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Aquaculture Laws and Regulations

Answering the questions you’ve been asking
about Maine Atlantic salmon aquaculture

The research and analysis employed in this effort are supported, in part by a Saltonstall-
Kennedy Grant (Grant # NA03NMF4270123); the University of Southern Maine; and the
University of Maine School of Law . Responses to this document can be forward to:
John A. Duff

This Question and Answer guide is intended as a tool for:
Aquaculture Industry Representatives- as a means to answer many of the questions that have
arisen regarding the legal and regulatory environment governing Atlantic salmon net pen
aquaculture in Maine.
Law and Policymakers - whose responsibilities include law and policymaking related to the
natural environment and the economic development.
Researchers – whose interests and studies might benefit from an overview of the questions that
have arisen in recent years related to the implications of implementation of federal and state laws
designed to fulfill the objectives of the Clean water Act and the Endangered Species Act.
Students – whose interest in the unique environmental, economic, and legal issues of net pen
aquaculture will be served by a review of contemporary; and,
Members of the General Public – who are interested in gaining a better awareness of working
environment of Atlantic salmon aquaculture in Maine.

For more information related to the legal and regulatory environment that governs salmon
aquaculture in Maine, readers may wish to visit the following:

Maine Aquaculture Task Force website:

Northeast Regional Aquaculture Center

Bibliography of Aquaculture Publications Funded by The National Sea Grant College

as well as those websites listed at

Clean Water Act enforcement related Questions
1. Is the EPA administrative determination that netpens are concentrated aquatic animal
production facilities" (CAAPF) valid?
Yes. In U.S. Public Interest Research Group v. Atlantic Salmon of Maine, LLC., D.Me.2002,
215 F.Supp.2d 239, Atlantic Salmon of Maine (ASM) challenged the EPA’s designation of their
operations as a CAAPF by asserting that the literal language of the EPA regulations, 40 CFR
122.24, focused on land based operations and additionally distinguished themselves from more
traditional notions of what a discrete point sources is. The court sustained the EPA designation of
ASM as a CAAPF based on a broader interpretation of language in 40 CFR 122.24. The court
reasoned it would not make sense to declare operations on land that dump pollutants into the
bays as CAAPFs, while not also categorizing operations which dump directly into the bays by
virtue of residing in those bays. In support of EPA’s determination, the court listed all of the
foreign materials that are put into the water as a result of operations. The court also held that
CAAPF operations fall within a broader construct of the term point source.
2. Is a Clean Water Act NPDES permit required?
Yes, see above. The opinion lists all of the materials which are discharged by the aquaculture
facilities and where they fall under the US Code definitions as pollutants.
3. Is "fish feces" a pollutant?
Yes. The court has held that fecal material from animals held in concentrated animal feed
operations is deemed agricultural waste. Higbee v. Starr, 598 F.Supp. 323, 330-331
(D.Ark.1984). The USPIRG court, employed this determination in the Maine cases.
4. Should a "general" NPDES/MPDES permit be established?
The State of Maine has implemented a general Maine Pollution Discharge Elimination System
(MPDES) permit for Atlantic Salmon aquaculture. This general permit was issued on J une 19th,
2003 and can be found at:
A general permit is a permit applicable to a class or category of dischargers (in this case Atlantic
Salmon aquaculture operators) who agree to conduct their activities in accordance with the
conditions spelled out in the general permit. The MPDES general permit outlines the general as
well as special conditions that apply to aquaculture facilities operating thereunder: The general
conditions outline the underlying authority of the permit and contain definitions and terms
related to notice and acceptance as well as the duration of applicability of the permit. The
special conditions spelled out in the general permit govern:
• General Limitations
• Feeding Rates and Monitoring
• Mixing Zones
• Narrative Limitations
• Monitoring Requirements
• Reference Sites
• Impact Thresholds
• Toxic Impacts
• Protection of Atlantic Salmon
• Best Management Practices for Operation of the Facility
• Husbandry Practices
• Best Management Practices for Disease Control
• Best Management Practices for Spill Control
• Quality Assurance
• Monitoring and Reporting

5. Isn’t there a new federal rule governing discharges from aquaculture operations? And
what impact would a new national rule have on companies operating under the exisiting
MPDES general permit?
On J une 30, 2004, EPA promulgated a final rule to establish wastewater controls for
concentrated aquatic animal production facilities (i.e., fish farms). The regulation applies to
facilities that generate wastewater from their operations and discharge that wastewater directly to
waters of the United States. The rule constitutes a set of requirements that are to be applied in
aquaculture NPDES permits. The final rule went into effect on September 22, 2004. The rule is
viewable at: and
applies to direct discharges of wastewater from the following types of existing and new facilities:
• Facilities that produce at least 100,000 pounds a year in flow-through and recirculating
systems that discharge wastewater at least 30 days a year (used primarily to raise trout,
salmon, hybrid striped bass and tilapia).
• Facilities that produce at least 100,000 pounds a year in net pens or submerged cage
systems (used primarily to raise salmon).
Since Maine DEP administers the general MPDES aquaculture permit pursuant to authority
granted by EPA, it is unlikely that the new national rule will displace the applicability of the
MPDES general permit.
6. Is an aquaculture operator insulated from Clean Water Act based injunctions upon
acquiring a state MPDES permit?
Not necessarily. While operation in compliance with a permit ordinarily shields a permittee from
enforcement actions, that insulation may not apply to consent decrees and court orders stemming
from Clean Water Act violations that occurred prior to operation under the permit. In 2003, two
aquaculture operators who had obtained a authority to operate under the MPDES permit were
enjoined from certain methods of operations even where those conditions would not violate the
permit. See US PIRG v. Atlantic Salmon of Maine 339 F.3d 23 (1
Cir. 2003). The court ruled
that the more stringent provisions of a previously formulated consent decree would remain in
effect to offset the harm resulting from the operators’ pre-MPDES operations. The court did
indicate that the more stringent provisions must necessarily continue forever however,
suggesting that the aquaculture operators could seek to eliminate certain provisions of a consent
decree upon a showing that previous harms had been remedied.
5. Can an aquaculture operator be held liable for paying an adverse party’s legal fees if a
Clean Water Act case is adjudicated in favor of that party?
Yes. In US PIRG v. Stolt Sea Farm, the court determined that the Clean Water Act’s provision
for the award of attorney’s fees to a prevailing plaintiff in a Clean Water Act case would support
an award payable from an aquaculture operator to an environmental organization. The court
awarded fees even though the underlying case was prompted in part by the failure of government
agencies to construct a regulatory and permitting system that might otherwise have allowed the
aquaculture operator to be in conformity with the law.

US PIRG v. Stolt Sea Farm, 301 F.Supp.2d 46 (D. Maine 2004).
Endangered Species Act related questions
1. How are Atlantic salmon aquaculture Operations linked to wild Atlantic salmon
recovery efforts?
In J une 2004, the National Marine Fisheries Service (NMFS) and the US Fish and Wildlife
Service published a Draft Recovery Plan for the Gulf of Maine Distinct Population Segment of
Atlantic Salmon (Salmo salar) in accordance with the Endangered Species Act.
The Draft
Recovery Plan (DRP) specifically refers to concerns related to aquaculture operations in the
vicinity of the distinct population segment of salmon sought to be protected.
In pertinent part, the DRP states:
Regarding aquaculture, comprehensive solutions to minimize the threat of interaction between
wild and aquaculture salmon have not yet been fully implemented. …
The lack of regulatory measures to address and prevent escapes from aquaculture hatcheries has
also been a concern. Two commercial hatcheries are located on DPS rivers (Heritage Salmon
hatcheries in East Machias, Maine at Gardner Lake and in Deblois, Maine), and cases of chronic
and large escapements from freshwater hatcheries in Maine have been documented.

And the DRP goes on to state:
The potential for interactions between wild Atlantic salmon and aquaculture escapees represents
a significant threat to the continued existence of endangered salmon in Maine (65 FR 69459;
NMFS and FWS 1999). Comprehensive protective solutions to minimize the threat of
interactions between wild and aquaculture salmon have not been implemented. …
Escaped aquaculture salmon pose a significant threat to the Gulf of Maine DPS because even at
low numbers they can represent a substantial portion of fish in some rivers. Aquaculture
escapees have been detected annually in Maine rivers since 1990.

2. How and to what degree should Atlantic salmon endangered species concerns be
addressed in lease applications?
To the extent that non-DPS salmon and the means to cultivate them threaten the biological
integrity of DPS habitat through the pollution of water, those concerns should be addressed in the
lease application and or the MPDES permit. The DRP recommends that the lease application
process include considerations regarding potential adverse impacts to the DPS of Atlantic

National Marine Fisheries Service and U.S. Fish and Wildlife Service. 2004. Draft
Recovery Plan for the Gulf of Maine Distinct Population Segment of Atlantic Salmon
(Salmo salar). [hereinafter Draft Recovery Plan]National Marine Fisheries Service, Silver
Spring, MD. Vieawable at:
Id. at 1-55
Id. at 1-57.
Id. at 4-6. “Evaluate new aquaculture lease and permit applications to ensure that net pens and equipment are
adequate for site location and potential storm impact”. Id.

3. What sanctions might apply if cultured species are accidentally released?
This might be a function of the degree of threat which the released fish posed and the extent of
the escapement. The greater the threat the greater the sanction. It may be that zero escapement is
the goal in which case the sanction should be appropriate to achieve this goal.
4. When is a Biological Assessment required?
The Endangered Species Act, 16 U.S.C. § 1536, says in part,
”Each Federal agency shall, in consultation with and with the assistance of the Secretary,
insure that any action authorized, funded, or carried out by such agency (hereinafter in this
section referred to as an ''agency action'') is not likely to jeopardize the continued existence
of any endangered species or threatened species or result in the destruction or adverse
modification of habitat of such species which is determined by the Secretary, after
consultation as appropriate with affected States, to be critical, unless such agency has been
granted an exemption for such action by the Committee pursuant to subsection (h) of this
section. In fulfilling the requirements of this paragraph each agency shall use the best
scientific and commercial data available.”

5. What is considered to be an adverse modification of critical habitat?
To the extent that critical habitat is affected by one of the activities listed in the “deemed” takes
list below, modification will be considered to have taken place. These would include
introduction of pesticides into the rivers at a level which would be toxic to the fish, reduction of
water levels in the rivers which would prevent migration and spawning activities, etc.
6. When is the continued existence of a listed species deemed to be "jeopardized" by
an aquaculture facility?
According to the implementation regulations of the Endangered Species Act,
“ ‘jeopardy’ has been deemed to occur whenever an activity ‘reasonably would be
expected to reduce the reproduction, numbers, or distribution of a listed species to such
an extent as to appreciably reduce the likelihood of the survival and recovery of that
species in the wild.’ 50 C.F.R. § 402.02.

16 U.S.C. §1356(a)(2) (West 2004).

In determining whether an endangered species is placed in jeopardy, the Endangered Species Act
requires that ‘each agency shall use the best scientific and commercial data available.’ 16 U.S.C.
§ 1536(a)(2).”

At least one federal court has interpreted the definition to mean that noted that “J eopardy
relates to the overall continued existence of a species, and examines the effects of an action on
the species.”

7. What are "reasonable and prudent" alternatives to avoid harm (including
technological solutions)?
"Reasonable and prudent alternatives" refer to alternative actions identified during formal
consultation that can be implemented in a manner consistent with the intended purpose of the
action, that can be implemented consistent with the scope of the Federal agency's legal authority
and jurisdiction, that is economically and technologically feasible, and that the Director believes
would avoid the likelihood of jeopardizing the continued existence of listed species or resulting
in the destruction or adverse modification of critical habitat.
The DRP suggests a number of steps to reduce risks of harm to the DPS that related to
commercial aquaculture operations, including:
• Improving containment at existing and future marine sites;
• Minimizing the effects of escaped farmed salmon;
• Minimize risks of disease and parasite transmission from farmed fish in marine pens to
wild fish; and,
• Reducing risk of juvenile escapement from freshwater aquaculture facilities into DPS

8. What activities will be deemed "takes" of endangered Atlantic salmon.
Activities that the Services believe could result in violation of section 9 prohibitions against
"take" of the Gulf of Maine DPS of anadromous Atlantic salmon include, but are not limited to,
the following:
(1) Targeted recreational and commercial fishing, bycatch associated with commercial and recreational
fisheries, and illegal harvest;
(2) The escapement of reproductively viable non-North American strain or non- North American hybrid
Atlantic salmon in freshwater hatcheries within the DPS range;

7 Conservation Law Foundation v. Watt, 560 F.Supp. 561 (D.C.Mass.,1983).
8 Greenpeace v. National Marine Fisheries Service, 55 F.Supp.2d 1248 (W.D.Wash.,1999).
Draft Recovery Plan at 4-51 – 4-57
(3) The escapement from marine cages or freshwater hatcheries of domesticated salmon such that they are
found entering or existing in rivers within the DPS range;
(4) Failure to adopt and implement fish health practices that adequately protect against the introduction and
spread of disease;
(5) Siting and/or operating aquaculture facilities in a manner that negatively impacts water quality and/or
benthic habitat;
(6) Discharging (point and non-point sources) or dumping toxic chemicals, silt, fertilizers, pesticides, heavy
metals, oil, organic wastes or other pollutants into waters supporting the DPS;
(7) Blocking migration routes;
(8) Destruction and/or alteration of the species' habitat (e.g., instream dredging, rock removal,
channelization, riparian and in-river damage due to livestock, discharge of fill material, operation of heavy
equipment within the stream channel, manipulation of river flow);
(9) Violations of discharge or water withdrawal permits that are protective of the DPS and its habitat;
(10) Pesticide or herbicide applications in compliance with or in violation of label restrictions; and
(11) Unauthorized collecting or handling of the species (permits to conduct these activities are available for
purposes of scientific research or to enhance the propagation or survival of the DPS).
Other activities not identified here will be reviewed on a case-by-case basis to determine if violation of
section 9 of the ESA may be likely to result from such activities. We do not consider these lists to be
exhaustive and provide them as information to the public.

The Services believe that, based on the best available information, the following actions are
unlikely to result in a violation of section 9:
• Possession of Atlantic salmon acquired lawfully by permit issued by the Services
pursuant to section 10 of the ESA, or by the terms of an incidental take statement in a
biological opinion pursuant to section 7 of the ESA;
• Federally approved projects that involve activities such as silviculture, agriculture, road
construction, dam construction and operation, discharge of fill material, siting of marine
cages for aquaculture, hatchery programs, and stream channelization or diversion for
which consultation under section 7 of the ESA has been completed, and when such
activity is conducted in accordance with any terms and conditions given by the Services
in an incidental take statement in a biological opinion pursuant to section 7 of the ESA;
• Routine culture and assessment techniques, including the FWS' river-specific
rehabilitation program at CBNFH; and
• Emergency responses to disease outbreaks.

See generally 65 Fed. Reg. 69459.

Magnuson-Stevens Act related questions

1. Do aquaculture operations require any review under essential fish habitat
(EFH)EFH provisions?
This is a question that does not have a clear answer resting on a solid legal footing.
Magnuson-Stevens Act is administered by the NMFS. NMFS has issued “guideline regulations”
that identify “fishing operations” which are not controlled by the Magnuson-Stevens Act. In
particular these rules indicate that aquaculture operations that are under state administration fall
within the category not controlled by the Magnuson-Stevens Act.

NMFS does issue conservation recommendations regarding EFH protection in the context
of the uncontrolled activities. In conjunction the Army Corps of Engineers, in there “Programatic
General Permit,” state that “[a]s part of the PGP screening process, the Corps will coordinate
with the National Marine Fisheries Service (NMFS) in accordance with the 1996
amendments to the Magnuson-Stevens Fishery and Conservation Management Act to
protect and conserve the habitat of marine, estuarine and anadromous finfish, mollusks, and
crustaceans. This habitat is termed ‘essential fish habitat (EFH)’, and is broadly defined to
include ‘those waters and substrate necessary to fish for spawning, breeding, feeding, or
growth to maturity.’ Applicants may be required to describe and identify potential impacts
to EFH based upon the location of the project, the activity proposed, and the species
present. Conservation recommendations made by NMFS will normally be included as a
permit requirement by the Corps.”

2. Is production from aquaculture facilities subject to the same kinds of management
measures as wild harvest fisheries (e. g., minimum size restrictions)?
I would suspect not as these are cultured fish as opposed to naturally reproducing fish. However
I will look further for legal precedence, or statutory exceptions.

STATE OF MAINE, available at <>.

Ocean Dumping Act related questions

33 USC 1401 AKA Marine Protection, Research, and Sanctuaries Act of 1972 (MPRSA)

1. Do EPA exemptions for "developing, maintaining, or harvesting fisheries
resources" Apply to aquaculture?
Water pollution is controlled by both the CWA and the Ocean Dumping Act. The demarcation
line for jurisdictional purposes is the 3 mile territorial water boundary. If aquaculture operations
are within the 3 mile boundary they are governed by the CWA and require NPDES permits.

2. What is the definition of "fish" wastes?
From what I can gather, it appears as though “fish waste” refers to the byproduct that
commercial fish processing facilities generate.

14Pacific Legal Foundation v. Quarles, 440 F.Supp. 316 (D.C.Cal. 1977).
60 Fed. Reg 12199,12200; 61 Fed. Reg 51196 (table “Examples of potentially regulated entities”)
Marine Mammal Protection Act related questions
1. Is an aquaculture facility entitled to an exemption as a type of commercial fishery?
While one could place aquaculture operations into the definition of a “fishery” the MMPA
statutes are more directed at fisheries of wild species rather than cultured species.
16 U.S.C. §1362(16) defines fishery as “one or more stocks of fish which can be treated as a unit
for purposes of conservation and management and which are identified on the basis of
geographical, scientific, technical, recreational and economic characteristics, and any fishing for
such stocks.” 16 U.S.C § 1371(a)(2) refers to an exception to “commercial fishing operations”.
“Marine mammals may be taken incidentally in the course of commercial
fishing operations and permits may be issued therefor under section 1374
of this title subject to regulations prescribed by the Secretary in
accordance with section 1373 of this title, or in lieu of such permits,
authorizations may be granted therefor under section 1387 of this title,
subject to regulations prescribed under that section by the Secretary
without regard to section 1373 of this title. Such authorizations may be
granted under subchapter IV of this chapter with respect to purse seine
fishing for yellowfin tuna in the eastern tropical Pacific Ocean, subject to
regulations prescribed under that subchapter by the Secretary without
regard to section 1373 of this title. In any event it shall be the immediate
goal that the incidental kill or incidental serious injury of marine mammals
permitted in the course of commercial fishing operations be reduced to
insignificant levels approaching a zero mortality and serious injury rate.
The Secretary of the Treasury shall ban the importation of commercial fish
or products from fish which have been caught with commercial fishing
technology which results in the incidental kill or incidental serious injury
of ocean mammals in excess of United States standards. For purposes of
applying the preceding sentence, the Secretary--

2. So what are commercial fishing operations?

The Marine Mammal Protection Act does not provide a clear definition. It alludes to what it is in
13 U.S.C. 1387 which states

“the provisions of this section shall govern the incidental taking of marine
mammals in the course of commercial fishing operations by persons using
vessels of the United States or vessels which have valid fishing permits
issued by the Secretary in accordance with section 1824(b) of this title.”

This language indicates that a fishing vessels must be involved for there to be a commercial
fishing operation.
3. Are permits for incidental take or incidental harassment authorizations
I found no case law which directly addresses whether aquaculture operations are required to
get permits under the Marine Mammal protection act.
4. How are nuisance marine mammals to be controlled?
Predatory barrier nets around the pens are currently used.

National Environmental Policy Act related questions

1. Do federally permitted aquaculture operations "affect the quality of the human
environment" such that Environmental Assessments and/or Environmental Impact
Statements must be constructed?
Maine aquaculture operations require two permits. One is a “NPDES” permit and the
other is an Army Corp of Engineers permit. Whether either permit requires that an
Environmental Impact Statement or and Environmental Assessment be performed depends on
whether the issuing of the permit represents a “major federal action” and federalizes the
permitted activity. Without a “major federal action one never gets to the question of whether a
federal action “affects the quality of the human environment.”
Within the context of the NPDES permit one must answer the question; who issues
permits for aquaculture operations, the federal government or the State of Maine?
In J anuary of 2001, the State of Maine assumed responsibility for the local administration of
the NPDES permitting program.

In 2003, the U.S. District Court, District of Columbia, in, Citizens Alert Regarding the
Environment v. EPA,
stated that once the state starts to issue permits it is no longer a federal
action, even with EPA oversight responsibilities.
One could extrapolate from this that the newly created Finfish aquaculture permit which
was developed by the state as part of its MEPDES administration responsibilities is also not a
“federal action” within the meaning of NEPA and as such would not be subject to EIS or EA
Aquaculture leases in Maine also require Army Corp of Engineer (ACE) permits as the
fish pens are place in navigable waters. Section 10 of the Rivers and Harbors Act of 1899
extends control to the ACE regarding structures in navigable waters.

AGENCY REGION 1, found at, <>; 64 Fed. Reg. 73552; 33
U.S.C. § 1342(c)
Regarding the Environment v. EPA, 259 F.Supp.2d 9, 18 (citing District of Columbia v. Schramm, 631 F.2d 854,
857 (D.C.Cir. 1980).
In two cases Pogliani v. US Army Corps of Engineers and Wetlands Action Network v.
US Army Corp of Engineers the court held that whether issuing of permits by the ACE
establishes a “major federal action “ requiring an EA or EIS depends on the permits relationship
to the over all project.

In the present case the ACE participation is minimal, siting the netpens out of the way of
navigational routes. This would probably not rise to a significant involvement and thus not a
“major federal action.”

Additional notes:
Factors to consider when construing “affect …human environment.” Fund for Animals v.
Williams, 246 F.Supp.2d 27, 41-42:
• Degree to which the effects on the quality of the Human environment are likely to be
highly controversial or highly uncertain
• Decree to which the action may establish a precedent for future actions.
• Degree to which the action may cause loss of significant scientific, cultural, or historic
• Degree to which action may adversely affect an endangered or threatened species.

Pogliani v. Unites States Army Corps of Engineers, 166 F.Supp.2d 673, 697 (2001); Wetlands Action Network v.
United States Army Corp of Engineers, 222 F.3d 1105, 1115 (2000).