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UNITED STATES ENVIRONMENTAL PROTECTION AGENCY 

WASHINGTON, D.C. 20460 

J U L 3 2012 

OFFICE OF 

WATER 

Helen Golde 

Acting Director, Office of Protected Resources 

National Marine Fisheries Service 

1315 East-West Highway, F/PR3 

Silver Spring, MD 20910 

RE: Initiation of Formal Consultation on EPA's Vessel General Permit for Discharges 

Incidental to the Normal Operation of Vessels (VGP) and Small Vessel General Permit for 

Discharges Incidental to the Normal Operation of Vessel Less than 79 Feet (sVGP) 

Dear Ms. Golde: 

Pursuant to Section 7(a)(2) of the Endangered Species Act (ESA) and the accompanying 

regulations at 50 CFR § 402.14(c), the U.S. Environmental Protection Agency (EPA) hereby 

requests the initiation of formal consultation with the National Marine Fisheries Service (NMFS) 

and the U.S. Fish and Wildlife Service (FWS) (collectively refen ed to as "the Services") on the 

reissuance of EPA's Vessel General Permit (VGP) and issuance of the new Small Vessel General 

Permit (sVGP), scheduled for November 2012. EPA's biological evaluation (BE) for both 

permits is attached (Attachment A). The draft VGP and sVGP (Attachments B and C, 

respectively), if finalized, may be effective for a period of up to five years. Also attached are the 

accompanying fact sheets for the VGP and sVGP (Attachments D and E), which include detailed 

information on the rationale for each proposed permit condition in the draft permits. 

EPA initiated informal consultation with the Services on the 2013 VGP in December 

2011. Informal consultation consisted of briefing you and your staff on the contents of the draft 

permits, discussing EPA's proposed outline and methodological approach of a BE for both 

permits, including'using a detailed analysis of expected constituents in and impacts from 

incidental vessel discharges, representative listed species, and reference action areas to inform 

the broader effects analysis. EPA also requested species lists, additional pertinent information 

from the Services, and discussed the penmit issuance timeline. We thank you for the insight, 

cooperation, and time that you and your staff have provided EPA in developing the BE outline 

and gathering the best data available. A brief discussion of how EPA responded to the Services' 

specific comments and requests made during informal consultation on the approach and outline 

for the biological evaluation is attached (Attachment F). 

I am now sending you a formal consultation package with the results of the Agencies' 

combined efforts, including EPA's BE for the 2013 VGP and sVGP. The BE was prepared using 

the best scientific and commercial information available for pollutant discharges from vessels 

Internet Address (URL) • http://www.epa.gov 

Recycled/Recyclable • Printed with Vegetable Oil Based Inks on 100%, Postconsumer, Process Chlorine Free Recycled Paper 
proposed to be regulated under the two separate permit actions: the 2013 re-issuance of the VGP 

and a new sVGP. This BE is intended to support the initiation of formal consultation, where 

appropriate. By this letter, EPA is requesting informal concurrence for not likely to adversely 

affect (NLAA) findings for 80 species. Although EPA believes that incidental vessel discharges 

are not likely to adversely impact all listed species, in light of limited data and uncertainty 

regarding Aquatic Nuisance Species (ANS) introductions, EPA is requesting initiation of fonnal 

consultation for the remaining 532 aquatic and aquatic dependent species. EPA determined 

either NLAA or "no effect" for the traditional pollutants (i.e., all pollutants originating from 

vessels except ANS) for all of these same 532 species. 

EPA's BE for the 2013 VGP and sVGP, has been substantially updated from a May 2008 

BE written for EPA's 2008 VGP. These updates reflect the Agency's actions of the 2013 reissuance of the VGP, as well as the new permit action of the proposed sVGP. In addition, this 

BE uses new infonmation found since completion of the 2008 BE, including new peer reviewed 

literature, government reports, and other information, and includes revisions that respond to 

concerns expressed in written comments provided by FWS in their July 22, 20081etter addressed 

to James Hanlon, Director of the USEPA Office of Wastewater Management, regarding the May 

2008 Draft BE and related correspondence. Additionally, this BE provides a quantitative 

screening modeling approach for evaluating the impacts of many traditional pollutants contained 

in the incidental discharges needing detailed analysis. 

The sections below provide the necessary information for initiating consultaoon pursuant 

to 50 CFR 402.14(c) for both proposed general permits. 

Description of Agency Actions 

The agency actions upon which EPA requests concurrence and formal consultation is the 

issuance of two National Pollutant Discharge Elimination System (NPDES) permits for 

discharges incidental to the normal operation of vessels, the VGP and sVGP. 

In December 2008 1 , EPA issued the VGP with an expiration date of December 2013. The 

reissuance of the VGP in 2012 includes improvements to the control measures implemented in 

the earlier 2008 VGP by making recommended changes and additions based on information 

gathered during the previous permit action. The updated VGP would continue to regulate the 26 

specific discharge categories that were contained in the 2008 permit and, for the first time, 

manage the discharge of fish hold effluent. A key new provision of the permit is a proposed 

numeric standard to control the release of non-indigenous invasive species in ballast water 

discharges. The new ballast water discharge standard addressing invasive species is based upon 

results from independent EPA Science Advisory Board and National Research Council National 

Academy of Sciences studies. These limits are generally consistent with those contained in the 

International Maritime Organization's 2004 Ballast Water Convention and the US C-oast Guard 

ballast water discharge standard rule finalized in March 2012. The new standard is expected to 

significantly reduce the risk of introduction and establishment of non-indigenous invasive 

species in U.S. waters. 

' Due to a subsequent extension of the vacatur date by the district court, NPDES permits were not required for 

incidental discharges from VGP vessels until February 6, 2009. 

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The draft VGP also contains updated conditions for mechanical systems that may leak 

lubricants into the water and exhaust gas scrubber washwater, which would reduce the ainount of 

oil and other pollutants that enter U.S. waters from unmanaged or unmitigated discharges. 

The sVGP would be the first permit under the Clean Water Act to address discharges 

incidental to the normal operation of commercial vessels less than 79 feet in length. Recognizing 

that small commercial vessels are substantially different in how they operate than their larger 

counterparts, the draft Small Vessel General Perinit is shorter and simpler. The draft permit 

specifies best management practices for several broad discharge management categories 

including fuel management, engine and oil control, solid and liquid tnaintenance, graywater 

management, fish hold effluent management and ballast water management, which includes 

specific measures to reduce the risk of spreading invasive species. EPA studied relevant 

discharges from vessels less than 79 feet and issued a Report to Congress, entitled "Study of 

Discharges Incidental to Normal Operation of Commercial Fishing Vessels and Other NonRecreational Vessels Less Than 79 Feet" in August 2010 (EPA, 2010). That report is available at 

http ://Cfpub. epa. ~;ov/npdes/vessel s/reportcongress. cfm. 

Section 2 of the BE includes more details about both the VGP and sVGP related to the 

scope of the proposed actions. Additional information about the scope and content of the VGP 

and sVGP can be found in the proposed VGP and proposed sVGP. 

H. Description of Action Area 

Based on the scope and nature of the proposed agency actions, the action area for the 

general permits includes "waters of the United States" as defined in 40 CFR§ 122.2. That 

provision defines "waters of United States" as certain inland waters and the territorial sea, which 

extends three miles from shore. 2Note that the CWA does not require NPDES permits for vessels 

or other floating craft operating beyond the territorial seas, i.e. in the contiguous zone or ocean. 

See CWA § 502(12) and 40 CFR §122.2 (definition of "discharge of a pollutant"). The action 

area for the proposed federal actions, therefore, does not extend to such waters. 

III. Description of Listed Species or Designated Critical Habitat That May Be Affected 

From an initial list of federally-listed species, EPA identified the subset of 612 aquatic and 

aquatic-dependent species that have more than limited exposure to "waters of the United States". 

EPA excluded listed species deemed to have only limited exposure to water (i.e., terrestrial 

species which do not have an important life-stage in aquatic systems and/or do not rely on 

aquatic systems for a substantial portion of their diet) and determined there would be no effect on 

these species. See Appendix E of the BE for additional discussion. 

EPA evaluated the full list of 612 aquatic and aquatic-dependent species for potential 

risks from vessel discharge-related ANS in the BE based on a conservative assumption that ANS 

could theoretically be transported or migrate through multiple pathways and mechanisms from 

2More specifically, CWA section 502(8) defines "territorial seas" as "the belt of the seas measured fl -om the line of 

the 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." 

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the original site of vessel's discharge. For pollutants and constituents of concerns in vessel 

discharges other than ANS, EPA narrowed the scope of listed species considered in the BE to 

only those species exposed to navigable waters traveled by vessels covered under the VGP and 

sVGP, because pollutant fate and transport is limited to dispersion and possibly downstream 

movement and dispersion (species selection methodology described in Appendix E of the BE, 

Attachment A). In this context, EPA included downstream waters and nearby tidally-influenced 

waters within the term navigable waters traveled by vessels covered under the VGP and sVGP. 

EPA identified 454 of the 612 aquatic and aquatic-dependent listed species for evaluation in the 

BE for potential impacts from pollutants other than ANS in vessel discharges covered under the 

VGP and sVGP. See Section 3.4 of the BE, Attachment A for more detailed discussion. 

IV.Descrintion of How AEency Actions May Affect Listed Snecies or Critical Habitat 

and Analysis of Cumulative Effects 

A detailed analysis of the direct and indirect effects of ANS and other pollutants in vessel 

discharges covered under the VGP and sVGP on the 82 aquatic and aquatic-dependent listed 

species present in the seven RAAs can be found in Section 5 of the BE. EPA used the risk 

conclusions for the 82 RAA listed species to inform the final effects determinations for a11612 

aquatic and aquatic-dependent species to which this BE applies (see Section 7 of the BE, 

Attachment A). Based on this analysis, EPA concluded that new introductions of A,NS from 

vessel discharges may affect 532 aquatic and aquatic-dependent species. However, EPA believes 

that the substantial mitigation of ANS from the actions of permit issuance will significantly 

reduce the overall potential risk to listed species, such that many of these species rnay not be 

exposed or susceptible to ANS. EPA further believes that given the most recent research on 

ANS, not likely to adversely affect (NLAA) determinations could reasonably be made for these 

532 species as none are likely to face jeopardy due to these permit actions. Nonetheless, based 

on uncertainties in the science and "a profound lack of data", EPA has concluded "may affect". 

In addition, EPA determined that vessel-related ANS are not likely to adversely affect 80 

aquatic-dependent species. 

For pollutants other than ANS, EPA concluded that 158 aquatic and aquatic-dependent 

species will experience no effect as these species are not present in "waters of the United States" 

navigable by vessels covered under the VGP and sVGP. EPA concluded that traditional 

pollutants identified for further analysis in the BE are not likely to adversely affect the remaining 

454 aquatic and aquatic-dependent listed species. See discussion in Section 7 of the BE, 

Attachment A for more detailed discussion. 

The 2008 VGP and the legislative moratorium on the exclusion of commercial fishing 

vessels and other non-recreational vessels less than 79 feet both expire on December 18, 2013. 

As noted earlier, it is EPA's intent to finalize and reissue the VGP and issue the sVGP by 

November 30, 2012. Given this limited timing, EPA requests that the Services confinm, in 

writing, that they have received a complete initiation package, and provide an estimate of the 

date on which the Services will provide EPA with the final biological opinion(s). Should the 

Services determine that additional data or information is needed to formulate the biological 

opinion(s), EPA asks that this request be made as soon as possible during the consultation 

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period. Finally, EPA asks that the Services share drafts of their biological opinions with EPA 

prior to finalization. 

V. Next Steps 

Thank you and your staff for assisting us in this effort. We have prepared this BE to assist 

in your development of your biological opinion, and have included and referenced the best 

scientiflc and commercially data and information available. Additionally, it is also my 

understanding that we have shared, among other things, our complete dataset collected for our 

2010 Report to Congress with your staff in May 2012 to aid in their advance preparation for this 

formal consultation. I believe that the contents of this package meet the requirements of 50 CFR 

402.14(c) for initiation of formal consultation, and therefore, it is my understanding that formal 

consultation has commenced upon submission of this consultation package, consistent with 50 

CFR 402.02. If for some reason, should the Services think additional data or information would 

be useful for formulating a biological opinion, I would request that the information be developed 

in the course of formal consultation in light of the November deadline for issuance of the 

permits. 

My staff and I have appreciated the positive, collaborative effort between our agencies 

that went into this BE and we look forward to continuing that relationship through the formal 

consultation process. As we have previously discussed, due to the EPA's obligation to issue the 

VGP by November 30, 2012, it is vitally important that the consultation be completed within the 

ESA's 135 day time period. I suggest that we briefly discuss this consultation package at our 

regularly scheduled meeting on July 9, 2012 to talk about the timeline for development of the 

draft and final biological opinion, including a target date for discussing the Services' preliminary 

risk or mitigation conclusions. My lead staff assigned to this consultation will follow up shortly 

after the July 9` hmeeting for more detailed discussions with your staff. Again, I request that you 

share copies of your draft biological opinion when they are available. 

Once again, thank you for your assistance and we look forward to working with you on 

this consultation. Please do not hesitate to call me at (202) 564-1185 or Ryan Albert of my staff 

at (202) 564-0763 if you or anyone on your staff has questions regarding this matter. 

Sincerely, 

Z

- -, - - /45; e A 

Deborah Nagle, Director 

Water Permits Division 

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Attachments: 

A. Biological Evaluation of the 2013 VGP and sVGP 

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

(VGP) 

C. Small Vessel General Permit for Discharges Incidental to the Normal Operation of Vessel 

Less than 79 Feet (sVGP) 

D. VGP Fact Sheet 

E. sVGP Fact Sheet 

F. EPA Responses to Services' Comments and Requests During Informal Consultation on 

the Approach and Outline for the Biological Evaluation of the 2013 VGP and sVGP 

m