enforcement

Self Inspections and Monitoring

Routine Visual Inspections. For vessels covered under the VGP, EPA requires vessel 

owners/operators to conduct a routine visual inspection at least once per voyage (but not more 

than once per day and not less than once per week. Vessel owners/operators are required to 

document the findings of each routine visual inspection including: the date and time of 

inspection, ship locations inspected, personnel conducting the inspection, location of any visual 

sampling and observations, any potential problems and sources of contamination found, any 
31

corrective actions taken, and the signature of the person conducting the inspection, who must be 

a signatory under 40 CFR § 122.22. These records must be available to EPA or its authorized 

representative upon request. Routine visual inspections must include

 Inspections of all accessible areas addressed in the VGP, including, but not limited to: 

cargo holds, boiler areas, machinery storage areas, welldecks, and other deck areas. 

Vessel owners/operators must ensure:

o areas are clear of garbage, exposed raw materials, oil, any visible pollutant or 

constituent of concern that could be discharged in any waste stream

o pollution prevention mechanisms are in proper working order

o pollution prevention procedures are in place to minimize the addition of pollutants to 

any waste stream. 

 Verification to the extent feasible that effluent limits and related requirements are being 

met and document any instances of noncompliance. 

 Visual inspection of safely accessible deck and cargo areas and all accessible areas 

where chemicals, oils, dry cargo, or other materials are stored, mixed, and used, whether 

or not the areas have been used since the last inspection. 

 Visual monitoring of the water around and behind the vessel for visible sheens, dust, 

chemicals, abnormal discoloration or foaming, and other indicators of pollutants or 

constituents of concern originating from the vessel during each watch.

 Corrective actions, if pollutants or constituents of concern are discharged in a manner 

that violates the limitations of the VGP

Extended Unmanned Period Inspections. For vessels covered under the VGP, the EPA provides 

vessels with the option of conducting extended unmanned period (EUP) inspections in lieu of 

vessels conducting routine visual inspections for vessels entering an unmanned period of 13 days 

or more. The extended unmanned period (EUP) inspection must include:

 A routine visual inspection as described above. 

 Ensuring material storage, and toxic and hazardous material requirements are met. 

 Ensuring all oils and oily machinery are properly secured, covered, and protected. Any 

spilled or leaked oils must be cleaned up immediately. If machinery or equipment is 

leaking oil, the leaks must be stopped or appropriate containment must be in place to 

capture any leaking oil. 

 Documenting whether automatic bilge water pump(s) will be engaged on the vessel 

during the EUP. 

 Documenting the amount of fuel on board. 

 Documenting the amount of ballast water on board. 

 Documenting the date the EUP began. 

While a vessel is in extended lay-up, the owner/operator must examine the outside of the vessel 

and surrounding waters at least once every two weeks for any evidence of leaks, loss of cargo, or 

any other spills which might result in an unauthorized discharge. If any deficiencies are observed 

while the vessel is in EUP, the vessel owner/operator must document those deficiencies and the 

corrective actions taken to resolve those deficiencies. If a visible sheen is noted on the surface of 
32

the surrounding water, the source of the oil must be identified and corrective action must be 

taken immediately. The vessel owner/operator must notify EPA of the visible sheen. All records 

must be available to EPA or its authorized representative upon request. Before a vessel reenters 

service, the EPA requires vessel owners/operators to conduct a post lay-up routine visual 

inspection. As part of this inspection, the owner/operator must document the date the EUP 

ended, whether fluids (e.g., fuel, ballast water) are at their pre-EUP levels, and whether any spills 

or leaks of oily materials are observed. Any deficiencies noted must be corrected before the 

vessel reenters service.

Comprehensive Annual Vessel Inspections. For vessels covered under the VGP, EPA requires

vessel owners/operators to conduct comprehensive vessel inspections at least once every 12 

months. These annual inspections must be conducted by qualified personnel, including: the 

Master or owner/operator of the vessel, if appropriately trained; appropriately trained marine or 

environmental engineers or technicians; or an appropriately trained representative of a vessel’s 

class society acting on behalf of the owner/operator. Comprehensive annual inspections must 

cover all areas of the vessel affected by the requirements in this permit that can be inspected 

without forcing a vessel into dry dock. Areas that inspectors must examine include, but are not 

limited to: 

 Vessel hull for attached living organisms, flaking anti-foulant paint, exposed TBT or 

other organotin surfaces; 

 Ballast water tanks, as applicable; 

 Bilges, pumps, and oily water separator sensors, as applicable; 

 Oil discharge monitoring system and electronic valve switching function, as applicable; 

 Protective seals for lubrication and any hydraulic oil leaks; 

 Oil and chemical storage areas, cargo areas, and waste storage areas; and 

 All visible pollution control measures to ensure that they are functioning properly. 

If any portions of the vessel are not inspectable without the vessel entering drydock, the vessel 

owner/operator must inspect these areas during their next drydock inspection. The EPA requires

vessel owner/operators to document areas not accessible during the annual inspection.

The annual inspections must also include a review of monitoring data collected in accordance 

with vessel-class-specific requirements, and routine maintenance records to ensure that required 

maintenance is being performed (e.g., annual tune-ups for small boats that have wet exhaust). 

The inspection must verify whether all monitoring, training, and inspections are logged and 

documented according to permit requirements. 

The EPA requires vessel owners/operators to take corrective action to resolve deficiencies

revealed by inspection, including violation of the effluent limits. Vessel owners/operators are 

required to record annual inspection results.

Dry Dock Inspections. For vessels covered under the VGP, EPA requires vessel 

owners/operators to make dry-dock reports available to EPA or an authorized representative of 
33

EPA upon request. The dry-dock report must note that: 

 The chain locker has been cleaned for both sediment and living organisms; 

 The vessel hull, propeller, rudder, thruster gratings, sea chest, and other surface areas of 

the vessel have been inspected for attached living organisms and those organisms have 

been removed or neutralized; 

 Any antifoulant hull coatings have been applied, maintained, and removed consistent 

with the FIFRA label if applicable; any exposed existing or any new coating does not 

contain biocides or toxics that are banned for use in the United States; 

 For all cathodic protection, anodes or dialectic coatings have been cleaned and/or 

replaced to reduce flaking; and 

 All pollution control equipment is properly functioning.

Recordkeeping

For vessels covered under the VGP, EPA requires vessel owners/operators to 

keep records on the vessel or accompanying tug that include the following information: 

1. Owner/Vessel information: 

a. Name, 

b. Owner and Vessel IMO Number (official number if IMO number not issued), 

c. Vessel type, 

d. Owner or operator company name, 

e. Owner or operator certifying official’s name, 

f. Address of owner/operator, 

g. Gross tonnage, 

h. Call sign, and 

i. Port of Registry (Flag). 

2. Voyage Log. Include the dates and ports of arrival, vessel agent(s), last port and country of 

call, and next port and country of call (when known). 

3. If vessel owners/operators have violated any effluent limit, they must document the violation 

and record:

a. A description of the violation, 

b. Date of the violation, 

c. Name, title, and signature of the person who identified the violation, 

d. Name, title, and signature of the person who is recording the violation (if different 

from person who identified the violation), 

e. If a Corrective Action Assessment pursuant to Part 3.2 is needed, attach a copy or 

indicate where the corrective action assessment is stored, and 
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f. If a Corrective Action Assessment was previously conducted pursuant to Part 3.2 (and 

revisions are not needed for this violation of the effluent limit), a reference to that 

previous corrective action assessment. 

4. Log of findings and any deficiencies and problems identified during routine visual inspections 

and extended unmanned inspections, including a discussion of any corrective actions, if 

applicable. Include date, inspector’s name, findings, and corrective actions planned or taken. If 

no deficiencies or problems are found during a routine visual inspection, the vessel 

owner/operator shall record that the inspection was completed with the inspector’s name and 

date. Routine visual inspections and extended unmanned inspections (if applicable) must be 

recorded as completed. 

5. Analytical results of all monitoring conducted, including sample documentation, results, and 

laboratory quality assurance (QA) documentation. Log of findings from comprehensive annual 

vessel inspections conducted, including a discussion of any corrective actions planned or taken 

required. Include date, inspector’s name, findings, and a description of the corrective actions 

taken. 

6. Log of findings from drydock inspections conducted including a discussion of any corrective 

actions planned or taken. Include date, inspector’s name, findings, and a description of the 

corrective actions taken. 

7. Record of any specific requirements given to your vessel by EPA or its authorized 

representative and how those requirements have been met.

8. Additional maintenance and discharge information to be recorded and kept in a log on the 

vessel: 

a. Deck maintenance. Record dates, materials used, application process, etc. for any 

significant maintenance of the deck surface(s) (e.g., more than routine, daily cleaning 

activities, such as sweeping). 

b. Bilgewater. Record dates, location, oil concentration (for MARPOL vessels) or visible 

sheen observation (non-MARPOL vessels), and estimated volume of bilgewater 

discharges. Record the same information for bilgewater disposed of at onshore locations. 

c. Paint application. Record dates, materials used, application process, etc. for any 

antifouling paint applied to the vessel. 

d. AFFF. Record dates, estimated volumes, and constituents of any discharges of AFFF. 

e. Chain locker inspections. Record dates of inspections and any rinsing conducted within 

waters subject to this permit. 

f. Controllable pitch propeller, stern tube, and other oil-to-sea interface maintenance. 

Record dates and locations of any maintenance of controllable pitch propellers that 

occurs while the vessel is in waters subject to this permit. 

g. Any emergencies requiring discharges otherwise prohibited to waters listed in 

Appendix G of the VGP. 
35

h. Gas Turbine Water Wash. Record dates and estimated volume of any discharge of gas 

turbine washwater within waters subject to this permit. If hauled or disposed of onshore, 

record log hauler and volume. 

i. Estimated volume and location of graywater discharged while in waters subject to this 

permit. 

9. All other documentation required pursuant to the VGP. 

10. Record of training completed as required by this permit, and where applicable, strategy for 

passenger training. For purposes of this part, if vessel owners/operators include their training 

plans as part of their ISM or similar environmental management plans, and they can document 

that they fully implement those plans, they will meet the recordkeeping requirements of this part. 

The EPA requires certification of accurate information for all NOIs, NOTs, the PARI form, and 

any report (including any monitoring data) submitted to EPA, pursuant to 40 CFR § 122.22. The 

vessel owner/operator are required to retain copies of all reports, certifications, records, 

monitoring data, and other information required by this permit, and records of all data used to 

complete the NOI to be covered by this permit, for a period of at least 3 years from the date that 

coverage under this permit expires or is terminated. The vessel master, owner/operator, or person 

in charge is required to make available to EPA or an authorized representative from EPA all 

records kept under this part upon request.

For vessels equipped with ballast tanks that are bound for a port or place in the United States, 

EPA requires the recordkeeping requirements of 33 CFR Part 151. The master, owner, operator, 

or person in charge of a vessel bound for a port or place in the United States is required to keep 

written records that include the following information: 

1. Total ballast water information. Include the total ballast water capacity, total volume of ballast 

water on board, total number of ballast water tanks, and total number of ballast water tanks in 

ballast. Use units of measurements such as metric tons (MT), cubic meters (m3), long tons (LT), 

and short tons (ST). 

2. Ballast water management. Include the total number of ballast tanks/holds that are to be 

discharged into the waters of the United States or to a reception facility. Indicate whether the 

vessel has a ballast water management plan and IMO guidelines on board, and whether the 

ballast water management plan is used. 

3. Information on ballast water tanks that are to be discharged into waters subject to this permit 

or to a reception facility. Include the following: 

a. The origin of ballast water. This includes date(s), locations(s) (including latitude and 

longitude and port [if relevant]), volume(s), and temperatures(s). If a tank has been 

exchanged, list the loading port of the ballast water that was discharged during the 

exchange. 
36

b. The date(s), location(s) (including latitude and longitude), volume(s), method, 

thoroughness (percentage exchanged if exchange conducted), sea height at time of 

exchange if exchange conducted, of any ballast water exchanged or otherwise managed. 

c. Specific records pertaining to treated ballast water (see Part 2.2.3.5 of the permit). 

d. The expected date, location, volume, and salinity of any ballast water to be discharged 

into the waters of the United States or a reception facility. 

4. Discharge of sediment. If sediment is to be discharged into a facility within the jurisdiction of 

the United States, include the location of the facility where the disposal will take place. 

The ballast water reporting forms must be kept on board the vessel and must be submitted to the 

National Ballast Information Clearinghouse before arriving to U.S. ports if required by the U.S. 

Coast Guard. In addition, all vessels that conduct saltwater flushing but do not report saltwater 

flushing to the NBIC, must instead keep a record of saltwater flushing to meet the requirements 

of this permit.

Reporting Requirements

For vessels covered under the VGP, the EPA requires vessel owners/operators to submit an 

Annual Report, i.e., the form available in Appendix H of the VGP. The EPA requires vessel 

owners/operators to report all instances of noncompliance as part of the Annual Report. The 

EPA requires vessel owners/operators to submit all analytical monitoring results as part of the 

Annual Report. Vessel owners/operators are required to answer all questions accurately and 

completely, and provide the necessary information and/or data to support each response. They 

are required to submit their Annual Report electronically unless exempted as described in the 

VGP. The EPA requires owners and operators of vessels greater than 300 gross tons or ballast 

water capacity of at least 8 cubic meters to submit a Notice of Intent (NOI). They require all 

other vessel owners/operators to complete a Permit Authorization and Record of Inspection Form 

(PARI) and keep it onboard at all times.

The following questions will be added to the Annual Report form available in Appendix H of the 

VGP:

 When is your next scheduled drydocking? (This question is optional for inland vessels 

less than 300 gross tons and unmanned, unpowered barges)

 When did you last conduct a below water (or drydock) hull inspection? (This question is 

optional for inland vessels less than 300 gross tons and unmanned, unpowered barges)

 Do you use anti-foulant paint? If so, what type of anti-fouling hull coating? [Select 

specific product from drop-down menu]. When was it last applied?

Corrective Action
37

Under the VGP, EPA has the authority to take enforcement action to require any remedy or 

corrective action necessary to achieve compliance as quickly as possible. They require vessel 

owners/operators to take action to ensure that the problem is eliminated and will not be repeated 

if they

 Violate one or more effluent limits or any other requirement of this permit, or if an 

inspection or evaluation of your vessel by an EPA official or an official agent acting on 

EPA’s behalf determines that modifications to the control measures are necessary to meet 

the effluent limits; 

 Become aware, or EPA determines, that their measures do not control discharges as 

stringently as necessary to meet applicable water quality standards; or 

 Become aware, or EPA determines, that their pollution control measures or best 

management practices are not being properly operated and maintained, or are not having 

the intended effect in minimizing pollutant discharges. 

Vessel owners/operators are required to conduct a corrective action assessment into the nature, 

cause, and potential options for eliminating these problems and to retain the records aboard their 

vessel. The EPA requires corrective actions to occur within 2 weeks for simple adjustments, 3 

months for adjustments that require new parts, and during the next dry dock for large repairs. 

The EPA considers the initial occurrence of a problem to be a violation of the permit; they 

consider failing to conduct a corrective action assessment and failing to correct the problem by 

the applicable deadline to be additional violations of the permit. 

Permit Compliance and Enforcement

The EPA requires vessel owners and operators to comply with the VGP requirements. Under the 

CWA, any person who knowingly falsifies, tampers with, or renders inaccurate any monitoring 

device or method required to be maintained under the CWA shall, upon conviction, be punished 

by a fine of not more than $10,000, or by imprisonment for not more than 2 years, or both. If a 

conviction of a person is for a violation committed after a first conviction of such person under 

this paragraph, punishment is a fine of not more than $20,000 per day of violation, or by 

imprisonment of not more than 4 years, or both. Any person who knowingly makes any false 

material statement, representation, or certification in any application, record, report, plan or other 

document filed or required to be maintained under the CWA shall, upon conviction, be punished 

by a fine of not more than $10,000 per violation, or by imprisonment for not more than 6 months 

per violation, or by both. In addition, false statements or representations, as well as alterations or 

false entries in documents, may be punishable by more severe criminal penalties pursuant to 18 

USC §1001 or 18 USC §1519. 

To monitor and insure compliance with its VGP, EPA will develop and implement a monitoring 

and compliance plan by December 2013 to assess the performance of the permit in protecting 

listed resources. Currently, the U.S. Coast Guard conducts all inspections of vessels covered 

under the VGP using EPA’s Job Aide, i.e., “Guidelines for Coast Guard Evaluations of 

Compliance with the US Environmental Protection Agency's (EPA) Vessel General Permit 

(VGP) for Discharges Incidental to the Normal Operation of Vessels.” To insure that the 
38

inspections assess new requirements of the proposed VGP, EPA will:

 Work with the U.S. Coast Guard, with the early input of the Services, to update the Job 

Aide to reflect requirements included in the new VGP. 

 Create an online training and/or a webinar training regarding the VGP 

requirements/prohibitions, within one year of final permit issuance.

 Create a comprehensive checklist of requirements for inspector training in conjunction 

with the U.S. EPA National Enforcement Training Institute, within one year of final 

permit issuance.

 Provide and continue to provide the U.S. Coast Guard with the title, office name, current 

address and phone number for points of contact at headquarters offices and in each EPA 

Region and USCG District. 

In addition, EPA’s Office of Enforcement and Compliance Assurance will meet with the 

Services to discuss enforcement under the VGP. The EPA will gather, review and analyze 

inspection data submitted by the Coast Guard; the results will be summarized (by type of vessel, 

location when available, type of deficiencies, and number of deficiencies) and provided to the 

Services annually. 

Small Vessel General Permit (sVGP)

The proposed sVGP authorizes owners/operators of eligible vessels less than 79 feet in length to 

release discharges incidental to the normal operation of a vessel into waters of the U.S. The 

following narrative describes the discharges authorized or prohibited should EPA issue the 

sVGP. It also describes the activities that EPA requires of vessel owners/operators for vessels 

covered under the sVGP, including reporting and compliance requirements. 

For vessels covered under the sVGP, the EPA authorizes discharges incidental to the normal 

operation of a vessel when operating as a means of transportation, including: anti-foulant hull 

coating leachate, bilgewater, deck runoff, fish hold effluent, graywater, non-contact engine 

cooling water, packing gland effluent, and underwater hull husbandry. 

The EPA does not authorize discharges that are not incidental to the normal operation of a vessel 

when operating as a means of transportation. They do not authorize the following discharges: 

industrial operations waste, medical waste, noxious liquid substance residue, sewage, used or 

spent oil, garbage or trash, tetrachloroethylene degreasers, and discharges covered by another 

NPDES permit. 

Discharges to be Authorized by the sVGP

For vessels covered under the sVGP, EPA requires vessel owners and operators to minimize 
39

vessel discharges. They define minimize as to reduce and/or eliminate to the extent achievable 

using control methods, including best management practices, that are technologically available 

and economically practible and achievable in light of best marine practices. The EPA prohibits 

the addition of any constituents to any discharge that are not incidental to the normal operation of 

a vessel. They require all vessel owner/operators to ensure adequate training for the master, 

operator, person-in-charge, and crew who manage or affect incidental discharges. They require 

that all discharges meet the following standards:

 Minimize the potential for substances or pollutants to accidentally enter the effluent, 

including spills. 

 May not contain visible garbage in the effluent. 

 May not use any dispersants, cleaners, chemicals, or other materials or emulsifiers that 

remove the appearance of a visible sheen. 

 Minimize the introduction of constituents of concern or pollutants, such as foam or 

floating solids. 

 Oil, including oily mixtures, may not be discharged in quantities that may be harmful or 

cause a visible sheen. 

 The discharge of antifreeze into waters subject to this permit must be minimized. For 

vessel engines that have been winterized, minimization can be achieved by draining 

antifreeze from the engine prior to startup or capturing antifreeze when discharged from 

the engine upon startup. The discharge of antifreeze with toxic or known carcinogenic 

additives, such as ethylene glycol and methanol, is prohibited. 

 When feasible, cleaning, maintenance, and repair jobs should be done while the vessel is 

out of the water or in drydock. 

 Any soaps, detergents or cleaners used must be non-toxic, phosphate-free, and 

biodegradable; EPA expects that non-toxic soaps will contain little to no nonylphenols. 

Phosphate-free soap contains by weight 0.5% or less of phosphates or derivatives of 

phosphates. 

 Any spill of oil or other harmful chemicals that are discharged in a quantity that may be 

harmful or cause a visible sheen as established under 40 CFR Part 110, 40 CFR Part 117, 

or 40 CFR Part 302, must be reported immediately to the National Response.

Water Quality-Based Effluent Limits

Impaired waters or “water quality limited segment[s]” are those which have been identified by a 

State or EPA pursuant to Section 303(d) of the CWA as not meeting applicable State water 

quality standards. Impaired waters may include both waters with EPA-approved or EPAestablished Total Maximum Daily Loads (TMDLs) and those for which EPA has not yet 

approved or established a TMDL. 

The EPA requires vessel owners/operators to comply with the requirements of this section, 
40

including any additional requirements that EPA may impose pursuant to this section, if the vessel 

discharges to an impaired water without an EPA-approved or established TMDL. This provision 

also applies to situations where EPA determines that a vessel’s discharge is not controlled as 

necessary to meet water quality standards in another water body, even if its discharge is to a 

receiving water that is not specifically identified on a Section 303(d) list. 

If a vessel discharges to an impaired water with an EPA-approved or established TMDL and 

EPA or state TMDL authorities have informed the owners/operators that a Waste Load 

Allocation (WLA) has been established that applies specifically to their vessel’s discharges, to 

discharges from vessels in their vessel class or type, or to discharges from vessels in general if 

applicable, EPA requires discharges to be consistent with the assumptions and requirements of 

that WLA. If such a WLA exists, EPA will inform vessel owners/operators if any additional 

limits or controls are necessary for discharges to be consistent with the assumptions of any 

available WLA in the TMDL, or whether an individual permit application is necessary. This 

provision also applies to situations where EPA determines that discharges are covered by the 

WLA in an EPA- approved or established TMDL for another water body, even if the discharge is 

to a receiving water that is not specifically identified on a Section 303(d) list. If an applicable 

TMDL exists either individually or categorically for a vessel or vessel class (including 

disallowing discharges from your vessel), EPA and/or state TMDL agencies will inform vessel 

operators of specific requirements via dock side postings, information made available from the 

Captain of the Port, or by specifically contacting vessel owners/operators.

Additional Technology-Based Effluent Limits

Fuel Management. For vessels covered under the sVGP, the EPA requires vessel 

owners/operators to:

 Have a functioning fuel-air separator or a fuel tank vent to prevent a fuel spill, for all 

motorized vessels constructed on or after December 19, 2013

 Prevent overfilling and refrain from topping off fuel tanks. 

 Use an oil absorbent material or other appropriate device while fueling the vessel to 

prevent any oil from entering waters subject to this permit, for motorized vessels that do 

not have a functioning fuel-air separator or a fuel tank vent.

 Regularly inspect the fuel and hydraulic systems for any damage or leaks, for instance 

during fueling and/or when performing routine maintenance.

 Fill portable tanks onshore, instead of on the dock or on your vessel, unless 

impracticable.

Engine and Oil Control. For vessels covered under the sVGP, the EPA requires vessel 

owners/operators to:
41

 Periodically inspect (at least once per quarter) the engine for any loose or leaking hoses, 

gaskets, and/or seals and if needed, repair or replace damaged parts as soon as possible. 

 Place oil absorbent material or other spill response equipment under the vessel engine or 

use other preventative practices to minimize oil entering the bilgewater. 

 Immediately clean up any spill or overflow of oil or other engine fluids . A supply of 

absorbent pads, pillows, or other materials should be kept onboard as appropriate for use 

in addressing or remediating any such spills or overflows, and supplies should be checked 

quarterly and restocked as necessary. 

 Dispose of used oil-absorbent materials onshore in containers designed for oily waste 

disposal. 

 If the vessel has a bilge oily water separator, check for the presence of a visible sheen in 

surrounding waters periodically while discharging. 

 If a visible sheen is observed as a result of this discharge, suspend discharge until the 

problem is corrected and clean up immediately. 

 Use an oil-absorbent material to remove any oil from the bilge before discharging, if a 

U.S. Coast Guard type-approved bilge oily water separator is not used. 

 Any discharge of packing gland or stuffing box effluent must not contain oil, including 

oily materials, in quantities that may be harmful. These discharges must not produce a 

visible sheen of oil or oily materials. If accessible, segregated water which contains drips 

from packing gland effluent or stuffing box effluent must be checked daily for the 

presence of a visible sheen, while the vessel is operational and manned. If not accessible 

while the vessel is operational and manned, then the surrounding water must be checked 

for the presence of a visible sheen (while operating). If a visible sheen is observed, 

appropriate measures such as the use of oil absorbent materials must be used to remove 

the presence of oil before the effluent may be discharged. Dispersants or emulsifiers that 

remove the appearance of a visible sheen must not be used. 

 If a visible sheen is observed in surrounding waters as a result of this discharge, suspend 

the discharge until the problem is corrected and clean up immediately. 

 Use environmentally acceptable lubricants in all machinery and equipment, including but 

not limited to stern tubes, wires, and two-stroke engines, where discharges of oil to 

surrounding waters are likely to occur, unless technically infeasible.

 Unless infeasible, prior to pumping the bilge, inspect the bilgewater for an oily sheen. 

While pumping the bilge, examine the surrounding water for the presence of a visible 

sheen. 

 If a visible sheen is observed as a result of this bilge pumping, suspend the discharge 

until the problem is corrected and clean up immediately. 

 Refrain from adding dispersants, detergents, emulsifiers, chemicals or other substances 

that remove the appearance of a visible sheen to the bilge. 

Solid and Liquid Waste Management. For vessels covered under the sVGP, the EPA requires

vessel owners/operators to:
42

 Prevent trash or garbage, including food waste, cigarette butts, bottles, and caps from 

entering any waste stream covered by this permit. 

 Have appropriate receptacles for retaining trash or garbage onboard the vessel. Examples 

of appropriate receptacles include secured trash bags or coolers, bins, or trash cans with 

secure lids. Store any used antifreeze, paint, out-of-date flares, or other toxics in secure 

containers and dispose of them properly at onshore disposal facilities. 

 Secure or otherwise prevent loose items on deck from entering any waste stream covered 

by this permit. 

 Prevent monofilament line, fishing nets, lines, lures, rope, bait boxes, and hooks from 

entering any waste stream covered by this permit. 

Deck Washdown and Runoff and Above Water Line Hull Cleaning. For vessels covered under 

the sVGP, the EPA requires vessel owners/operators to:

 Use all soaps and cleaners as directed by the label. 

 Use non-toxic, phosphate-free, and biodegradable soaps, detergents, or cleaners; EPA 

expects that soaps that are “minimally toxic” will contain little to no nonylphenols. The 

use of soaps that are labeled toxic or highly toxic is prohibited under the sVGP. 

 Prevent the introduction of on-deck debris, garbage, residue, and spills into deck 

washdown and runoff discharges. 

 Minimize the discharge of paint chips and residue, especially during cleaning, 

maintenance, paint application, and reapplication. When performing these activities, 

collect and then dispose of chips and residues onshore in accordance with applicable 

requirements for the facility where operations are performed. 

Vessel Hull Maintenance. For vessels covered under the sVGP, the EPA requires vessel 

owners/operators to:

 Minimize the impact of any anti-foulant system or the discharges resulting from antifoulant paints on the aquatic environment. Use less toxic alternatives to copper based 

paints to the extent practicable and available. 

 Minimize hull husbandry in designated critical habitat for ESA listed aquatic species.

 Do not use anti-fouling coatings if not needed, where drying or hull cleaning at haul-out 

is adequate for managing fouling (e.g., for vessels that are hauled frequently or for overwinter storage). 

 Avoid discharges of tributyltin (TBT), i.e., zero-discharge standard by avoiding TBT 

coatings; or having an effective overcoating that completely eliminates TBT discharges. 

 Avoid cleaning anti-foulant paint which releases biocides for the first 90 days after 

application. 

 If the anti-foulant paint requires cleaning, gently clean hulls on a regular basis (this 

minimizes the need for stronger cleaners and more abrasive brushes). 
43

 When cleaning hulls coated with anti-fouling paint while the vessel is in the water, use 

only soft sponges. Examine the water while cleaning to avoid forming a plume of paint. 

Stop immediately if any visible plume of paint appears in the water. Consider hiring a 

qualified, professional hull cleaner to do the work, and ensure that they follow 

environmental guidelines. 

 When cleaning hulls coated with anti-fouling paint while the vessel is out of the water, 

always work away from the water in a location where paint chips and dust will not be 

washed into the water. Place a tarp under the area to catch loose particles, and properly 

dispose of paint chips, dust, and other particles. 

 Vessel hulls must be periodically inspected (at least once per quarter), and if necessary, 

cleaned to prevent the spread or dispersal of potentially invasive species. 

 Minimize the transport of any visible living organism from one waterbody to another by 

regularly cleaning and maintaining the hull. If a vessel’s hull is severely fouled the 

cleaning has not occurred regularly. Hence, severe fouling could be a permit violation.

 Prior to transporting the vessel from one waterbody to another overland, inspect the 

visible areas of the vessel for any attached or visible stowaway living organisms. If 

organisms are found, they must be removed and appropriately discarded onshore. 

Removed organisms may not be discharged into waters subject to the sVGP. 

Graywater. For vessels covered under the sVGP, the EPA requires vessel owners/operators to:

 Minimize graywater discharges in areas that have heavy vessel traffic or heavy 

recreational use and in marine sanctuaries, national wildlife refuges, national wild and 

scenic rivers, and national wilderness areas. If the vessel has the capacity to store 

graywater in these waters, it should be stored and later discharged in other waters or 

onshore. 

 Minimize the production of graywater while the vessel is stationary in confined waters 

(e.g., marinas, harbors). If the vessel has the capacity to store graywater, it should be 

stored and discharged at an appropriately equipped onshore facility or discharged while 

the vessel is underway. 

 Use soaps, detergents and cleaners that are phosphate free, non-toxic, and biodegradable 

for any activities that may result in their introduction into graywater; EPA expects that 

non-toxic soaps will contain little to no nonylphenols. Excess oils, including animal fats 

and vegetable oils, used during cooking must not be added to the graywater system or 

into any other discharge covered by this permit. 

Fish Hold Effluent. For vessels covered under the sVGP, the EPA requires vessel 

owners/operators to:
44

 Discharge your effluent (including dirty ice) to a shore-based facility instead of 

discharging to surrounding waters, if a shore-based discharge facility is available and 

economically achievable.

 Avoid discarding any unused live bait overboard, unless caught in that waterbody or 

watershed. Unused live bait purchased from a bait shop or dealer may not be discharged 

overboard. 

 Minimize the discharge of fish hold water or ice while in port. All reasonable steps must 

be taken to prevent the discharge of excess fish hold water and ice while the vessel is 

stationary at the pier. If solid fish waste is contained in the fish hold effluent, the fish 

hold effluent may not be discharged while in port, unless a physical separation method is 

used (e.g. filters or removal of residuals). 

 Use non-toxic, phosphate-free, and biodegradable soaps and cleaners when cleaning fish 

holds. While pierside and stationary, avoid washing any residual solids into surrounding 

waters. 

Ballast Water. For vessels covered under the sVGP, the EPA requires vessel owners/operators 

to:

 Avoid the discharge or uptake of ballast water in areas within, or that may directly affect, 

marine sanctuaries, marine preserves, marine parks, shellfish beds, or coral reefs. 

 Minimize or avoid uptake of ballast water in the following areas and situations: 

designated critical habitat for ESA listed species; areas known to have infestations or 

populations of harmful organisms and pathogens (e.g., toxic algal blooms); areas near 

sewage outfalls; areas near dredging operations; areas where tidal flushing is known to be 

poor or times when a tidal stream is known to be turbid; in darkness, when bottomdwelling organisms may rise up in the water column; where propellers may stir up the 

sediment; areas with pods of whales, convergence zones, and boundaries of major 

currents. 

 Discharge only the minimal amount of ballast water essential for vessel operations. 

 When feasible, use one of the following measures to reduce the potential for transfer or 

introduction of organisms to waters of the U.S.: use potable water for ballasting; utilize 

onshore treatment or disposal methods for ballast water; for vessels that conduct fixed 

routes, capture and reuse ballast water in each port. 

Seawater Cooling Overboard Discharge. For vessels covered under the sVGP, the EPA requires

vessel owners/operators to:

 Discharge seawater cooling overboard discharge when the vessel is underway to 

minimize any thermal impacts to the receiving water, when possible. 
45

 To reduce the production and discharge of seawater cooling overboard discharge, EPA 

recommends that vessel owner/operators use shore-based power when the vessel is in 

port if: 

o Shore power is readily available for vessel owner/operators from utilities or port 

authorities; 

o Shore-based power supply systems are capable of providing all needed electricity 

required for vessel operations; and 

o The vessel is equipped to connect to shore-based power and such systems are 

compatible with the available shore power. 

sVGP Recordkeeping, Inspections, Compliance, and Enforcement

Recordkeeping Requirements

For vessels covered under the sVGP, the EPA requires vessel owners/operators to read and sign a 

PARI and keep it on board at all times. 

Quarterly Visual Inspection Requirements

For vessels covered under the sVGP, the EPA requires vessel owners/operators to conduct 

quarterly visual inspection. The inspection must cover all discharges and all applicable areas 

which impact discharges covered by the permit and at minimum, the visible portions of the hull. 

The inspection must ensure that all areas are clear of garbage, exposed raw materials, oil, or any 

other materials that could be discharged into any waste stream or receiving waters and that there 

is no uncontrolled or unmanaged sources of these pollutants. The EPA will develop a discharge 

requirement checklist or other implementation tool for vessel owners/operators to use to assist in 

their quarterly self-inspections; this tool will be developed within one year of the final sVGP 

permit issuance (December 2013). The EPA requires vessel owners/operators to:

 Frequently check the area around and behind the vessel to ensure that no visible sheen, 

dust, chemicals, or discoloration is originating from the vessel, while the vessel engine is 

operating. 

 Check to ensure that all equipment on board is in proper working condition. This 

equipment includes, as appropriate, oily water separators, monitors, bilges, pumps, and 

generators. 

 Check all protective seals for lubrication and hydraulic oil leaks. 

 Document any problem(s) requiring corrective action and corrective actions that were 

taken to resolve the problem(s). The dates of these inspections must be documented on 

the sVGP PARI Form along with any corrective actions taken. 

Corrective Action

The EPA retains the right to request any information required to determine whether cause exists 
46

for modifying, revoking and reissuing, or terminating the sVGP or to determine compliance with 

the sVGP. They require vessel owners/operators to provide any requested information within a 

reasonable time following the request. The vessel owner or operator is required to allow EPA or 

an authorized representative to: 

1. Inspect any vessel, equipment (including monitoring and control equipment), practices, or 

operations regulated or required under this permit; and 

2. Sample or monitor, for the purpose of assuring permit compliance or as otherwise authorized 

by the Act, any substances or parameters at any location. 

Authorized representatives include the U.S. Coast Guard, an authorized contractor acting as a 

representative of the Administrator or Director, or an appropriate state agency. Authorized 

representatives should present their credentials to the vessel owner or operator before inspecting 

or entering any vessel. The EPA retains authorities under Section 308 of the CWA, including the 

authority to enter, access, inspect, sample, monitor, and obtain information to verify compliance 

with the CWA. 

Permit Compliance and Enforcement

The EPA requires vessel owners and operators to comply with the sVGP requirements. Under 

the CWA, any person who knowingly falsifies, tampers with, or renders inaccurate any 

monitoring device or method required to be maintained under the sVGP shall, upon conviction, 

be punished by a fine of not more than $10,000, or by imprisonment for not more than 2 years, or 

both. If a conviction of a person is for a violation committed after a first conviction of such 

person under this paragraph, punishment is a fine of not more than $20,000 per day of violation, 

or by imprisonment of not more than 4 years, or both. Any person who knowingly makes any 

false material statement, representation, or certification in any record or other document 

submitted or required to be maintained under the sVGP shall, upon conviction, be punished by a 

fine of not more than $10,000 per violation, or by imprisonment for not more than 6 months per 

violation, or by both. In addition, false statements or representations, as well as alterations or 

false entries in documents, may be punishable by more severe criminal penalties pursuant to 18 

USC §1001 or 18 USC §1519.

To monitor and insure compliance with its sVGP, EPA will:

 Develop and implement a monitoring and compliance plan within 1 year of finalization 

of the permit to assess the performance of the permit in protecting listed resources; 

 Organize a meeting with their Office of Enforcement and Compliance Assurance for the 

Services to discuss and provide input to OECA’s inspection and enforcement plans for 

the sVGP;

 Work with USCG, with the input of the Services, to update the inspection and 

enforcement document inspection checklist (i.e., Job Aide) to reflect sVGP requirements;
47

 Conduct outreach to the states to raise awareness about small vessel requirements; EPA 

will encourage States to check records of quarterly self-inspection records and visible 

portions of the hull while inspecting vessels when implementing their own programs;

 Develop trainings covering the small vessel requirements and share these with the Coast 

Guard and States.

The EPA will provide the Services with a yearly summary of the number of inspections (by 

EPA, the Coast Guard, States or other sources) and results (including number of inspections by 

type of vessel, location when available, and number and type of deficiencies). 

Additional Specific Actions Taken by EPA to Conserve Listed Resources

Reinitiation Clause

The VGPs include permit reopener clauses which state that the permits are subject to 

modification based on the receipt of new information that was not available at the time of permit 

issuance and would have justified the application of different permit conditions at the time of 

permit issuance. This new information may include data on ANS invasion rates, available 

technologies to minimize ANS invasions, discharge concentrations or volumes, pollutant risks, 

compliance or lack thereof, and adverse affects to listed resources. This information would also 

allow EPA to determine whether reinititation of formal ESA Section 7 consultation would be 

required as provided in 50 CFR 402.16, as described in the Fact Sheets.

VGP Requirements

During the course of the Section 7 consultation, EPA agreed to include the following language in 

the VGP Fact Sheet to minimize exposure and/or adverse affects to listed resources. The EPA

requires vessel owners/operators to:

 Regularly inspect the fuel and hydraulic systems for any damages or leaks, for instance 

during fueling, when performing routine maintenance on the auxiliary vessel, and/or 

during deployments for testing.

 Avoid discharging ballast water in critical habitat when feasible 

(http://www.nmfs.noaa.gov/pr/species/criticalhabitat.htm)

 Minimize hull husbandry in critical habitat for aquatic species 

(http://www.nmfs.noaa.gov/pr/species/criticalhabitat.htm)

 Use soaps and detergents that are minimally toxic; EPA expects that soaps that are 

““minimally toxic” will contain little to no nonylphenols”

 Add the following questions to the Annual Report:

o When is your next scheduled drydocking? (This question is optional for inland 

vessels less than 300 gross tons and unmanned, unpowered barges)
48

o When did you last conduct a below water (or drydock) hull inspection? (This question 

is optional for inland vessels less than 300 gross tons and unmanned, unpowered 

barges)

o Do you use anti-foulant paint? If so, what type of anti-fouling hull coating? [Select 

specific product from drop-down menu]. When was it last applied?

sVGP Requirements

During the course of the Section 7 consultation, EPA agreed to include the following language in

the sVGP Fact Sheet. The EPA requires vessel owners/operators to:

 Regularly inspect the fuel and hydraulic systems for any damages or leaks, for instance 

during fueling and/or when performing routine maintenance;

 Periodically inspect (at least once per quarter) the engine for any loose or leaking hoses, 

gaskets, and/or seals and if needed, repair or replace damaged parts as soon as possible;

 Check for the presence of a visible sheen surrounding waters periodically while 

discharging bilgewater;

 Visible portions of the vessel hulls must be periodically inspected (at least once per 

quarter), and if necessary, cleaned to prevent the spread or dispersal of potentially 

invasive species;

 Minimize the transport of any visible living organism from one waterbody to another by 

regularly cleaning and maintaining the hull;

 Minimize hull husbandry in critical habitat for aquatic species 

(http://www.nmfs.noaa.gov/pr/species/criticalhabitat.htm);

 Avoid discharging ballast water in critical habitat when feasible 

(http://www.nmfs.noaa.gov/pr/species/criticalhabitat.htm);

 Use soaps and detergents that are minimally toxic; EPA expects that soaps that are 

““minimally toxic” will contain little to no nonylphenols”;

 EPA will develop a discharge requirement checklist or other implementation tool for 

vessel owners/operators to use to assist in their quarterly self-inspections. This tool will 

be developed within one year of the final sVGP permit issuance (December 2013). 

VGP Compliance

To monitor and insure compliance with its VGP, EPA will develop and implement a monitoring 

and compliance plan by December 2013 to assess the performance of the permit in protecting 

listed resources. Currently, the U.S. Coast Guard conducts all inspections of vessels covered 

under the VGP and uses a EPA/USCG jointly developed Job Aide as a tool, i.e., “Guidelines for 

Coast Guard Evaluations of Compliance with the US Environmental Protection Agency's (EPA) 
49

Vessel General Permit (VGP) for Discharges Incidental to the Normal Operation of Vessels.” To 

insure that the inspections assess new requirements of the proposed VGP, EPA will:

 Work with the U.S. Coast Guard, with the early input of the Services, to update the Job 

Aide to reflect requirements included in the new VGP. 

 Create an online training and/or a webinar training regarding the VGP 

requirements/prohibitions, within one year of final permit issuance.

 Create a comprehensive checklist of requirements for inspector training in conjunction 

with the U.S. EPA National Enforcement Training Institute, within one year of final 

permit issuance.

 Provide and continue to provide the U.S. Coast Guard with the title, office name, current 

address and phone number for points of contact at headquarters offices and in each EPA 

Region and USCG District. 

In addition, EPA’s Office of Enforcement and Compliance Assurance will meet with the 

Services to discuss enforcement under the VGP. The EPA will gather, review and analyze 

inspection data submitted by the Coast Guard; the results will be summarized (by type of vessel, 

location when available, type of deficiencies, and number of deficiencies) and provided to the 

Services annually. 

sVGP Compliance

To monitor and insure compliance with its sVGP, EPA will:

 Develop and implement a monitoring and compliance plan within one year of permit 

issuance to assess the performance of the permit in protecting listed resources. 

 Organize a meeting with their Office of Enforcement and Compliance Assurance for the 

Services to discuss and provide input to OECA’s inspection and enforcement plans for 

the sVGP. 

 Work with USCG, with the early input of the Services, to update the inspection and 

enforcement document inspection checklist (i.e., Job Aide) to reflect sVGP requirements

 Conduct outreach to the states to raise awareness about small vessel requirements; EPA

will encourage States to check records of quarterly self-inspection records and visible 

portions of the hull while inspecting vessels when implementing their own programs. 

 Develop trainings covering the small vessel requirements and share these with the Coast 

Guard and States

The EPA will provide the Services with a yearly summary of the number of inspections (by 

EPA, the Coast Guard, States or other sources) and results (including number of inspections by 
50

type of vessel, location when available, and number and type of deficiencies). 

Monitoring of Stressors (ANS and Pollutants)

Annually, EPA will summarize data from Annual Reports (which include all instances of 

noncompliance and unavoidable discharges authorized by the VGP) and Discharge Monitoring 

Reports and provide this summary to the Services. The Discharge Monitoring Reports include:

 Ballast water treatment system testing results, including results from: 

o Functionality monitoring (at least monthly)

o Biological organism monitoring (2 or 4 times annually, depending on system)

o Residual biocides (After initial monitoring, 2 or 4 times annually, depending on 

system)

 Graywater from cruise ships (Quarterly, after initial monitoring)

o BOD, fecal coliform, suspended solids, pH, and total residual chlorine

o E. coli, total phosphorus, ammonia, nitrate/nitrite, and total Kjeldahl nitrogen

 Bilgewater (annual oil content monitoring, for new builds on or before December 19, 

2013)

In addition, EPA has committed to the following:

Copper

Within 1 year of finalization of the VGPs, EPA will develop, in cooperation with the Services, 

and implement a monitoring and reporting plan for copper. The plan will contain the following 

elements:

1) EPA, with the technical assistance of the Services, will identify metrics for assessing 

copper loadings to waters inhabited by ESA listed species (i.e., using the number of ships 

reporting copper hull treatments in eNOIs for particular areas as a proxy).

2) EPA will compile eNOI and annual report information regarding the number and type of 

vessels that use copper-based anti-fouling hull coating and/or exhaust gas scrubbers, their 

home port/most frequented US port, and US ports anticipated visiting during the permit 

term.

3) Twice, once by December 2014 (to summarize eNOI data) and another before EPA 

transmits the next draft VGP/sVGP to OMB for interagency review (to evaluate annual 

reports in time to make changes for the next permit cycle, if need be), EPA will evaluate 

vessel data and identify ports/locations where the metric has been exceeded. If the metric 
51

has been exceeded, EPA will, as appropriate, identify and implement additional actions to 

reduce any unacceptable risks.

Potential Selenium Discharges in Exhaust Gas Scrubber (EGS)

Within 1 year of finalization of the VGPs, EPA will develop, in cooperation with the Services, 

and implement a monitoring and reporting plan for gas-scrubber discharges. The plan will 

contain the following elements:

1) EPA, with the technical assistance of the Services, will identify metrics for assessing 

selenium loadings to waters inhabited by ESA listed species (i.e., using the number of 

ships reporting exhaust gas scrubbers in eNOIs for particular areas combined with 

expected and/or reported volume and concentration values as proxies).

2) EPA will state that vessel operators should analyze selenium in saline EGS discharges 

using methods capable of accurately measuring selenium in saline samples (e.g., 

Octopole Reaction Cell ICP-MS or Hydride generation AA methods or other methods 

which reduce matrix interference for selenium).

3) EPA will compile NOI and annual report information regarding the number and type of 

vessels that use exhaust gas scrubbers, discharge monitoring data for pollutants including 

selenium and copper, their home port/most frequented US port, and US ports anticipated 

visiting during the permit term.

4) Twice, once by December 2014 (to summarize eNOI data) and another before EPA 

transmits the next draft VGP/sVGP to OMB for interagency review (to evaluate annual 

reports in time to make changes for the next permit cycle, if need be), EPA will evaluate 

vessel data and identify ports/locations where the metric has been exceeded. If the metric 

has been exceeded, EPA will, as appropriate, identify and implement additional actions to 

reduce any unacceptable risk.

ANS

Within 1 year of finalization of the VGPs, EPA will develop, in cooperation with the Services, 

and implement a monitoring and reporting plan for vessel-mediated ANS invasions. The plan 

will contain the following elements:

1) EPA, with the technical assistance of the Services, will identify metrics to evaluate 

whether vessel mediated ANS invasion rates are being reduced over time.

2) EPA will track information from ANS invasions that might be potentially tied to vessel 

vectors. Information tracked may include:

a. Dr. Greg Ruiz (Smithsonian Institution) conducts systematic surveys for ANS 

invasions caused by hull-fouling and ballast water in San Francisco, Chesapeake, 

and Tampa Bays to track changes in the rate of ANS invasions.
52

b. Nationwide NEMESIS database for all newly documented, marine, ballast water 

and hull fouling ANS invasions. 

http://invasions.si.edu/nemesis/browseDB/searchQuery.jsp

c. National USGS NAS database for all newly documented, freshwater, shippingrelated ANS invasions. http://nas.er.usgs.gov/queries/SpSearch.aspx

EPA and the Services acknowledge that new invasions observed from any of these 

sources are not necessarily linked to discharges authorized by the VGPs. Nonetheless, 

over a multi-permit lifespan, tracking invasions, and improving EPA’s methodologies 

and understanding of the risk-release relationship, could provide a long-term perspective 

about ballast water discharge standards, antifouling technologies, and other practices to 

reduce invasions.

3) EPA will report to the Services once per year that they have reviewed this information 

and whether notable new invasions have been recorded in the previous year that could 

have been previously caused by vessel discharges. The Services note that they are 

requesting a short review (approximately one hour per year) to ensure that EPA continues 

to track aquatic bioinvasions. As discussed above, EPA and the Services agree that these 

observations are being used to inform EPA’s general understanding of continued and 

ongoing invasion rates.

If needed, EPA will identify and implement, as appropriate, additional actions (e.g., require antifouling coatings; require debris containment systems; require more stringent ballast water 

standards) as soon as practicable (including in future permit iterations) to ensure the protection of 

listed species.

AFCs and Debris Containment Technology

Before EPA transmits the next draft of the VGPs to OMB for interagency review:

1) EPA will compile information on new developments in AFCs (to minimize exposure to 

hull-fouling ANS and copper loading) and debris containment systems (to minimize the 

release of ANS and biocides during underwater husbandry).

2) EPA, with the technical assistance of the Services, will identify whether there are more 

efficacious BMPs or technologies for underwater husbandry and for anti-fouling coatings 

with fewer secondary environmental impacts that could be required of vessels.

Approach to the Assessment
53

Overview of FWS’ Assessment Framework

Section 7(a)(2) of the Endangered Species Act of 1973, as amended, requires federal agencies, in 

consultation with and with the assistance of the Services, to insure 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, FWS fulfills its 

obligations 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 effect on the environment (we use the term “potential stressors” 

for these components of an action); we then determine whether listed species or designated 

critical habitat are likely to be exposed to those potential stressors; we estimate how 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 

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 specific effects of a specific 

proposal, are not designed to deal with the spatial and temporal scales and level of uncertainty 

that is typical of consultations on general permits. 

Instead of trying to adapt traditional consultation approaches to programmatic consultations, we 

have developed an assessment framework that specifically allows us to help Federal agencies 

insure that their programs comply with the requirements of section 7(a)(2) of the ESA as 

described in the Interagency Endangered Species Consultation Handbook (FWS and NMFS 

1998a; Chapter 5). Our assessment framework for general permits first assesses whether the 

general permits are likely to adversely affect listed species or critical habitats by estimating 

exposure and response, as described above for traditional consultations. If listed species and 

critical habitats are likely to be adversely affected we then assess how the permit is structured to 

comply with section 7(a)(2). Specifically, our programmatic consultations on general permits 

examine the decision-making processes that are integrated into Federal Agency programs to 

determine whether those decision-making processes are likely to insure that specific actions the 

agency authorizes, funds, or carries out through the program comply with the requirements of 

section 7(a)(2). That is, during programmatic consultations we ask whether or to what degree the 

Federal action agency (in this case, EPA) has structured its proposed general permit so that the 

agency (1) collects the information necessary to allow it to know or reliably estimate the 

probable individual and cumulative consequences of its actions on listed resources; (2) evaluates 

the information it collects to assess how its actions have affected endangered species, threatened 

species, and designated critical habitat specifically; and (3) use its authorities to bring those 

activities into compliance with the requirements of section 7(a)(2) of the ESA, if the information 
54

it collects suggests that it is necessary. Here, “permit structure” refers to the decision-making 

processes, applications of standards and criteria (including standards of information and 

treatment of uncertainty), feedback loops and internal audits, and controls (including permit 

conditions) that agencies rely upon to fulfill their obligations under the ESA.

Figure 2.1 displays a normative model of a decision-making process that includes these program 

elements and feedback loops. The process trigger on the left-hand side of the figure (Box D1) 

might represent an application from a prospective permittee or licensee, a request for prospective 

funding, or a prospective proposal to be undertaken by a Federal Agency. These process triggers 

are typically subjected to two screening processes (Box D2): 

1. an initial screening process that are designed to insure that proposals minimally comply with statutory, 

regulatory, or policy requirements that are applicable to requests for permits, licenses, or funding and

2. secondary screening processes that are designed to insure that an agency satisfies the statutory, regulatory, 

or policy requirements or criteria that must be met before an agency can issue a permit, license, or funding.

For example, the screening process the EPA applies to general permits includes reviews for 

completeness; analyses for compliance with Clean Water Act (CWA) guidelines; compliance 

with State water quality standards; compliance with toxic effluent standards; and compliance 

with the requirements of section 7(a)(2) of the ESA. 

Agency screening processes typically produce recommendations to agency decision-makers, who 

have the authority to make final decisions on Agency Actions (Figure 2.1, Box D3). Following 

those decisions, the Action Agency, permittee, licensee, or funding recipient undertakes the 

action, including any terms or conditions the Action Agency has attached (Figure 2.1, Box O1). 

The action produces a set of direct, indirect, and cumulative effects on the environment and any 

living organisms that occur in or rely on the environment that is affected by the action (Figure 

2.1, Box O2) and the condition of the environment changes in response to those effects (Figure 

2.1, Box O3). 

Figure 2.1 also displays a program that contains an audit function represented by a monitoring 

component (Figure 2.1, Lines M1 to M4), a feedback component (Figure 2.1, Lines F1 to F4), 

and an information gathering and evaluation component that informs a screening process (Figure 

2.1, Box D2.1). The monitoring component would collect empirical information on individual 

actions or a sample of individual actions to (a) identify what action actually occurred for 

comparison with the action that had been proposed and approved (implementation monitoring; 

Figure 2.1, Line M1); (b) identify which terms and conditions, if any, were satisfied, including 

any mitigation measures that were required (implementation monitoring; Figure 2.1, Line M1), 

(c) gather empirical information on 
55

Figure 2.1. A normative model of a decision-making process that includes these program elements and feedback loops. See text for 

further explanation
56

the action’s direct and indirect effects on the environment, including the effectiveness of any 

mitigation measures that had been required (validation and compliance monitoring; Figure 2.1, 

Line M2), (d) gather the empirical evidence to determine whether or to what degree the 

environment changed in response to those effects (Figure 2.1, Line M3); and (e) gather the 

empirical evidence sufficient to determine whether a proposal contributed to environmental 

conditions that fail to meet program purposes and standards (compliance monitoring; Figure 2.1, 

Line M4). The feedback component evaluates empirical data collected by monitoring and 

incorporates those data into agency decisions about prior or subsequent actions (Figure 2.1, 

Lines F1 through F4).

Regardless of whether an agency’s decision-making processes corresponds to the model 

presented in Figure 2.1, five components of an agency’s decision-making process are critical to 

our assessment of whether a general permit would be expected to insure that individual actions 

authorized, funded, or carried out by the program comply with the requirements of section 

7(a)(2) of the ESA. The first critical component is the screening process an agency applies to 

specific actions authorized, funded, or carried out by a program. When we examine this 

component of an Agency’s decision-making process, questions we ask include: What standards 

apply to the screening process? How rigorous are those standards? How rigorously does the 

Action Agency apply those standards? Are proposals assumed to comply with an Agency’s 

statute barring evidence of non-compliance or vice versa? Which party (prospective permittees 

or the Action Agency) bears the responsibility for presenting the evidence that supports their 

position? Does an Agency’s record of performance allow us to conclude that the screening 

process works as designed by filtering out proposals that do not satisfy applicable environmental 

mandates, standards, criteria, and program purposes?

The second critical component is the information that forms the foundation for the agency’s 

screening process (Figure 2.1, Boxes D1.1, D2.1, and D2.2). When we examine this component 

of an agency’s decision-making process, questions we ask include: Does the agency assess the 

individual and cumulative impacts of specific proposals? Does the agency’s methodology 

consider all of the variables that would have to be considered to determine whether a specific 

proposal is likely to have adverse consequence for endangered or threatened species and 

designated critical habitat? Do assessments employ data acquisition procedures that are likely to 

identify, gather, and analyze all of the information that would be relevant to identify the presence 

or absence of consequence for endangered or threatened species and designated critical habitat? 

Does the assessment process incorporate quality assurance and quality control procedures? Are 

those procedures designed to prevent Type I decision error (falsely concluding that a proposal 

had an adverse impact), Type II decision error (falsely concluding that a proposal had no adverse 

impact), or both?

The third critical component is an Action Agency’s decision-making process, which includes the 

information and variables that inform the Agency’s decision on whether or not to authorize, 

fund, or implement an action, the decisions the Agency makes, and any conditions or terms the 

Agency attaches to its decision. 

The fourth critical component is an audit function. Does the Action Agency regularly or 
57

continuously audit the results of its actions? Are the monitoring and feedback loops (Figure 2.1, 

lines M1 to M4 and F1 to F4) designed to allow the Agency to (a) collect empirical information 

that allows them to insure that specific actions they authorize, fund, or carry out are undertaken 

as designed (including any terms, conditions, or mitigation measures associated with the 

proposal), (b) assess the actual effects of those actions, and (c) determine whether the program is 

fulfilling its mandate, purposes, and goals. 

The final critical component is the agency’s authority to modify its prior and subsequent 

decisions when new information (particularly information provided by the audit function) reveals 

that particular authorizations have not satisfied applicable environmental mandates, standards, 

criteria, and program purposes (the applicable environmental mandates includes compliance with 

section 7(a)(2) of the ESA).

We organize our programmatic consultations on general permits using a sequence of questions 

that focus on the agency’s decision-making process, in general, and the five critical components 

we just described. Those questions focus on whether and to what degree an Agency has 

structured a program so that the Agency is in a position to know or reliably estimate whether 

endangered or threatened species or designated critical habitat are likely to be (a) exposed to 

stressors associated with specific actions a program would authorize, fund, or carry out; (b) 

respond to that exposure; and (c) experience individual-level, population-level, or species-level 

risks as a result of those responses. Further, we ask whether or to what degree an agency actively 

gathers that information, whether or to what degree an agency incorporates that information into 

its decision-making processes about specific actions, and whether or to what degree an agency 

changes the decisions it makes about specific actions based on that information.

Application of this Approach in this Consultation 

As we have already discussed, we treat the issuance of the proposed VGPs as “programs” that 

would authorize discharges of pollutants over a five-year period. As we described earlier, during 

general permit consultations we ask whether or to what degree the programs: 

 Collect or will have access to the information necessary to allow it to know how the 

actions it permits affect listed resources; 

 Evaluate that information to assess how its actions have affected endangered species, 

threatened species, and designated critical habitat; and 

 Uses its authorities to bring those activities into compliance.

Specific questions we ask about the proposed VGPs 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
58

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 (that is, the stressors produced by the actual discharges to waters of the U.S.)?

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 

elements of critical habitat?

5. Responses of Listed Resources

Does the general permit have an 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, 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: 
59

a) at concentrations, durations, or frequencies that are potentially harmful to individual 

listed organisms, populations, or the species, or; 

b) to ecological consequences that are potentially harmful to individual listed organisms, 

populations, the species or Primary Constituent Elements of designated critical habitat? 

As with all of our consultations, we conduct our section 7 analyses through a series of steps. 

These include: a examination of the action; identification of the action area; exposure analyses; 

response analyses; analyses of aggregate impacts; and risk analyses. These steps are described 

below.

PROPOSED ACTION

In reviewing the proposed action and biological evaluation, the Services will examine the 

activities that would be authorized by the proposed VGPs. This step of our analyses identifies 

spatial and temporal patterns associated with each category of activity; specifically (a) the 

geographic distribution of the different activities; (b) the number activities; (c) the amounts of 

pollutants that are likely to be discharged; and (d) the rate of discharges.

Our analysis will evaluate the effects of all discharges of biological and chemical pollutants to 

waters of the US incidental to the normal operation of all eligible vessels that would be 

authorized by the VGPs. In addition, the Services must consider the effects of interrelated and 

interdependent actions of the proposed action. Interdependent actions are actions having no 

independent utility apart from the proposed action (50 CFR 402-021). They are typically a 

consequence of the proposed action. For example, if our consultation were evaluating the effects 

of building a road, an interdependent action would be the planned construction of homes and 

other structures that would not be accessible without the presence of that road. Interrelated 

actions are actions that are part of a larger action and depend on the larger action for their 

justification (50 CFR 402-023). They are actions that are typically associated with the proposed 

action.

In this consultation, NMFS would address the potential effects of the proposed action for marine, 

coastal, estuarine, or anadromous endangered species, threatened species, and critical habitat that 

has been designated for those species in those ecosystems under its jurisdiction; FWS would 

address the potential effects of the proposed action for terrestrial, freshwater, and resident 

estuarine endangered species, threatened species, and critical habitat that has been designated for 

those species under FWS’ jurisdiction in those ecosystems. 

ACTION AREA

We determine the degree of geographic and temporal overlap between the activities that would 

be authorized by the proposed VGPs and endangered and threatened species and designated 

critical habitat. 

 

1

See: http://cfr.vlex.com/vid/402-02-definitions-19895209
60

EXPOSURE ANALYSES

Before assessing an agency’s decision-making process (as described above), the FWS will first 

establish whether the proposed action could expose listed species and critical habitat to 

potentially harmful stressors and whether listed species and critical habitats are likely to respond 

adversely. If exposure to stressors and adverse responses are not likely to occur, we do not 

assess the agency’s decision-making process.

Our assessment will focus on whether and to what degree the EPA structured the VGPs in ways 

that would prevent or minimize endangered or threatened species or critical habitat that has been 

designated for those species 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. For example, once individual plants and animals are 

exposed to a discharge containing pollutants, their responses to the exposure is controlled by the 

concentration, duration, and frequency associated with the exposure, their sensitivity to the 

discharged materials, other physical, chemical, or biotic stressors they are exposed to in the same 

time interval, their pre-existing physiological state, and their constitutional endowment. 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 exposure itself. For that reason, our assessment focuses on whether and to what degree the 

VGPs prevent or minimize 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 VGPs. Rather than discuss the literature for each species, it would be only be 

necessary to discuss the risks of exposing species groups (for example, Pacific Salmon; 

Sturgeon; Sea Turtles; etc.).

RESPONSE ANALYSES

We conduct a detailed review of the literature available on the physical, physiological, 

behavioral, social, and ecological responses of endangered or threatened species or constituent 

elements of critical habitat given exposure to harmful discharges into waters of the United States 

or to the effects of those discharges and the activities associated with those activities on the 

ecology of the watersheds in which they occur (that is, effects resulting from changes in 

populations of prey, predators, competitors, symbionts, etc.). Rather than discuss the literature 

for each species, we organize the data using species groups (for example, Pacific Salmon; 

Sturgeon; Sea Turtles; etc.). We summarize the probable consequences of the identified 

responses for populations of endangered and threatened species and designated critical habitat. 

TREATMENT OF AGGREGATE IMPACTS 

To address the question of whether the activities that would be authorized by the proposed VGPs 

have direct and indirect effects on listed resources that are sufficiently small both individually 

and in aggregate, we explicitly consider the aggregate impacts of the proposed permits in the 

Effects of the Action chapter of our Opinion. This usage of “aggregate impacts” is distinct from 

the term “cumulative effects” which the section 7 regulations defines as “those effects of future 

State or private activities, not involving Federal activities, that are reasonably certain to occur 
61

within the action area of the Federal action subject to consultation” (50 CFR 402.02). 

Aggregate impacts include: (1) time-crowded perturbations or perturbations that are so close in 

time that the effects of one perturbation do not dissipate before a subsequent perturbation occurs; 

(2) space-crowded perturbations or perturbations that are so close in space that their effects 

overlap; (3) interactions or perturbations that have qualitatively and quantitatively different 

consequences for the ecosystems, ecological communities, populations, or individuals exposed to 

them because of synergism (when stressors produce fundamentally different effects in 

combination than they do individually), additivity, magnification (when a combination of 

stressors have effects that are more than additive), or antagonism (when two or more stressors 

have less effect in combination than they do individually); and (4) nibbling or incremental and 

decremental effects are often, but not always, involved in each of the preceding three categories 

(NRC 1986).

RISK ANALYSES 

We help Action Agencies determine whether or to what degree they have complied with the 

requirements of section 7(a)(2) of the ESA by assessing whether and to what degree an Agency 

has structured a program so that the Agency is in a position to know or reliably estimate: (a) 

whether endangered or threatened species are likely to be placed at increased risk of extinction, 

or (b) if those species avoid extinction, whether they are likely to experience increased risk of 

failing to recover from having been endangered or threatened because of the actions the program 

authorizes, funds, or carries out. 

Our consideration of how well an Agency’s program manages risks to endangered and 

threatened species reflects the relationship between a listed species, the populations it comprises, 

and the individuals those populations comprise. The continued existence of a species is 

determined by the fate of the populations it comprises and the continued existence of a 

population is determined by the fate of the individuals they comprise. Populations grow or 

decline as the individuals they comprise live, die, grow, mature, migrate, and reproduce, or fail 

to do so. When we assess whether or to what degree an Agency’s program is likely to eliminate 

or avoid risks to endangered or threatened species, we are mindful of the distinction between 

species, the populations they comprise, and the individuals comprised by those populations.

When we assess whether or to what degree an Agency’s program is likely to eliminate or avoid 

risks to individual members of endangered or threatened species, we think in terms of the 

individuals’ fitness, which integrates an individuals’ longevity with its current and future 

reproductive success. In particular, we examine the scientific and commercial data available to 

determine if an individual’s probable response to stressors produced by an Action would 

reasonably be expected to reduce the individual’s current or expected future reproductive success 

by increasing an individual’s likelihood of dying prematurely, increasing the age at which it 

becomes reproductively mature, reducing the age at which it stops reproducing, reducing the 

number of live births it produces during any reproductive bout, reducing the number of 

reproductive bouts it engages in over its reproductive lifespan (in animals that reproduce 

multiple times), or causing the individual’s progeny to experience any of these phenomena 
62

(Brommer 2000, Brommer et al. 1998, 2002; Clutton-Brock 1998, Coulson et al. 2006, Kotiaho 

et al. 2005, McGraw and Caswell 1996, Newton and Rothery 1997, Oli and Dobson 2003, Roff 

2002, Stearns 1992, Turchin 2003).

We evaluate whether individual members of an endangered or threatened species experience 

reductions in their current or expected future reproductive success or experience reductions in 

the rates at which they grow, mature, or become reproductively active. Then we determine if 

those reductions also reduce the abundance, reproduction rates, and growth rates (or increase 

variance in one or more of these rates) of the populations those individuals represent (see Stearns 

1992). Similarly, we determine if those population-level reductions reduce the viability of the 

species those population(s) comprise. Our general permit assessments focus on whether or to 

what degree an Agency’s program is likely to insure 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.

Our consideration of how well an Agency’s program manages risks to designated critical habitat 

focuses on the value of the physical, chemical, or biotic phenomena of the critical habitat for the 

conservation of the endangered and threatened species for which the critical habitat was 

designated. In this step of our assessment, we consider information about the contribution of 

constituent elements of critical habitat (or of the physical, chemical, or biotic features that give 

the designated area value for the conservation of listed species, particularly for older critical 

habitat designations that have no constituent elements) to the conservation value of those areas of 

critical habitat that occur in the action area. Then we consider the contribution of the 

conservation value of those areas to the conservation value of the entire critical habitat 

designation. Our general permit assessments focus on whether or to what degree an Agency’s 

program is likely to insure that the direct or indirect effects of actions the program would 

authorize are not likely to reduce the value of the physical, chemical, or biotic phenomena of the 

critical habitat areas affected or are not likely to reduce that value of the physical, chemical, or 

biotic phenomena to a degree that would be sufficient to reduce the value of the entire critical 

habitat for the conservation of the endangered and threatened species for which the critical 

habitat was designated.

Evidence Available for the Consultation

For all of the above analyses, the Services will rely on two bodies of evidence for this 

consultation (including EPA’s BE). We will use the first body of evidence to determine whether 

or to what degree the proposed general permits can insure that vessel discharges on, over, or near 

waters of the United States are not likely to jeopardize the continued existence of endangered or 

threatened species or result in the destruction or adverse modification of critical habitat that has 

been designated for those species. To build this body of evidence, we will search for, gather, and 

analyze published and unpublished sources that examine the effectiveness of previous programs, 

and whether or to what degree the program has had: (1) adverse consequences for natural flora 

and fauna that have some dependency on the quality of waters of the United States, or (2) 

adverse consequences for species that have been listed as endangered or threatened. In 
63

particular, we will consider information contained in biological assessments, program reviews of 

effectiveness, compliance monitoring databases, risk assessments and ESA Section 7 

consultations on similar actions, species status reviews, listing documents, recovery plans, 

reports on the status and trends of water quality, past and current research and population 

dynamics modeling. We will supplement this information by searching for compliance data 

from available databases that track the number of inspections and enforcement actions over time. 

We will use a second body of evidence to assess the probable consequences of authorizing 

discharges of pollutants on, over, or near waters of the United States to endangered or threatened 

species or critical habitat that has been designated for those species. To assemble this body of 

information, we shall search peer-reviewed scientific literature, master’s theses and doctoral 

dissertations, government reports and studies and reports from commercial vendors. For 

example, the National Library of Medicine’s Hazardous Substance Data Bank, TOXNET, 

Toxline, EXTOXNET pesticide information profiles provide information on the toxicity of the 

pollutants. These searches will focus on identifying recent information on the biology, ecology, 

distribution, status, and trends of the threatened and endangered species considered in this 

consultation. We will consider the results of these searches based on the quality of their study 

design, sample sizes and study results. Studies that relied on large sample sizes with small 

variances will be generally ranked higher than studies that relied on small sample sizes or large 

variances.

Treatment of “Cumulative Impacts” (in the sense of NEPA)

To address the question of whether the activities that would be authorized by VGPs have direct 

and indirect effects on the environment that are small both individually and cumulatively, we 

explicitly consider the cumulative impacts of the proposed permits in a “cumulative impact” 

section of the Effects of the Action chapter of this Opinion. Here, we use the term “cumulative

impact” in the NEPA sense of the term (the U.S. Council on Environmental Quality defines them 

under the term “cumulative effects” but we refer to them as “cumulative impacts” to distinguish 

between NEPA and ESA uses of “cumulative effects”). That is, we mean “cumulative impacts” 

as “the impact on the environment which results from the incremental impact of the action when 

added to other past, present, and reasonably foreseeable future actions regardless of what agency 

(Federal or non-federal) or person undertakes such other actions” (40 CFR 1508.7). The effects 

analyses of biological opinions considered the “impacts” on listed species and designated critical 

habitat that result from the incremental impact of an action by identifying natural and 

anthropogenic stressors that affect endangered and threatened species throughout their range (the 

Status of the Species) and within an Action Area (the Environmental Baseline, which articulate 

the pre-existing impacts of activities that occur in an Action Area, including the past, 

contemporaneous, and future impacts of those activities). We assess the effects of a proposed 

action by adding their direct and indirect effects to the impacts of the activities we identify in an 

Environmental Baseline (50 CFR 402.02), in light of the impacts of the status of the listed 

species and designated critical habitat throughout their range; as a result, the results of our effects 

analyses are equivalent to those contained in the “cumulative impact” sections of NEPA

documents.
64

This usage of “cumulative impacts” is distinct from the term “cumulative effects” which the 

section 7 regulations defines as “those effects of future State or private activities, not involving 

Federal activities, that are reasonably certain to occur within the action area of the Federal action 

subject to consultation” (50 CFR 402.02). 

As we discussed previously, cumulative impacts includes (1) time-crowded perturbations or 

perturbations that are so close in time that the effects of one perturbation do not dissipate before 

a subsequent perturbation occurs; (2) space-crowded perturbations or perturbations that are so 

close in space that their effects overlap; (3) interactions or perturbations that have qualitatively 

and quantitatively different consequences for the ecosystems, ecological communities, 

populations, or individuals exposed to them because of synergism (when stressors produce 

fundamentally different effects in combination than they do individually), additivity, 

magnification (when a combination of stressors have effects that are more than additive), or 

antagonism (when two or more stressors have less effect in combination than they do 

individually); and (4) nibbling or incremental and decremental effects are often, but not always, 

involved in each of the preceding three categories (NRC 1986).

Action Area

The Action Area for this consultation consists of all waters of the United States in the United 

States, its territories, and its possessions (which includes American Samoa, Baker Island, Guam, 

Howland Island, Jarvis Island, Johnston Atoll, Midway Islands, Navassa Island, the 

Commonwealth of the Northern Mariana Islands, Palmyra Atoll, Puerto Rico, the U.S. Virgin 

Islands, and Wake Island) where discharges incidental to the normal operation of all nonrecreational and non-military vessels are to be authorized by the EPA’s VGPs. Waters of the 

U.S. extend to the outer reach of the three mile territorial sea, defined in section 502(8) of the 

CWA as the belt of the seas measured from the line of ordinary low water along that portion of 

the coast which is in direct contact with the open sea and the line marking the seaward limit of 

inland waters, and extending seaward a distance of three miles.

Waters of the U.S. (as defined in 40 CFR 122.2) are:

1. All waters which are currently used, were used in the past, or may be susceptible to use in 

interstate or foreign commerce, including all waters which are subject to the ebb and flow 

of the tide;

2. All interstate waters, including interstate “wetlands;”

3. All other waters such as intrastate lakes, rivers, streams (including intermittent streams), 

mudflats, sandflats, “wetlands,” sloughs, prairie potholes, wet meadows, playa lakes, or 

natural ponds the use, degradation, or destruction of which would affect or could affect 

interstate or foreign commerce including any such waters:
65

a. Which are or could be used by interstate or foreign travelers for recreational or 

other purposes;

b. From which fish or shellfish are or could be taken and sold in interstate or foreign 

commerce; or

c. Which are used or could be used for industrial purposes by industries in interstate 

commerce;

4. All impoundments of waters otherwise defined as waters of the United States under this 

definition;

5. Tributaries of those waters described above;

6. The territorial sea; and

7. “Wetlands” adjacent to waters (other than waters that are themselves wetlands).

The action area also includes other wetland or aquatic sites that do not meet the definition of 

“Waters of the U.S.” and adjacent upland areas that may be affected by the introduction and 

spread of aquatic nuisance species.

Status of the Species and Critical Habitat and Environmental Baseline

In this section of this Opinion we describe the proposed and listed threatened and endangered 

species2and their proposed and designated critical habitat that occur in the action area and may 

be exposed to the direct or indirect effects of discharges authorized by the proposed VGPs. We 

also consider candidate species and treat these species as “proposed” for the purpose of this 

analysis. All species within FWS’ jurisdiction, listed below, are “aquatic” or “aquatic 

dependent” and may occur within portions of the action area. FWS has determined that the 

following species and critical habitat “may be affected” by EPA’s proposed VGPs (Table 1). 

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Amphibians

Salamander, California Tiger (Santa Barbara DPS)* Ambystoma californiense Endangered

 

2 We use the word “species” as it has been defined in section 3 of the ESA, which include “species, subspecies, and any distinct 

population segment of any species of vertebrate fish or wildlife which interbreeds when mature (16 U.S.C. 1533)”. Some species, 

such as California tiger salamanders, have been listed as endangered or threatened distinct population segments (DPS) of 

California tiger salamanders. Any DPS is a “species” for the purposes of the ESA. 
66

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Salamander, California Tiger (Sonoma DPS)* Ambystoma californiense Endangered

Salamander, California Tiger (Central V alley DPS)* Ambystoma californiense Threatened

Salamander, Frosted Flatwoods Ambystoma cingulatum Threatened

Salamander, Santa Cruz long-toed Ambystoma macrodactylum croceum Endangered

Salamander, Sonora tiger Ambystoma tigrinum stebbinsi Endangered

Salamander, desert slender Batrachoseps aridus Endangered

Toad, Wyoming Bufo baxteri (=hemiophrys) Endangered

Toad, arroyo (=arroyo southwestern)* Bufo californicus (=microscaphus) Endangered

Toad, Yosemite Bufo canorus Candidate

Toad, Houston* Bufo houstonensis Endangered

Hellbender, Ozark

Cryptobranchus alleganiensis 

bishopi

Endangered

Guajon* Eleutherodactylus cooki Threatened

Salamander, Salado Eurycea chisholmensis Proposed Endangered

Salamander, San Marcos* Eurycea nana Threatened

Salamander, Georgetown Eurycea naufragia Proposed Endangered

Salamander, Barton Springs Eurycea sosorum Endangered

Salamander, Jollyville Plateau Eurycea tonkawae Proposed Endangered

Salamander, Austin blind Eurycea waterlooensis Proposed Endangered

Treefrog, Arizona Hyla wrightorum Candidate

Waterdog, black warrior (=Sipsey Fork) Necturus alabamensis Candidate

Salamander, Cheat Mountain Plethodon nettingi Threatened

Frog, California red-legged* Rana aurora draytonii Threatened

Frog, Chiricahua leopard* Rana chiricahuensis Threatened

Frog, Columbia spotted Rana luteiventris Candidate

Frog, mountain yellow-legged (southern California)* Rana muscosa Endangered

Frog, mountain yellow-legged (northern California) Rana muscosa Candidate

Frog, relict leopard Rana onca Candidate

Frog, Oregon spotted Rana pretiosa Candidate

Salamander, Texas blind Typhlomolge rathbuni Endangered

 Fish

Cavefish, Ozark Amblyopsis rosae Threatened

Sucker, Zuni bluehead Catostomus discobolus yarrowi Candidate

Sucker, Modoc* Catostomus microps Endangered

Sucker, Santa Ana* Catostomus santaanae Threatened

Sucker, Warner* Catostomus warnerensis Threatened

Sucker, shortnose Chasmistes brevirostris Endangered
67

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Cui-ui Chasmistes cujus Endangered

Sucker, June* Chasmistes liorus Endangered

Sculpin, pygmy Cottus paulus (=pygmaeus) Threatened

Sculpin, grotto Cottus sp. Proposed Endangered

Springfish, White River* Crenichthys baileyi baileyi Endangered

Springfish, Hiko White River* Crenichthys baileyi grandis Endangered

Springfish, Railroad Valley* Crenichthys nevadae Threatened

Shiner, blue Cyprinella caerulea Threatened

Shiner, beautiful* Cyprinella formosa Threatened

Pupfish, Leon Springs* Cyprinodon bovinus Endangered

Pupfish, Devils Hole Cyprinodon diabolis Endangered

Pupfish, Comanche Springs Cyprinodon elegans Endangered

Pupfish, desert* Cyprinodon macularius Endangered

Pupfish, Ash Meadows Amargosa* Cyprinodon nevadensis mionectes Endangered

Pupfish, Warm Springs Cyprinodon nevadensis pectoralis Endangered

Pupfish, Owens Cyprinodon radiosus Endangered

Sucker, Lost River Deltistes luxatus Endangered

Minnow, Devils River* Dionda diaboli Threatened

Poolfish, Pahrump Empetrichthys latos Endangered

Dace, desert* Eremichthys acros Threatened

Chub, spotfin* Erimonax monachus Threatened;XN

Chub, slender* Erimystax cahni Threatened;XN

Darter, slackwater* Etheostoma boschungi Threatened

Darter, vermilion* Etheostoma chermocki Endangered

Darter, relict Etheostoma chienense Endangered

Darter, Arkansas Etheostoma cragini Candidate

Darter, Etowah Etheostoma etowahae Endangered

Darter, fountain* Etheostoma fonticola Endangered

Darter, yellowcheek Etheostoma moorei Endangered

Darter, Niangua* Etheostoma nianguae Threatened

Darter, watercress Etheostoma nuchale Endangered

Darter, Okaloosa Etheostoma okaloosae Endangered

Darter, duskytail Etheostoma percnurum Endangered;XN

Darter, rush Etheostoma phytophilum Endangered

Darter, bayou Etheostoma rubrum Threatened

Darter, Cherokee Etheostoma scotti Threatened

Darter, Maryland* Etheostoma sellare Endangered

Darter, bluemask (=jewel) Etheostoma sp. Endangered
68

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Darter, Cumberland Etheostoma susanae Endangered

Darter, boulder Etheostoma wapiti Endangered;XN

Goby, tidewater* Eucyclogobius newberryi Endangered

Gambusia, Big Bend Gambusia gaigei Endangered

Gambusia, San Marcos* Gambusia georgei Endangered

Gambusia, Clear Creek Gambusia heterochir Endangered

Gambusia, Pecos Gambusia nobilis Endangered

Stickleback, unarmored threespine Gasterosteus aculeatus williamsoni Endangered

Chub, Mohave tui Gila bicolor mohavensis Endangered

Chub, Owens tui* Gila bicolor snyderi Endangered

Chub, Hutton tui Gila bicolor ssp. Threatened

Chub, Borax Lake* Gila boraxobius Endangered

Chub, humpback* Gila cypha Endangered

Chub, Sonora* Gila ditaenia Threatened

Chub, bonytail* Gila elegans Endangered

Chub, Gila* Gila intermedia Endangered

Chub, headwater Gila nigra Candidate

Chub, Chihuahua Gila nigrescens Threatened

Chub, Yaqui* Gila purpurea Endangered

Chub, Pahranagat roundtail Gila robusta jordani Endangered

Chub, Virgin River* Gila seminuda (=robusta) Endangered

Minnow, Rio Grande silvery* Hybognathus amarus Endangered

Smelt, delta* Hypomesus transpacificus Threatened

Catfish, Yaqui* Ictalurus pricei Threatened

Spinedace, White River* Lepidomeda albivallis Endangered

Spinedace, Big Spring* Lepidomeda mollispinis pratensis Threatened

Spinedace, Little Colorado* Lepidomeda vittata Threatened

Spikedace* Meda fulgida Threatened

Silverside, Waccamaw* Menidia extensa Threatened

Dace, Moapa Moapa coriacea Endangered

Redhorse, Sicklefin Moxostoma sp. Candidate

Shiner, palezone Notropis albizonatus Endangered

Shiner, smalleye Notropis buccula Candidate

Shiner, Cahaba Notropis cahabae Endangered

Shiner, Arkansas River* Notropis girardi Threatened

Shiner, Cape Fear* Notropis mekistocholas Endangered

Shiner, sharpnose Notropis oxyrhynchus Candidate

Shiner, Pecos bluntnose* Notropis simus pecosensis Threatened
69

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Shiner, Topeka* Notropis topeka (=tristis) Endangered

Madtom, smoky* Noturus baileyi Endangered;XN

Madtom, chucky Noturus crypticus Endangered

Madtom, yellowfin* Noturus flavipinnis Threatened;XN

Madtom, Neosho Noturus placidus Threatened

Madtom, pygmy Noturus stanauli Endangered;XN

Madtom, Scioto Noturus trautmani Endangered

Trout, Little Kern golden* Oncorhynchus aguabonita whitei Threatened

Trout, Apache Oncorhynchus apache Threatened

Trout, Lahontan cutthroat Oncorhynchus clarki henshawi Threatened

Trout, Paiute cutthroat Oncorhynchus clarki seleniris Threatened

Trout, greenback cutthroat Oncorhynchus clarki stomias Threatened

Trout, Gila Oncorhynchus gilae Threatened

Chub, Oregon* Oregonichthys crameri Endangered

Darter, amber* Percina antesella Endangered

Darter, goldline Percina aurolineata Threatened

Darter, Pearl Percina aurora Candidate

Logperch, Conasauga* Percina jenkinsi Endangered

Darter, leopard* Percina pantherina Threatened

Logperch, Roanoke Percina rex Endangered

Darter, snail* Percina tanasi Threatened

Dace, blackside Phoxinus cumberlandensis Threatened

dace, Laurel Phoxinus saylori Endangered

Woundfin* Plagopterus argentissimus Endangered;XN

Topminnow, Gila (incl. Yaqui) Poeciliopsis occidentalis Endangered

Pikeminnow (=squawfish), Colorado* Ptychocheilus lucius Endangered;XN

Dace, Independence Valley speckled Rhinichthys osculus lethoporus Endangered

Dace, Ash Meadows speckled* Rhinichthys osculus nevadensis Endangered

Dace, Clover Valley speckled Rhinichthys osculus oligoporus Endangered

Dace, Foskett speckled Rhinichthys osculus ssp. Threatened

Dace, Kendall Warm Springs Rhinichthys osculus thermalis Endangered

Trout, bull* Salvelinus confluentus Threatened

Sturgeon, Alabama* Scaphirhynchus suttkusi Endangered

Cavefish, Alabama* Speoplatyrhinus poulsoni Endangered

Minnow, loach* Tiaroga cobitis Threatened

Sucker, razorback* Xyrauchen texanus Endangered

 Reptiles
70

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Alligator, American Alligator mississippiensis SAT

Lizard, St. Croix ground* Ameiva polops Endangered

Sea turtle, loggerhead Caretta caretta Threatened

Sea turtle, green Chelonia mydas Endangered;T

Turtle, bog (=Muhlenberg) Clemmys muhlenbergii

Threatened;

Threatened (S/A)

Crocodile, American* Crocodylus acutus Endangered;T

Sea turtle, leatherback Dermochelys coriacea Endangered

Snake, eastern indigo Drymarchon corais couperi Threatened

Sea turtle, hawksbill Eretmochelys imbricata Endangered

Lizard, blunt-nosed leopard Gambelia silus Endangered

Turtle, yellow-blotched map Graptemys flavimaculata Threatened

Turtle, ringed map Graptemys oculifera Threatened

Turtle, Sonoyta mud

Kinosternon sonoriense 

longifemorale Candidate

Whipsnake (=striped racer), Alameda* Masticophis lateralis euryxanthus Threatened

Snake, Atlantic salt marsh Nerodia clarkii taeniata Threatened

Snake, copperbelly water Nerodia erythrogaster neglecta Threatened

Snake, Concho water Nerodia paucimaculata Threatened

Snake, Lake Erie water Nerodia sipedon insularum Threatened

Turtle, Alabama red-belly Pseudemys alabamensis Endangered

Plymouth Red-Bellied Turtle* Pseudemys rubriventris bangsi Endangered

Massasauga (=rattlesnake), eastern Sistrurus catenatus catenatus Candidate

Turtle, flattened musk Sternotherus depressus Threatened

Snake, giant garter Thamnophis gigas Threatened

Snake, San Francisco garter Thamnophis sirtalis tetrataenia Endangered

 Birds

Warbler, nightingale reed (old world warbler) Acrocephalus luscinia Endangered

Sparrow, Cape Sable seaside* Ammodramus maritimus mirabilis Endangered

Duck, Laysan Anas laysanensis Endangered

Duck, Hawaiian (=koloa) Anas wyvilliana Endangered

Murrelet, Kittlitz's Brachyramphus brevirostris Candidate

Murrelet, marbled* Brachyramphus marmoratus Threatened

Hawk, Puerto Rican broad-winged Buteo platypterus brunnescens Endangered

Knot, red Calidris canutus rufa Candidate

Grouse, greater sage Centrocercus urophasianus Candidate

Grouse, Gunnison sage Centrocercus minimus Candidate
71

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Plover, western snowy (Pacific Coast Population)* Charadrius alexandrinus nivosus Threatened

Plover, piping* Charadrius melodus Endangered;T

Elepaio, Oahu* Chasiempis sandwichensis ibidis Endangered

Cuckoo, yellow-billed Coccyzus americanus Candidate

Bobwhite, masked (quail) Colinus virginianus ridgwayi Endangered

Crow, Mariana (=aga)* Corvus kubaryi Endangered

Flycatcher, southwestern willow* Empidonax traillii extimus Endangered

Coot, Hawaiian Fulica americana alai Endangered

Moorhen, Mariana common Gallinula chloropus guami Endangered

Moorhen, Hawaiian common Gallinula chloropus sandvicensis Endangered

Crane, whooping* Grus americana Endangered;XN

Crane, Mississippi sandhill* Grus canadensis pulla Endangered

Stilt, Hawaiian Himantopus mexicanus knudseni Endangered

Thrush, small Kauai (=puaiohi) Myadestes palmeri Endangered

Stork, wood Mycteria americana Endangered

Curlew, Eskimo Numenius borealis Endangered

Storm-petrel, band-rumped Oceanodroma castro Candidate

Pelican, brown Pelecanus occidentalis Endangered;DM

Albatross, short-tailed Phoebastria (=Diomedea) albatrus Endangered

Gnatcatcher, coastal California* Polioptila californica californica Threatened

Caracara, Audubon's crested Polyborus plancus audubonii Threatened

Eider, Steller's* Polysticta stelleri Threatened

Crake, spotless Porzana tabuensis Candidate

Petrel, Hawaiian dark-rumped

Pterodroma phaeopygia 

sandwichensis Endangered

Shearwater, Newell's Townsend's Puffinus auricularis newelli Threatened

Rail, light-footed clapper Rallus longirostris levipes Endangered

Rail, California clapper Rallus longirostris obsoletus Endangered

Rail, Yuma clapper Rallus longirostris yumanensis Endangered

Kite, Everglade snail* Rostrhamus sociabilis plumbeus Endangered

Eider, spectacled* Somateria fischeri Threatened

Tern, least Sterna antillarum Endangered

Tern, California least Sterna antillarum browni Endangered

Tern, roseate Sterna dougallii dougallii Endangered;T

Murrelet, Xantus's Synthliboramphus hypoleucus Candidate

Vireo, least Bell's* Vireo bellii pusillus Endangered

Mammals
72

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Wolf, red Canis rufus Endangered;XN

Bat, Ozark big-eared

Corynorhinus (=Plecotus) 

townsendii ingens Endangered

Bat, Virginia big-eared*

Corynorhinus (=Plecotus) 

townsendii virginianus Endangered

Otter, Northern Sea* Enhydra lutris kenyoni Threatened

Otter, southern sea Enhydra lutris nereis Threatened;XN

Jaguarundi, Gulf Coast

Herpailurus (=Felis) yagouaroundi 

cacomitli Endangered

Jaguarundi, Sinaloan

Herpailurus (=Felis) yagouaroundi 

tolteca Endangered

Bat, Hawaiian hoary Lasiurus cinereus semotus Endangered

Ocelot Leopardus (=Felis) pardalis Endangered

Vole, Amargosa* Microtus californicus scirpensis Endangered

Vole, Florida salt marsh

Microtus pennsylvanicus 

dukecampbelli Endangered

Bat, gray Myotis grisescens Endangered

Bat, Indiana* Myotis sodalis Endangered

Woodrat, riparian (=San Joaquin Valley) Neotoma fuscipes riparia Endangered

Mouse, Pacific pocket Perognathus longimembris pacificus Endangered

Mouse, southeastern beach Peromyscus polionotus niveiventris Threatened

Mouse, Anastasia Island beach Peromyscus polionotus phasma Endangered

Panther, Florida Puma (=Felis) concolor coryi Endangered

Mouse, salt marsh harvest Reithrodontomys raviventris Endangered

Shrew, Buena Vista Lake ornate* Sorex ornatus relictus Endangered

Manatee, West Indian* Trichechus manatus Endangered

Bear, American black Ursus americanus SAT

Bear, Louisiana black* Ursus americanus luteolus Threatened

Bear, grizzly Ursus arctos horribilis Threatened;XN

Bear, polar* Ursus maritimus Threatened

 Arachnids

Pseudoscorpion, Tooth Cave Tartarocreagris texana Endangered

 Crustaceans

Isopod, Madison Cave Antrolana lira Threatened

Fairy shrimp, Conservancy* Branchinecta conservatio Endangered

Fairy shrimp, longhorn* Branchinecta longiantenna Endangered

Fairy shrimp, vernal pool* Branchinecta lynchi Threatened
73

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Fairy shrimp, San Diego* Branchinecta sandiegonensis Endangered

Crayfish, cave Cambarus aculabrum Endangered

Crayfish, cave Cambarus zophonastes Endangered

Amphipod, Illinois cave Gammarus acherondytes Endangered

Amphipod, Noel's* Gammarus desperatus Endangered

Amphipod, diminutive Gammarus hyalleloides Proposed Endangered

Tadpole shrimp, vernal pool Lepidurus packardi Endangered

Isopod, Lee County cave Lirceus usdagalun Endangered

Shrimp, anchialine pool Metabetaeus lohena Candidate

Crayfish, Nashville Orconectes shoupi Endangered

Crayfish, Shasta Pacifastacus fortis Endangered

Shrimp, anchialine pool Palaemonella burnsi Candidate

Shrimp, Squirrel Chimney Cave Palaemonetes cummingi Threatened

Shrimp, Alabama cave Palaemonias alabamae Endangered

Shrimp, Kentucky cave* Palaemonias ganteri Endangered

Shrimp, anchialine pool Procaris hawaiana Candidate

Amphipod, Kauai cave* Spelaeorchestia koloana Endangered

Fairy shrimp, Riverside* Streptocephalus woottoni Endangered

Amphipod, Peck's cave* Stygobromus (=Stygonectes) pecki Endangered

Amphipod, Hay's Spring Stygobromus hayi Endangered

Shrimp, California freshwater Syncaris pacifica Endangered

Isopod, Socorro Thermosphaeroma thermophilus Endangered

Shrimp, anchialine pool Vetericaris chaceorum Proposed Endangered

 Insects

Naucorid, Ash Meadows* Ambrysus amargosus Threatened

Naucorid bug (=Furnace Creek), Nevares Spring Ambrysus funebris Candidate

Beetle, Hungerford's crawling water Brychius hungerfordi Endangered

Tiger beetle, northeastern beach Cicindela dorsalis dorsalis Threatened

Tiger beetle, Salt Creek* Cicindela nevadica lincolniana Endangered

Tiger beetle, Puritan Cicindela puritana Threatened

Beetle, valley elderberry*

Desmocerus californicus

dimorphus Threatened (proposed 

delist)

Beetle, delta green ground* Elaphrus viridis Threatened

Caddisfly, Sequatchie Glyphopsyche sequatchie Candidate

Beetle, Comal Springs riffle* Heterelmis comalensis Endangered

Riffle beetle, Stephan's Heterelmis stephani Candidate

Butterfly, lotis blue Lycaeides argyrognomon lotis Endangered
74

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Damselfly, crimson Hawaiian Megalagrion leptodemus Endangered

Damselfly, flying earwig Hawaiian Megalagrion nesiotes Endangered

Damselfly, blackline Hawaiian

Megalagrion nigrohamatum 

nigrolineatum Endangered

Damselfly, oceanic Hawaiian Megalagrion oceanicum Endangered

Damselfly, Pacific Hawaiian Megalagrion pacificum Endangered

Damselfly, orangeblack Hawaiian Megalagrion xanthomelas Candidate

Butterfly, Saint Francis' satyr Neonympha mitchellii francisci Endangered

Butterfly, Mitchell's satyr Neonympha mitchellii mitchellii Endangered

Skipper, Carson wandering Pseudocopaeodes eunus obscurus Endangered

Skipper, Laguna Mountains* Pyrgus ruralis lagunae Endangered

Dragonfly, Hine's emerald* Somatochlora hineana Endangered

Beetle, Comal Springs dryopid* Stygoparnus comalensis Endangered

 Snails

Cavesnail, Tumbling Creek* Antrobia culveri Endangered

Snail, Pecos assiminea* Assiminea pecos Endangered

Riversnail, Anthony's Athearnia anthonyi Endangered;XN

Campeloma, slender Campeloma decampi Endangered

Snail, Phantom Cave Cochliopa texana Proposed Endangered

Elimia, lacy (snail) Elimia crenatella Threatened

Mudalia, black Elimia melanoides Candidate

Snail, Newcomb's* Erinna newcombi Threatened

Springsnail, Koster's* Juturnia kosteri Endangered

Limpet, Banbury Springs Lanx sp. Endangered

Rocksnail, round Leptoxis ampla Threatened

Rocksnail, interrupted (=Georgia)* Leptoxis foremani Endangered

Rocksnail, plicate Leptoxis plicata Endangered

Rocksnail, painted Leptoxis taeniata Threatened

Pebblesnail, flat Lepyrium showalteri Endangered

Lioplax, cylindrical (snail) Lioplax cyclostomaformis Endangered

Ambersnail, Kanab Oxyloma haydeni kanabensis Endangered

Snail, Snake River physa Physa natricina Endangered

Hornsnail, rough* Pleurocera foremani Endangered

Snail, Diamond Y Spring

Pseudotryonia (=Tryonia) 

adamantina Proposed Endangered

Snail, armored Pyrgulopsis (=Marstonia) pachyta Endangered

Springsnail, San Bernadino* Pyrgulopsis bernardina Endangered
75

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Springsnail, Bruneau Hot Pyrgulopsis bruneauensis Endangered

Springsnail, Chupadera Pyrgulopsis chupaderae Endangered

Springsnail, Page Pyrgulopsis morrisoni Candidate

Springsnail, Socorro Pyrgulopsis neomexicana Endangered

Springsnail, elongate mud meadows Pyrgulopsis notidicola Candidate

Marstonia, royal (snail) Pyrgulopsis ogmorhaphe Endangered

Springsnail, Roswell* Pyrgulopsis roswellensis Endangered

Springsnail, Huachuca Pyrgulopsis thompsoni Candidate

Springsnail, Three Forks* Pyrgulopsis trivialis Endangered

Snail, Chittenango ovate amber Succinea chittenangoensis Threatened

Snail, Bliss Rapids Taylorconcha serpenticola Threatened

Springsnail, Alamosa Tryonia alamosae Endangered

Springsnail (=Tryonia), Phantom Tryonia cheatumi Proposed Endangered

Springsnail, Gonzales

Tryonia 

circumstriata(=stocktonensis) Proposed Endangered

Snail, tulotoma Tulotoma magnifica Endangered

Snail, Utah valvata Valvata utahensis Endangered

 Bivalves

Elktoe, Cumberland* Alasmidonta atropurpurea Endangered

Wedgemussel, dwarf Alasmidonta heterodon Endangered

Elktoe, Appalachian* Alasmidonta raveneliana Endangered

Three-ridge, fat (mussel)* Amblema neislerii Endangered

Pocketbook, Ouachita rock Arkansia wheeleri Endangered

Pearlymussel, birdwing Conradilla caelata Endangered;XN

Spectaclecase Cumberlandia monodonta Endangered

Fanshell Cyprogenia stegaria Endangered;XN

Pearlymussel, dromedary Dromus dromas Endangered;XN

Slabshell, Chipola* Elliptio chipolaensis Threatened

Spinymussel, Altamaha* Elliptio spinosa Endangered

Spinymussel, Tar River Elliptio steinstansana Endangered

Bankclimber, purple (mussel)* Elliptoideus sloatianus Threatened

Combshell, Cumberlandian* Epioblasma brevidens Endangered;XN

Mussel, oyster* Epioblasma capsaeformis Endangered;XN

Pearlymussel, Curtis Epioblasma florentina curtisii Endangered

Blossom, yellow (pearlymussel) Epioblasma florentina florentina Endangered;XN

Riffleshell, tan

Epioblasma florentina walkeri (=E. 

walkeri) Endangered
76

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Combshell, upland* Epioblasma metastriata Endangered

Catspaw (=purple cat's paw pearlymussel) Epioblasma obliquata obliquata Endangered;XN

Catspaw, white (pearlymussel) Epioblasma obliquata perobliqua Endangered

Acornshell, southern* Epioblasma othcaloogensis Endangered

Combshell, southern Epioblasma penita Endangered

Blossom, green (pearlymussel) Epioblasma torulosa gubernaculum Endangered

Riffleshell, northern Epioblasma torulosa rangiana Endangered

Blossom, tubercled (pearlymussel) Epioblasma torulosa torulosa Endangered;XN

Mussel, snuffbox Epioblasma triquetra Endangered

Blossom, turgid (pearlymussel) Epioblasma turgidula Endangered;XN

Pigtoe, shiny Fusconaia cor Endangered;XN

Pigtoe, finerayed Fusconaia cuneolus Endangered;XN

Pigtoe, narrow Fusconaia escambia Threatened

Ebonyshell, round Fusconaia rotulata Endangered

sandshell, Southern Hamiota (=Lampsilis) australis Proposed Endangered

Pearlymussel, cracking Hemistena lata Endangered;XN

Mucket, pink (pearlymussel) Lampsilis abrupta Endangered

Pocketbook, finelined* Lampsilis altilis Threatened

Higgins eye (pearlymussel) Lampsilis higginsii Endangered

Mucket, orangenacre* Lampsilis perovalis Threatened

Fatmucket, Arkansas Lampsilis powelli Threatened

Mucket, Neosho Lampsilis rafinesqueana Proposed Endangered

Pocketbook, speckled Lampsilis streckeri Endangered

Pocketbook, shinyrayed* Lampsilis subangulata Endangered

Lampmussel, Alabama Lampsilis virescens Endangered;XN

Heelsplitter, Carolina* Lasmigona decorata Endangered

Mussel, scaleshell Leptodea leptodon Endangered

Pearlymussel, slabside Lexingtonia dolabelloides Proposed Endangered

Pearlshell, Louisiana Margaritifera hembeli Threatened

Pearlshell, Alabama Margaritifera marrianae Endangered

Moccasinshell, Alabama* Medionidus acutissimus Threatened

Moccasinshell, Coosa* Medionidus parvulus Endangered

Moccasinshell, Gulf* Medionidus penicillatus Endangered

Moccasinshell, Ochlockonee* Medionidus simpsonianus Endangered

Ring pink (mussel) Obovaria retusa Endangered;XN

Pearlymussel, littlewing Pegias fabula Endangered

Wartyback, white (pearlymussel) Plethobasus cicatricosus Endangered;XN

Pimpleback, orangefoot (pearlymussel) Plethobasus cooperianus Endangered;XN
77

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Mussel, sheepnose Plethobasus cyphyus Endangered

Clubshell Pleurobema clava Endangered;XN

Spinymussel, James Pleurobema collina Endangered

Clubshell, black Pleurobema curtum Endangered

Clubshell, southern* Pleurobema decisum Endangered

Pigtoe, dark* Pleurobema furvum Endangered

Pigtoe, southern* Pleurobema georgianum Endangered

Pigtoe, Cumberland Pleurobema gibberum Endangered

Pigtoe, Georgia* Pleurobema hanleyianum Endangered

Pigtoe, flat Pleurobema marshalli Endangered

Clubshell, ovate* Pleurobema perovatum Endangered

Pigtoe, rough Pleurobema plenum Endangered;XN

Pigtoe, oval* Pleurobema pyriforme Endangered

Pigtoe, fuzzy Pleurobema strodeanum Threatened

Pigtoe, heavy Pleurobema taitianum Endangered

Hornshell, Texas Popenaias popei Candidate

Pocketbook, fat Potamilus capax Endangered

Heelsplitter, Alabama (=inflated) Potamilus inflatus Threatened

Kidneyshell, triangular* Ptychobranchus greenii Endangered

Kidneyshell, southern Ptychobranchus jonesi Endangered

Kidneyshell, fluted Ptychobranchus subtentum Proposed Endangered

Rabbitsfoot, rough* Quadrula cylindrica strigillata Endangered

Mapleleaf, winged Quadrula fragosa Endangered;XN

Monkeyface, Cumberland (pearlymussel) Quadrula intermedia Endangered;XN

Monkeyface, Appalachian (pearlymussel) Quadrula sparsa Endangered;XN

Stirrupshell Quadrula stapes Endangered

Pigtoe, tapered Quincuncina burkei Threatened

Lilliput, pale (pearlymussel) Toxolasma cylindrellus Endangered

Bean, Choctaw Villosa choctawensis Endangered

Bean, rayed Villosa fabalis Endangered

Bean, purple* Villosa perpurpurea Endangered

Bean, Cumberland (pearlymussel) Villosa trabalis Endangered;XN

Ferns and Allies

Quillwort, Louisiana Isoetes louisianensis Endangered

Quillwort, black spored Isoetes melanospora Endangered

Quillwort, mat-forming Isoetes tegetiformans Endangered

Ihi`ihi* Marsilea villosa Endangered
78

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

No common name* Pteris lidgatei Endangered

 Flowering Plants

Liliwai* Acaena exigua Endangered

Monkshood, northern wild Aconitum noveboracense Threatened

Joint-vetch, sensitive Aeschynomene virginica Threatened

Seabeach Amaranth Amaranthus pumilus Threatened

Sandwort, Marsh Arenaria paludicola Endangered

Silversword, Mauna Loa (=Ka'u)* Argyroxiphium kauense Endangered

Milk-vetch, Fish Slough*

Astragalus lentiginosus var. 

piscinensis Threatened

Milk-vetch, Ash meadows* Astragalus phoenix Threatened

Milk-vetch, coastal dunes Astragalus tener var. titi Endangered

Crownscale, San Jacinto Valley* Atriplex coronata var. notatior Endangered

Ko`oko`olau Bidens conjuncta Proposed Endangered

Sunshine, Sonoma Blennosperma bakeri Endangered

Aster, decurrent false Boltonia decurrens Threatened

Brodiaea, thread-leaved* Brodiaea filifolia Threatened

Brodiaea, Chinese Camp Brodiaea pallida Threatened

Reedgrass, Maui Calamagrostis expansa Candidate

Bellflower, Brooksville Campanula robinsiae Endangered

Bittercress, small-anthered Cardamine micranthera Endangered

Sedge, golden* Carex lutea Endangered

Sedge, Navajo* Carex specuicola Threatened

Owl's-clover, fleshy* Castilleja campestris ssp. succulenta Threatened

Centaury, spring-loving* Centaurium namophilum Threatened

Prickly-apple, fragrant Cereus eriophorus var. fragrans Endangered

Spurge, Hoover's* Chamaesyce hooveri Threatened

Thistle, fountain Cirsium fontinale var. fontinale Endangered

Thistle, Chorro Creek bog Cirsium fontinale var. obispoense Endangered

Thistle, Suisun*

Cirsium hydrophilum var. 

hydrophilum Endangered

Thistle, La Graciosa* Cirsium loncholepis Endangered

Thistle, Sacramento Mountains Cirsium vinaceum Threatened

`Oha wai*

Clermontia oblongifolia ssp. 

mauiensis Endangered

No common name Cordia bellonis Endangered

Bird's-beak, salt marsh

Cordylanthus maritimus ssp. 

maritimus Endangered
79

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Bird's-beak, soft* Cordylanthus mollis ssp. mollis Endangered

Higuero de sierra Crescentia portoricensis Endangered

Haha* Cyanea grimesiana ssp. grimesiana Endangered

Pu`uka`a* Cyperus trachysanthos Endangered

Pawpaw, beautiful Deeringothamnus pulchellus Endangered

Pawpaw, Rugel's Deeringothamnus rugelii Endangered

Panic grass, Hirst Brothers' Dichanthelium (=Panicum) hirstii Candidate

Daisy, Willamette* Erigeron decumbens var. decumbens Endangered

Button-celery, San Diego Eryngium aristulatum var. parishii Endangered

Thistle, Loch Lomond coyote Eryngium constancei Endangered

Mustard, Penland alpine fen Eutrema penlandii Threatened

Heau* Exocarpos luteolus Endangered

Butterfly plant, Colorado*

Gaura neomexicana var. 

coloradensis Threatened

Nohoanu* Geranium multiflorum Endangered

No common name Gesneria pauciflora Threatened

Gilia, Monterey Gilia tenuiflora ssp. arenaria Endangered

Gumplant, Ash Meadows* Grindelia fraxino-pratensis Threatened

Beauty, Harper's Harperocallis flava Endangered

Kampua`a Hedyotis fluviatilis Candidate

Sneezeweed, Virginia Helenium virginicum Threatened

Sunflower, Pecos (=puzzle, =paradox)* Helianthus paradoxus Threatened

Pink, swamp Helonias bullata Threatened

Heartleaf, dwarf-flowered Hexastylis naniflora Threatened

Rose-mallow, Neches River Hibiscus dasycalyx Proposed Threatened

Howellia, water Howellia aquatilis Threatened

Ivesia, Ash Meadows* Ivesia kingii var. eremica Threatened

Goldfields, Burke's Lasthenia burkei Endangered

Goldfields, Contra Costa* Lasthenia conjugens Endangered

Water-umbel, Huachuca*

Lilaeopsis schaffneriana var. 

recurva Endangered

Lily, Western Lilium occidentale Endangered

Lily, Pitkin Marsh Lilium pardalinum ssp. pitkinense Endangered

Meadowfoam, Butte County* Limnanthes floccosa ssp. californica Endangered

Meadowfoam, large-flowered woolly* Limnanthes floccosa ssp. grandiflora Endangered

Pondberry Lindera melissifolia Endangered

Desert-parsley, Bradshaw's Lomatium bradshawii Endangered

Lomatium, Cook's* Lomatium cookii Endangered
80

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Loosestrife, rough-leaved Lysimachia asperulaefolia Endangered

No common name* Lysimachia filifolia Endangered

Birds-in-a-nest, white Macbridea alba Threatened

Button, Mohr's Barbara Marshallia mohrii Threatened

Blazingstar, Ash Meadows* Mentzelia leucophylla Threatened

Monkey-flower, Michigan

Mimulus glabratus var. 

michiganensis Endangered

Asphodel, bog Narthecium americanum Candidate

Navarretia, spreading* Navarretia fossalis Threatened

Navarretia, few-flowered

Navarretia leucocephala ssp. 

pauciflora (=N. pauciflora) Endangered

Navarretia, many-flowered

Navarretia leucocephala ssp. 

plieantha Endangered

Grass, Colusa* Neostapfia colusana Threatened

No common name Nesogenes rotensis Endangered

Niterwort, Amargosa* Nitrophila mohavensis Endangered

Orcutt grass, California Orcuttia californica Endangered

Orcutt grass, San Joaquin* Orcuttia inaequalis Threatened

Orcutt grass, hairy* Orcuttia pilosa Endangered

Orcutt grass, slender* Orcuttia tenuis Threatened

Orcutt grass, Sacramento* Orcuttia viscida Endangered

Dropwort, Canby's Oxypolis canbyi Endangered

Locoweed, Fassett's Oxytropis campestris var. chartacea Threatened

Stonecrop, Lake County Parvisedum leiocarpum Endangered

Beardtongue, Penland Penstemon penlandii Endangered

Butterwort, Godfrey's Pinguicula ionantha Threatened

Popcornflower, rough Plagiobothrys hirtus Endangered

Kuahiwi laukahi* Plantago princeps Endangered

No common name* Platanthera holochila Endangered

Orchid, white fringeless Platanthera integrilabia Candidate

Orchid, eastern prairie fringed Platanthera leucophaea Threatened

Mesa-mint, Otay Pogogyne nudiuscula Endangered

Pondweed, Little Aguja (=Creek) Potamogeton clystocarpus Endangered

Cinquefoil, Soldier Meadows Potentilla basaltica Candidate

Potentilla, Hickman's Potentilla hickmanii Endangered

Primrose, Maguire Primula maguirei Threatened

Lo`ulu, (=Na`ena`e) Pritchardia hardyi Endangered

Lo`ulu Pritchardia kaalae Endangered
81

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Lo`ulu Pritchardia napaliensis Endangered

Lo`ulu* Pritchardia remota Endangered

Kopiko* Psychotria grandiflora Endangered

Kopiko* Psychotria hobdyi Endangered

Harperella Ptilimnium nodosum Endangered

Buttercup, autumn Ranunculus aestivalis (=acriformis) Endangered

Makou Ranunculus mauiensis Candidate

Rhododendron, Chapman Rhododendron chapmanii Endangered

Beaked-rush, Knieskern's Rhynchospora knieskernii Threatened

Watercress, Gambel's Rorippa gambellii Endangered

Cress, Tahoe yellow Rorippa subumbellata Candidate

Arrowhead, bunched Sagittaria fasciculata Endangered

Water-plantain, Kral's Sagittaria secundifolia Threatened

No common name* Sanicula purpurea Endangered

Pitcher-plant, green Sarracenia oreophila Endangered

Pitcher-plant, Alabama canebrake Sarracenia rubra alabamensis Endangered

Pitcher-plant, mountain sweet Sarracenia rubra ssp. jonesii Endangered

Chaffseed, American Schwalbea americana Endangered

Bulrush, Northeastern Scirpus ancistrochaetus Endangered

Skullcap, Florida Scutellaria floridana Threatened

Roseroot, Leedy's Sedum integrifolium ssp. leedyi Threatened

Checker-mallow, Nelson's Sidalcea nelsoniana Threatened

Checker-mallow, Kenwood Marsh Sidalcea oregana ssp. valida Endangered

Checkermallow, Wenatchee Mountains* Sidalcea oregana var. calva Endangered

Checker-mallow, pedate Sidalcea pedata Endangered

Goldenrod, Houghton's Solidago houghtonii Threatened

Goldenrod, Yadkin River Solidago plumosa Candidate

Spiraea, Virginia Spiraea virginiana Threatened

Ladies'-tresses, Canelo Hills Spiranthes delitescens Endangered

Ladies'-tresses, Ute Spiranthes diluvialis Threatened

Ladies'-tresses, Navasota Spiranthes parksii Endangered

Cobana negra Stahlia monosperma Threatened

Seablite, California Suaeda californica Endangered

Meadowrue, Cooley's Thalictrum cooleyi Endangered

Bluecurls, Hidden Lake

Trichostema austromontanum ssp. 

compactum Threatened

Clover, showy Indian Trifolium amoenum Endangered

Tuctoria, Greene's* Tuctoria greenei Endangered
82

Table 1. Species Listed or Proposed as Threatened, Endangered, and their Designated and Proposed Critical Habitat 

(Denoted by Asterisk) in the Action Area. Double Asterisks Denote Proposed Critical Habitat. There are 45 Candidates for 

listing also included and treated herein as “Proposed.”

Common Name Scientific Name Status

Solano Grass Tuctoria mucronata Endangered

Vervain, Red Hills Verbena californica Threatened

Pamakani*

Viola chamissoniana ssp. 

chamissoniana Endangered

No common name* Viola helenae Endangered

Nani wai`ale`ale* Viola kauaiensis var. wahiawaensis Endangered

Grass, Tennessee yellow-eyed Xyris tennesseensis Endangered

Wild-rice, Texas* Zizania texana Endangered

NMFS and the FWS have joint jurisdiction over sea turtles, gulf sturgeon and Atlantic salmon. 

To avoid redundancy, these shared species have been wholly addressed within NMFS biological 

opinion. The FWS is generally responsible for endangered and threatened sea turtles above mean 

higher high water (when they are on their nesting beaches as opposed to when they are in or 

beyond the surf zone) and for Gulf sturgeon and Atlantic salmon when they are in fresh water (as 

opposed to when they are in estuarine or marine water). 

Species and Critical Habitat Not Likely to be Adversely Affected by the Proposed 

Action

As described in the Approach to the Assessment, FWS uses two criteria to identify those 

endangered or threatened species or critical habitat that are not likely to be adversely affected by 

the discharges that would be authorized by the proposed VGPs. The first criterion is exposure or 

some reasonable expectation of a co-occurrence between direct and indirect effects of the 

discharges authorized by the proposed permits and a particular listed species or designated 

critical habitat: if we conclude that a listed species or designated critical habitat is not likely to be 

exposed to those discharges or the resultant stressors, we must also conclude that the critical 

habitat is not likely to be adversely affected by those activities. The second criterion is the 

probability of a response given exposure, which considers susceptibility: species that may be 

exposed to a discharge, but are likely to be unaffected by the discharge (at levels they are likely 

to be exposed to) are also not likely to be adversely affected by that discharge. We applied these 

criteria to the species listed in Table 2.

The FWS has determined that there is a reasonable expectation that any aquatic and aquaticdependent species and their critical habitats listed in Table 2 may be adversely affected by 

stressors associated with the proposed action. This determination is based primarily on the 

potential for aquatic nuisance species to have effects far from the site of an original introduction. 

Species and Critical Habitat Likely to be Adversely Affected by the Proposed 

Action

For more information regarding the individual species and critical habitats listed in Table 1 and 
83

the factors affecting their conservation status, please refer to proposed and final listing 

determinations, critical habitat designations, recovery plans, and five-year reviews available at: 

http://ecos.fws.gov/ecos/indexPublic.do; and EPA’s BE prepared for this consultation (EPA 

2012a). 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. The discussion also describes, 

generally, the physical and biological features (or primary constituent elements) of critical 

habitat that are essential to the conservation of species and may be exposed to the stressors of the 

proposed action. 

Environmental Baseline

By regulation, the environmental baseline includes the past and present impacts of all state, 

Federal or private actions and other human activities in the action area, the anticipated impacts of 

all proposed Federal projects in the action area that have already undergone formal or early 

Section 7 consultation, and the impact of State or private actions which are contemporaneous 

with the consultation in process (50 CFR 402.02). The environmental baseline for this Biological 

Opinion includes the effects of several activities that affect the conservation of endangered and 

threatened species and their critical habitats in the Action Area. 

A number of human activities have contributed to the current status of populations of endangered 

and threatened species and their critical habitats in the action area. Some of those activities 

occurred extensively in the past, ended, and no longer appear to occur, although the effects of 

population reductions likely persist today. Other human activities are ongoing and appear to 

continue to affect populations of endangered and threatened species in the Action Area. The 

following discussion summarizes the principal phenomena in the Action Area that are known to 

affect the likelihood that these endangered and threatened species will survive and recover in the 

wild.

Because this is a programmatic consultation on a continuing action with a geographic scope that 

encompasses all waters of the United States, its territories and possessions, this Environmental 

Baseline serves a slightly different purpose. First, because this is both a programmatic and 

national consultation that does not assess the consequences of EPA’s proposed VGPs for specific 

sites or listed resources that occur at those sites, 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. As such, this Environmental Baseline elaborates on some of the 

narratives we have already presented in our treatments of the Status of Listed resources by 

focusing on the status and trends of waters of the United States at a national scale. 

We begin this Environmental Baseline with a discussion of the status and trends of waters of the 

United States. Because the status and trends of those waters, and the endangered and threatened 

species that depend on them, has been strongly influenced by wetland ecosystems in the United 
84

States, we summarize the status and trends of wetlands in the United States as a second step. We 

summarize large-scale impacts to coastal and wetland habitat, including aquatic nuisance 

species, pollutants, and the impacts of global climate change. Then we summarize the effect of 

Federal programs designed to protect and restore waters of the United States. We conclude by 

integrating and synthesizing this information to assess the effect of these programs on 

endangered species, threatened species, and designated critical habitat.

The Changing Landscapes of the United States

The continental United States has a land area of about 2.3 billion acres. Since colonial times, the 

landscapes of the United States reflect the abundance, distribution and economics of the human 

population. In 1790, the United States had a resident population that was slightly less than 4 

million and a population density of 4.5 people per square mile. By 2010, that population had 

grown to slightly more than 308 million people and the population density had increased to 85 

per square mile. Most of the population growth in the United States occurred in urban areas, first 

in central cities and later suburbs. In 1910, three times more Americans lived in central cities 

than in suburban areas; by 1970, slightly more Americans lived in suburban areas than in either 

cities or rural areas. From 1950 to 1996, the urban population increased by 63 percent, the rural 

population decreased by 19 percent, and the greatest relative change occurred in the suburban 

population, an increase of 274 percent. 

Most of the urban or suburban areas occur in the South and Midwest, but cities and suburbs 

account for less than 2 percent of the land area in those regions. In comparison, urban and 

suburban lands in the Northeast made up over 5 percent of the landscape. The percentage of 

“undeveloped” land or natural areas in the South, Northeast and West was almost the same as the 

percentage of urban and suburban area in those regions (about 22 percent). The Midwest had the 

lowest percentage of these lands (17 percent). In the Northeast and South, these lands are 

represented by forest cover; in the Midwest, these lands are represented by farmland, and in the 

West the lands are represented by grassland and shrub cover. About half of all natural lands in 

urban and suburban areas consist of patches that are smaller than 10 acres. Nationally, less than 5 

percent of all natural areas consist of patches at least 1,000 acres in size. The northeast States 

have a higher percentage of natural areas between 100 and 1,000 acres and 1,000 to 10,000 acres 

in size than the other regions. Only western States have natural areas greater than 10,000 acres; 

these natural areas, however, account for 0.3 percent of all natural lands in urban and suburban 

areas.

In some cases suburbs developed along major highways and transportation systems to connect 

pre-existing, rural communities with nearby urban areas. In other cases, suburbs developed in 

areas that had previously been agricultural or had been dominated by natural communities 

because of favorable environmental conditions, zoning ordinances or land costs (Abler 1976; 

Matlack 1997). As a result, most modern metropolitan areas encompass a mosaic of different 

land covers and uses (Hart 1991). 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). 
85

Other human activities that have altered the landscapes of the United States include agricultural 

practices that include land conversion, sod busting, and applications of pesticides; forest 

practices that include timber harvests, silviculture, and the construction of logging roads; mining 

practices that include open-pit mining, mountain-top mining, placer mining, heap-leach mining, 

and removal of overburden materials; road construction practices that include alteration of land 

in the right of way, spraying herbicides to maintain the right of way, and construction of quarries 

for source materials; civil works projects that include canals, drainage ditches, projects to deliver 

water to arid lands in the western States, projects to drain wetlands in southeastern States, 

projects to control flooding in mid-western and eastern States, port construction, projects to 

maintain shipping channels, and the construction of more than 8,100 major dams on rivers and 

streams in the United States, Puerto Rico, and the U.S. Virgin Islands. 

The direct and indirect effects of these changes in land-use and land-cover change have had a 

lasting effect on the quantity, quality and distribution of every major terrestrial, aquatic, and 

coastal ecosystem in the United States, its territories and possessions. By the mid-1990s, at least 

27 types of ecosystems had declined by more than 98 percent (Noss & Murphy 1995). These 

include old growth and virgin forests in the eastern United States, pine barrens across 

Connecticut, Maine, Massachusetts, New Hampshire, New Jersey, New York, Pennsylvania, 

Rhode Island (Cryan 1985); more than 95 percent of the natural barrier island beaches in 

Maryland had been destroyed along with more than 50 percent of barrier island dunes. By 1986, 

more than 98 percent of the pre-settlement longleaf pine (Pinus palustris) forests in the 

southeastern coastal plain had been destroyed (Noss & Murphy 1995; Ware et al. 1993). Many 

other native ecosystems have experienced substantial reductions in area. About 90 percent of the 

original 58 million hectares of tallgrass prairie had been destroyed; 99 percent of the tallgrass 

prairie east of the Missouri River and 85 percent of the tallgrass prairie west of the Missouri 

River has been destroyed (Klopatek et al. 1979). 

Aquatic and semi-aquatic ecosystems have not fared much better than these terrestrial 

ecosystems. Between the 1780s and 1980s, 30 percent of the nation’s wetlands had been 

destroyed, including 74 percent of the wetlands in Connecticut, 73 percent of the wetlands in 

Maryland, 52 percent of the wetlands in Texas, 91 percent of all wetlands in California, 

including 94 percent of all inland wetlands (Dahl 1990). From 1982 to 1987, the wetland area 

throughout the conterminous United States declined by 1.1 percent and the expansion of urban –

suburban metropolitan areas accounted for 48 percent of this decline (Brady & Flather. 1994).

Because of these changes in land use, many of the native plant and animal species that inhabited 

those native ecosystems over the past have become extinct or extinct in the wild over the past 

200 years. The last passenger pigeon, a species that once numbered in the billions and covered 

most of the eastern and mid-western United States, became extinct in 1912. In the same year, the 

Louisiana parakeet (Conuropsis carolinensis ludoviciana) became extinct followed two years 

later by the extinction of its relative, the Carolina parakeet (C. c. carolinensis). The heath hen 

became extinct in the mid-1920s, the June sucker (Chasmistes liorus liorus) in the mid-1930s, 

Tecopa pupfish (Cyprinodon nevadensis calidae) in the early 1940s, and Ash Meadows killifish 

(Empetrichthys merriami) and Thicktail chub (Gila crassicauda) in the 1950s. Over the past 200 

years, a substantial portion of the bird fauna of the Hawaiian islands -including the Oahu akepa, 
86

Kona finch, Lanai creeper, black mamo, and Hawai’i o’o- became extinct combined with the 

extinction of substantial portions of the freshwater mussel fauna of the Mississippi, Ohio, and 

Tennessee Rivers and regional extirpations of the flora and fauna of California, Florida, Oregon, 

Puerto Rico, and the desert states.

Status and Trends of Waters of the United States

All of the endangered and threatened species and designated critical habitat considered in this 

biological opinion depend on the health of aquatic ecosystems for their survival. These species 

were listed as endangered or threatened, at least in part, because of the consequences of human 

activities on the aquatic ecosystems -the 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 determines the status and trends 

of these species and the critical habitat that has been designated for them.

Over the past 30 to 40 years, the nation’s aquatic ecosystems have improved substantially. In 

particular, pollution from point sources has been significantly reduced over the past 35 years. 

Sewage and industrial discharges into aquatic ecosystems have been controlled and some 

agricultural pesticides have been restricted or banned. Programs like the Conservation Reserve 

Program have taken highly erodible lands out of production. Despite this progress, however, 

many aquatic ecosystems remain highly polluted. Of the waters bodies they assessed -39 percent 

of the river and stream miles, 46 percent of the lake area and 51 percent of the estuarine areaone or more designated uses are impaired. Non-point pollution from urban and agricultural land 

(e.g. siltation, nutrients, bacteria, metals and oxygen depleting substances) that is transported by 

precipitation and runoff was the primary cause of the impairment.

These water quality problems, particularly the problem of non-point sources of pollution, have

resulted from the changes humans have imposed on the landscapes of the United States over the 

past 100 – 200 years. One way of relating these changes in water quality to land uses relies on 

the surface area of a watershed that is covered by porous versus impervious surfaces. Most land 

areas that are 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 -roads, rooftops, 

parking lots, driveways and sidewalks- in those landscapes. 

The amount of impervious surface in a watershed is a reliable indicator of a suite of phenomena 

that influence a watershed’s hydrology (Center for Watershed Protection, 2003). Above certain 

thresholds, landscapes with impervious surfaces respond to precipitation differently than other 

land-uses: rain that would normally infiltrate in forest, grassland and wetland soils 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.
87

Aquatic Nuisance Species

Aquatic nuisance species (ANS) are aquatic and terrestrial organisms, introduced into new 

habitats throughout the United States and other areas of the world, that produce harmful impacts 

on aquatic natural resources in these ecosystems and on the human use of these resources 

(http://www.anstaskforce.gov). They are also referred to as invasive, alien, or nonindigenous 

species. Introduction of these species is cited as a major threat to biodiversity, second only to 

habitat loss (Wilcove et al. 1998). They have been implicated in the endangerment of 48% of 

the species listed under ESA (Czech and Krausman 1997). In Hawaii, 343 marine aquatic 

invasive species have been documented. Over 250 nonindigenous species of invertebrates, 

algae, and microorganisms have established themselves in the coastal marine ecosystems of 

California, whose waters have been the subject of most in-depth analyses of aquatic invasions in 

the U.S. More than 180 invaders have been detected and described in the Great Lakes, which are 

among the best studied freshwater systems in the world. 

Climate Change

All species discussed in this Opinion are or will be threatened by the direct and indirect effects of 

global climatic change. There is now widespread consensus within the scientific community that 

atmospheric temperatures on earth are increasing (warming) and that these increases will 

continue for at least the next several decades (IPCC 2001). The Intergovernmental Panel on 

Climate Change (IPCC) estimated that average global land and sea surface temperature has 

increased by 0.6°C (± 0.2) since the mid-1800s, with most of the change occurring since 1976. 

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 & Berner 2001). The IPCC

reviewed computer simulations of the effect of greenhouse gas emissions on observed climate 

variations that have been recorded in the past and evaluated the influence of natural phenomena 

such as solar and volcanic activity. Based on their review, the IPCC concluded that natural 

phenomena are insufficient to explain the increasing trend in land and sea surface temperature, 

and that atmospheric warming observed over the last 50 years is probably attributable to human 

activities (IPCC 2001b). Climatic models estimate that global temperatures would increase 

between 1.4 to 5.8°C from 1990 to 2100 if humans do nothing to reduce greenhouse gas 

emissions from current levels (IPCC 2001b). 

In the Northeast, annual average temperatures have increased by 2°F since 1970, with winter 

temperatures increasing by up to 4°F (Karl et al. 2009). Over the same time interval, the 

Northeast has experienced more days with temperatures greater than 90°F, a longer growing 

season, increased heavy precipitation, more winter precipitation falling as rain than as snow, 

reduced snowpack, earlier breakup of winter ice on lakes and rivers, earlier spring snowmelt 

resulting in earlier peak river flows, rising sea surface temperatures and sea level. 

Over the next several decades, the Northeast is expected to experience temperatures increases of 

another 2.5 to 4°F during the winter season and 1.5 to 3.5°F during the summer season as a result 

of carbon emissions that have already occurred (Burakowski et al. 2008; Karl et al. 2009). 

Forecasts beyond the middle of this century are sensitive to the level of carbon emissions 

produced today. If carbon emissions are not reduced, the length of the winter snow season would 

be cut in half across northern New York, Vermont, New Hampshire, and Maine, and reduced to a 
88

week or two in southern parts of the region; the Northeast would have fewer cold days during the 

winter and experience more precipitation (Hayhoe et al. 2007; Karl et al. 2009).

Cities in the Northeast that currently experience temperatures greater than 100°F for a few days 

each summer would experience an average of 20 days of such temperatures each summer; some 

cities in the Northeast -- Hartford, Connecticut, and Philadelphia, Pennsylvania, for example --

would experience an average of 30 days of such temperatures each summer (Karl et al. 2009). 

Hot summer conditions would arrive three weeks earlier and last three weeks longer into the fall. 

Droughts lasting from one- to three-months are projected to occur as frequently as once each 

summer in the Catskill and Adirondack Mountains, and across the New England states. Finally, 

sea levels in this region are projected to rise more than the global average, which would increase 

coastal flooding and coastal erosion (Karl et al. 2009; Kirshen et al. 2008).

In the Pacific Northwest, annual average temperatures have increased by about 1.5°F over the 

past century with some areas experiencing increases of up to 4°F (Elsner & Hamlet 2010; Karl et 

al. 2009; Littell et al. 2009). Higher temperatures during the cool season (October through 

March) have caused more precipitation to fall as rain rather than snow and contribute to earlier 

snowmelt. The amount of snowpack remaining on April 1, which is a key indicator of natural 

water storage available for the warm season, has declined substantially throughout the Northwest 

region. In the Cascade Mountains, for example, the snowpack remaining on April 1 declined by 

an average of 25 percent over the past 40 to 70 years; most of this decline is attributed to the 

2.5°F increase in temperatures during the winter season over the time interval (Christensen et al. 

2007; Payne et al. 2004).

Over the next century, average temperatures in the Northwest Region are projected to increase 

by another 3 to 10°F, with higher emissions scenarios resulting in warming in the upper end of 

this range (Christensen et al. 2007; Karl et al. 2009). Increases in winter precipitation and 

decreases in summer precipitation are projected by many climate models, though these 

projections are less certain than those are for temperature. 

There is consensus within the scientific community that warming trends will continue to alter 

current weather patterns and patterns of natural phenomena that are influenced by climate, 

including the timing and intensity of extreme events such as heat-waves, floods, storms, and wetdry cycles. Oceanographic models project a weakening of the thermohaline circulation resulting 

in a reduction of heat transport into high latitudes of Europe, an increase in the mass of the 

Antarctic ice sheet, and a decrease in the Greenland ice sheet, although the magnitude of these 

changes remain unknown (Levermann et al. 2007; Schmittner et al. 2005). As ice melts in the 

Earth’s polar regions in response to increases in temperature, increases in the distribution and 

abundance of cold water are projected to influence oceanic currents, which would further alter 

weather patterns. In addition to influencing atmospheric temperatures and weather patterns, 

increases in greenhouse gases in the Earth’s atmosphere have begun to increase rates of carbon 

capture and storage in the oceans: as carbon dioxide levels in the oceans increase, the waters will 

become more acidic, which would affect the physiology of large marine animals and cause 

structures made of calcium carbonate (for example, corals) to dissolve (IPCC, 2001).
89

Climate change is projected to have substantial direct and indirect effects on individuals, 

populations, species, and the structure and function of marine, coastal, and terrestrial ecosystems 

in the foreseeable future (McCarthy et al. 2001; Parry et al. 2007) (see Table 2). Climatemediated changes in the global distribution and abundance are expected to reduce the 

productivity of the oceans by affecting keystone prey species in marine ecosystems such as 

phytoplankton, krill, cephalopods. 

Increasing atmospheric temperatures have already contributed to changes in the quality of the 

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). 

Changes in temperature and precipitation projected over the next few decades are projected to 

decrease snow pack, affect stream flow and water quality throughout the Pacific Northwest 

region (Knowles et al. 2006; Mote et al. 2008; Rauscher et al. 2008; Stewart et al. ; 2004). 

Warmer temperatures are expected to reduce snow accumulation and increase stream flows 

during the winter, cause spring snowmelt to occur earlier in the year causing spring stream flows 

to peak 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).

The States of Idaho, Oregon, and Washington, are likely to experience increased forest growth 

over the next few decades followed by decreased forest growth as temperature increases 

overwhelm the ability of trees to make use of higher winter precipitation and higher carbon 

dioxide. In coastal areas, climate change is forecast to increase coastal erosion and beach loss 

(caused by rising sea levels), increase the number of landslides caused by higher winter rainfall, 

and inundate areas in southern Puget Sound around the city of Olympia, Washington (Littell et 

al. 2009).

Table 2. Phenomena associated with projections of global climate change including levels of confidence 

associated with projections (adapted from IPCC 2001 and Campbell-Lendrum Woodruff 2007)

Phenomenon

Confidence in Observed 

Changes (observed in the 

latter 20th Century)

Confidence in Projected 

Changes (during the 21st

Century)

Higher maximum temperatures and a greater 

number of hot days over almost all land areas Likely Very likely

Higher minimum temperatures with fewer cold 

days and frost days over almost all land areas Very likely Very likely

Reduced diurnal temperature range over most 

land areas Very likely Very likely

Increased heat index over most land areas Likely over many areas Very likely over most 

areas

More intense precipitation events

Likely over many mid- to highlatitude areas in Northern 

Hemisphere

Very likely over many 

areas

Increased summer continental drying and Likely in a few areas Likely over most mid-
90

associated probability of drought latitude continental 

interiors (projections are

inconsistent for other 

areas)

Increase in peak wind intensities in tropical 

cyclones Not observed Likely over some areas

Increase in mean and peak precipitation 

intensities in tropical cyclones Insufficient data Likely over some areas

Rising stream temperatures will likely reduce the quality and extent of freshwater salmon habitat. 

The duration of periods that cause thermal stress and migration barriers to salmon is projected to 

at least double by the 2080s for most analyzed streams and lakes (Littell et al. 2009). 

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. 

Clean Water Act

The Federal Water Pollution Control Act, or Clean Water Act, is the principal law concerned 

with polluting activity in streams, lakes and estuaries in the United States. The original 1948 

statute was totally re-written in 1972 (P. L. 92-500) 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 

Clean Water Act in the Water Quality Act of 1987 (P. L. 100-4) in response to the significant 

and persistent water quality problems.

The Clean Water Act uses two primary approaches to achieve its goal. The first approach uses 

regulations to achieve a goal of zero discharge of pollutants into waters of the United States. The 

second approach provides Federal technical assistance for municipal wastewater treatment 

construction. Both approaches are supported by research activities, permits and provisions for 

enforcement. 

To achieve its objectives, the Clean Water Act generally prohibits all discharges into the nation’s 

waters, unless they are specifically authorized by a permit. For example, the National Pollutant 

Discharge Elimination System or NPDES program regulates discharges of pollutants like 

bacteria, oxygen-consuming materials, and toxic pollutants like heavy metals, pesticides, and 

other organic chemicals. 

Most states have been authorized to administer the NPDES program in lieu of EPA (see CWA 

§402(b)). However, we note that the VGPs (Clean Water Act NPDES permits) are both issued 

and administered by EPA nationwide. 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 Clean Water Act permits or the regulatory requirements. Instead, non-point sources of 

pollution are regulated by State programs.
91

San Francisco Bay as an Example of the Impact

San Francisco Bay provides and illustrative example of the impacts of the environmental 

baseline on endangered and threatened species under FWS’ jurisdiction. In the 1830s, San 

Francisco Bay covered almost 700 square miles, with almost a million fish passing through the 

estuary and 69 million acres of water flowing down from mountain headwaters toward the sea 

(San Francisco Estuary Project, 1997; EPA BE 2012a). But in 1848, the Gold Rush began, and 

hydraulic mining plugged the rivers and bays with more than one billion cubic yards of 

sediments. Over time, farmers and city builders filled up more than 750 square miles of tidal 

marsh, and engineers built dams to block and store the rush of water from the mountains into the 

SFBE, as well as massive pumps and canals to convey this water to cities and farms throughout 

the state (San Francisco Estuary Project, 1997; EPA BE 2012a).

More than 95% of the historic tidal marshes have been leveed and filled, leading to subsequent 

losses in fish and wildlife habitat. Harbor and channel dredging has altered water flow patterns 

and salinity. Beginning in the early 1900s, water development for flood control, agricultural and 

municipal uses altered the volume and timing of freshwater inflows (San Francisco Estuary 

Project, 1997; EPA BE 2012a). For a number of the estuary’s fish and invertebrate species, it 

was estimated that a 10 km upstream shift in the location of the mixing zone in the spring around 

this time period corresponded to a two- to five-fold decrease in abundance or survival. The 

freshwater inflow can vary significantly from year to year from natural conditions. However 

since the 1940s, large dams on the estuary’s tributary rivers have captured and stored the 

majority of fresh water, resulting in less input to the estuary. Analyses of the spring time mixing 

zone location benchmarks reveal a steady decline in open water habitat (SFEP, 2011; EPA BE

2012a). Diversions to cities, farms and other uses remove an average of more than half the water 

that would otherwise reach the SFBE. Though about 70% of the state's available water supply is 

carried by Northern California rivers and streams, 80% of the present demand for water comes 

from the San Joaquin Valley and south of the Tehachapi Mountains (the Los Angeles area) (San 

Francisco Estuary Project, 1997; EPA BE 2012a).

Additionally, the amount and quality of the fresh water entering into the SFBE from nearby 

watersheds can have a significant impact on the overall health of the system. The local 

watersheds surrounding San Francisco Bay have been dramatically altered due to development, 

water diversions, and urban runoff. This has caused erosion and sedimentation and negatively 

impacted water quality, hydrology, and habitat for fish and other aquatic species (SCCC, 2010; 

EPA BE 2012a).

There have been numerous projects that have improved the conditions in the SFBE over the last 

20 to 25 years, including, but not limited to: wetland restoration and enhancement; the 

development of an integrated Regional Water Management Plan; and the implementation of 

several invasive species prevention control and eradication programs. One particularly 

noteworthy program is the Long Term Management Strategy for the Placement of Dredged 

Material. Until the late 1980s most of the dredged material from shipping lanes was disposed of 

in one of three areas in the Bay (SFEP, 2011; EPA BE 2012a). As a result of this management 
92

plan and subsequent actions, there has been a significant decrease in the amount of in-Bay 

disposal of dredged material with nearly 20 million cubic yards of dredged material being reused 

for beneficial purposes. Currently the program is on track to meet its long-term goal to reduce 

in-Bay disposal to 1.25 million cubic yards of material per year (SFEP, 2011; EPA BE 2012a).

The California San Francisco Bay Regional Water Quality Control Board 2010 303(d) list of 

water quality impaired waters includes more than 270 listings in 88 water bodies (EPA BE

2012a). TMDL projects are currently being developed to address more than 160 of the 270 

303(d) listings; however, one TMDL may address multiple listings. For example, the 

Diazinon/Pesticide Toxicity TMDL for urban creeks addressed more than 30 impaired creeks or 

creek segments.

ANS have been introduced in California waters via transoceanic ships, aquaculture, the aquarium 

trade, the bait industry, recreational activities, biological research, environmental restoration 

projects, and freshwater deliveries up and down the state (SCDFG, 2008; EPA BE 2012a). 

However, in the San Francisco Bay Estuary, unmanaged or untreated ballast water from 

international ships has been cited as the principal cause of invasive species (SCDFG, 2008; EPA 

BE 2012a). Statewide, researchers have now identified 607 introduced or likely introduced 

species in California’s estuarine waters. In San Francisco Bay, the rate at which ANS were 

becoming established increased from an average of one new species every 55 weeks prior to 

1960, to one new species every 14 weeks between 1961 and 1995 (Cohen and Carlton, 1998; 

EPA BE 2012a). 

More than 250 non-native species have been found in the San Francisco Bay-Delta Estuary 

(SCDFG, 2008). Some of the most problematic ANS that have become established in California 

include the European green crab (Carcinus maenas), the Chinese mitten crab (Eriocheir 

sinensis), the Asian overbite clam (Corbula amurensis), as well as a plethora of aquatic plants 

with origins as far away as Brazil and Japan (SCFDG, 2008; EPA BE 2012a).

These ANS cause major impacts: disrupting agriculture, shipping, water delivery, recreational 

and commercial fishing; undermining levees, docks and environmental restoration activities; 

impeding navigation and enjoyment of the state’s waterways; and damaging native habitats and 

the species that depend on them (SCDFG, 2008; EPA BE 2012a).

Integration and Synthesis of the Environmental Baseline

The direct and indirect effects of changes in land-use and land-cover of the United States have 

had lasting effect on the quantity, quality, and distribution of every major terrestrial, aquatic, and 

coastal ecosystems. Many native ecosystems exist as small isolated fragments surrounded by 

expanses of urban and suburban landscapes or “natural” areas that are dominated by non-native 

species. As a result, many of the native plant and animal species that inhabited those native 

ecosystems over the past have become extinct, extinct in the wild, endangered, or threatened 

over the past 200 years. 

Beginning in the 1960s, a wide variety of programs undertaken by Federal, State, and local 
93

governments, non-governmental organizations, and private individuals have been established to 

protect or restore our nation’s forests, grasslands, wetlands, estuaries, rivers, lakes, and streams. 

Those programs have helped slow and, for many ecosystems, reverse declining trends that began 

in the past. However, those efforts have benefited some ecosystems and their associated flora and 

fauna more than other ecosystems. Despite the efforts of agencies at every level of government, 

non-governmental organizations, and private individuals, non-point sources of pollution and 

ANS invasions still degraded our rivers, lakes, and streams; freshwater aquifers in coastal areas 

remain at risk from saltwater intrusion because of water withdrawals; nutrients transported down 

the Mississippi River remains sufficient to produce an hypoxic zone in the Gulf of Mexico that 

had more than doubled in size; and the acreage of wetland declined from slightly more than 274 

million acres of wetlands to about 107.7 million acres between the 1980s and 2004 (Dahl 2006).

Water quality is important to all of the above listed resources, either directly, as for fishes and 

invertebrates, or indirectly, as for cetaceans who are affected through their diet. In some cases,

detriments to water quality have led to the endangerment of 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. For example, stressors that 

affect only a limited number of individuals were once tolerated with little impact to the species, 

whereas now, the same stressors are likely to reduce population viability. It is with this 

understanding of the environmental baseline that we consider the effects of the proposed action, 

including the likely effects that ANS and pollutants will have on endangered and threatened 

species and their designated critical habitat. 

Effects of the Proposed Action, Traditional Approach

The Effects of the Action is the primary focus of an Opinion. For this Opinion, our analysis of the 

probable effects of the proposed VGPs on proposed and listed endangered and threatened species 

and proposed and designated critical habitat are divided into two sections, the Traditional 

Approach, described here, and the Programmatic Approach, described below. 

Following the Traditional Approach, we first describe the population of vessels covered under 

the VGPs. We then examine the consequences of exposing endangered and threatened species 

and designated critical habitat to the discharges authorized by EPA’s proposed VGPs. We 

organize our analyses by general stressor type, i.e., aquatic nuisance species (ANS) and 

pollutants. Under each section, we describe discharges authorized by the VGPs that are likely to

produce either ANS or pollutant stressors. For example, ballast water, hull fouling, and chain 

locker effluent are grouped as discharges that carry aquatic nuisance species (ANS). We first 

characterize exposure of ESA listed species to the discharges authorized by the VGPs; we also 

describe the actions EPA will take to prevent exposure of listed resources to authorized 

discharges. Next, we identify the physical, chemical, and biological stressors associated with 
94

vessel discharges. Then we review the literature describing the responses of threatened and 

endangered individuals, given exposure to these stressors. Finally, we summarize the risks posed

to the continued existence of populations, species, or designated critical habitat. Our purpose is 

not to provide a comprehensive review of the probable responses of and consequences to 

endangered or threatened species; instead, our intention is to identify the range of representative 

responses and consequences we would expect given exposure to vessel discharges authorized by 

EPA’s VGPs. 

Vessel Populations Covered by the VGPs

The demographics of the vessels to be covered under the VGPs influence loading of stressors. 

Vessel size affects discharge volume. Vessel service class and age generally determines the type 

and performance of equipment used onboard vessels and therefore the characteristics of 

discharges from the equipment. Vessel age structure also indirectly indicates the implementation 

rate of build-date dependent protective measures over the 5-year permit period. Finally, 

distribution of vessel service classes among ports and harbors influences pollutant loading from 

VGP authorized discharges. The following paragraphs, describing the vessel service classes 

authorized to discharge to waters of the U.S. under the VGPs, are summarized in Table 3 and 

Table 4. 

The types of vessels covered under the 2013 VGP include approximately 2,000 large commercial 

fishing vessels greater than 79 feet along with cruise ships, ferries, barges, mobile offshore 

drilling units, oil tankers or petroleum tankers, bulk carriers, cargo ships, container ships, other 

cargo freighters, refrigerant ships, research vessels, emergency response vessels, including 

firefighting and police vessels, and any other vessels operating in a capacity as a means of 

transportation. Approximately half of the vessels covered under the sVGP are commercial 

fishing vessels involved in such activities as fish catching (e.g., longliner, shrimper, and trawler), 

fish processing, fishing tendering, and charter fishing. The other half are distributed among a 

variety of vessel types, including passenger vessels (e.g., water taxis, tour boats, harbor cruise 

ships, dive boats), utility vessels (e.g., tug/tow boats, research vessels, offshore supply boats), 

and freight barges (USEPA 2010b). These vessels and their relative abundance are described 

below.

VGP Vessels

EPA’s Notices of Intent (NOIs) database cannot be used alone to estimate the total number of 

vessels covered by the VGP Permit because only vessels greater than 300 gross tons or with the 

capacity to carry more than 8 cubic meters of ballast water were required to submit NOIs under 

the 2008 VGP. To estimate the population of domestically-flagged vessels subject to the VGP, 

EPA used two existing databases, the Marine Information for Safety and Law Enforcement 

(MISLE) and Waterborne Transportation Lines of the United States (WTLUS) databases, to 

create a master database identifying approximately 60,000 vessels eligible for coverage. Using 
95

the Foreign Traffic Vessel Entrances and Clearances (FTVEC) database3, EPA estimated 

approximately 12,400 additional foreign-flagged vessels also subject to the VGP requirements, 

making a total estimated vessel population of 72,400 vessels. From these vessels, 43,431 active 

NOIs were submitted under the 2008 VGP as of August 2010. This represents about 60% of the 

estimated vessel population covered. The NOI form listed nine types of vessels under which the 

vessel owners/operators could classify their vessel along with an option of selecting vessel 

service class “Other,” with space to designate vessel type in writing. In addition to the vessels 

identified in Table 4, about 10,000 were identified as “other”. These include 9,839 vessels for 

which no vessel class was specified, while 2,044 others self-identified as some variety of cargo 

vessel, 143 as tug/tow boats, 115 as crew/supply/support vessels, 83 as chemical/oil tankers, 34 

as barges, and 18 as passenger vessels. These vessels are integrated into the table of relative 

service class distribution and demographic properties for vessels submitting NOIs and with 

tonnage/ballast water capacity (Table 4).

The EPA-provided metrics in Table 3 include median4 values for vessel gross tonnage, ballast 

capacity and maximum persons aboard along with the proportion of vessels with on board 

treatment and using antifouling coatings. In addition to these metrics, FWS used the build dates 

reported in the NOI database to estimate the proportion of vessels within each service class that 

are 5 years of age or younger. This provides an index of the expected implementation rate of 

build date-dependent measures5 within the permit. 

Barges. Barges represent the greatest number of vessels permitted under the VGP, with 20,444 

uniquely identified vessels. Barges are large, flat-bottomed boats typically used to move cargo 

in inland waterways. There are many types of barges, including hopper barges, chemical barges, 

fuel barges, crane barges, dry bulk cargo barges, etc. Barges are usually not powered vessels, but 

are instead pushed or pulled by tugboats. Build dates for barges reported in the NOI indicate that 

21% of barges are less than 5 years old. Because of their relatively small size (vessel tonnage), 

ballast capacity, and maximum persons aboard, most discharges incidental to the normal 

operation of these vessels are of limited concern. EPA included barges in its analysis due to the 

large number of barges in operation. 

Oil and Gas Tankers. Oil and gas tankers represent the second greatest number of vessels 

permitted under the VGP, with 3,363 uniquely identified vessels. Oil tankers are designed to 

carry oil and other petroleum products in bulk tanks. Oil and gas tankers are large utility vessels, 

 

3 The FTVEC database provides information on foreign vessels entering or clearing U.S. Customs ports in calendar

year 2008, the most recent year for which data are published (USACE, 2010).

4 The median of a set of observations is the center value in the dataset where half of the observations are below and 

half are above. As a measure of central tendency, the median is robust against the influence of outliers and extreme 

values found in skewed data, that is, not distributed symmetrically around the mean. When the mean is greater than 

the median, it suggests the data are skewed such that it is influenced by a few larger values. 

5 The VGP requires biannual graywater monitoring for vessels with a maximum capacity to overnight 10 or more 

crewmembers and constructed on after December 19, 2013. In addition, all vessels constructed on or after 

December 19, 2013 must use an environmentally acceptable lubricant in all oil-to-sea interfaces. Older vessels 

technically able to use environmentally acceptable lubricants must do so and those which cannot, must report the use 

of unsafe lubricants in their Annual Report to EPA.
96

second only to large cruise ships in size (median tonnage equal to approximately 25,000 gross 

tons). Moreover, the median ballast water capacity of these vessels is very relatively large 

(24,000 m3). Nearly all oil and gas tankers also use anti foulant coatings to reduce attachment of 

organisms to the vessel hull. Approximately half of these vessels (47%) are less than 5 years old. 

EPA included oil and gas tankers in their analysis because of their prevalence at certain ports, 

their overall size, their large ballast water capacity, likelihood they are engaged in long distance 

voyages, and their use of AFCs.

Large Commercial Fishing Vessels6. Large commercial fishing vessels are those greater than 

79 feet in length that are engaged in the catching, taking, or harvesting of fish, crabs, lobster, 

shrimp, or other aquatic organisms for commercial sale. The MISLE7 database (USCG 2009)

indicates there are 2,326 commercial fishing vessels larger than 79 feet in length that are eligible 

for coverage under the VGP. The median ballast water capacity of these vessels is moderately 

high (1,388 m3), as is the number of crew/passengers aboard. In addition, only 13 percent of the 

large commercial fishing vessels are less than 5 years old. Commercial fishing vessels generate 

fish hold and fish hold cleaning waste streams that are unique to commercial fishing vessels, and 

these waste streams have been shown to contain relatively high concentrations of conventional 

pollutants and nutrients (USEPA 2010b). Since most large commercial fishing vessels are 

concentrated in a limited number of home ports, and since fish holds are frequently discharged 

and cleaned by vessel crews between catches, EPA included large commercial fishing vessels in 

its analysis. (Note that industrial operations from vessels used as seafood processing facilities are 

not subject to the VGP because these operations are not incidental to the normal operation of a 

vessel engaged in a capacity of transportation). 

Large Cruise Ships. Large cruise ships are the largest vessels (by size) covered under the VGP. 

Median vessel tonnage (53,526 gross tons) is approximately twice that of even the large oil and 

gas tankers. While the actual number of large cruise ships seeking coverage under the 2008 VGP 

is low (only 127 vessels), the number of crew and passengers aboard is relatively high -

approximately 3,500 per vessel. EPA NOI data indicate that 20% of large cruise ships are less 

than 5 years old. Because of the large number of crew and passengers living on-board cruise 

ships, graywater generation can average nearly 600 m3/day (158,500 gal/day). Median ballast 

water capacity of large cruise ships vessels is moderate (3,136 m3). A high percentage of large 

cruise ships also use AFC. Moreover, since aesthetics are important to the industry, deck 

washdowns may be performed more frequently on cruise ships than other types of vessels. The 

 

6

Public Law 110-299 subsequently extended by Public Law 111-215 provided for a temporary moratorium on 

NPDES permitting for all commercial fishing vessels. The moratorium on NPDES permitting for commercial 

fishing vessels expires on December 18, 2013 and therefore all commercial fishing vessels larger than 79 feet will be 

required to obtain permit coverage under the VGP in the event the moratorium is not extended.

7 The U.S. Coast Guard’s Marine Information for Safety and Law Enforcement (MISLE) database provides a wide 

range of information regarding vessel and facility characteristics, accidents, marine pollution incidents, and other 

pertinent information tracked by the U.S. Coast Guard. The USCG MISLE database provides information on a wide 

ensemble of vessels, including identification numbers, vessel category, size, area of operation, passenger and crew 

capacity, propulsion method, construction material and design, and year built or age.
97

above factors led EPA to include large cruise ships in its analysis. 

Medium Cruise Ships. Medium cruise ships are those ships authorized to carry 100 to 499 

passengers for hire and provide overnight accommodations to those passengers. Although only 

22 medium cruise ships are included in EPA’s NOI database, these vessels are relatively large, 

ranging in size from approximately 1,500 gross tons up to 5,000 gross tons, and have ballast 

capacities ranging from approximately 350 to 400 m3. Only 14% of these vessels are less than 5 

years old. With passenger and crew capacities up to 499 persons, medium cruise ships have the 

potential to generate more than 20,000 gallons/day of graywater. Untreated graywater from 

medium cruise ships has been shown to contain similar pollutants to those in untreated graywater 

discharges from large cruise ships (ADEC 2006; 2007). In addition, most medium cruise ships 

use AFC to prevent biofouling of the vessel hull. 

Large Ferries. The NOI database includes 118 large ferries, 12 percent of which are less than 5 

years old. Large ferries are vessels for hire that are designed to carry passengers and/or vehicles 

between two ports, usually in inland, coastal, or nearshore waters. For purposes of the VGP, 

large ferries are those ferries authorized to carry a) more than 100 tons of cars, trucks, trains, or 

other land-based transportation or b) 250 or more people. Large ferries usually travel the same 

route several times a day but do not provide overnight accommodations to their passengers. 

Because many ferries can travel the same route several times per day, they can discharge 

pollutants from a variety of sources (e.g., graywater, bilgewater, and seawater engine and 

exhaust cooling) to same water body. EPA included large ferries in its analysis due to these 

potential discharges. 

Cargo [Bulk] and Other Carriers. Cargo carriers (e.g., bulk carrier, freighters, roll-on/roll-off, 

container ships) comprise the majority of the “Other” vessels classified in the NOI database. The 

attributes of this group of vessels are similar to those of the oil and gas tankers in terms of vessel 

size (median tonnage equal to approximately 16,000 gross tons) and median ballast water 

capacity (10,198 m3). Approximately 61 percent of the owners/operators of these vessels 

reported using on-board treatment systems to treat the various waste streams aboard the vessels, 

and fewer use AFC. This is the youngest vessel population reporting in the NOI, with 56% of 

the vessels less than 5 years old. EPA included cargo carriers in its analysis due to their ballast 

water capacity and prevalence at certain ports. 

Emergency and Research Vessels. The emergency and research vessels types include relatively 

few numbers of vessels and are relatively small in size, ballast capacity, and number of 

passengers/crew. Build date data indicate that 16% of research vessels are less than 5 years old 

and only 3% of emergency vessels are less than 5 years old. Additionally, these vessels do not 

tend to engage on longer voyages where they can serve as a vector for invasive species 

(exceptions on voyage movements include large research vessels such as those operated by 

NOAA and the maritime services industry). Furthermore, the areas of operation for these vessels 

are not centrally located in any one home port or region. For these reasons, EPA considered 

discharges from these vessels to be discountable for purposes of the Endangered Species Act and 

does not consider that these vessel types warrant extensive analysis in the BE. 
98

Table 3. Distribution of vessel service classes, equipment, and metrics among VGP covered 

vessels submitting NOIs and reporting vessel tonnage/ballast water capacity(USEPA 

2012a).

Vessel 

Service 

Class

Estimated 

Number of 

Vessels 

Median 

Gross 

Tonnage

Median 

Ballast 

Capacity 

(m3)

Median 

Maximum 

Persons 

Aboard 

% Vessels 

w/On-board 

Treatment 

% Vessels 

Using Antifouling Hull 

Coatings 

% Vessels 

0-5 Years of 

Age

Barges 20,444

a

705 206 4 1 4 21

Oil and Gas 

Tankers

3,363b24,908 23,893 22 78 80 47

Large 

Commercial 

Fishing

2,326c1,997 1,388 29 41 85 13

Large 

Cruise 

Ships

127 53,526 3,136 3,455 79 84 20

Large 

Ferries

118 1,451 404 559 45 86 12

Medium 

Cruise 

Ships

22 4,584 364 315 50 82 14

Bulk Cargo 

and Other 

Carriers

2,044d15,939 10,198 25 61 65 56

Research 

Vessels

82 1,780 425 41 78 95 16

Emergency 

Vessels

56 563 332 16 43 96 3

a

“Other” was selected for 34 NOIs and some variety of barge was designated.

b

“Other” was selected for 83 NOIs and some variety of oil/chemical tanker was designated.

c

 Fishing vessels greater than 79 feet long, data from (USCG 2009)

d

 “Other” was selected for all 2,044 bulk cargo and other carriers with some variety of carrier specified. These were 

were dominated by: general cargo/not otherwise specified (91percent); car/truck carrier (3.6 percent); refrigerated 

cargo (2.3 percent); log/lumber/woodchip carrier (1.2 percent); and roll-on roll-off cargo, cement, grain/ore and 

ore/oil (cumulatively less than one percent) (USEPA 2012b).

sVGP Vessels

EPA estimates that between 115,000 and 138,000 vessels may be covered by the sVGP. The 

primary source of information used to characterize these vessels and their discharges is EPA’s 

Study Report to Congress: Study of Discharges Incidental to Normal Operation of Commercial 

Fishing Vessels and Other Non-recreational Vessels Less than 79 Feet (USEPA 2010b). EPA’s 

BE and the Report to Congress do not provide the same level of detail on the distribution of 

ballast capacity, onboard treatment and the presence of antifouling coatings for sVGP vessels as 

was provided for VGP covered vessels. Details for sVGP eligible vessels are provided for hull 

material and horsepower (Table 4). 

Approximately half of the sVGP eligible vessels are commercial fishing vessels involved in such 
99

activities as fish catching (111,094 vessels, e.g., longliner, shrimper, and trawler), fish 

processing, fishing tendering, and charter fishing. The other half are distributed among a variety 

of vessel types, including passenger vessels (34,609 vessels, e.g., water taxis, tour boats, harbor 

cruise ships, dive boats), utility vessels (18,743 vessels, e.g., tug/tow boats, research vessels, 

offshore supply boats), freight barges (11,596 vessels), freight ships (1,102 vessels) along with 

35,578 vessels with unspecified service class (USEPA 2010b)(USCG 2009). Recreational 

vessels are generally excluded because a separate act (the Clean Boating Act of 2008 (P.L. 110-

288)) exempts discharges incidental to the normal operation of these vessels from NPDES 

permitting requirements. The Clean Boating Act defines recreational vessels as those that are 

either 1) manufactured or used primarily for pleasure or 2) leased, rented, or chartered to a 

person to use for pleasure. Furthermore, vessels that are subject to U.S. Coast Guard inspection 

and that are either engaged in commercial use or that carry paying passengers are not considered 

recreational vessels under the Clean Boating Act.

Hull Materials. According to the analysis in EPA’s report to Congress, the three most common 

hull material types among sVGP eligible vessels are fiberglass, wood, and steel in order of most 

common usage. Commercial fishing vessels with wood hulls account for over three quarters of 

the total number of wood hulled vessels, although wood is also used in the hulls of a significant 

share of freight ships and passenger vessels less than 79 feet in length. The type of hull material 

affects the type of anti-foulant coatings that are applied and has implications on vessel discharges 

and receiving water quality. For example, steel hulls often have an anti-corrosive as well as antifoulant hull coatings. The type of hull material may also affect the frequency with which certain 

maintenance procedures such as hull inspections are conducted(USEPA 2010b).

Vessels less than 5 years old. Vessel age, for the purposes of this Biological Opinion, is an 

indicator of the implementation rate for build date dependent measures specified by the VGPs. 

The sVGP requires that “All motorized vessels constructed on or after December 19, 2013 must 

have a functioning fuel-air separator or a fuel tank vent to prevent a fuel spill.” In addition, for 

both VGPs, all vessels constructed on or after December 19, 2013 must use an environmentally 

acceptable lubricant in all oil-to-sea interfaces. Older vessels technically able to use 

environmentally acceptable lubricants must do so and those which cannot, must report the use of 

unsafe lubricants in their Annual Report to EPA. 

Self Propelled Vessels and Horsepower Ahead. Not all vessels covered by the sVGP are selfpropelled; rather they are moved about by other vessels (e.g. tug boats, tow boats). Horsepower 

ahead represents the rated power of a vessel’s engine in forward motion (as opposed to 

horsepower astern) and is expressed as the work accomplished per unit of time (e.g., 1 hp = 550 

foot-pounds of work per second). This power is transferred to the propulsion mode (e.g., jet or 

propeller) to create thrust and determines the vessel’s speed at any given weight, or the weight 

that can be moved at any given speed. Vessel power rating may determine the amount and 

characteristics of discharges from operating vessels by affecting the size, type, and complexity of 

onboard propulsion equipment. Most sVGP eligible vessels have a horsepower rating between 

100 and 500 hp, with fewer having horsepower ratings of 500 to 1,000 hp.
100

Table 4. Vessel metrics for sVGP eligible vessels with specified length less than 79 (USEPA 

2012a).

Vessel Service 

Class

Number of 

Vessels

Distribution of 3 

Most Common Hull 

Materials 

Number 

Vessels 0-5 

Years of 

Agea,b

Number of 

Self Propelled 

Vesselsa

Horsepower Ahead for 

Vessels Reporting 

Horsepowerc

Commercial 

Fishing Vessel

111,094 fiberglass 19,433

wood 21,479

steel 7,805

3,125 54,258 5k or more 21

1 – 5k 443

500 – 1k 1732

100 – 500 8478

<100 1364

Passenger 

Vessel

34,609 Fiberglass 8,022

wood 5,002

steel 1,633

2,502 17,061 5k or more 1

1 – 5k 642

500 – 1k 1,808

100 – 500 4,473

<100 1,059

Unspecified 37,578 fiberglass 6,595

wood 859

steel 1,998

2,648 16,392 1 – 5k 27

500 – 1k 142

100 – 500 1,570

<100 606

Utility Vessel 18,743 fiberglass 408

wood 510

steel 7,082

920 8,698 5k or more 2

1 – 5k 711

500 – 1k 1,174

100 – 500 1,159

<100 111

Freight Barge 11,596 fiberglass 20

wood 87

steel 4,391

321 320 1 – 5k 1

500 – 1k 4

100 – 500 13

<100 4

Freight Ship 1,102 fiberglass 38

wood 285

steel 224

19 610 5k or more 1

1 – 5k 5

500 – 1k 16

100 – 500 54

<100 9

Tank Barge 1,144 fiberglass 4

wood 2

steel 323

50 48 500 – 1k 6

100 – 500 1

<100 2

Public Vessel, 

unclassified

684 fiberglass 16

wood 1

steel 5

13 123 5k or more 2

1 – 5k 1

500 – 1k 2

100 – 500 4

<100 2

Tank Ship 220 fiberglass 0

wood 6

steel 43

5 85 1 – 5k 1

500 – 1k 2

100 – 500 19

<100 10

a Based on operational, U.S. flagged commercial fishing vessels and other non-recreational vessel less than 79 feet 

(including vessels of unspecified length) identified in the 2009 MISLE database (USEPA 2010)

b Vessel age was either not reported or an invalid age (i.e. less than zero) was reported for approximately 43,000 

vessels. 

c Horsepower ahead was not reported or an invalid value was reported for approximately 114,000 vessels. 
101

Aquatic Nuisance Species

Exposure Analysis

The introduction of non-native species is one of the leading causes of species endangerment and 

extinction, second only to habitat loss (Wilcove et al. 1998). Shipping has led to more ANS 

introductions than any other source (Fofonoff et al. 2003). Within the broad category of 

shipping, ballast water and hull fouling are the primary vectors for ANS introduction to coastal 

and marine environments (Ruiz et al. 2000), which are among the most heavily invaded systems 

on earth (Grosholz 2002). 

Globally, hull fouling and ballast water have been identified as the source of 228 (57%) marine 

ANS invasions (Molnar 2008). In North America, these vectors were identified as the source for 

164 of 316 (52 percent) marine invertebrate and algal invasions; these vectors were identified as 

a possible source for another 87 (27.5 percent) invasions, for a total of 251 (80 percent) invasions

(Fofonoff et al. 2003). At least 40 introductions of 32 non-native fish species have been linked 

to ballast water transport (Wonham et al. 2000). As indicated in the BE, biofouling is likely a 

greater threat than ballast water. Globally, 39% of marine ANS invasions were linked to hull 

fouling, whereas 31% of marine ANS invasions were likely to have been transported via ballast 

water (Molnar 2008). Bax et al. (2003) identified hull fouling as the source of 36% of the

nonnative coastal marine species established in continental North America (Bax et al. 2003), 

whereas ballast water only accounted for 20% (Carlton 2001). 

Propagule pressure is the quantity, quality, and frequency with which propagules (ANS or their 

larvae, eggs, spores, etc.) are introduced to a given location (NAS, 2011). The invasion process 

begins when an organism survives transport by a vector and is released into a novel environment. 

It may survive, reproduce, and spread throughout its environment; however, its successful 

establishment depends upon a myriad of factors, including: basic climatic factors, food 

resources, its reproductive strategy, competition, predation, and parasitism (Carlton, 1996). 

While species are most likely to be adversely affected by ANS after establishment, even limited 

exposure to an ANS organism can result in adverse effects, such as disease transmission.

The rate of ANS introductions has increased over time as vessel traffic has increased. For 

example, in the San Francisco Bay/Inland Delta, ANS were introduced an average of once every 

36 weeks from 1850 to 1995, but in the last ten years (from 1985 to 1995), ANS were introduced 

once every 12 weeks (http://anstaskforce.gov/more_impacts.php). Invasion rates also differ by 

location. In the Lower Columbia River Basin, the ANS invasion rate is one every 20 weeks

(Sytsma, 2004); in the Great Lakes the rate was one invasion every 28 weeks, although no new 

invasions have been documented in the Great Lakes since 2006 (USEPA, 2012a). 

For the vectors described below, we estimate the number of vessels authorized by the VGPs and 

overall discharge volumes. We also attempt to provide a broad estimate of the number of ANS
102

released to waters of the U.S., as authorized under the VGPs. We describe EPA’s proposed 

actions that are likely to minimize the exposure of listed resources to ANS. Finally, we 

summarize the likelihood that ESA listed resources would be exposed to ANS as a result of 

vessel discharges. When possible, we provide quantitative estimates, but in most instances, these 

data are not available. We therefore review the best available scientific data to provide a 

qualitative analysis of the risk of ANS invasion and the exposure of listed resources (NAS 2011; 

G. Ruiz, J. Carlton, pers. comm.). 

Hull Fouling

Biofouling of hulls is a significant, if not the single greatest, source of ANS invasions. 

For example, 90 percent of the 343 marine aquatic invasive species in Hawaii are thought to 

have arrived via hull fouling (Carlton 2001), while 36 percent of the nonnative coastal marine 

species established in continental North America are attributed to hull fouling (Bax et al. 2003). 

Approximately 800 million square meters of hull area arrives in the U.S. annually (Miller et al. 

2007). As described in EPA’s BE (EPA 2012a), Miller et al. (2007) investigated the extent of 

biofouling on 21commercial vessels and found that even the best-maintained commercial vessels 

had biofouling on up to 5% of their wetted surface, while 10 drydocked ships were covered over 

5 to >90% of their wetted surface. Container ships are expected to have the lowest levels of 

biofouling due to their fast speeds and short port durations. In a study of 22 in-service container 

ships at the Port of Oakland, Davidson et al. (2009) found low levels of biofouling on 21 hulls; 

however, biofouling covered 90% of one hull. Taxonomic richness was high among all 

container ships. A study of underwater video and scrapings taken from 20 vessels shortly after 

their arrival to the Great Lakes estimated that total abundance averaged > 170,000 invertebrates 

per vessel, belonging to 109 species (Sylvester and MacIsaac 2010). A study of 40 transoceanic 

vessels arriving in Vancouver and Halifax estimated that total abundance averaged up to 600,000 

invertebrates per ship belonging to 156 species (Sylvester et al., 2011). 

Hull fouling ANS are generally bottom-associated sessile and sedentary organisms

(http://www.serc.si.edu/labs/marine_invasions/vector_ecology/fouling.aspx). They attach in

succession: a slime layer of bacteria and algae colonizes first; barnacles, bryozoans, and tube 

worms follow; and with this base established, mollusks, sponges, sea squirts, and seedweed are 

able to colonize (BE). Highly developed fouling communities may provide microhabitats for 

mobile organisms, such as fish, crabs, and sea stars (Underwater Husbandry). These organisms 

are able to release themselves, gametes, or fragments into aquatic environments encountered by 

the vessel, including novel harbors and waterways. 

To remove biofouling organisms, and to reduce or slow the attachment of new organisms, 

vessels perform underwater ship husbandry or hull husbandry, i.e., the maintenance of the 

underwater portions of a vessel. Hull husbandry includes the application of antifouling coatings 

(AFCs) and removal of biofouling organisms during dry dock periods, as well in-water hull 

cleaning. The shipping industry performs hull husbandry primarily for economic reasons. 

Biofouling on a ship’s hull increases the hydrodynamic drag of the vessel and leads to increased 
103

fuel consumption (Chambers et al., 2006). It has been estimated that fouling increases the annual 

fuel consumption of the world’s commercial shipping fleet by 40 percent, or 120 million tons of 

fuel at a cost of about $ 7.5 billion per year, in year 2000 dollars (GISP, 2008). 

Underwater hull cleaning can be quite effective at removing marine fouling; however, the 

effluent stream from cleaning is difficult to control. The potential for ANS release resulting from 

the uncontained discharge of underwater cleaning effluent is widely recognized. For example, 

underwater hull cleaning has been banned by the ANZECC Code of Practice (ANZECC, 1997). 

Underwater hull cleaning is also prohibited in California, Maine, and Massachusetts (Underwater 

husbandry). 

As described in the BE, underwater hull husbandry has the potential to spread ANS by releasing 

them into the environment. To examine the ANS risks posed by various hull cleaning

operations, researchers from the New Zealand National Institute of Water and Atmospheric

Research (NIWA) visited hull cleaning facilities in four New Zealand ports where vessels were

removed from the water for cleaning (drydock and haul-out facilities) or where fouling

organisms were removed underwater by divers (Floerl, 2005). For the operations examined, 

physical removal of fouling assemblages from vessel hulls did not result in mortality of all 

organisms. Most fouling organisms (72%) survived and remained viable after removal using 

underwater hull cleaning methods, which did not involve exposure to air or high-pressure water 

blasting. The overall viability of organisms removed from hulls was lowest in haul-out facilities 

(16 %) and drydock facilities (43 %), where fouling organisms were often exposed to air, highpressure freshwater blasting, and trampling.

Vessel hull fouling and underwater husbandry thus provide two pathways for ANS invasions. 

To address these concerns, EPA included the following requirements in the VGP (suggested 

measures are not included; for example, the VGP does not require AFCs, but if owners/operators 

use AFCs, they are required to “give consideration” to selecting products that maximize efficacy 

but minimize adverse environmental effects): 

 Minimize the transport of attached living organisms when traveling into U.S. waters from 

outside the U.S. economic zone or between Captain of the Port zones. 

 For underwater hull cleaning, vessel owners/operators must, when feasible, use a vacuum 

or other control technologies to minimize the release of dispersion of fouling organisms 

into the water column

To address ANS hull fouling concerns, EPA included the following requirements in the sVGP: 

 Minimize the transport of any visible living aquatic organisms from one waterbody to 

another by regularly cleaning and maintaining the hull 

 Vessel hulls must be periodically inspected, and if necessary, cleaned to prevent the 

spread or dispersal of potentially invasive species 

 Prior to transporting the vessel from one waterbody to another overland, you must inspect 

the visible areas of the vessel for any attached or visible stowaway living organisms. If 

organisms are found, they must be removed and appropriately discarded onshore. 

Removed organisms may not be discharged into waters subject to this permit. 
104

It is not clear, from reading the BE or the permits, the extent to which these requirements will 

minimize the risk of ANS invasions. For example, EPA requires vessel owners to minimize the 

transport of ANS, but EPA does not require anti-fouling coatings in either the VGP or the sVGP. 

If vessel owners/operators use AFCs, EPA requires that they “give consideration” to selecting 

the most effective product for their vessel type, but EPA does not provide guidance on which 

AFCs are the best available technology for each vessel type. The sVGP requires hull cleaning 

but does not require that debris containment systems be used to collect ANS. The VGP requires 

the use of such technology when feasible; however, the BE states that vacuum systems “are not 

widely commercially available; hence EPA has not required that they must be used in this 

permit,” (BE). We conclude that listed resources retain appreciable exposure to ANS via hull 

fouling and hull husbandry despite measures in the VGPs to reduce this exposure.

The permit requirements to “minimize” ANS are not likely to result in major changes to vessel 

operations. Therefore, we will use the above estimates of hull area and hull fouling coverage to 

provide a rough estimate of fouling organisms. It is important to note that not all hull fouling 

organisms are non-native; not all are likely to become invasive; and not all are likely to affect 

listed species and critical habitat. We do not have data to tease out these variables; therefore, our 

estimate is the worst-case scenario of biofouling. 

According to the U.S. Maritime Administration, there are ~60,000 vessel calls at U.S. ports 

annually (http://www.marad.dot.gov). As described above, Sylvester et al. (2011) estimated hull 

fouling propagule pressure at 600,000 invertebrates per vessel. This provides a rough estimate of 

36 billion hull fouling organisms entering waters of the U.S. annually. This estimate does not 

differentiate between native and non-native species and does not account for multiple calls made 

by the same vessel. 

While we are unable to quantitatively estimate how many of these organisms are likely to 

become established in waters of the U.S. (NAS 2011), we used the NEMESIS database to 

quantify the annual number of newly documented hull-fouling ANS, since the first year of the 

previous VGP (2008). It should be noted that this database does not include all ANS that were 

introduced by hull fouling; rather, it represents the number of ANS, introduced by hull fouling, 

which were documented, nationwide. In using this database, we expect considerable 

ascertainment bias, i.e., greater effort is likely to increase the number of ANS detected. Also, 

this number of documented ANS likely underestimates the total number of invasions because 

there are no monitoring programs throughout many of the waters of the U.S., and funding cuts 

are likely to further reduce the number of programs looking for ANS. Still, these data provide a 

qualitative measure of exposure. From 2008 to 2011, the annual mean was 13.5 newly 

documented hull-fouling ANS invasions nationwide (95% CI: 11.3 – 15.7). 

The VGPs require few explicitly mandated anti-fouling/hull husbandry practices or technologies; 

their requirements are not likely to result in substantial changes to biofouling ANS invasion 

rates. We estimate that a minimum of 14 hull-mediated ANS invasions are likely to occur 

nationwide each year the permit is in effect. As described above, we expect this to be a gross

underestimate of ANS invasions. Although not all ANS introductions may result from VGP or 

sVGP-regulated vessels and not all introductions will ultimately overlap with listed resources; 
105

we conclude that there is at least a small likelihood that listed resources would be exposed to 

ANS invasions as a result of hull fouling and hull husbandry of VGP and sVGP vessels. 

Ballast Water

Ballast water is water taken onboard in large volumes to assist with vessel draft, buoyancy, and 

stability. It is taken from coastal port areas and transported with the ship to the next port of call,

where the water may be discharged or exchanged. If a ship is receiving or delivering cargo to a 

number of ports, it may release or take on a portion of ballast water at each port. Large 

commercial vessels (e.g., container ships, bulk carriers, other cargo vessels, tankers, and 

passenger vessels) normally have ballast tanks dedicated to this purpose, and some vessels may 

also ballast empty cargo holds. The discharge volume varies by vessel type, ballast tank capacity, 

and type of deballasting equipment. 

According to the BE, the VGP would authorize discharges from approximately 72,000 vessels; 

many of these vessels utilize ballast water. The sVGP would authorize discharges from 115,000 

to 138,000 vessels; however these vessels (i.e., commercial fishing vessels less than 79 feet, 

passenger vessels, and utility vessels) tend to not utilize ballast water frequently, in high 

volumes, nor do they tend to engage on long international voyages. Further, the BE notes that 

according to the U.S. Coast Guard: vessels less than 100 feet “typically operate in more sheltered 

environments and do not load and discharge ballast. Their stability characteristics generally 

accommodate the amount and type of cargo they carry, precluding the need to use ballast as a 

stability enhancer.”(USCG 2008)

A National Academy of Science study estimates that ~52 billion gallons (196 million metric 

tons) of ballast water are discharged annually (NAS). Ballast water that originated from outside 

of North America (i.e., that was taken on from a foreign source port) accounted for 28.5 percent 

of the total discharge volume, and the remainder came from other ports or locations within the 

U.S. and Canada (NAS).

Vessel class estimates of ballast water discharge volumes reported in the BE are based on 

median ballast water capacity for those vessels that have ballast tanks (USEPA 2011a). The 

median is the middle observation in a dataset or 50th percentile. It a more robust measure of 

central tendency than the mean when the data are not symmetrically distributed around the mean 

(i.e., the data are skewed). However, reporting the median alone does not provide much useful 

information about the distribution of the data such as the direction of skew or range of 

observations, nor does it represent a plausible worst case scenario. FWS used data reported to 

the NOI database to generate a more complete characterization of the distribution of ballast water 

capacity among VGP eligible vessels (Table 5). The distribution of ballast water capacity is 

strongly positively skewed for all vessel service classes, meaning that the majority of the 

observations are below the mathematical mean. The skew is particularly strong for barges, cargo 

carriers and large cruise ships. 
106

Table 5. Vessel service class relative distribution of ballast water capacity reported in the NOI database (all values except 

skew are m3).

Vessel Service Class Number of 

Vessels Reporting 

Ballast Water 

Capacity

Mean Standard 

Deviation

Minimum Median

(50th

Percentile)

75th

Percentile

Maximum Skew

Barge 4692 2,477 57,302 8 447 1,030 3,543,700 54.9

Bulk Cargo and Other 

Carriers

6311 23,950 37,565 9 16,618 30,887 1,567,953 21.4

Commercial Fishing 

Vessel

211 6,691 12,765 12 594 6,775 78,007 2.9

Emergency Vessel 41 3,003 16,211 12 332 468 104,036 5.9

Large Cruise Ship 146 15,527 145,092 19 3,041 4,625 1,756,454 11.8

Large Ferry 44 2,806 8,022 17 387 1,625 51,224 5.0

Medium Cruise Ship 29 2,273 5,845 9 404 1,689 26,744 3.3

Oil or Gas Tanker 3955 32,522 29,951 17 23,473 42,018 662,128 3.6

Passenger 47 5,469 35,332 11 80 213 242,423 6.4

Utility 832 3,550 19,401 8 190 780 255,680 8.4
107

The uptake and discharge of ballast water potentially transports planktonic (i.e., occur in the 

water column) ANS to novel water bodies. Benthic ANS can also be transferred when sediments 

are taken in along with ballast water. Ballasting and deballasting occur through openings in 

vessel hulls, which are usually covered by protective gates that are permeable to viruses, 

bacteria, diatoms, algae, and invertebrate larvae (especially mollusks and crustaceans); however, 

corrosion or the loss of these grates permits larger organisms, including postlarval fish, to be 

ballasted (Wonham et al. 2000). 

On any given day, approximately 7,000 individual species may be “in motion” in ballast tanks 

(Carlton 2001), and there is no evidence that ship age, seasonal timing, or age of ballast water 

affects the abundance of individuals or species in the ballast tanks (Drake and Lodge 2007). 

When species in ballast tanks are transported between water bodies and discharged, they have 

the potential for establishing new, non-indigenous populations that can cause severe economic 

and ecological impacts to waters of the U.S. It is not possible to quantitatively assess the number 

and type of ANS that have the ability to establish a viable population from the 7,000 individual 

species currently being carried in ballast tanks (NAS 2011). 

It is possible, however, to link past ANS invasions to ballast water (NAS 2011). In the 

Laurentian Great Lakes, which are among the best-studied freshwater ecosystems in North

America, 55 – 70% of the 180 ANS invasions are attributed to ballast water release (Ricciardi, 

2006; Kelly et al., 2009; Holeck et al., 2004). For coastal marine ecosystems in western North 

America, 10-50% of over 250 invasions are attributed to ballast water release (Carlton 1979; 

Cohen and Carlton 1995; Ruiz et al. 2011). 

Though the density of organisms in ballast water is just one of many variables that influence the 

probability that an invasive species will successfully establish a population in U.S. waters, there 

is evidence that significantly reducing the density of organisms in ballast water will reduce the 

probability of invasions, when controlling for all other variables (NAS 2011). Thus, establishing 

a benchmark discharge standard to reduce concentrations of coastal organisms below current 

levels is a logical first step.

Under current U.S. laws, regulations, and permitting requirements, existing best management 

practices are required to help reduce the potential impacts of ANS from ballast water discharges. 

These include ballast water exchange8 and saltwater flushing8

9

for certain vessels/voyages. These 

 

8

“Ballast Water Exchange” means to replace the water in a ballast tank using either “Flow through exchange” or “Empty/refill

exchange”. “Flow through exchange” means to flush out “ballast water” by pumping in water from the “mid-ocean” or “coastal

exchange zone” (as applicable) into the bottom of the tank and continuously overflowing the tank from the top until three full

volumes of water has been changed to minimize the number of original organisms remaining in the tank. “Empty/refill exchange”

means to pump out the “ballast water” taken on in ports, estuarine, or territorial waters until the tank is empty, then refilling it

with water from the “mid-ocean” or “coastal exchange zone” (as applicable); when conducting empty/refill exchange,

masters/operators should pump out as close to 100 percent of the “ballast water” as is safe to do so (adapted from 33 C.F.R

151.2025(b) (definition of “exchange”)).

9

“Saltwater flushing” means the addition of “mid-ocean” or “coastal exchange zone” water to empty ballast water tanks; the
108

practices have been shown to offer some protection in mitigating the transfer and potential 

introduction of invasive species. While useful in reducing the presence of potentially invasive 

organisms in ballast water, ballast water exchange is not feasible for all vessels (e.g., vessels that 

cannot voyage offshore), can have variable effectiveness, and in some circumstances may not be 

feasible due to vessel safety concerns (Albert et al. 2010). 

One way to address these limitations associated with ballast water exchange is to require 

treatment of ballast water prior to discharge to meet an established standard for the concentration 

of living organisms. On March 23, 2012, the US Coast Guard published final regulations to

phase in ballast water treatment requirements which became effective on June 21 of that year. 

These regulations established a standard for the allowable concentration of living organisms 

contained in ships’ ballast water discharges. 

Similarly, to reduce the number of ANS in ballast water, EPA has included several requirements 

in the VGP. The following requirements are likely to reduce the exposure of listed species to 

ANS:

 Minimize or avoid ballast water discharge and update in critical habitat

 Ballast water numeric discharge limits (consistent with the Coast Guards 2012 

standards):

 < 10 living organisms/m3ballast water, for organisms greater than or equal to 50 

micrometers

 < 10 living organisms/mL ballast water, for organisms less than 50 micrometers and 

greater than or equal to 10 micrometers

 Vessels may meet the above standards by one of the following management methods

 Onshore treatment of ballast water

 Use of public water supply for ballast water

 No discharge of ballast water

 Ballast water treatment system (with additional testing, calibration, and reporting 

requirements)

The EPA concluded that their VGP numeric effluent limits are likely to result in a “very small 

absolute risk of invasion” (USEPA 2012a). As described in their BE, an estimated 196 million 

m

3

of ballast water is released into U.S. waters annually. Therefore, EPA requirements authorize

an annual discharge of:

 < 1.96 billion living organisms, greater than or equal to 50 micrometers

 < 1.96 trillion living organisms, less than 50 micrometers and greater than or equal to 

10 micrometers

 

mixing of the added water with residual ballast water and sediment through the motion of the vessel; and the discharge of the

mixed water until loss of suction, such that the resulting residual water remaining in the tank has either a salinity greater than or

equal to 30 parts per thousand (ppt) or a salinity concentration equal to the ambient salinity of the location where the uptake of

the added water took place (adapted from 33 C.F.R. 401.30(f)(1)).
109

For the above calculation, we assumed that all released ballast water in waters of the U.S. would 

be subjected to the numeric discharge limits of the VGP; however, we know that some vessels 

are allowed to discharge without meeting numeric limitations. This is a confounding factor 

which may make our methodology result in an underestimate of the numbers of living organisms 

discharged. There are several vessel types that are not subject to the numeric limits of the VGP 

(e.g., vessels covered by the sVGP). On the other hand, we assume that all vessels will discharge 

at the maximum allowable concentration for their full discharge events; a situation which results 

in the overestimation of the actual number of living organisms discharged by these vessels. For 

our estimates, we calculated the annual number of living organisms that EPA authorized to be 

released in ballast water using the VGP numeric effluent limits. Because some vessels would not 

be required to meet numeric treatment limits, the total number of living organisms in ballast 

water that EPA authorizes to be released into waters of the U.S. is likely:

 > 1.96 billion living organisms, greater than or equal to 50 micrometers

 > 1.96 trillion living organisms, less than 50 micrometers and greater than or equal to 

10 micrometers

While we are unable to quantitatively estimate how many of these organisms are likely to 

become established in waters of the U.S. (NAS 2011), we used the NEMESIS database to 

quantify the annual number of newly documented ballast water ANS, since the first year of the 

previous VGP (2008). It should be noted that this database does not include all ANS that were 

introduced by ballast water; rather, it represents the number of ANS, which were documented

nationwide and attributed to ballast water. In using this database, we expect considerable 

ascertainment bias, i.e., greater effort is likely to increase the number of ANS detected. The

number of documented ANS grossly underestimates the total number of invasions because there 

are no monitoring programs throughout many of the waters of the U.S., and funding cuts are 

likely to further reduce the number of programs looking for ANS invasions. Still, this provides a 

qualitative measure of how many ballast water organisms result in ANS invasions. From 2008 to 

2011, the annual mean was 5.75 newly documented ballast water ANS invasions nationwide 

(95% CI: 4.5 – 7.0). 

The numeric standards in the VGP are likely to reduce ballast-water-mediated ANS invasion 

rates; therefore, we expect that the number of documented ANS invasions is likely to be reduced 

over the life of the permit. Equivalent standards are not required in the sVGP. Thus there 

remains a small likelihood that listed resources would be exposed to ANS invasions as a result of 

ballast water discharges authorized by the VGPs. 

Other Vectors

Several other discharges incidental to the normal operation of a vessel serve as potential vectors 

for ANS. These include effluent from chain lockers, seawater cooling systems, and use and 

disposal of live bait. Less is known about these discharges and their potential to serve as ANS 

vectors; however, they are generally considered to be significantly less important than hull 

fouling and ballast water.
110

Chain locker effluent is water that collects in the below-deck storage area during anchor

retrieval. A sump collects the liquids and materials that enter the chain locker and discharges it

overboard or into the bilge. Chain locker effluent may contain marine organisms including ANS. 

The sVGP does not require any actions to minimize ANS transfer in chain locker effluent. To 

minimize the number of ANS in chain locker effluent, EPA has included the following 

requirements in the VGP:

 The anchor chain must be carefully and thoroughly washed down (i.e., more than a 

cursory rinse) as it is being hauled out of the water to remove sediment and marine 

organisms. 

 Chain lockers must be thoroughly cleaned during dry-docking

The surfaces of seawater cooling systems, especially sea chest intakes and seawater piping, can 

support the growth of fouling organisms including ANS. In vessel sea chests, Coutts et al. 

(2003) found typical fouling organisms, the introduced European clam (Corbula gibba), an 

invasive sea-star (Asterias amurensis), several species of small fish, and three introduced Green 

crabs (Carcinus maenas), two of which were ovigerous females capable of releasing viable 

propagules. Coutts and Dodgshun (2007) found that marine growth protection systems 

significantly reduce fouling by sessile and sedentary organisms, but have little influence on the

mobile species within sea-chests. The sVGP does not require any actions to minimize ANS 

transfer in seawater cooling systems. To minimize the spread of ANS through seawater piping, 

EPA has included the following requirements in the VGP:

 Vessel owners/operators must remove fouling organisms from seawater piping on a 

regular basis and dispose of removed substances in accordance with local, state, and 

federal regulations (regular basis is not defined)

 Removed fouling organisms shall not be discharged into waters of the U.S.

Fish hold effluent also has the potential to introduce ANS into receiving waters from fish

waste or water transported from one port to another. To minimize the spread of ANS through 

fish hold effluent, EPA has included the following requirements in the VGP and the sVGP:

 Minimize the discharge of fish hold water and/or ice while in port and at the pier.

 If fish waste is contained in the fish hold effluent, it may not be discharged while in port 

unless a physical separation method is used. 

 The discharge of fish hold effluent (including dirty ice) is prohibited if a shore-based 

discharge facility is available. 

 The discharge of unused bait overboard is prohibited, unless bait was caught in the same 

water body or watershed. 

The fish hold effluent requirements including in the VGPs are stringent, specific, and 

enforceable. They are likely to minimize the exposure of listed resources to ANS transported in 

fish hold effluent. The sVGP does not require any actions to minimize ANS transfer in seawater 

cooling systems or chain locker effluent, although these vessels’ characteristics are typically 

different than on larger vessels and should present lesser risk compared to VGP vessels (e.g., 

there are not typically large chain lockers where sediment and organisms could accumulate). 
111

Furthermore, the VGP is vague on its requirements for the “regular” removal of organisms from 

seawater piping. Thus, it is not clear how or to what extent the VGPs will minimize the risk of 

ANS invasions from seawater cooling systems or chain lockers. Though these vectors are 

responsible for fewer ANS invasions than hull fouling and ballast water, they are regarding as 

ANS “hotspots” and cannot be discounted. Therefore, there is a small likelihood that that listed 

resources will be exposed to ANS invasions as a result of EPA’s authorization of discharges 

from seawater cooling systems and chain lockers. 

Stressors

Established ANS are stressors that have the potential to jeopardize the future existence of 

threatened and endangered species through the following mechanisms: 

 Predation

 Competition

 Food web alterations

 Alteration of the structure or function of ecosystems

 Introgressive hybidization

 Transfer of disease and parasites

 Destruction or modification of critical habitat

These stressors are the mechanisms by which ANS adversely affect native species; they are often 

multifold and interlinked. Here we highlight two examples of the multitude of stressors caused 

by ANS included in EPA’s Biological Evaluation. Introduction of the green crab (Carcinus 

maenus) has been implicated in the destruction of soft-shell clam (Mya arenaria) fisheries in 

New England (Cohen and Carlton, 1995) and the reduction of populations of other commercially

important bivalves including the scallop, Argopecten irradians, and the northern quahog,

Mercenaria mercenaria (Morgan et al. 1980; Walton, unpublished data as cited in Grosholz and

Ruiz, 2002). In Connecticut, weekly rates of crab predation on scallops were as high as 70%

leading Tettlebach (1986) to observe that green crabs were responsible for most observed

mortality in scallops and were a limiting factor in population size. MacPhail et al. (1955)

concluded that the green crab was "one of the worst, if not the worst, clam predators we know."

Their ability to out-compete native species for food resources, high reproductive capacity, and

wide environmental tolerances enable them to fundamentally alter community structure in 

coastal ecosystems. 

Many ANS are filter feeders which, upon reaching high densities, can deplete phytoplankton that 

serve as the diet for zooplankton, juvenile life stages, and planktivorous fish. The Asian clam 

(Potamocorbula amurensis) invasion of the San Francisco Bay is closely correlated to the 

shutdown of the spring phytoplankton bloom in the bay, which usually fuels much of the pelagic

ecosystem (i.e., zooplankton and larval fish). Most of this primary production is transferred to 

the benthic food webs, which are dominated by benthic invertebrates and bottom-feeding fishes 

(Grosholz 2002). The overbite clam (Corbula amurensis) spread throughout the waterways 

surrounding San Francisco Bay within two years of being detected in 1986. The clam accounts 
112

for up to 95 % of the living biomass in some shallow portions of the bay floor. It is believed to 

be a major contributor to the decline of several pelagic fish species in the Sacramento-San 

Joaquin River Delta, including the threatened delta smelt, by reducing the planktonic food base 

of the ecosystem (Takata et al., 2011).

Response Analysis

Here we consider the probable responses of ESA listed species to ANS invasions. We group 

species together into a generalized discussion because of the large number of species potentially 

affected; the mechanisms of impact are similar across very different taxonomic groupings and in 

both estuarine and freshwater systems. We discuss responses to the following ANS-related 

stressors: predation, competition, trophic alteration, ecosystem alteration, disease transmission, 

and habitat modification. We determine whether these responses are likely to reduce an 

individual’s fitness (i.e., survival and reproduction). 

Estuarine Systems

A large number of estuarine systems have been highly invaded by ANS. For example, in San 

Francisco Bay, which hosts threatened and endangered fish, tidal marsh birds, mammals and 

plants, over two hundred ANS have been identified, such as the Chinese mitten crab (Cohen and 

Carlton, 1998). Additionally, non-indigenous microorganisms have become established in many 

estuarine waters. The introduction of nonnative pathogens, such as VHS, which negatively 

impact native organisms through parasite or disease transmission, can be particularly destructive 

to the estuarine ecosystem (USEPA, 2008a).

For coastal marine ecosystems, California and western North America have received the most indepth analyses of aquatic invasions, with over 250 nonindigenous species of invertebrates, algae, 

and microorganisms having become established in tidal (marine and estuarine) waters of 

California alone. Of these, only about 10% are attributed solely to ballast water as a vector, but 

greater than 50% include ballast water as a possible vector among others (NAS, 2011). 

There have also been extensive introductions of nonindigenous mollusks in estuarine ecosystems 

throughout North America since the early 19th century. Thirty species have become established 

on the Pacific Coast, eight on the Atlantic Coast and one on the Gulf Coast. Nineteen of the 30 

Pacific Coast ANS occur in San Francisco Bay alone (Carlton, 1992). There, the Asian clam has 

reached high densities at the expense of native biota (Carlton, 1992). The overbite clam (Corbula 

amurensis) spread throughout the waterways surrounding San Francisco Bay within two years of 

being detected in 1986. The clam accounts for up to 95 % of the living biomass in some shallow 

portions of the bay floor. It is believed to be a major contributor to the decline of several pelagic 

fish species in the Sacramento-San Joaquin River Delta, including the threatened delta smelt, by 

reducing the planktonic food base of the ecosystem (Takata et al., 2011).

Invertebrate ANS have had severe ecological impacts in many regions of the U.S. The elevated 

densities of Asian clams and other introduced invertebrates have become the primary mechanism 

controlling phytoplankton biomass in portions of the San Francisco Bay. This has impacted 
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native zooplankton, shrimp, and fish populations (Cohen and Carlton, 1995). Such breakdowns 

of established ecosystems can result in alterations of physical processes, such as sedimentation 

rates and nutrient cycling. The physical environment may experience elevated erosion rates due 

to burrowing by invertebrate ANS (e.g., isopods, crayfish, and crabs) (Cohen and Carlton, 1995).

There is relatively little research published on ballast water transport of plant species. However, 

it is known that floating and detached seaweeds and seagrasses may be entrained in ballast water 

(NRC, 1996). It is well established that the consequences of nonindigenous aquatic plants have 

been extensive. The introduction of ANS can have deleterious effects on native aquatic plants as 

well as serious implications beyond the aquatic ecosystem level. In the San Francisco Bay 

estuary, more than 20 nonindigenous plant species have been identified (Cohen and Carlton, 

1995). The potential adverse impacts of these species include competitive replacement of native 

cordgrass; altered habitat for wetland plants and animals; altered sediment dynamics; and loss of 

shorebird foraging habitat (USCG, 2012).

Estuarine wetlands have been invaded and adversely affected by animal and plant ANS from 

ballast water and other sources (USEPA, 2004). For example, the Chinese mitten crab, 

potentially introduced via ballast water discharge, has affected native invertebrates and the 

ecological structure of estuarine wetland communities in California. It disrupts fishing operations 

by competing with and preying on native species, damaging native habitats, and reducing 

biodiversity (Cohen and Carlton, 1997). The current species composition of U.S. estuarine plants 

includes many ANS that have become widely established over time. In the waters of Florida 

alone, 23 nonindigenous aquatic plant species have become established (USCG, 2012).

Freshwater Systems

U.S. freshwater ecosystem species have been significantly affected by ANS introductions. For 

example, ANS have become a significant component of the food web in the Great Lakes with 

162 ANS identified by 2001 (NOAA, 2004). Transoceanic shipping activities are attributed with 

55% to 70% of an estimated 56 aquatic ANS invasions recorded in the Great Lakes since 1959 

(Bailey et al., 2011). They assembled data on dates of discovery of shipmediated aquatic ANS 

reported in the Great Lakes after the opening of the modern St. Lawrence Seaway in 1959. Their 

analysis revealed 34 aquatic ship-mediated ANS reported from the Great Lakes after that date. 

The rate of aquatic ANS discovery was relatively linear between 1959 and the mid-1980s, after 

which time it began to increase. The peak number of discoveries occurred in 1992 when six ANS 

were reported, including five parasitic species associated with the Eurasion ruffe; the discovery 

rate begins to decline rapidly after the peak. The authors note that this decline in ANS discovery 

corresponds with two to six-year time lags following the inception of ballast water management 

practices. Since 2000, shipping activities have been responsible for three of eight (37.5%) 

aquatic ANS introductions and no new species have been reported since 2006; this is the first 

time there has been a four-year gap in ship-mediated aquatic ANS discoveries since 1974-1977 

(Bailey et al., 2011).

In the Mississippi River, more than 100 ANS have been identified across at least nine taxonomic 

groups (USGS, 2004). In the lower and middle Columbia River alone, 134 nonindigenous 

species have been identified (USGS, 2009). North America's rivers and stream species are being 
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extirpated five times faster than animals living on land and three times faster than marine 

mammals (American Rivers, 2005). This is due in great measure to the threat posed by ANS to 

such fauna and the ease with which they spread in freshwater ecosystems (USCG, 2012).

Perhaps the best-known example of freshwater invasion is the zebra mussel in the Great Lakes 

and Mississippi River. This mollusk attaches itself to surfaces in such high densities that it can 

clog pipes and foul other important structures, such as boat hulls or buoy bases. Zebra mussels 

also have the capacity to crowd out native mollusk species or interfere with such basic functions 

as respiration, reproduction, feeding, growth, and movement. Zebra mussels are filter feeders and 

can remove algae from the water column that other native species depend on as a food source 

and, therefore, zebra mussels outcompete native (and sometimes endangered) mollusks and other 

filter feeders.

Native mollusk communities have been affected by ANS – one estimate is that another 127 

freshwater mussel species will become extinct in the next 100 years if no conservation efforts are 

initiated (Ricciardi and Rasmussen, 1998; Williams and Neves, 2003). The Eurasian zebra 

mussel and the Asiatic clam, two alien nonunionoid species, have caused significant harm to 

North American unionoids (Lydeard et al., 2004). By attaching to native mussels such as the

northern riffleshell in great numbers, zebra mussels make it difficult for the mussel to move and

feed properly, thereby suffocating and killing the native species (USFWS, 1997). Studies of

zebra mussels on unionids in Great Lakes waterways have confirmed that unionid mortality may

approach 100% when unionids are heavily encrusted with zebra mussels (Schloesser et al.,

1998).

Other non-native species may also impact unionid survival through the reduction or

redistribution of native fishes, of which the larval (glochidia) life-stage is parasitic. Nonnative

fish species such as the Eurasian ruffe (Gymnocephalus cernuus) and round goby (Neogobius

melanostomus) can completely displace native fish, thus causing the functional extirpation of

local unionid populations (USEPA, 2007a). Glochidia of freshwater mussels generally display

varying degrees of host specificity. Closely related mollusks have been shown to use banded 

sculpin, as well as dusky, redline, and spotted darters (Yeager, 1986). Other possible hosts 

include: banded sculpin, greenside darter, logperch, redline darter, snubnose darter, and spotted 

darter (Yeager and Saylor, 1995).

In 2005, a freshwater strain of VHS was discovered in freshwater drum from Lake Ontario, and 

subsequently it was found in numerous freshwater species throughout much of the Great Lakes. 

It has also been found in preserved samples from as far back as 2003. Since 1988 the virus, a 

finfish pathogen, was only known to exist in marine fish off both coasts (USDA, 2006). Genetic 

studies have determined that the strain in the Great Lakes is most closely related to the North 

Atlantic strain (Gagné et al., 2007). Ballast water is a plausible vector; however, there is no way 

to definitivelydetermine how this pathogen arrived in the Great Lakes. (USCG, 2012).

Eurasian watermilfoil (Myriophyllum spicatum) is a stringy and submerged plant that is highly 

invasive and aggressively competes with native plant communities, reducing biodiversity. Dense 

mats of watermilfoil have less value as a food source for waterfowl than the native plants it 
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replaces (Aiken et al., 1979). Although fish may initially experience a favorable edge effect,

overabundant growth of watermilfoil negates any short-term benefits that it may provide fish in

healthy waters, because its high densities cause a lower abundance and diversity of invertebrates

that serve as fish food (Keast, 1984). The growth and aging of the thick watermilfoil vegetation

also degrades water quality and depletes dissolved oxygen levels (Engel, 1995; Honnell et al.,

1992).

The common reed (Phragmites australis) is is another vigorous plant competitor. It can grow up 

to more than four meters tall and form dense monospecific stands. Common reed is native to the 

United States, but more invasive European strains may have been unintentionally introduced in 

ships’ ballast (Saltonstall, 2008). Involuntary transport of Phragmites seeds and rhizome 

fragments by commercial and recreational vessels can promote the spread of this weed. Other 

aquatic nuisance species that pose a similar threat include the purple loosestrife (Lythrum

salicaria) and the yellow iris (Iris pseudacorus). Both taxa can out-compete native plants and

spread through transport of seeds and propagules by vessels.

Once established in a new environment, fish can spread over broad geographic areas. A classic 

example is the Eurasian ruffe (Gymnocephalus cernuus), which was introduced via ballast water 

to the St. Lawrence River in the mid-1980s. Since its introduction, it has spread rapidly through 

rivers, bays, and lakes in the Great Lakes area. Furthermore, the ecological and geographical 

expansion of the ruffe has injured native fish populations (OTA, 1993). Other nonindigenous 

fish, such as the round goby (Neogobius melanostomus), the common carp (Cyprinus carpio), the 

alewife (Alosa pseudoharengus), the white perch (Morone americana), and the sea lamprey 

(Petromyzon marinus) have spread rapidly and caused major environmental and economic 

problems (USCG, 2012).

Competition and predation by introduced non-native species may have been factors that

contributed to the decline of the Rio Grande silvery minnow within its historic range (USFWS,

2007), and their survival continues to be threatened by interactions with non-native fishes

(NatureServe, assessed April 2008). The intentional or accidental introductions and transfers of 

indigenous and non-indigenous minnows, e.g., live minnows from other drainages, may threaten 

wild Rio Grande silvery minnow populations by imposing genetic threats, increasing competition 

for food or habitat, or spreading diseases. It is also possible that rapid increases in abundance of 

other non-indigenous species (e.g., guppy Poecilia reticulata, goldfish Carassius auratus) may 

affect Rio Grande silvery minnow food sources (e.g., diatoms, algae) and/or introduce new 

predators to compete for resources of Rio Grande silvery minnow.

Mechanisms of Impact

ANS threaten the diversity or abundance of native species and the ecological stability of the 

aquatic ecosystems they infest. They can permanently reduce biodiversity by preying on, 

parasitizing, out-competing, causing or carrying diseases, or altering habitats of native species 

(Convention on Biological Diversity, 2005). Marine ANS can change food webs and disrupt 

ecosystem services provided by marine wetland plants (salt marshes, sea grasses). Many of these 

impacts were noted above in the examples of ANS invasions. This section describes specific 

mechanisms by which ANS impact native species.
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An introduced species might become invasive if it can outcompete native species for resources, 

such as nutrients, light, physical space or food. If the introduced species evolved under great 

competition or predation, the new environment may host fewer able competitors, allowing the 

invader to proliferate quickly. For example, zebra mussels are capable of reaching such high 

densities that they crowd out or encrust native mollusk species; furthermore, their filtration rates 

are so high that they outcompete native filter feeders for available phytoplankton.As an 

additional example, a variety of coral species have been introduced into United States waters via 

ballast water discharge and other sources. Nonindigenous coral species can harm native coral 

species by colonizing the native species’ habitat. This is a competition between invasive and 

native species over limited, overlapping resource needs, with the invaders ultimately replacing 

native species within the ecosystem.

Introduction of nonnative pathogens, such as viral hemorrhagic septicemia (VHS), can 

negatively impact native organisms through parasite or disease transmission. VHS is caused by 

the Viral hemorrhagic septicemia virus, a finfish pathogen. It afflicts over 50 species of 

freshwater and marine fish in several parts of the northern hemisphere (Disease Factsheets: Viral 

Hemorrhagic Septicemia. Iowa State University, The Center for Food Security & Public Health. 

(http://www.cfsph.iastate.edu/Factsheets/pdfs/viral_hemorrhagic_septicemia.pdf, accessed June 

15, 2012)). In 2005, a freshwater strain of VHS was discovered in freshwater drum from Lake 

Ontario, and subsequently it was found in numerous freshwater species throughout much of the 

Great Lakes. It has also been found in preserved samples from as far back as 2003. Since 2005, 

massive die-offs have occurred amongst a wide variety of freshwater species in the Great Lakes 

region. As another example, sturgeon species appear to be susceptible to viruses enzootic to the 

west coast of the U.S., and fish introductions could further spread these diseases (NatureServe,

accessed April 2008).

HAB can produce toxic compounds, including brevetoxin, saxitoxin and microcystins. Toxins 

can bioaccumulate in high trophic level marine animals, which can accumulate relatively large 

amounts of the toxin and show symptoms of contamination (Bushaw-Newton and Sellner, 1999). 

The adverse effects of HAB on marine mammals can range from cell and tissue damage to 

organism mortality. Immune system responses have been affected by brevetoxin exposure in the 

endangered Loggerhead sea turtle.

Additional marine mammal species, like the endangered North Atlantic Right Whale, have been 

exposed to neurotoxins by preying on highly contaminated zooplankton (Durbin et al. 2002). 

The summertime habitat of the North Atlantic Right Whale overlaps with seasonal blooms of the 

toxic dinoflagellate Alexandrium fundyense. Foraging right whales will ingest large 

concentrations of contaminated copepods, resulting in affects on respiratory capabilities, feeding 

behavior, and ultimately the reproductive condition of the population (Durbin et al. 2002).

Many of the negative affects of ANS are related to changes in community structure. Species 

invasion causes a breakdown in structure and rapid reorganization (Sanders et al. 2003). ANS 

can exert bottom-up or top-down controls. Many ANS are filter feeders which, upon reaching 

high densities, can deplete phytoplankton that serve as the diet for many native species (native 
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zooplankton, shrimp, and fish populations), including their juvenile life stages. These effects 

may continue through the food web to fish, for example reducing the biomass of planktivorous 

fish.

Invasive species may be an inferior food. An example is the invasive diatom Melosira, which at 

certain times in the year can be the most abundant species of phytoplankton. This diatom grows 

in long chains and is very difficult for zooplankton to graze on; thus the change in composition 

and abundance of zooplankton may also be tied to the increased importance of this diatom. 

Bythotrephes longimanus, the spiny water flea, is another invasive species that may be an 

inferior food for planktivores in the Great Lakes.

Invasive species may be highly effective predators capable of reducing the abundance of various 

life history stages of native species. For example, the endangered Columbia spotted frog is 

particularly susceptible to displacement or predation by introduced species. For example, various 

studies have documented the vulnerability of Columbia spotted frogs to nonnative salmonid and 

Centrarchid (e.g., bass) species (Bull and Marx, 2002; Pilliod and Peterson, 2001; Werner et al., 

1998). Other non-native fishes thought to be potentially important predators of Columbia spotted 

frogs include char and goldfish (Carrasius auratus) (Amphibiaweb.org website, accessed April 

17, 2008). Invasive crayfish and American bullfrogs (R. catesbeiana) might also be aggressive 

predators of various life history stages of spotted frogs, including eggs and tadpoles (Reaser, 

1997).

The effects of introduced species on the listed California Freshwater Shrimp are mainly 

associated with predation. The shrimp is prey for native fish species at all life stages. The 

riparian habitat protects the shrimp from many native species, as do the intermittent pools that 

the shrimp also inhabit. Introduced species are a threat to the populations of S. pacifica

particularly in areas where native fish species are not abundant. These pools sometimes are of 

lesser water quality which protects the shrimp from many native species. However, the nonnative 

fish species, green sunfish (Lepomis cyanellus), is capable of surviving at extreme conditions, 

including high temperatures, low oxygen, and high alkalinities (USFWS, 1998).

Invasive species can affect water quality (negatively or positively) in marine, estuarine, and 

riverine freshwater environments by altering processes such as sedimentation rates and nutrient 

cycling. Introduced non-native algal species from ballast water (as well as other sources) 

combined with nutrient overloading may increase the intensity and frequency of algal blooms. 

An overabundance of algae can degrade water quality upon bacterial decomposition, which 

depletes oxygen levels in an ecosystem. Oxygen depletion can result in “dead zones,” murky 

water, seagrass and coral habitat degradation, and large-scale fish kills (Deegan and Buchsbaum, 

2005).

Breakdowns of established ecosystems can result in alterations of physical habitat. The physical 

environment may experience elevated erosion rates due to burrowing by invertebrate ANS. ANS 

can also alter the environment to favor introductions of additional nonnative species. Simberloff 

and Von Holle (1999) referred to this positive feedback loop as “invasional meltdown.” A recent 

series of invasions by euryhaline organisms from the Black and Caspian seas might be the start 
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of an invasional meltdown in the North American Great Lakes (Rahel, 2002). It seems likely 

that zebra mussels have altered the benthic environment of the Great Lakes so as to facilitate 

invasions by additional exotic species. Zebra mussels have also increased the habitat complexity 

on lake floors, providing crevices in which invertebrates live. This increase in complexity, 

together with the nutrition provided by the waste products of mussel filter-feeding, increases the 

density and diversity of benthic invertebrate communities.

Documented impacts on Listed Species

Some endangered species face threat from the combined impact of ANS introduction and the 

existing environmental circumstances (USCG, 2012). For example, almost 40 native mussel 

species occur in the Mississippi River, some of which are federally listed as threatened or 

endangered (USFWS, 2003). The zebra mussel threatens some of these indigenous species of 

mussel with extinction (USCG, 2012).

ANS have been identified as a contributing factor in the listing as threatened or endangered of 

more than 50% of fish species and 33% of invertebrates, which includes mollusks and 

crustaceans (USCG, 2012). Shortnose sturgeon (Acipenser brevirostrum) are endangered and 

under many threats, amongst them habitat degradation and dredging operations. It is also 

anticipated that rapid increases in abundance of other non-indigenous species (e.g., Asian clams, 

zebra mussels, blue and flathead catfish) in some rivers will affect sturgeon prey and/or 

introduce new predators to compete for resources of shortnose sturgeon (NMFS and USFWS, 

1998).

Over 145 nonnative species have become established in the North American Great Lakes (Mills 

et al., 1993). Especially noteworthy is that since 1985, 70% of the invading species are native to 

fresh and brackish waters of the Ponto-Caspian region (Black, Caspian, and Azov seas) 

(Ricciardi and Maclsaac, 2000). Some of these species have achieved high abundance and now 

play a major role in Great Lakes food webs. Examples include ruffe Gymnocephalus cemuus, 

round goby Neogobius melanostomus, tubenose goby Proterorhinus marmoratus, zebra mussel, 

quagga mussel Dreissena bugensis, and the amphipod Echinogammarus ischnus. Most of the 

invasions resulted from ship ballast water release (Rahel, 2002).

Freshwater mussels in the families Margaritiferidae and Unionidae are worldwide in distribution 

but reach their greatest diversity in North America with 281 species and 16 subspecies (Williams 

et al., 1993). They are the most imperiled freshwater fauna with 12% of the taxa listed as 

probably extinct and 60% considered endangered, threatened, or of special concern (Ricciardi et 

al., 1998). During the twentieth century, the most important source of imperilment was 

destruction of habitat by damming, dredging, and channelization of rivers, especially in the 

southeastern United States (Rahel, 2002).

In the 1990s, a significant new threat was added with the establishment of the zebra mussel that 

smothered the shells of other mollusks and competed with them for food (Nalepa et al., 1996). 

The biological impacts of zebra mussels have the potential to harm native mussels in North 

America by interfering with their feeding, growth, movement, respiration, and reproduction. This 

species has rapidly spread throughout the Great Lakes and the Mississippi River basin, often 
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reaching densities in excess of 3,000 individuals per square meter and extirpating native mussel 

species within 4 to 8 years. Ricciardi et al. (1998) projected that if the current rate (as of 1998) of 

spread continues, the zebra mussel will accelerate the regional extinction rates of North 

American freshwater mussels by ten-fold and will threaten the existence of over 60 endemic 

species in the Mississippi River basin.

Researchers are observing some of these effects as they study interactions between zebra mussels 

and native mussels in the Great Lakes. In one study, biologists found that where zebra mussel 

densities were highest, in Lake St. Clair and in the western basin of Lake Erie, native mussels 

had declined after only two years of zebra mussel colonization (Bensen, 2012) and other studies 

have shown an inverse correlation between zebra mussel biomass and the density of native 

mussels.

Zebra mussels are also believed to negatively impact native fish populations. Among benthicfeeding fish, lake sturgeon (Acipenser fulvescens) are of particular concern. Lake sturgeon are 

threatened or endangered throughout much of their range. This species is native to lakes and 

large rivers in the Atlantic watershed of North America including the Hudson Bay, Laurentian, 

and Gulf of Mexico catchments (Lee et al., 1980). Through much of this range, lake sturgeon 

populations have been reduced from viable populations to threatened or endangered status owing 

to overfishing and habitat destruction (Auer, 1999). Zebra mussels now co-occur with lake 

sturgeon over much of their range, including the Laurentian Great Lakes and portions of the 

Mississippi and Hudson Bay catchments, and may represent a novel threat to lake sturgeon. 

Juvenile sturgeon use sandy and silty habitats extensively during their growth. Invasive zebra 

mussels change the nature of these sandy and silty habitats because they settle on and coat the 

habitat with the shells of living and dead individuals. McCabe et al. (2006) assessed juvenile lake 

sturgeon habitat choice in laboratory experiments, and zebra mussel impact on the foraging

success of juvenile lake sturgeon on three different prey species was measured. Sturgeon avoided 

the zebra-mussel covered habitat more than 90% of the time. This combination of zebra mussel 

avoidance and reduced foraging in the presence of zebra mussels was suggested to be detrimental 

to sturgeon restocking programs utilizing smaller sturgeon in zebra-mussel-infested waterways.

Existing ANS are a persistent problem in U.S. coastal and inland waters. In coastal 

environments, commercial shipping is the most important means of introducing new ANS, and 

unmanaged ballast water discharge and biofouling are the vectors responsible for the 

introduction of the majority of ANS in the U.S. ANS pose several dangers to aquatic ecosystems, 

including outcompeting native species, damaging habitat, changing food webs, and altering the 

chemical and physical aquatic environment. Numerous studies have concluded that the reduced 

discharge of viable organisms capable of establishing a viable population of the organism in U.S. 

waters reduces the risk of invasions. While it is presently not possible to calculate the risk of

ANS invasion associated with specific ANS concentrations in ballast water discharges, EPA 

believes that the two permits (VGP/sVGP) will reduce the propagule pressure substantially 

associated with vessel discharges, which will significantly reduce the risk that new ANS 

introductions pose to listed species.
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The individuals and populations of the aquatic species listed in Table 1 are vulnerable to the 

impacts of ANS through predation, competition, trophic alteration, ecosystem alteration, disease 

transmission, and habitat modification. The aquatic-dependent species are vulnerable to 

ecosystem and habitat alteration especially as it affects the prey base of piscivorous birds and 

mammals. 

Extinction and Endangerment as a Result of ANS Invasions

In our Exposure Analysis, we concluded that threatened and endangered species and their 

designated critical habitat were likely to be exposed to ANS in the following discharges: ballast 

water, hull fouling/underwater husbandry, sea cooling systems, and chain lockers. In our 

Response Analysis, we concluded that listed individuals exposed to ANS invasions are likely to 

experience reduced fitness as a result. Here we ask whether these reductions in fitness are likely 

to reduce the viability of populations and species. We start by reviewing the literature species 

endangerment and extinction as a result of ANS invasions. 

The introduction of non-native species poses one of the greatest threats to biodiversity, second 

only to habitat loss (Wilcove et al. 1998). In the United States, more than 40% of species listed 

under the ESA are threatened by invasive species (Wilcove et al. 1998). The ANS Task Force 

identifies ANS as a major cause of decline of species and a significant impediment to their 

recovery (ANS Task Force website). The detrimental effects of ANS have contributed to 68% of 

North American fish extinctions over the past century, including two Oncorhynchus species 

(Miller et al. 1989). A study by USGS (2012) identified ANS as a contributing factor in the 

listing of more than 50% of fish species and 33% of invertebrate species listed under the ESA. 

Some argue whether invasive species are the primary cause of endangerment or extinction, but it 

is widely agreed that listed species become further imperiled as a result of ANS invasions 

(Clavero & Garcia-Berthou 2005; Gurevitch & Padilla 2004). 

While there are many examples of fresh water species extinctions as a result of ANS, marine 

equivalents are less prevalent in the literature; however this may be a result of underreporting 

and low detection power (Roberts & Hawkins 1999). As terrestrial animals, humans are less 

likely to notice declines and extinctions in the marine environment; furthermore, many marine 

species have yet to be described, and their extinction would go unnoticed. Though we were 

unable to find any examples of marine extinctions caused exclusively by ANS, there are several 

examples where ANS invasions led to the decline of native species. For example, egg predation 

by an introduced starfish (Asterias amurensis) led to the decline of the critically endangered 

spotted handfish (Brachionichthys hirsutus) in Australia. In California, the introduced Japanese 

mud snail (Batillaria attramentaria) outcompetes the native snail (Cerithidea californica) and is 

predicted to eventually replace the native species (Byers 2000). Molecular analyses of museum 

specimens suggest that alien mussels (Mytilus galloprovincialis) displaced the native mussel (M. 

trossulus) in southern California, some time in the last century (Geller 1999).

We present statistics on ANS-related extinctions and endangerments to illustrate that ANS 

invasions have reduced the viability of numerous populations and species and are likely to do so 

in the future. As described above, ANS invasions affect species by predation, competition for 
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habitat or prey, reduction of the prey base, habitat alteration, disease transmission, and 

ecosystem restructuring. These types of impacts rarely affect one or a few individuals; they are 

more likely to affect many individuals or an entire population. For example, we described 

several diseases that ANS are likely to transmit to listed fish, abalone, corals, and seagrass. 

These infectious diseases would first affect exposed individuals, but they would quickly spread 

through these small immunologically naïve populations, which often exhibit low genetic 

diversity a reduced ability to mount an effective immune response. Ultimately, such ANStransmitted diseases would reduce the viability of the population, and the loss of populations 

would reduce the viability of species. Similarly, we described above how ANS are likely to 

reduce the survival of salmonids and Pacific eulachon through competition, predation, disease 

transmission, habitat loss, and ecosystem restructuring. Again, these mechanisms are likely to 

affect many individuals, reducing the viability of populations, and thus the species (or listed 

DPS). A significant loss in the abundance of salmonids and Pacific eulachon is likely to reduce 

the fitness of many Cook Inlet beluga whales and southern resident killer whales that depend on 

these species as their primary prey. These DPSs have already experienced severe population 

declines, in part as a result of reduction in their prey base. Additional reductions would reduce 

the viability of these species. In conclusion, ANS invasions, which are likely to occur as a result 

of the discharges authorized by EPA, are likely to result in reduced population and species 

viability of listed fish, marine mammal, invertebrate, and plant species.

Critical Habitat

Invasive species are likely to adversely affect water quality in marine, estuarine, and riverine 

freshwater environments by altering processes such as sedimentation rates and nutrient cycling. 

Introduced non-native algal species from ballast water (as well as other sources) combined with 

nutrient overloading may increase the intensity and frequency of algal blooms. An 

overabundance of algae can degrade water quality upon bacterial decomposition, which

depletes oxygen levels in an ecosystem. Oxygen depletion can result in “dead zones,” murky

water, seagrass and coral habitat degradation, and large-scale fish kills (Deegan and Buchsbaum,

2005, BE). Therefore, successful ANS invasions are likely to adversely affect the critical habitat 

of listed species, especially when ANS threaten the prey that has been designated as a primary 

constituent element, i.e., physical or biological features that are essential to the conservation of a 

given species, including: space for individual and population growth and for normal behavior; 

food, water, air, light, minerals, or other nutritional or physiological requirements; cover or 

shelter; sites for breeding, reproduction, and rearing of offspring; and habitats that are protected 

from disturbance or are representative of the historical geographical and ecological distribution 

of a species (50 CFR 424.12(b)). 

For the species listed in Table 1 with designated critical habitat, the primary constituent 

elements, or the physical and biological features essential to species conservation, include many 

habitat characteristics. These include elements or features such as areas for breeding, feeding, 

and sheltering, sufficient prey to support normal individual and population growth, physical 

structure of habitat such as substrate characteristics for egg laying, and presence of specific plant 

species.
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As described above, ANS invasions are likely to reduce the availability of prey and thus 

adversely affect some critical habitats. In addition, invasive plant species are likely to adversely 

affect the critical habitat of endangered species by altering the physical structure and species 

composition of critical habitat. Two introduced plants, purple loosestrife (Lythrum salicaria) 

and Eurasian water milfoil (Myriophyllum spicatum), have displaced native wetlands vegetation 

in many parts of the United States. The rapidly decomposing purple loosestrife produces a 

seasonal shift in local nutrient availability. Eurasian water milfoil forms dense mats of 

vegetation that can depress dissolved oxygen concentrations (Cronin et al. 2006; Unmuth et al. 

2000). These invasive plants, which were likely introduced via shipping, are likely to change the 

structure and function of the ecosystem (Sanderson et al. 2009). 

In conclusion, there is a likelihood that listed resources will be exposed to ANS as a result of 

discharges authorized by EPA’s VGPs. If exposed, individuals are likely to experience 

reductions in fitness. If the invasion is sufficiently large in extent and magnitude, population 

viability and species conservation status is likely to be diminished. In addition, exposure to ANS 

is likely to adversely affect designated critical habitat. 

Traditional Pollutants

Exposure Analysis

The constituents of the discharges authorized by the proposed VGPs are mixtures of pollutants 

capable of producing adverse effects to endangered or threatened species and their critical 

habitat. This section first reviews the vessel discharges authorized by the VGPs in terms of 

discharge volumes and constituent mixtures then summarizes pollutant loads and EPA’s modeled 

estimates of final harbor concentrations. Pollutant load, expressed in terms of mass per day, is 

the net amount of pollutant discharged based on discharge volume and pollutant concentration. 

Many pollutants are found in more than one discharge source, with some sources being more 

significant pollutant load contributors than others by virtue of their greater volume or constituent 

concentrations. 

The vessels discharge information used by EPA in its BE were taken from the Report to 

Congress and other sources such as the Uniform National Discharge Standards for Vessels of the 

Armed Services Technical Development document (USDOD/USEPA 1999) and several reports 

generated by EPA in support of the VGPs (USEPA 2008, 2011b, a). The BE relied heavily on 

discharge volume and constituents data in the Report to Congress: Study of Discharges 

Incidental to Normal Operation of Commercial Fishing Vessels and Other Non--Recreational 

Vessels Less than 79 Feet (EPA 2010). It is important to note this data represents opportunistic 

sampling from a total of 61 vessels intended to represent a population of the greater than 90,000 
123

non-recreational small vessels10 tracked in the MISLE database. Not all discharge types were 

sampled each vessel. The same constituents were not analyzed for in all discharges due to 

sample volume constraints or decisions made regarding whether or not the discharge would 

contain a given analyte or analyte group (e.g. nonylphenols in engine exhaust). In a few cases, 

target analytes differed for the same discharge type within vessel classes, for example, additional 

analytes were included for samples when an unexpected analyte source was observed. These 

data properties limit systematic characterization of discharges within and among vessel service 

types. Taken with the very limited number of vessels examined, inferences made based on these 

data regarding discharges from other vessels, particularly the larger vessels covered by the VGP,

are accompanied by high levels of uncertainty. After describing exposure data used in the BE 

we provide a summary of the uncertainties acknowledged by EPA for estimates made within this 

vessel population and for extrapolating to larger vessels authorized to discharge under the VGPs. 

This Exposure Analysis section is followed by the Response Analysis which describes the 

potential effects of discharge constituents and the consequences of exposing our species to those 

constituents.

Discharges Authorized by the VGP and sVGP

EPA identified 27 specific effluent streams as discharges eligible for coverage under the VGP 

while the sVGP authorizes discharges or discharge creating activities conducted in the normal 

operation of vessels. The VGP and sVGP authorized discharges are cross walked in Table 6. 

Several of discharges authorized by the VGP, such as sonar dome and elevator pit effluent, are 

specific to larger vessels and are therefore not included in the sVGP. Many sVGP discharge 

activities are either identical to VGP-authorized discharges (e.g., ballast water) or are broader 

discharge classifications. For example, the “Engine and Oil Control” discharge activity covered 

by the sVGP conceptually includes the “Bilgewater/Oily Water Separator Effluent” and 

“Controllable Pitch Propeller and Thruster Hydraulic Fluid and Other Oil-to-Sea Interfaces...” 

discharges authorized under the VGP. 

Table 6. Discharge classes authorized under the Vessels General Permit and small vessels 

general permit.

VGP Authorized Discharge sVGP Authorized Discharge

Anti-Fouling Hull Coatings/Hull Coating Leachate 

Underwater Ship Husbandry Discharges Vessel Hull Maintenance 

Cathodic Protection 

Ballast Water Ballast Water

Bilgewater/Oily Water Separator Effluent 

Engine and Oil Control Boat Engine Wet Exhaust 

 

10 Small recreational vessels far outnumber small non-recreational vessels, but are covered under the Clean Boating Act and are 

not subject to the sVGP.
124

Controllable Pitch Propeller and Thruster 

Hydraulic Fluid and Other Oil-to-Sea Interfaces 

Including Lubrication Discharges from Paddle 

Wheel Propulsion, Stern Tubes, Thruster Bearings, 

Stabilizers, Rudder Bearings, Azimuth Thrusters, 

Propulsion Pod Lubrication, and Wire Rope and 

Mechanical Equipment Subject to Immersion. 

Motor Gasoline and Compensating Discharge Fuel Management 

Fish Hold Effluent Fish Hold Effluent

Boiler/Economizer Blowdown 

These discharges are not typically associated with 

sVGP eligible vessels

Welldeck Discharges

Refrigeration and Air Condensate Discharge 

Exhaust Gas Scrubber Washwater Discharge 

Freshwater Layup

Gas Turbine Washwater 

Non-Oily Machinery Wastewater 

Seawater Piping Biofouling Prevention 

Seawater Cooling Overboard Discharge

Sonar Dome Discharge

Aqueous Film Forming Foam (AFFF)

Elevator Pit Effluent 

Graywater Mixed with Sewage 

Distillation and Reverse Osmosis Brine

Firemain Systems

Graywater Graywater 

Not an explicit category in the VGP Solid and Liquid Waste Management 

Deck Washdown and Runoff and Above Water 

Line Hull Cleaning 

Deck Washdown and Runoff and Above Water 

Line Hull Cleaning 

The decision process EPA followed in its selection of which discharges to analyze for risk in the 

BE was based on the relative number of vessels releasing the discharge, the volume of the 

discharge, and the potential risk posed by the concentration and constituents of that discharge. 

The following sections briefly describes each discharge selected for evaluation in the BE. This is 

followed with a table summarizing those discharges not evaluated in the BE and EPAs decision 

process for each. 

Anti-Fouling Leachate from Anti-Fouling Hull Coatings. Anti-fouling coatings are applied to 

the vessel hull and seawater piping systems to limit attachment of aquatic species. Virtually all 

vessels that are permanently kept in saltwater use anti-fouling coatings. Biocides such as copper 

contained in anti-fouling coatings continuously leach into surrounding waters. EPA analyzed the 

risk of this discharge in its BE due to the high number of vessels discharging, the large volume 

and frequency of discharges, along with the potentially high risk posed by the concentration and 
125

types of pollutant discharged. In its supplement to the BE, EPA estimates pollutant loadings 

from antifouling coatings (Table 7).

Table 7. Copper loading AFC of various vessel service classes

Vessel Type Average 

Vessel 

Length (ft) 

Estimated 

Vessel 

Draft (ft) 

Wetted 

Hull 

Area 

(ft2) 

Average 

Copper 

Leaching 

Rate 

(μg/cm2/day)j

Estimated 

CopperLeaching 

Rate 

(lbs/day/vessel) 

Barges 175a 10d 3,500 10.5 0.075n 

Oil and Gas Tankers 797b 75e 

120,257 

10.5 2.6 

Large Commercial Fishing 

Vessels 

250a 17f 8,500 10.5 0.18 

Large Cruise Ships 995c 28g 55,706 10.5 1.2 

Large Ferries 200a 15.5h 6,200 10.5 0.13 

Medium Cruise Ships 325a 15.5h 10,075 10.5 0.22 

Bulk Cargo and Other Carriers 663b 38i 50,355 10.5 1.1 

Small Commercial Fishing 

Vessels 

33k 4l 264 10.5 0.0057 

Passenger Vessels (tour boats, 

water taxis, etc.) 

45k 4m 360 10.5 0.0077 

Utility Vessels (tug boats, offshore vessels, etc.) 

50k 4m 400 10.5 0.0086

a) Average length estimated from Figure 1.3 of USEPA’s Report to Congress (USEPA, 2010). 

b) Average length for oil tankers and bulk cargo carriers from Chamber of Shipping of America, MSD Survey, 2010. 

c) Average cruise ship length calculated from the following cruise ships: Carnival Freedom, Disy Magic, Golden Princess 

and Freedom of the Sea. 

d) Estimated draft for barges based on Barge Number 4727, Ingram, Nashville, TN. 

e) Estimated draft for oil and gas tankers based on a Suezmax tanker, 

http://people.hofstra.edu/geotrans/eng/ch5en/appl5en/tankers.html 

f) Estimated draft for large commercial fishing boats based on trawlers, http://maritimesales.com/fishing%20vessels.htm 

g) Estimated draft for large cruise ships based on Royal Caribbean Freedom of the Seas. 

h) Estimated draft for large ferries and medium cruise ships based on Washington State Department of Transportation’s 

M/V Sealth, passenger/auto ferry. 

i) Estimated draft for bulk cargo vessels based on Golden Pegasus Navigation S.A High Glow vessel. 

j) Average copper leaching rate from USEPA Underwater Ship Husbandry Discharges, (USEPA, 2011b). 

k) Average length estimated from Figure 1.5 of USEPA’s Report to Congress (USEPA, 2010). 

l) Estimated draft for small commercial fishing boats 30 to 40 feet in length, 

http://pacificboatbrokers.com/fishing/licvess.asp. 

m) Estimated draft for various passenger and utility vessels, http://www.taxi-boat.com/, http://commercial.apolloduck.com/, 

http://allmandboats.com/. 

n) Per EPA’s Notice of Intent database, very few barges use anti-fouling coatings. EPA assumes these barges are engaged 

in coastwise trade of bulk cargo. 

Bilgewater. Bilgewater is generated by all vessels and consists of water and other residue that 

accumulates in a compartment of the vessel’s hull. The source of bilgewater is typically drainage 

from interior machinery, engine rooms, and from deck drainage. EPA analyzed the risk of this 
126

discharge in its BE due to the high number of vessels discharging, the large volume and 

frequency of discharges, along with the potentially high risk posed by the concentration and 

types of pollutant discharged.

The amount of bilgewater generated by a vessel varies based on vessel size, age, and the amount 

below-deck mechanical systems; discharges typically occur several times per week (Table 8). 

Cruise ship bilgewater volumes are estimated at 25,000 gallons per week (3,570 gal/day) 

(USEPA 2008). Bilgewater discharges from fishing vessels are estimated to range from a few 

gallons per day up to 750 gallons/day (USEPA 2010). Bilgewater water discharges rates for tour 

boats are approximately 11 gallons/day (0.04 m3/day) and for water taxis are approximately 34 

gallons/day (0.13 m3/day). Tow and salvage boats discharge approximately 37 gallons/day

(0.139 m3/day) of bilgewater (USEPA 2010). To estimate bilgewater flow rates for medium 

cruise ships, large ferries, barges, cargo/bulk carriers, and oil tankers, EPA compared the vessel 

gross tons (see Table 3-1) to large cruise ships and multiplied by the bilgewater generation rate 

for large cruise ships. The example below shows how daily bilgewater discharge was estimated 

for cargo/bulk carriers using information for large cruise ships.

Example: 

15,939 gross tons (cargo/bulk carrier)/53,526 gross tons (large cruise ship) x 3,570 g/day = 1,063 g/day

Table 8. Estimated Bilgewater Discharge Rates used in EPAs BE Analyses.

Vessel Type Estimated Bilgewater Discharge 

Rates

(m3/day) (gallons/day) 

Barges 0.18 47 

Cargo/Bulk Carriers 4.0 1,063 

Commercial Fishing 1.4 375 

Large Cruise Ships 13.5 3,570 

Medium Cruise Ships 2.0 305 

Large Ferries 2.0 97 

Oil and Gas Tankers 6.3 1,661 

Passenger Vessels (e.g., water taxis, tour 

boats) 

0.08 22 

Utility Boats (tugs and tow boats) 0.14 37 

EPA estimated concentrations of bilgewater pollutants based on data for vessels examined in the 

Report to Congress. A total of eight bilgewater samples were collected from seven vessels with 

a total of 128 analytes detected. The vessels sampled included two fishing vessels, two 

tow/salvage vessels, a tour boat and two water taxis. Contaminants of concern in bilgewater 

identified by EPA are listed in Table 9 and include conventional pollutants, nutrients, metals and 

volatile/semivolatile organic chemicals (sVOCs/VOCs). Table 9 includes additional information 
127

for these analytes from the Report to Congress, which provides details on the detection 

frequency and distribution of all analytes detected in bilge water. 

Table 9. Estimated Bilgewater Pollutant Concentrations used in EPAs Biological 

Evaluation

Pollutant

Point 

Estimate Used 

in BE

Detection 

frequency Mean (range) 50th/75th/90thPercentilesb

Nutrients and Conventional Pollutants

Ammonia Nitrogen

(mg/L) 1.7 4/5 1.7 (nd-7.6) 0.24/4/7.6

Total Phosphorous

(mg/L) 3

5/5 3 (0.084-13) 0.47/7.1/13

Total Residual Chlorine

(TRC, μg/L)

0.077 3/7 0.077 (nda

-0.16) ncc/0.13/0.16

Total Suspended Solids

(TSS, mg/L)

39 7/7 39 (3.7-88) 38/71/88

Biochemical Oxygen 

Demand (BOD, mg/L)

190 7/7 190 (2-770) 14/330/770

Hexane Extractable Oil 

and Grease (HEM, mg/L)

9.3 7/7 9.3 (1.1-44) 5.2/7/44

Silica Gel TreatedHexane Extractable Oil 

and Grease (SGT-HEM, 

mg/L)

4.4 7/7 4.4 (1.1-18) 2.4/3.5/18

Metals

Aluminum (total, μg/L)

370 7/7 370 (26-940) 330/640/940

Cadmium (dissolved, 

μg/L)

1.9 1/7 1.9 (nd-10) nc/nc/10

Chromium (dissolved, 

μg/L)

12 5/7 12 (nd-56) 1.6/17/56

Copper (dissolved, μg/L)

100 7/7 100 (6.6-350) 56/120/350

Nickel (dissolved, μg/L)

9.2 6/7 9.2 (nd-15) 8.8/14/15

Zinc (dissolved, μg/L)

130 7/7 130 (53-250) 100/190/250

sVOCs and VOCs

2,4,6-Trichlorophenol 

(μg/L)

7

1/7 7 (nd-24) nc/nc/24

Benzene (μg/L)

61 4/7 61 (nd-410) 0.1/1.3/410

Bis (2-ethylhexyl)-

phthalate (μg/L)

15 4/7 15 (nd-71) 1.4/21/71

Trichloroethene (μg/L)

2.6 1/7 2.6 (nd-0.3) nc/nc/0.3

a

Nondetect (censored) concentrations were replaced with 1⁄2 of the reporting limit for calculating average 

concentrations. 

b Percentiles are the concentrations of each analyte below which at least that percentage of the values fall. 
128

So the 75th percentile is the concentration below which at least 75% of the observations were found.

c

Distribution statistics were only calculated when analytes were detected at a sufficient frequency.

Deck Washdown. Deck washdown occurs from all vessels as a result of deck cleaning. 

Constituents in the discharge can include detergent, soap, deck surface components (e.g., rust, 

paint chips) and anything dropped, spilled, dripped, or scattered onto the deck surface. Deck 

washdown volumes vary widely and are highly dependent on a vessel’s purpose, service, and 

practices. For example, since aesthetics are important to the industry, deck washdowns may be 

performed more frequently on cruise ships than other types of vessels. EPA analyzed the risk of 

this discharge in its BE due to the high number of vessels discharging, the large volume and 

frequency of discharges, along with the potentially high risk posed by the concentration and 

types of pollutant discharged.

EPA used information for commercial fishing vessels, passenger vessels and utility boats to 

estimate deck washdown volumes (USEPA 2010) for barges, cargo/bulk carriers, and oil and gas 

tankers (Table 10). EPA estimated the deck washdown volumes by comparing vessel gross tons 

for these vessels with the gross tons of a typical utility vessel. EPA estimated utility vessels are 

80 gross tons based on 50% of the utility vessels being approximately 65 feet long (USEPA 

2010). For medium and large cruise ships and large ferries, EPA estimated deck washdown 

volumes by comparing vessel gross tons for these vessels with that of a typical passenger vessel. 

EPA estimated passenger vessels are 35 gross tons based on 50% of passenger vessels being 45 

feet long (USEPA 2010). The example below shows how EPA used the vessel gross tons and 

deck washdown discharge volume for passenger vessels to estimate the deck washdown flow for 

large ferries.

Example:

1,451 gross tons (large ferry)/35 gross tons (passenger vessel) x 27 g/day = 1,083 g/day

Table 10. Estimated Deck Washdown Discharge Rates used in EPAs BE Analysis.

Vessel Type Estimated Deck Washdown 

Discharge Rate

m

3

/day gallons/day

Barges 0.88 232 

Cargo/Bulk Carriers 19.9 5,259 

Commercial Fishing (average shrimper, trawler 

and troller) 

0.39 103 

Large Cruise Ships 152.9 40,396 

Medium Cruise Ships 13.1 3,461 

Large Ferries 4.1 1,083 

Oil and Gas Tankers 31.1 8,216 
129

Passenger Vessels (average water taxi, tour 

boat)

0.10 27 

Utility Boats (average fire boat, supply boat, tow 

boat and tug boat)

0.05 14

EPA estimated concentrations of deckwash pollutants based on data for the vessel types 

examined in the Report to Congress (Table 11). Deck washwater was collected from a total of 

32 vessels: 11 fishing vessels, nine tugboats, six tow/salvage vessels, two tour boats, a water taxi, a 

fire boat, a supply boat, and a recreational boat. A total of 88 analytes were detected in deckwass 

samples. Table 11 includes the point estimates used in EPAs BE plus additional information for 

these analytes from the Report to Congress, which provides details on the detection frequency 

and distribution of all analytes detected.

Table 11. Estimated Deckwash Pollutant Concentrations used in EPAs Biological 

Evaluation.

Pollutant

Point 

Estimate 

Used in BE

Detection 

frequency Mean (range) 50th/75th/90thPercentilesb

Total Phosphorus (mg/L) 1.7 31/31 1.7 (0.06-22) 0.79/1.6/2.9

Total Residual Chlorine (mg/L) 0.12 7/31 0.12 (nda-0.8) ncc/nc/0.37

Total Suspended Solids (TSS, 

mg/L) 170 32/32 170 (27-530) 120/250/470

Biochemical Oxygen Demand 

(BOD, mg/L) 110 30/32 110 (nd-830) 56/92/370

Hexane Extractable Material 

(HEM, mg/L) 14 (130) 26/29 14 (nd-130) 2.8/12/39

Silica Gel Treated HEM (SGTHEM, mg/L) 7.0 (84) 22/29 7 (nd-84) 1.7/3.8/13

Aluminum, Total (μg/L) 3400 30/31 3400 (nd13000) 1900/4700/8300

Cadmium, Dissolved (μg/L) 1.3 2/31 1.3 (nd-22) nc/nc/nc

Copper, Dissolved (μg/L) 42 29/31 42 (nd-200) 23/59/120

Lead, Dissolved (μg/L) 615/31 6 (nd-54) nc/4.7/19

Zinc (dissolved, μg/L) () 260 31/31 260 (16-1200) 120/430/620
130

Bis (2-ethylhexyl) phthalate 

(μg/L) 13 1/2 4.7 (nd-6.7) 6.7/6.7/6.7

Bromodichloromethane (μg/L) 4.7 1/2 13 (nd-1.2) 1.2/1.2/1.2

Dibromochloromethane (μg/L) 13 1/2 13 (nd-0.7) 0.7/0.7/0.7

a

Nondetect (censored) concentrations were replaced with 1⁄2 of the reporting limit for calculating average 

concentrations. 

b Percentiles are the concentrations of each analyte below which at least that percentage of the values fall. 

So the 75th percentile is the concentration below which at least 75% of the observations were found.

c

Distribution statistics were only calculated when analytes were detected at a sufficient frequency.

Engine Wet Exhaust Effluent. Engine wet exhaust effluent is generated when gasoline or 

diesel engine cooling water is injected into the engine exhaust. The engine cooling water 

decreases the exhaust temperature, reduces engine noise and reduces exhaust emissions. Engine 

wet exhaust discharge rates can range from 5 to 10 gallons per minute for electrical generators to 

more than 100 gallons per minute on larger diesel engines operating at high inputs. Most 

passenger vessels, a large number of fishing vessels, and utility vessels use engines that generate 

wet engine exhaust. Large commercial vessels occasionally operate small auxiliary craft that 

discharge engine wet exhaust (e.g., life boats on cruise ships); however, discharge volumes for 

these vessels are negligible. EPA analyzed the risk of this discharge in its BE due to the high 

number of vessels discharging, the large volume and frequency of discharges, along with the 

potentially high risk posed by the concentration and types of pollutant discharged.

Large engines, like those found on VGP eligible vessels (e.g., large ferries, medium and large 

cruise ships, tankers and cargo/bulk container ships) use dry engine exhaust systems and 

therefore do not generate engine wet exhaust effluent. Barges do not have engines and therefore 

do not generate engine wet exhaust effluent. Estimated volume of wet engine exhaust from the 

EPA report to congress were directly applied to EPA’s BE (EPA 2010a).

Table 12. Estimated Propulsion and Generator Engine Wet Exhaust Discharge Rates used 

in EPAs Analysis.

Vessel Type Estimated 

Propulsion Engine 

Wet Exhaust 

Discharge Rate

Estimated 

Generator Engine 

Wet Exhaust 

Discharge Rate

m3/day gallons/day m3/day gallons/day

Commercial Fishinga 15.8 4,161 1.41 372 

Passenger Vessels (e.g., water taxis, tour 

boats)b 

41 10,832 6.45 1,704 

Utility Boats (fire boat, tugs)c 36.3 9,590 1.80 475 

EPA estimated concentrations of engine wet exhaust pollutants based on data from the Report to 
131

Congress (Table 13). A total of 90 analytes were detected. EPA collected engine cooling water 

discharge samples from a variety of vessel classes with different engine types. Two of the sampled 

vessels are recreational vessels and are not study vessels. These vessels and four of the six sampled 

tow/salvage vessels (those with outboard propulsion engines) were manufactured for pleasure. EPA 

sampled engine effluent from these vessels because all of the sampled engines can be installed on 

either recreational or nonrecreational vessels and are representative of engines on study vessels. 

Contaminants of concern include copper and volatile/semivolatile organic chemicals 

(sVOCs/VOCs). Table 13 includes additional information for these analytes from the Report to 

Congress, which provides details on the detection frequency and distribution of all analytes 

detected [put RtC data in an appendix?]. 

Table 13. Estimated Engine Wet Exhaust Pollutant Concentrations used in EPAs 

Biological Evaluation.

Pollutant

Point 

Estimate 

Used in 

BE

Detection 

frequency

Mean 

(range)

50th/75th/90th

Percentilesb

Copper, Dissolved (μg/L) 16 12/13 16 (nd-53) 6.6/23/51

Benzene (μg/L) 12 9/12 12 (nd-120) 2.3/5.4/84

Benzo (a)anthracene (μg/L) 3.3 1/12 3.3 (nd-18) nc/nc/13

Benzo (a)pyrene (μg/L) 3.2 1/12 3.2 (nd-16) nc/nc/11

Benzo (b)fluoranthene 

(μg/L) 2.8 1/12 2.8 (nd-11) nc/nc/7.8

Benzo (k)fluoranthene 

(μg/L) 3.1 1/12 3.1 (nd-15) nc/nc/11

Chrysene (μg/L) 1.7 1/12 3.3 (nd-18) nc/nc/12

Indeno (1,2,3-cd) pyrene 

(μg/L) 3.3 1/12 2.5 (nd-8) nc/nc/5.6

a

Nondetect (censored) concentrations were replaced with 1⁄2 of the reporting limit for 

calculating average concentrations.

b Percentiles are the concentrations of each analyte below which at least that percentage of 

the values fall. So the 75th percentile is the concentration below which at least 75% of the 

observations were found.

c

Distribution statistics were only calculated when analytes were detected at a sufficient 

frequency.

Exhaust Gas Scrubber Washwater Effluent. Exhaust gas scrubber washwater discharge 

occurs as a result of cleaning the exhaust gas system on marine diesel engines. The washwater 

discharge can be highly acidic, and can also contain traces of oil, polycyclic aromatic 

hydrocarbons (PAHs), heavy metals and nitrogen. Washwater volumes of 2.8 million gallons per 

day are estimated from a 10 MWh engine. While EPA anticipates very low numbers of vessels 

will potentially be releasing this discharge, the risk of this discharge was analyzed in the BE due 

to the very large volume and frequency of discharges, along with the potentially high risk posed 

by the concentration and types of pollutant discharged.
132

Exhaust gas scrubbers would be used on large vessels such as oil and gas tankers, cargo/bulk 

carriers, large ferries and medium and large cruise ships burning high-sulfur bunker oil (USEPA 

2011c). The exhaust gas scrubbers remove sulfur dioxide generated by the vessel engines during 

combustion of the bunker oil. Exhaust gas scrubber systems using seawater typically generate 45 

m3 (11,900 gallons) of washwater per megawatt-hour (MWh) for scrubbing (MEPC 2008). 

Closed freshwater exhaust gas scrubber systems have much smaller discharge rates than seawater 

scrubbers. Freshwater closed loop scrubbers generate 0.1 to 0.3 m3/MWh (26 to 79 

gallons/MWh) of scrubber washwater (MEPC 2008). To estimate exhaust gas scrubber 

washwater flows for vessels like tankers, cargo/bulk carriers, ferries and cruise ships, EPA used 

information on the engine sizes for each type of vessel. Table 14 shows the range of engine sizes 

by vessel type and the estimated seawater and freshwater exhaust gas scrubber washwater flow 

rates based on engine size. The size of the propulsion engines for large cruise ships and large 

ferries was obtained from EPA’s Technical Development Document for Exhaust Gas Scrubber 

Washwater Effluent (USEPA 2011c). EPA assumed that the power requirements for propulsion 

engines on large ferries are similar to those for medium cruise ships. For oil and gas tankers and 

cargo/bulk carriers, EPA used information for the 80 MW (109,000 HP) engine onboard the 

Emma Maersk large container ship (Technology 2011). EPA assumed that for smaller vessels 

such as tour boats, water taxis, fishing boats and tug boats using low sulfur fuels will be a less 

expensive compliance alternative than installing and operating exhaust gas scrubbers; therefore, 

exhaust gas scrubber washwater flows for these vessel types were not estimated.

Table 14. Estimated Exhaust Gas Scrubber Washwater Discharge Rates used in EPAs 

Analysis

Vessel Type Average 

Propulsion 

Power (MW)

Estimated Saltwater 

Exhaust Gas Scrubber 

Washwater Discharge Rate

Estimated Freshwater 

Exhaust Gas Scrubber 

Washwater Discharge Rate

m3/hr gallons/hr m3/hr gallons/hr

Cargo/Bulk 

Carriersaa 

80 3,600 951,000 16 4,227 

Large Cruise 

Shipsb 

45 2,025 535,000 9 2,377 

Medium Cruise 

Shipsc 

4.8 216 57,000 1 264 

Large Ferriesc 4.8 216 57,000 1 264 

Oil and Gas 

Tankersa 

80 3,600 951,000 16 4,227

EPA estimated concentrations of exhaust gas scrubber washwater pollutants based on data from 

the Zaandam Scrubber Trial ((KRYSTALLON 2010, USEPA 2011c)Table 15). Data provided 

in the trial report were point values and did not include details on analytical observations.
133

Table 15. Estimated Exhaust Gas Scrubber Washwater Pollutant Concentrations used in 

EPAs Biological Evaluation.

Pollutant Point 

Estimate 

used in 

BE (μg/L)

Arsenic (dissolved) 81

Arsenic (total) 81

Copper (dissolved) 15

Nickel (dissolved) 12

Selenium (dissolved) 94

Selenium (total) 100

Benzo (a)-anthracene 0.262

Benzo (a)-pyrene 0.136

Chrysene 0.373

Fish Hold and Fish Hold Cleaning Effluent. All fishing vessels generate some form of fish 

hold effluent. Fish hold effluent is composed of seawater, ice-melt, or ice slurry collected inside 

fish hold tanks. Fish hold effluent contains pollutants which result from seafood catch and other 

onboard vessel sources. These pollutants can include biological wastes, metals, and nutrients, as 

well as wastewater resulting from fish hold cleaning activities. 

Table 16 shows the volume of water discharged from various commercial fishing vessels during 

fish holds in operation and during tank cleaning. Fish hold effluent discharge rates can range 

from as low as 211 gal/day for a gillnetter to as high as 5,090 gallons per day for a tender vessel 

while cleaning volumes range from 283 gal/day for purse seiners to 58 gallons per day for 

trawlers (USEPA 2010b). The volume of fish hold effluent can vary from less than 100 gallons 

during off-loading to tens of thousands of gallons for large fish tenders. EPA analyzed the risk 

of this discharge in its BE due to the high number of vessels discharging, the large volume and 

frequency of discharges, along with the potentially high risk posed by the concentration and 

types of pollutant discharged. 

Table 16. Fish Hold Effluent and Cleaning Effluent Discharge Rates (USEPA 2010b).

Commercial Fishing 

Vessel Type 

Estimated Fish 

Hold Effluent 

Discharge Rate

Estimated Fish 

Hold Cleaning 

Effluent Discharge 

Rate

m3/day gal/day m3/day gal/day

Gillnetter 0.80 211 

Lobster Boat 2.83 748 
134

Longliner 2.83 748 

Purse Seiner 16.3 4,306 1.07 283 

Shrimper 1.25 330 

Tender 19.3 5,099 0.66 174 

Trawler 1.25 330 0.22 58 

Troller 3.04 803 0.66 174 

EPA estimated concentrations of fish hold and fish hold cleaning effluent pollutants based on 

data for the vessel types examined in the Report to Congress (Table 17). Contaminants 

identified in fish hold and fish hold cleaning effluent include metals and volatile/semivolatile 

organic chemicals (sVOCs/VOCs).
135

Table 17. Estimated Fish Hold and Fish Hold Cleaning Effluent Pollutant Concentrations used in EPAs Biological Evaluation.

Pollutant

Fish Hold Effluent Fish Hold Cleaning Effluent

BE Point 

Estimate 

Detection 

Frequency

Mean (range) 50th/75th/90th

Percentileb

BE Point 

Estimate 

Detection 

Frequency

Mean (range) 50th/75th/90th

Percentile

Ammonia Nitrogen 12 25/26 12 (nda-160) 2.1/6.7/160 16 7/9 16 (nd-97) 4.8/18/97

Total Phosphorous 13 25/26 13 (nd-76) 9.7/17/76 8.5 7/9 8.5 (nd-20) 11/17/20

Total Residual Chlorine 0.096 10/26 0.096 (nd-0.3) ncc/0.13/0.3 0.29 6/9 0.29 (nd-1.5) 0.11/0.29/1.5

Total Suspended Solids

(TSS) 210 26/26 210 (10-1100) 130/190/1100 190 9/9 190 (16-460) 84/400/460

Biochemical Oxygen 

Demand (BOD) 840 24/26 840 (nd-5100) 440/830/5100 470 6/9 470 (nd-1800) 300/770/1800

Hexane Extractable Oil 

and Grease (HEM) 3.2 18/26 3.2 (nd-16) 1.5/2.9/16 5.4 6/9 5.4 (nd-28) 1.4/4.2/28

Silica Gel Treated-Hexane 

Extractable Oil and Grease

(SGT-HEM)

3.4 15/26 3.4 (nd-4.4) 0.98/2.2/4.4 4.9 4/9 4.9 (nd-12) nc/2.8/12

Aluminum (total) 827 24/26 490 (nd-1000) 670/850/1000 1100 9/9 1100 (850-

1700) 930/1500/1700

Arsenic (dissolved) 31 10/26 31 (nd-350) nc/5.7/350 22 5/9 22 (nd-97) 5.3/38/97

Arsenic (total) 40 16/26 40 (nd-380) 4.8/13/380 35 5/9 35 (nd-150) 8.7/64/150

Cadmium (dissolved) 0.77 1/26 0.77 (nd-1.4) nc/nc/1.4

Copper (dissolved) 96 23/26 96 (nd-920) 15/38/920 34 8/9 34 (nd-180) 12/32/180

Lead (dissolved) 0 3/26 2.3 (nd-8) nc/nc/8 2.7 1/9 2.7 (nd-8.7) nc/nc/8.7

Selenium (dissolved) 9.2 6/26 9.2 (nd-61) nc/2.5/61 6 1/9 6 (nd-14) nc/nc/14

Zinc (dissolved) 180 26/26 180 (24-790) 120/240/790 190 8/9 190 (nd-640) 53/420/640

a

Nondetect (censored) concentrations were replaced with 1⁄2 of the reporting limit for calculating average concentrations.

b Percentiles are the concentration below which that percentage of the values fall. So 75 percent of observations occur below the 75th percentile.

c

Distribution statistics were only calculated when analytes were detected at a sufficient frequency.
136

Graywater and Graywater Mixed with Sewage. Graywater volumes depends primarily on the 

type of vessel and the number of passengers and crew onboard (Table 18). For example, cruise 

ships generate more graywater than cargo ships since they have many more passengers and crew. 

Further, cruise ships also generate higher graywater volumes per capita than cargo ships because 

passengers and crew on these vessels use galleys and accommodations (sinks and showers) to a 

greater extent than crew on cargo ships. Estimated graywater generation rates reported in 

response to EPA’s 2004 cruise ship survey ranged from 36 to 119 gallons/day/person, with an 

average of 67 gallons/day/person (USEPA 2008) for large cruise ships. Finland’s Ministry of the 

Environment estimated cruise ship grey water generation at 120 liters per day (32 

gallons/day/person) ((BMEPC) 2007). During EPA’s 2004 Alaskan cruise ship sampling 

program, graywater generation on one ship was 45 gallons/day/person (USEPA, 2006). 

Table 18. Estimated Graywater Discharge Rates Used in EPAs BE.

Vessel Type

Number of 

Passengers 

and Crewa

Estimated Graywater

Discharge Rated

gal/day m3/day

Barges 4 61e 0.23

Cargo/Bulk Carriers 25 1,125 4.2

Commercial Fishing Vessels 29 1,305 4.9

Large Cruise Ships 3,455 155,475 588

Medium Cruise Ships 315 14,175 53.6

Large Ferries 559 25,155 95.2

Oil and Gas Tankers 22 990 3.7

Passenger Vessels (tour boats, water taxis, etc.) 282b 12,690 48

Utility Vessels (tug boats, off-shore vessels, 

etc.) 6c 1 270

a) Number of crew and passengers from EPA’s NOI Report (USEPA, 2011a) unless otherwise specified.

b) Average number of passengers and crew calculated based on information gathered from both personnel 

communication with operators and web site marketing data for tour boats, dinner cruise vessels, wedding party 

boats, whale watching tours, and shuttle service vessels. Vessels do not provide overnight accommodations.

c) Based on personal contact with AEP River Operations.

d) Based on a graywater generation rate of 45 gallons per person per day (USEPA, Sampling Episode Report 

for Holland America Veendam, Sampling Episode 6503) Washington, DC (USEPA. 2006).

e) Average flow adjusted based on an estimated 33.8% of barges are manned and would therefore generate 

graywater (USEPA, 2011a, Section 2.2.1.5 and Figure 2.1-1)

Graywater can contain high levels of pathogens, nutrients, soaps and detergents, and organics. 

EPA analyzed the risk of this discharge in its BE due to the high number of vessels discharging, 

the large volume and frequency of discharges, along with the potentially high risk posed by the 

concentration and types of pollutant discharged. EPA estimated concentrations of graywater 

pollutants based on data for the vessel types examined in the Report to Congress (Table 19). 

Contaminants identified in graywater include metals oil and grease and nutrients.
137

Table 19. Estimated Graywater Pollutant Concentrations used in EPAs Biological 

Evaluation.

Pollutant

Point 

Estimate 

Used in BE

Detection 

Frequency Mean (range) 50th/75th/90thPercentilesc

Ammonia as Nitrogen (NH3-N, 

mg/L) 1.3 (2.1)a

8/8 1.3 (0.19-4.5) 0.75/1.8/4.5

Total Phosphorus (mg/L) 1.4 (10) 8/8 1.4 (0.42-3.4) 1.2/2.2/3.4

Total Residual Chlorine (mg/L) 0.12 6/8 0.12 (ndb-0.11) 0.02/ncd/0.11

Total Suspended Solids (TSS)

(mg/L) 52 8/8 52 (14-81) 58/69/81

Hexane Extractable Material

(HEM) (mg/L) 39 (149) 8/8 39 (9.4-100) 29/68/100

Silica Gel Treated HEM (SGT-HEM)

(mg/L) 8.1 (36.6) 6/8 8.1 (nd-35) 1.5/9.4/35

Aluminum (total, μg/L ) 380 8/8 380 (50-910) 420/540/910

Arsenic (total, μg/L ) 2 2/8 2 (-2.9) /1.5/2.93

Copper (dissolved, μg/L) 55 8/8 55 (5.3-280) 17/60/280

Lead (dissolved, μg/L) 2.5 4/8 2.5 (nd-6) 1.1/4.2/6

Zinc (dissolved, μg/L) 400 8/8 400 (70-1500) 240/610/1500

a

Values in parentheses are for large cruise ships.

b

Nondetect (censored) concentrations were replaced with 1⁄2 of the reporting limit for calculating 

average concentrations.

c

Percentiles are the concentrations of each analyte below which at least that percentage of the 

values fall. So the 75th percentile is the concentration below which at least 75% of the observations 

were found.

d

Distribution statistics were only calculated when analytes were detected at a sufficient frequency.

Stern Tube Packing Gland Effluent and Other Oil/Water Interfaces. A stuffing box packed 

with greased flax rings is designed to leak a few drops per minute of ambient water (EPA 

estimate, 4 to 8 gallons per day(USEPA 2010b) to cool the gland when a vessel is underway. 

Stuffing boxes are also used to seal rudder stocks that penetrate the hull below the waterline. The 

packing gland effluent water is often collected in a segregated section of the bilge that contains 

an automatic bilge pump.

To estimate stern tube effluent discharge rates for the other vessel types requiring detailed 

analysis for the BE, EPA used the size of a utility vessel (measured as gross tons), compared this 

vessel size to the other vessel types, and applied an average stern tube packing gland discharge 

rate of 6 gallons per day as shown in the example calculation below.

Example: 

25 gross tons (fishing vessel)/80 gross tons (utility vessel) x 6 g/day = 2 g/day

Pollutants in the stern tube packing gland effluent include metals, oil and grease, suspended 

solids, organics, and phthalates. Oil to sea interfaces include any mechanical or other equipment 
138

where seals or surfaces may release small quantities of oil and grease into the sea. Examples 

include controllable pitch propellers, rudder bearings and wire ropes and cables that have 

lubricated (greased) surfaces which are submerged in seawater during use. EPA analyzed the 

risk of this discharge in its BE due to the high number of vessels discharging, the large volume 

and frequency of discharges, along with the potentially high risk posed by the concentration and 

types of pollutant discharged.

Table 20 shows the vessel sizes and the estimated stern tube packing gland discharge rates for 

the vessel types requiring detailed analysis. Flows range from as little as 2 gal/day for 

commercial fishing vessels to as great as 4,000 gal/day for large cruise ships.

Table 20. Estimated Stern Tube Packing Gland Effluent Discharge Rates used in EPAs 

BE.

Vessel Type 

Vessel Size

(gross 

tons)a 

Estimated Stern Tube 

Packing Gland Effluent 

Discharge Rates

m3/day gallons/day

Barges 705 0e 0e 

Cargo/Bulk Carriers 15,939 4.5 1,195 

Commercial Fishing 25b 0.008 2 

Large Cruise Ships 53,526 15.1 4,014 

Medium Cruise Ships 4,584 1.3 343 

Large Ferries 1,451 0.4 108 

Oil and Gas Tankers 24,908 7.1 1,868 

Passenger Vessels (e.g., water taxis, tour 

boats) 35c 0.01 2.6 

Utility Boats (tugs and tow boats) 80d 0.02 6 

a) Vessel size from EPA’s NOI Report (USEPA, 2011a) unless otherwise specified.

b) Vessel gross tons estimated assuming 50% of commercial fishing vessels are 40 feet long

(USEPA, 2010).

c) Vessel gross tons estimated assuming 50% of passenger vessels are 45 feet long (USEPA, 2010).

d) Vessel gross tons estimated assuming 50% of utility vessels are 65 feet long (USEPA, 2010).

e) Barges do not have propeller shafts and associated stern tube packing glands.

EPA estimated concentrations of stern tube packing gland effluent pollutants based on data for 

the vessel types examined in the Report to Congress (Table 21). Contaminants identified in stern 

tube packing gland effluent includes metals and volatile/semivolatile organic chemicals 

(sVOCs/VOCs).

Table 21. Estimated Stern Tube Packing Gland Effluent Pollutant Concentrations used in 

EPAs Biological Evaluation.

Pollutant Point 

Estimate 

Detection 

Frequency Mean (range) 50th/75th/90thPercentilesb
139

Used in 

BE

Total Phosphorus (mg/L) 0.13 7/9 0.13 (nda

-0.25) 0.1/0.22/0.25

Total Suspended Solids (TSS, mg/l) 59 9/9 59 (5.6-270) 28/81/270

Hexane Extractable Material (HEM, mg/l) 14 5/9 14 (nd-67) 1.65/23/67

Chromium, (dissolved, μg/L) 13 5/9 19 (nd-110) 3.8/20/110

Silica Gel Treated HEM (SGT-HEM, mg/l) 19 5/9 13 (nd-56) 1.7/19/56

Copper (dissolved, μg/L) 22 4/9 22 (nd-92) ncc

/38/92

Nickel (dissolved, μg/L) 210 6/9 210 (nd-1000) 13/370/1000

Nickel (total, μg/L) 610 8/9 610 (nd-3200) 45/970/3200

Bis (2-ethylhexyl)phthalate (μg/L) 4.7 3/9 4.7 (nd-24) nc/4.1/24

Tetrachloroethene (μg/L) 1.4 1/9 1.4 (nd-0.2) nc/nc/0.2

a

Nondetect (censored) concentrations were replaced with 1⁄2 of the reporting limit for calculating average 

concentrations.

b Percentiles are the concentrations of each analyte below which at least that percentage of the values fall. 

So the 75th percentile is the concentration below which at least 75% of the observations were found.

c

Distribution statistics were only calculated when analytes were detected at a sufficient frequency.

Underwater Ship Husbandry Discharges. Although discharges from underwater ship 

husbandry is considered a low volume and low frequency discharge generated by a low number 

of vessels, EPA analyzed the risk of this discharge in its BE due to the high potential risk posed 

by the concentration and types of pollutant discharged. Underwater husbandry discharge 

volumes were not estimated because EPA was unable to find available data to accurately 

estimate volume of these discharges. Furthermore, EPA round approached ANS risk 

qualitatively, so volume estimates were not necessary. EPA’s Report to Congress did provide 

copper release estimates for underwater ship husbandry events (Table 22).

Table 22. Dissolved Copper Release from Vessel AFSs During an Underwater Hull 

Cleaning “Event” ((Schiff et al. 2003), after (USEPA 2010)).

AFS Cleaning Method Copper Release

(μg/cm2/event)

Epoxy copper 

antifouling paint

Less abrasive management practices 8.6

No management practices 17.4

Hard vinyl/Teflon 

copper antifouling 

paint

Less abrasive management practices 3.8

No management practices 4.2

Biocide-free coating

Less abrasive management practices 0.03

No management practices 0.05

Discharges not Evaluated in the BE. EPA’s decision process identified a number of discharges 

that would not be evaluated in the BE due to the relative number of vessels releasing the 

discharge, the volume of the discharge, and/or the potential risk posed by the concentration and 

constituents of that discharge. Table 23 summarizes each discharge not evaluated in the BE and 
140

EPAs decision process for each. Details on discharge estimates and other information EPA used 

in arriving at these decisions are provided in footnotes to table 3-3 in the BE.
141

Table 23. Decision Process for those Vessel Discharges Not Evaluated in EPA's BE.

Vessel Discharge Description Number of 

Vessels 

Discharging

Discharge 

Volume 

and 

Frequency 

Amount and 

Types of 

Pollutants 

Present in the 

Discharge 

Evaluated 

in BE

Firemain Systems Firemain systems are found on a large number of vessels and 

draw in water through the sea chest to supply water for fire 

hose stations and sprinkler systems. Systems are activated 

during testing or during an actual fire. Small amounts of 

metals may be added to the fire water from vessel piping 

system.

High Low Low No

Well Deck 

Discharges

The welldeck is a floodable platform used for launching or 

loading small satellite vessels, vehicles, and cargo from select 

vessels. Welldeck discharges may include water from 

precipitation, welldeck and storage area washdowns, 

equipment and engine washdowns, and leaks and spills from 

stored machinery. Potential constituents of welldeck 

discharges include fresh water, distilled water, firemain water, 

graywater, air-conditioning condensate, sea-salt residues, paint 

chips, wood splinters, dirt, sand, organic debris and marine 

organisms, oil, grease, fuel, detergents, combustion byproducts, and lumber treatment chemicals.

Low High Low No

Aqueous Film 

Forming Foam 

(AFFF)

Firefighting agent added to fire suppression systems on some 

vessels to create foam. Used infrequently (annually or semiannually) to test equipment for maintenance, certification, or 

training. Constituents include fluorosurfactants and/or 

fluoroproteins.

Low Low Potentially 

High

No

Freshwater Layup Freshwater layup is generated when a vessel is pier side or in 

port for more than a few days, the main steam plant is shut 

down, and the condensers do not circulate. A freshwater layup 

includes replacing the seawater in the system with potable or 

Low Low Low No
142

Vessel Discharge Description Number of 

Vessels 

Discharging

Discharge 

Volume 

and 

Frequency 

Amount and 

Types of 

Pollutants 

Present in the 

Discharge 

Evaluated 

in BE

surrounding freshwater (e.g., lake water). Freshwater layup 

discharges can be as large as 6,000 gallons per evolution and 

can contain residual saltwater, freshwater, tap water, and 

possibly metals leached from the pipes or machinery.

Gas Turbine 

Water Wash

Gas turbines are used for propulsion and electricity generation 

on some vessels. Occasionally, they must be cleaned to 

remove byproducts that can accumulate and affect their 

operation. Although not subject to the VGP but similar in 

operation to VGP vessels regarding this discharge, large naval 

vessels can generate up to 244 gallons of washwater per day. 

Wash water can include salts, lubricants, and combustion 

residuals.

Low Low Potentially 

High

No

Boiler/Economizer 

Blowdown

Boiler blowdown occurs on vessels with steam propulsion or a 

steam generator and is used to control the concentration of 

scaling constituents in boiler systems. Boiler blowdown are 

infrequent, of short duration (seconds), in small volumes, and 

at high pressure. The blowdown can contain water and steam 

or sludge-bearing water at elevated temperatures (above 

325°F). The discharge can contain metals or boiler water 

treatment chemicals.

Low Low Low No

Motor Gasoline 

and 

Compensating 

Discharge

Motor gasoline is transported on vessels to operate vehicles 

and other machinery. As the fuel is used, ambient water is 

added to the fuel tanks to replace the weight. This ambient 

water is discharged when the vessel refills the tanks with 

gasoline or when performing maintenance. Most vessels are 

designed not to have motor gasoline and compensating 

discharge. The volume of the compensating discharge is 

expected to range from less than 50 gallons to up a few 

hundred gallons. The discharge can contain small amounts of 

Low Low Potentially 

High

No
143

Vessel Discharge Description Number of 

Vessels 

Discharging

Discharge 

Volume 

and 

Frequency 

Amount and 

Types of 

Pollutants 

Present in the 

Discharge 

Evaluated 

in BE

fuel and other fuel-related pollutants.

Cathodic 

Protection

Nearly all vessels having steel hulls or metal hull appendages 

use cathodic protection systems to prevent corrosion. Based on 

underwater hull inspections and maintenance records, one-half 

of anodes are consumed after three years. The primary 

pollutant released from cathodic protection is zinc. Average 

pierside and underway zinc generation rates are 1.3 x 10-6 and 

5.1 x 10-6 (lb zinc/square foot of underwater surface area)/hr, 

respectively. Concentrations modeled for military vessels using a 

mixing zone envelope approach indicate that zinc, aluminum and 

mercury concentrations were below WQS within 0.5, 0.1 and 0.1 

feet from the vessels surface, respectively (USDOD/USEPA 1999). 

High Low Low No

Non-oily 

Machinery 

Wastewater

Some larger vessels are expected to have some non-oily 

machinery discharges, such as distilling plants start-up 

discharge, chilled water condensate drains, fresh-and saltwater 

pump drains, and potable water tank overflows. These flows 

are generally low in volume and are not expected to contain 

significant amounts of pollutants.

Low Low Low No

Refrigeration and 

Air Condensate 

Discharge

Condensation from cold refrigeration or evaporator coils of air 

conditioning systems drips from the coils and collects in drip 

troughs which typically empty to a drainage system. Large 

numbers of vessels are equipped with refrigeration systems to 

keep food and other perishable items from spoiling. Air 

conditioning systems are also used for passenger and crew 

comfort. Condensates may contain very small amounts of 

pollutants such as metals derived from vessel piping systems.

High Low Low No

Coal Ash from 

Coal Fired 

Propulsion 

Combusting coal in boilers produces a residue of combustible 

flue constituents known as ash. Some of the ash consists of 

very fine particles that are entrained in the flue gas and carries 

Low High Potentially 

High

No
144

Vessel Discharge Description Number of 

Vessels 

Discharging

Discharge 

Volume 

and 

Frequency 

Amount and 

Types of 

Pollutants 

Present in the 

Discharge 

Evaluated 

in BE

Systems on 

Ferries

out of the furnace (fly ash), while heavier ash settles at the 

bottom of the boiler (bottom ash). Bottom ash may be 

hydraulically conveyed (i.e., sluiced with water). The 

discharge of coal ash slurry from coal fired propulsion systems 

on a ferry is authorized by the 2008 VGP until December 19, 

2012.

Seawater Cooling 

Overboard 

Dischargenn

Seawater cooling systems use ambient water to absorb the heat 

from heat exchangers, propulsion systems, and mechanical 

auxiliary systems. The water is typically circulated through an 

enclosed system that does not come in direct contact with 

machinery, but still may contain sediment from water intake, 

traces of hydraulic or lubricating oils, and trace metals leached 

or eroded from the piping within the system. Additionally, 

because it is used for cooling, the effluent will have an 

increased temperature.

High Low Low No

Distillation and 

Reverse Osmosis 

Brine

Discharges of brine can occur on vessels that do not bunker 

potable water but instead use onboard plants to distill seawater 

or desalinate seawater using reverse osmosis (RO) to generate 

fresh water. Distillation units generate brine at a rate of 17 

gallons of brine for every gallon of fresh water produced. 

Reverse osmosis units generate approximately 4 gallons of 

brine for every gallon of fresh water produced. The three 

sources of the constituents of brine discharge are: 1) influent 

seawater; 2) anti-scaling treatment chemicals; and 3) the 

purification plant components, including heat exchangers, 

casings, pumps, piping and fittings. The primary constituents 

of the brine discharge are identical to those in seawater; 

however, they are more concentrated due to volume reduction.

Low High Low No

Seawater Piping Some vessels that use seawater cooling systems introduce Low Low Potentially No
145

Vessel Discharge Description Number of 

Vessels 

Discharging

Discharge 

Volume 

and 

Frequency 

Amount and 

Types of 

Pollutants 

Present in the 

Discharge 

Evaluated 

in BE

Biofouling anti-fouling compounds (e.g., sodium hypochlorite) in their 

interior piping and component surfaces to inhibit the growth of 

fouling organisms. These anti-fouling compounds are then 

typically discharged overboard. Most vessels that have 

seawater piping systems are expected to use piping materials 

such as copper to prevent biofouling rather than injecting high 

concentrations of anti-fouling compounds into their piping 

systems.

High

Elevator Pit 

Effluent

Large vessels with multiple decks are equipped with elevators 

to facilitate the transportation of maintenance equipment, 

people, and cargo between decks. A pit at the bottom of the 

elevator shaft collects small amounts of liquids and debris 

from elevator operations and deck washdown and runoff 

depending on the elevator configuration. Water entering the 

elevator pit can contain materials that were on the deck, 

including fuel, hydraulic fluid, lubricating oil, residual water, 

and AFFF. The runoff may also contain lubricant applied to 

the elevator doors, door tracks, and other moving elevator 

parts. Residue in the elevator car from the transport of 

materials may also be washed into the elevator pit. The 

cleaning solvent used during maintenance cleaning operations, 

as well as liquid wastes generated by the cleaning process, can 

also drain into the elevator pit sump.

Low Low Potentially 

High

No

Sonar Dome 

Discharge

Water is used to maintain the shape and pressure of domes that 

house sonar detection, navigation, and ranging equipment on 

large vessels. Discharges occasionally occur when the water 

must be drained for maintenance or repair or from the exterior 

of the sonar dome. Although not subject to the VGP but 

similar in operation to VGP vessels regarding this discharge, 

Low Low Low No
146

Vessel Discharge Description Number of 

Vessels 

Discharging

Discharge 

Volume 

and 

Frequency 

Amount and 

Types of 

Pollutants 

Present in the 

Discharge 

Evaluated 

in BE

sonar dome discharge volumes on naval vessels can range 

from 300 gallons per event up to 74,000 gallons per event. 

Pollutant levels are expected to be low due to the ban on the 

use of tributyl tin.

Underwater Ship 

Husbandry 

Discharges

Underwater ship husbandry is grooming, maintenance, and 

repair activities of hulls or hull appendages performed while 

the vessel is located in the water. Underwater ship husbandry 

discharges can contain aquatic organisms and residue such as 

rust and biocide from AFC. Underwater ship husbandry is 

typically performed only when excessive biological growth is 

causing vessel drag and excessive fuel consumption outside of 

regular dry dock inspections.

Low Low Potentially 

High

ANS only

Chain Locker 

Effluent

Chain locker effluent is water that drips from the anchor chain 

and anchor during anchor retrieval. Discharge volumes are 

small and chain locker effluent is expected to contain zinc, 

rust, paint, grease, and any constituents from the firemain 

water. The small volume of chain locker effluent results in 

small mass loadings and provides opportunity for the transfer 

of non-indigenous species.

High Low Low ANS only
147

Estimates of Exposure Resulting from Discharges Authorized by the VGP and 

sVGP

This section summarizes the modeling approach EPA used to estimate exposure of threatened 

and endangered species and their critical habitat to VGP-authorized discharges. Greater detail is 

provided in section 5 of EPA’s BE. Representative Action Areas (RAAs) were selected by EPA 

after consultation with the Services to be used to evaluate the potential exposure and effects of 

permitted discharges on listed aquatic and aquatic-dependent species, as well as their designated 

critical habitats. The following selection criteria were used to identify the RAAs evaluated in the 

BE:

 High density of vessels covered under the VGP and sVGP to capture a reasonable “worst 

case” scenario;

 Varying percentages of vessel types present to capture the variability in pollutant loading 

rates;

 Selection of RAAs that provide broad coverage of diverse ecosystem types and broad

geographical representation; and Selection of “special interest” locations with known or 

expected sensitivities for specific taxa and their critical habitats (i.e., Pacific coast 

salmonid populations, sea turtles in Gulf of Mexico, etc.) and/or specific vulnerabilities

(e.g., historic introduction and spread of ANS in the Great Lakes).

EPA’s NOI Summary Report and EPA’s Report to Congress on Vessel Discharges were used to 

identify the top Home/Hailing Ports for each vessel type. For both groups of covered vessels 

(large and small), New York, NY; Houston, TX, and Seattle, WA were consistently among the 

top 10 port cities, as well as other ports such New Orleans, LA; Miami, FL; Los Angeles, CA; 

Norfolk, VA; Pittsburgh, PA; and St. Louis, MO (to name a few). Among these port cities, 

nearly all are representative of estuarine/marine ecosystems, except for inland port cities such as 

Jeffersonville (Indiana), Pittsburgh, St. Louis and Cincinnati (top port cities for barges on large 

inland rivers). Port cities on a large freshwater lake (Great Lakes) system do not appear to be 

among the most heavily trafficked. From this initial list of port cities, EPA selected seven RAAs 

for detailed evaluation in the BE that were both ecologically and geographically diverse and 

captured several special interest locations identified during preliminary informal consultation 

meetings with the Services (Table 24). 

Table 24. RAAs Selected for Exposure Assessment Modeling to Represent Water Bodies 

and Ecosystems Inhabited by Listed Resources.

Reference 

Port/Harbor

Waterbody 

Represented

Ecosystem 

Represented

Justification

Duluth, MN Lake Superior 

Harbor

Freshwater 

[Great] Lake

Major port in sensitive “cold-water” Great Lakes 

area with known ANS issues. 

Houston, 

TX

Galveston Bay Estuarine/Marine RAA with large population of oil and gas tankers, 

barges, and cargo carriers. This area also 
148

encompasses nesting ground of listed sea turtles. 

Miami, FL Biscayne Bay Estuarine/Marine RAA with significant populations of cargo/bulk 

carriers and large population of cruise ships. Area 

encompasses extensive listed Johnson’s seagrass 

beds and represents a portion of Florida’s coral 

reef tract. In addition, Miami was requested to be 

an additional RAA during informal consultation 

with Services, in light of the presence of 

endangered species and their critical habitats with 

unique characteristics not found in other RAAs 

New York, 

NY

Upper and 

Lower New 

York Bay

Estuarine/Marine RAA with significant presence of all major vessel 

types, and in proximity to listed short nose 

sturgeon population along the Hudson River. RAA 

includes multiple critical habitat areas. 

San 

Francisco, 

CA

San Francisco 

Bay Estuary

Estuarine/Marine RAA with significant populations of cargo bulk 

carriers, utility boats, and commercial fishing 

vessels. Estuary is emblematic of one subjected to 

heavy ANS invasion. In addition, San Francisco 

was requested to be an additional RAA during 

informal consultation with Services due to the 

presence of a significant number of endangered 

and threatened species from a broad range of taxa 

and critical habitat areas. 

St. Louis, 

MO

Upper 

Mississippi 

River

Large 

Freshwater River

RAA with large barge and supporting utility vessel

presence. The upper Mississippi River near St. 

Louis also represents a large freshwater river 

ecosystem home to a sensitive listed freshwater 

unionid mussel species. 

Seattle, WA Puget Sound Estuarine/marine RAA with significant large and small commercial 

fishing vessel presence. Puget Sound near Seattle 

is home to several Pacific Northwest salmonid 

populations. Includes multiple critical habitats. 

EPA selected simple screening-level models to estimate exposure concentrations in the receiving 

water from vessel discharges covered under the VGP and sVGP. EPA selected the “fraction of 

freshwater model” to calculate receiving water concentrations in a estuarine harbor and a dilution 

equation to estimate receiving water concentrations in a river harbor. 

For the fraction of freshwater model, EPA identified two types of estuarine systems in 

commonly found in the port areas:

 Estuaries where tidal influence is the primary driver for mixing in the estuary as indicated 

by a lower river flow and higher salinity value; and

 Estuaries where the freshwater inflow is the primary driver for mixing in the estuary as 

indicated by a higher river flow and lower salinity value.
149

For the river harbor model, the dilution equation requires the average annual river flow rate to 

calculate a receiving water concentration. EPA selected the minimum and maximum river flow 

rates from the nine river harbors to represent the bounding conditions for the river harbors, 

resulting in two river harbor scenarios for the BE effects analysis.

A range of water body flow, salinity, vessel populations, and loading assumptions were applied 

to the model to explore different “likely” and “worst-case” scenarios pollutant exposure 

concentrations resulting from vessel discharges covered under the VGP and sVGP. Vessel 

population scenarios were developed for each RAA based on data provided by the RAA port 

authorities, available Department of Transportation port call data, and other vessel related 

literature to characterize the average daily vessel equivalents present in the RAA by vessel class.. 

Vessel discharges were expressed as vessel equivalents where a vessel equivalent represents a 

single vessel discharging 24-hours per day in the harbor. For example, 1 vessel equivalent could 

represent 24 vessels that each operate (and discharge) for 1 hour in the modeled harbor each day. 

EPA also collected receiving water characteristic data from a variety of estuaries and rivers 

where vessels covered under VGP and sVGP are known to travel. 

EPA identified 32 pollutants to include in the modeling analysis based on pre-permit frequency, 

vessel discharge flow rates and pollutant concentrations as described in Discharges Authorized 

by the VGP and sVGP. EPA then estimated reductions in vessel discharge pollutant 

concentrations and flow rates anticipated to occur as the result of issuance of the VGP and sVGP 

for the pollutants, discharges and vessel types evaluated. Harbor specific pollutant loads were 

estimated for each of the seven RAAs by multiplying vessel and discharge specific pollutant 

loads by the number of vessel equivalents present in the RAA harbors. EPA used this 

information to model 14 scenarios addressing harbor specific pollutant loads for 7 RAAs and 

receiving water characteristics representing minimum and maximum dilution conditions for 

estuary and river ports (Table 25). 

Table 25. Receiving Water Model Scenarios Assessed by EPA.

Model 

Scenario 

Number

Harbor Scenario RAA Loading Scenario

1 Estuary mixing driven by tidal influence Seattle Pollutant Load

2 Estuary mixing driven by tidal influence Houston Pollutant Load

3 Estuary mixing driven by tidal influence New York Pollutant Load

4 Estuary mixing driven by tidal influence San Francisco Pollutant Load

5 Estuary mixing driven by tidal influence Miami Pollutant Load

6 Estuary mixing driven by river inflow Seattle Pollutant Load

7 Estuary mixing driven by river inflow Houston Pollutant Load

8 Estuary mixing driven by river inflow New York Pollutant Load

9 Estuary mixing driven by river inflow San Francisco Pollutant Load

10 Estuary mixing driven by river inflow Miami Pollutant Load
150

11 Minimum river flow St. Louis Pollutant Load

12 Minimum river flow Duluth Pollutant Load

13 Maximum river flow St. Louis Pollutant Load

14 Maximum river flow Duluth Pollutant Load

EPA stated that it believed the scenarios modeled to be representative of the types of water 

bodies where VGP and sVGP vessels likely operate based on the wide geographical range of 

waterbodies used to develop the input values. By selecting the minimum water characteristic 

values for the harbor scenarios, and evaluating the maximum pollutant loading values from the 

seven RAAs, EPA also believed that the model scenarios reasonably capture a “worst case” 

scenario within the action area applicable to the BE. Table 26 lists the receiving water 

concentrations estimated from the 10 estuary harbor exposure scenarios modeled. Table 27 lists 

the receiving water concentrations estimated from the four river harbor exposure scenarios 

modeled. 
151

Table 26. Estimated Receiving Water Concentrations Resulting from Vessel Discharge Pollutant Loadings Under Estuary 

Mixing Conditions.

Polutant 

Class Analyte 

Pre VGP and sVGP Receiving 

Water Average (range)

Post VGP and sVGP Receiving 

Water

Average (range)

Percent Reduction 

Average Scenario Loading

(worst-best case scenarios) 

Units 

Classicals Biochemical Oxygen 

Demand (BOD) 

mg/L 0.195 (0.00629-0.915) 0.162 (0.0053-0.676) 17% (16%-26%)

Classicals Hexane Extractable 

Material (HEM) 

mg/L 0.0264 (0.00146-0.0656) 0.013 (0.000701-0.0324) Approximately 50%a

Classicals Silica Gel Treated 

HEM (SGT-HEM) 

mg/L 0.00684 (0.000438-0.0169) 0.00343 (0.000215-0.0089) Approximately 50%

Classicals Total Residual 

Chlorine 

mg/L 0.000281 (0.0000032-0.00214) 0.000103 (0.00000238-0.00066) 63% (26%-69%)

Classicals Total Suspended 

Solids (TSS) 

mg/L 0.0435 (0.00335-0.202) 0.0281 (0.0015-0.13) 35% (36%-55%)

Metals Aluminum, Total μg/L 0.405 (0.0542-1.28) 0.293 (0.0357-1.02) 28% (20%-34%)

Metals Arsenic, Dissolved μg/L 0.681 (0.0483-1.94) 0.68 (0.0476-1.94) Minimal change (<10%)

Metals Arsenic, Total μg/L 0.682 (0.0493-1.94) 0.681 (0.0484-1.94) Minimal change (<10%)

Metals Cadmium, Dissolved μg/L 0.000189 (0.0000215-0.000867) 0.000132 (0.0000123-0.000697) 30% (20%-43%)

Metals Chromium, Dissolved μg/L 0.000463 (0.0000565-0.00191) 0.000418 (0.0000465-0.00185) 10% (3%-18%)

Metals Copper, Dissolved μg/L 0.999 (0.14-2.99) 0.999 (0.11-2.33) 0% (0%-22%)

Metals Lead, Dissolved μg/L 0.0011 (0.000116-0.00295) 0.000934 (0.00008-0.00262) 15% (11%-31%)

Metals Nickel, Dissolved μg/L 0.102 (0.00718-0.291) 0.102 (0.00701-0.291) No change

Metals Nickel, Total μg/L 0.00507 (0.000654-0.0125) 0.00507 (0.000654-0.0125) No change
152

Polutant 

Class 

Analyte Pre VGP and sVGP Receiving 

Water Average (range)

Post VGP and sVGP Receiving 

Water

Average (range)

Percent Reduction 

Average Scenario Loading

(worst-best case scenarios) 

Metals Selenium, Dissolved μg/L 0.788 (0.0538-2.25) 0.788 (0.0536-2.25)11 No change

Metals Selenium, Total μg/L 0.837 (0.0565-2.39) 0.837 (0.0565-2.39) No change

Metals Zinc, Dissolved μg/L 0.145 (0.00813-0.493) 0.134 (0.00635-0.452) Minimal change (<10%)

Nutrients Ammonia As Nitrogen 

(NH3-N) 

mg/L 0.00149 (0.0000232-0.00954) 0.00123 (0.0000209-0.00742) 17% (10%-22%)

Nutrients Total Phosphorus mg/L 0.00267 (0.000112-0.0119) 0.0000905 (0.00000632-

0.000543)

Greater than 94%

SVOC 2,4,6-Trichlorophenol μg/L 0.000178 (0.000012-0.00103) 0.0000927 (0.00000607-

0.000514)

Approximately 50%

SVOC Benzo (a)anthracene μg/L 0.00306 (0.000393-0.00685) 0.00306 (0.000393-0.00685) No change

SVOC Benzo (a)pyrene μg/L 0.00198 (0.000214-0.00614) 0.00198 (0.000214-0.00614) No change

SVOC Benzo (b)fluoranthene μg/L 0.000733 (0.0000185-0.00486) 0.000733 (0.0000185-0.00486) No change

SVOC Benzo (k)fluoranthene μg/L 0.000812 (0.0000205-0.00538) 0.000812 (0.0000205-0.00538) No change

SVOC Bis (2-ethylhexyl) 

phthalate 

μg/L 0.00117 (0.000122-0.00569) 0.000754 (0.000048-0.00424) 36% (25%-61%)

SVOC Chrysene μg/L 0.00399 (0.00055-0.00943) 0.00399 (0.00055-0.00943) No change

SVOC Ideno (1,2,3-

cd)pyrene 

μg/L 0.000655 (0.0000165-0.00434) 0.000655 (0.0000165-0.00434) No change

VOC Benzene μg/L 0.00554 (0.000393-0.0311) 0.0042 (0.000186-0.0258) 24% (17%-53%)

 

11 EPA recalculated selenium concentrations to reflect fewere vessels using this technology. We were not provided revised harbor model estimates, only revised total loadings and 

RQs.
153

Polutant 

Class 

Analyte Pre VGP and sVGP Receiving 

Water Average (range)

Post VGP and sVGP Receiving 

Water

Average (range)

Percent Reduction 

Average Scenario Loading

(worst-best case scenarios) 

VOC

Bromodichloromethane 

μg/L 0.00085 (0.000139-0.00195) 0.00025 (0.0000364-0.000573) Approximately 70%

VOC

Dibromochloromethane 

μg/L 0.00085 (0.000139-0.00195) 0.00025 (0.0000364-0.000573) Approximately 70%

VOC Tetrachloroethene μg/L 0.0000116 (0.0000015-

0.0000288)

0.00000582 (0.00000075-

0.0000144)

50% reduction regardless of 

scenario

VOC Trichloroethene μg/L 0.159 (0.00122-1.14) 0.0000344 (0.00000225-

0.000191)

Eliminated

a

generalized for cases where the average, minimum and maximum reductions are within 5% of each other

Table 27. Estimated Receiving Water Concentrations Resulting from Vessel Discharge Pollutant Loadings Under River 

Mixing Conditions.

Polutant 

Class Analyte Units

Pre VGP and sVGP Receiving 

Water

Average (range)

Post VGP and sVGP Receiving 

Water

Average (range)

Percent Reduction 

Average Scenario Loading

(worst-best case scenarios)

Classicals Biochemical Oxygen 

Demand (BOD) 

μg/L 4.38 (0.0506-9.2) 4.17 (0.0459-9.11) 5% (1%-9%)

Classicals Hexane Extractable 

Material (HEM) 

μg/L 0.396 (0.00445-0.855) 0.149 (0.00173-0.311) 62% (61%-64%)

Classicals Silica Gel Treated 

HEM (SGT-HEM) 

μg/L 0.102 (0.00117-0.214) 0.041 (0.00049-0.0837) 60% (58%-61%)

Classicals Total Residual 

Chlorine 

μg/L 0.00152 (0.0000169-0.00328) 0.00139 (0.0000144-0.00319) 9% (3%-15%)

Classicals Total Suspended Solids

(TSS) 

μg/L 1.1 (0.0126-2.33) 0.72 (0.00764-1.62) 35% (30%-39%)

Metals Aluminum, Total μg/L 0.015 (0.000162-0.0334) 0.0119 (0.000102-0.0309) 21% (7%-37%)

Metals Arsenic, Dissolved μg/L 0.0413 (0-0.164) 0.0413 (0-0.164) no change
154

Polutant 

Class Analyte Units

Pre VGP and sVGP Receiving 

Water

Average (range)

Post VGP and sVGP Receiving 

Water

Average (range)

Percent Reduction 

Average Scenario Loading

(worst-best case scenarios)

Metals Arsenic, Total μg/L 0.0413 (0.000000231-0.164) 0.0413 (0.000000231-0.164) no change

Metals Cadmium, Dissolved μg/L 0.0000059 (0.0000000653-

0.0000129)

0.00000446 (0.0000000366-

0.0000118)

24% (9%-44%)

Metals Chromium, Dissolved μg/L 0.0000158 (0.000000142-

0.0000399)

0.0000141 (0.000000137-

0.0000338)

11% (4%-15%)

Metals Copper, Dissolved μg/L 0.047 (0.000136-0.164) 0.037229 (0.000106-0.131) 21% (20%-22%)

Metals Lead, Dissolved μg/L 0.0000416 (0.00000045-

0.0000922)

0.0000362 (0.000000345-

0.0000878)

13% (5%-23%)

Metals Nickel, Dissolved μg/L 0.0062 (0.000000338-0.0246) 0.0062 (0.000000334-0.0246) minimal change <2%

Metals Nickel, Total μg/L 0.000211 (0.000000716-

0.000723)

0.000211 (0.000000716-

0.000723)

no change

Metals Selenium, Dissolved μg/L 0.0479 (0-0.191) 0.0479 (0-0.191) no change

Metals Selenium, Total μg/L 0.051 (0-0.203) 0.051 (0-0.203) no change

Metals Zinc, Dissolved μg/L 0.00446 (0.0000496-0.00968) 0.00418 (0.0000439-0.00948) 6% (2%-11%)

Nutrients Ammonia As Nitrogen

(NH3-N) 

μg/L 0.0149 (0.000167-0.032) 0.014 (0.000167-0.0285) 6% (0%-11%)

Nutrients Total Phosphorus μg/L 0.0225 (0.000271-0.0453) 0.00248 (0.0000242-0.00594) 89% (87%-91%)

SVOC 2,4,6-Trichlorophenol μg/L 0.00000539 (0.0000000626-

0.0000113)

0.00000376 (0.0000000313-

0.00000986)

30% (13%-50%)

SVOC Benzo (a)anthracene μg/L 0.000268 (0.00000164-0.0008) 0.000268 (0.00000164-0.0008) no change

SVOC Benzo (a)pyrene μg/L 0.0002 (0.00000159-0.000536) 0.0002 (0.00000159-0.000536) no change

SVOC Benzo (b)fluoranthene μg/L 0.000114 (0.00000139-0.000228) 0.000114 (0.00000139-0.000228) no change
155

Polutant 

Class Analyte Units

Pre VGP and sVGP Receiving 

Water

Average (range)

Post VGP and sVGP Receiving 

Water

Average (range)

Percent Reduction 

Average Scenario Loading

(worst-best case scenarios)

SVOC Benzo (k)fluoranthene μg/L 0.000126 (0.00000154-0.000252) 0.000126 (0.00000154-0.000252) no change

SVOC Bis (2-ethylhexyl) 

phthalate 

μg/L 0.0000981 (0.00000118-

0.000198)

0.0000839 (0.000000979-

0.000175)

14% (12%-17%)

SVOC Chrysene μg/L 0.000325 (0.00000164-0.00102) 0.000325 (0.00000164-0.00102) no change

SVOC Ideno (1,2,3-cd)pyrene μg/L 0.000102 (0.00000124-0.000203) 0.000102 (0.00000124-0.000203) no change

VOC Benzene μg/L 0.000579 (0.00000701-0.00117) 0.000538 (0.00000641-0.0011) <10%

VOC

Bromodichloromethane 

μg/L 0.0000431 (0.000000451-

0.0000981)

0.0000159 (0.000000116-

0.0000443)

63% (55%-74%)

VOC

Dibromochloromethane 

μg/L 0.0000431 (0.000000451-

0.0000981)

0.0000159 (0.000000116-

0.0000443)

63% (55%-74%)

VOC Tetrachloroethene μg/L 0.000000484 (0.00000000164-

0.00000166)

0.000000242 (0.000000000821-

0.00000083)

50%

VOC Trichloroethene μg/L 0.0595 (0.0000000232-0.237) 0.0000014 (0.0000000116-

0.00000366)

100% (50%-100%)
156

Geographical Distribution and Overlap of Discharges Authorized by the VGP and 

sVGP with Threatened and Endangered Species

In order to determine whether listed resources will be exposed to these discharges, it is necessary 

to characterize the overlap of vessel operations with species and their critical habitat. In its BE, 

EPA modeled exposures for several Representative Action Areas (RAAs) selected after 

consultation with the Services to evaluate the potential effects of the permit actions on listed 

aquatic and aquatic-dependent species, as well as their designated critical habitats. 

The Services provided EPA with a list of over 1,900 federally-listed species, 612 of which were 

identified by EPA as aquatic and aquatic-dependent animal and plant species with more than 

limited exposure to “waters of the United States” and may be affected by ANS or pollutants from 

vessel discharges covered under the proposed actions. The EPA species list (see Appendix E, 

BE; EPA 2012a) included 44 mammals, 44 birds, 24 reptiles, 27 amphibians, 135 fish, 27 

crustaceans, 34 snails, 93 bivalve mollusks (clams and abalone), 25 insects, 2 corals, 157 sea 

grasses and aquatic and wetland plants and 217 designated critical habitats that may be affected 

by the permits. The ranges for 454 of these aquatic and aquatic-dependent animal and plant 

species are concurrent with waters generally navigable by vessels covered under the VGP and 

sVGP. The list of 454 aquatic and aquatic-dependent animal and plant species identified in 

EPA’s analysis constitute the full range of species and their designated critical habitats that may 

be affected by both ANS and traditional pollutants from the permit actions, while all 612 were

identified as potentially affected by ANS. The FWS addresses 568 endangered, threatened, 

proposed, and candidate species and their critical habitats in this biological and conference 

opinion. The list of species addressed by EPA’s RAA analysis included 59 of the 568 FWS

species. 

The remaining FWS listed, proposed, and candidate species are not located in the specific RAAs 

examined by EPA, but are also likely to be exposed to effects of vessel discharges because their 

ranges are concurrent with waters generally navigable by vessels covered under the VGP and 

sVGP, or exist in or rely on wetlands and waters of the U.S. that are vulnerable to ANS 

invasions.

The VGPs include limits on certain discharges in Waters Federally Protected Wholly or in Part 

for Conservation. This list includes marine sanctuaries, units of the National Park System, units 

of the National Wildlife Refuge System, National Wilderness areas, national wild and scenic 

rivers system components and any water body designated as an Outstanding National Resource 

Water (ONRW) by a State or Tribe. 

These discharge limitations for Waters Federally Protected Wholly or in Part for Conservation

include:

 Bilgewater may not be discharged into Waters Federally Protected Wholly or in Part for 

Conservation unless the discharge is necessary to maintain the safety and stability of the 

ship. 
157

 Ballast water discharge or uptake must be avoided in/into waters within, or that may 

directly affect, marine sanctuaries, marine preserves marine parks, or coral reefs or 

Waters Federally Protected Wholly or in Part for Conservation.

 Unexchanged or untreated ballast water or sediment may not be discharged to Waters 

Federally Protected Wholly or in Part for Conservation by: 

o Any vessels that carry ballast water that was taken on in areas less than 200 

nautical miles from any shore that will subsequently operate beyond the Exclusive 

Economic Zone (EEZ) and more than 200 nm from any shore

o Vessels Carrying Ballast Water Engaged in Pacific Nearshore Voyages 

o Vessels with any Ballast Water Tanks that are Empty or have Unpumpable 

Residual Water 

o Vessels Engaged in Pacific Nearshore Voyages with Unpumpable Ballast Water 

and Residual Sediment (including NOBOBs)

 AFFF discharges may not occur in or within 1 nm of Waters Federally Protected Wholly 

or in Part for Conservation unless:

o For emergency purposes; 

o By rescue vessels such as fireboats for firefighting purposes; or 

o By vessels owned or under contract to do business exclusively in or within 1 nm 

of those protected areas by the United States government or state or local 

governments. 

 Boiler/economizer blowdown may not be discharged In Waters Federally Protected 

Wholly or in Part for Conservation except for safety purposes. 

 Firemain systems may not be discharged Waters Federally Protected Wholly or in Part 

for Conservation except for safety purposes. 

 Graywater may not be discharged Waters Federally Protected Wholly or in Part for 

Conservation by vessels with the capacity to store graywater. Vessels which cannot store 

graywater must minimize graywater production.

Response Analysis

The previous Exposure Analysis section reviewed the discharges in terms of their volume and 

constituent mixtures, then described EPAs harbor modeling methodology and results. This 

section summarizes the modeled harbor discharge constituent concentrations for each pollutant 

class and the relative importance of discharge sources before reviewing the responses of listed, 

or surrogate, species to exposures to these pollutants. 

Nutrients 
158

In their Biological Evaluation EPA acknowledged that Nutrient pollution is one of the leading 

causes of water quality impairment in the nation, primarily because the quantity of nutrients 

reaching the nations waters has dramatically escalated over the past 50 years (USEPA, 2009). 

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).

Nutrients in Vessel Discharges

EPA reported that nutrients, particularly ammonia nitrogen and total phosphorus, were 

constituents commonly found in bilgewater, deck washdown, fish hold and fish hold cleaning 

effluent, and graywater. Based on studies of pollutants in vessel discharges EPA reported that 

average ammonia nitrogen concentrations were above their screening level benchmark of 1.2 

mg/L in both fish hold effluent and fish hold cleaning effluent (USEPA, 2010) (see Appendix D 

of EPA’s BE for more information regarding screening level benchmarks). Protein, free amino 

acids, and nucleotides from fish and fish by-products are all potential sources of nitrogen in the 

fish hold effluent and fish hold cleaning effluent. EPA also reported that ammonia nitrogen 

concentrations can also be above screening level benchmarks in graywater. EPA found the 

average ammonia nitrogen concentration from all graywater sources on cruise ships was 2.1 

mg/L (USEPA, 2008). Average phosphorous concentrations were above EPAs screening level 

benchmark of 0.1 mg/L in bilgewater, graywater, deck washdown discharges, fish hold effluent, 

and fish hold cleaning effluent. EPA suggested that the likely source of phosphorous in 

bilgewater and deck washdown water was liquid detergents used on board for deck washing. 

They also indicated that sources of phosphorous in graywater and fish hold effluent may reflect 

food or other wastes. Table 28 shows the average concentrations of ammonia nitrogen and total 

phosphorous in the various vessel discharges requiring detailed analysis.
159

Table 28. Average nutrient concentrations in vessel discharges at levels above screening 

level benchmarks. [Adapted from Table 3-14, USEPA, 2012a]

Vessel Discharge Requiring 

Detailed Analysis

Average Ammonia 

Nitrogen (mg/L)

Average Total 

Phosphorus (mg/L)

Bilgewater 1.7 3.0

Deck Washdown NA 1.7

Fish Hold Effluent 12 13

Fish Hold Cleaning Effluent 16 8.5

Graywater 1.3

2.1a

1.4

10a

Source: USEPA, 2010, unless otherwise specified.

NA: Pollutant does not exceed the screening level benchmark for this vessel discharge (see Appendix D of this BE for more

information regarding screening level benchmarks).

a) Average concentration in graywater from large cruise ships (USEPA, 2008, EPA sampling data).

Direct effects of Ammonia Nitrogen

As mentioned above, nitrogen is essential for primary production in aquatic ecosystems and 

over-enrichment can lead to eutrophication and water quality impairments. Ammonia nitrogen 

(NH3 and NH4-) can also be highly toxic. Recent studies have shown that freshwater mollusks 

(mussels and snails) are particularly sensitive ammonia (Wang et al. 2007a; Wang et al. 2007b; 

Besser et al. 2009). In fact, they are more sensitive than previously tested species. As a result, 

EPA is revising their 304a aquatic life criteria for ammonia to include these new mollusk data so 

that freshwater mussels, snails and other mollusks are adequately protected. A draft of the 

updated ammonia criteria document was published in the federal register for public comment in 

2009.

EPA used the freshwater mussel Lampsilis siliquoidea (Fatmucket) as a surrogate to represent 

freshwater invertebrates in their response analysis. The IC20 for Fatmucket (0.3027 mg N/L) 

was the lowest chronic effects thresholds (CTET) among all taxa (freshwater or marine) 

considered in the analysis (EPA BE Table 5-49). EPA predicted the concentrations of ammonia 

nitrogen in river and estuarine harbors, resulting from vessel discharges, to be 0.0000285 (mg 

N/L) and 0.00742 (mg N/L), respectively. These concentrations are orders of magnitude below 

the Fatmucket IC20 and the resulting risk quotients were extremely low (EPA BE Table 5-50). 

Therefore risks from chronic exposure to ammonia nitrogen in harbors, where vessel discharges 

are the sole source, should be very low. 
160

Phosphorus

EPA noted in their BE that under natural conditions, freshwater ecosystems generally have low 

phosphorous concentrations (< 100 μg/L), but each waterbody is different, and there are 

numerous factors which impact how any particular waterbody will respond to excess nutrient 

loading, including hydraulic residence time, freshwater inflow, clarity and light attenuation, 

geologic substrate, depth, temperature, and degree of physical alterations, such as channelizing. 

Additionally, excessive phosphorus and the resulting problems associated with nutrient 

enrichment in general are frequently widespread and manifested at a location remote from the 

sources, and may not show themselves for some time after significant inputs to the system have 

occurred (WERF, 2010). Because of the above, EPA chose to use the lowest statewide and/or 

site-specific water quality criteria for total phosphorus (10 μg/L) as the basis for CTETA,W in the 

analysis.

Services Conclusion. Since the Services assessment for ammonia nitrogen is based on EPAs 

exposure analysis which assumed that vessel discharges would be completely mixed within the 

harbor area, acute or short term exposure of species to pollutants in close proximity to vessels, 

i.e. within discharge mixing zones, is not considered. The uncertainty associate with this 

assumption is discussed in the section entitled “Services Assessment of Uncertainty in the 

Exposure Analysis.” Although, high ammonia concentrations are predicted for discharges (fish 

hold and fish hold cleaning effluent) from some vessels, the infrequent occurrence of those 

vessels (fishing vessels) in freshwater river RAA harbors (EPA BE) suggest that the likelihood 

that sensitive listed species will be exposed, short term, to acutely toxic concentrations of 

ammonia is low. In addition, effluent limits and BMPs in the VGP/sVGP for nutrient reduction 

should further reduce the chance of hazardous exposures. 

EPA estimated that vessel discharges would result in phosphorus concentrations of 0.00594 ug/L 

in freshwater environments and 0.543 ug/L in Estuarine/Marine Environments. These values are 

well below the most protective phosphorus criteria (at this time). Low expected phosphorus 

concentrations along with effluent limits and BMPs required by the VGP/sVGP for nutrient 

reduction suggest that vessel discharges will not produce the adverse effects associated with 

nutrient enrichment. 

Effluent limitations and BMPs in the 2013 VGP and sVGP are expected to reduce/minimize 

nutrient loadings from vessel discharges. The Services conclude that adverse effects of nutrient 

loading by vessel discharges under the VGPs should not adversely affect listed resources.

Oil and Grease

Oil and grease are expressed in the BE in terms of hexane extractable material (HEM) and silica 

gel treated hexane extractable material (SGT-HEM). HEM contains relatively nontoxic 

nonvolatile hydrocarbons, oils, fats and waxes. SGT-HEM contains non polar substances, 

including toxic partially combusted hydrocarbons and petrochemical constituents such as 

polycyclic aromatic hydrocarbons, benzene, toluene, ethylbenzene and xylene (SVOCs and 
161

VOCs). EPA’s estuarine harbor model estimated post permit HEM concentrations to average 

0.013 mg/L and range from 0.0007 to 0.03 mg/L. These values represent an approximately 50 

percent reduction in hexane extractable material for all scenarios. For the river harbor model, 

EPA's average estimated post permit hexane extractable material concentration was 0.15 mg/L 

and ranged from 0.002 to 0.3 mg/L, suggesting approximately 60% reduction in discharged 

hexane extractable material. 

EPA states that it was necessary for the BE to examine the physical and toxic effects of oil and 

grease separately because a qualitative assessment was required for the HEM and quantitative 

assessments were required for the individual toxic constituents in the SGT-HEM in the section 

evaluating SVOCs and VOCs. While HEM averaged below the 15 mg/L U.S. Coast Guard and 

EPA standard screening level benchmark in most discharges, all discharges had at least one 

observation which exceeded this benchmark. Graywater was the only discharge with an average 

concentration exceeding the benchmark, at 39 mg/L, greater than twice the benchmark. EPA 

acknowledged that, due to the highly variable graywater generation volumes possible within 

vessel classes, EPA was unable to fully define graywater generation rates. 

Given the particularly high concentrations of HEM in gray water and the large volume of 

graywater relative to other discharges, graywater accounts for greater than 90% of the oil and 

grease discharged incidental to the normal operation of vessels. Loads range from as little as 4 

grams per day from utility boats to as much as 600 kg per day (0.6 tons) from large cruise 

vessels. The source of oil and grease found in graywater is expected to originate from oils, fats 

and grease used in cooking or personal care products. Oil and grease in fish hold effluent, which 

is estimated at 5 kg/and day accounts for less than 1% of a fishing vessels oil and grease 

discharge, is likely from the tissues of the fish contained in the hold. Such products (i.e., nonvolatile hydrocarbons, vegetable oils, animal fats, waxes, and greases) nominally represented by 

HEM minus SGT-HEM are both biodegradable and less toxic to aquatic and aquatic-dependent 

wildlife ((USEPA 2011d). The available data support this expectation, with relative SGT-HEM 

representing a much smaller fraction of graywater HEM (17%) relative to engine associated 

discharges (32-57%). Fish hold and deckwash discharges also have higher relative SGT-HEM, 

33-51%, which could be contributed by lubricants and other petroleum products used on the 

vessel. World-wide scale, transportation activities estimated to contribute 24% of the total oil 

input into the oceans (Tong et al. 1999). Among other vessel sources of oil and grease, bilge 

water contributes an estimated 1-12 grams oil and grease per vessel per day and deckwash (an 

intermittent exposure) contributes 1-14 grams per day, depending on vessel class. 

The BE indicates that most information on oil and grease exposures and effects for listed species 

or surrogates is associated with accidents rather than discharges due to incidental vessel 

operation. After searching the scientific literature and reports from nongovernment and 

government agencies, FWS concurs with that finding. Both petroleum and non-petroleum oils 

have similar physical properties that can harm wildlife (USEPA, 1997) such as sticking to fur 

and feathers and reducing their insulative properties. Although pre-permit oil and grease 

discharges exceeded the USCG limits, these are not be at the intensities encountered during oil 

spill events and do not likely result in effects caused by the physical characteristics of this 
162

pollutant class. Further, surface fouling by oil and grease due to VGP authorized discharges is 

not expected because post permit HEM estimates are far below those observed in the Report to 

Congress and discharges which produce a sheen must be eliminated under the VGPs. 

Metals

EPA estimates that concentrations of metals (aluminum, arsenic, cadmium, chromium, lead, 

nickel, and zinc) associated with vessel discharges are likely to be below levels that may cause 

adverse effects to listed species. Under EPAs estuarine harbor model, the overall average of post 

permit metals concentrations were 5% less that of pre permit conditions for worst case conditions 

and 13% less that of pre permit conditions for best case reductions. The range in estimated 

reductions of individual metals among the estuarine harbor models was broad, with worst case 

reductions of selenium, nickel and arsenic at 0% up to approximately 40% reduction in cadmium 

under best case conditions. For the river harbor model, the overall average post permit metals 

concentrations were 2% less that of pre permit conditions for worst case conditions and 11% less 

that of pre permit conditions for best case reductions. The range in estimated reductions for 

individual metals under the river harbor models was 0% for worst case reductions of selenium, 

nickel and arsenic up to 44% reductions in cadmium under best case conditions. Cumulative 

RQs for metals ranged up to 0.311 for exposures of estuarine/marine invertebrates, with copper 

accounting for about 95% of the cumulative RQ. Given the uncertainties in EPA’s exposure 

analysis (reviewed in the section entitled “Services Assessment of Uncertainty in the Exposure 

Analysis”), we believe that these concentrations may be higher than modeled. EPA also omitted 

discharges from zinc sacrificial anodes in its analysis. Our rough estimate of this metals source 

increases the cumulative RQ for estuarine/marine invertebrates to 0.422. In addition, vessel 

discharges are likely to combine with other sources of metals in waterways, resulting in exposure 

to species at concentrations greater than considered in this analysis. 

Metals are a diverse group of pollutants, many of which can be toxic to aquatic and aquaticdependent species. As described by EPA, vessel discharges can contain a variety of metal 

constituents which can come from a variety of on-board sources. For example, EPA’s study of 

cruise ship graywater found a total of 13 different metals in at least 10% of samples, with copper, 

nickel and zinc detected in 100% of samples (US EPA 2008). Bilgewater has also been shown to 

contain numerous metals, the exact constituents of which vary dependent upon on-board 

activities on the vessel and the materials used in the construction of the vessel. Other metals, 

such as copper, are known to leach from vessel hulls and can cause exceedances of water quality 

standards. For example, Srinivasan and Swain (2007) found significant leaching of copper from 

the hulls of sailboats, powerboats, and cruise ships. 

While some metals, including copper, nickel and zinc, are known to be essential to organism 

function, many others, including thallium and arsenic, are non-essential and/or are known to 

have only adverse impacts. Exposure to metals at toxic levels (which is partially dependent on 

the essentiality of the metal) can cause a variety of changes in biochemical, physiological, 

morphological, and behavioral patterns in aquatic and aquatic-dependent organisms. In the 

aquatic environment, elevated concentrations of dissolved metals can be toxic to many species of 
163

algae, crustaceans, and fish because it is this dissolved form of the metal that is most readily 

available and taken up and internalized by an organism. Additionally, metals may not be fully 

eliminated from blood and tissues processes, and may bioaccumulate in predatory and 

scavenging organisms further up the food chain, including fish, birds, reptiles, and mammals.

One of the key factors in evaluating risk from exposure to metals is the bioavailability of the 

metal to an organism. As indicated above, some metals have a strong tendency to adsorb to 

suspended organic matter and clay minerals, or to precipitate out of solution, thus removing the 

metal from the water column. The tendency of a given metal to adsorb to suspended particles is 

typically controlled by the pH and salinity of the waterbody, as well as the organic carbon 

content of the suspended particles. If the metal is highly sorbed to particulate matter, then it is 

likely to not be in a dissolved form that aquatic organisms can process, i.e., bioavailable. 

Accordingly, the protection of aquatic life for metals is typically expressed in the dissolved metal 

form. 

In contrast, evaluation of total metals is more appropriate for aquatic-dependent animals where 

the primary route of exposure is assumed to be through the consumption of aquatic organisms, 

and where the digestive process is assumed to transform all forms of metals to the dissolved 

phase, thus increasing the amount of biologically available metals. This latter is also applicable 

in aquatic animals exposed to metalloids such as arsenic and selenium. 

EPA describes effects of aluminum, arsenic, cadmium, chromium, lead, nickel, and zinc that 

result in measured changes to survival, growth, and reproduction. In addition, each of these 

elements may result in sublethal effects to aquatic and aquatic-dependent wildlife that may affect 

a species’ fitness, either alone or in combination with other physiological or environmental 

stressors. Exposure to metals may result in a wide range of effects to endpoints such as behavior, 

enzyme activity, blood chemistry, osmoregulation, respiration, disease resistance, and other 

physiolological parameters. In many cases, these effects have been found to occur at 

concentrations lower than those used in established aquatic life criteria (Eisler 2000). 

One example of a particular sensitive endpoint is avoidance behavior in fish, observed at 

concentrations as low as 23.9 ug/L nickel and 10 ug/L zinc in rainbow trout (Eisler 2000). Other 

sublethal effects of metals were recorded at concentrations generally consistent with those 

observed to effect survival, growth, and reproduction.

While abundant data are available for metal effects in most aquatic species, information on 

metals in marine mammals is generally limited to tissue concentrations (Varanasi et al. 1994, 

Sanpera et al. 1996, Wagemann et al. 1996, Wood and VanVleet 1996, Sydeman and Jarman 

1998, Meador et al. 1999, Welfinger-Smith et al. 2011). There are a few in vitro investigations 

demonstrating cytolotoxic, genotoxic and immunotoxic effects of metals in marine mammal 

tissues (DeGuise et al. 1996, Kakuschke et al. 2008, Frouin et al. 2010, Chen et al. 2012). While 

data from in vitro studies are difficult to interpret in ecological terms, they identify the 

mechanisms by which pollutants affect organisms. 

Because EPA’s modeled concentrations of the metals aluminum, arsenic, cadmium, chromium, 

lead, nickel, and zinc are well below levels documented to cause adverse effects in aquatic and 
164

aquatic-dependent species, we do not anticipate adverse effects to listed species from therse 

metals discharged from vessels, even given the uncertainties associated with the assessment. We 

believe that monitoring of discharges from new builds will assist in the reduction of uncertainty 

regarding these concentrations and assist in the verification of assumptions made herein.

Copper

Copper concentrations estimated by EPA from anti-fouling hull coatings and other discharges 

range up to 2.99 ug/L pre-permit and 2.33 ug/L post-permit in hypothetical estuarine harbor 

scenarios, and up to 0.164 ug/L pre-permit and 0.131 ug/L post-permit in hypothetical river 

harbor scenarios, suggesting an approximately 20 percent reduction in discharges of dissolved 

copper. Post permit copper estimates fell below the response thresholds selected by EPA for 

evaluating risks of exposure to copper. These thresholds ranged from 3.5 to 119 ug/L for 

freshwater organisms and from 7.9 ug/L to 249 ug/L for estuarine/marine organisms. The 

threshold values EPA selected for freshwater and estuarine/marine invertebrates and for marine 

vertebrates were derived from NOECs and LOECs. The invertebrates NOECs were 2.5 ug/L and 

6.1 for freshwater and estuarine/marine organisms, respectively. The NOEC for 

estuarine/marine vertebrates was 249 ug/L.

EPA predicts that high-end concentrations are likely to be overestimations of even worst-case 

scenarios. However, we believe that given the uncertainties in EPA’s exposure analysis 

(reviewed in the section entitled “Services Assessment of Uncertainty in the Exposure 

Analysis”), species may be exposed to copper concentrations from vessel discharges that not 

only meet, but exceed estimates calculated by EPA. In addition, vessel discharges are likely to 

combine with other sources of copper in waterways to produce even higher concentrations than 

those predicted in this analysis. At present, copper impairs 14,000 miles of rivers and streams 

(12% of impaired rivers and streams) and 964 square miles of bays and estuaries (43% of

impaired bays and estuaries). Due to the high sensitivity of aquatic species to copper, adverse 

effects to listed species are likely to occur if copper discharges from vessels reach concentrations 

predicted in this analysis.

As described by EPA, copper is a nutritionally essential inorganic element for all species, both 

plant and animal, and thus has the potential to accumulate in tissues of aquatic animals. As long 

as water column or dietary concentrations are not so high as to overwhelm homeostatic 

mechanisms, aquatic species are able to regulate their internal body burden of copper. Aquatic 

organism exposure to copper concentrations in excess of nutritional needs via other potential 

routes of exposure in addition to direct waterborne toxicity (e.g. dietary toxicity) may pose a 

threat to listed species. Toxicity of copper to aquatic organisms is dependent on pH, temperature, 

alkalinity, hardness, and concentrations of bicarbonate, sulfide, and organic ligands. Synergistic 

toxicity is suggested for mixtures of copper and aluminum, iron, zinc, mercury, anionic 

detergents, or various organophosphorus insecticides (Eisler 2010). 

In its BE, EPA describes effects of copper from studies that directly measure changes to survival, 

growth, and reproduction. In addition to these endpoints, exposure to contaminants may result in 

sublethal effects to aquatic and aquatic-dependent wildlife that may affect a species’ fitness, 
165

either alone or in combination with other physiological or environmental stressors. In many 

cases, these effects have been found to occur at concentrations lower than those that directly 

affect survival, growth, or reproduction. They may also be lower than criteria that have been 

deemed protective of aquatic life. In the case of copper, effects upon chemoreception and 

behavior have been particularly well-studied and documented in aquatic species. Though not 

discussed in the BE, EPA describes these effects in its report to Congress:

At relatively low concentrations, copper is toxic to a wide range of aquatic 

organisms, not just fouling organisms (CRWQCB, 2005). Concentrations as low as 5 to 

25 μg/L can be lethal for marine invertebrates (Chambers et al., 2006). Elevated copper 

levels affect growth, development, feeding, reproduction, and survival at various life 

stages of fish, mussels, oysters, scallops, crustaceans, and sea urchins. High copper levels 

also change the types of phytoplankton that thrive in boat basins (Calabrese et al., 1984). 

Low levels of dissolved copper affect the olfactory capabilities in juvenile Coho salmon, 

which is critical for homing, foraging, and predator avoidance (Baldwin et al., 2004). The 

effect of copper on olfaction of juvenile salmonids suggests that copper might affect 

other fish species, too. Most effects on fish are sublethal (e.g., they may hinder metabolic 

processes, reproduction, development, activity levels and behavior). Thus, the damage is 

chronic and less noticeable than, for example, fish kills caused by sudden oxygen 

depletion (Evans et al., 1994). 

Hecht et al (2007) compiled data on sensory effects to juvenile salmonids exposed to dissolved 

copper. In their analysis, benchmark concentrations ranged from 0.18 – 2.1 μg/L, corresponding 

to reductions in predator avoidance behavior from approximately 8 – 57%. Recent work is 

consistent with previous observations (Baldwin et al. 2011, McIntyre et al. 2012). These effects 

can manifest over a period of minutes to hours and can persist for weeks. In aquatic systems, 

chemoreception is one of oldest and most important sensory systems used by animals to collect 

information on their environment and generate behaviors involved in growth, reproduction, and 

survival (Pyle and Mirza 2007). These behaviors include recognition of conspecifics, mates and 

predators, food search, defense, schooling, spawning and migration. Stimuli are perceived by 

sensory structures and converted to electrical signals that are conducted to the central nervous 

system where the information is integrated and appropriate behavioral responses are generated 

(Baatrup 1991). Detection of chemical signals involves not only recognition of a spectrum of 

unique compounds or mixtures but also their spatial and temporal distribution in the medium 

(Atema 1995). Sensory receptors are in direct contact with the environment, and therefore 

pollutants may disrupt normal chemosensory function by masking or counteracting biologically 

relevant chemical signals or by causing direct morphological and physiological damage to the 

receptors (Baatrup 1991). 

These concentration thresholds for juvenile salmonid sensory and behavioral responses fall 

within the range of other sublethal endpoints affected by dissolved copper, such as behavior, 

growth, and primary production (Hecht et al 2007). In addition to sensory effects, impaired 

disease resistance, hyperactivity, impaired respiration, disrupted osmoregulation, pathology of 

kidneys, liver, and gills, impaired function of olfactory organs and brain, altered blood 

chemistry, and enzyme activity have been documented in fish, with effects thresholds as low as 
166

0.1 ug/L (Eisler 2000). Like olfactory effects, other sublethal effects may manifest quickly and 

persist after exposure ceases. For example, Munoz et al. (1991) observed rapid elevations of 

plasma cortisol, an indicator of stress, in rainbow trout after a 1-hour exposure to approximately 

0.2 μg/L of copper at a hardness of 12 mg/L. The elevated plasma cortisol levels were 

maintained throughout the experiment’s duration of 21 days. Elevated plasma cortisol levels are 

indicative of stress, and potentially represent a diversion of energy from normal physiological 

processes that may render salmonids more vulnerable to disease. 

Information for effects on other anadromous species groups are limited to data for white 

sturgeon. This species, particularly early life stages, is highly sensitive to copper, with LC20 

response thresholds falling within the range of concentrations causing sensory effects in 

salmonids as described by Hecht (2007) (Vardy et al. 2011, Little et al. 2012). Data on copper 

for marine mammals are limited to tissue concentrations (Varanasi et al. 1994, Sanpera et al. 

1996, Wagemann et al. 1996, Wood and VanVleet 1996, Sydeman and Jarman 1998, Meador et 

al. 1999, Welfinger-Smith et al. 2011).

Sublethal effects from low levels of copper have also been documented in mussels and other 

mollusks. Exposure to copper at concentrations <10 ug/L has been demonstrated to affect valve 

closure rate, ability of glochidia to infect host fish, growth, swimming behavior, oxygen 

consumption, ammonia excretion, and spawning frequency (Eisler 2000). In freshwater mussels, 

mean 10% inhibition concentrations were as low as 3.1 ug/L for survival and 5.5 ug/L for growth 

following 28 days of exposure (Wang et al. 2009). Even lower concentrations produced effects to 

biomass and survival in rainbow mussels (Villosa iris) (Wang et al. 2011). Both metrics varied 

with concentration of dissolved organic content (DOC), and resulted in reductions to biomass at 

levels as low as 0.8 ug/L (biotic ligand model normalized EC20; 2.5 mg/L DOC) and to survival 

at levels as low as 1.7 ug/L (biotic ligand model normalized EC20; 10 mg/L DOC) (Wang et al 

2011). 

As described above, effects of copper can manifest following very short exposures to copper 

(minutes to hours). Therefore, the potential for species to be exposed can result from both 

chronic loading and acute discharges. EPA’s Report to Congress indicated that average 

concentrations of dissolved copper were found to exceed benchmark screening levels in every 

sampled discharge type except for outboard engine and generator engine effluents. 

Concentrations in these discharges ranged from 22 – 100 ug/L, far exceeding effect thresholds 

described above.

EPA’s copper monitoring plan will identify areas of high concentrations of ships with copperhull coatings. Where these areas overlap with sensitive listed species, additional actions will be 

taken to reduce exposure. Because copper toxicity can manifest quickly (minutes to hour) at 

very low concentrations, we expect adverse effects such as disrupted chemoreception to occur 

even with this monitoring in place. However, we expect that EPA’s monitoring plan will prevent 

these effects from rising to the level of jeopardy. 
167

Selenium

EPA reported that selenium was detected in several vessel discharges authorized by the VGPs 

(USEPA 2010, USEPA 2012a). Among those, discharges from Exhaust Gas Scrubbers have the 

potential to generate substantial selenium loadings. As described in the section entitled 

“Discharges Authorized by the VGP and sVGP,” exhaust gas scrubbers are used to clean the 

exhaust gas system on marine diesel engines. These discharges can be highly acidic, and can 

contain traces of oil, polycyclic aromatic hydrocarbons (PAHs), nitrogen, selenium and other 

metals. Relatively few vessels currently use seawater scrubber technology, however, more 

restrictive air emissions standards, adopted in 2008, will become enforceable in 2012 (EPA 

2011). To comply with these new standards, which require lower emissions of SOx, vessels can 

either burn low sulfur fuel oil or clean the exhaust gas. Cleaning, or scrubbing, the exhaust gas 

is generally accepted to be more economical (EPA 2011). Therefore, EPA anticipates that the 

number of vessels using exhaust gas scrubbers may increase significantly (EPA BE Table 3-3).

In their Biological Evaluation, EPA estimated selenium loadings to Reference Action Area 

(RAA) harbors from vessel discharges authorized under the VGPs, resulting concentrations of 

selenium in harbor waters, and risk to listed species from selenium exposure. EPA modeled 

several RAA harbor scenarios using different values for selected parameters, i.e. flushing time, 

percentage of vessels equipped with wet exhaust gas scrubbers, and concentration of selenium in 

scrubber effluent. Scenarios expected to produce the highest selenium concentrations in water 

also predicted the highest selenium loading. For some harbors, loads exceeded 30 lb Se/day and 

would represent a significant new source of selenium. For example, recent studies of the San 

Francisco Bay-Delta report selenium loading from oil refineries, which along with agricultural 

drainage comprise the two major sources of selenium to the system, of 1287 lb Se/year in 2009 

or about 3.5 lb Se/day (Presser and Luoma 2010a). EPA predicted selenium loading to San 

Francisco Bay, from vessel discharges, of 30.3 lb Se/day (Post-permit: EPA BE Table G-9), 

which is nearly 9 times greater than loading from refineries and more than twice the combined 

load from refineries and agriculture.

Following discussions with the Services, EPA re-assessed their original loading estimates for 

selenium. They acknowledged that their initial predictions of the number of vessels that would 

be using exhaust gas scrubbers (10% of vessels in specific classes) were unrealistically high. 

They also re-examined the analytical data for selenium in exhaust gas scrubber washwater 

effluent and concluded that concentrations may be unexpectedly high because of matrix 

interferences found in seawater. EPA revised their loading estimates for selenium using two 

approaches to account for potential interferences (USEPA 2012c). The revised selenium 

loadings and predicted concentrations of selenium in RAA harbors and substantially lower than 

the original estimates (USEPA 2012c).

It is worth noting that while EPA considers their original loading estimates to be unrealistically 

high they, nevertheless, concluded that risks to listed species from these high selenium 

discharges would be “negligible” (for anadromous salmonids/sturgeons and marine mammals) or 

“remote” (for all other taxa) (EPA BE Table 5-42). These conclusions were based on risk 

quotients which ranged from 0.002 to 0.136 for surrogate animal taxa. In addition, to account for 
168

any possible (although unexpected) difference in sensitivity between a listed species and its 

surrogate, EPA opted to apply its recently published safety adjustment factor of 2.0 (see Mayer 

et al., 2008) to the Agency’s criterion continuous concentration (i.e. chronic criterion) to further 

evaluate risk to listed species. Risk quotients using the safety adjustment factor approach were 

0.06 for saltwater and 0.1 for freshwater (EPA BE Table 5-56). Considering the relative 

magnitude of these predicted loadings (based on original estimates) compared to known 

anthropogenic sources of selenium, such as described above for the San Francisco Bay-Delta, it 

is surprising that EPAs methodology predicted that risks to listed species would so low. 

As we analyzed the potential effects, on listed species, of selenium-containing vessel discharges 

we became aware of information regarding the chemical/biological dynamics of selenium in 

aquatic environments and effects to aquatic and aquatic-dependent species that did not appear to 

be considered by EPA in their risk assessment. Much of this information was produced as the 

outcome of prior consultations with EPA on water quality criteria for selenium in California. 

The following excerpt from a 2010 USGS report by Presser and Luoma (2010a) describes the 

history and context for the derivation of selenium criteria intended to protect listed fish and 

wildlife species in California which, we believe, will help inform the risk assessment for the 

VGPs:

“Adjustments to the development of Se criteria specifically for California were called for 

by 1) the USEPA through the National Toxics Rule (NTR) and the California Toxics 

Rule (CTR) (USEPA, 1992; 2000); and 2) the USFWS and National Marine Fisheries 

Service (NMFS) through their Biological Opinion (USFWS and NMFS 2000). In general, 

these adjustments were necessary to consider 1) the bioaccumulative nature of Se in 

aquatic systems; 2) Se’s long-term persistence in aquatic sediments and food webs; 3) the 

importance of dietary pathways in determining toxicity; and 4) protection of threatened 

and endangered species.” 

Specifically, pursuant to section 7(a) of the U.S. Endangered Species Act (ESA) (1973), the 

USEPA consulted with the USFWS and NMFS concerning USEPA’s rulemaking action for 

California. USEPA submitted a Biological Evaluation for their review as part of the consultation 

process in 1994. This evaluation found that the proposed CTR was not likely to jeopardize the 

continued existence of any federally listed species or result in the destruction or adverse 

modification of designated critical habitat. In April of 1998, the Services sent USEPA a draft 

Biological Opinion that found that USEPA’s proposed rule would jeopardize federally listed 

species. After discussions with the USFWS and NMFS, the USEPA agreed to several changes in 

the final rule and USFWS and NMFS, in turn, issued a final Biological Opinion finding that 

USEPA’s action would not likely jeopardize the continued existence of federally listed species. 

The agencies agreed that federally listed fish and wildlife species that are aquatic system foragers 

would be protected under future criteria and procedures for site-specific adjustments.

To achieve these goals and as part of the remedy for these problems, the USEPA initiated an 

interagency project with the USFWS and the U.S. Geological Survey (USGS) to address issues 

of 1) a methodology for translation of a tissue guidelines to protective site-specific dissolved Se 

concentrations (implementation of tissue criteria); 2) inclusion of protection of wildlife species 
169

(i.e., federally listed species) in regulatory methodologies; and 3) site-specific criteria 

development for the Bay-Delta (USEPA, 1999). 

A methodology for ecosystem-scale modeling of Se is now available (see Appendices A and B, 

Luoma and Presser, 2009; Presser and Luoma, 2010). Analysis from this biodynamically-based 

methodology showed, in general, that:

 a crucial factor ultimately defining Se toxicity is the link between dissolved and 

particulate phases at the base of the food web (i.e., Kd); 

 collection of particulate material phases and analysis of their Se concentrations are key to 

representing the dynamics of the system; 

 bioaccumulation in invertebrates is a major source of variability in Se exposure of 

predators within an ecosystem, although that variability can be explained by invertebrate 

physiology (i.e., TTFinvertebrate); 

 TTFfish is relatively constant over the range of species considered here; and 

 Se concentrations are at least conserved and usually magnified at every step in a food 

web.”

The ecosystem-scale model developed by Presser and Luoma (2010a & b) reveals the 

importance of understanding the biodynamics of selenium in aquatic environments to more 

accurately predict selenium toxicity. Conventional methods that relate water column selenium 

concentrations to tissue concentrations using bioaccumulation factors (BAFs), as was used in in 

the BE, have a high degree of uncertainty (Presser and Luoma, 2010b). We reevaluated the risk 

assessment for selenium to examine how the analysis might benefit from a more informed, 

ecosystem-scale, approach. We adapted the model used to support criteria development (Error! 

Reference source not found.) to estimate tissue concentrations (referred to as ECT values in the 

BE) from concentrations of selenium in water (Error! Reference source not found.). For this 

evaluation we selected parameter estimates (Kd’s and TTFs; Error! Reference source not 

found.) that were developed by Presser and Luoma (2010a) for the San Francisco Bay-Delta 

system, as well as, estimates used to represent a hypothetical estuary (Presser and Luoma 

2010b). We incorporated effects estimates for fish and bird reproduction (i.e. larval 

edema/skeletal defects and hatchability) and survival that were derived by the USFWS and used 

by Pressor and Luoma (2010a) to predict water concentrations necessary for protecting sensitive 

listed fish and bird species in the San Francisco Bay-Delta.

Our revaluation indicates that EPAs, BAF-based, analysis likely underestimates risks of 

selenium exposure to listed species. As previously mentioned, EPA concluded (based on their 

original loading estimates) that risks to listed species from selenium discharged by vessels would 

be negligible for some taxa and remote for others. In contrast, risk quotients calculated using the 

ecosystem-scale approach ranged from 2.05 to 79.8 (Error! Reference source not found.), 

indicated that significant effects on reproduction and survival would likely occur. Risk quotients 

for the alternative exposure scenarios A and B (where fewer vessels are discharging EGS 

washwater and the Se effluent concentrations are lower; USEPA 2012c) were substantially 

lower. However, even at the lower exposures predicted under scenarios A and B some of the 
170

risk quotients for the San Francisco Bay-Delta model approached or equaled 1.0 for fish and 

exceeded 1 for birds using our methodology discussed above. These results suggest that 

selenium from vessel discharges could pose a risk to listed species in the future if the number of 

vessels utilizing exhaust gas scrubbers increase beyond what is anticipated. 

EPA has agreed to develop and implement a monitoring plan for gas-scrubber discharges. With 

technical assistance from the Services, EPA will identify metrics for assessing selenium loadings 

in waters inhabited by ESA listed species. They will also state which analytical methods should 

be used to accurately measure selenium in saline gas-scrubber discharges. EPA will also 

compile NOI and annual report information regarding the number and type of vessels using 

exhaust gas scrubbers and discharge monitoring data for selenium. And finally, EPA will 

evaluate vessel data, identify ports/locations where the metric has been exceeded and will, as 

appropriate, identify and implement additional actions to reduce any unacceptable risk.

Table 29. Generalized steps in ecosystem-scale methodology for translation of a tissue Se 

concentration to a water-column Se concentration for protection of fish and aquaticdependent wildlife. [Adapted from Table 2, Presser and Luoma, 2010a, 2010b]

Translation of Tissue Criterion to Water-Column Concentration

 Develop a conceptual model of food webs in watershed.

 Choose toxicity guideline for fish or aquatic bird species in estuary

 Choose fish or bird species to be protected in watershed.

 For fish, choose species-specific TTFfish or use default TTFfish of 1.1: for birds, choose 

species-specific TTFbird or use default TTFbird of 2.0.

 Identify appropriate food web(s) for selected fish or bird species based on speciesspecific diet.

 Choose site-specific TTFinvertebrate for invertebrates in selected food web(s) or use default 

TTFinvertebrate for species of invertebrates (see list in Presser and Luoma, 2010b).

 Choose site-specific Kd or use Kd indicative of a) generalized source of Se and receiving 

water conditions or b) site-specific hydrologic type and speciation; or a default Kd of 

1000 (see list in Presser and Luoma, 2010b).

 Solve equation(s) for allowable water-column concentration for protection of fish or 

birds (i.e. predator):

 If assume single invertebrate diet, then

 • Cwater = (Cpredator) ÷ (TTFpredator)(Kd)(TTFinvertebrate)

 If assume a mixed diet of invertebrates, then

 • Cwater = (Cpredator) ÷ (TTFpredator)(Kd)[(TTFinvertebrate a)(prey fraction)]

 + [(TTFinvertebrate b) (prey fraction)] + [(TTFinvertebrate c) (prey fraction)]
171

 If assume sequential bioaccumulation in longer food webs, then

 • Cwater = (Cpredator) ÷ (TTFpredator)(Kd)(TTFinvertebrate a) (TTFforage fish)

 • Cwater = (Cpredator) ÷ (TTFpredator)(Kd)(TTFTL2 invertebrate)(TTFTL3 invertebrate)( TTFTL3 fish)

 where TL=trophic level

Table 30. Equations used to calculate Fish and Bird ECT’s for the Biological Opinion.

[Adapted from Presser and Luoma, 2010a.]

Translation of Water-Column Selenium Concentrations to

Tissue Concentrations

 Fish ECT = Cfish-clam pathway = (Cwater )(Kd)(TTFclam)(TTFfish)

 Fish ECT = Cfish-invertebrate pathway = (Cwater)(Kd)(TTFinvert)(TTFfish)

 Bird ECT = Cbird-clam pathway = (Cwater)(Kd)(TTFclam)(TTFbird)

Table 311. Kd and TTF values used to calculate fish and bird ECT’s.

Kd and TFF values

San Francisco 

Bay-Delta1

Hypothetical 

Estuary2

Kd 5784 3000

TTFinvertebrate 2.8 1.3

TTFclam 17.1 6.25

TTFfish 1.1 1.1

TTFbird 2.6 1.8
172

1

from Presser and Luoma 2010a, Kd value is average of four time periods (Table 17)

2

from Presser and Luoma 2010b, Figure 6D&E.
173

Table 32. Application of the Ecosystem-scale approach to: a) estimate tissue concentrations of selenium from water 

concentrations predicted from vessel discharges, and b) calculating risk quotients for sensitive fish and bird species (adapted 

from Presser and Luoma 2010a&b).

Risk Quotients (ECT/EC10 or NEC)

Percentage of vessels 

with EGS

1

Selenium concentration 

in EGS discharge 

(ug/L)

1

Max Selenium 

concentration among 

RAA Harbors (ug/L)

1

Fish EC

T (insect food 

web) (ug/g dw)

Fish EC

T (clam food 

web) (ug/g dw)

Bird EC

T (clam food 

web) (ug/g dw)

Adult female sturgeon 

[EC10 for larval edema 

and skeletal 

defects=8.1ug/g dw]

Juvenile salmon [whole 

body EC10 for mortality 

= 1.8 ug/g dw]

Generic insect-eating 

fish [whole body 

NEC=5.0 ug/g dw]

Bird (scoter and scaup) 

egg [EC10 for 

hatchability=7.7 ug/g 

dw]

San Francisco Bay-Delta

Original BE 

estimate 10 100 2.39 42.6 260.0 614.6 32.1 23.7 8.5 79.8

Revised estimateScenario A 1 14.5 0.035 0.6 3.8 9.0 0.5 0.3 0.1 1.2

Revised estimateScenario B 1 31.2 0.075 1.3 8.2 19.3 1.0 0.7 0.3 2.5

Hypothetical Estuary

Original BE

estimate 10 100 2.39 10.3 49.3 80.7 6.09 5.70 2.05 10.48

Revised estimateScenario A 1 14.5 0.035 0.2 0.7 1.2 0.09 0.08 0.03 0.15
174

Revised estimateScenario B 1 31.2 0.075 0.3 1.5 2.5 0.19 0.18 0.06 0.33

1

data from USEPA 2012c (Addendum to the Biological Evaluation)
175

Classical Pollutants

Classical pollutants combine several standard water quality parameters such as conductivity, 

salinity, temperature, pH, Biochemical Oxygen Demand (BOD), etc. along with other parameters 

EPA defined as conventional pollutants such as total suspended solids (TSS) and total residual 

chlorine (TRC). In its BE, EPA limited its analysis to TRC and TSS. EPA also stated that only 

those pollutants with toxic effects (i.e., TRC) to aquatic and aquatic-dependent species lend 

themselves to analysis of quantitative effects.

Biological Oxygen Demand (BOD). BOD is a measure of the oxygen used by microorganisms 

to oxidize organic matter present in water. Bacteria working to decompose organic matter 

consume oxygen in the process, exerting an oxygen demand in wastewater and receiving waters, 

thereby depressing dissolved oxygen (DO) concentrations. If there is a large quantity of organic 

waste in water, there will be substantial demand for oxygen, resulting in a high BOD and the 

associated potential to depress DO concentrations in receiving waters. As the waste is consumed 

or dispersed through the water, BOD levels will begin to decline.

Vessel discharges that exert relatively high oxygen demand include fish hold effluent, 

bilgewater, deckwash and graywater. BOD levels in these discharges exceed the screening level 

benchmark for wastewater discharges of 30 mg/L12 by at least an order of magnitude. Although 

BOD is highest in fish hold effluent, averaging 840 mg/L, the net oxygen demand only accounts 

for less than 3% of a the total organic matter discharge from a fishing vessel. Due to its greater 

volume, graywater accounts for 90% or more of a vessel’s organic matter discharge even though 

BOD levels are barely over half that of fish hold effluent, averaging 430 mg/L. Deck washdown 

and bilge water BOD levels are 430 and 190 mg/L, respectively and account for less than 0-6% 

of a vessels organic matter discharge, depending on service class. EPA estimated post permit 

BOD in the estuarine harbor model averaged 0.16 mg/L and ranged from 0.005 to 0.68 mg/L, 

suggesting a 16 to 26 percent reduction in organic material discharged. For the river harbor 

model, EPA's average estimated post permit BOD was 4.17 mg/L and ranged from 0.0459 to 

9.11 mg/L, suggesting a 1 to 9 percent reduction in organic material discharged. 

The implications of BOD loading on dissolved oxygen in receiving waters was not evaluated by 

EPA. However, organic enrichment and oxygen depletion is the fourth most common cause for 

impairment among 303(d) listed waters. Nearly 4250 waters of the United States are listed with 

this impairment, with about 550 of them marine environments (388 miles of coastline and 3000 

square miles of ocean, bays and estuaries). Low dissolved oxygen alters biological assemblages 

and the food webs of which they are a part. The oxygen status of water also influences 

biologically mediated environmental fate processes of pollutants like mercury methylation and 

metabolism of organic chemicals. While organic loading from the many land based sources are 

 

12 The screening level benchmark for BOD is based on the 1984 secondary treatment limit for publically owned

treatment works (see 49 FR 37006, Sept. 20, 1984).
176

orders of magnitude larger than that from vessels, vessel discharges pose yet another incremental

source to those land based loadings. Data are not available to place vessel organic loading in 

context of consequences for our species. We review the effect of low dissolved oxygen on listed 

resources and their surrogates to acknowledge the potential effects of this discharge constituent 

on listed resouces.

Intergravel dissolved oxygen concentrations for survival of embryo and larval salmonids need to 

be at least 8 mg/L dissolved oxygen, which requires dissolved oxygen levels of 11 mg/L in 

overlying water. Other salmonid lifestages require 8 mg/L in the water column, with 

impairments to productivity occurring when levels decline to 6 mg/L or lower (LD and CA 

20056). Sturgeon basal metabolism, growth, consumption and survival are all very sensitive to 

changes in oxygen levels, which may indicate their relatively poor ability to oxyregulate. Based 

on bioenergetics and behavioral responses of young of the year juveniles aged 30 to 200 days, 

productivity losses occurred at oxygen saturation levels below 60 percent, which corresponds to 

5 mg/liter at 25oC (Wirth et al. 2000). Accordingly, dissolved oxygen levels of 5 mg/L and 

above are also considered protective of sturgeon (Southworth et al. 2011). 

Services Conclusion. Direct linkage of BOD with adverse effects on listed species is 

complicated by extrapolating the organic loading represented by BOD to actual levels of the 

proximate stressor, low dissolved oxygen. The VGPs limit discharges into impaired waters, 

discharges of high BOD waste streams in protected areas, and requires BOD monitoring of 

graywater in new build vessels. These restrictions lead FWS to conclude that BOD contributions 

from vessels compliant with the VGPs are not likely tip the balance between neutral and harmful 

levels of organic loading to waters where our species occur.

Total Residual Chlorine (TRC). Chlorine gas released into water first dissolves and then 

undergoes immediate conversion into two forms of free chlorine: hypochlorous acid (HOCl) and 

the hypochlorite ion (OCl-). If the water contains ammonia, the solution will likely also contain 

two forms of combined chlorine: monochloramine and dichloramine. Because all four of these 

forms of chlorine can be toxic to aquatic organisms, the term “total residual chlorine or TRC” is 

used to refer to the sum of free chlorine and combined chlorine in fresh water. However, because 

salt water contains bromide, addition of chlorine also produces hypobromous acid (HOBr), 

hypobromous ion (OBr-), and bromamines (USEPA 2010). These products are referred to as 

chlorine produced oxidants. Total residual chlorine was detected in bilgewater, deck washdown, 

and graywater discharges. Eighty eight to nearly 100% of the total residual chlorine load from 

vessels is discharged in graywater at concentrations ranging from 13 mg/day from utility vessels 

to nearly 2 kg per day from large Cruise ships (USEPA 2010). 

The post permit TRC concentrations in EPA’s estuarine harbor model averaged 0.1 ug/L and 

ranged from 0.002 ug/L to 0.0007 mg/L, suggesting an approximately 25 to 70 percent reduction 

in TRC discharged. For the river harbor model, EPA's average post permit TRC was 0.0014

mg/L and ranged from 0.0144 ug/Lto 0.0032 mg/L, suggesting a 3 to 15 percent reduction the 

amount of TRC discharged. These post permit TRC estimates fell below the response thresholds 

selected by EPA for evaluating risks of exposure to TRC. These thresholds ranged from 3.7 to 
177

50 mg/L for freshwater organisms and from 7.5 ml/L to 46.5 ml/L for estuarine/marine 

organisms. The threshold values EPA selected for freshwater and estuarine/marine vertebrates 

and for freshwater vertebrates were derived from NOECs and LOECs. The vertebrate NOECs 

were 6 ml/L and 40 ml/L for freshwater and estuarine/marine organisms, respectively. The 

NOEC for freshwater invertebrates was 2 ug/L.

Services Conclusion. Chlorine is not expected to bioaccumulate in plants or animals since it 

reacts with the moist tissues of living systems (Compton, 1987; Schreuder and Brewer, 2001; 

Schmittinger et al., 2006). Also, chlorine is toxic to microbial communities; therefore, 

biodegradation is not considered to be a relevant fate process (Vetrano, 2001). In general, the 

hypochlorous acid formed during the dissolution of chlorine in natural waters reacts with organic 

and inorganic materials, ultimately forming chloride ion, oxidized inorganics, chloramines, 

trihalomethanes, oxygen, and nitrogen. Consequently, chlorine does not persist in the aquatic 

environment in the form in which it was discharged. As such listed species and their critical 

habitat are not expected to be exposed to total residual chlorine at levels which could cause 

adverse effects.

Total Suspended Solids 

EPA’s estimated post permit TSS concentrations in the estuarine harbor model averaged 0.0281 

mg/L and ranged from 0.0015 to 0.13 mg/L, suggesting a 35 to 55 percent reduction in TSS

discharges. For the river harbor model, EPA's post permit TSS averaged 0.72 mg/L and ranged 

from 0.00764 to 1.62 mg/L, suggesting a 35 to 40 percent reduction in TSS discharges. Post 

permit TSS estimates fell below the response threshold of 3.33 mg/L selected by EPA for 

evaluating risks of exposure to TSS. This threshold is based on EPAs existing ambient water 

quality criteria converted into TSS equivalents. 

Direct effects of suspended materials on invertebrates and fish are complex, ranging from 

behavioral to physiological to toxicological. Suspended sediments have been documented to 

have a negative effect on the survival of fish, freshwater mussels, and other benthic organisms. 

In a frequently cited review paper prepared by Newcombe and Jensen (1996), sublethal effects 

(e.g. increased respiration rate) were observed in eggs and larvae of salmonids and 

nonsalmonids, as well as in adult estuarine and freshwater non-salmonids, when exposed to Total 

Suspended Solids concentrations as low as 55 mg/L for one hour. Mussels compensate for 

increased levels of suspended sediment by increasing filtration rates, increasing the proportion of 

filtered material that is rejected, and increasing the selection efficiency for organic matter. 

Excess sediment smothers benthic organisms and the surface layer of the benthos can be heavily 

impacted and altered. Increased turbidity associated with suspended sediments can reduce 

primary productivity of algae as well as growth and reproduction of submerged vegetation (Jha, 

2003). In addition, once in the system, resuspension and deposition can “recycle” sediments so 

that they exert water column and benthic effects repeatedly over time and in multiple locations.

Services Conclusion. A review of effects thresholds described in studies published between 

1969 and 2001 supports EPAs conclusion that TSS discharges authorized by the VGPs alone 
178

would not result in adverse effects (Rowe et al. 2003). While TSS loading from the many land 

based sources are orders of magnitude larger than that from vessels, vessel discharges pose yet 

another incremental source to those land based loadings. The RQ for vessel associated TSS 

loading in freshwater environments is 3 orders of magnitude lower than the threshold for a risk 

conclusion of “remote” (RQ=0.1). The RQ for eastuarine/marine environments is higher, but 

still ~ an order of magnitude below the threshold for a risk conclusion of “remote” (RQ=0.1). 

FWS concludes that TSS contributions from vessels are therefore not expected to tip the balance 

between neutral and harmful levels of TSS in waters where our species occur.

VOCs and SVOCS

The toxicity of oil and grease measured as SGT-HEM to aquatic and aquatic-dependent animals 

is most often attributed to the water-soluble monocyclic aromatic hydrocarbons or MAHs 

(benzene, toluene, ethylbenzene, and xylene, otherwise known as BTEX), and the polycyclic 

aromatic hydrocarbons or PAHs (McGrath and DiToro, 2009). EPA’s study of cruise ship 

graywater found a total of 17 different volatile and semi-volatile organic compounds in at least 

10 percent of samples, for which the most significant rates and levels of detection were 

phthalates, phenol, and tetrachloroethylene. EPA also found elevated pththalates (bis(2-

ethylhexyl)phthalate) in a few bilgewater and stern tube packing gland effluent samples, as well 

as benzene in bilgewater (USEPA 2010). 

EPA stated that for many of the VOCs and SVOCs, there are no definitive chronic toxicity test 

data available for aquatic organisms, as well as no data to support selection of response 

thresholds based on growth or reproduction. FWS concurs with EPA regarding the availability 

of response thresholds for the many VOC and SVOC substances detected in vessel discharges. 

Those organics for which EPA conducted quantitative analysis include PAH and MAH 

compounds, bis(2-ethylhexyl) phthalate and 2,4,6-trichlorophenol. The MAH compounds like 

benzene are low-molecular-weight compounds that usually do not persist in the environment 

because they are volatile and highly biodegradable. Conversely, the PAH compounds 

(particularly those with four or more carbon rings) are high-molecular-weight compounds that 

are less volatile and degrade more slowly, and thus, persist in the aquatic environment. The 

services are supplementing EPAs assessment of VOCs and SVOCS to include nonylphenol and 

octylphenol ethoxylates due to the greater toxicity and environmental persistence the degradate 

nonylphenol (NP). 

PAH and MAH. Because MAHs and PAHs are Type I narcotic compounds, the toxicity of 

these compounds in water (and sediments) is most easily assessed using what is called the target 

lipid model or TLM (DiToro and McGrath, 2000). Under the TLM, acute and chronic toxicity of 

MAHs and PAHs to aquatic animals is predicted as single pollutants and as mixtures by 

calculating the critical body burden in the target lipid of an organism. EPA used the critical body 

burden of benzo(a)pyene and benzene in lipid to develop its response thresholds against which 

modeled environmental concentrations would be compared. Under EPAs estuarine harbor 

model, average post permit PAH and MAH concentrations were unchanged for all analytes but 

benzene, which was reduced between 17 and 53 percent under worst case and best case 
179

conditions, respectively. For the river harbor model, average post permit PAH and MAH 

concentrations were unchanged for all but benzene, which was reduced between 6 and 9 percent, 

depending on scenario. 

The TLM guidelines proposed by McGrath and DiToro (2009) are equivalent to a HC5, which is 

the hazard concentration considered to protect 95% of the tested species. Thresholds for 

individual analytes ranged from 0.286 ug/L for bezo(a)pyrene to 2,433 for benzene ug/L. 

Average RQs calculated by EPA for individual analytes in modeled estuarine/marine harbors 

ranged from <0.0001 to about 0.022 while modeled river harbors ranged from <0.0001 to 

approximately 0.002. Since these thresholds are all based on the same mechanisms of action, 

narcosis, EPA summed the individual RQs to estimate the aggregate toxic risk of MAH and PAH 

using the modeled harbor concentrations. RQs for PAH and MAH ranged from 0.002 to 0.08 in 

estuarine/marine scenarios and from <0.0001 to 0.0022 in river scenarios.

PAHs (and to a lesser extent, MAHs) accumulate in tissues of aquatic organisms as well as 

biomagnify up the food chain, through partitioning and subsequent bioaccumulation in the lipid 

fraction of organisms. TLM-calculated critical body burdens, when paired with tissue 

concentrations predicted by multiplying the maximum toxicant concentration in receiving water 

with the freely dissolved BAF in prey species, provides the critical body burden in the lipid of 

prey organisms which serves as a dietary response threshold. EPA chose to include on multiple 

routes of exposure in the BE, but limited its analysis to potential risks for bioaccumulations to 

just benzo(a)pyrene and benzene because: 1) benzo(a)pyrene is the most toxic of the PAHs being 

considered here, and thus, the most relevant for evaluating risk, and 2) benzene is the only MAH 

for which a critical lipid body burden exists to support risk evaluation from multiple routes of 

exposure (as well as exposure via oral ingestion by wildlife). In describing this decision, EPA 

noted that PAHs are biotransformed and detoxified in organisms, so they generally do not 

bioaccumulate to particularly high levels. RQs calculated for freshwater vertebrates and 

invertebrates based on estimated concentrations accumulated in tissues from continuous 

exposure to maximum concentrations of benzo(a)pyrene and benzene in ambient receiving 

waters under post-permit conditions were all below 0.01.

Information on the toxicity of hydrocarbons to coral species is extremely limited. A recent 

review compiled information on molecular mechanisms and effects of pollutants on coral 

(Rotchell and Ostrander 2011). The limited amount of information on this species group do not 

indicate effects at concentrations suggested by EPA’s modeling. Responses ranged from 

alterations in enzyme activity at 5 ug/L after 1 day exposure to benzo(a) pyrene, an order of 

magnitude higher than EPA’s HC5 TLM for benzo(a)pyrene 0.28 ug/L. The services were 

unable to identify information on the effects of PAH and MAH substances on aquatic vegetation.

In addition to survival and reproductive effects assessed by EPA, PAHs have been identified as 

having immunotoxic (Reynaud and Deschaux 2006, Bravo et al. 2011) and neurodevelopmental 

(Danion et al. 2011, He et al. 2011, He et al. 2012, Shi et al. 2012) effects in marine and 

anadromous fish. A recent investigation of PAH implications for threatened and endangered 

Chinook salmon reported mean PAH concentrations measured in some stomach content samples 

from wild caught fish were near the threshold concentrations associated with variability and 
180

immune dysfunction in juvenile salmonids (Yanagida et al. 2012). This study demonstrated that 

dietary PAH exposure, rather than water column concentrations (which ranged from 0.001 to 

0.005 ug/L), was the primary source of exposure for juvenile salmonids. Dietary threshold 

concentrations calculated for pink salmon in EPAs BE were 38.7 and 71.7 mg/kg wet weight for 

benzo(a)pyrene and benzene, respectively. However, these thresholds were for PAH induced 

mortality alone and did not take into account other effects which may also lead to mortality, such 

as effects on immune function. Mortality was 60% after 14 days among Chinook salmon fed 

16.5 +/- 0.1 mg/kg total PAH and challenged with Listonella anguillarum. Mortality among 

vaccinated PAH exposed fish was markedly lower (approximately 16%, read from figure). The 

PAH exposure mixture which only contained about 0.72% benzo(a)pyrene, was formulated to 

approximate the actual PAH profile observed in the stomach contents of juvenile wild Chinook 

(Palm et al. 2003). Increased spinal curvature rates in rockfish embryos occurred after 7 days 

exposure to ambient concentrations of benzo(a)pyrene as low as 0.126 ug/L. While statistically 

significant, the difference between controls and embryos exposed to 0.126 ug/ml B(a)P appeared 

to be less than 5% (read from figure). The incidence rate for spinal deformities was 80% at 1.26 

ug/L B(a)P (He et al. 2011). 

Information regarding PAH and MAH marine turtles is limited to tissue concentrations (Alam 

and Brim 2000, Camacho et al. 2012) and much of the information on PAH and MAH for marine 

mammals are tissue concentrations (Hellou et al. 1991, Fair et al. 2010, Godard-Codding et al. 

2011). Tissue concentration information confirms exposure and uptake of PAHs by marine 

turtles occurs, the ecological implications of such exposures are difficult to interpret. There are 

also a few biomarker and in vitro studies for marine mammals. Two investigations establish 

point of effect exposures by identifying DNA adducts or biomarkers of exposure/toxicant 

metabolism for marine mammals (Wilson et al. 2005, Godard-Codding et al. 2011). 

Environmental PAH concentrations and the presence of PAH DNA adducts have been of 

implicated in the occurrence of cancer within the St. Lawrence population of beluga whale (Ray 

et al. 1991, Beland et al. 1993, Martineau et al. 1994). One in vitro investigation demonstrated 

cytolotoxic effects of benzo(a) pyrene in cell cultures from Northern Right Whale, with greatest 

toxicity found for testis. Another investigation exposing harbor seal lymphoma cell lines to 

benzo(a)pyrene identified genototic, but not immunotoxic effects (Frouin et al. 2010). While 

data from biomarker and in vitro studies are difficult to interpret in ecological terms, they 

identify the mechanisms by which pollutants can affect organisms. 

Services Conclusion. Both pre and post permit receiving water concentrations are orders of 

magnitude below individual toxicant effects thresholds identified by EPA and those thresholds 

identified through our review of recent literature as was the net PAH-MAH toxicity for 

freshwater taxa. The aggregate PAH-MAH toxicity for saltwater organisms was somewhat 

higher, with an RQ of 0.08, approaching the threshold between “remote” and “no effect”. FWS

concludes that PAH-MAH contributions from vessels are not expected to tip the balance between 

neutral and harmful levels in waters where our species occur.

2,4,6-Trichlorophenol. 
181

EPA post permit 2,4,6-trichlorophenol in the estuarine harbor model to average 0.0927 ng/L and 

ranged from 0.00607 to 0. 514 ng/L, suggesting a 48 to 50 percent reduction in 2,4,6-

trichlorophenol discharged. For the river harbor model, EPA's average post permit 2,4,6-

trichlorophenol was 0.00376 ng/L and ranged from 0.0000313 to 0. 00986 ng/L, suggesting a 30 

to 67 percent reduction in 2,4,6-trichlorophenol discharged. Post permit 2,4,6-trichlorophenol 

estimates fell below the response thresholds selected by EPA for evaluating risks of exposure to 

2,4,6-trichlorophenol. These thresholds ranged from 0.46 to 5,923 ug/L for freshwater 

organisms. The threshold values EPA selected for freshwater vertebrates were derived from a 

NOEC and LOEC, with the NOECs being 530 ug/L. EPA stated that threshold values were not 

available for estuarine/marine organisms. After review of the available literature, concurs with 

EPA’s conclusion. Further, FWS literature searches did not identify information of effects 

important to our species such as olfaction, immune function or behavior.

Services Conclusion. Both pre and post permit receiving water concentrations are greater than 3 

orders of magnitude below toxicant effects thresholds identified by EPA and thresholds below 

those identified by EPA or for effects not considered by EPA were not found through FWS

literature reviews. FWS concludes that 2,4,6-trichlorophenol contributions from vessels are not 

expected to tip the balance between neutral and harmful levels in waters where our species occur.

Bis(2-Ethylhexyl) Phthalate (DEHP). EPA estimated post permit DEHP in the estuarine 

harbor model to average 0.754 ng/L and range from 0.048 to 4.24 ng/L, suggesting a 25 to 61 

percent reduction in DEHP discharged. For the river harbor model, EPA's average post permit 

DEHP was 0.0839 ng/L and ranged from 0.000979 to 0.175 ng/L, suggesting a 14 to 58 percent

reduction in DEHP discharged. EPA stated that it was unable to find threshold response data for 

DEHP useful in evaluating risk to aquatic organisms. 

FWS identified several studies evaluating DEHP as an endocrine disruptor. California EPA 

reviewed these and other studies evaluating more traditional effects (Carlisle et al. 2009). 

Response threshold data were reviewed for effects on development and maturation, growth, and 

reproductive tissue metrics. The concentrations at which responses were reported ranged from 

0.01 to 10,000 ug/L. The only responses that occurred at concentrations at or below those 

modeled by EPA for its hypothetical harbors used the standard laboratory species medaka. 

Mortality rates were higher and male body weights were lower for adult individuals hatched from 

eggs exposed to as little as 0.01 ug/L DEHP. Exposure did not affect female body weights or the 

gonadosomatic index (GSI) of either sex (Chikae et al., 2004a – after Carlisle et al 2009). A later 

study by the same workers reported declines in female body weights at 0.1, 1.0, and 10.0 μg/L and 

reduction of male GSI at 0.01 – 10 ug/L (Chikae et al., 2004b – after Carlisle et al 2009). 

Interpretation of the ecological implications of such data in the light of conflicting results reported by 

the same research group leads us to exclude this study from consideration when evaluating EPAs 

post permit DEHP estimates.

Services Conclusion. FWS concludes that DEHP contributions from vessels are not expected to 

tip the balance between neutral and harmful levels in waters where our species occur. The bulk 

of the response thresholds reviewed in Carlisle et al. (2009) occurred at concentrations that were 

orders of magnitude greater than ambient water concentrations modeled by EPA; and conflicting data 
182

from the same research group were reported for those responses observed at or near EPAs modeled 

concentrations. 

Nonylphenol and Octylphenol Ethoxylates. EPAs Report to Congress describes the 

environmental fate and transport of nonylphenol and octylphenol ethoxylates in vessel discharges 

(USEPA 2010), yet the BE does not acknowledge this discharge constituent class. These substances 

are often collectively referred to as nonylphenols and represent two distinct subsets of the broader 

family of alkylphenols that are commonly used in many products such as liquid detergents and soaps. 

Longer chain nonylphenol and octylphenol ethoxylates degrade to shorter chained ethoxylates under 

aerobic conditions. In general, the shorter the chain, the more hydrophobic, persistent, and toxic the 

substance becomes. 4-Nonylphenol (NP) is a shorter-chain nonylphenol that has been found in 

surface water and is toxic to aquatic life. NP is formed from the longer chain nonylphenol and 

octylphenol ethoxylates as they break down. In general, the hydrophobicity, persistence, and toxicity 

of the substance all increase as the ethoxylate chain becomes shorter. NP accumulates in sediment,

occurring at concentrations several orders of magnitude greater in sediment than in water. The 

short-chained isomers may be quite persistent once they are buried in the sediment, and bottomfeeding fish can be significantly exposed to these persistent and toxic compounds (USEPA 2010). 

EPA’s Report to Congress indicated that there were no analytical results which could be directly 

compared with EPA's 1.7 ug/L marine acute benchmark for the degradate, NP. The Services 

note that Toxic Equivalency Factors are available for adjusting for NPE mixtures. An alternative 

to a Toxic Equivalency analysis would be to estimate NP degradate loading equivalents based on 

moles NP producing substances in vessel discharges.

Toxicity data indicate that some listed species are greater than the proposed correction factor of 

two more sensitive to these substances than standard test species (e.g., LC50s for atlantic 

sturgeon is 50 ug/L, shortnose sturgeon and spotfin chub LC50s were reported at 80 ug/L 

(Dwyer et al 2005), Fathead minnow LC50s averaged 290 ug/L and sheepshead minnow 

averages 460 ug/L in EPAs ECOTOX database). NP is a common adjuvant used in pesticides 

and was reviewed by NMFS in its Biological Opinion for the EPA-NMFS consultation on 

Pesticides Containing Chlorpyrifos, Diazinon, and Malathion (NMFS 2008). In a review of 

ECOTOX data in this Biological Opinion, the lowest fish LOEC reported was 0.15 ug/L for 

fathead minnow reproduction. Numerous fish studies reported LOECs at or below 10 ug/L. 

Additionally, salmonid prey species are also sensitive to sublethal effects of nonylphenol. The 

amphipod, Corophium volutator, grew less and had disrupted sexual differentiation (Brown et al. 

1999). Multiple studies with fish indicated that nonylphenol disrupts fish endocrine systems by 

mimicking the female hormone 17B-estradiol (Arsenault et al. 2004; Brown and Fairchild 2003; 

Hutchinson et al. 2006; Jardine et al. 2005; Lerner et al. 2007a; Lerner et al. 2007b; Luo et al. 

2005; Madsen et al. 2004; McCormick et al. 2005; Segner 2005). NP induced the production of 

vitellogenin in fish at concentrations ranging from 5-100 ug/L (Arukwe and Roe 2008; Hemmer 

et al. 2002; Ishibashi et al. 2006; Schoenfuss et al. 2008). Vitellogenin is an egg yolk protein 

produced by mature females in response to 17-β estradiol, however immature male fish contain 

the capacity to produce vitellogenin if exposed to estrogenic compounds. As such, vitellogenin is 

a robust biomarker of exposure. A retrospective analysis of an Atlantic salmon population crash 

suggested the crash was due to NP applied as an adjuvant in a series of pesticide applications in
183

Canada (Brown and Fairchild 2003; Fairchild et al. 1999). Additionally, processes involved in 

sea water adaptation of salmonid smolts are impaired by NP (Jardine et al. 2005; Lerner et al. 

2007a; Lerner et al. 2007b; Luo et al. 2005; Madsen et al. 2004; McCormick et al. 2005). 

Services Conclusion. Since graywater discharges primarily contain the NP precursors, there is 

little concern that direct acute exposures to NP discharge plumes would occur. Additionally 

EPA proposes to add the following sentence to the VGP and sVGP fact sheets definition of 

minimally toxic: “EPA expects that soaps that are “minimally toxic” will contain little to no 

nonylphenols.” For these reasons, FWS concludes that nonylphenols from vessel discharges are 

not expected to result in harmful levels in waters where our species occur.

Effects of the Proposed Action, Programmatic Approach

In our Programmatic Approach, we examine whether and to what degree EPA has structured the 

VGPs, as well as monitoring and compliance, to insure that vessel discharges into waters of the 

U.S. 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. In this evaluation, we 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. 

(1) Scope

In this section, we ask whether EPA is aware of the scope of their Action. Section 7 regulations 

define an action as “all activities or programs of any kind authorized, funded, or carried out, in 

whole or in part, by Federal agencies in the United States or upon the high seas.” It defines 

effects of the action as the “direct and indirect effects of an action on the species or critical 

habitat, together with the effects of other activities that are interrelated or interdependent with

that action, that will be added to the environmental baseline. Indirect effects are those that are 

caused by the proposed action and are later in time, but still are reasonably certain to occur. 

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.”

As described earlier, the scope of the action includes all aspects of EPA’s issuance and 

implementation of the VGPs, including the monitoring of discharges authorized by the permits
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and enforcement of the permits. The VGPs include several references to monitoring, compliance, 

and enforcement, all of which will be conducted by EPA as part of their action. In sections 1.4 

of the VGP and 4.3 of the sVGP, EPA requires permit compliance and affirms its authority to 

determine enforcement responses to permit violations including fines, requirements, and 

schedules for taking corrective actions. Section 3.1 of the VGP discusses EPA's authority (either 

an EPA official or official agent acting on EPA's behalf) to determine that effluent limits/water 

quality standards/pollution control measures/BMPs have not been met and how an applicant can 

take corrective actions. Section 4.5 of the sVGP discusses EPA's authority to inspect any vessel, 

equipment, practices, or operations regulated under the permit; and to sample or monitor for the 

purpose of assuring permit compliance. It also discusses EPA’s authorities under Section 308 of 

the Clean Water Act, including its authority to enter, access, inspect, sample, monitor, and obtain 

information to verify compliance with the CWA. 

In addition to specific references to these activities, through the course of our consultation, EPA 

has committed to several monitoring, compliance, and enforcement-related activities, discussed 

in the relative sections below (see 4, 6, and 7). Therefore, we conclude that EPA is aware of the 

full scope of its action. 

To reliably estimate the probable individual or cumulative effects to ESA listed species or 

designated critical habitat, the EPA would need to know or reliably estimate the probable 

number of discharges that it would authorize under the VGPs. Therefore, we also ask whether 

EPA has structured their general permits to reliably estimate the probable number, location, and 

timing of discharges that would be authorized by their VGPs. For the VGP, EPA requires a 

Notice of Intent (NOI) for all vessels greater than or equal to 300 gross tons or with the capacity 

for 8 cubic meters of ballast water. This NOI must be submitted electronically no later than 

December 12, 2013 for existing vessels, by date of transfer for resale vessels, and seven days 

prior to entering waters of the U.S. for new builds. The NOI asks for location information, 

including homeport, anticipated port visits during the term of the permit, and whether the vessel 

is engaged in nearshore voyages. The NOI also asks information on the types waste streams that 

would be discharged (e.g. exhaust gas scrubber, graywater, ballast water). The EPA used the 

NOI data from the 2008 VGP to estimate the number of discharges that would be authorized 

under the VGP. They did not estimate the location and timing of discharges, nor did the account 

for the vessels that do not submit NOIs; for this they should use the annual reports in the future. 

The sVGP is a new permit; unlike the VGP, it will not require NOIs or annual reports. 

Therefore, even after the permit goes into effect, EPA will not know or be able to reliably 

estimate the number or location of the vessels authorized to discharge under the sVGP. Instead, 

EPA uses (and would continue to use) the U.S. Coast Guard’s MISLE database to search for

vessels that are less than 79 feet in length, except for recreational and military vessels. They 

estimate that 115,000 to 138,000 vessels would be eligible for coverage under the sVGP. They 

do not estimate how many vessels of these vessels are likely be covered under the sVGP, nor 

how many vessel owners/operators will consider themselves to be covered under the sVGP or 

self-identify (i.e., have the knowledge that they are discharging wastes under a Federal permit). 

Accurate self-identification is a problem among general permits. For example, self-identification 
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by municipal and industrial storm water dischargers was among the metrics evaluated in a study 

of 136 facilities subject to stormwater General Permit requirements (Cross & Duke 2008). 

Among these facilities, approximately 21% were aware that their discharges were subject to the 

permit even though stormwater permits had been in place over 15 years. The authors suggested 

that outreach might improve compliance among dischargers. The rates of self-identification 

among municipal and industrial storm water dischargers do not necessarily apply to vessels 

authorized to discharge under the either of the VGPs. In General, the shipping industry is 

accostumed to regulation and the well-defined vessel populations and discharges specified under 

the VGPs should lead to greater awareness of vessel operator obligations under these permits. 

An online query for information on the VGPs indicated information sharing activity during and 

after the VGPs comment period among professional associations, service providers, state and 

federal agencies within the US and US trading partners.

Although there is evidence that self-identification rates for the VGPs may be greater than that for 

other General Permits, EPA has not at this time reliably estimated the actual number, location, 

and timing of discharges authorized by the sVGP. EPA will conduct an inspection of a random 

sample of small vessels, useful as a means to extrapolate to the larger population of small 

vessels, as one way that might address these estimates. As described below (under the 

compliance section, number 6), one question that will be asked during small vessel inspections is 

whether vessel owners/operators consider their vessels to be authorized under the sVGP and 

perform actions (e.g., signing a PARI form and quarterly inspections) required of the permit. 

We conclude that EPA is aware of the scope of their Action and has reliably estimated the 

probable number of discharges that it would authorize under the VGP. Though EPA has not 

reliably estimated the probable number of discharges that it would authorize under the sVGP, we 

believe that their proposed inspection and compliance plan, coupled with other information 

sources, will provide data with which to estimate the number of discharges throughout the term 

of the permit. 

(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 vessel discharges that would be 

authorized by the VGPs. We also ask whether the EPA would know or be able to reliably 

estimate whether those discharges have occurred in concentrations, frequencies, or for durations 

that violate the terms of the proposed VGPs. 

ANS

In the BE, EPA identifies ANS as one of the greatest threats to biodiversity globally and one of 

the largest threats to coastal and freshwater ecosystems. They describe invasive species as the 

second largest threat to endangered species after habitat loss and indicate that some scientists 

believe the impact of invasive species is greater than that of habitat loss. They identify 

commercial shipping as the “most important means of introducing ANS to coastal environments” 

and the “predominant vector for the human transport of invasive species in marine 
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environments.” 

The EPA identifies several mechanisms by which ANS are likely to adversely affect listed 

resources. These include: outcompeting native species, damaging habitat, changing food webs, 

and altering the chemical and physical aquatic environment. They also identify the taxonomic 

range of possible ANS, dividing the organisms by those likely to be transported via ballast water 

(planktonic, but also benthic organisms) and biofouling organisms. 

The EPA does not estimate the concentrations, frequencies, or durations of discharges carrying 

ANS. In the BE, EPA suggests that the lack of species-specific chronic response data for ANS 

precludes calculation of a risk quotient to support a quantitative effects analysis. We found 

several datasets describing actual or potential responses to ANS. In our analyses, we used past 

documented ANS invasions from a nationwide database to determine that listed resources are 

likely to be exposed to ANS, but our analyses do not include all ANS invasions and do not 

represent invasion probabilities. Instead, we agree with the conclusion of the NAS study, which 

states that “the data are not sufficient in present form to characterize a biologically meaningful 

relationship, much less estimate the associated uncertainty, to be able to identify with confidence 

the invasion probabilities associated with particular discharge standards.” For this reason, EPA 

cannot quantify ANS invasion probabilities associated with authorized ballast water discharge, 

hull fouling/hull husbandry, and other vessel discharges. Instead, EPA uses a qualitative 

approach to estimate exposure (discussed below in section 3). 

The EPA has identified ANS as potentially harmful stressors that are likely to be released into 

the waters of the U.S. as a direct or indirect result of the vessel discharges that would be 

authorized by the VGPs. To date, EPA has not been able to reliably estimate whether those 

discharges have occurred in concentrations, frequencies, or for durations that are consistent with

the terms of the proposed VGPs; however, their monitoring and reporting plan, discussed below 

(section 4) will allow EPA to more reliably estimate the volumes of discharges that are likely to 

carry ANS and the number of living organisms carried in ballast water. 

Pollutants 

In their BE, EPA used pollutant data collected for the Report to Congress as a primary data 

source to characterize the discharges the VGPs will authorize. This required extrapolation from 

the sampled 61 vessels and their discharges to the universe of vessels authorized to discharge 

under the VGPs. Given that the sVGP authorizes discharges from between 115,000 and 139,000 

vessels, discharge estimates are based on data from approximately 0.05% of the permitted 

population. The vessels sampled for the report were commercial fishing vessels and other nonrecreational vessels less than 79 feet, that is to say, sVGP-authorized vessels. Vessels described 

in the Report to Congress volunteered to allow EPA to sample discharges. This “opportunity 

sampling” approach likely favored participation of operators who were confident that their vessel 

discharges were low impact. 

In its report, EPA discussed whether these data could be extrapolated to other vessels, including 

larger vessels, such as those authorized to discharge under the VGP. EPA cautioned against 

extrapolating bilgewater data to vessels not sampled for the Report to Congress (e.g., cruise 
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ships, ferries, barges, tankers) because these vessels differ considerably in design, construction, 

and operation. The BE did use information from a 2008 report on cruise ship discharges 

(USEPA 2008), but this report only provides data for bilgewater volume in these larger vessels, 

not data on the pollutants present in bilgewater Ultimately EPA characterized VGP bilgewater 

discharges using bilgewater pollutant data from the Report to Congress and bilgewater volume 

data from the cruise ship discharges report. In its report to Congress, EPA also cautioned against 

extrapolating deckwash and graywater volume and constituents among vessels because these 

would differ due to activities conducted on board. For example, fishing vessels and cruise ships 

would have very different graywater and deckwash characterisitcs. Nevertheless, voluntary 

discharge data from 61 small vessels were used to characterize discharges from VGP vessels.

EPA considered zinc discharges from cathodic protection sacrificial anodes to be of too low 

volume and toxicity to be considered in the BE. FWS calculated zinc load using the discharge 

rate reported in BE Table 3-3 and the wetted hull area estimates reported in BE table 3-18. 

These calculations indicate that sacrificial anode discharges can actually make up a substantial 

portion of the zinc load from some vessels. Sacrificial anodes contribute approximately 20% to 

80% of the zinc discharged from barges, cargo ships and oil tankers at pierside and 

approximately 50 to 95% of zinc discharges from these vessels while underway. Under worst 

case conditions (i.e. oil tanker anodes), including anode discharges would increase a vessel’s 

zinc loading five-fold pierside and 17 fold while underway. Fortunately, increasing the modeled 

zinc estimates by 17 fold does not appreciably change the risk conclusions of the BE analysis. 

While the analyte list examined in the BE was extensive, there were a number of omissions that 

should be noted:

 EPA states that mercury was not evaluated because it was not possible to sample away 

from sources of metals or sources of airborne mercury such as engines or generators 

which may contaminate the sample. In stating this, EPA indirectly acknowledges that 

mercury is a contaminant generated on vessels and that it does not know the relative 

sources or extent to which mercury is discharged from vessels. 

 EPA acknowledges that pharmaceuticals and personal care products (PPCPs) would 

occur in graywater and sewage mixed with graywater but stated that PPCPs were not 

analyzed due to a lack of resources. EPA therefore does not know the types of PPCPs 

and extent to which they are discharged by vessels. 

 While the Report to Congress included data for nonylphenols, EPA did not acknowledge 

this data in the body of its BE. 

Due to data limitations, there are substantial gaps and uncertainty in EPA’s analyses which 

resulted in EPA relying on assumptions to fill these gaps and uncertainties. This results in a 

reduction of precision in the final risk assessement. Additionally, while the Services 

acknowledge that uncertainty exists in all risk analyses, the magnitude of uncertainty with EPA’s

BE analysis due to the insufficient quantity and quality of data available to characterize

authorized discharges is substantial. This further emphasizes the need to monitor discharges to 

gather additional information to more accurately identify stressors and determine which may be 
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problematic. 

(3) Exposure to potentially harmful impacts

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. EPA identified uncertainties in their effects analysis that could potentially limit the 

interpretation of results and conclusions. In order to address whether EPA has demonstrated 

sufficient knowledge of the exposures resulting from discharges authorized by the VGP, we must 

first review these uncertainties acknowledged by EPA for the BE’s assessment. 

Uncertainties in Exposure Estimates Identified by EPA

The models to represent the estuarine and river water bodies to estimate the exposure 

concentrations evaluated in the risk analysis all U.S. waters navigable by vessels covered under 

the VGP and sVGP are simple screening models. EPA acknowledged that the use of such 

screening-level models is typically limited to identifying major water quality issues and to 

identify data gaps, not to perform risk analyses as they were used in the BE. 

EPA acknowledged that uncertainty was added to the analysis by the extrapolations needed to fill 

data gaps for the various combinations of vessel types, discharges, pollutants, and vessel 

populations. These extrapolations were required to develop the pollutant loads used in the 

modeling analysis. EPA also assumed that the background concentration for all pollutants in the 

harbor scenarios was zero. Therefore, the model output used to inform the effects analysis does 

not directly evaluate the potential for vessels to contribute to pollutant impairments or quantify if 

vessel pollutant loads serve as the “tipping point” between exceeding and not exceeding a given 

effect threshold. Rather than assess pollutant load contribution to existing baseline levels in the 

RAAs it modeled, EPA relied on the magnitude of risk quotients to provide a sense as to whether 

incidental vessel discharges covered under the VGP and sVGP would make notable or sizable 

contributions to existing harbor pollutant levels. 

Impacts on a local scale potentially occurring in stagnant side embayments, coves within the 

larger water bodies or occurring as a result of large volume discharges are not addressed in EPAs 

assessment because screening models assume instantaneous and universal mixing within the 

modeled harbor. EPA concluded that by using model parameters to bound in the analysis and 

reflect a “worst case” scenario (e.g., minimum river flow from the nine rivers considered in the 

analysis), the screening-level models appropriately characterize the range of potential exposure 

concentrations and subsequent pollutant risk. 

EPA believes that the analysis also represents vessel discharges to intracoastal waterways 

because several of the major water bodies (e.g., Elizabeth River, Charleston Harbor, Biscayne 

Bay) that are part of the Atlantic and Gulf intracoastal waterway were considered in developing 

the receiving characteristics for the estuary model. Even though a significant amount of vessel 

traffic travels these waters on a daily basis, the daily vessel equivalent population is assumed to 
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be significantly lower in these waters than in a harbor environment. EPA acknowledged that 

listed species present in intracoastal waterways may be directly exposed to a vessel discharge 

plume, but stated that the exposure duration is expected to be brief such that the chronic effects

thresholds considered in the BE are not of concern. 

Although the environmental concentrations calculated for the effects analysis do not specifically 

account for localized effects, EPA considered the potential risk posed by vessel discharges in 

other unique environments and determined vessel discharges are unlikely a concern. For 

example, in the case of localized changes in buffering capacity due to climate change, untreated 

exhaust gas scrubber discharges have the greatest potential to depress pH values in receiving 

waters as the discharge can have pH values as low as 3(USEPA 2011c). EPA originally relied 

on its economic and benefits analysis for the 2013 VGP and concluded that that a maximum of 5 

to 10 percent of affected vessels would install this treatment by the end of the permit period. 

EPA has since revised this estimate to reflect far fewer vessels plying this technology. EPA 

assumed that the concurrence of site-specific changes in buffering capacity with a significant 

population of vessels discharging exhaust gas scrubber water is highly unlikely to occur. Similar 

to the assessment of intracoastal waterways, EPA assumed that any localized effects caused by 

direct exposure to an exhaust gas scrubber discharge plume would be brief such that risk effects 

to listed species considered in the BE are not of concern. However, the discharge volume and

concentrations of selenium associated with this discharge was identified by the Services as a

potential major contributor to existing selenium issues in the San Francisco Bay estuary.

Lakes and reservoirs isolated from the major rivers navigable by vessels covered under the VGP 

and sVGP represent another unique environment that was not specifically modeled in the EC 

analysis. EPA believes that the maximum exposure concentrations estimated in the hypothetical 

river harbor can be used to inform effects determinations for species identified in the lake 

environment. EPA determined that vessel populations operating on lakes and reservoirs are 

significantly smaller than vessel populations operating in river harbors, and that the vessels also 

operate (and discharge) for limited periods of time. Therefore, EPA concluded that the permitted 

vessel equivalents in lake environments are very likely to be significantly lower than the vessel 

equivalents estimated in the two river RAAs included in the effects analysis, which would result 

in lower estimated pollutant concentrations in a lake environment than the maximum exposure 

concentration calculated for the hypothetical river harbor. Given this assumption, EPA believes 

that the calculated river EC values and subsequent risk conclusions for freshwater species 

adequately capture the potential “worst case” scenario pollutant concentrations and risks in a 

lake environment.

Services Assessment of Uncertainty in the Exposure Analysis

In order to determine if EPA’s decision process in evaluating its action has insured against 

jeopardizing listed species, the Services must evaluate EPA’s acknowledged uncertainties and 

how they were addressed by EPA along with additional uncertainties identified by the Services. 

The Service took EPA’s acknowledged uncertainties into consideration while identifying 

discharges and stressors that posed the greatest risk to listed species. Additional monitoring 
190

agreed to by EPA is expected to provide mechanisms for identifying unacceptable risks and 

implementing corrective measures.

Perhaps the greatest source of uncertainty in the effects analysis lies in EPA’s ability to predict 

exposure. EPA identified three major uncertainties in their exposure analysis, including: model 

pollutant load inputs reflect the data limitations in available vessel discharge data (discharge 

flow, discharge concentrations, and vessel populations); model inputs assume no background 

concentrations of pollutants are present in the receiving water; and the model is not designed to 

evaluate localized impacts or stressors.

Uncertainties regarding EPA’s estimation of pollutant loadings from vessel discharges arise 

primarily for the limited amount of data for discharges, i.e., discharge volumes and 

concentrations of pollutants in those discharges for different discharge/vessel types. In terms of 

pollutant concentrations, where sample data were available EPA based their estimates on median 

values (EPA report to Congress). Predictions based on medians may underestimate the full 

breath of potential exposures. Data collected as part of the monitoring requirements proposed in 

VGP and sVGP should improve the quality of information used for EPA’s future analyses. 

Models used to predict concentrations of pollutants in water assumed no background 

concentrations in the receiving water. While these predictions may capture pollutant 

concentrations attributable to vessel discharges, they likely underestimate actual exposures 

because other sources of pollution are not considered. In addition, the models assume complete 

mixing throughout the harbor and are not designed to evaluate localized impacts or stressors. 

Organisms that reside in close proximity to vessels may be exposed to higher pollutant 

concentrations. Risks associated with these acute exposures will be dependent on the overlap 

between species and vessel locations, proximity to discharges, and duration of exposure. Sessile 

species will likely be most vulnerable to these types of exposures. Because of the scope of the 

VGP and sVGP, EPA evaluated exposure using Reference Action Area (RAA) harbors. The 

RAA harbors are expected to represent areas where the greatest numbers of vessels are located. 

EPA modeled several different harbor scenarios and based their risk assessment on the maximum 

predicted pollutant concentration (among all harbor scenarios). The RAA harbor approach and 

use of maximum predicted pollutant concentrations should help balance the uncertainties 

mentioned above and reduces the likelihood that pollutant exposures used in the effects analysis 

are underestimated.

ANS

For ballast water, EPA concluded that its proposed ballast water standards in the VGP are likely 

to result in a “very small absolute risk of invasion.” Using the NEMESIS database (with the 

caveats listed above), we estimated an annual average of 5.75 documented ANS invasions 

nationwide that were attributed to ballast water discharge. The proposed VGP ballast water 

numeric discharge limitations are likely to reduce the number of ANS invasions over time; 

however, similar standards are not required of small vessels. We conclude that there is a small 

likelihood that listed resources will be exposed to ANS invasions as a result of ballast water 
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discharges authorized by the VGPs. 

As with ballast water EPA provided a qualitative analysis, but did not provide a quantitative 

estimate of exposure of listed resources to hull fouling ANS. We used the NEMESIS database to 

estimate an annual average of 13.5 ANS invasions nationwide that were attributed to hull 

fouling. This number represents a minimum number of ANS invasions annually. The VGPs 

require few anti-fouling/hull husbandry practices or technologies that are likely to result in 

substantial changes to biofouling ANS invasion rates. Therefore, there is at least a small 

likelihood that listed resources would be exposed to ANS invasions as a result of hull fouling and 

hull husbandry as authorized by the VGPs. 

We conclude that EPA has not reliably estimated whether, and to what degree, listed resources 

are likely to be exposed to potentially harmful impacts of discharges authorized by the permit. 

We acknowledge that several, substantial uncertainties prevent or complicate the reliable 

estimation of exposure to several of these stressors. These uncertainties emphasize the need for 

additional monitoring and data collection, as described in the following section. 

(4) Monitoring/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 owners/operators to self-monitor their discharges as one means to identify, 

collect, and analyze information to determine whether vessel discharges into waters of the U.S. 

expose listed resources to ANS or pollutants at concentrations, durations, or frequencies that are 

known or suspected to produce adverse effects. Under requirements of the VGP, permittees are 

required to monitor and report any unavoidable or unauthorized discharges. Without oversight, 

we expect the rates of disclosure of unauthorized discharges will likely be low. It is unclear 

whether the required self-monitoring and self-reporting alone will allow EPA to continually 

identify, collect and analyze information to accurately characterize exposure or adverse effects. 

Therefore, EPA will conduct additional assessments of discharges with the greatest potential to 

adversely affect listed resources. These include: ballast water, bilge water, graywater, copper 

(from anti-fouling hull coatings and gas scrubber effluent), selenium (from gas scrubbers 

effluent), and vessel-mediated ANS.

Annually, EPA will collect and review information on the ballast water treatment system

discharges through the electronic submittal of reports by all vessels using such systems. All 

ballast water treatment systems must meet the ballast water numeric discharge limitations, as 

described in the proposed VGP, which limits the number of biological organisms discharged to 

waters of the U.S. In addition, EPA will monitor the following data, submitted annually by 

vessel owners/operators:

 Monthly indicators of ballast water treatment system functionality 

 Results of analytical tests for biological indicators (i.e., total heterotrophic bacteria, E.

coli, and Enterococci) to ascertain compliance with ballast water numeric discharge 

limitations
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 Results of analytical tests for residual biocides and derivatives used in the treatment 

process (e.g., chlorine dioxide, chlorine, ozone, peracetic acid, and hydrogen peroxide). 

Annually, EPA will collect and review information on treated graywater through the electronic 

submittal of reports by large and medium-sized cruise vessels covered under the VGP. 

Quarterly, cruise ship owners/operators must collect and analyze graywater samples for the 

following constituents: BOD, fecal coliform, suspended solids, pH, total residual chlorine, E. 

coli, TP ammonia, nitrate/nitrite, and TKN. They must submit these results to EPA on an annual 

basis.

For new build vessels (constructed on or after December 19, 2013) greater than 400 gross tons 

that elect to discharge bilgewater into waters subject to this permit, vessel owners/operators must 

collect and analyze a sample of the bilgewater effluent for oil content annually; they must submit 

these data electronically to EPA. 

Biannually, EPA will summarize data from Annual Reports (which include all instances of 

noncompliance and unavoidable discharges authorized by the VGP) and Discharge Monitoring 

Reports and provide summaries to the Services. 

For copper, EPA will develop, in cooperation with the Services, and implement a monitoring and 

reporting plan, within 1 year of finalization of the VGPs. The plan will contain the following 

elements:

1) EPA, with the technical assistance of the Services, will identify metrics for assessing 

copper loadings to waters inhabited by ESA listed species (i.e., using the number of ships 

reporting copper hull treatments in eNOIs for particular areas as a proxy).

2) EPA will compile eNOI and annual report information regarding the number and type of 

vessels that use copper-based anti-fouling hull coating and/or exhaust gas scrubbers, their 

home port/most frequented US port, and US ports anticipated visiting during the permit 

term.

3) Twice, once by December 2014 (to summarize eNOI data) and another before EPA 

transmits the next draft VGP/sVGP to OMB for interagency review (to evaluate annual 

reports in time to make changes for the next permit cycle, if need be), EPA will evaluate 

vessel data and identify ports/locations where the metric has been exceeded. If the metric 

has been exceeded, EPA will, as appropriate, identify and implement additional actions to 

reduce any unacceptable risks.

For potential selenium discharges in exhaust gas-scrubber discharges, EPA will develop, in 

cooperation with the Services, and implement a monitoring and reporting plan, within 1 year of 

finalization of the VGPs. The plan will contain the following elements:

1) EPA, with the technical assistance of the Services, will identify metrics for assessing 

selenium loadings to waters inhabited by ESA listed species (i.e., using the number of 
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ships reporting exhaust gas scrubbers in eNOIs for particular areas combined with 

expected and/or reported volume and concentration values as proxies).

2) EPA will state that vessel operators should analyze selenium in saline EGS discharges 

using methods capable of accurately measuring selenium in saline samples (e.g., 

Octopole Reaction Cell ICP-MS or Hydride generation AA methods or other methods 

which reduce matrix interference for selenium).

3) EPA will compile NOI and annual report information regarding the number and type of 

vessels that use exhaust gas scrubbers, discharge monitoring data for pollutants including 

selenium and copper, their home port/most frequented US port, and US ports anticipated 

visiting during the permit term.

4) Twice, once by December 2014 (to summarize eNOI data) and another before EPA 

transmits the next draft VGP/sVGP to OMB for interagency review (to evaluate annual 

reports in time to make changes for the next permit cycle, if need be), EPA will evaluate 

vessel data and identify ports/locations where the metric has been exceeded. If the metric 

has been exceeded, EPA will, as appropriate, identify and implement additional actions to 

reduce any unacceptable risk.

EPA will do the following regarding vessel-mediated ANS invasions. Within 1 year of 

finalization of VGP/sVGP, EPA will develop, in cooperation with the Services, and implement a 

monitoring and reporting plan for vessel-mediated ANS invasions. The plan will contain the 

following elements:

1) EPA, with the technical assistance of the Services, will identify metrics to evaluate 

whether vessel mediated ANS invasion rates are being reduced over time.

2) EPA will track information from ANS invasions that might be potentially tied to vessel 

vectors. Information tracked may include:

a. Dr. Greg Ruiz (Smithsonian Institution) conducts systematic surveys for ANS 

invasions caused by hull-fouling and ballast water in San Francisco, Chesapeake, and 

Tampa Bays to track changes in the rate of ANS invasions.

b. Nationwide NEMESIS database for all newly documented, marine, ballast water and 

hull fouling ANS invasions. 

http://invasions.si.edu/nemesis/browseDB/searchQuery.jsp

c. National USGS NAS database for all newly documented, freshwater, shipping-related 

ANS invasions. http://nas.er.usgs.gov/queries/SpSearch.aspx

EPA and the Services acknowledge that new invasions observed from any of these sources 

are not necessarily linked to discharges authorized by the VGPs. Nonetheless, over a multipermit lifespan, tracking invasions, and improving our methodologies and understanding of 

the risk-release relationship, could provide a long term perspective about ballast water 

discharge standards, antifouling technologies, and other practices to reduce invasions.
194

3) EPA will report to the Services once per year that they have reviewed this information 

and whether notable new invasions have been recorded in the previous year that could 

have been previously caused by vessel discharges. The Services note that they are 

requesting a short review (approximately one hour per year) to ensure EPA continues to 

track aquatic bioinvasions. As discussed above, EPA and the Services agree that these 

observations are being used to inform EPA’s general understanding of continued and 

ongoing invasion rates.

4) EPA will identify and implement, as appropriate, additional actions (e.g., require antifouling coatings; require debris containment systems; require more stringent ballast water 

standards) as soon as practicable (including in future permit iterations) to ensure the 

protection of listed species if needed.

These ANS monitoring methods were chosen to provide an indicator of how invasion rates 

change over time. For example, researchers at the Smithsonian Environmental Research Center 

(SERC)13 have has conducted systematic surveys for non-native species in San Francisco Bay 

(past 12 years) as well as Tampa and Chesapeake Bays (past year). These studies were designed 

to provide an indicator of how ANS invasion rates change over time as regulations change. Data 

analyses include identifying the source location (e.g., South China Sea) of the ANS as well as the 

vector for the ANS (e.g., ballast water, biofouling, etc.). The databases provide a nationwide 

repository for newly reported ANS invasions in marine (NEMESIS) and freshwater (USGS 

NAS) environments; they do not account for changes in effort as above.

The Services spoke with Dr. Greg Ruiz of SERC and Peg Brady, NOAA’s Senior Liaison to the 

ANS Task Force, to determine whether these methods would be informative and whether they 

could be used as a gross measure of the efficacy of the VGPs. Both agreed that the systematic 

surveys were a good method to track the effectiveness of the permit. They acknowledged the lag 

time for ANS invasions (months to years after introduction) but were confident that the metric

would be meaningful within the life of the permit (i.e., 5 years). They also saw the value in 

establishing base and trend lines in the early years of the permits and stated it was possible to 

tailor their data analyses to link invasion rates directly to the VGPs.

As they pertain to ballast water, EPA’s monitoring measures can be compared to USCG’s Ballast 

Water Rulemaking. Under the VGP, permittees are responsible for self-inspections and 

monitoring, and report on them annually. According to EPA, those data will be submitted to an 

electronic reporting tool and database currently in development. EPA plans to make data 

submitted to the Agency in electronic form available to the public in electronic form. In 

comparison, the U.S. Coast Guard program includes mandatory reporting and a system for 

receiving and archiving report information, and inspections to corroborate report claims (NAS 

2011). EPA has noted they have access to all ballast water data submitted to SERC, and EPA 

plans on sharing its data collected with the Coast Guard. For vessels covered under the sVGP, 

 

13 See: http://www.serc.si.edu/labs/marine_invasions/index.aspx
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self-monitoring reports are kept on board; though never sent to EPA, these reports could be

checked during an inspection.

We conclude that EPA is likely to identify, collect, and analyze important information about its 

authorized discharges under its VGP; their ability to collect monitoring data on vessel discharges 

authorized under the sVGP is partially dependent on their inspections and other compliance 

assistance activities being developed, described below (under compliance, section 6). This 

monitoring information is essential because it will provide EPA with data needed to reliably

estimate stressors and exposure throughout the life of the permit. It will also provide EPA with a 

additional means to determine the efficacy of its permit in protecting waters of the U.S. and the 

listed resources that depend upon them (as discussed further below, number 7).

(5) Effects on 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, 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.

As with uncertainties in its exposure analysis, EPA also identified uncertainties in the response 

analysis. In section 5.2.6.2 of the BE, EPA provided a comprehensive discussion of uncertainties 

associated with the selection of chronic toxicity values. In order to address whether EPA has 

demonstrated sufficient knowledge of the effects on listed resulting from exposures to discharges 

authorized by the VGP, we must first review these uncertainties for the BE’s assessment and 

how EPA addressed them, then evaluate the additional uncertainties identified by the Services. 

Uncertainty in Effects Analysis Identified by EPA

EPA acknowledged the uncertainty added to its analysis by the interspecies extrapolations 

necessary to fill data gaps in response toxicity threshold information for threatened and 

endangered species. The use of chronic effects data from tests with surrogate species 

traditionally requires applying data for the closest taxonomically related species with appropriate 

data. EPA chose to data for the most sensitive surrogate species rather than the closest 

taxonomically related species. This decision provides an added measure of conservatism in the 
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risk analysis. EPA also assumed that listed species may be uniquely sensitive to pollutants 

compared to surrogate species. Comparative analysis of the extreme chronic sensitivity of the 

darter species, Etheostoma fonticola, and the generally-sensitive surrogate species rainbow trout, 

to copper (Besser et al., 2005a) along with comparisons made in a number of related studies by 

the same group of investigators, suggests that dividing water quality guidelines by a factor of 2.0 

may be a reasonable safety factor (e.g., Dwyer et al. 2005; Gensemer et al. 2007; Mayer et al. 

2008). 

 

In addition to uncertainty associated with the use of effects data for standard lab species, there 

are associated with response to the net toxicity of vessel discharges as mixtures. Organisms are

simultaneously exposed to multiple pollutants in their natural environment, yet risk assessment, 

as a science, still focuses on effects based on exposures to single pollutants. Accordingly, the 

bulk of EPAs analysis evaluated toxicity on a single stressor basis. Mixture toxicity is extremely 

complicated to assess due to the vast number of combinations of pollutants that could be present 

in a mixture which differ in mechanism of action, biological availability and propensity to 

interact with coocurring toxicants or water quality characteristics which influence toxicity and 

bioavailability. To address this uncertainty, EPA applied a concentration addition approach, 

summing the RQs for pollutants with the same toxicological mechanism of action: metals, which

cause oxidative injury of biological tissues (Stohs and Bagchi 1995), and type 1 narcotics, such 

as PAHs which induce stupor through altering nerve transmission (USEPA, 2005; McGrath and 

DiToro, 2009). In this analysis, EPA summed the RQs for water-column only exposure based on 

a mixture of metals or PAHs to give a total RQ representative of the risk of those mixtures to 

listed aquatic species. 

EPA acknowledged issues with its use of NOECs (no observable effect concentration)/ LOECs 

(lowest observable effect concentration)/MATCs (maximum acceptable toxicant concentration), 

as sources of uncertainty that have the potential to influence the response analysis. EPA 

described the shortcomings of NOECs/ LOECs/MATCs as follows: “Historically, most chronic 

toxicity data were evaluated using hypothesis testing to derive a no observed effect concentration 

(NOEC) and lowest observed effect concentration (LOEC) (and resultant maximum acceptable 

toxicant concentration or MATC) from the test concentration series. The resulting values are 

highly dependent on the test concentrations selected, and the number of replicates at each 

treatment level. In many cases, the level of protection afforded by the NOEC-LOEC approach is 

driven more by study design and data precision than ecological significance (see Mount et al., 

2003 for more discussion).” EPA did acknowledge that use of point estimates of chronic 

toxicity, such as the EC10 or EC20, overcome many of the shortcomings of the NOEC-LOEC 

approach, but the availability of point estimates associated with chronic effects is limited, and 

debate continues with regards to the significance to the individual organism (and population) of 

an estimated 10% reduction in chronic response, such as growth.

EPA also asserted that it was correct in not considering sublethal and nontraditional effects when 

selecting its response thresholds. EPA stated that:
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“As a general rule, the use of alternative endpoints is discouraged unless a compelling 

argument can be made that inclusion would reduce the overall level of uncertainty in the 

analysis towards achieving the assessment goal.” 

And:

“EPA relies on the 1985 Guidelines data requirements and data selection process as the 

process by which information is fully-vetted for its utility and applicability in the BE 

analysis. “

Services Assessment of Uncertainty in the Repose Analysis

EPAs decisions to select the most sensitive surrogate species, assess risk of metals and PAH 

mixtures, and perform risk threshold analyses using water quality criteria adjusted by a factor of 

two to account for potential increased sensitivity of threatened and endangered species are, for 

this permit, appropriate adjustments for the uncertainties introduced by interspecies extrapolation

(except as noted for selenium). However, EPA did not acknowledge that an adjustment of water 

quality criteria by a factor of two may also be necessary to account for the greater significance of 

effects on individuals to the survival of a population when protecting threatened and endangered 

species.

When selecting its response thresholds, EPA stated that it relies on the 1985 Guidelines data 

requirements and data selection process. However, the services these guidelines also state: 

"For any threshold material, continuous exposure to any combination of concentrations below the 

threshold will not cause an unacceptable effect ... However, it is important to note that this is a 

threshold of unacceptable effect, not a threshold of adverse effect. Some adverse effect, possibly 

even a small reduction in the survival, growth, or reproduction of a commercially or recreationally 

important species, will probably occur at, and possibly even below, the threshold. The Criterion 

Continuous Concentration (CCC) is intended to be a good estimate of this threshold of 

unacceptable effect."

What constitutes an unacceptable effect for threatened and endangered species was not addressed 

in EPA’s guidelines. For some sublethal effects, such as olfaction, effects may occur at 

concentrations below which traditional endpoints (survival growth and reproduction) are affected 

(reference Copper section of the BO). If such responses are not considered when selecting 

chronic toxicity values, the resulting effects analyses my underestimate risk to susceptible 

species. 

The services also have further comment on the ecological relevance of NOECs/LOECs and 

MATCs. Due to the hypothesis driven selection of response thresholds, the underlying “level of 

effect” associated with NOECs, LOECs, and MATCs may be high. For example, Suter et al. 

(1987) reported that MATC’s for fish fecundity, on average, corresponded to a 42% level of 

adverse effect. These shortcomings can be addressed by using a regression approach to derive 

point estimates of chronic toxicity, such as the EC10.
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In conclusion, the Service evaluated EPAs BE and identified specific discharges (anti-fouling 

hull coatings and exhaust gas scrubbers) and pollutants (copper and selenium) that could pose 

substantial risks to listed species. Considering the uncertainties described above, EPA, with the 

technical assistance of the Services, will identify metrics for assessing selenium and copper 

loadings to waters inhabited by ESA listed species. EPA will evaluate vessel data and identify 

ports/locations where the metric has been exceeded and, as appropriate, identify and implement 

additional actions to reduce any unacceptable risk.

ANS

According to the BE, EPA considered the individual life history for 612 threatened and 

endangered species (those identified by EPA to represent all listed species that occur in the 

action area) to assess exposure and the likelihood of adverse effects from ANS. They anticipate 

that both permits will “significantly benefit listed species due to the anticipated reduction in 

potential ANS release from ballast water due to the requirements of the VGP and sVGP.” While 

we agree that ANS invasions are likely to be reduced as a result of the VGP ballast water 

numeric standards, we do not believe the requirements in the sVGP are as robust. Furthermore, 

requirements to minimize or prevent the introduction of ANS through hull fouling, underwater 

hull husbandry, and other discharges (i.e., chain lockers, seachests, and fish holds) are not as 

well developed this permit cycle. EPA’s literature review identifies invasive species 

introductions as the second greatest threat to biodiversity, and shipping as the greatest source of 

ANS introductions to marine and coastal ecosystems. Our literature review similarly indicates 

that ANS introductions have contributed to the endangerment of species. Therefore, there is a 

high potential for adverse impacts from ANS introductions.

Despite anticipating a reduction in ANS introductions, EPA does not believe that ANS invasions 

will cease as a result of authorized vessel discharges. In light of limited data and uncertainty 

quantifying the risk of ANS introduction, EPA concluded that ANS introductions as a result of 

their action “may affect” aquatic species and their critical habitat. They concluded that aquatic 

listed species, including all listed species under FWS’ authority, may be affected by new vesseldischarge-related ANS, and thus made a “may affect” determination for these species. We agree 

that the species considered by EPA may be affected by discharges containing ANS that are 

authorized by their VGPs. 

(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 

VGPs. 

To monitor and insure compliance with its VGP, EPA will, within one year of finalizing the 

permit, develop and implement a monitoring and compliance plan to assess the performance of 

the permit in protecting listed resources. Currently, the U.S. Coast Guard conducts inspections 

of vessels covered under the VGP using EPA and USCG jointly developed Job Aide, i.e., 

“Guidelines for Coast Guard Evaluations of Compliance with the US Environmental Protection 
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Agency's (EPA) Vessel General Permit (VGP) for Discharges Incidental to the Normal

Operation of Vessels.” To insure that the inspections assess new requirements of the proposed 

VGP, EPA will:

 Work with the U.S. Coast Guard, with the early input of the Services, to update the Job 

Aide to reflect requirements included in the new VGP. 

 Create an online training and/or a webinar training regarding the VGP 

requirements/prohibitions, within one year of final permit issuance.

 Create a comprehensive checklist of requirements for inspector training in conjunction 

with the U.S. EPA National Enforcement Training Institute, within one year of final 

permit issuance.

 Provide and continue to provide the U.S. Coast Guard with the title, office name, current 

address and phone number for points of contact at headquarters offices and in each EPA 

Region and USCG District. 

In addition, EPA’s Office of Enforcement and Compliance Assurance will meet with the 

Services to discuss enforcement under the VGP. The EPA will gather, review and analyze 

inspection data submitted by the Coast Guard; the results will be summarized (by type of vessel, 

location when available, type of deficiencies, and number of deficiencies) and provided to the 

Services annually. 

To monitor and insure compliance with its sVGP, EPA will, within one year of finalizing the 

permit, develop and implement a monitoring and compliance plan to assess the performance of 

the permit in protecting listed resources. To insure inspection of a sample of small vessels, EPA 

will: 

 Organize a meeting with their Office of Enforcement and Compliance Assurance for the 

Services to discuss and provide input to OECA’s inspection and enforcement plans for 

the sVGP. 

 Work with USCG, with the early input of the Services, to update the inspection and 

enforcement document inspection checklist (i.e., Job Aide) to reflect sVGP requirements

 Conduct outreach to the states to raise awareness about small vessel requirements; EPA 

will encourage States to check records of quarterly self-inspection records and visible 

portions of the hull while inspecting vessels when implementing their own programs. 

 Develop trainings covering the small vessel requirements and share these with the Coast 

Guard and States

The EPA will provide the Services with a yearly summary of the number of inspections (by 

EPA, the Coast Guard, States or other sources) and results (including number of inspections by 

type of vessel, location when available and number and type of deficiencies) based on data 

available to EPA. 

Unanticipated, low levels of compliance for either the VGP or sVGP would constitute new 

information. This information would allow EPA to determine whether reinititation of formal 

ESA Section 7 consultation would be required as provided in 50 CFR 402.16, as described in the 
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Fact Sheets. EPA’s “permit reopener clause” allows EPA to modify its permits, if necessary, 

during the permit period. The VGP requires that vessel operators inform EPA of instances of 

noncompliance with the permit terms, including the results of monitoring, in annual reports 

submitted to EPA. EPA has partnered with the USCG, and will rely on the USCG’s VGP 

inspections. VGP inspection and compliance data will be entered into the USCG MISLE 

database. EPA may also partner with States and others who may provide equivalent inspection 

and compliance data for the sVGP, though these partnerships have not yet been established. The

monitoring of compliance EPA ultimately establishes will support their ability to know whether 

discharges by individual permittees have complied with the terms of the proposed VGPs. 

In the sections on the Water Quality-Based Effluent Limitations, the VGPs include statements 

that if at any time the permittee becomes aware, or EPA determines, that the discharge causes or 

contributes to an exceedance of applicable water quality standards, the permittee must take 

corrective action. However, the VGPs do not require monitoring for such exceedances for the 

vast majority of the discharges to be authorized, so it is likely that exceedances of a water quality 

standard would infrequently be detected. As such, it is uncertain whether EPA can know or 

reliably estimate the physical, chemical or biotic stressors that are likely to be produced as a 

direct or indirect result of the activities to be authorized by the proposed permits.

It is important to note that the first stage of compliance under a general permit, accurate selfidentification of discharges requiring coverage under the permit, is a recognized barrier to permit 

effectiveness. Accurate self-identification of dischargers under municipal and industrial storm 

water general permits was among the metrics evaluated in a study of 136 facilities subject to the 

stormwater permit requirements (Cross & Duke 2008). Among these facilities, approximately 

21% were aware that their discharges were subject to the permit and only 10% had completed the

first stages of complying with the permit, even though stormwater permits had been in place over 

15 years. While the authors suggested that outreach regarding the duty to comply might 

stimulate greater compliance among dischargers they also noted that compliance would still 

likely be low because among those facilities whose managers were aware of their duty to 

comply, fewer than half pursued the required actions. The authors attributed the low rate of 

compliance to penalties that were not sufficiently strict to motivate compliance. 

Issues identified with self-identification among EPA’s other general permits do not necessarily 

apply to vessels authorized to discharge under the either of the VGPs due to cultural differences 

among these regulated communities and the well-defined vessel populations specified under the 

VGPs. It is important to note that self-identification for sVGP dischargers is particularly 

essential to compliance with the sVGP. A query for information on the VGPs demonstrated 

information sharing activity during and after the VGPs comment period along with offers of 

compliance assistance among professional associations, service providers, state and federal 

agencies within the US and US trading partners.14 EPA has noted that it has received

approximately 50,000 NOIs submitted for the 2008 VGP, roughly how many the Agency 

 
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expected to be submitted. Addtionally, Coast Guard inspectors alert EPA when certain vessels 

have not completed NOIs or met other self-reporting and self inspection requirements of the 

permit. Hence, to date, EPA reported to the Services that they believe the VGP has had high 

levels of self-identification and implementation with the 2008 VGP.

In the course of consultation, the Services requested existing inspection and compliance 

information from EPA. EPA provided a powerpoint illustration identifying a total of 182 

deficiencies found in the course of 22,500 inspections conducted by USCG between March and 

September 2011. EPA indicated that most deficiencies were corrected upon discovery and a 

total of 10 warning letters were sent out. 

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 its Permit Compliance System (PCS) and Integrated 

Compliance Information System - National Pollutant Discharge Elimination System (ICISNPDES) databases. The PCS and ICIS-NPDES databases track the number of inspections and 

enforcement actions over five years, along with the number of non-compliance and effluent 

exceedances over three years. The data are classified for major and minor dischargers. VGP 

compliance data are not tracked in EPAs databases and compliance inspections are conducted by 

the USCG which maintains inspection and compliance data in its database. The VGP and sVGP 

are conceptually analogous to the major and minor discharger classification used for permits 

tracked in its databases. While we cannot know in advance the compliance rate for the sVGP, 

the compliance rates of existing general permits, taken in context of reported compliance with 

the VGP, provide insight. 

General Permit Compliance

We downloaded and analyzed EPA’s compliance databases in September of 201215. The analysis 

focused on general and individual permits for entities where EPA is the permitting authority. To 

avoid bias from permits with multiple inspections, we converted the frequency data into 

presence/absence of inspection, compliance and enforcement events. In this way, each permit 

was equally weighted in the analysis. All major dischargers under general permits were inspected 

at least once in the past 5 years. However, among minor dischargers, a much smaller proportion 

of general permittees (51%) were inspected relative to the proportion of individual permittees 

inspected (88%). 

The most common type of inspections for all inspected Permit Groups (i.e., major vs. minor, 

general vs. individual) are compliance evaluations, followed by sampling inspections. No other 

type of inspection was conducted for major discharges under general permits. Reconnaissance 

inspections, which serve to “Expand regulatory presence with limited inspection resources to 

 

15 The PCS was the original tracking mechanism for NPDES permits and currently includes data for 21 states. State by state, the 

data in PCS is being migrated into the newer ICIS-NPDES. The ICIS-NPDES currently tracks data for the remaining states not 

represented in PCS, U.S. territories, the Navajo Nation, and the St. Regis Tribe.
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verify basic compliance data” (USEPA 1989), were the third most common type of inspection, 

but were half as frequent among minor dischargers covered under a general permit (6% of 

inspections) as under those with an individual permit (12% of inspections). Plan reviews for 

minor dischargers under a general permit (3% of inspections) were half the frequency of plan 

reviews for minor dischargers holding individual permits (6% of inspections). 

One aspect of enforcement and compliance that demonstrates EPAs ability to identify and 

correct problems is the role inspections play in detecting permit violations. The analysis 

revealed an increased rate of permit violations among inspected minor dischargers relative to 

uninspected minor dischargers holding general permits (violations 16% inspected vs 4% of 

uninspected permits). Permit violations for inspected facilities with individual permits were 

higher than inspected facilities general permits (violations in 59% inspected vs 17% uninspected 

permits). Recall that among minor dischargers, 88% of those holding individual permits were 

inspected while only 51% of those holding general permits were inspected. Three violation 

types appear to contribute to the difference between general and individual permits; reportable 

noncompliance (35% of permits), effluent violations (24% of permits), and compliance schedule 

violations (10% of permits). 

The role of effluent limits in permit compliance rates among minor dischargers. 

The difference in the rate of permit violations between minor dischargers holding a general 

permit versus those with individual permits appears to be due to the absence of effluent limits 

among the general permits. Effluent limits require discharge monitoring to ensure compliance 

with permit requirements and, for impaired waters, load allocation for individual dischargers. 

Ninety two percent of the minor dischargers with individual permits have effluent limits while 

only 54% of general permit holders have effluent limits. Individual permit holders with effluent 

limits were more likely to report exceeding their effluent limits (nearly 70%) than submit an 

incomplete DMR (19%). The opposite is true for general permit holders with effluent limits, 

which were more likely to submit an incomplete DMR (58%) than report exceeding effluent 

limits (23%). Taken together, 80% of general permit holders and 88% of individual permit 

holders either reported effluent limit exceedences or submitted an incomplete DMR. While this 

suggests a difference in compliance behavior between general and individual permit holders, it 

indicates a similar fundamental compliance rate among minor dischargers with effluent limits, 

regardless of permit type. This suggests that discharges from permits lacking discharge limits 

have similar rates of compliance, but are not detected and are therefore not actionable.

The absence of effluent limits in nearly half of EPA’s General Permits eliminates one of EPA’s 

potential tools for identifying noncompliance, leaving only schedule violations to identify 

permittee activities which may harm water quality. Reanalyzing compliance rates for permits 

lacking effluent limits leaves 56 individual permits held by minor dischargers and 389 general 

permits held by minor dischargers. Among the minor dischargers with individual permits, six 

permits had violations, these specifically include; three reportable noncompliance violations, two 

permit schedule violations, a compliance schedule non-receipt, and one single event violation. 

Among the minor dischargers with general permits, two permits had violations, these specifically 

include; one reportable noncompliance violations and one permit schedule violation. These data 

indicate that the absence of effluent limits that is characteristic of general permits likely results in 
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substantial numbers of undetected discharges that are not in compliance.

Discharge sampling and analysis required under the VGP is limited to the following subset of 

discharges; 1) ballast water samples from vessels with ballast water treatment systems, 2) 

graywater samples from vessels housing 10 or more persons and built after December 2013, and 

3) exhaust gas scrubber waste water from vessels employing that technology. These represent a 

relatively small portion of vessels and discharges subject to the VGP. Other terms affect most 

vessels covered by the VGPs. These include visual monitoring for oily sheen and restricted 

discharges within 1 nm of shore or into Waters Federally Protected wholly or in part for 

Conservation Purposes. Discharge sampling and analysis is not required under the sVGP. 

The role of enforcement in permit compliance.

The severity of a given violation should be reflected by the enforcement action taken. Formal 

enforcement actions are triggered by the failure to achieve compliance within a specified period 

of time under informal enforcement measures or for violations of sufficiently serious nature 

triggering formal enforcement action with subsequent penalty order or judicial action.16 Informal 

enforcement actions were twice more common than formal enforcement actions among general 

permits for minor dischargers. Minor dischargers under general permits were also less likely to 

have violations met with any enforcement action as those with individual permits. 

The lack of an enforcement action could indicate either return to compliance or lapsed 

enforcement. Using the number of quarters in noncompliance as a surrogate for “return to 

compliance”, a comparison of permits with violations which were and were not subjected to 

enforcement action shows that, with the exception of minor dischargers with general permits, the 

number of quarters in noncompliance has no bearing on whether or not facilities are subjected to 

enforcement. The number of quarters in noncompliance was only a determinant of whether or 

not a facility is subjected to an enforcement action for minor dischargers with general permits. 

Those operators receiving an enforcement action had an average of 7 quarters in noncompliance 

while those with no enforcement averaged 3 quarters in noncompliance. Among both minor and 

major dischargers with individual permits, the number of quarters in noncompliance was higher 

(8-10 quarters) and had no bearing on enforcement. Major dischargers holding general permits 

averaged 4 quarters in noncompliance, irrespective of enforcement. 

The disparity in the average number of quarters in noncompliance among individual and general 

permits could be due to the differing nature of their discharges and the specificity of the 

constraints listed within the permits. Individual permittees are largely wastewater treatment 

facilities and industrial dischargers releasing effluents with known constituents (more or less) at 

a predictable rate from discrete point sources. This allows more specific monitoring and 

reporting requirements within a permit and, as a consequence, a greater probability of detecting a 

violation of the permit conditions. Additionally, discharges from a point source at a known rate 

are more easily monitored than the diffuse, episodic discharges typical of general permits. 

 

16 USEPA 1989. The Enforcement Management System: National Pollutant Discharge Elimination System, (Clean Water Act). 

Office of Water. # PB95-156527
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Data from the USCG regarding compliance under the existing VGP indicate high rates of 

inspection and compliance. Data for the VGP indicated a violation rate of 182 deficiencies 

among 22,500 inspections (<1%) while 33% percent of major dischargers and 10% of minor 

dischargers were found in violation among General Permit holders whose compliance is tracked 

in EPAs databases. Analysis of EPAs compliance databases does indicate that inspections and 

effluent limits positively influence detections of permit violations. 

(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 primary 

constituent elements of designated critical habitat. 

In the VGPs, EPA includes a “Permit Reopener Clause.” This clause reiterates in detail the 

CWA’s regulatory framework that allows EPA to modify its permits or require individual 

permits if, for example, new information becomes available or if water quality standards are 

exceeded. The VGPs include permit reopener clauses which state that the permits are subject to 

modification based on the receipt of new information that was not available at the time of permit 

issuance and would have justified the application of different permit conditions at the time of 

permit issuance. This new information may include data on ANS invasion rates, information 

regarding available technologies to minimize ANS invasions, discharge concentrations or 

volumes, pollutant risks, compliance or lack thereof, and adverse effects to listed resources. This 

information would also allow EPA to determine whether to request reinitiation of formal ESA 

Section 7 consultation as provided in 50 CFR 402.16 and described in the Fact Sheets.

For the VGP, with respect to ballast water discharges, new information that will be considered in 

determining whether to modify this permit includes, but is not limited to, data or information

from permittees, the general public, states, academia, scientific or technical articles or studies, 

and results of monitoring conducted under this permit indicating that: 

• Treatment technology has improved such that these improved technologies would have 

justified the application of significantly more stringent effluent limitations or other permit 

conditions had they been known at the time of permit issuance; 

• Treatment technologies known of at the time of permit issuance perform better than 

understood at the time of permit issuance such that this improved performance would 

have justified the application of significantly more stringent effluent limitations or other 

permit conditions had this been understood at the time of permit issuance; 

• Scientific understanding of pollutant effects or of invasion biology has evolved such 

that this new information would have justified the application of significantly more 

stringent effluent limitations or other permit conditions had this been understood at the

time of permit issuance; or 

• The cumulative effects of any discharge authorized by the VGP on the environment are 
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unacceptable. 

As they pertain to ballast water, EPA’s reopener clause can be compared to USCG’s Ballast 

Water Rulemaking’s practicality review. As an NPDES permit, the VGP must be reissued every 

5 years. The permit reissuance process is essentially a mandatory periodic review during which 

the permit’s requirements are evaluated to ensure that they reflect best available technology and 

remain sufficiently protective of water quality. At the conclusion of that systematic review, EPA 

issues a new permit with updated requirements, including, as appropriate, more stringent 

requirements. Under the VGP, EPA can modify their permit and reinitiate if “new information” 

becomes available that triggers the need. In comparison, the U.S. Coast Guard program includes 

a mandatory review of ballast water numeric standards after three years. The Coast Guard 

results from their three-year review will be available to EPA, and the Agency can determine 

whether these results constitute new information.

As described in the Exposure Section, the VGPs require few anti-fouling/hull husbandry 

practices or technologies that are likely to result in substantial changes to biofouling ANS 

invasion rates. This is partially because developing technologies are not yet widely available. 

To ensure the protection of listed species, EPA will identify and implement, as appropriate, 

additional actions (e.g., require anti-fouling coatings (AFCs); require debris containment 

systems; require more stringent ballast water standards) as soon as practicable (including in 

future permit iterations). Before they transmit the next draft of the VGPs to OMB for 

interagency review, they will 

1) Compile information on new developments in AFCs (to minimize exposure to hullfouling ANS and copper loading) and debris containment systems (to minimize the 

release of ANS and biocides during underwater husbandry).

2) Identify whether there are more efficacious BMPs or technologies for underwater 

husbandry and for anti-fouling coatings with fewer secondary environmental impacts that 

could be required of vessels.

With the technical assistance of the Services, EPA will identify metrics to evaluate whether 

vessel mediated ANS invasion rates are being reduced over time. If needed, EPA will, as 

appropriate, identify and implement additional actions (e.g., require anti-fouling coatings; require 

debris containment systems; require more stringent ballast water standards) as soon as 

practicable (including in future permit iterations) to ensure the protection of listed species.

With the technical assistance of the Services, EPA will identify metrics for assessing vesselrelated copper loadings to waters inhabited by ESA listed species (i.e., using the number of ships 

reporting copper hull treatments in eNOIs for particular areas as a proxy). If the metric has been 

exceeded, EPA will, as appropriate, identify and implement additional actions to reduce any 

unacceptable risks.

With the technical assistance of the Services, EPA will identify metrics for assessing exhaust gas 

scrubber selenium loadings to waters inhabited by ESA listed species (i.e., using the number of 

ships reporting exhaust gas scrubbers in eNOIs for particular areas combined with expected 
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and/or reported volume and concentration values as proxies). If the metric has been exceeded, 

EPA will, as appropriate, identify and implement additional actions to reduce any unacceptable 

risk.

Aquatic nuisance species, copper, and selenium, are the stressors most likely to reduce individual 

fitness and population viability for listed species. In addition, ANS are likely to adversely affect 

the primary constituent elements of designated critical habitat. For vessel discharges associated 

with these stressors, EPA has committed to monitoring metrics, which if exceeded, will trigger 

additional protective measures. In addition, EPA will monitor, and implement when practicable, 

new technologies designed to minimize ANS invasions. Finally, if new information becomes 

available that would have justified different permit requirements, EPA may modify their permits 

and/or request reinitiation of Section 7 consultation. We conclude that EPA has several 

mechanisms to prevent or minimize listed resources’ exposure to stressors in discharges. 

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 Biological 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 ESA. 

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 and that would not require Federal authorization, Federal

funding, or the actions of a Federal agency. During this consultation, FWS searched for 

information on future State, Tribal, local or private actions that were reasonably certain to occur 

in the action area. FWS conducted electronic searches of business journals, trade journals and 

newspapers using First Search, Google and other electronic search engines. Those searches 

produced no evidence of future private action in the action area that would not require Federal

authorization or funding and is reasonably certain to occur. As a result, FWS is not aware of any 

actions of this kind that are likely to occur in the action area during the near future.

Integration and Synthesis

The EPA proposes to issue and implement the Vessel General Permit (VGP) and the Small

Vessel General Permit (sVGP), which authorize discharges incidental to the normal operation of 

non-recreational and non-military vessels into waters of the U.S. 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 VGP was first issued by EPA in 2008; the sVGP 
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is a new permit. 

The EPA expects that vessels greater than 79 feet in length or with 8 cubic meters or more of 

ballast water capacity will seek coverage under the VGP. Vessels less than 79 feet and with less 

than 8 cubic meters of ballast water capacity may be eligible for coverage under the sVGP, 

which has less stringent restrictions and fewer reporting requirements. The EPA estimates that 

approximately 72,000 vessels may be eligible for coverage under the VGP and approximately

138,000 vessels may be eligible for coverage under the sVGP. 

The action will occur throughout the waters of the U.S., i.e., the action area. The proposed 

action is likely to likely to adversely affect the species and critical habitats listed in Table 1. 

This is primarily a function of the potential effects of ANS. 

In the Opinion, we described the status of each species and the environmental baseline. We also 

discussed the effects of the action, i.e., exposure, stressors, response, and risks. Here, we 

integrate this information to describe stressors of the greatest concern (i.e., ANS, copper, and 

selenium) and the likely consequences of exposing listed resources to these stressors. 

Aquatic nuisance species (carried in ballast water, on hulls, and in chain lockers, seachests, and 

fish holds of vessels) may be discharged into waters of the U.S. While ANS are themselves 

stressors, the mechanisms by which they adversely affect listed resources include: predation, 

competition, trophic alteration, ecosystem alteration, disease transmission, and genetic 

introgression. Because of the magnitude of these mechanisms, ANS are likely to reduce the 

fitness (i.e., survival and/or reproduction) of exposed individuals. 

Fishes are often threatened by some combination of the four Hs: habitat loss, harvest, hydrology 

alterations, and for some species, hatcheries. These species are highly dependent upon waters of 

the U.S., and thus are sensitive to the introduction of pollutants and ANS. Invasive species have 

been found to prey on juveniles, compete for prey resources, alter essential habitat, and transmit 

infectious diseases. ANS invasions pose a very significant threat because ANS have the potential 

to reduce the fitness of a large number of listed individuals through a multitude of mechanisms. 

ANS invasions are likely to reduce population and species viability. Invasions are also likely to 

adversely affect the critical habitat of these species, which includes prey resources as a principle 

constituent element. Copper affects chemoreception of fish, reducing their ability to forage, 

migrate, avoid predators, and find mates. It also impairs their disease resistance, respiration, 

osmoregulation, blood chemistry, enzyme activity, and internal organ functions. Selenium can 

reduce reproductive potential in fishes and birds. Therefore, exposure to high concentrations of 

copper and/or selenium is likely to reduce population and species viability.

Threatened and endangered invertebrates have experienced dramatic declines as a result of 

ecosystem restructuring, overharvest, environmental changes, and disease. Their reproductive 

strategies (e.g., broadcast spawning) make them susceptible to detrimental Allee effects at small 

population sizes. They are especially vulnerable to the introduction ANS invasions which would 

lower the fitness of individuals through the introduction of novel pathogens and competition for 

space and prey. These mechanisms are likely to affect a large number of individuals through the 

spread of disease and niche replacement. Therefore, ANS invasions are likely to reduce 
208

population and species viability of listed invertebrates. Invasions are also likely to adversely 

affect the critical habitat of these species, which includes prey resources and suitable substrate as 

principle constituent elements. Copper has been shown to reduce the survival and reproduction 

of mollusks. 

Listed plant species have declined primarily as a result of habitat modification and destruction

and altered water quality. Their limited habitat range provides little resilience to ecosystem or 

environmental perturbations. Invasive species are likely to transmit infectious diseases and 

compete for resources (including space). Disease is likely to spread quickly through the small 

population and a competitor could easily overgrow native plants with small habitat ranges. 

Therefore, ANS invasions are likely to reduce population and species viability of listed plants. 

Our Programmatic Effects Analyses assess whether and to what degree EPA structured the 

VGPs, as well as monitoring and compliance, to insure that vessel discharges into waters of the 

U.S. 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. 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 VGPs, which includes monitoring and compliance. Second, while there 

were gaps in EPA’s identification of stressors of the action, EPA will use monitoring programs 

to fill these gaps in knowledge. Third, EPA was unable to reliably estimate exposure of ESA 

listed resources to these stressors, but again, they will use monitoring programs to estimate 

exposure through the life of the permit. Fourth, EPA will collect and monitor information on 

authorized activities throughout the life of the permit. Fifth, EPA concluded that vessel 

discharges carrying ANS may affect listed resources. Though EPA initially underestimated the 

impact of pollutants on listed resources, they have incorporated new knowledge into their 

analyses and will continue to monitor pollutants of concern (i.e., copper and selenium). Sixth, 

EPA has programs in place for the VGP and is developing a program for the sVGP to monitor 

for compliance; they have the authority to enforce both permits. Seventh, EPA has committed to 

considering modification of its action if new information (including inadequate protection for 

species or low levels of compliance) becomes available and reopening the permit is appropriate. 

Modifications may include additional actions or requirements, reopening of the permits, and 

reinitiation of Section 7 consultation. Though this programmatic review gives us confidence in 

EPA’s ability to insure that vessel discharges into waters of the U.S. 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; however, we 

must address our final area of concern: exposure.

Given exposure to ANS invasions and pollutants, listed resources are likely to be adversely 

affected, resulting in reduced viability of populations and species. Therefore, it is imperative 

that EPA reduce to the extent practicable the exposure of listed resources to vessel-mediated

ANS invasions and harmful concentrations of pollutants. There is a small likelihood that listed 

resources would be exposed to ANS or harmful concentrations of pollutants. To reduce this 

likelihood of exposure even further, EPA will implement the following four-step feed-back loop: 

permit requirements, monitoring and collecting new information, additional actions to reduce 
209

any unacceptable risks, and, as appropriate, reopening the permit and/or reinitiating consultation 

to reassess permit requirements.

First, EPA includes several requirements in their VGPs to reduce the exposure of listed resources 

to ANS and pollutants, For ANS, EPA requires vessel owners/operators to “minimize the 

transport of attached living organisms” into waters of the U.S. For many vessels covered under 

the VGP, EPA requires that discharges meet numeric ballast water standards. They require 

vessel owners/operators to minimize hull husbandry and avoid discharging ballast water in 

designated critical habitat, when feasible. For pollutants, ANS requires that vessel 

owners/operators meet technology-based and water-quality based effluent limits.

Second, EPA will monitor pollutants and ANS. To monitor pollutants in VGP discharges, EPA 

requires and reviews the annual analytical test results for treated ballast water, exhaust gas 

scrubber effluent, bilgewater (new builds), and graywater (cruise ships). For copper and 

selenium, EPA will develop and implement a monitoring and reporting plan within one year of 

the finalization of the VGPs. They will identify metrics for copper and selenium and compile 

data through NOIs and annual reports. They will review the data twice during the term of the 

permit to determine whether the metrics have been exceeded. For ANS invasions, they will 

annually track new vessel-mediated invasions using nationwide ANS databases; they will also 

review invasion rates as estimated by systematic surveys of ANS in San Francisco, Tampa, and 

Chesapeake Bays. To identify improvements in technology designed to minimize the transport 

of biofouling ANS, EPA will compile information on new developments in AFCs (to minimize 

exposure to hull-fouling ANS and copper loading) and debris containment systems (to minimize 

the release of ANS and biocides during underwater husbandry). They will identify whether there 

are more efficacious BMPs or technologies for underwater husbandry and for anti-fouling 

coatings with fewer secondary environmental impacts that could be required of vessels.

Third, EPA will, if necessary, identify and implement additional actions to reduce any 

unacceptable risks associated with vessel mediated ANS or pollutants. For example, EPA will, if 

necessary, require additional requirements to minimize the transport of ANS (e.g., anti-fouling 

coatings, debris containment systems, or more stringent ballast water standards) as soon as 

practicable. These additional actions would be designed to further reduce exposure of listed 

resources to ANS and traditional pollutants.

Fourth, EPA will, as appropriate, reopen and modify their permits if they receive new 

information (including that discussed above) that was not available at the time of permit issuance 

and would have justified the application of different permit conditions at the time of permit 

issuance. This new information may include data on ANS invasion rates, available technologies 

to minimize ANS invasions, discharge concentrations or volumes, pollutant risks, compliance or 

lack thereof, and adverse affects to listed resources. This information would also allow EPA to 

determine whether to request reinititation of formal ESA Section 7 consultation as provided in 50

CFR 402.16 and described in the Fact Sheets. Either of these actions (reopening the permit or 

requesting reinitiation of Section 7 consultation) under the fourth step provides a mechanism for

EPA to revise the permit requirements, thus restarting the feedback loop at step one to reduce to 

the extent practicable the exposure of listed resources to vessel-mediated ANS invasions and 
210

traditional pollutants. 

To assess and encourage compliance, EPA authorizes and/or conducts vessel inspections. In this 

endeavor, EPA has created an MOA with the U.S. Coast Guard, which potentially inspects all 

vessels covered under the VGP on an annual basis. EPA will create and implement a plan to 

assess the performance of the VGP based on inspections of a subset of vessels covered under the 

sVGP. The EPA will review annual reports and inspection data to insure that vessel 

owners/operators are complying with the requirements of the permits. Lower than anticipated 

compliance levels could constitute new information, as described in the fourth step, and provide 

a mechanism to reopen/modify the permit or reinitiate Section 7 consultation. In this manner, 

EPA has the ability to increase compliance through additional requirements to their permits or 

through additional actions (steps one and three of the feedback mechanism).

This four-step feedback mechanism provides continual monitoring of potential exposure of listed 

resources to potentially harmful stressors. If metrics indicate the possibility of exposure to 

potentially harmful levels of ANS and pollutants, EPA can implement measures to reduce these 

threats before individuals are exposed. This iterative process first minimizes the likelihood of 

exposure; if there is exposure, it minimizes the number of exposed individuals exposed; and if 

individuals are exposed, it minimizes the likelihood that an entire population or species will be 

affected. In this manner, EPA has insured that their action is not likely to jeopardize the 

continued existed of any listed species and is not likely to adversely modify or destroy 

designated critical habitat. 

Conclusion

After reviewing the current status of the listed species, the environmental baseline for the action 

area, the potential direct and indirect effects of EPA’s proposal to issue and implement the VGPs 

which would authorize discharges incidental to the normal operation of vessels into waters of the 

United States, an examination of the controls EPA proposes to implement to mitigate these 

effects, and cumulative effects, it is our Biological and Conference Opinion that EPA has insured 

that its action is not likely to jeopardize the continued existence of any listed or proposed species 

under FWS’ jurisdiction. 

After reviewing the current status of the critical habitat that has been designated for endangered 

and threatened species, the environmental baseline of the action area, the potential direct and 

indirect effects of the action, an examination of the controls EPA proposes to implement to 

mitigate these effects, and cumulative effects, it is our Biological and Conference Opinion that 

EPA has insured that its action is not likely to destroy or adversely modify designated or 

proposed critical habitat. 
211

Incidental Take Statement

Section 9 of the ESA and Federal regulations 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 further defined by FWS to include significant 

habitat modification or degradation that results in death or injury to ESA listed species by 

significantly impairing essential behavioral patterns, including breeding, feeding or sheltering. 

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 Act provided that such taking is in compliance with the terms and conditions of 

this Incidental Take Statement.

Section 7(b)(4) and 7(o)(2) of the Act generally do not apply to listed plant species. However, 

limited protecton of listed plants from take is provided to the extent that the Act prohibits the 

removel and reduction to possession of Federally listed endangered plants or the malicious 

damage of such plants on areas under Federal jurisdiction, or the destruction of endangered 

plants on non-Federal areas in violation of State law or regulation or in the course of any 

violation of a State criminal trespass law.

The prohibitions against taking the species found in section 9 of the Act do not apply until the 

species is listed. However, the Service advises the EPA to consider implementing the following 

following reasonable and prudent measures. If this conference opinion is adopted as a biological 

opinion following a listing or designation, these measures, with their implementing terms and 

conditions, will be non-discretionary.

Amount or Extent of Take

This programmatic consultation focuses on whether the EPA has insured 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 address the specific individual actions that the general permit would 

authorize. The controls and measures in the general permits are designed to reduce or in most 

cases prevent the exposure of endangered or threatened species under FWS’ jurisdiction to 

adverse impacts as a result of activities authorized by the general permits. However, it is 

possible that such exposures may still take place as a result of those activities, and it is possible 

that these exposures may cause incidental take. As a result, incidental take of endangered or 

threatened species is possible over the duration of the proposed general permit.

Because of the large scale and broad scope of the proposed action, even the best scientific and 

commercial data available are not sufficient to enable FWS to estimate the specific amount of 

potential incidental take associated with the action. Therefore, FWS identifies, as a surrogate for 

the allowable extent of take, the ability of this action to proceed without any adverse incident to 
212

any species listed in Table 1 that is attributed to any discharge in accordance with the general 

permit in the range of listed endangered or threatened species under FWS’ jurisdiction. 

An adverse incident is considered attributable to a discharge in accordance with the general 

permit if a discharge of a pollutant authorized by the general permit is known to, or reasonably 

presumed to have occurred prior to, and near or upstream from the adverse incident, and if the 

pollutant is detected in local water samples or in tissue samples of affected fish, or –in the case 

of aquatic nuisance species– that adverse incident is directly attributable to the introduction of 

any aquatic nuisance species known or reasonably presumed to have occurred from discharges 

authorized by the general permit. 

Reasonable and Prudent Measures

The measures to avoid or minimize take described below are non-discretionary and must be 

implemented by the EPA so that they become a binding condition on any applicant, as 

appropriate, for the exemption in section 7(o)(2) to apply. The EPA has a continuing duty to 

regulate the activity covered by this incidental take statement. The protective coverage of 

section 7(o)(2) may lapse if the EPA: (1) fails to assume and implement the terms and 

conditions; or (2) fails to require any applicant to adhere to the terms and conditions of the 

incidental take statement through enforceable terms that are added to the general permit. In 

order to monitor the impact of incidental take, the EPA must report the progress of the action and 

its impact on the species to FWS as specified in the incidental take statement (50 

CFR§402.14(i)(3)). 

The EPA shall utilize its authority to regulate vessel discharges in an adaptive framework by 

monitoring implementation of the action, its effects, and development of new technologies, and 

incorporating new control technologies that are developed, as appropriate, in order to minimize 

risk from pollutant exposures and ANS.

Terms and Conditions

To be exempt from the prohibitions of section 9 of the ESA, the EPA must comply with the 

following condition. This condition implements the reasonable and prudent measure described 

above. This term and condition is non-discretionary. 

The EPA shall implement the action as proposed.

Reporting Requirements

Incidents where any listed species under the FWS’s jurisdiction appear injured or killed as a 

result of discharges into Waters of the United States from discharges authorized by this permit 

shall be reported by EPA to the U.S. Fish and Wildlife Service, Endangered Species Program,

Chief, Branch of Consultations and HCPs, at (703) 358.2171. The finder should leave the plant 
213

or animal alone, make note of any circumstances likely causing the death or injury, note the 

location and number of individuals involved and, if possible, take photographs. Adult animals 

should not be disturbed unless circumstances arise where it is obviously injured or killed by 

discharge exposure, or some unnatural cause. The finder may be asked to carry out instructions 

provided by FWS to collect specimens or take other measures to ensure that evidence intrinsic to 

the specimen is preserved. This information should be communicated to operators covered by 

the permit.

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 ESA listed species or critical habitat, 

to help implement recovery plans, or to develop information.

The following conservation recommendations would provide information for future consultation 

involving EPA’s issuance and implementation of VGPs:

1. Review more stringent ballast water, hull fouling, and hull husbandry requirements of 

States and other nations to evaluate their practicability for incorporation in future 

permits.

2. Begin information ESA Section 7 consultation (“preconsultation”) well in advance of 

the publishing the draft permits in the Federal Register for public comment. This will 

allow EPA to incorporate recommended actions designed to protect listed resources 

into its permits at an early stage and receive public comment on these actions.

In order to keep FWS informed of actions minimizing or avoiding adverse effects, or benefiting 

ESA listed species or their habitats, the U.S. Environmental Protection Agency should notify the 

FWS of any conservation recommendations they implement in their final action.

Reinitiation Notice

This concludes formal consultation on the U.S. Environmental Protection Agency’s issuance of 

the Vessel General Permit and the Small Vessel General Permit. 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) New information 

reveals effects of the agency action that may affect endangered or threatened species under FWS’ 

jurisdiction or to designated critical habitat in a manner or to an extent not considered in this 

Opinion; (2) The agency action is subsequently modified in a manner that causes an effect to the 
214

ESA listed species or critical habitat not considered in this Opinion; (3) A new species is listed 

or critical habitat designated that may be affected by the action; or (4) The amount or extent to 

take specified in the incidental take statement is exceeded. In instances where the amount or 

extent of take specified in the incidental take statement is exceeded, the U.S. Environmental 

Protection Agency must immediately request reinitiation of Section 7 consultation.

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