Final Recovery Plan for the 

Gulf of Maine Distinct Population Segment 

of Atlantic Salmon (Salmo salar)

November, 2005

Prepared by

NOAA’s National Marine Fisheries Service

(NMFS)

Silver Spring, Maryland

and

Northeastern Region

U.S. Fish and Wildlife Service

Hadley, Massachusetts
Recovery Plan for the 

Gulf of Maine Distinct Population Segment 

of Atlantic Salmon (Salmo salar) 

November, 2005 

Prepared by 

NOAA's National Marine Fisheries Service 

(NMFS) 

Silver Spring, Maryland 

and 

Northeastern Region 

U.S. Fish and Wildlife Service 

Hadley, Massachusetts 

Approved: 

Assistant Administrator for Fisheries 

NOAA's National Marine Fisheries Service 

Date 

Regional Director, U.S. Fish and Wildlife Service Date 
DISCLAIMER 

Recovery plans delineate actions that are thought to be necessary to recover andlor 

protect endangered species. Recovery plans are prepared by NOAA's National Marine 

Fisheries Service (NMFS) and the U.S. Fish and Wildlife Service (FWS) and sometimes 

with the assistance of recovery teams, contractors, state agencies and others. This 

Recovery Plan for the Gulf of Maine (GOM) Distinct Population Segment (DPS) of 

Atlantic Salmon (Salmo salar) was prepared by the staff of the Northeast Regional 

Offices of NMFS with the assistance of the FWS and the Maine Atlantic Salmon 

Commission (ASC). While the State of Maine provided recommendations for this plan, 

it was developed using federal guidelines and policies pertaining to recovery plans for 

federally listed species. Recovery plans are not regulatory or decision documents. The 

recommendations in a recovery plan are not considered final decisions unless and until 

they are actually proposed for implementation. Objectives will only be attained and 

hnds expended contingent upon appropriations, priorities and other budgetary 

constraints. Nothing in this plan should be construed as a commitment or requirement 

that any federal agency obligate or pay hnds in contravention of the Anti-Deficiency 

Act, 3 1 U.S.C. 1341, or any other law or regulation. Recovery plans do not necessarily 

represent the views nor the official positions or approval of any individuals or agencies, 

other than those of NMFS and FWS. They will represent the official positions of NMFS 

and FWS only after they have been signed as approved by the NOAA Assistant 

Administrator for Fisheries and FWS Regional Director. Approved recovery plans are 

subject to modification as dictated by new findings, changes in species status and the 

completion of Recovery Actions. 

LITERATURE CITATION SHOULD READ AS FOLLOWS: 

National Marine Fisheries Service and U.S. Fish and Wildlife Service. 2005. Recovery 

Plan for the Gulf of Maine Distinct Population Segment of Atlantic Salmon (Salmo 

salar). National Marine Fisheries Service, Silver Spring, MD. 

ADDITIONAL COPIES MAY BE OBTAINED FROM: 

National Marine Fisheries Service 

One Blackburn Drive 

Gloucester, Massachusetts 0 1930 

978-28 1-9328 

Recovery plans can be downloaded via the Internet at: 

http ://www .nmfs.noaa.gov/pr/ 

http://endangered. fws.gov. 
iii

ACKNOWLEDGMENTS 

This recovery plan was prepared by the staff of the National Marine Fisheries Service, 

Northeast Regional Office, Protected Resource Division with the assistance of the United 

States Fish and Wildlife Service (FWS) and Maine Atlantic Salmon Commission (ASC). 

Mark Minton, NMFS’ Atlantic Salmon Recovery Plan Coordinator, served as the primary 

author. 

This recovery plan builds on and expands recovery actions identified in the State of 

Maine’s Atlantic Salmon Conservation Plan for Seven Maine Rivers (MASCP). The 

MASCP (1997) provides the basis for many important on-going Atlantic salmon 

conservation and recovery activities. The Services intend to maintain and expand 

ongoing collaborative recovery efforts implemented as part of the MASCP. The MASCP 

is further discussed in section VIII of the recovery plan. 

The authors of the Atlantic salmon recovery plan sought the individual review and input 

of a number technical experts from a variety of fields, agencies and organizations in the 

development of this draft recovery plan. This recovery plan has undergone extensive 

internal technical review by NMFS (NEFSC, NWFSC, NERO, F/PR), ASC1

 and FWS 

staff. This recovery plan has also been reviewed by the technical staff of many other 

state and federal agencies including the Maine Department of Environmental Protection 

(DEP), Maine Department of Inland Fish and Wildlife (IFW), the Maine Forest Service 

(MFS), the Maine Department of Marine Resources (DMR) and the U.S. Geological 

Survey (USGS). The comments received from these agencies and groups have been fully 

considered. In addition, the Services met with stakeholders throughout the recovery 

planning process. This included holding public meetings in Maine seeking input on 

recovery strategies that provide overarching principles intended to guide all recovery 

activities conducted under the plan. Furthermore, NMFS published a Federal Register 

notice in September 2001 (66 FR 47452), requesting public input on threats and 

information that should be considered in the development of the recovery plan. 

In June 2004, the Services published a draft recovery plan for public review and 

comment. During the 90-day public comment period the Services held two formal public 

hearings as well as numerous meetings and briefings with federal, state, local and private 

stakeholders to discuss the recovery plan. In addition to public review the recovery plan 

underwent peer-review. Based on public comments received on the draft plan the 

Services and the Maine ASC conducted a two-day Threats Assessment Workshop in 

December 2004. The public and peer review comments received during the public 

comment period have been fully considered in the preparation of this recovery plan. In 

addition, the Services have reviewed and considered the recommendations of the recent 

National Research Council’s (NRC) report (see NRC 2004) and this recovery plan has 

incorporated the recommendations of the NRC Report as appropriate. 

 

1 The ASC distributed the draft plan for review to all the state agencies and organizations that were 

involved in the development and implementation of the Atlantic Salmon Conservation Plan for 

Seven Maine Rivers.
iv

The authors of this plan would like to thank the many individuals that have contributed 

material used in its development and who have reviewed and commented on this plan. 

These have improved the accuracy and usefulness of the plan. 

Lastly the authors would like to extend recognition to all the many individuals who have 

worked over the years to conserve Atlantic Salmon. This recovery plan builds on the 

dedication of these individuals and their efforts to preserve this national treasure for the 

citizens of Maine and the nation. 
v

EXECUTIVE SUMMARY FOR THE GULF OF MAINE DPS OF ATLANTIC 

SALMON 

Current Species Status: The Gulf of Maine Distinct Population Segment (DPS) of 

Atlantic salmon was listed as endangered on December 17, 2000. The DPS includes all 

naturally reproducing remnant populations of Atlantic salmon from the Kennebec River 

downstream of the former Edwards Dam site, northward to the mouth of the St. Croix 

River. DPS salmon taken for hatchery rearing for broodstock purposes and any captive 

progeny from these salmon are also included as part of the DPS. These hatchery-held 

fish, however, do not count toward a delisting or reclassification goal as this goal refers 

to the status of naturally-spawned salmon in the wild. 

Historically, the Androscoggin River delineated the range of the DPS to the south. In the 

listing determination, the Services deferred a decision whether the Gulf of Maine DPS 

range included the mainstem of the Penobscot River and its tributaries above the former 

site of the Bangor dam (65 FR 69459). Presently a status review is underway to 

determine the relationship of large river systems (e.g., Penobscot, Kennebec) to the DPS 

as currently delineated. This review will also determine the status of current salmon 

populations within these large river systems, as well as any other additional salmon 

populations present outside the geographic range of the DPS. Decisions regarding the 

status of these populations may have significant implications for the recovery strategy 

and recovery criteria. The Services will consider the implications of these decisions for 

the overall recovery program and revise the recovery plan accordingly. 

At the time of listing, there were at least eight rivers in the geographic range of the DPS 

known to still support wild Atlantic salmon populations (Dennys, East Machias, Machias, 

Pleasant, Narraguagus, Ducktrap and Sheepscot rivers and Cove Brook). In addition to 

these eight rivers, there are at least fourteen small coastal rivers within the historic range 

of the DPS from which wild salmon populations have been extirpated. 

The Gulf of Maine DPS has declined to critically low levels. Adult returns, juvenile 

abundance estimates and survival have continued to decline since the listing. In 2004, 

total adult returns to the eight rivers still supporting wild Atlantic salmon populations 

within the DPS were estimated to range from 60 to 113 individuals. No adults were 

documented in three of the eight rivers. Declining smolt production has also been 

documented in recent years, despite fry stocking. For example, from 1996 through 1999, 

annual smolt production in the Narraguagus River was estimated to average about 3,000 

fish. Smolt production declined significantly in 2000 and for the past three years has 

averaged only about 1,500 fish per year. Overwinter survival in the Narraguagus River 

since 1997 has only averaged about 12%, approximately half of the survival rate of 

previous years and significantly less than the 30% previously accepted for the region. 

Habitat Requirements and Limiting Factors: The Atlantic salmon is an anadromous 

fish, typically spending 2-3 years in freshwater, migrating to the ocean where it also 

spends 2-3 years, and returning to its natal river to spawn. 
vi

Suitable spawning habitat consists of coarse substrate (gravel or rubble) in areas of 

moving water. Eggs incubate slowly due to cold winter water temperatures, hatch in 

March or April and become fry. Fry remain buried in the gravel for about six weeks. 

The fry emerge from the gravel about mid-May and start feeding on plankton and small 

invertebrates. Emergent fry quickly disperse from the redd, develop parr marks along 

their sides and enter the parr stage. Parr habitat (often called “nursery habitat”) is 

typically riffle areas characterized by adequate cover (gravel and rubble up to 20 cm), 

moderate water depth (10-60 cm) and moderate to fast water flow (30-90 cm/sec). 

Salmon parr spend two to three years in the freshwater environment then undergo a 

physiological transformation called smoltification that prepares them for life in a marine 

habitat. Atlantic salmon leave Maine rivers in the spring and reach Newfoundland and 

Labrador by mid-summer. They spend their first winter at sea in the area of the Labrador 

Sea south of Greenland. After the first winter at sea, a small percentage return to Maine 

while the majority spend a second year at sea, feeding off the southwest or (to a much 

lesser extent) southeast coast of Greenland. Some Maine salmon are also found in waters 

along the Labrador coast. After a second winter in the Labrador Sea, most Maine salmon 

return to rivers in Maine, with a small number returning the following year as three sea 

winter (3SW) fish. 

The habitat within the range of the DPS is generally characterized as being free-flowing, 

medium gradient, cool in-water temperature and suitable for spawning in gravel substrate 

areas. The watershed structure, available Atlantic salmon habitat, and abundance of 

Atlantic salmon stocks at various life stages are best known for the seven largest salmon 

rivers with remnant Atlantic salmon populations. There is less known about the habitat 

of smaller rivers within the historic range of the DPS, with the exception of Cove Brook. 

Reasons for Listing 

Among the numerous factors that led to the endangered designation of Atlantic salmon 

populations in the Gulf of Maine DPS were the following: 

• Critically low adult returns make the DPS especially vulnerable and susceptible to 

threats 

• Continued low marine survival rates for U.S. stocks of Atlantic salmon 

• Excessive or unregulated water withdrawal 

• Multiple factors that are likely affecting the quality of freshwater habitat in the 

DPS 

• Continuation of the commercial fishery in Greenland 

• The threat of disease to the DPS from Infectious Salmon Anemia (ISA) and 

Salmon Swimbladder Sarcoma (SSS) 

• Increased likelihood of predation because of low numbers of returning adults and 

increases in some predators 

• Existing aquaculture practices, including the use of European Atlantic salmon, 

pose ecological and genetic risks 
vii

These threats, which were key factors in the listing determination, continue to imperil the 

continued existence of Atlantic salmon. 

Threat Assessment: As part of the Recovery Planning process, the Services assembled a 

team of technical experts from Maine ASC, NMFS and USFWS to conduct a structured 

threats analysis. This evaluation of the geographic extent and life stage affected by 

threats, and the severity of these effects, resulted in the following threats being identified 

as high priority for action to reverse the decline of Atlantic salmon populations in the 

Gulf of Maine DPS: 

• Acidified water and associated aluminum toxicity which decrease juvenile 

survival 

• Aquaculture practices, which pose ecological and genetic risks 

• Avian predation 

• Changing land use patterns (e.g., development, agriculture, forestry) 

• Climate change 

• Depleted diadromous fish communities 

• Incidental capture of adults and parr by recreational fishermen 

• Introduced fish species that compete or prey on Atlantic salmon 

• Low marine survival 

• Poaching of adults in DPS rivers 

• Recovery hatchery program (potential for artificial selection/domestication) 

• Sedimentation 

• Water extraction 

Recovery Strategy: The initial focus of the recovery program will be on the eight 

populations in the DPS that were extant at the time of the listing. Without immediate 

action to conserve and protect these core populations and the remnant genetic variation 

they represent, long-term success and attainment of self-sustaining populations will be 

severely compromised. 

Certain categories of actions will be high priority for the first phase of recovery plan 

implementation. The cornerstone of the initial phase of recovery will be the immediate 

implementation of priority 1 recovery actions that will reduce the severest threats. In 

addition, actions that can be initiated quickly and have the potential to significantly 

improve survival, thereby helping to reverse the decline of DPS populations, also will 

receive high priority for expeditious implementation. Actions to address critical 

information needs are a third category of actions that are high priority for immediate 

implementation. Research is needed to increase understanding of certain threats and how 

best to address them. 

After the initial phase of recovery plan implementation is completed, efforts will focus on 

addressing remaining threats and information needs. Throughout all phases of recovery 

plan implementation, an adaptive management approach will be used. 
viii

Recovery Goal, Objectives and Criteria: The goal of the recovery program is removal 

of the Gulf of Maine DPS of Atlantic salmon from the Federal List of Endangered and 

Threatened Wildlife and Plants. Recovery will be achieved when conditions have been 

attained that allow self-sustaining populations to persist under minimal ongoing 

management and investment of resources. In order to achieve the goal of recovery, a 

stepwise approach will be adopted which addresses the critically low numbers of adult 

Atlantic salmon returns then builds toward full recovery. 

The Services have concluded that it is not practicable at this time to establish final 

demographic criteria for reclassification and delisting of the DPS. The Recovery Plan 

does, however, contain both preliminary demographic and threat reduction recovery 

criteria. The first objective of the plan is to halt the decline of the DPS and demonstrate a 

persistent increase in population abundance trends such that the overall probability of 

long-term survival is increased. To meet Objective 1 of the plan, the following criteria 

must be met: 

Criterion 1. Atlantic salmon are perpetuated in at least the eight rivers within the Gulf 

of Maine DPS that had extant populations at the time of listing; and 

Criterion 2. The replacement rate (5-year geometric mean) of adult salmon within DPS 

rivers is greater than 1.0. 

Once Objective 1 has been achieved, the second step or objective necessary to achieve 

the recovery goal is to establish self-sustaining populations, and the third is to ensure that 

threats have been diminished such that the self-sustaining populations will remain viable 

over the long-term. These last two objectives relate to conditions necessary for 

reclassification and delisting. 

Actions Needed: The major areas of action are designed to stop and reverse the 

downward population trends of the remnant eight wild Atlantic salmon populations and 

minimize the potential for human activities to result in the degradation or destruction of 

Atlantic salmon habitat essential to survival and recovery. For full recovery the 

following actions are needed: 

1. Protect and restore freshwater and estuarine habitat 

2. Minimize potential for take in freshwater, estuarine and marine fisheries 

3. Reduce predation and competition on all life stages of Atlantic salmon 

4. Reduce risks from commercial aquaculture operations 

5. Supplement wild populations with hatchery-reared DPS salmon 

6. Conserve the genetic integrity of the DPS 

7. Assess stock status of key life stages 

8. Promote salmon recovery through increased public and government awareness 

9. Assess effectiveness of recovery actions and revise as appropriate 

Total Estimated Cost of Recovery: The total cost of recovery is undeterminable at this 

time. It is impossible to estimate the cost of recovery for the DPS. The species continues 
ix

to decline and its status is precarious. Even when we achieve a complete reversal of 

downward trends and population growth, it is not possible to estimate the cost of 

recovery of the DPS. 

Despite ongoing efforts to arrest and reverse the decline of the DPS adult salmon returns 

to DPS rivers remain at historic lows (an estimated 60 to 113 adult returns in 2004). 

The initial focus of the recovery program will be on the 8 rivers within the DPS with 

extant populations at the time of the listing. The initial goal of recovery efforts is to 

immediately halt the decline of the DPS and demonstrate a persistent increase in 

population abundance such that the overall probability of long-term survival is increased. 

Research is ongoing to help identify the causes for the species continued decline and 

identify appropriate measures to mitigate threats and recover the DPS. Pending the 

results of the recommended research it is not yet possible to identify recovery actions and 

strategies to mitigate the threats. Specific research needs, including estimated times and 

costs, are identified in Part 4 of this plan and prioritized in the implementation schedule. 

In the face of this continued uncertainty of the overall causes of the species decline it is 

not possible to identify all recovery actions that may be necessary to recover the DPS and 

therefore be able to estimate costs for full recovery of the DPS. 

As noted, the Services have concluded that it is not practicable at this time to establish 

final demographic criteria for reclassification and delisting of the DPS. The Recovery 

Plan does, however, contain both preliminary demographic and threat reduction recovery 

criteria. The first objective of the plan is to halt the decline of the DPS and demonstrate a 

persistent increase in population abundance trends such that the overall probability of 

long-term survival is increased. In the absence of final measurable and objective criteria 

it is not possible at this time to provide a full estimate of the cost of achieving the 

conditions that will constitute a secure and recovered DPS. 

The Implementation Schedule, however, does contain cost estimates for individual tasks. 

The total estimated minimum cost of recovery actions identified for year 1 to year 3 is 

$36.6 million. 

Estimated Date of Recovery: It is impossible to estimate the date of recovery for the 

DPS. The species continues to decline and its status is precarious. Even when we 

achieve a complete reversal of downward trends and population growth, it is not possible 

to estimate the date of recovery of the DPS. 
x

LIST OF ABBREVIATIONS 

 

ABF Aquatic base flow 

ACOE Army Corps of Engineers (U.S.) 

ASA Atlantic Salmon Authority (Maine) 

ASC Atlantic Salmon Commission (Maine) 

ASCP Atlantic Salmon Conservation Plan (Maine) 

ASRSC Atlantic Sea Run Salmon Commission (Maine) 

ATV All terrain vehicle 

BKD Bacterial kidney disease 

BMP Best management practice 

BPC Board of Pesticides Control (Maine) 

BRT Biological Review Team 

CBNFH Craig Brook National Fish Hatchery 

CCP Critical control points 

CFR Code of Federal Regulations (U.S.) 

CMLT Coastal Mountains Land Trust 

CMS Containment management system 

COSEWIC Committee on the Status of Endangered Wildlife 

CPUE Catch per unit effort 

CSE Conservation spawning escapement 

CWD Coldwater disease 

DEP Department of Environmental Protection (Maine) 

DFO Department of Fisheries and Oceans (Canadian) 

DMR Department of Marine Resources (Maine) 

DO Dissolved oxygen 

DOC Dissolved organic carbon 

DPS Distinct Population Segment, Gulf of Maine 

DRESS Dennys River Eastern Surplus Superfund 
xi

EEZ Exclusive Economic Zone 

EIS Environmental impact statement 

ESA Endangered Species Act 

EPA Environmental Protection Agency 

ERM Enteric redmouth disease 

FAMP Finfish Aquaculture Monitoring Program 

FMP Fishery Management Plan 

FON Forest operations notification 

FWS U.S. Fish and Wildlife Service 

GLNFH Green Lake National Fish Hatchery 

GOM Gulf of Maine 

HACCP Hazard analysis critical control point 

HCP Habitat Conservation Plan 

ICES International Council for the Exploration of the Sea 

ICM Integrated crop management 

IFIM Instream flow incremental methodology 

IFW Inland Fisheries and Wildlife, Department of (Maine) 

IPN Infectious pancreatic necrosis 

HKS Hemorrhagic kidney syndrome 

HMSC Huntsman Marine Science Center 

ISA Infectious salmon anemia 

LCP Loss control plans 

LFHC Lamar Fish Health Center (FWS) 

LMF Land for Maine’s Future (Program) 

LURC Land Use Regulation Commission (Maine) 

LWRC Land and Water Resource Council (Maine) 

MBTA Migratory Bird Treaty Act 

MDOT Maine Department of Transportation 

MEPDES Maine pollutant discharge elimination system 
xii

MFS Maine Forest Service 

MGS Maine Geological Survey 

MNAP Maine Natural Areas Program 

MMPA Marine Mammal Protection Act 

MOA Memorandum of agreement 

MSFCMA Magnuson-Stevens Fishery Conservation and Management Act 

NGO Non-Governmental Organization 

NAC North American Committee 

NASSG North American Salmon Study Group (ICES) 

NASWG North Atlantic Salmon Working Group (ICES) 

NANFH North Attleboro National Fish Hatchery (Massachusetts) 

NASCO North Atlantic Salmon Conservation Organization (international) 

NEST Northeast Salmon Team (NMFS) 

NFWF National Fish and Wildlife Foundation 

NEFMC New England Fishery Management Council 

NMFS National Marine Fisheries Service 

NPDES National pollutant discharge elimination system 

NWFSC Northwest Fisheries Science Center (NMFS) 

NPS Non-point source 

OBD Overboard discharge 

PCR Polymerase chain reaction 

PIT Passive integrated transponder 

PVA Population viability analysis 

SFI Sustainable Forest Initiative 

SWCD Soil and Water Conservation Districts (Maine) 

SSSV Salmon Swimbladder Sarcoma vrius 

SST Sea surface temperature 

SFI Sustainable Forestry Initiative 

TAC Technical Advisory Committee (Maine) 
xiii

USASAC United States Atlantic Salmon Assessment Committee 

USDA/APHIS U.S. Department of Agriculture/Animal and Plant Health Inspection Services 

USFS U.S. Forest Service 

USGS U.S. Geological Survey 

WUMP Water Use Management Plan (Maine) 
xiv

LIST OF FIGURES AND TABLES 

Figure 1. Map of the Gulf of Maine DPS of Atlantic salmon (p. 1-2) 

Figure 2. Maine Rivers (1-3) 

Figure 3. Major historic New England Atlantic salmon rivers (p. 1-6) 

Figure 4. Documented adult returns to the Narraguagus River (p.1-8) 

Figure 5. Estimated adult returns to rivers within the DPS (p.1-8) 

Figure 6: Replacement rates for the Narraguagus River (p. 1-9) 

Figure 7. Atlantic salmon life cycle (p. 1-11) 

Figure 8. Marine migration routes of U.S.-origin Atlantic salmon (p. 1-15) 

Figure 9. Narraguagus River water temperature (p. 1-47) 

Figure 10. Expansion of Development Statewide 1940 – 2050 (1-48) 

Figure 11. Salmon Annual flow patterns in four DPS rivers (p. 4-14) 

Table 1. Atlantic salmon temperature requirements (p. 1-45) 

Table 2. Atlantic salmon habitat w/in DPS and other Maine rivers (p. 4-72) 
xv

TABLE OF CONTENTS 

DISCLAIMER .................................................................................................................... ii 

ACKNOWLEDGMENTS .................................................................................................iii 

EXECUTIVE SUMMARY FOR THE GULF OF MAINE DPS OF ATLANTIC 

SALMON............................................................................................................................ v 

LIST OF ABBREVIATIONS............................................................................................. x 

LIST OF FIGURES AND TABLES................................................................................ xiv 

TABLE OF CONTENTS.................................................................................................. xv 

PART ONE: BACKGROUND........................................................................................ 1-1 

I. GULF OF MAINE DISTINCT POPULATION SEGMENT..................................1-1 

II. TAXONOMY AND DESCRIPTION...................................................................... 1-4 

III. DISTRIBUTION AND ABUNDANCE.............................................................. 1-5 

IV. LIFE HISTORY AND HABITAT REQUIREMENTS.......................................1-7 

A. Adult Spawning ................................................................................................. 1-10 

B. Early Freshwater Development..........................................................................1-12 

C. Parr Stage...........................................................................................................1-13 

D. Smolt Stage ........................................................................................................1-14 

E. Marine Stage ...................................................................................................... 1-14 

V. ECOLOGICAL RELATIONSHIP OF OTHER NATIVE DIADROMOUS 

SPECIES........................................................................................................................1-14 

VI. HISTORICAL STOCKING OF SALMON WITHIN THE DISTINCT 

POPULATION SEGMENT RANGE............................................................................ 1-17 

A. Stocks Used for Artificial Propagation..............................................................1-17 

B. Life Stages and Numbers Stocked .....................................................................1-18 

C. Impacts of Past Stocking....................................................................................1-19 

VI. REASONS FOR LISTING................................................................................ 1-20 

A. PRESENT OR THREATENED DESTRUCTION, MODIFICATION OR 

CURTAILMENT OF HABITAT OR RANGE............................................................. 1-21 

1. Water Use...........................................................................................................1-25 

2. Water Quality.....................................................................................................1-28 

i. Acidified water and aluminum...................................................................1-28 

ii. Pesticides, other contaminants and endocrine disruption ..........................1-32 

iii. Sedimentation ............................................................................................1-40 

iv. Excess Nutrients.........................................................................................1-44 

v. Elevated Water Temperature .....................................................................1-44 

vi. Environmental Impacts of Changing Landuse Patterns.............................1-47 

3. Obstruction to Passage/Habitat Connectivity ....................................................1-49 

i. Manmade Barriers......................................................................................1-49 

ii. Natural Barriers..........................................................................................1-51 
xvi

B. OVERUTILIZATION FOR COMMERCIAL, RECREATIONAL, SCIENTIFIC 

OR EDUCATIONAL PURPOSES................................................................................ 1-52 

1. Commercial and Recreational Fisheries ............................................................ 1-52 

A. U.S. Fisheries............................................................................................. 1-52 

B. Canadian Fisheries..................................................................................... 1-55 

C. West Greenland Fishery.............................................................................1-56 

D. St. Pierre et Miquelon Fishery ...................................................................1-57 

2. Research and Monitoring................................................................................... 1-57 

C. DISEASE ............................................................................................................... 1-58 

1. Infectious Salmon Anemia (ISA).......................................................................1-60 

2. Salmon Swimbladder Sarcoma (SSS)................................................................1-64 

D. PREDATION AND COMPETITION ................................................................... 1-64 

1. Marine Mammals............................................................................................... 1-65 

2. Avian Predators.................................................................................................. 1-67 

i. Double-crested Cormorant.........................................................................1-67 

ii. Mergansers.................................................................................................1-69 

3. Piscine Predators and Competitors ....................................................................1-69 

i. Freshwater..................................................................................................1-69 

ii. Estuarine and marine..................................................................................1-75 

E. INADEQUACY OF EXISTING REGULATORY MECHANISMS.................... 1-76 

F. OTHER NATURAL AND ANTHROPOGENIC FACTORS AFFECTING THE 

SPECIES’ CONTINUED EXISTENCE........................................................................ 1-78 

1. Salmon Aquaculture...........................................................................................1-78 

2. Marine Survival ................................................................................................. 1-86 

3. Hatcheries ..........................................................................................................1-89 

4. Depleted Diadromous Fish Communities..........................................................1-90 

5. Climate Change..................................................................................................1-91 

VII. THREATS ASSESSMENT............................................................................... 1-92 

VIII. CURRENT CONSERVATION EFFORTS....................................................... 1-99 

PART TWO: RECOVERY STRATEGY........................................................................ 2-1 

PART THREE: RECOVERY GOAL, OBJECTIVES AND CRITERIA....................... 3-1 

PART FOUR: RECOVERY PROGRAM ....................................................................... 4-1 

A. RECOVERY ACTION OUTLINE...................................................................... 4-1 

B. RECOVERY ACTION NARRATIVE.............................................................. 4-12 

1. Protect and restore freshwater and estuarine habitats........................................4-12 

1.1 Protect hydrologic conditions to ensure instream flows (volume, velocity, 

depth, temperature) adequate for Atlantic salmon.................................................4-12 

1.2 Ensure water quality to support healthy and productive salmon 

populations............................................................................................................ 4-20 

1.3 Ensure timely passage for each life-stage, including connectivity of 

spawning and nursery habitats, downstream passage for smolts and upstream 

passage for returning spawners..............................................................................4-29 

1.4 Secure long term protections for freshwater and estuarine habitats ..........4-32 
xvii

1.5 Restore degraded stream and estuarine salmon habitat .............................4-36 

2. Minimize potential for take in freshwater, estuarine, and marine fisheries.......4-39 

2.1 Prevent Directed Take of Atlantic salmon................................................. 4-39 

2.2 Avoid bycatch of Atlantic salmon .............................................................4-41 

3. Reduce predation and competition on all life-stages of Atlantic salmon ..........4-44 

3.1 Assess impacts of predation on wild and hatchery-reared river-specific 

salmon populations and develop methods for reducing adverse affects from 

predation ................................................................................................................ 4-44 

3.2 Reduce predation and competition between Atlantic salmon and other 

freshwater fish species ........................................................................................... 4-51 

4. Reduce risks from commercial aquaculture operations..................................... 4-53 

4.1 Improve containment at existing and future marine sites ..........................4-53 

4.2 Minimize the effects of escaped farmed salmon........................................4-57 

4.3 Minimize risks of disease and parasite transmission from farmed fish in 

marine pens to wild fish.........................................................................................4-61 

4.4 Reduce risk of juvenile escapement from freshwater aquaculture facilities 

into DPS rivers....................................................................................................... 4-66 

5. Supplement wild populations with hatchery-reared DPS salmon...................... 4-67 

5.1 Stock cultured fish in natal rivers to supplement contributions of wildspawned fish........................................................................................................... 4-67 

5.2 Maintain Fish Health Practices to Minimize Potential Introduction of Disease 

to Hatchery Stocks and transmission to Wild Populations ....................................4-74 

5.3 Maintain practices to prevent escapement from federal hatcheries...........4-76 

6. Conserve the genetic integrity of the DPS......................................................... 4-77 

6.1 Ensure that culture and stocking programs conserve the genetic integrity of 

the DPS .................................................................................................................. 4-77 

6.2 Ensure that management plans consider and avoid negative genetic effects 

of management actions and promote preservation of adaptive variation ..............4-78 

6.3 Explore methods for long-term preservation of gametes and genes for future 

use...... .................................................................................................................. 4-78 

6.4 Monitor genetic diversity, including important trait variation and parentage 

of smolts and returning adults................................................................................4-78 

7. Assess stock status of key life stages................................................................. 4-78 

7.1 Assess abundance and survival of Atlantic salmon at key freshwater and 

marine life-stages...................................................................................................4-79 

8 Promote salmon recovery through increased public and government 

awareness..... ............................................................................................................. 4-87 

8.1 Develop a comprehensive Education and Outreach Program for the Gulf of 

Maine DPS of Atlantic salmon ..............................................................................4-87 

8.2 Maintain, and if necessary increase, coordination/communications between 

government and local agencies on issues pertaining to Atlantic salmon 

recovery................................................................................................................ 4-89 

9. Assess effectiveness of recovery actions and revise as appropriate ..................4-90 

9.1 Appoint a Recovery Implementation Team to coordinate implementation of 

recovery plan objectives ........................................................................................4-90 

9.2 Review implementation of Recovery Plan tasks annually and assess need for 
xviii

revisions, including changes in priorities...............................................................4-90 

9.3 Complete necessary addenda, updates and revisions to the Recovery 

Plan...... ................................................................................................................ 4-91 

PART FIVE: IMPLEMENTATION SCHEDULE..........................................................5-1 

LITERATURE CITED .................................................................................................... 6-1 

APPENDIX 1: LISTING FACTORS (THREATS) AND RECOVERY TASKS........... 7-1 

APPENDIX 2: REGULATORY PROTECTIONS ......................................................... 8-1 

APPENDIX 3: ESTABLISHED EDUCATION AND OUTREACH PROGRAMS AND 

GROUPS IN MAINE ...................................................................................................... 9-1 

APPENDIX 4: GLOSSARY OF TERMS ..................................................................... 10-1 

APPENDIX 5: GULF OF MAINE DPS OF ATLANTIC SALMON THREATS 

ASSESSMENT.............................................................................................................. 11-1 

APPENDIX 6: RESPONSE TO PUBLIC AND PEER-REVIEW COMMENTS ........ 12-1 

APPENDIX 7: PUBLIC AND PEER REVIEW COMMENTS................................... 13-1

APPENDIX 8: RECOVERY ACTIONS...................................................14-1 
1-1

PART ONE: BACKGROUND 

The overall goal of the Endangered Species Act of 1973 (Act) is to recover species listed 

as endangered or threatened to the point at which they are no longer in danger of 

extinction and are unlikely to become so in the foreseeable future. To help achieve this 

goal, the Act requires a recovery plan for each listed species unless such a plan will not 

promote its conservation. The Act states that recovery plans shall, to the maximum 

extent practicable, incorporate, objective, measurable criteria for assessing recovery 

progress, management actions needed to recover and/or protect the listed species and the 

ecosystem upon which it depends, and time and cost estimates for reaching recovery 

objectives. 

The subject of this recovery plan is the Gulf of Maine (GOM) distinct population 

segment (DPS) of Atlantic salmon. The National Marine Fisheries Service (NMFS) and 

the U.S. Fish and Wildlife Service (FWS) listed the Atlantic salmon GOM DPS as 

endangered on December 17, 2000 (65 FR 69459). The listing was made in accordance 

with both the Act, which defines distinct population segments of vertebrate fish or 

wildlife as “species” eligible for protection, and the 1996 DPS policy issued by the U.S. 

Fish and Wildlife Service and the National Oceanic and Atmospheric Administration (61 

FR 47223). 

The following Background sections describe the Gulf of Maine DPS of Atlantic salmon 

and assess its current status, continuing threats to its survival and recovery, and 

conservation efforts to date. The intent is to provide the context for the recovery strategy, 

objectives and actions recommended in Parts Two, Three and Four of this plan. 

I. GULF OF MAINE DISTINCT POPULATION SEGMENT 

Historically, the geographic range of the DPS within the U.S. extended from the 

Androscoggin River in the south, northward to the mouth of the St. Croix River on the 

United States-Canada border (NMFS-USFWS 1999)(see figure 1 and 2). This 

delineation was based on examination of life history, biogeographical, genetic, and 

environmental information. Zoogeographic maps helped identify boundaries between 

areas that likely exert different selective pressures on Atlantic salmon populations and 

have substantial differences in riverine-marine ecosystem structure and function. Key 

elements to the delineation included: (1) spatial arrangements of river systems to create 

isolation, and (2) watershed location within ecological provinces and subregions that 

affect the productivity and ecology of riverine-marine ecosystem complexes (NMFS and 

FWS 1999). 

The Gulf of Maine DPS includes all naturally reproducing remnant populations of 

Atlantic salmon from the Kennebec River downstream of the former Edwards dam site, 

northward to the mouth of the St. Croix River. The Penobscot and its tributaries 

downstream from the site of the Bangor Dam are included in the range of the Gulf of 

Maine DPS (65 FR 69459). At the time of the listing, there were at least eight rivers 
Figure 1: Geographic Range of the

Gulf of Maine DPS of Atlantic Salmon

0 60 120 180

Kilometers

.

Legend

DPS Watershed Delineation

1-2
%

%

Kennebec

Bangor Dam

(removed)

Cove Brook

Ducktrap

Sheepscot

East Machias

Machias

Narraguagus

Pleasant

Dennys

Penobscot

St. Croix

Androscoggin

St. John

Indian Chandler

Orange

Hobart

Pennamaquan

Boyden Stream

Eaton Brook

Felts Brook

Kenduskeag

Piscataquis

Marsh Stream

Little

Orland

St. George

Medomak Pemaquid

Aroostook

Prestile

Meduxnekeag

Union

Edwards Dam

(removed)

 ̄ 0 25 50 75

Kilometers

Maine Rivers

Figure 2

1-3
1-4

within the geographic range of the Gulf of Maine DPS that still contained functioning 

wild salmon populations, although at substantially reduced abundance levels (65 

69459)(hereinafter referred to as “DPS rivers”). The core of these remnant populations is 

located in the Dennys, East Machias, Machias, Pleasant, Narraguagus, Ducktrap and 

Sheepscot rivers and Cove Brook (65 FR 69459). DPS salmon taken for hatchery rearing 

for broodstock purposes and any captive progeny of these salmon, are included as part of 

the DPS. These hatchery-held fish do not count toward a delisting or reclassification goal 

as this goal refers to the status of the salmon in the wild (see Part Three). 

At the time of the listing, the Services deferred a decision whether the Gulf of Maine 

DPS range included the mainstem of the Penobscot River and its tributaries above the 

former site of the Bangor dam (65 FR 69459). Presently a status review is underway to 

determine the relationship of large river systems (e.g., Penobscot, Kennebec) to the DPS 

as currently delineated. This review will also determine the status of current salmon 

populations within these large river systems, as well as any other additional salmon 

populations present outside the geographic range of the DPS. Decisions regarding the 

status of these populations may have significant implications for the recovery strategy 

and recovery criteria. The Services will consider the implications of these decisions for 

the overall recovery program and revise the recovery plan accordingly. 

II. TAXONOMY AND DESCRIPTION 

The Atlantic salmon, Salmo salar, is of the order Salmoniformes and family Salmonidae. 

Atlantic salmon is one of only two members of the genus Salmo found in North America. 

The Atlantic salmon is an anadromous fish, spending its first two to three years in 

freshwater, migrating to the ocean where it spends typically two years, and returning to 

its natal river to spawn. A non-anadromous variety (recognized in the past by some 

taxonomists as the subspecies S. salar sebago) is found in some lakes and rivers, but for 

purposes of this Recovery Plan the term “Atlantic salmon” refers to the anadromous form 

while “landlocked salmon” refers to members of the non-anadromous populations. The 

other member of the genus Salmo is Salmo trutta, brown trout, which was introduced 

from Europe. 

Atlantic salmon have a fusiform body shape, i.e., like a spindle, rounded, broadest in the 

middle and tapering at each end. The shape is somewhat flattened towards the sides 

which is typical of salmonids in general. The head is relatively small, comprising 

approximately one-fifth of body length. Ventral paired fins are prominent, especially on 

juveniles. 

Parr (juvenile salmon before they enter salt water) have eight to eleven vertical dark bars 

(known as “parr marks”) on silvery sides. After smoltification, the physiological process 

that enables juvenile salmon to transition from freshwater to salt-water and enter the sea, 

the typical silver coloration with small, dark dorsal spots of the sea-run pre-adult 

predominates. Spawning adults darken to a bronze color after entering freshwater and 

darken further after spawning. They are often referred to as “black salmon” at this stage. 

The silver coloring returns after re-entering the sea. 
1-5

Outmigrating Atlantic salmon smolts in Maine average 14-18 cm in length. The size of 

returning adults depends on the time spent at sea. Grilse, young salmon returning to 

freshwater after one winter at sea (1SW), average 50-60 cm and weigh 1-2 kg while 2SW 

salmon (adult salmon returning after two years at sea) range from 70-80 cm and 3.5-4.5 

kg. Salmon that are 3SW (adult salmon returning after three years at sea) are 80-90 cm 

long and often weigh more than 7 kg (Baum 1997). 

III. DISTRIBUTION AND ABUNDANCE 

Atlantic salmon reproduce in coastal rivers of northeastern North America, Iceland, 

Europe and northwestern Russia and migrate through various portions of the North 

Atlantic Ocean. There are three generally recognized groups of Atlantic salmon: North 

American, European and Baltic. 

The North American group historically ranged from the Ungava area of northern Quebec, 

southeast to Newfoundland and southwest to Long Island Sound. It includes Canadian 

populations (e.g., St. Lawrence River Basin, outer Maritimes, Bay of Fundy and 

Newfoundland-Labrador) and U.S. populations, including the Gulf of Maine DPS of 

Atlantic salmon as described above. 

In Canada, significant reproducing populations remain throughout the historic range, 

though many populations are severely depleted. In May 2001, Atlantic salmon 

populations in several rivers in the upper Bay of Fundy were designated as endangered by 

the Canadian Committee on the Status of Endangered Wildlife2

 (COSEWIC). 

Subsequently, the Species at Risk Act (SARA) was passed in October 2002. The Atlantic 

Salmon Inner Bay of Fundy populations are protected under SARA. 

In the U.S., nearly every major coastal river north of the Hudson River historically 

supported an Atlantic salmon population (figure 3). These populations have been divided 

into three Distinct Population Segments: Long Island Sound, Central New England and 

Gulf of Maine (NMFS-FWS 1999). At one time, at least eight rivers in the Long Island 

Sound DPS had Atlantic salmon runs. The Central New England DPS ranged from the 

Merrimack River in the south to the Royal River (Yarmouth, Maine) in the north. All 

wild populations in the Long Island Sound and Central New England DPS’s have been 

extirpated. Efforts to restore these salmon runs (e.g., Saco, Merrimack, Pawcatuck and 

Connecticut rivers) have been underway for the past thirty years. 

 

2

 COSEWIC is an independent committee of experts that assesses the status of species suspected of 

being at risk of extinction. While Canadian federal, provincial and territorial governments 

recognize COSEWIC as the source of independent advice on the status of species at risk and to 

work cooperatively to protect these species, COSEWIC designations have no legal standing.
1

2

3

4

5

6

7

8

9

11 10

12

13

14 15

16

17

18

19

20

21

Major Historic Atlantic

Salmon Rivers of

New England

- Figure 3

1-6

0 20 40 60

Kilometers

1. Aroostook

2. St. Croix

3. Dennys

4. East Machias

5. Machias

6. Pleasant

7. Narraguagus

8. Union

9. Penobscot

10. Ducktrap

11. Sheepscot

12. Kennebec

13. Androscoggin

14. Royal

15. Saco

16. Cocheco

17. Lamprey

18. Merrimack

19. Pawcatuck

20. Connecticut

21. Housatonic
1-7

Persistent reproducing wild populations of Atlantic salmon occur within the Gulf of 

Maine DPS but have declined to critically low levels (see page 1-7). Since the listing, 

adult returns, as well as juvenile abundance estimates and survival have continued to 

decline. In 2004, the total number of adult returns to the eight rivers still supporting wild 

Atlantic salmon populations within the DPS was estimated to range from 60 to 113 

(USASAC 2005). The best long-term data for adult DPS returns is for the Narraguagus 

River, which indicates greatly reduced numbers since 1967 (Figure 4). The estimated 

number of adult returns to other DPS rivers over the past 11 years indicates a similar 

decline (Figure 5). Replacement rates of adult salmon in the Narraguagus River for the 

years 1996 to 2002 all averaged less than 1.0, with the lowest value of 0.2 occurring in 

2002 (Figure 6). Population assessments on the DPS by USASAC show a current 5-year 

geometric mean replacement rate of 0.54 (USASAC 2004). 

IV. LIFE HISTORY AND HABITAT REQUIREMENTS 

Differences in life history among United States and Canadian stocks of Atlantic salmon 

were identified as early as 1874 (Atkins 1874). Both environmental and genetic factors 

make the DPS markedly different from other populations of Atlantic salmon in their life 

history and ecology (NMFS and FWS 1999). Differences in life history characteristics 

have contributed to making the Gulf of Maine DPS distinct (NMFS and FWS 1999). 

Remnant DPS populations have maintained the most characteristic of these factors: 

smoltification at a mean age of two and predominant adult returns at age four after two 

winters at sea (2SW fish). 

Wild salmon in Maine DPS rivers are genetically different from European and Canadian 

Atlantic salmon (NRC 2002, and references therein). U.S. Atlantic salmon stocks are 

composed of predominately 2SW salmon (> 80%) (Atkins 1874; Kendall 1935; 

USASAC 1999), while many Canadian and several European stocks have a much higher 

grilse component and a lower 2SW component (frequently <50%) (Hutchings and Jones 

1998). The proportion of 2SW fish in an Atlantic salmon stock has a documented genetic 

basis (Glebe and Saunders 1986; Ritter et al. 1986; Hutchings and Jones 1998; Palm and 

Ryman 1999). In 1999, a Biological Review Team (BRT)3

 completed a status review and 

concluded that the Gulf of Maine DPS has unique life history characteristics that have a 

heritable basis (NMFS and FWS 1999). The pattern of homing to their natal streams 

leads to a variety of local adaptations in life history features such as timing of spawning 

runs and growth rates (NRC 2002 and references cited therein). The NRC Committee on 

Atlantic salmon in Maine concluded that the large genetic differences among populations 

suggest biologically important genetic isolation and that the genetic differences among 

tributaries within large watersheds are suggestive of local adaptations (NRC 2002). 

 

3 Section 4(b)(1)(a) of the ESA provides that the Secretaries of the Interior and of Commerce shall 

make listing determinations based solely on the basis of the best scientific and commercial data 

available, after conducting a review of the status of the species and after taking into account those 

efforts being made by any state or foreign nation to protect such species. Under the ESA, 

biological review teams can be convened to review the status of species in accordance with section 

4(b)(1)(a) of the Act. 
1-8

Figure 4: Documented Adult returns to the Narraguagus River 

1967-2002 Documented Narraguagus Adult Returns

0

50

100

150

200

250

300

350

400

1967 1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000

Figure 5: Estimated Adult returns to rivers within the DPS (1991-2002) 

0

50

100

150

200

250

300

350

400

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002

95%CL High

Mean

95%CL Low
1-9

 Figure 6: Replacement Rate for Narraguagus River
1-10

The occurrence of at least some straying among locally adapted populations allows the 

development of a metapopulation4 structure. Genetic data on Atlantic salmon in Maine 

indicate that they may constitute one or more metapopulations, which are distinct from 

other populations in North America (Spidle et al. 2003). 

The relatively complex life cycle of anadromous Atlantic salmon is described in the 

Status Review (NMFS and FWS 1999) and is extensively treated by Baum (1997) and 

Gibson (1993)(figure 7). The typical cycle for Maine salmon is summarized below by 

life stage.5

A. Adult Spawning 

Historically (through the early 1980s), salmon runs in Maine were comprised of 

approximately 5% 1SW fish and 3SW fish, or repeat spawners, were more prevalent than 

today (Ed Baum, Atlantic Salmon Unlimited, personal communication). Presently, the 

majority of returning adult salmon are 2SW fish (80%) while approximately 15 to 20% of 

the run are 1SW fish. A small proportion of the run is comprised of 3SW fish and repeat 

spawners. While most 1SW fish are males, the older returning salmon are predominantly 

females at approximately a 2:1 ratio. 

Spawning adults return from the sea to Maine rivers from May through October. The 

majority of a spawning run (60-70%) enters freshwater before August. The 

predominance of 2SW fish influences spawning-run timing because they typically enter 

rivers earlier than grilse (1 SW). Historically, the majority of salmon in the Penobscot, 

Dennys, East Machias, Machias, Narraguagus, Kennebec, Androscoggin and Saco rivers 

entered freshwater between May and mid-July and were therefore called “early run,” 

whereas the majority of those returning to the Ducktrap River entered freshwater after 

mid-July and were called “late run” (Baum 1997). Some rivers, such as the Sheepscot 

and Pleasant, had both an early run and late run of Atlantic salmon (Baum 1997). The 

current trend in spawning-run timing is difficult to discern due to low abundance and the 

lack of collection facilities on all rivers. Analysis of historic recreational catch data in 

some Maine rivers indicates that the timing has changed little in the past fifty years 

(Baum 1997). 

The upstream migration of adult Atlantic salmon is a complex response to different 

environmental stimuli at different times in the migration. Increasing water flows and 

temperatures stimulate upstream migration. Solomon et al. (1999) describe two Atlantic 

salmon migration phases: the first includes river entry and a period of holding, the second 

includes instream movement to spawning areas. Olfaction is important in the first phase 

of migration, when salmon locate and enter their natal river. Once in the river, olfaction 

is overshadowed by the influence of flow and temperature. The low flows that are typical 

of Maine rivers in late summer constrain movement. As a result of these constraints, 

 

4

 A metapopulation is a set of populations (sometimes referred to as subpopulations) connected by 

straying at low to moderate rates.

5

 See appendix 2 for glossary of terms relating to the life history of Atlantic salmon. 
Figure 7: Life Cycle of the Atlantic Salmon

(Salmo salar)

Spawned-out salmon, called kelts or 

black salmon, return to the ocean or overwinter in the river

Adult salmon begin returning in the spring to their native stream to repeat the spawning cycle Adult female

Smolts are silver colored and approximately 6 inches long. In the spring, smolt body chemistry changes; they now weigh about 2 ounces and are ready to enter salt waters. They migrate to the ocean where they will develop in about 2-3 years into mature salmon weighting about 8-15 pounds. 

Fry quickly develop into parr with camoflaging

vertical stripes. The parr are two inches long. They feed and grow for one to three years in their native stream before becoming smolts.

Adult male

In late autumn, the fertilized eggs in strgravel nests called 

The eggs hatch into alevin or sac fry in late spring, and the yolk sac is gradually absorbed

Three to six weeks after hemerge from the gravel to called fry

1-11
1-12

Maine salmon typically hold for long periods before the second migration phase. In the 

second migration phase, flow becomes increasingly important as the salmon move to 

smaller tributaries farther upstream in the watershed (Solomon et al. 1999). Salmon may 

await the fall rains that typically occur in Maine before making their final move to 

spawning reaches. Water temperatures above 22.8oC or dissolved oxygen levels below 5 

ppm will inhibit migration (DeCola 1970). In Maine rivers, high summer temperatures 

constrain adult salmon movements and result in mortality (Shepard 1995). 

Spawning occurs predominantly from mid-October to mid-November when water 

temperatures are between 7-10oC. The female seeks gravel substrate within riffle areas 

and digs out a redd (nest or depression) with her tail. She deposits 7,000-8,000 eggs in 

several redds 12-20 centimeters (cm) under the gravel with 22-76 cm of water flowing 

over them at 27-83 centimeters per second (cm/sec). The eggs are fertilized by milt 

released from nearby males, which may include several different age groups (possibly 

five to six), including precocious parr that have never gone to sea. While the homing 

fidelity of salmon tends to limit the exchange of genetic material between populations of 

different rivers (particularly distant rivers), the participation of several age groups in a 

single spawning season promotes genetic exchange among generations within a river. 

The downstream movement of post-spawned adults (kelts) may be triggered by increased 

water temperatures or flows. Some migrate toward the sea immediately, either moving 

partway downstream or returning to the ocean (Ruggles 1980; Don Pugh, U.S. 

Geological Survey (USGS) personal communication). The majority, however, 

overwinter in the river and migrate to sea in the spring as “black salmon.” Kelts that 

remain in the river appear to survive well through the winter (Ruggles 1980; Jonsson et 

al. 1990). The relative survival of kelts, however, has not been calculated for Maine 

rivers. After reaching the ocean, few kelt survive. Few rivers have a spawning run with 

a significant proportion of repeat spawners. 

B. Early Freshwater Development 

Atlantic salmon deposit their eggs 12-20 cm under the gravel in redds. As noted, water 

depths of 22-76 cm and flow rates of 27-83 cm/sec are needed to provide adequate 

protection and water movement for the developing embryos. Eggs incubate slowly due to 

cold winter water temperatures and hatch in March or April. The newly hatched preemergent fry (alevins) rely on their yolk sac for nourishment while remaining deeply 

buried in the gravel. The fry emerge from the gravel about mid-May and start feeding on 

plankton and small invertebrates. Studies in Maine indicate less than 10% of the eggs 

spawned in the autumn will survive to emerge as feeding fry the following spring (Baum 

1997). Sources of egg mortality include de-watering, freezing, mechanical destruction 

(i.e., sedimentation) and predation. From the egg through the juvenile stages, salmon 

need clean gravel and cobble substrate through which water can easily flow (Stanley and 

Trial 1995). 

The timing of hatching and emergence, relative to spring runoff, affects egg to fry 

mortality and survival. Low flows in the thirty days prior to spring runoff may cause 
1-13

high mortality among pre-emergent alevins (Frenette et al. 1984). Unusually high spring 

runoff may scour redds, causing pre-emergent alevins to drift downstream prematurely. 

High flows within one week after emergence can cause fry mortality or displace fry to 

sub-optimal habitats (Jensen and Johnson 1999). 

C. Parr Stage 

Emergent fry quickly disperse from the redd, develop parr marks along their sides and 

enter the parr stage. The parr stage may last for one to three years in Maine rivers, with 

two years being typical. Parr habitat (often called “nursery habitat”) is typically riffle 

areas characterized by adequate cover (gravel and rubble up to 20 cm), moderate water 

depth (10-60 cm) and moderate to fast water flow (30-90 cm/sec) (Symons and Heland 

1978). Parr are very territorial and spend much time on the bottom, holding their position 

in the current aided by large pectoral fins. They feed on invertebrates and some small 

fish. 

The growth rate of juvenile salmon is determined by the productivity of the water 

(nutrient supply) and temperature. Temperatures during the growing season range from 

around 7-25oC (Elson 1975; Symons 1979). Temperatures above 28oC can be harmful to 

juvenile salmon (Fry 1947). If water temperatures exceed 24oC for extended time, 

growth may be affected and may be affected and fish may not reach adequate size to 

over-winter successfully. While environmental factors have a strong influence on 

juvenile growth and maturation, genetic differences between stocks also influence growth 

and performance (Kincaid et al. 1994; Hutchings and Jones 1998). 

The low flows that typically occur in late summer in Maine salmon rivers can limit parr 

populations (Havey 1974; Power 1981; Gibson and Myers 1988; Frenette et al. 1984). 

Parr growth and survival during the summer are positively correlated with various flow 

rates, demonstrating that the low flows limit parr populations. Population reductions 

during low flows probably occur because of reduction in habitat quantity and quality and 

possibly reduced foraging opportunities (Frenette et al. 1984). This reduction in habitat 

quantity and quality can cause salmon parr to shift to sub-optimal habitat, reducing 

foraging opportunities and thereby impairing growth and survival. Frenette et al. (1984) 

found that the abundance of large parr (generally 2+ parr6

 in their study) was significantly 

correlated with mean July flow the preceding year and mean August flow two years 

earlier. Power (1981) found correlation’s between low summer flows and the abundance 

of adult salmon returning to Canadian rivers. 

Similarly, low flows in winter are associated with reduced parr and pre-smolt abundance 

(Hvidsten 1993). Low winter flows can reduce habitat quantity and exacerbate ice 

conditions that cause parr mortality (Whalen and Parrish 1999). 

 

6 The period from July 1 to December 31 two years after hatching. 
1-14

D. Smolt Stage 

Parr larger than 12 cm undergo a physiological transformation called smoltification that 

prepares them for life in a marine habitat. In Maine, this usually occurs the second spring 

after hatching. The outward signs include a color transformation with the loss of the parr 

marks and silvering of the body (except along the back), a more streamlined body form 

(less weight per unit of length), a decline in territorial behavior and a change in 

swimming orientation from facing upstream to facing downstream. Fundamental 

physiological changes also occur, especially with osmoregulatory processes, that enable 

the transition from the freshwater environment to the marine environment. 

Migration to sea is triggered by a number of environmental cues including water flow, 

temperature and photoperiod changes. Smolt migrations in Maine rivers occur primarily 

at night after peak spring flows and at temperatures above about 10°C (Ruggles 1980; 

Shepard 1991). In Maine rivers, downstream migration occurs primarily from mid-April 

through mid-June (Baum 1997). Migrating smolts swim actively in the river and the 

estuary, but the migration also includes periods of holding and may include periods of 

passive drift with the current (LaBar et al. 1978; Shepard 1991; Peake and McKinley 

1998). Higher flows accelerate the timing of the migration and shorten the duration. 

Differences in the timing of smolt migration occur between rivers. 

E. Marine Stage 

The marine stage of Atlantic salmon life history is the least understood. Post-smolts 

leaving Maine rivers in spring migrate northeasterly, reaching Newfoundland and 

Labrador by mid-summer (figure 8). They spend their first winter at sea in the area of the 

Labrador Sea south of Greenland. After the first winter at sea, a small percentage will 

return to Maine while the majority will spend a second year at sea, feeding off the 

southwest or, to a much lesser extent, southeast coast of Greenland. Some Maine salmon 

are also found in waters along the Labrador coast. After a second winter in the Labrador 

Sea most Maine salmon return to rivers in Maine, with a small number returning the 

following year as 3SW fish. The homing instinct is high for Maine Atlantic salmon; 

generally less than 2% have been observed to stray to non-natal rivers (Baum 1997). 

V. ECOLOGICAL RELATIONSHIP OF OTHER NATIVE DIADROMOUS 

SPECIES 

Maine Atlantic salmon rivers historically supported abundant populations of other native 

diadromous fish species including alewives, blueback herring, American shad, sea 

lamprey, anadromous rainbow smelt, Atlantic sturgeon, shortnose sturgeon and American 

eel. Salmon co-evolved over time with these and other aquatic organisms native to 

Maine rivers. Large populations of clupeids, such as shad, alewife, and blueback herring, 

used rivers within the DPS as migratory corridors, spawning grounds and juvenile 

nursery habitat. As these fish completed their life cycles, they likely performed 

important ecological functions that may have been important to Atlantic salmon in 

completing their life cycle. Primarily, these functions may be categorized under three 
Figure 8

1-15
1-16

broad categories: prey buffering, marine derived nutrient cycling and habitat modification 

and enhancement. 

Predation Buffer 

Clupeids likely provided an alternative forage base (or prey buffer) for predators of 

salmon in freshwater and estuarine habitats. Specifically, pre-spawn adult alewives 

migrate upstream at the same time as salmon smolts would be moving downstream to the 

estuary through the same river reaches. Conversely, post-spawn adult alewives migrate 

downstream at the end of the smolt migration period later in the spring. Alewives, 

similar in size to Atlantic salmon smolts, likely exceeded outmigrating salmon smolts in 

abundance by several orders of magnitude. Alewives were likely a substantial prey 

buffer against predation on Atlantic salmon smolts within common migratory corridors 

by native predators such as cormorants, otters, ospreys and bald eagles, (Schulze 1996, 

USASAC 2004). Similarly, adult shad migrations that coincided with adult salmon 

migrations likely served as a prey buffer against seal predation. In addition, the presence 

of abundant juvenile clupeids (e.g., alewives and shad) would buffer juvenile Atlantic 

salmon against bird (e.g., cormorant, merganser), and mammal (e.g., mink) predation as 

these species share similar instream rearing habitat. 

Marine Derived Nutrients 

In addition to providing a buffer against predation, a diverse and abundant diadromous 

fish community likely shaped nutrient cycling regimes in the rivers within the DPS. The 

annual addition of marine derived nutrients (MDNs) was potentially very important for 

wild Atlantic salmon because rivers in Maine are relatively nutrient poor (Richardson 

1993). The upstream migrations of large populations of adult clupeids and sea lampreys, 

along with adult salmon themselves, may have provided a conduit for the annual import 

and deposition of marine derived nutrients and biomass into the freshwater environment 

of these rivers. Mechanisms of direct deposition included discharge of urea, discharge of 

gametes on the spawning grounds and deposition of post-spawn adult carcasses (Garman 

and Macko 1998, MacAvoy et al. 2000). 

In addition to clupeids sea lampreys were probably much more abundant historically than 

they are today (Kircheis 2004). Sea lampreys are more habitat selective than clupeids, 

prefering spawning habitat very similar in location and physical characteristics to that 

used by Atlantic salmon (e.g., headwater reaches of moderate to large tributaries) 

(Kircheis 2004). Unlike clupeids, lampreys’ experience 100% post-spawning mortality, 

all of which occurs right on the spawning grounds (Kircheis 2004). This mortality occurs 

at time that salmon fry are emerging from redds and beginning to occupy adjacent 

juvenile production habitats. The decomposition of sea lamprey carcasses likely resulted 

in substantial depositions of MDNs directly into juvenile salmon rearing habitats. These 

nutrients probably enhance the primary production capability of these habitats for weeks 

or even months. Moreover these MDNs would gradually be transferred throughout the 

trophic structure of the ecosystem, including those components most important to 

juvenile salmon (e.g., macroinvertebrate production). Clupeids also serve as an 
1-17

important vector of MDN, experiencing 20% to 50% post-spawning mortality (Collette 

and Klein-MacPhee 2002). While clupeid spawning generally occurs in middle to lower 

river reaches (i.e., below salmon spawning), the resulting MDN influx may still be 

substantial to a river system as a whole; if not to Atlantic salmon populations specifically. 

Additional MDNs may not always translate to higher primary productivity levels 

(Ambrose et al. 2004) but many studies from west coast ecosystems describe the 

ecological significance of this nutrient cycling function among co-evolved Pacific salmon 

species (Bilby et al. 1996, Cederholm et al. 1999, Gresh et al. 2000). The scientific basis 

and biological significance to Atlantic salmon of any parallel nutrient cycling role that 

co-evolved clupeids, sea lamprey, or Atlantic salmon themselves might represent in east 

coast salmon rivers is not well studied and therefore not thoroughly understood at this 

time. 

Habitat Modification/Enhancement 

Sea lamprey spawning activity can enhance instream substrate structure and thereby 

benefit other species including Atlantic salmon (Kircheis 2004). Sea lamprey spawning 

activity loosens and cleans substrate making the site more suited for spawning sites for 

other salmonids including Atlantic salmon (Kircheis 2004). The disturbance of substrate 

results in increased permeability and water quality that may enhance salmon egg and fry 

survival as well as benefiting other important aquatic species such as insects and 

invertebrates (Kircheis 2004). 

VI. HISTORICAL STOCKING OF SALMON WITHIN THE DISTINCT 

POPULATION SEGMENT RANGE 

A. Stocks Used for Artificial Propagation 

The first stocking of Atlantic salmon within the range of the Gulf of Maine DPS (see 

page 1-1) occurred in 1871 with the release of 1,500 parr of Canadian origin into the 

Sheepscot River. At the same time, a hatchery was established in the lower Penobscot 

River drainage and the practice of purchasing wild adult salmon harvested by commercial 

trap-netters for use as broodstock was initiated. The Penobscot River was the primary 

source of Atlantic salmon eggs for artificial propagation within the region for the next 

fifty years. Between 1871 and 1886 about 24 million eggs were taken from wild 

Penobscot sea-run salmon. Most of these eggs were used to stock waters outside of the 

DPS area, including inland lakes to create or enhance landlocked salmon populations 

(Baum 1997). 

In the early 20th century, declining salmon runs and price disputes with commercial trapnetters resulted in a decline of Penobscot eggs available for artificial salmon propagation. 

As a result, Canadian salmon stocks, primarily from the Miramichi and Gaspé rivers, 

were used throughout the 1920s and 1930s as a source of eggs for the Craig Brook 

National Fish Hatchery (CBNFH) in East Orland, Maine. The use of Canadian eggs 

declined in the 1940s when the Machias River and, for a brief time the Penobscot River, 

became sources of broodstock. During the 1950s and 1960s, a lack of Penobscot River 
1-18

fish once again resulted in Canadian salmon being used as the primary source of eggs. 

These were supplemented with Atlantic salmon eggs from adults collected from the 

Machias and Narraguagus rivers. 

In the late 1960s, efforts to rehabilitate the Penobscot salmon run were initiated through a 

combination of construction of new and/or improved fish passage facilities, improved 

water quality7

 and restocking utilizing smolts of mostly Machias and Narraguagus River 

origin (Baum 1997). By the 1970s, the adult returns made the Penobscot River 

propagation program self-sufficient for eggs and enabled it to support the egg needs of 

other hatcheries in Maine. Since 1992, rivers within the range of DPS still supporting 

wild salmon populations have been stocked only with juvenile salmon that are the 

offspring of parr taken from that specific river and raised to broodstock or mature fish 

(i.e., river-specific stocking). 

B. Life Stages and Numbers Stocked 

The stocking strategy in the U.S. from the start of the artificial propagation program in 

the 1870s through the 1930s depended heavily on releasing fry. Most records indicate 

that early fry stocking methods were dominated by cluster stocking in limited areas of a 

river. After a sixty-year period of predominantly fry releases, with unsatisfactory 

success, the strategy shifted to parr stocking which continued through the 1950s. By the 

mid-1960s, due to poor results from the parr stocking program, a smolt stocking program 

was implemented (Baum 1997). 

The numbers of fish produced and stocked varied greatly depending on the stocking 

strategy (i.e., fry vs. parr vs. smolt). The greatest numbers of fish were stocked between 

1896 and 1936. Fry were the focus of the stocking program during this period, with 

millions of fry stocked each year. In the 1930s, hatcheries began retaining fry for rearing 

to the parr stage. As a result of this change in stocking strategy, the number of fish 

stocked annually fell from one to three million fry to 100,000-300,000 parr. This 

reduction was due to hatchery capacity limitations. During the 1940s and 1950s, adult 

returns were poor despite the stocking of hundreds of thousands of hatchery-reared fry 

and parr (Baum 1997). 

Beginning in the early 1960s, the stocking program shifted to smolt production. The 

construction of Green Lake National Fish Hatchery (GLNFH) in 1974 and a change in 

rearing regime from 2-year-old smolts to 1-year-old smolts increased production capacity 

to 600,000 annually. Nearly all these smolts are stocked into the Penobscot River. 

In 1991, based on the recommendation of the Maine Atlantic Salmon Technical Advisory 

Committee (TAC)8

, the current river-specific stocking program was initiated. The river-

 

7

 These improvements were made under the auspices of the Anadromous Fish Conservation Act of 

1965, and Clean Water Act of 1972. 

8 The Maine TAC provides scientific and technical advice concerning Maine Atlantic salmon to the 

Regional Administrator of the National Marine Fisheries Service, Regional Director of the U.S. 

Fish and Wildlife Service and the Chair of the Maine Atlantic Salmon Commission. The TAC is 
1-19

specific stocking program stocks fish at the fry life-stage as the primary management 

strategy to recover Atlantic salmon populations in the DPS (see Recovery Action 5). 

This program stocks the progeny of salmon collected from DPS rivers into the river of 

origin (i.e., river-specific stocking). This strategy was intended to help protect the 

genetic integrity and metapopulation structure of the DPS and restore declining numbers 

of wild salmon. 

C. Impacts of Past Stocking 

Despite previous stocking efforts, the natural populations remaining in Maine rivers are 

distinguishable from each other with a level of genetic distinctiveness typical of that 

found in natural salmon populations in other parts of the world (NRC 2002). Historic 

stocking practices may have had an adverse effect upon the genetic integrity of the wild 

stocks persisting in rivers within the DPS (i.e., the geographic range, see page 1-1) 

(NMFS-USFWS 1999). These early programs, however, were limited in technology, 

distribution capabilities and knowledge of stocking strategies. Evidence suggests that 

these early efforts probably resulted in only negligible adult returns. For example, a 

recent study found no evidence of genetic influence on the Penobscot River salmon 

population from Miramichi stocks introduced in the late 1960s (Spidle et al. 2001). Poor 

hatchery return rates coupled with remnant natural stocks suggest that while some 

negative effects upon the genetic integrity of these stocks are possible, there is no 

evidence that stocks of hatchery origin have supplanted or homogenized the wild 

populations existing in these rivers. Genetic studies and review of these data (King et al. 

2000, 2001; NRC 2002) have demonstrated that genetic structure continues to exist 

among the wild populations in the DPS rivers. 

In June 2001, a multi-disciplinary committee was formed by the National Research 

Council (NRC), the principal operating agency of the National Academies of Science, to 

review the available scientific information on the status of wild Atlantic salmon 

populations in Maine. Part of the committee’s charge was to assess how Maine salmon 

populations differ from other Atlantic salmon populations. The NRC committee was 

tasked with assessing whether North American Atlantic salmon are genetically different 

from European salmon, whether Maine salmon are genetically different from Canadian 

salmon and the level of genetic distinctiveness, if any, between Atlantic salmon 

populations in the Gulf of Maine DPS. The committee concluded that North American 

populations of Atlantic salmon are clearly genetically distinct from European Atlantic 

salmon populations; Atlantic salmon in Maine are genetically distinct from Atlantic 

salmon in Canada; and, there is considerable genetic divergence among the remnant 

populations of Atlantic salmon in the Gulf of Maine DPS (NRC 2002). In addition, the 

committee concluded that the pattern of genetic divergence among Maine streams is 

similar to patterns seen elsewhere and is the degree of genetic divergence expected in 

natural salmon populations in the Northern hemisphere (NRC 2002). 

 comprised of representatives of the Maine ASC, Maine DMR, Maine IFW, NMFS, FWS and the 

Penobscot Indian Nation.
1-20

The NRC committee on Atlantic salmon in Maine reviewed the available scientific 

information on this subject and concluded that, despite many years of non-river specific 

stocking, substantial genetic divergence remains among populations (NRC 2002). The 

committee also concluded that the remnant stocks in the Gulf of Maine DPS are not 

simply hatchery products; rather they display typical metapopulation structure. Wild 

salmon populations in Maine display the degree of genetic divergence characteristic of 

wild salmon populations where stocking has not occurred or has been minimal. 

VI. REASONS FOR LISTING 

Documented adult returns of Maine salmon declined significantly in the 1980s and 

remain at critically low levels of abundance. Among the numerous factors that led to the 

endangered designation of Atlantic salmon populations in the Gulf of Maine DPS were 

the following: 

• Critically low adult returns make the DPS especially vulnerable and susceptible to 

threats 

• Continued low marine survival rates for U.S. stocks of Atlantic salmon 

• Excessive or unregulated water withdrawal 

• Multiple factors that are likely affecting the quality of freshwater habitat in the 

DPS 

• Continuation of the commercial fishery in Greenland9

• The threat of disease to the DPS from Infectious Salmon Anemia (ISA) and 

Salmon Swimbladder Sarcoma (SSS) 

• Increased likelihood of predation because of low numbers of returning adults and 

increases in some predators 

• Existing aquaculture practices, including the use of European Atlantic salmon10, 

pose ecological and genetic risks 

These threats, which were key factors in the listing determination, continue to imperil the 

continued existence of Atlantic salmon. 

As part of the Recovery Planning process, the Services assembled a team of technical 

experts from Maine ASC, NMFS and USFWS to conduct a structured threats analysis. 

This evaluation of the geographic extent and life stage affected by threats, and the 

 

9 The Services determined that at the time of listing the continuation of the internal use fishery in Greenland 

posed a reduced but continuing concern to the DPS. However, the Services concluded that the best available 

data did not show that overutilization was creating a danger of extinction. In August 2002, commercial 

fishing for Atlantic salmon within Greenland territorial waters was provisionally suspended for five years 

(see page 1-56). The internal use fishery is not included in the agreement. 

10 In May 2003, U.S. District Judge Gene Carter issued a ruling prohibiting the use of European salmon by 

Atlantic Salmon of Maine and Stolt Sea Farm Inc. The ruling was part of a lawsuit brought against the 

aquaculture industry under the Clean Water Act for operating without a NPDES permit as required under the 

Act. Heritage Salmon, the other major salmon producer in Maine, had already agreed to not stock any nonNorth American salmon as part of an earlier consent degree. In 2003, the Maine DEP issued a MEPDES 

general permit for Atlantic salmon aquaculture. The permit contains conditions for finfish aquaculture 

operations including the prohibition of the use of non-North American strains of Atlantic salmon.
1-21

severity of these effects, resulted in the following threats being identified as high priority 

for action to reverse the decline of Atlantic salmon populations in the Gulf of Maine 

DPS: 

• Acidified water and associated aluminum toxicity which decrease juvenile 

survival 

• Aquaculture practices, which pose ecological and genetic risks 

• Avian Predation 

• Changing land use patterns (development, agriculture, forestry etc.) 

• Climate Change 

• Depleted Diadromous Fish Communities 

• Incidental capture of adults and parr by recreational fishermen 

• Introduced fish species that compete or prey on Atlantic salmon 

• Low Marine Survival 

• Poaching of adults in DPS rivers 

• Recovery Hatchery Program (potential for artificial selection/domestication) 

• Sedimentation 

• Water extraction 

No single factor can be pinpointed as the cause of the continuing decline of the DPS, 

rather, all the threats that were key factors in the listing determination in addition to other 

recently identified threats, have the potential to adversely affect Atlantic salmon and/or 

their habitat. Continuing research and assessment is needed to understand the impacts 

and interactions of all of the threats faced by the DPS. Not all threats are pervasive 

throughout DPS rivers (e.g., excess nutrients may only be a threat in the Sheepscot River, 

Maine TAC 2002) and not all threats would be expected to adversely affect the DPS if 

populations were stable (i.e., predation and competition would not be expected to be a 

threat if Atlantic salmon populations were not at critically low levels). The discussion of 

threats below includes identification of threats, the impact the threat has on the species 

and/or its habitat, and the source of the threat. 

A. PRESENT OR THREATENED DESTRUCTION, MODIFICATION OR 

CURTAILMENT OF HABITAT OR RANGE 

The following section examines the multiple threats and types of impacts (stressors) that 

may affect Atlantic salmon habitat. As discussed (see below), many historical land-use 

activities have likely had a significant impact on the quantity and quality of Atlantic 

salmon habitat throughout Maine. In addition, numerous current activities (sources) have 

the potential to affect salmon habitat. The following section examines various threats to 

habitat and, where appropriate identifies activities that may affect habitat thereby 

impeding the recovery and conservation of the DPS. In many cases there are multiple 

potential sources that may contribute to impacts that may affect Atlantic salmon habitat. 

For example, numerous activities if not conducted properly in accordance with best 

management practices (BMPs) or in violation of existing regulatory measures may result 

in sedimentation that has the potential to affect salmon habitat, both quantity and quality. 
1-22

Historic Impacts 

Many historical land and water use activities have altered, and in some cases destroyed, 

habitat needed by Atlantic salmon for spawning, growth and migration. The effects are 

evident from the headwater lakes, streams and springs that feed the rivers all the way to 

the estuaries and into the Gulf of Maine. Atlantic salmon habitat in Maine has changed 

dramatically over the last two hundred years due to a number of factors including dams, 

log drives, stream channelization, accelerated sedimentation and road crossings. These 

factors have altered important habitat features including channel widths and depths, poolto-pool spacing, modification of floodplain flowage patterns and functionality and 

substrate composition. 

Historically, timber harvests likely had a significant impact on Atlantic salmon 

populations and habitat. Salmon and their habitat were likely impacted through direct 

and indirect effects of timber removal and transport. Historical practices such as log 

driving, channel clearing and large-scale clear cutting have largely been eliminated. 

Forest management activity, including timber and pulpwood harvesting is still common 

in the DPS river watersheds. The Maine Forest Service (MFS; a bureau within the Maine 

Department of Conservation) estimates that 1-2% of the area of these watersheds are 

harvested annually, slightly below the statewide average of approximately 3.3%. Natural 

regeneration of harvested areas is typically profuse on most sites in Maine and planting is 

relatively uncommon. The Services believe that current forest management activities, 

including timber harvesting, do not represent a significant threat under current 

management measures and harvest practices. Similarly, the NRC (2004) concluded that 

current forestry practices do not appear to be an important problem for Atlantic salmon in 

Maine. However, some forest practices (e.g., inappropriate road construction and 

maintenance, removal of riparian vegetation) have the potential to adversely affect 

salmon habitat quality and availability and therefore needs to be monitored (NRC 2004). 

While many historic land-use practices have largely been eliminated, changes to the 

physical, chemical and biological structure of rivers and streams may remain for many 

decades after the activity has been terminated. Current smolt population and survival 

studies strongly suggest that habitat-related factors in freshwater may significantly impact 

smolt production and survival (NMFS and FWS 1999). Incongruity between the 

increases in early juvenile abundance due to fry stocking and the corresponding parr and 

smolt survival rates suggest that the quality of the freshwater habitat may be negatively 

impacted by multiple factors within the rivers. 

Current Habitat Quality 

Despite the impacts of past human activities, much of the habitat within the DPS can be 

generally characterized as being free-flowing, medium gradient, cool in-water 

temperature and suitable for spawning in gravel substrate areas. While habitat quantity is 

generally known for rivers within the DPS, the quality of existing salmon habitat has not 

been fully assessed. The extent to which historic habitat disturbances/alterations continue 

to impact salmon habitat has not been adequately assessed. Information documenting 
1-23

pre-disturbance conditions is generally lacking making restoration of degraded habitat 

and ecological processes more difficult. Many physical alterations/factors may be 

affecting the quality of habitat in rivers and streams within the DPS including; substrate 

embeddedness, stream channel alteration, diminished habitat complexity and multiple 

water quality issues. 

Substrate Embeddedness and Permeability 

The degree by which fine sediments surround coarse substrates on the surface is often 

referred to as embeddedness (Sylte 2002). Increased embeddedness may block juvenile 

salmon from seeking shelter beneath substrates during cold temperatures. Recent studies 

on the Downeast11 rivers found indications that juvenile densities were inversely related 

to embeddedness levels (Atkinson et al. 2005). The full extent of embeddedness in rivers 

within the DPS is not well documented. Additional research into this issue is warranted 

(see page 4-29). 

Many studies have documented the relationship between substrate permeability and 

salmonid survival during egg incubation and through fry emergence (Wicket 1958, 

Peterson 1978, McKenzie 1985 and Gustafson-Marjaene 1982). Substrate permeability is 

reduced when fine sediments are deposited in stream beds. Reduced permeability can 

lead to lower dissolved oxygen rates and greater concentrations of metabolic wastes 

around incubating eggs. In Maine, several studies have found similar trends for both 

natural and artificially created redds. McKenzie (1985) and Gustafson-Marjanen, (1982) 

found permeability was related to emergence from wild redds in several Downeast rivers. 

These studies, while somewhat limited in sample size, indicate permeability has a 

significant affect on survival to emergence of salmon. The Maine Atlantic Salmon 

Commission has begun studies to estimate permeability in spawning areas on Downeast 

Rivers in order to try to relate salmon survival to permeability (Sheller 2005). 

Stream Channel Alteration 

Many reaches of rivers within the DPS display very large channel width to depth ratios. 

This suggests that in some areas stream channels are overly wide. These shallow 

channels may be a result of disturbance or a function of bedrock geology. Channels with 

large width to depth ratios tend to experience more rapid water temperature fluctuations, 

cooling and heating more quickly than narrow deep channels (Cunjak et al. 1998). 

Changes in channel geometry could also increase embeddedness as wider channels could 

decrease bed mobility (e.g., reduce sediment transport). 

Alterations of the physical instream habitat have been documented on a number of DPS 

rivers. For example, an inventory of historic impacts to habitat, prepared for Project 

SHARE, details a wide variety of instream channel changes on the Machias River 

(Abbott 2004). Documented stream channel alterations on the Machias River include 

 

11 Generally, Downeast Maine encompasses coastal Maine, east of the Penobscot River including Washington 

and Hancock Counties. 
1-24

widening at the outlet of First Machias Lake, diversions below Holmes Falls and areas of 

the river bottom covered with slabs of wood. 

Diminished Habitat Complexity 

Large instream structures such as boulders, large woody debris (LWD) and organic 

debris can influence sediment sorting and storage, spacing of pool-riffle sequences and 

overall channel geometry. All of these structures are important for the formation and 

maintenance of channel morphology including gradient, pool depths and sequencing of 

features. Structural elements affect channel processes at all scales from distribution of 

bed materials to valley formation. At a local level, structural controls can create scour 

conditions that form and maintain pools. At a reach level, LWD can influence pool-riffle 

sequencing, bank erosion and bar formation. At a valley level, LWD can influence 

interaction between rivers and their floodplains. 

Large instream structure such as boulders, LWD and root wads provide habitat required 

by Atlantic salmon for survival. In winter, salmon require habitat that provides adequate 

shelter from adverse physical conditions, particularly high flows as well as protection 

from predaceous mammals and birds (Cunjak et al. 1998). Availability of winter habitat 

may influence salmon survival and has been identified as a potential limiting factor for 

Maine salmon populations (NMFS 2003, unpublished report). 

Large Woody Debris (LWD) 

Habitat surveys conducted through the 1990’s evaluated the presence of large woody 

debris (LWD) in streams and rivers in Maine including DPS rivers (USFWS 2004). The 

data indicate that, in channels less than 10 meters wide, 65% of pool, run and riffle 

habitat features on the Downeast rivers lack LWD. 

A 10 meter channel width is used as a threshold as larger channels would be less likely to 

retain LWD due to higher flows and the absence of trees with channel spanning heights. 

The significance of the lack of LWD is not known and historic LWD volumes are 

unavailable for the Downeast rivers. A comprehensive study of LWD, funded by the 

National Fish and Wildlife Foundation, is currently underway. 

Large woody debris (LWD) may be important for Atlantic salmon during several lifehistory stages. Nislow et al. (1999) found that survival of salmon fry in small streams in 

Vermont was strongly correlated with the availability of lateral, low-velocity 

microhabitats12. The addition of LWD increased the availability of these habitats 

(Nislow et al. 1999). LWD may be even more important for older juvenile life-stages. 

Salmon parr appear to use instream cover extensively, including LWD, particularly 

during winter (Cunjak et al. 1998). This issue may be particularly relevant to Atlantic 

salmon in Maine. Data collected from index stream sites indicate that there is a high 

mortality rate for large (pre-smolt) salmon parr during the winter prior to their 

 

12 Microhabitats habitats away from the main channel (e.g., near banks, lateral channels) that 

maintain velocities < 0.18 m/sec during the early fry stage. 
1-25

outmigration as smolts (John Kocik, NMFS, unpublished data). The low over-winter 

survival rate for large (pre-smolt) salmon parr is having a significant affect on overall 

smolt production from these systems. This may constitute a bottleneck to population 

recruitment. If pre-smolt winter survival is linked to the availability of appropriate 

habitat, increasing the amount of LWD cover may increase overwinter survival and smolt 

production. 

Boulders 

While it is clear that juvenile Atlantic salmon use boulders and loose cobble as shelter 

during winter, few studies have examined habitat preferences for other types of cover. 

Whalen et al. (1999) found that at night, rock and root wad complexes had higher 

concentrations of Atlantic salmon parr relative to other locations in the stream, especially 

during the ice and post-ice periods. These researchers also found parr sheltering in quiet 

water formed by boulders, woody debris and stream edges (Whalen et al. 1999). 

As noted, most of the rivers within the DPS were historically used for log drives. 

Streams were reportedly channelized and, meanders removed in order to transport logs to 

sawmills. Similarly large instream structures such as boulders were apparently removed 

where they might obstruct or hinder the downstream transport of timber. For example, in 

the Machias River, known habitat alterations include the removal of boulders on the 

mainstem below Third Machias Lake and above the confluence with the West Branch. In 

the Narraguagus and Machias rivers, historic alterations also included removal of midchannel boulders and diking along lower reaches of the Machias River. 

As noted above, large instream structure such as LWD and boulders are important for the 

formation and maintenance of stream channel morphology including gradient, pool 

depths and sequencing of features. These features provide the habitat complexity that is 

required by Atlantic salmon. It is known that juvenile Atlantic salmon require a diversity 

of habitats including unembedded substrate and instream structures such as boulders, root 

wads and woody debris. For stream restoration efforts to be successful it is necessary to 

consider the habitat requirements for all lifestages as well as seasonal and temporal 

needs. 

1. Water Use 

Water withdrawals for agricultural irrigation was identified as a key threat to Atlantic 

salmon (65 FR 69459; NMFS and FWS 1999; MASCP 1997). The Services have 

concluded that water extraction remains a high level threat to the conservation of the 

DPS. Water extraction has the potential to expose or reduce salmon habitat. It is the 

most immediate habitat threat posed in some DPS rivers (65 FR 69475). Adequate water 

quantity and quality are critical to all life stages of Atlantic salmon, including spawning, 

egg survival, fry emergence, juvenile survival and smolt emigration. Water quantity and 

quality can be affected by the withdrawal of water for irrigation and other purposes. 
1-26

In the Pleasant, Narraguagus and Machias river watersheds, commercial wild blueberry 

growers irrigate with water withdrawn from streams supporting wild Atlantic salmon. 

These water withdrawals pose a threat to Atlantic salmon and their habitat (65 FR 

69477). This threat, if not adequately addressed, is likely to grow based on industry 

projections of expansion of berry production and processing. Approximately 6,000 acres 

of blueberries are irrigated annually. Water is needed for irrigation, frost protection and 

berry processing (NMFS and FWS 1999). 

The potential impacts of water withdrawals from DPS rivers and streams include limiting 

summer habitat for parr, low winter flow effects on redds and egg incubation as well as 

adult immigration (requires fall increases in flows) and smolt emigration. Timing of 

emigration is cued by day length, temperature and discharge. Speed of out movement 

may be related to discharge. If reservoirs are to be used, the effects of capturing spring 

flows on the emigration of smolts needs to be evaluated. Changes in streamflow due to 

withdrawal can change basic sediment transport functions and result in stream channel 

changes. 

The State of Maine and its partners have completed a water use management plan 

(WUMP) for the Narraguagus and Pleasant rivers and for Mopang Stream (MSPO 

2001)13. The WUMP concludes that withdrawal of surface water during low flows poses 

the greatest risk to Atlantic salmon habitat. The WUMP also concludes that “...irrigation 

of existing acreage with a well replacing the major direct withdrawal seems to affect 

habitat only at the lowest flows.” 

As a result of the WUMP, there has been a net reduction in the number of large growers 

withdrawing water directly from streams covered under the WUMP (Nate Pennell, 

Washington County Soil and Water Conservation Service, personal communication). In 

recent years, wild blueberry growers have begun to move away from withdrawing water 

directly from rivers in these watersheds, relying instead on groundwater withdrawals to 

meet their needs. Little information is available to assess the potential impacts of these 

withdrawals on water quality in DPS rivers. Water withdrawal from groundwater 

aquifers may affect cold groundwater discharge rates from springs. During periods of 

elevated water temperatures typical of summer conditions, salmon rely on cold water 

refugia to survive. Numerous smaller wild blueberry growers continue to rely on direct 

water withdrawals from rivers to meet their irrigation needs. 

The Maine Land Use Regulation Commission (LURC; a bureau of the Maine Department 

of Conservation) regulates water withdrawals from surface waters and groundwater 

within unorganized territories in the State of Maine. The LURC must approve requests 

for withdrawals for irrigation and can curtail withdrawals if water levels fall below what 

is considered necessary for the well being of fish and wildlife or other natural resources. 

In 1999, LURC limited the amount of water that could be drawn from the Pleasant, 

Narraguagus and Machias rivers based on instream flow incremental methodology 

 

13 The WUMP identifies a hierarchical approach for using water intended to ensure adequate stream 

flows that are protective of Atlantic salmon while addressing the irrigation needs of the blueberry 

industry within the watersheds for which the plan was developed.
1-27

(IFIM) studies of Mopang Stream (a major tributary of the Machias River), Narraguagus 

and Pleasant rivers. The LURC has worked with the Services during review of water 

withdrawal permit applications to ensure that permits are sufficiently protective of 

salmon. 

In addition, the DEP is in the process of developing in-stream flow standards that will 

apply to all state waters. These standards are specified in 38 MRSA Section 470E. 

These standards will recognize existing standards developed for Downeast rivers under 

the WUMP process. The DEP recognizes that there may be differences between IFIM 

and low flow analyses to document suitable flow limits and intends to carefully evaluate 

available information to determine the appropriate stream flow statistic that will protect 

salmon habitat. 

The Maine DEP has the authority to regulate water withdrawals from organized 

municipalities within the State. Water withdrawals in organized municipalities are not 

currently regulated. This multi-jurisdictional arrangement results in situations where 

water withdrawals from a water body whose shores are located in both organized and 

unorganized towns can be regulated on one bank and not on the opposite bank. 

In addition to the agricultural demand for water, population growth and development in 

Maine has accelerated in recent years, especially in the mid-coast region. This trend is 

projected to continue (Gulf of Maine, Council on the Maine Environmental 2001) and 

will undoubtedly result in increased municipal water use demands. This change in land 

use patterns and resource demands, including water use, will need to be managed in order 

to protect salmon and their habitat. 

In addition to direct withdrawal for irrigation and other purposes, impoundments used to 

regulate instream flow affect the hydrologic conditions of DPS rivers. Several DPS 

rivers have small dams on lakes and ponds within the drainage used to manipulate river 

flows. For example, the ASC manages low flows in the Dennys River using 

Meddybemps Dam and there are dams on Cathance Stream that may influence flows. 

The IFW manages Bog Brook Flowage for waterfowl production, influencing the flow of 

a tributary to the Narraguagus River. Gardner Lake Dam has partial control of flow in 

Chase Mill Stream, a tributary to the East Machias River. Pleasant River Lake, source of 

the Pleasant River, has a dammed outlet. The potential for regulating low flows by 

impoundments on ponds in the Sheepscot River drainage has not been evaluated. The 

potential to use stream flow augmentation to meet Atlantic salmon flow needs and 

increase juvenile production should be investigated (see page 4-38). 

The effect that these impoundments have on the hydrologic conditions of individual 

watersheds and Atlantic salmon habitat has not been assessed. One recent event does 

underscore the potential for negative impacts on Atlantic salmon. In spring 2002 vandals 

blocked the fishway at the Meddybemps Lake Dam on the Dennys River, thereby 

reducing flow in the river, eliminating fish passage into the lake (probably not a major 

problem for salmon directly, but an ecosystem issue), and increasing the risk of 

catastrophic dam failure. The water in the lake was high, and blocking the fishway 
1-28

reduced the amount of water flowing out of the lake. If a major storm had occurred, it is 

conceivable that the dam could have been overflowed. The result of this occurrence was 

that some salmon habitat in the Meddybemps area had much lower flows than intended. 

2. Water Quality 

There are a number of water quality issues that have the potential to adversely affect the 

recovery of the DPS. Non-point source (NPS) pollution problems occur on all DPS 

rivers. Sources of NPS pollution include agriculture, airborne pollutants (e.g., acid rain), 

livestock grazing, septic systems, forestry timber harvest activities not conducted in 

accordance with BMPs, public and private roads, overboard discharges (OBD, a type of 

waste water treatment system), stream channel alteration and urban runoff. The most 

common NPS pollutants are sediment and nutrients. Other NPS pollutants include 

agricultural pesticides, heavy metals, pathogens (bacteria and viruses) and toxic 

chemicals. The prevailing land use patterns and disturbances within DPS river 

watersheds result in varying amounts of NPS pollution within DPS rivers. While NPS 

pollution issues are noticeable in all rivers within the DPS, the cumulative effect on water 

quality is most evident in the Sheepscot River watershed (Maine TAC 2002). The 

Sheepscot River has elevated levels of nutrients, bacteria, organic loading, temperature 

and also has depressed dissolved oxygen (Maine TAC 2002). Local watershed councils, 

with assistance from state and federal agencies, have identified and remediated numerous 

non-point source pollution sites in DPS river watersheds. 

There are few point sources of pollution on the eight salmon rivers. Maine DEP issues 

permits for licensed discharges. These permits are conditioned to maintain the existing 

water quality classification. The Maine DEP has issued discharge permits to blueberry 

processors on the Narraguagus River, a municipal waste treatment facility in Machias, the 

Maine Department of Inland Fisheries and Wildlife (IFW) Palermo Rearing Station 

(Sheepscot River) and commercial salmon aquaculture hatcheries operated by Heritage 

Salmon (Connors Brothers) located on the Pleasant River in Deblois (CLOSED) and on 

Chase Mills Stream (tributary to East Machias River). 

In 2001, the Signatories to the Maine Atlantic Salmon Cooperative Agreement (ASC, 

NMFS, FWS) asked the Maine TAC to assess whether water quality issues threaten the 

recovery of the DPS. The Maine TAC (2002) concluded that sufficient evidence exists 

that several water quality issues are affecting DPS Atlantic salmon populations in Maine. 

i. Acidified water and aluminum 

The Maine TAC Water Quality Committee concluded that acidification and endocrine 

disruption are the most significant water quality threats to the DPS. The Services and the 

NRC (2004) have concluded that water quality problems related to acidification pose a 

high level threat to the survival and recovery of the DPS. 
1-29

Acidified Water and Acid Rain 

The physiological effects of chronically low pH on freshwater life stages of Atlantic salmon 

are well documented. Exposure to pH less than 4.5 causes rapid plasma ion loss and death, 

apparently from circulatory collapse. Eggs are susceptible to delayed hatching when 

exposed to low pH water since spring is a normal time for Maine salmon rivers to 

experience episodes of low pH. Delayed hatch could put alevin behind with regard to 

timing of emergence, food availability, and seasonal river temperatures and flow. Alevins 

(sac-fry) are the most susceptible life stage. This transitional life stage experiences high 

mortality even in healthy populations with high quality habitat. Chronic exposure to 

depressed pH results in reduced feeding and growth of juvenile Atlantic salmon (Haya et al. 

1985). Chronically low pH also results in altered behavior and gill damage (Jagoe and 

Haines 1990). Perhaps the most severe effect of low pH is the disruption of osmoregulatory 

ability, particularly after smolts enter seawater (Staurnes et al. 1993). Like alevins, the 

smolt stage is a life cycle bottleneck for stocks of Atlantic salmon, even healthy stocks 

experience high mortality during the transition to a marine environment. Low pH further 

stresses smolting salmon during a critical physiological transition period. 

Atlantic salmon populations cannot persist in chronically low pH environments. The 

effects are most severe in river systems that have a low buffering capacity, such as the 

granitic bedrock watersheds of Nova Scotia. By 1980, the mean annual pH in nine Nova 

Scotia rivers that historically contained salmon populations had dropped below 4.7 and as a 

result, the salmon were extirpated (Watt 1981). Large portions of the DPS river watersheds 

share this poor buffering capacity and chronically low pH has been documented in streams 

such as the West Branch Narraguagus River (Beland et al. 1994). 

In addition to chronic low pH levels, recent research has shown that pulses of low pH can 

impact some life stages of Atlantic salmon. Acidity in DPS rivers varies in predictable 

geographic and seasonal patterns. Seasonally, the most significant pH depression occurs 

during spring runoff when acidity stored in the snow pack is released into rivers and the 

greater volume of water dilutes the river’s acid neutralizing capacity. This low pH pulse 

occurs as smolts are beginning to migrate and are altering their physiology in preparation 

for life in marine habitats and when alevins are preparing to emerge from the gravel as fry. 

Pulses of low pH can also occur in response to stormwater runoff (Staurnes et al. 1993), 

such as during fall rains that typically increase the flows in the DPS rivers. 

Geographically, the DPS rivers that are located east of the Penobscot River have a lower pH 

than those located west of the Penobscot (Haines 1981; Haines et al. 1990). This is due to 

the granitic bedrock underlying much of eastern Maine and the low acid neutralizing 

capacity of the overlying soils. Within a given river system, pH is typically lower in 

headwater streams and at higher elevations (Schofield 1981). This is evident in the 

Narraguagus River, where pH measurements from 1990 through 1993 in tributaries such as 

Sinclair Brook were often below 5.0, while the main stem Narraguagus consistently 

remained above 5.0 (Beland et al. 1994). West Kerwin Brook, a tributary of the Machias 

River, also has lower pH relative to the main stem (Haines 1981).
1-30

Regional trends indicate a move toward Northeast waters becoming more dilute (i.e., 

fewer dissolved solids) with very little bicarbonate acid neutralizing capacity. However, 

there is currently no supporting data for the DPS rivers at this time (Steve Kahl, George 

Mitchell Center, personal communication). Bicarbonate buffering will typically maintain 

pH 6-7 in receiving waters, while the depletion of bicarbonates can lead to pH levels 

below 5.0 in aquatic systems (Schofield 1981; Haines et al. 1990; Stoddard et al. 1999; 

Norton et al. 1999). Previously, it was believed that over time acid rain depleted the 

bicarbonate-based acid-neutralizing capacity of forest soils, shifting the buffering system 

to other chemical reactions (Schofield 1981; Haines et al. 1990). More recent evidence 

suggests that soil capacity to absorb sulfate and nitrate is the most important factor 

controlling acidity of surface waters, along with cation exchange and mineral weathering 

(Driscoll et al. 2001; Galloway 2001; Terry Haines, USGS, personal communication). 

Exposure to acid rain has been responsible for the decline and extirpation of Atlantic 

salmon populations from certain Norwegian and Canadian rivers (Watt 1981; Watt et al. 

1983; Watt et al. 2000; Sandøy and Langåker 2001). In Nova Scotia, chronically 

depressed pH linked to anthropogenic sources, specifically airborne sulfates and nitrates 

that originate largely from fossil fuel combustion, is the likely cause of salmon 

mortalities (Terry Haines, USGS, personal communication). In Norway, however, the 

mortalities are primarily caused by aluminum and occur at much higher pH levels, as 

high as pH 5.8 to 6.2 as compared to the pH levels in Nova Scotia ranging from pH 4.2 to 

4.7 (Terry Haines, USGS, personal communication). 

Peat bogs are a common natural landscape feature in much of Maine, especially in the 

Downeast region. Waters draining peat bogs typically have lower pH due to naturally 

occurring organic acids produced in low oxygen environments associated with peat bogs. 

Runoff from peat deposits (bogs) also depresses pH in DPS rivers. For example, in the 

Pleasant River pH is lower downstream of the Great Heath relative to upstream 

monitoring locations (Beland et al. 1994). This also occurs in the West Branch 

Narraguagus River where pH was found to be lower downstream of Denbo Heath than 

upstream of this peat bog (Beland et al. 1994). 

Historically, runoff from peat mining operations may have exacerbated depressed pH in 

rivers within the DPS (NMFS and FWS 1999). The only peat mining operation in the 

DPS river watersheds is the Downeast Peat plant in Deblois, which is in the West Branch 

of the Narraguagus River. Recent improvements in state and federal licensing programs 

have greatly improved the water quality from drainage ditches in peat mining operations. 

Ownership of the peat mining facility changed control in the early 1990s. With the 

assistance of the DEP, the facility was brought into compliance with stormwater and 

other water discharge standards. Analysis of upstream and downstream sites on the West 

Branch and on McCoy Brook (a tributary to the main stem) have shown no difference in 

water quality since monitoring began in 1994 (Mark Whiting, Maine DEP, personal 

communication). 

Current integrated crop management (ICM) programs for blueberries recommend that 

soil pH be maintained at 4.5 for weed control (the desired range is pH 4.3 to 4.8). If the 
1-31

soil pH is not already low, Maine Cooperative Extension recommends the addition of 

sulfur. If the soil is too acidic, growers are advised to use lime. Either of these practices 

can affect surface water pH. Some tributaries (e.g., Big Springy Brook in the Machias 

River drainage) have a springtime pH that is more acidic than rainfall (the mean pH of 

rainfall over the last two years in Maine is 4.8). This suggests that soil acidity might also 

have a role in governing pH in streams (Mark Whiting, Maine DEP, personal 

communication). While the addition of sulfur to blueberry fields to lower soil pH is a 

standard Cooperative Extension recommendation, reportedly neither Cherryfield Foods 

or Jasper Wyman and Sons, Inc., the two largest wild blueberry growers in Downeast 

Maine, engage in this practice (Fred Olday, Jasper Wyman & Son, personal 

communication). It is not known whether, or to what extent, small growers apply this 

practice. 

Acidified Water and Aluminum 

Laboratory and field studies demonstrate that low pH leaches aluminum and potentially 

increases its toxicity to fish. Aluminum’s solubility increases exponentially as pH 

declines below 7.0 (Haines 2001). The aqueous chemistry of aluminum is complex, the 

most toxic species are collectively termed labile forms14. Dissolved organic carbon 

(DOC) readily binds with labile aluminum (as well as other metals) and these organic 

carbon/aluminum complexes are not toxic. 

Osmoregulatory failure seems to be the most significant impact of acidified water and 

aluminum. This toxic effect is significant for developing alevins and migrating smolts, 

life stages that are undergoing significant physiological transitions and already 

experience high mortality. Conditions during this critical period of Atlantic salmon’s life 

cycle directly affects adult return rates to the DPS rivers. 

The toxic effects of aluminum have been well studied in Norwegian salmon rivers. 

Salmon populations in twenty-four rivers were not affected by labile aluminum less than 

8 ug/l, pH greater than 6.0 and at least 50 ueq/l of acid neutralizing capacity (Staurnes et 

al. 1995). Varying degrees of impact were observed in twenty-six Norwegian streams 

with intermediate pH (5.2 to 6.2), greater amounts of labile aluminum (10 to 60 ug/l), and 

acid neutralizing capacity between 20 and 40 ueq/l (Staurnes et al. 1995). Salmon were 

extirpated from twenty-two Norwegian rivers with pH less than 5.7, labile aluminum 

levels in excess of 20 ug/l and acid neutralizing capacity less than 10 ueq/l (Staurnes et 

al. 1995). Laboratory experiments using Norwegian salmon stocks showed that smolts 

experienced osmoregulatory failure and 60 to 75% mortality when exposed to freshwater 

conditions at pH 5 with 50ug labile aluminum and then subjected to a 24-hour seawater 

challenge (Staurnes et al. 1993; Rosseland et al. 2001; Kroglund et al. 2001). 

In contrast to the Norwegian salmon studies, North American studies have shown smolts 

to be more tolerant of low pH and elevated aluminum. Pauwels (1990) recorded a 

significant reduction of plasma chloride concentration but no mortality of smolts exposed 

 

14 These include AlOH++, AlOH2+, AlF++, AlF 2+ and Al+++ (hereafter referred to as labile aluminum).
1-32

for eleven days to pH 4.6-5.5 with 20-84ug labile aluminum. About 4% mortality 

occurred on the thirteenth day with no additional mortality occurring until the twenty-first 

day. However, these fish were never challenged with seawater. Magee et al. (2001) 

documented altered behavior of migrating salmon smolts after exposure to constant low 

pH and elevated aluminum. This may affect smolt survival. Magee et al. (2001) also 

documented, during the same study that the migratory behavior of salmon smolts in the 

Narraguagus River was similar to that of hatchery smolts exposed to acidified water in 

the study. Magee et al. (2001) found no mortality occurred after a fourteen-day exposure 

to stream water with pH declining from 6.0 to 5.1 and a short (<24 hr) acidic pulse to pH 

4.5. In a separate study, there was substantial mortality when smolts, exposed to both a 

constant low pH and pulsed exposure, were then placed in seawater (Magee 1999; Magee 

et al. 2003). Saunders et al. (1983) reported ionoregulatory disruption within four weeks 

but only 24% mortality after ten weeks at pH 4.2-4.7. Farmer et al. (1989) reported that 

pH 5.0 elicited no significant reduction in plasma osmolality, hematocrit, chloride 

concentration, branchial Na+/K+ ATPase activity, or mortality during a 112-day period 

in spring. In contrast, fry growth was reduced and mortality increased when pH was 

decreased to 5.5 with aluminum causing little increase in mortality above acid addition 

alone (Haines et al. 1990). 

The mean pH of precipitation falling in Maine is about 4.8 and large amounts of 

aluminum are mobilized from Maine soils to the aquatic environments of DPS rivers. 

The synergistic effect of aluminum toxicity exacerbates the stress from acidity (Kroglund 

et al. 2001). DPS river watersheds located east of Penobscot Bay are dilute with very 

little acid-neutralizing capacity and low pH, which mobilizes toxic aluminum. The pH 

depression that accompanies spring runoff may exacerbate this toxic effect. 

Increased gill sodium/potassium ATPase activity is associated with smoltification and 

recent research has demonstrated that smolts in DPS rivers have unusually low levels of 

sodium/potassium ATPase activity relative to Maine hatchery smolts and smolts from 

several New Brunswick and Newfoundland rivers (McCormick et al. 2002). This is an 

area that requires additional study (see page 4-25), but it may indicate that conditions in 

the DPS rivers produce smolts that are poorly equipped for the marine environment. 

These impacts are associated with the extirpation of salmon from many Norwegian 

rivers. The relatively high levels of DOC in some of the DPS rivers may mitigate the 

toxic effects of labile aluminum and acidity. More study is needed on the synergistic 

effect of these water chemistry parameters, particularly the seasonal variation and 

influence of precipitation. 

ii. Pesticides, other contaminants and endocrine disruption 

Pesticides 

Pesticides include insecticides, fungicides and herbicides. Of these, insecticides are 

generally the most toxic to Atlantic salmon, followed by fungicides and herbicides 

(Maine TAC 2002). Improper applications of pesticides may introduce pesticides into 

DPS rivers and tributary streams. Potential sources of pesticide to Maine rivers and 
1-33

surface waters include low bush blueberry applications, forestry, roadside and powerline 

applications, municipal sewage, industrial and waste discharges, and possibly 

atmospheric deposition (Maine TAC 2002). 

The effects of pesticide exposure to Atlantic salmon have not been fully investigated. 

Pesticide effects on salmonids may range from acute (i.e., lethal), to chronic (i.e., 

sublethal). Effects on aquatic life depend primarily on the concentration and duration of 

exposure. Specific effects of pesticides on Atlantic salmon are influenced by factors such 

as concentration, toxicity, water quality (e.g., pH, temperature, conductivity, alkalinity), 

and stream flow velocity. Salmonid LC50's (lethal concentration to 50% of the 

individuals in a given time) are known for most of the pesticides used in Maine 

agriculture (Maine TAC 2002). The effects of mixtures of pesticides upon fish have not 

been adequately studied (see page 4-25). All available data show that pesticides occur in 

the DPS rivers at concentrations that are several orders of magnitude less than published 

thresholds for acute toxicity (Maine TAC 2002). 

The effects of chronic or sublethal pesticide exposure to sensitive life stages of Atlantic 

salmon such as fry emergence and smoltification are not well understood. Sublethal 

concentrations of pesticides may impair behavior or physiological functions in fish (Trial 

1986, Scholz et al. 2000, Waring and Moore 2004). Moore and Waring (1996, 2001) 

documented the effect of several pesticides on Atlantic salmon olfactory capabilities. 

The Maine Board of Pesticides Control (Maine BPC) has conducted most of the recent 

environmental monitoring of pesticides used on blueberry fields. In 1987, the Maine 

BPC conducted a drift study during an azinphos-methyl (brand or trade name: Guthion) 

aerial application. During the sprays, approximately 3% of the spray was estimated to 

have been deposited off-target (Jennings 1987). Most of the residues were close to the 

spray area and concentrations decreased with distance from the blueberry fields. Very 

small amounts of drift were found as far as 400 feet from the spray site (the farthest point 

were monitoring cards were located). 

From 1991 to 1994, the Maine ASC and Maine BPC sampled and analyzed surface water 

from the Narraguagus, Pleasant, and Machias river drainages for pesticide residues. 

Samples were screened for all pesticides used in blueberry fields. Only hexazinone 

(Velpar) was routinely identified in the Narraguagus and Pleasant rivers, where it was 

found throughout the year (Magee 2001). No other pesticides in the analytical suite were 

detected. DDT and DDE were found in some samples in the Narraguagus River ranging 

from 12-314 ppb and 12-39 ppb, respectively (Magee 2001). In recent years, other 

pesticides have been detected in surface water from Washington County rivers including 

terbacil (Sinbar; Chizmas 2000), phosmet (Imidan; Chizmas 2001), triforine (Beland et 

al. 1995), azinphos-methyl (Guthion; Magee 2001), and benomyl (Benlate; Magee 2001). 

In 1997, the Maine BPC began a survey of seven of the then official salmon rivers. Of 33 

different pesticides tested in surface water samples, only hexazinone was detected in the 

rivers. Hexazinone was found in 19 of the 64 samples taken, and was only found in the 

Narraguagus, Pleasant, and Machias Rivers. Concentrations in these three rivers ranged 
1-34

from 0.1-1.7 ppb (Chizmas 1999). In 1999, another study of drift during aerial pesticide 

applications was conducted by the Maine BPC. Hexazinone (max. concentration 3.8 

ppb) was found in 11 of 13 samples taken from the Narraguagus and Pleasant Rivers. 

Terbacil (Sinbar) was also detected at 0.148 ppb. 

In the 2000 field season, the Maine BPC continued their investigation of pesticide drift. 

Both hexazinone and phosmet were found in off-target areas on drift cards. Water 

samples were also analyzed in the study. Hexazinone was found in most water samples 

taken near blueberry barrens. Phosmet was found in three agricultural ponds that are 

tributaries to the Narraguagus and Pleasant River. The ponds are located immediately 

adjacent to blueberry fields and are used seasonally as sources of irrigation water. The 

ponds overflow in the spring, but not in the summer. Phosmet concentrations in pond 

surface water ranged from 0.08-0.52 ppb (Chizmas 2001). 

In 2001, pesticide drift during spray operations was examined by the Maine BPC at three 

locations on the Narraguagus River and four locations on the Pleasant River (Chizmas 

2002). In addition to drift cards, an automated water sampler (Iscos ®) was used to 

collect a time-series of surface water samples during spray events. Drift during 

propiconazole and phosmet applications was detected on filter cards, but not in water 

samples on the Narraguagus River. In the Pleasant River, chlorothalonil (0.103 - 0.79 

ppb) and phosmet (0.155 - 3.76 ppb) were detected in water samples and drift cards. 

Hexazinone was detected in water samples at two Narraguagus River locations (0.084 - 

1.22 ppb) and at three Pleasant River locations (0.41 - 2.45 ppb). 

The Maine BPC continued its drift studies associated with spray applications in 2003 and 

placed an automated water sampler and drift cards at eight locations on the Narrraguagus 

(n=2) and Pleasant Rivers (n=6). Phosmet was found on drift cards at one location on the 

Narraguagus River, and in water (0.28 - 1.95 ppb) and on drift cards from Montegail 

Pond, a waterbody that discharges to the Pleasant River. Pesticide drift was detected 

1,500 feet from one of the spray sites (Jackson 2003). 

As noted, hexazinone has been detected at numerous sites in trace amounts in the 

Narraguagus, Pleasant and Machias rivers (Beland et al. 1995; Chizmas 1999; Chizmas 

2000, Chizmas 2002, Maine TAC 2002). The pervasive presence of hexazinone in 

surface water sampled at low flow periods suggests that the material is entering the river 

through groundwater flow rather than storm runoff (Beland et al. 1993). Although 

hexazinone has been detected in surface water samples in the range of 4-9 ppb, 

concentrations are typically less than 1 ppb. Some groundwater (e.g., wells) samples 

have hexazinone levels approaching 30 ppb. Groundwater does not appear to be an 

important pathway for other pesticides that have been reported in DPS rivers (Maine 

TAC 2002). 

Monitoring the presence of pesticides in aquatic habitats is complicated by the fact that 

several compounds (e.g., organophosphate pesticides), are very short-lived in the 

environment or are not very water-soluble (hexazinone is an exception) and are thus 

difficult to detect in water or fish tissue. Pesticides can adsorb to soils and be transported 
1-35

to watercourses during storm events. Sediment analyses are one possible means to detect 

pesticide residues. However, recent analyses of sediments collected above and below 

areas of blueberry cultivation in the Narraguagus River did not detect any pesticide 

residues (Spaulding 2005). Pesticide concentrations in sediments of the other DPS rivers 

have not been determined. 

Wild Blueberry Production and Pesticide Use 

Wild blueberry production is the primary agricultural land use in the Downeast DPS 

watersheds. Approximately 60,000 acres of blueberry land is currently in production 

(only half of which is actually harvested any given year). Approximately 60-70% of this 

acreage is located in Washington County (Maine TAC 2002). As noted above, there are 

a number of pesticides used by wild blueberry growers in Maine (brand or trade names in 

parentheses). Insecticides include azinophos-methyl (Guthion, Sniper 2E), carbaryl 

(Sevin), diazinon, malathion (Cythion), methoxychlor (Marlate) phosmet (Imidan), and 

Bacillus thuringiensis (BT)(Javeline, Biobit - BT is a bacterium). Herbicides include 

fluazifo-p butyl (Fusilade), glyphosate (Roundup), hexazinone (Velpar), sethoxydim 

(Poast), terbacil (Sinbar) and 2,4-D ester. Fungicides include propiconazole (Orbit), 

chlorothalonil (Bravo), benomyl (Benlate), captan and captec (Captan) and triflorine 

(Funginex) (MASCP 1997). 

Most of these chemicals have not been routinely detected in historical water samples 

from the DPS rivers with the exception of hexazinone. DDT (banned since 1972 but its 

metabolites persist in the environment), phosmet, guthion, propiconazole and 

chlorothalonil have been detected intermittently at low concentrations. Increased joint 

monitoring by Maine DEP, Maine BPC, and other agencies is needed to accurately detect 

levels of pesticides in DPS river watersheds and to determine transport mechanisms, fate 

and toxicity (see page 4-26). 

As noted, hexazinone has been detected at numerous sites in trace amounts in the 

Narraguagus, Pleasant and Machias rivers (Beland et al. 1995; Chizmas 1999; Chizmas 

2000, Chizmas 2002, Maine TAC 2002). Pesticide applications occur from May through 

June, but hexazinone has been detected in water samples year-round. 

Forestry and Pesticide Use 

Forest is the dominant cover type and commercial forestry is a major land use bordering 

most of the Downeast salmon rivers. Along the Pleasant River and Narraguagus River, 

forested areas are interspersed with tracts of blueberry barrens. Historically, pesticides 

have been used in commercial forestry to control insect outbreaks such as the spruce 

budworm. Currently, biological agents (e.g., Bacillus thuringiensis also referred to as Bt) 

are used to control outbreaks of defoliating insects. These agents are specific to target 

organisms (e.g., moth larvae). Herbicides are occasionally used to control post-harvest 

hardwood growth, promote softwood regeneration, and to prepare sites for planting15. 

 

15 Triclopyr (Garlon) and glyphosate (Accord) may be sprayed. Generally, sprays are used on one 

site for no more than a year or two, no more than one spray a year. Since the harvest frequency is 
1-36

During herbicide applications, there is the potential for these chemical compounds to 

enter streams through runoff and drift. Best management practices (BMPs) are 

recommended to minimize herbicide use (MFS 2004). Statewide, use of forestry 

herbicides has been declining in recent years as land ownership patterns change and 

different methods of forest management are applied. While no broad-scale insect control 

efforts are currently occurring in the managed forests within the DPS watersheds, insect 

and disease outbreaks in the future could trigger a response with a pesticide component. 

Road Maintenance and Pesticide Use 

The maintenance of road rights-of-way in Maine includes herbicide spraying for brush 

control. In the past few years, sprays have not been used in Washington and Hancock 

Counties (Maine Department of Transportation, Division 2) due to concerns about the 

health of Atlantic salmon (Maine TAC 2002). 

Outside of Maine DOT Division 2, a 50/50 mix of triclopyr (Garlon) and tricamba 

(Vanquish) are used in most roadside spray applications. No-spray buffers of 100 feet 

are maintained along the Sheepscot and Ducktrap Rivers and Cove Brook, and within 50 

feet of other surface waters. Herbicide sprays are not applied during spring, on standing 

water or bedrock. All road maintenance crews receive training in Maine DOT’s spray 

protocols. Due to the relatively low toxicity of herbicides and the low application rate, 

roadside maintenance is not thought to represent a threat to the health of Atlantic salmon 

(Maine TAC 2002). 

Existing Regulatory Measures and Best Management Practices 

The application, storage and disposal of pesticides in the state are regulated by the Maine 

BPC. The Maine BPC has the authority to designate areas where pesticide use is 

restricted to protect health, welfare and environment. Through the Maine BPC, farmers 

are encouraged to adopt integrated crop management practices including integrated pest 

management to minimize pesticide usage. These integrated management practices have 

reduced the rates and frequency of agricultural chemical applications. The use of 

hexazinone, for example, in recent years is about one third of historic application rates 

(Maine TAC 2002). In addition, Maine has developed a State Management Plan for 

Pesticides and Groundwater, a strategy for Managing Nonpoint Source Pollution from 

Agricultural Sources, Best Management System Guidelines and a Coast Nonpoint Source 

Control Program. These water quality programs address potential pollution associated 

with pesticides, sediments, nutrients, manure, grazing management and wastewater from 

confined animal facilities. 

The Maine Cooperative Extension Service (2002, 2004) has developed fact sheets 

outlining best management practices for wild blueberry production and to minimize offtarget deposition of pesticide applications. Fact Sheet 251 describes best management 

practices including proper monitoring, identification of pests, and choice of the least toxic 

 about 35-40 years for pulpwood and 80 years for saw logs, the spray frequency is no more than 

twice in that period. 
1-37

effective material to control when warranted. Fact Sheet 303 describes methods for 

reducing pesticide drift during ground and aerial applications and avoidance of sensitive 

areas including fish-bearing waters. Integrated pest management (IPM) and integrated 

crop management (ICM) principles are taught to growers and scouts by the Cooperative 

Extension Service at three ICM field sessions and at spring grower meetings. In addition, 

planted or natural vegetation buffers, especially buffers comprised of evergreen species, 

are highly recommended whenever there are sensitive nearby surface waters. 

Other Contaminants 

Besides the pesticides listed above, Atlantic salmon may be affected by suites of other 

environmental contaminants including organochlorine compounds (e.g., DDT and its 

metabolites, polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins, and 

polychlorinated dibenzofurans), trace elements (e.g., mercury), and other chlorines (e.g., 

calcium hypochlorite). 

Organchlorine compounds 

The class of chemical compounds known as organochlorines (or chlorinated organics) is 

composed of hundreds of chemicals, many of which are structurally complex, and all of 

which have at least one chlorine atom and one “benzene ring” (C6H6). Many 

organochlorines of industrial origin have yet to be fully identified or chemically 

speciated. The most widely recognized and studied contaminant groups within this class 

are dioxins, furans, and polychlorinated biphenyls (Maine TAC 2002). 

A variety of natural processes, such as forest fires, can generate small amounts of a few 

of these compounds (e.g., dioxins) that can end up in surface waters. Surface waters may 

also receive dioxins and dioxin-like compounds through atmospheric deposition and trace 

discharges from municipal sewage treatment plants (Maine TAC 2002). Within Maine 

DPS rivers, the source of these compounds include landfill and hazardous waste disposal 

sites (e.g., the Eastern Surplus Superfund site on the Dennys River). 

Dioxins, furans, and PCBs can impart sublethal and lethal physiological effects to 

exposed fish in at least three ways: (1) through direct/acute toxicity to the exposed 

organism; (2) through chronic bioaccumulation in fatty tissue; (3) through maternal 

transfer to eggs of exposed gravid females (Maine TAC 2002). Documented effects of 

exposure by one or more of these routes, in studies using several species of salmonids, 

include visual/motor function (Carvalho and Tillitt 2004), reduced adult and fry survival 

(Giesy et al. 2002), total length and cranial length (Carvalho et al. 2004), general 

physiological and endocrine dysfunction, decreased egg viability, and fry survival 

(Walker and Peterson 1994; Zabel et al. 1995), abnormal gene expression, genetic 

fragmentation (genotoxicity), and, in extreme cases, direct mortality (Sijm and 

Opperhuizen 1996). Notably, few studies have involved anadromous Atlantic salmon. 

Results in one relevant study involving Atlantic salmon from two Massachusetts rivers 

(Rees et al. 2003) indicate that parr with PCB burdens exhibited amplified expression in a 
1-38

widely used biomarker (cytochrome P4501A or CYP1A). This amplified expression 

was expressed by two orders of magnitude (i.e., 100 fold) or more in gill tissue using a 

more sensitive technique to detect induction (i.e., quantitative reverse transcription 

polymerase chain reaction - RT-PCR; Rees et al. 2003). Although this work was not 

intended to determine the ultimate effects of amplified expression on the affected 

organism, such investigation would represent the next logical step. NOAA Fisheries 

initiated a similar study in 2003 using the same biomarker in gill tissue with parr from the 

Dennys River (a PCB affected river) and Cathance Stream (an unimpacted tributary). 

The results were less conclusive than the Massachusetts study, in part because of small 

sample sizes at the two Maine sites. 

Individual organochlorine compounds, and even isomers of the same compound, appear 

to have substantially different toxicities to aquatic life and humans. Generally, the total 

contaminant burden present in an exposed organism’s tissue is calculated and expressed 

as a weighted sum, termed the “Toxicity Equivalent Quotient” (TEQ). The TEQ value is 

derived by adding the concentrations of congeners of the compounds adjusted by a toxic 

equivalency factor relative to the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (Van 

den Berg et al. 1998). This method is only used for dioxin-like compounds (e.g., dioxins, 

furans, and several PCB congeners). 

Organochlorines have a tendency toward high environmental persistence, warranting an 

examination of historical legacies (e.g. sediment repositories) as well as direct discharges, 

when assessing potential impacts to aquatic life migrating through contaminated water or 

inhabiting contaminated habitats or substrates (Maine TAC 2002). 

Trace Elements 

Trace elements, such as mercury and cadmium, have been detected in sediments and 

resident fish tissue (e.g., white suckers) in the DPS rivers. These contaminants are taken 

up by fish through diet or water. Chronic dietary exposure to elevated levels of mercury 

causes pathological injuries to Atlantic salmon parr including oxidative stress and brain 

lesions (Berntssen et al. 2003). In other fish species, mercury exposure affected predator 

avoidance (Webber and Haines 2003). 

Chlorines 

The effects of chlorine compounds on salmon olfactory senses and homing behavior is 

currently unknown and should be studied (Maine TAC 2002). While the potential effects 

of chlorine compounds on Atlantic salmon are unknown, the density of overboard 

discharges (OBD)16 in Cherryfield on the Narraguagus River, is a matter of concern to 

salmon recovery efforts in this watershed (Maine TAC 2002). OBDs use chlorine tablets 

(calcium hypochlorite) in the chlorinator unit. There are thirty-seven OBD units in 

 

16 An overboard discharge (OBD) is an alternative wastewater treatment system for sites where 

municipal sewer connection is not possible and where a traditional septic system is not feasible. 

The simplest kind of overboard discharge (OBD) is a holding tank with a chlorinator for the 

overflow pipe (Maine TAC 2002). 
1-39

Cherryfield. OBDs in rivers other than the Narraguagus should also be assessed to 

determine the extent and level of threat to the DPS rivers. 

Since 1987, the construction of new OBDs has been prohibited in Maine. In 1990, the 

Maine OBD program was initiated by the State legislature (38 MRSA Section 411-A) to 

help fund replacement systems that would eliminate OBDs in certain areas. Currently, 

the focus of the replacement program is in shellfish areas that would be open to 

shellfishing if the OBDs were removed. Maine DEP is responsible for annually 

inspecting all OBD systems and generating a priority list for replacement. In addition to 

the Maine DEP, the Farmers Home Administration and the Maine State Housing 

Authority can provide grants or low interest loans to towns or community groups for 

replacement of OBDs. This program to replace OBDs with less environmentally harmful 

wastewater treatment systems should be continued (see page 4-24). 

Endocrine Disruption 

Endocrine disrupting chemicals are substances that disrupt sex hormone systems in 

animals. The effects can occur in many life stages, and are often delayed in expression. 

A large number of chemical compounds have been found to have endocrine disrupting 

activity, including herbicides (2,4-D, atrazine), fungicides (benomyl, zineb), insecticides 

(DDT, methoxychlor, synthetic pyrethoids), industrial chemicals (dioxin, PCB, 

nonylphenols, phthalates), and trace metals (cadmium, lead, mercury). 

The Maine TAC (2002) concluded that there are not sufficient water quality data to 

determine the extent of exposure of Atlantic salmon to endocrine disrupting chemicals in 

the DPS rivers. Moreover, existing data are not sufficient research to ascertain the 

potential effects of endocrine disruptors on salmon restoration (Maine TAC 2002). The 

available weight-of-evidence, however, indicates that endocrine disrupting environmental 

contaminants may be an important factor in Atlantic salmon restoration (Maine TAC 

2002). 

Endocrine disruptors are believed to affect smoltification in Atlantic salmon by 

disrupting hormone systems that facilitate the physiological processes necessary for 

seawater adaptation (Fairchild et al. 1999). In New Brunswick, Fairchild et al. (1999) 

documented a decline in returning adult Atlantic salmon in areas where the insecticide 

Matacil 1.8D had been sprayed to control an outbreak of spruce budworm17 during the 

time of smolt out-migration. The particular pesticide used was not an endocrine 

disrupting compound, but the formulation included a known endocrine disruptor (4-

nonylphenol) as an emulsifying agent. Exposure to 4-nonylphenol induced vitellogenin 

(an egg yolk protein) in Atlantic salmon smolts in the same manner as exposure to 17 βestradiol (Sherry et al. 2001). Moore and Lower (2001) showed that exposure to atrazine 

(a triazine herbicide) and pentabromodiphenyl ether (a brominated fire retardant) reduced 

gill Na+/K+ ATPase activity, caused osmoregulatory disruption and elevated cortisol 

 

17 Spruce budworm outbreaks are cyclical over 40-80 year periods and are not expected in the next 

10-20 years 
1-40

levels, reduced survival in sea water, and reduced migratory activity. These are the same 

effects reported by Magee et al. (2001) for Narraguagus River smolts. 

The E-SCREEN bioassay (Soto et al. 1995) has been used to demonstrate that several 

pesticide active ingredients used in blueberry operations exhibited estrogenic activity of 

50 to 75% of 17β estradiol, and several commercial formulations had activities of 25% or 

greater (Van Beneden and Morrill 2002, Haines and Van Beneden 2003). Among these 

pesticides, 2,4-D, propiconazole, methoyclor, phosmet, and hexazinone exhibited the 

activity of a xenoestrogen (a foreign substance that may act like estrogen). 

In a recent study at the University of Maine, endocrine disruption was not exhibited in 

Atlantic salmon pre-smolts exposed to several pesticides (Spaulding 2005). Pre-smolts 

were exposed to mixtures of hexazinone, propiconazole, 2,4-D, terbacil, and phosmet in 

five weekly, 24-hour tests. The exposures did not affect smoltification, mortality 

following saltwater challenge tests, body length or weight, hematocrit levels, or plasma 

steroid concentrations. 

Both nonylphenol and diethylhexyl phthalate, demonstrated endocrine disruptors, are on 

the U.S. Environmental Protection Agency List 1 inert ingredients and are incorporated 

into a large number of agricultural and industrial chemicals. These substances are 

commonly found in municipal sewage. Studies to determine the possible presence of 

these compounds have not been conducted in the DPS rivers. 

Endocrine disrupting organochlorine compounds have been detected in Maine Atlantic 

salmon rivers including dioxin, PCBs, and DDT metabolites (all fish tissue values 

following expressed in wet weight). In the Pleasant River, DDT metabolites (8.1 - 11.2 

ppb) and PCBs (5.3 - 8.6 ppb) have been found in brook trout and white suckers (Maine 

Department of Environmental Protection 1999). DDE (3 - 5 ppb) has been detected in 

white suckers from the Narraguagus River, Pleasant River, and Cove Brook (USFWS 

2005 unpublished data). PCBs have been found in smallmouth bass (91 - 168 ppb), white 

suckers (52 - 54 ppb), and sediments from the Dennys River, downstream from the 

Eastern Surplus Superfund Site (Mierzykowski and Carr 1998, EPA 2005 unpublished 

data) and in smallmouth bass (23 ppb) and white suckers (12 ppb) from the East Machias 

River (Mierzykowski and Carr 1998). 

iii. Sedimentation 

The Services have concluded that sedimentation poses a high level threat to the recovery 

of the DPS. Sedimentation from a variety of sources may be altering habitat and 

rendering it incapable of supporting Atlantic salmon (65 FR 69459). Sedimentation may 

be affecting the quality of habitat in rivers and streams within the DPS including 

substrate embeddedness, diminished habitat complexity and stream channel alteration. 

Sources of sedimentation within DPS rivers include natural stream bank erosion, poorly 

maintained roads, improperly constructed culverts, unstable bridge abutments, improper 

road ditching, road construction and maintenance, poor agricultural practices, stream 
1-41

crossings, recreational all terrain vehicles (ATVs), timber harvest activities not conducted 

in accordance with BMPs, dredging, and salt and sand from winter road maintenance. 

Excessive removal of riparian vegetation can accelerate erosion and sedimentation and 

contribute to thermal loading. Upland and wetland vegetation help prevent NPS 

pollutants from entering streams. 

Sediment can impact salmon habitat in a number of ways. Excessive sedimentation can 

result in direct mortality to early life stages of Atlantic salmon (i.e., eggs and fry) due to 

smothering (Shaw and Maga 1943; Shelton 1955; Hall and Lantz 1969; Platts et al. 1979; 

Bjornn and Reiser 1991). McCrimmon (1954) compared several factors (sediment 

temperature and food) affecting stocked Atlantic salmon fry. He concluded that 

sedimentation had the most significant deleterious effect on the survival of fry. 

Sediment changes the physical structure of a river’s substrate, a critical factor in salmon 

survival. Excess sedimentation can fill pools, resulting in decreased depths and total 

area, thus reducing the amount of habitat available for juveniles and adults during the 

summer and winter months (Cordone and Kelley 1961). Excess sedimentation in pools 

has been cited as a reason for numerous salmonid populations declines (Saunders and 

Smith 1965; Peters 1967; Elwood and Waters 1969; Barton 1977). 

Sedimentation can adversely affect benthic macroinvertebrate populations (Bjornn et al. 

1974, 1977 and McClelland and Brusven 1980). The affected organisms consist mainly 

of insect orders that are generally the forms most readily available to foraging fish 

(Waters 1995). Substrate embeddedness and decreased interstitial space can decrease 

macroinvertebrate production resulting in reduced food supply (Atkinson and Mackey 

2005). Reduced food supply may further cause fish to defend larger territories, 

decreasing the density of fish. Increased substrate embeddedness can result in decreased 

habitat complexity, reducing visual isolation among individual fish, creating larger 

territories and lower densities of fish (Atkinson and Mackey 2005). 

Sedimentation can result in increased substrate embeddedness (the measure of the extent 

a rock particle is buried, or embedded in the substrate). Substrate embeddedness can 

result in a number of changes to habitat that may adversely affect Atlantic salmon. 

Substrate embeddedness may reduce over-winter sheltering habitat. Bjornn et al. (1974, 

1977) found that embedding cobble substrates in sediment reduced the amount of habitat 

available for juvenile salmonids (salmon and trout) affecting their density and 

distribution. Increased embeddedness may block juvenile salmon from seeking shelter 

beneath substrates during cold temperatures and lower overwinter survival rates 

(Atkinson and Mackey 2005). The loss of shelter in interstitial gravel and cobble spaces 

can result in increased predation (Cordone and Kelley 1961; Bjornn et al. 1974). 

Estimates of embeddedness can be used to assess habitat degradation or identify stream 

reaches that may benefit from habitat restoration (Atkinson and Mackey 2005). A less 

embedded streambed has a lower proportion of fine sediments than a more embedded 

one. Embeddedness can be used to assess the impact of non-point source pollution 

sources such as erosion at road crossings (Atkinson and Mackey 2005). Estimates of 
1-42

embeddedness are useful in evaluating habitat quality, i.e. available living spaces, for 

juvenile salmonids, and may provide a measure of habitat quality for salmon rearing and 

spawning, and for benthic macroinvertebrates. 

While there have been a number of NPS surveys conducted on DPS rivers (see below), 

the full extent of sedimentation and embeddedness is not well documented. In 2004, the 

ASC surveyed at a number of sites on the Narraguagus River to determine cobble 

embeddedness levels. The goal of the survey was to assess changes in substrate 

embeddedness since a previous survey of embeddedness conducted on the Narraguagus 

in 1993. Preliminary analysis indicates that embeddedness levels may have decreased 

over the eleven year period (Atkinson and Mackey 2005). The ASC also assessed the 

interstitial space index (ISI)18 of substrate at the sites sampled. While the preliminary 

results suggest an improvement in overall embeddedness levels, ISI seems to be reduced 

from 1993 to 2004. The reason for this decline is not apparent. Additional analyses will 

be required to better understand these findings (Atkinson and Mackey 2005). 

The ASC also conducted substrate embeddedness surveys on a number of sites on the 

Dennys River. The surveys were conducted to estimate substrate embeddedness levels in 

the drainage and examine the relationship between embeddedness and juvenile Atlantic 

salmon densities (parr) (Atkinson and Mackey 2005). An additional goal was to 

determine, if possible, a threshold at which high levels of embeddedness significantly 

affect parr densities (Atkinson and Mackey 2005). Atkinson and Mackey (2005) found 

indications that young of the year (YOY) salmon densities were inversely related to 

embeddedness levels (Atkinson and Mackey 2005). 

The ASC has begun studies to estimate permeability in spawning areas on Downeast 

Rivers in order to try to relate salmon survival to permeability (Sheller 2005). As noted 

above (see also, page 1-23), substrate permeability is reduced when fine sediments are 

deposited in streambeds. Available studies suggest that substrate permeability has a 

significant affect on survival to emergence of salmon (McKenzie 1985; GustafsonMarjanen 1982). 

Field evidence suggests that elevated levels of sediment have compromised spawning 

habitat along certain reaches in several DPS rivers (65 FR 69459). Local organizations 

have conducted NPS surveys on DPS rivers identifying numerous NPS sites. The 

majority of the sites are related to erosion resulting in sedimentation problems. These 

efforts have identified 800 NPS sites on the five Downeast Rivers and over 400 NPS sites 

on the Sheepscot River (Steve Koenig, Project SHARE, personal communication, see 

also DRWC NPS inventory, NRWC NPS inventory). 

On the Dennys River, NPS surveys, conducted between 1999 and 2003, have 

documented 69 NPS sites, 84% of which are associated with unpaved roads (logging, 

 

18 ISI is an index of the three dimensional interstitial space available for salmonids and other 

organisms. Atlantic salmon juveniles use the interstitial spaces for shelter from fast moving 

currents and to find thermal refuge, particularly during winter months. 
1-43

blueberry-access, town, county, or residential/private)19. The problems on these roads 

include faulty culverts, poor ditching, road runoff and unstable shoulders (DRWC 2005). 

On the Narraguagus River, a total of seven NPS surveys have been conducted since 1999, 

approximately 75% of the watershed has been surveyed to date. These surveys 

documented over 175 NPS sites (NRWC 2003). Approximately 50% of these sites have 

either been fully repaired or are in the process of completion (NRWC 2003). The NWRC 

(2003) identifies several potential sources of sedimentation in the Narraguagus River 

watershed. These include: ATV use, poorly maintained roads (e.g., logging roads, state 

and municipal roads, private roads, blueberry roads)20 and timber harvesting practices 

(NRWC 2003). 

On the Sheepscot River, large sections of the river turn cloudy in the spring and fall; 

turbidity can last for four to six weeks during the spring freshet. This watershed has the 

highest density of year-round roads in DPS river watersheds (Maine TAC 2002). 

There are no documented NPS sites associated with timber harvesting in either the 

Dennys or Narraguagus river watersheds (NRWC 2003; DRWC 2005). One recent 

incident, however, highlights the potential for activities related to timber harvesting to 

result in NPS pollution when not conducted in accordance with BMPs. In June 2004, an 

evaluation of a logging operation in Dennysville found a sediment plume covering 50% 

of the width of the Dennys River (DRWC 2005). The sediment discharge was the result 

of a skidder21 crossing an intermittent stream in a very wet area with silt/loam/clay soils. 

The event appears to have been caused by failure to employ recommended BMPs during 

the harvest activity (DRWC 2005). 

Cooperative efforts among landowners and watershed councils have identified and 

remedied chronic NPS sites where sedimentation of streams was a concern. Regulatory 

authority over water quality issues related to forestry currently resides with the Maine 

Department of Environmental Protection (DEP). In 2006, MFS will assume this 

authority upon implementation of statewide water quality standards, anticipated in 2006. 

In the interim, MFS continues to make statewide routine harvest inspections. MFS also 

continues to work collaboratively with DEP and LURC through existing MOUs that 

provides MFS authority for early intervention and correction of water quality problems. 

Significant water quality issues are resolved through DEP and LURC regulatory process 

with assistance from MFS. In addition, landowners filing a Forest Operations 

Notification (FONs) within municipal boundaries that contain a DPS salmon watershed 

receive a notification letter alerting them to potential critical salmon habitat and an offer 

of assistance from MFS. Recent revisions to this letter now include distribution to 

stakeholders such as the Atlantic Salmon Commission. 

 

19 The Narraguagus River Watershed Council (NRWC) and the Dennys River Watershed Council 

(DRWC), in cooperation with Project SHARE, have developed NPS management plans for the 

Narraguagus and Dennys rivers. 

20 The problems on these roads include faulty culverts, poor ditching, road runoff, sand/salt buildup, 

and unstable shoulders. 

21 Skidders are used to move logs from the woods to the landing 
1-44

iv. Excess Nutrients 

Excessive nutrient enrichment of a river can increase growth of aquatic vegetation and 

may reduce the carrying capacity for Atlantic salmon. Increased respiration and 

decomposition of plants may cause dissolved oxygen to fall below levels optimal for 

Atlantic salmon. Increased algae in the water column can decrease visibility for sight 

feeding salmon. 

Excess nutrients can enter a river either in surface runoff or groundwater. Sources of 

excess nutrients include agricultural facilities, sewage treatment plants, failing septic 

systems, manufacturing or processing plants and hatcheries. Increased nutrients from 

improper manure storage and manure spreading can significantly impact water quality 

making habitats less suitable for the spawning, rearing and migration of Atlantic salmon. 

As long as manure spreading is done in accordance with existing state regulations and 

with proper oversight, there is minimal potential for deleterious water quality effects 

(Maine TAC 2002). Passage of the Nutrient Management Act with the requirement for 

nutrient management plans and funding for the construction of manure storages has 

helped reduce the potential for deleterious water quality effects (MDAFRR personal 

observations). 

The available water quality data for DPS rivers indicate that excess nutrients are not a 

problem, except for in the Sheepscot River. The relative contribution of agricultural uses 

versus suburban development and runoff is not known (Mark Whiting, Maine 

Department of Environmental Protection (DEP), personal communication 2001). 

v. Elevated Water Temperature 

The Services have concluded that elevated water temperature poses a medium level threat 

to the recovery of the DPS. Maine rivers lie near the southern extent of the Atlantic 

salmon’s range in North America, and are vulnerable to elevated water temperature 

regimes (Maine TAC 2002). Factors that may contribute to elevated water temperatures 

include improper or unregulated land use practices, impoundment of free-flowing 

reaches, discharge of industrial processing or cooling water, low flows that increase net 

insolation (exposure to sun) and broad climatic changes (Maine TAC 2002). Water 

temperature may be an important factor limiting Atlantic salmon rearing habitat in Maine 

rivers (Maine TAC 2002). Water temperature may be important alone or in combination 

with other factors (Maine TAC 2002). The Maine TAC (2002) concluded that there was 

insufficient information to determine the effect that increased water temperature, from 

land-use factors, impoundments, industrial cooling water and global climate change may 

have on Atlantic salmon recovery efforts. 

The temperature requirements of the various salmon life stages are well understood. 

Table 1. summarizes published optimal temperature ranges along with maximum and 

minimum thermal tolerance criteria. Relatively minor increases in water temperature 

may cause lethal or sub-lethal physiological effects for adult and juvenile salmon (Maine 
1-45

TAC 2002). Juvenile salmon can survive for several days at temperatures of 26-27°C 

(Garside 1973; Elliott 1991). However, adult salmon mortalities have often been 

observed at temperatures of 26-27°C. 

Table 1 - Atlantic salmon temperature (°C) requirements for freshwater life stages. Data are from published 

studies on Atlantic salmon, including experimental data and in situ measurements over the range of the species 

(North America and Europe). 

Life Stage 

Optimum 

Range Min.1 Max. References 

Spawning 5-8 4.4 10 DeCola ‘70; Danie et al. ‘84; McLaughlin and Knight ‘87 

Incubation 4-7.2 0.5 12 DeCola ‘70; Gunnes ‘79; Danie et al. ‘84; McLaughlin and 

Knight ‘87 

Early Fry 8-19 0.5 23.5 Danie et al. ‘84; Jensen et al. ‘91 

Juveniles 

Feeding 

Survival 

15-19 

0.5-20 

3.8 

0 

22.5 2

29.0 3

DeCola ‘70; Elson ‘75; Danie et al. ‘84; Elliott ‘91 

Garside ‘73; Elliott ‘91 

River Migration 

Smolt 

Adult 

7-14.3 

14-20 

5 

8 

19 

23 4

Bakshtansky et al. ‘76; LaBar et al. ‘78; Ruggles ‘80; 

Jonsson and Rudd-Hansen ‘85; Duston et al. ‘91; Shepard 

‘91 

Elson ‘69; DeCola ‘70; Danie et al. ‘84; Hawkins ‘89; 

Shepard ‘95 

Notes: 

1. 

2. 

3. 

4. 

Minimum water temperatures reflect the requirements of southern populations and include winter temperature 

requirements. Northern populations have lower minima for some life stages (not included). 

Highest temperature for feeding after acclimation at 20.0°C. 

Highest temperature for 1000 minute survival after acclimation at 25.0-27.0°C. 

Highest temperature for normal upstream migration. The lethal temperature for adult salmon is approximately 

27.0°C, depending upon acclimation and duration of exposure. 

In addition to direct mortality, elevated water temperature may diminish habitat 

suitability and adversely affect the production potential of a river or stream (Maine TAC 

2002). The optimal temperature range for juvenile salmon feeding and growth in streams 

is 15-19°C and the maximum limit for feeding is 22.5°C (DeCola 1970; Elson 1975; 

Danie et al. 1984; Elliott 1991). If temperatures exceed 24°C for extended time, growth 

may be affected and fish may not reach adequate size to over-winter successfully. At 

over 27°C salmon will seek cooler habitat. With Maine’s non-native warm water 

predators, having to move can result in predation losses. Increased water temperatures 

can also reduce dissolved oxygen levels in aquatic environments. Dissolved oxygen 

levels below 6 mg/l are not suitable for salmonids (Maine TAC 2002). On the Sheepscot 

River, dissolved oxygen (DO) levels often drop below 7 milligrams per liter (mg/l) 

during summer coinciding with high bacteria counts (Maine TAC 2002). Water 

temperature above 23°C inhibits spawning migrations (Elson 1969; DeCola 1970; Danie 

et al. 1984; Hawkins 1989; Shepard 1995). 

Recent water temperature data (last 10 years) exist to some extent for most Maine salmon 

rivers, with the Penobscot and Narraguagus rivers having historical temperature data 

dating back to the mid 1950’s22. High water temperatures have been documented on DPS 

 

22 In January 2002, ASC produced a database with the intent of assimilating available temperature 

data into one central location. This database will greatly facilitate intra- and inter-river 

comparisons of water temperatures and long-term trend analysis for Maine salmon rivers. 
1-46

rivers including the Sheepscot River. High water temperatures have been documented on 

the main stem of the Sheepscot River at Head Tide. In 2001, 2002 and 2003, days during 

a period between late June and early August water temperatures exceeded 27°C on at 

least 7 days and exceeded 30°C on four (ASC 2002). Nighttime temperatures during this 

same period remained between 20 and 25°C. On at least one occasion, water 

temperatures reached 31.1°C and was followed by a fish kill upstream in Alna (ASC 

2004). ASC data indicates that Long Rips on the Sheepscot also reaches temperatures 

that may limit production of salmon. In 1994 and 1995, the river reach below the 

Coopers Mills dam experienced several consecutive days where water temperatures never 

dropped below 22.5°C (Arter 2004; KRIS 2005). 

Elevated water temperatures occur on other DPS rivers. The ASC has recorded 

continuous water temperatures at several sites on the Narraguagus River (Figure 9). 

These data show that daily maximum water temperatures often exceed the feeding 

threshold of 22.5°C in warm years and occasionally in cool years such as 1992 and 1996. 

At the Deblois station, the feeding threshold (22.5°C) is exceeded on >50 days or 

approximately one-third of the growing season (May to September) in 5 out of the 8 

years of data presented. These data indicate the potential for serious reductions in growth 

and survival of juvenile salmon due to the cessation of feeding activities. In addition, 

Figure 9 shows that while daily maximum temperatures exceeded 26°C (threshold for 

adult mortality) on about ten days during the warmer years, but seldom exceeded this 

level in cool years. In 2003, the main stem of the Narraguagus exceeded 22.5°C at nine 

sites and exceeded 27°C at 11 sites. The West Branch at Sprague Falls exceeded 22.5°C 

on 17 days and exceeded 27°C on six days (ASC 2002). 

In 2003, three sites in the Dennys River exceeded 22.5°C. In the Ducktrap River, one 

site exceeded 22.5°C on nine days and the same site exceeded 27°C on one day. The 

Machias River had three sites that exceeded 22.5°C, two of which also exceeded 27°C on 

two days. Old Stream also had a site that exceeded 22.5°C on 7 days and exceeded 27°C 

on 14 days. The Pleasant River exceeded 22.5°C at four sites and exceeded 27°C at three 

of those sites on multiple days. Staff reports from the Atlantic Salmon Authority (ASA; 

predecessor agency to ASC) indicate that high water temperature may be a problem in 

some years in Cathance Stream in the Dennys River and certain sections of the mainstem 

of the East Machias River ((Beland et al. 1995; Horton et al. 1995, ASA 1998). 

The potential for water temperature elevation in the vicinity of berry processing water 

discharges has been identified as a water quality issue (MASCP 1997). Two berry 

processing plants on the Narraguagus River and one on the Machias River discharge 

water used in the processing of blueberries directly into the river (MASCP 1997). 

Processing plants are allowed to discharge 627,000 gallons of agricultural process water 

in to the Narraguagus River per day (0.97 cfs). Up to 100,000 gallons per day (0.15 cfs) 

is allowed to attain a discharge temperature of 26°C. Up to 70,000 gallons per day (0.11 

cfs) of agricultural process water is allowed to be discharged into the Machias River with 

a maximum temperature of 32°C, a temperature lethal to both juveniles and adult salmon. 

No monitoring of the effect of these discharges on the river temperature and Atlantic 

salmon has been conducted. In addition to lethal effects, areas of elevated water 
1-47

temperature may adversely affect salmon by acting as a thermal barrier to passage 

thereby inhibiting migration. 

vi. Environmental Impacts of Changing Landuse Patterns 

The Services have concluded that changing landuse and development poses a high level 

threat to the conservation of the DPS. Changing land-use patterns, particularly 

development, population growth and land conversion creates a number of issues that may 

affect the DPS. Population growth and development in Maine has accelerated in recent 

years, especially in the mid-coast region. The Maine State Planning Office (SPO) projects 

that the southern, mid-coast and Penobscot regions of Maine will continue to experience 

changes from current rural land-use to urban/suburban in the next several decades (see 

Figure 10). Associated with increased population growth, land conversion and 

development are increased infrastructure needs including road construction and resource 

demands such as increased water use and water pollution control/treatment. 

The Downeast Region of Maine is also experiencing changes in land use patterns 

particularly land ownership. The Downeast watersheds are sparsely populated and 

historically have been managed for the growth and harvest of forest products and 

lowbush blueberries. In the Dennys, East Machias, Machias, Pleasant and Narraguagus 

watersheds, forestry has historically been the dominant land use. International Paper 

(IP), until recently the principle land owner Downeast23, had begun to sell forest lands in 

 

23 In November 2004, International Paper sold its Maine and New Hampshire forestlands, totaling 

approximately 1.1 million acres, to GMO Renewable Resources, LLC, (GMORR) a private forest 

0

10

20

30

40

50

60

1991 1992 1993 1994 1995 1996 1997 1998

No. of Days 

Exceeded

(Deblois)

> 22.5

> 26.0

0

10

20

30

40

50

60

1978 1979 1981 1992 1993 1994 1995 1996 1997 1998

No. of Days 

Exceeded 

(Cherryfield)

Figure 9 – Number of days when the Narraguagus River daily maximum water temperature 

exceeded 22.5 or 26 EC at Deblois (upper) and Cherryfield (lower). Data from the Maine ASC.
1-48

this region. The sale of this property reportedly attracted liquidation timber harvesters 

and developers, known for intensive logging, followed quickly by subdivision and resale 

of property. The State of Maine, in response to concerns about the possible impacts of 

liquidation harvesting, recently enacted legislation intended to control and restrict this 

practice. It is anticipated that the recent adoption of standards by the Maine Legislature 

will result in a reduction of this risk by essentially eliminating liquidation harvesting. 

Nevertheless, the subdivision of what historically have been large tracts of industrial 

forest into smaller tracts has given rise to concerns about intense localized harvests and 

conversion to other land uses (e.g., vacation homes, subdivisions). 

 

The changing land use patterns occurring in Maine have the potential to result in a 

number of ecological impacts that may affect salmon habitat. Increased development and 

population growth results in land clearing and construction of infrastructure such as 

roads, road crossing and buildings. These activities can alter and disrupt the hydrological 

process in the system and result in a decline in water and habitat quality. Changes in land 

cover and land and water use can result in adverse impacts to freshwater ecosystems. For 

example, increasing the amount of impervious surface (e.g. roads, parking lots) in a 

watershed can increase sedimentation/erosion and pollutant loads entering streams and 

rivers. Land management activities, particularly land clearing for agriculture, 

 investment management company. The new landowner plans on keeping the land in the 

Sustainable Forestry Initiative (SFI) certification program. 

Figure 10. – Projected Expansion of Development 1980-2050 (Maine State Planning Office.

http://www.state.me.us/spo/landuse/techassist/expansion/state.php 
1-49

development, and timber harvest, have the potential to impact geomorphological and 

riparian processes (Boyer et al. 2003, NRC 2004). Changing land use patterns and 

resource demands will need to be managed in order to protect salmon and their habitat. 

The construction of new roads facilitates increased access into relatively undisturbed and 

previously inaccessible areas. Roads are often built in association with logging, 

agriculture and the development of homes or industrial or commercial projects. All these 

activities can result in a number of ecological effects. Depending on a large number of 

factors, the effects of roads on the ecological health of a landscape can be quite severe 

(Trombulak and Frissell 2000). 

Roads can alter many ecological functions and characteristics including the pattern of 

runoff and surface water flow, sedimentation and increased nutrient loading and chemical 

contaminants (Trombulak and Frissell 2000). Numerous studies have correlated declines 

in the ecological health and habitat quality of streams and rivers in relation increasing 

road density (Trombulak and Frissell 2000). Roads can result in the direct transfer of 

sediment and other material to streams and other water bodies at road crossings. Roads 

and bridges can directly alter the development of stream channels. Road crossings 

commonly act as barriers to the movement of fish. Maintenance and use of roads 

contribute at least four different general classes of chemicals to the environment: heavy 

metals, salt, organic molecules, and nutrients (Trombulak and Frissell 2000). 

Among the DPS rivers, the Sheepscot River currently has a higher road density and more 

stream crossings than the other DPS rivers (Maine TAC 2002). The most common 

roadway impact in Downeast watersheds is related to secondary (paved or unpaved) road 

crossings of tributary streams. These small streams are relatively fragile and collectively 

comprise the majority of stream miles and drainage area of each watershed (SHARE 

2004). 

3. Obstruction to Passage/Habitat Connectivity 

i. Manmade Barriers 

Historically, dams were a major cause of the decline of Atlantic salmon runs in many 

Maine rivers and streams (Baum 1997). At one time, dams existed at various times on all 

eight rivers within the DPS known to still support wild Atlantic salmon. Dams were 

constructed to produce electricity, operate mills, transport logs and as ice control 

structures. Historic records indicate that many of the old, low-head timber crib dams had 

significant leakage and were not complete barriers to fish passage. The Services have 

concluded that manmade obstructions to passage is not a high level threat to the survival 

and conservation of the DPS. Dams that obstruct passage of salmon do, however, exist 

on several rivers within the range of the DPS that no longer known to support wild 

salmon populations (e.g., Orange River, St. George River, Marsh River). Dams exist 

within the DPS that impede the passage of other diadromous species whose recovery 

could benefit Atlantic salmon. 
1-50

In the late 1940s, the presence of dams on the Narraguagus, Machias, East Machias and 

Pleasant rivers was identified as a threat to the continued existence of Atlantic salmon in 

those rivers (Rounsefell and Bond 1949). According to Rounsefell and Bond (1949), the 

Atlantic salmon run in the Dennys River was almost always in peril during the 1880s 

because of dams. In the Sheepscot River, twenty-four obstructions, including a dam at 

the head of tide in Alna, threatened salmon returns until the early 1960s (Meister 1982). 

Today, most of the dams on DPS rivers have either been removed or breached and no 

longer threaten salmon migration. Coopers Mills Dam on the Sheepscot River and the 

Stillwater Dam on the Narraguagus are the only remaining dams with potential to 

significantly obstruct access to valuable spawning and rearing habitat. The Head Tide 

Dam on the Sheepscot River was effectively breached on the eastern shore in 1968 to 

allow free passage into the river (Meister 1982). Today, most of the structure still exists 

and though it no longer obstructs fish passage, it still impacts spawning and rearing 

habitat by altering normal flow conditions. All other obstructions on these rivers (e.g., 

ice-control dam in Cherryfield, Meddybemps Lake outlet dam) have fishways. The 

efficiency of these fishways has not been well documented (Baum et al. 1992). 

The Coopers Mills Dam, located below the long pond on the mainstem of the Sheepscot 

River, was retrofitted in 1960 with a Denil fishway, which IFW maintains (Meister 

1982). In recent years, the dam has developed leaks that reduce attraction to the fishway. 

In addition, a screen in the fishway to block lamprey passage and to assist in the alewife 

fishery, in combination with the deterioration of the dam’s structural integrity, greatly 

reduces or prevents the passage of migrating salmon during the spring migration period. 

The U.S. Army Corps of Engineers (ACOE) constructed the Stillwater Dam in 

Cherryfield, Maine on the Narraguagus River in 1961 as a flood- ice-control structure 

(Baum and Jordan 1982). The dam is equipped with a Denil fishway which most fish 

normally use. During high water, salmon are often observed swimming over the top of 

the spillway (Baum and Jordan 1982). ASC has been working with the Town of 

Cherryfield to repair the fishway at the ice control dam (USASAC 2005). 

Other obstructions to passage, including poorly designed road crossings and culverts, 

remain a potential hindrance to salmon recovery. Improperly placed or designed culverts 

can create barriers to fish passage through hanging outfalls, increased water velocities or 

insufficient water velocity and quantity within the culvert. Poorly placed or undersized 

culverts (usually from road building and maintenance) can also hinder fish passage, thus 

reducing access to potential habitat. The extent of impacts on salmon populations within 

the DPS from improperly installed or designed culverts, damaged riparian areas and 

associated fish passage problems is not well known. 

In addition, concerns exist about the potential for barrier weirs to impede passage24. 

Seasonal weirs have been located on the Narraguagus, Pleasant and Dennys rivers. The 

Recovery Plan recommends (see page 4-58) that barrier weirs be maintained as a means 

 

24 The construction, operation and maintenance of weirs on DPS rivers has been an integral 

component of the efforts to conserve and restore wild Atlantic salmon in Maine.
1-51

to prohibit passage of aquaculture salmon in DPS rivers and enable data collection. The 

potential of weirs to impede up and downstream passage of salmon should continue to be 

assessed (see page 4-30). Weirs should be constructed with state-of-the-art technology 

and operate continuously from ice out to ice in and effectively without hindering the 

passage of wild Atlantic salmon or other species (see page 4-58). 

ii. Natural Barriers 

Natural geological falls occur in most of the rivers within the DPS known to still support 

wild salmon populations and sometimes act as temporary barriers or deterrents to fish 

passage during certain flow conditions. Fish ladders have been constructed at Bad Little 

Falls on the Machias River in Machias (Fletcher et al. 1982), at Saco Falls on the Pleasant 

River (Dube and Jordan 1982) and at Marion Falls on Cathance Stream (a tributary of the 

Dennys River). The Bad Little Falls fishway provides passage around the dam that was 

constructed at the head of the Machias Gorge. In order to facilitate upstream passage, 

concrete defectors were built to provide eddies and resting areas for salmon moving 

upstream through the gorge at Bad Little Falls. In 1970, the dam was breached by the 

spring freshets and now fish most often use the west channel to pass above the falls rather 

than the fishway, which is in the center channel (Fletcher et al. 1982). On the Pleasant 

River a fish ladder was constructed at Saco Falls in 1955 to improve fish passage around 

this natural obstruction (Dube and Jordan 1982). The Saco Falls fish ladder needs repairs 

but is functional. 

Beaver dams and debris jams are perennial events on Maine rivers. These dams are 

typically temporary partial obstructions (Havey and Fletcher 1956). They can 

temporarily alter habitat and block access to spawning habitat, thereby reducing salmon 

productivity. While Atlantic salmon and beavers have always coexisted, the problems 

associated with beaver dams may be exacerbated by very high beaver populations and 

very low salmon populations. Beaver populations in Maine have expanded in the 

absence of natural predators. Beaver populations have also increased as demand for their 

fur has decreased. 

Generally, beaver dams do not limit upstream migration for adult Atlantic salmon in the 

main stem of the Dennys, East Machias, Machias and Narraguagus rivers. Tributaries to 

the East Machias, Machias and Narraguagus rivers contain some spawning habitat that 

may be blocked by beaver dams. In years of low water conditions, beaver dams may 

prevent access to some spawning areas on these rivers (ASA 1998). Currently, biologists 

and volunteers remove debris jams on DPS rivers and tributaries as time permits. 

First-order and smaller second-order streams are those most likely to have chronic beaver 

dam obstructions, yet these streams are the least likely to be used by a significant portion 

of salmon run. Typically, spawning salmon use these smaller streams only in years with 

ample autumn flows and significant salmon runs. In third-order and smaller second-order 

streams, beaver dams can obstruct access or inundate spawning areas, and occasionally 

have significant local effects on salmon production. An ongoing study on Venture Brook 
1-52

(Dennys) conducted by UMaine-Machias seeks to understand the effects of opening up a 

beaver dam choked small stream 

B. OVERUTILIZATION FOR COMMERCIAL, RECREATIONAL, 

SCIENTIFIC OR EDUCATIONAL PURPOSES 

1. Commercial and Recreational Fisheries 

Both commercial and recreational fisheries, especially marine, have historically played a 

role in the decline of the DPS. Today, U.S. fishery regulations prohibit commercial and 

recreational harvest of sea-run Atlantic salmon in state and federal waters. Canadian 

regulations prohibit all commercial harvest of Atlantic salmon off Labrador and 

Newfoundland. In Greenland, commercial harvest of Atlantic salmon is regulated 

through cooperative international management. Currently, the only marine fishery not 

under state, federal or international management that poses a potential threat to 

endangered salmon occurs in the French territory of St. Pierre et Miquelon off the coast 

of Newfoundland. 

A. U.S. Fisheries 

In 1987, the New England Fishery Management Council (NEFMC), pursuant to its 

authority under the Magnuson-Stevens Fishery Conservation and Management Act 

(MSFCMA) (16 USC. 1801 et seq.) prepared and implemented a federal Fishery 

Management Plan (FMP) for Atlantic salmon. The FMP prohibits possession of Atlantic 

salmon in the U.S. exclusive economic zone (EEZ). The FMP was intended to safeguard 

U.S. Atlantic salmon, protect the U.S. investment in the state-federal restoration program 

and strengthen the U.S. position in international negotiations. In addition, Section 9 of 

the ESA prohibits the take of endangered Atlantic salmon. The term take means to 

“harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or attempt to 

engage in any such conduct.” 

The State of Maine currently prohibits all recreational and commercial harvest of wild 

Atlantic salmon in state waters. From the 1960s through the early 1980s, the estimated 

average recreational catch25 rate in Maine rivers ranged from approximately 20% to more 

than 25% of the run (Beland 1984; Baum 1997). This level of harvest was likely too 

high, especially in light of the extensive commercial marine harvest at that time. In 

response to declining salmon returns, the State of Maine enacted new regulation of the 

recreational harvest of salmon. These measures included reducing the allowable annual 

harvest from ten salmon in the 1980s to one salmon in 1994. In 1995, regulations were 

implemented permitting only catch-and-release fishing for Atlantic salmon in Maine, 

closing the last remaining recreational harvest opportunities for wild Atlantic salmon in 

the U.S. In December 1999, the State of Maine adopted regulations prohibiting all 

angling for sea-run salmon statewide. 

 

25 During this period catch and release was generally not practiced. 
1-53

Despite these strict state and federal regulations, both juvenile and adult Atlantic salmon 

remain vulnerable to injury and mortality due to incidental capture by recreational anglers 

and as bycatch in commercial fisheries. Returning adult sea-run Atlantic salmon are 

vulnerable to capture by recreational anglers when holding in deep, cold water pools 

during the summer months prior to spawning. The best available information indicates 

that Atlantic salmon are still often incidentally caught by recreational anglers in many of 

these pools. The Services have concluded that the incidental capture of Atlantic salmon 

is high level threat to the conservation of the DPS. 

In addition to inadvertent capture by recreational fishermen, Atlantic salmon are 

vulnerable to intentional capture. Documented poaching in 1998 and 2000 indicate that 

poaching continues to pose a threat to Atlantic salmon. In 2003, two Atlantic salmon 

kelts were reportedly taken by a fisherman on the Sheepscot River. Reports of the 

deliberate targeting and capture of Atlantic salmon in the Narraguagus and Machias 

rivers by recreational fishermen also raise serious concerns. The Services have also 

concluded that poaching is a high level threat to the DPS. 

In August 2003, the Maine IFW closed all fishing in the portion of the Narraguagus River 

from the ice control dam to the Railroad Bridge in Cherryfield through an emergency 

measure. This river reach includes the Stillwater, Cable and Maple Pools. Atlantic 

salmon were being fished for and hooked under the guise of angling for shad on the 

Narraguagus River. ASC biologists monitoring returning adults at the fishway trap at the 

ice control dam documented hooking and line wounds on 3 of 12 Atlantic salmon 

captured (25%). The ASC received a request from the Narraguagus and Pleasant River 

Watershed Councils to pursue this closure. The Maine IFW has permanently closed the 

Cable and Maple Pools to all fishing while leaving open, for the time period that shad are 

migrating, (May 1 to June 10) the Stillwater Pool (100 and 450 feet from the ice control 

dam) where shad are more likely to be caught than Atlantic salmon. 

The potential also exists for recreational anglers to keep juvenile Atlantic salmon 

misidentified as brook trout, brown trout or landlocked salmon. To reduce the potential 

for keeping salmon parr misidentified as other salmonid species, the State established a 

minimum size (8 inches) restriction on trout caught after June 30 of each year in the DPS 

river watersheds. Atlantic salmon kelts may also be kept by ice fishermen who 

misidentify them as landlocked salmon. In an attempt to avoid this potential source of 

accidental sea-run Atlantic salmon harvest, a maximum length for landlocked salmon and 

brown trout (25 inches) was implemented by the State. There is no way to accurately 

estimate the number of Atlantic salmon caught as recreational bycatch or the resultant 

mortality (LWRC 1999). 

The biological effects that incidental catch and subsequent release may have on Atlantic 

salmon are not well understood (Brobbel et al. 1996). Several studies have concluded 

that exhaustive exertion associated with angling may result in significant physiological 

disturbances including mortality (Bouck and Ball 1966; Beggs et al. 1980; Graham et al. 

1982; Wood et al. 1983; Brobbel et al. 1996). For example, Brobbel et al. (1996) 

compared the effects of catch and release fishing on kelts and bright salmon on the 
1-54

Miramachi River in New Brunswick. It was determined that compared to kelts, bright 

salmon26 were more disturbed by angling and were more likely to suffer mortality. 

Several factors, such as degree of starvation, osmoregulatory status and environmental 

temperature, probably influenced the physiological response of Atlantic salmon at 

different life-stages. In contrast, other researchers have found that extreme exertion does 

not always result in significant levels of mortality (Wydoski et al. 1976; Tufts et al. 1991; 

Booth et al. 1995). 

While studies conducted under controlled or laboratory settings have resulted in zero 

mortality to Atlantic salmon caught and properly released, it is highly unlikely that such 

favorable conditions would be consistently present in the natural environment. 

Conditions that contribute to mortality include elevated water temperatures, exposure of 

the fish to air after it has been captured, extremely soft water, low oxygen levels, low 

river flow and improper handling (Booth et al. 1995). Further, as returning adult salmon 

rely on fixed energy reserves (e.g., they eat very little once in river) to complete 

migration and spawning, the exertion expended in a catch and release event may have 

significant impacts. These possible impacts include comprising its ability to complete the 

migration to spawn and diversion of energy necessary to complete gamete formation 

(especially eggs). Given current wild Atlantic salmon population levels, any bycatch 

mortality would adversely affect the DPS and its recovery. 

There are only a few studies on the sub-lethal effects of hook and release of Atlantic 

salmon. These have focused on post exercise physiology (Wilkey et al. 1996, Wilkey et 

al. 1997) and post hooking migration (Whoriskey et al. 2000, UK Environmental Agency, 

2003, Makinen et al. 2000). 

The potential also exists for juvenile and adult Atlantic salmon to be incidentally taken as 

bycatch in commercial fisheries. Commercial fisheries deploying small mesh active gear 

(pelagic trawls and purse seines within ten meters of the surface) have the potential to 

incidentally take post-smolts. Results from a 2001 and 2002 post-smolt trawl survey in 

Penobscot Bay and the nearshore waters of the Gulf of Maine indicate that Atlantic 

salmon post-smolts are prevalent in the upper water column throughout this area in midto-late May (Russell Brown, NOAA Fisheries, personal communication). 

One current fishery operating in near-shore marine waters within proximity of salmon 

rivers within the DPS is the Atlantic herring fishery. In September 1999, NOAA 

Fisheries completed a Biological Opinion (BO) under section 7(a)(2) of the ESA for the 

Atlantic herring fishery. The BO concluded that the continued operation of the fishery 

was not likely to result in jeopardy to any ESA-listed species under NOAA Fisheries’ 

jurisdiction. In 2004, NOAA reinitiated formal consultation27 for the herring fishery. 

 

26 a salmon that has entered its natal stream upon return from the sea. 

27 Reinitiation of formal consultation is required should anyone of several triggers be met (e.g., a 

new species is listed that may be affected by the action, new information becomes available, the 

level of permitted incidental take is exceeded. On December 17, 2000 the Gulf of Maine Distinct 

Population Segment (DPS) of Atlantic salmon was listed as endangered under the ESA. 
1-57

to the recovery of the DPS, the West Greenland internal use fishery is not currently 

jeopardizing the continued existence of the species. 

D. St. Pierre et Miquelon Fishery 

A small commercial fishery occurs off St. Pierre et Miquelon, a French territory off the 

coast of Newfoundland. Historically, the fishery has been very limited in scope (2-3 mt 

per year). There is great interest by the U.S. and Canada in sampling this catch to gain 

more information on stock composition. In recent years there has been a reported small 

increase in the number of fishermen participating in this fishery. In 2004, a sampling 

program was initiated through the efforts of the North Atlantic Salmon Conservation 

Organization (NASCO). The goal of the sampling program is to determine the stock 

composition of the catch to estimate the level of take and potential threat this fishery may 

pose to the continued survival and recovery of the DPS. 

2. Research and Monitoring 

Research and monitoring is needed to help managers monitor the status and trends of 

wild Atlantic salmon populations in Maine. Research is necessary to reduce uncertainties 

about the cause of the decline of wild salmon populations in Maine and evaluate current 

and alternative stocking strategies. Current gaps in the understanding of the reasons for 

the species continued decline makes it difficult to identify and implement effective 

management actions needed to reverse the decline of the DPS and recover the species. 

Further, research and monitoring are key elements in assessing the effectiveness of 

management actions whereby managers are able to employ an adaptive strategy as part of 

the overall recovery program. 

The NRC Report on Atlantic salmon in Maine (2004) raised concerns about potential 

mortality associated with research and monitoring. The NRC (2004) concluded that 

while in most cases the research mortality is so minimal as not to be a serious 

consideration, in several Maine rivers the populations are so small that any mortality 

would be of concern. The NRC (2004) concluded that research that increases the risk of 

death to wild fish should be examined thoroughly. The NRC (2004) specifically 

identified research that requires fish to be anaesthetized, samples of blood or scales from 

very small fish, sampling that held fish for long-periods in strong current (e.g., rotary 

screw traps for smolts during high flows). 

The Services and the ASC have conducted a structured analysis of the threats faced by 

the DPS including the risk associated with research and monitoring (see page 1-93 

Threats Assessment). The Services and ASC concluded that, given the high natural 

mortality and low mortality rates associated with sampling, the low probability of 

encountering a wild fish, research and monitoring poses a low risk to the species. The 

Services agree with the NAS that the value of information obtained through research and 

monitoring activities must be carefully weighed against the possible impact to wild 

populations that could result from mortality associated with the activity. 
1-55

The BO again concluded that the herring fishery was not likely to adversely affect the 

DPS. 

While there is potential for Atlantic salmon bycatch to be occurring in pelagic and 

midwater fisheries due to an overlap in space and time of the fish and gear, there are few 

observations of it actually happening. Beginning in 2005, observer coverage in the 

midwater trawl herring fleet was increased and should improve the ability to assess the 

potential for Atlantic salmon bycatch to occur in the herring fishery. Detection of 

potential Atlantic salmon smolt bycatch in the midwater trawl herring fishery is 

complicated by the volume of herring landed and the similarity in size, shape and 

coloration of the two species. 

In addition to outmigrating post-smolts, the potential also exists for returning adults to be 

taken as bycatch in commercial fisheries. For example, in 2001 a commercial fishing 

vessel captured an adult salmon subsequently determined to be an escaped aquaculture 

fish. While a review of existing commercial fishery records does not indicate that 

bycatch of Atlantic salmon is a significant threat, additional investigation is warranted 

(see page 4-44). 

In addition to marine fisheries, commercial fisheries in estuarine and freshwater 

environments have the potential to incidentally take Atlantic salmon. For example, a 

commercial elver (juvenile eels) fishery harvests small eels returning to Maine rivers 

from their ocean spawning areas. Intense market demand in the Far East (Japan, China, 

Taiwan and Korea) makes elvers a highly valuable commercial catadromous species. In 

Maine, elvers begin to migrate into Gulf of Maine watersheds in March with peak 

migrations occurring in April and May. Elver harvest methods are restricted to fyke nets 

(a funnel shaped net) and hand dip nets. Regulation of the elver fishery includes a season 

from March 22 to May 31, a ban on harvest of elvers upriver of the head-of-tide and 

limits on the length of fyke nets that can be set in waterways. Regulations also prohibit 

nets from the middle third of any waterway and require finfish excluder panels to 

minimize bycatch and adverse impacts on non-target species. Fishing effort for elvers 

has decreased in recent years due to license restrictions and a significant reduction in the 

market price (65 FR 69470). In recent years, no incidental take of juvenile or adult 

Atlantic salmon has been documented in this fishery. 

A recent event highlights the potential for other commercial fisheries to adversely affect 

Atlantic salmon and the need to continue to monitor these fisheries. In 2001, in violation 

of existing regulations, access to the Dyer River (a tributary to the Sheepscot River) was 

entirely blocked by an alewife net. The problem was brought to the attention of state and 

federal agencies by a member of a local conservation organization. 

B. Canadian Fisheries 

In February 1999, the Canadian Department of Fisheries and Oceans (DFO) instituted a 

three-year moratorium on the commercial harvest of Atlantic salmon in Newfoundland 

and Labrador. This moratorium has been extended indefinitely. In addition, the DFO 
1-56

implemented regulations for recreational fisheries, including the requirement to use only 

barbless hooks in Newfoundland and Labrador. Currently, recreational fisheries for 

Atlantic salmon are regulated through in-season adjustments to the total allowable catch 

rates based on salmon returns. Since these recreational fisheries occur in Canadian 

rivers, they do not impact DPS fish. 

C. West Greenland Fishery 

Until recently, the West Greenland fishery was one of the last directed Atlantic salmon 

fisheries in the Northwest Atlantic. In August 2002, commercial fishing for Atlantic 

salmon within Greenland territorial waters was provisionally suspended for five years 

(see page 1-20). The internal use fishery is not included in the agreement. From 2002-

2004, the internal use fishery landed an estimated 19, 19 and 25 metric tons (mt) annually 

(reported and unreported catch, ICES 2005)). This fishery is a mixed stock fishery, 

catching both North American and European fish. The North American component of 

this mixed stock includes both Canadian and United States salmon. Maine-origin salmon 

including endangered salmon are taken in low numbers by this fishery28. Based upon tag 

returns, the commercial fisheries of Newfoundland and Labrador historically intercepted 

far greater number of Maine-origin salmon than the West Greenland fishery (Baum 

1997). Nevertheless, concerns exist about the potential of the West Greenland fishery to 

harvest endangered U.S. salmon. 

Beginning in 1982, Atlantic salmon catch has been sampled from the West Greenland 

fishery to determine continent of origin. The information is used in the scientific model 

that predicts pre-fishery abundance and to make science-based management decisions for 

this fishery. The results of this research are integral to the completion of stock 

assessments of Atlantic salmon through the ICES North Atlantic Salmon Working Group. 

Historically, the overall proportion of European to North American fish taken was 

roughly 50/50 (Baum 1997). In recent years, the proportion of North American fish 

taken in this fishery has increased. Based on discriminant analysis of characteristics from 

scales sampled in the fishery, 91% of fish harvested in 1999 were of North American 

origin, the highest proportion on record (ICES 2005). The reasons for this are not 

understood but may relate to changes in the fish migration patterns of Atlantic salmon, or 

differential rates of decline in the stocks of long-range migrating Atlantic salmon 

originating from North American and European sources. The proportion of North 

American salmon has dropped to approximately 70% in contemporary times (2000-2004 

range of 65-72). This may be due to a shifting of fishing effort southward along the coast 

of West Greenland relative to 1999, with fishing effort disproportionately distributed in 

the southern divisions (NAFO subareas 1D & 1F, ICES 2005). 

In view of elimination of the directed commercial fishery in Maine and changes in the 

high seas fishery, the existing fishery off West Greenland is not thought to be limiting the 

survival of the DPS. The best available data indicate that, while a potential impediment 

 

28 In 2002, based on reported and unreported catch estimates, between 0 and 8 (90% confidence 

interval) DPS fish may have been caught in the fishery (USASAC 2005).
1-58

Section 10(a)(1)(A) of the Endangered Species provides for exemption to the Acts 

prohibition of “take” for research and other activities designed to further the recovery and 

survival of the species (insert ESA language). Currently all research and assessment 

activities conducted by the Services and the ASC are conducted under the authority of 

Section 10 scientific research permits. As part of the permit application process the 

impacts of the proposed research activities have been assessed, including the potential 

mortality of fish and how any potential impacts will be avoided or minimized. Permit 

conditions require that all mortalities be reported. In response to the NAS report, FWS is 

reassessing existing procedures for the issuance of Section 10(a)(1)(A) permits to ensure 

that mortality related to scientific research is minimized. 

The Services and ASC have developed sampling protocols designed specifically to 

minimize the risk of harm to all fish captured and handled as part of ongoing research and 

assessment activities. The Services continue to investigate ways to minimize any 

potential adverse effects from research and develop non-invasive ways to acquire the 

necessary data. For example, the ASC and NOAA have provided support to a University 

of Maine student to study alternatives to electrofishing as a means to minimize impacts to 

salmon populations and are assessing the feasibility of hydroacoustics to monitors smolts 

and returning adults. 

In addition to state and federal agencies responsible for Atlantic salmon, the Maine IFW, 

DEP and DMR, and US EPA, conduct research and assessment activities to monitor other 

species in waters containing DPS fish. These activities may result in the capture of wild 

Atlantic salmon. To date, these agencies have not pursued an ESA take permit. 

C. DISEASE 

Atlantic salmon are susceptible to a number of diseases that can result in direct or indirect 

mortality. Indirect mortality involves debilitation that leads to increased mortality from 

other sources and causes. Disease-related mortality is more apparent and easier to 

document in fish culture facilities than in the wild. The final rule listing the DPS as 

endangered identified disease as a serious threat to the continued survival and recovery of 

the species (65 FR 69459). The Maine TAC (2002) concluded that fish pathogens may 

be a significant factor affecting recovery of Atlantic salmon populations, particularly in 

rivers with salmon net-pen facilities at their mouth or hatcheries in the watershed. 

The Atlantic Salmon Status Review (NMFS and FWS 1999) provides a detailed 

description of common salmonid diseases that may adversely affect wild salmon 

populations in Maine. These diseases include both viral and bacterial pathogens. There 

are at least a dozen common fish diseases that are a threat to Atlantic salmon. To some 

degree, the immediacy of the threat and the basic approach for control are related to 

geographic proximity and frequency of occurrence of the disease relative to the DPS 

population. For convenience of discussion, these diseases are grouped below on that 

basis. 
1-59

There are three basic categories of disease: (a) those not endemic to the geographic range 

of the DPS; (b) those commonly occurring within the geographic range of the DPS; and 

(c) those present to a limited extent within the geographic range of the DPS. The 

significance of each disease within a group, relative to management and severity of 

threat, depends on a number of characteristics of the particular pathogen. These factors 

include the rate of mortality, ease of control, ease of detection and method and rate of 

spread. Diseases not endemic to the DPS include non-marine Viral Hemorrhagic 

Septicemia (VHS), Infectious Hematopoietic Necrosis (IHN), Oncorhynchus Masou 

Virus Disease, Whirling Disease and Ceratomyxosis. Those commonly occurring within 

the geographic range of the DPS include Bacterial Kidney Disease (BKD), Infectious 

Pancreatic Necrosis (IPN), Enteric Redmouth (ERM), Furunculosis, Coldwater Disease 

(CWD) and Vibrio. Those present to a limited extent within the geographic range of the 

DPS include Infectious Salmon Anemia (ISA) and Salmon Swimbladder Sarcoma (SSS) 

(Mills 1971; Gaston 1988; Olafsen and Roberts 1993; Egusa 1992). 

The threats posed by diseases in group (a) are best controlled through strict importation 

and transfer regulations and protocols. State regulations in Maine are some of the most 

restrictive in the U.S. The State’s current salmonid fish health inspection and importation 

regulations (09-137 Code of Maine Rules Chapter 2.03-A) identify exotic and endemic 

infectious pathogens of regulatory concern. These regulations also prohibit the transfer 

of live salmonids or gametes among culture facilities until the fish are tested and certified 

pathogen free, outlaws the sale of clinically ill fish, outlines a standardized annual testing 

and monitoring protocol for all salmonids in public and private facilities and requires that 

fish taken from the wild be isolated until inspected for diseases. These regulations also 

outline stringent regulations for salmonid importation into the State and outline a 

standard protocol for action in the case of a confirmed disease outbreak. Applicable 

federal import regulations (Title 50) apply only to a limited number of pathogens and 

need to be revised to include the ISA virus. Guidelines and protocols, such as the 

American Fisheries Society/Fish Health Section (AFS/FHS) Suggested Procedures for 

the Detection and Identification of Certain Finfish and Shellfish Pathogens (2004), the 

New England Salmonid Health (NESH) Guidelines (2001) and the North American 

Commission of NASCO Protocols for Salmonid Introductions and Transfers (1992), 

provide guidance to control the introduction and spread of group (a) pathogens beyond 

their current distribution. 

The relatively common diseases found in group (b) are most often a problem in fish 

culture situations (hatchery and pens) of high population densities. Mitigation of the 

disease threats posed by group (b) pathogens primarily requires proper fish culture 

practices. In addition to impacting hatcheries and net-pens, group (b) diseases can also 

impact salmon in the wild. For example, furunculosis is a bacterial disease that is more 

common under crowded hatchery conditions but also occurs in the wild. The bacterium 

causing this disease, Aeromonas salmonicida, is highly infectious in freshwater and 

sufficiently salt tolerant for transmission to occur in seawater. This disease can cause 

mortality if not recognized and treated at an early stage. In New England, furunculosis is 

the only documented epizootic source of mortality in wild Atlantic salmon (Bley 1987). 

Outbreaks of this disease are most common when environmental conditions become 
1-60

stressful, such as during high water temperature situations that can occur with low water 

levels. Thus, this threat needs to be considered as a factor in maintaining proper flow 

levels in DPS rivers. In Norway, furunculosis was found for the first time after the 

importation of rainbow trout from Denmark (Heggberget et al. 1993). Another example 

of how group (b) diseases can be a problem in culture situations would be with 

Flavobacterium psychrophilum, the bacterium causing cold water disease (CWD). 

Although this bacterium is considered ubiquitous in the aquatic environment, it is an 

opportunistic, rather than obligate, pathogen so the impact of horizontal transmission may 

not be very significant. However, the bacterium has caused acute and chronic mortality 

in the early life stages of salmon raised in hatchery environments. Experiments strongly 

suggest that F. psychrophilum can be vertically transmitted within salmon eggs and that 

surviving infected fry may be adversely affected in the natural environment. 

1. Infectious Salmon Anemia (ISA) 

The concern about disease raised in the final listing rule (65 FR 69459) relates primarily 

to the recent occurrence of two salmonid diseases previously unknown in the geographic 

range of the DPS: ISA and SSS; these diseases are discussed below. 

ISA is a contagious and untreatable viral disease that affects a fish’s kidneys and 

circulatory system with a variable mortality rate from 3% to more than 50% in one 

production cycle (USDA APHIS 2001). Atlantic salmon infected with clinical ISA are 

anemic, typically lethargic, swim near the surface and fail to swim upright. Experimental 

studies have demonstrated that the virus is transmissible through mucous, feces and blood 

of infected/diseased fishes (Nylund et al., 1994). This results in cultured fishes being 

particularly susceptible to exposure to ISAV by infected cagemates. Studies in Norway 

indicate that penned salmon populations held within five kilometers (km) of each other or 

the discharge of slaughter wastes are at greatest risk of contracting ISA (Jarp and 

Karlsen, 1997). There is no evidence that the virus spreads vertically (from parents to 

offspring) although poor disinfection of fertilized eggs may allow for external transfer of 

the virus. Poor culture practices in fish hatcheries and net-pens in an Atlantic salmon 

watershed could increase the risk of a wild population's exposure to disease. 

ISA is the most significant known disease threat to the DPS. The threat of ISA to the 

recovery of the DPS is both direct, through infection of wild fish, and indirect by 

compromising hatchery supplementation of the DPS. The infection of emigrating smolts 

or adults passing near infected net-pens may cause mortality. This risk is greatest in 

those rivers whose approaches are nearest the highest concentration of net-pens, 

specifically the Dennys, East Machias and Machias. Other DPS river populations may 

also be at risk if they migrate through areas where aquaculture facilities are concentrated. 

ISA has the potential to compromise CBNFH and the GLNFH if ISA-infected fish are 

inadvertently brought into one of these facilities. For example, an ISA-infected salmon 

brought into CBNFH for broodstock purposes could potentially infect other fish at the 

facility. In fact in 2001, a Penobscot sea run salmon brought to CBNFH for use as 

broodstock initially tested positive for ISA. Subsequent tests were negative and no 
1-61

additional fish were found to be infected. Outbreaks of ISA in freshwater hatcheries have 

not been reported from major salmon producing countries that have experienced ISA 

outbreaks. Still the potential for juveniles that have never entered salt water to be carriers 

of the virus is currently unknown. 

ISA has already had an impact on Atlantic salmon recovery efforts. An adult stocking 

experiment (see page 4-69) was not fully optimized due to ISA concerns. These concerns 

resulted in more than 50% of the net-pen reared broodstock being destroyed. This 

decision was made because fish health experts felt the close proximity of these fish to 

fish infected with the ISA virus (ISAV) in commercial aquaculture pens was a substantial 

risk to wild populations. This concern was later affirmed by the outbreak of ISA in 

marine pens in the Cobscook Bay region (see page 1-82). 

ISA was first reported in Norway in 1984 (Thorud and Djupvik 1988). In more recent 

years, cases of the disease have been reported from eastern Canada (Mullins et al. 1998), 

Scotland (Rodger et al. 1998), the Faroe Islands (OIE 2000), and in Cobscook Bay, 

Maine (Bouchard et al. 2001). The virus has also been associated with disease in 

cultured coho salmon in Chile (Kibenge et al. 2001) and very recently has been detected 

in cultured rainbow trout in Ireland. 

The ISA virus has been known to cause disease in cultured fishes, principally in Atlantic 

salmon, although other species may act as carriers of the virus without signs of the 

disease. Species other than Atlantic salmon can become infected with ISAV and must be 

considered in the epizootiology of outbreaks and management of ISA. In laboratory 

studies, brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) have been 

shown to be asymptomatic carriers of the ISA virus that can transmit the virus to salmon 

by co-habitation (Nylund and Jakobsen 1995; Nylund et al. 1995; Nylund et al. 1997). 

Escaped or caged rainbow trout may pose a threat to wild Atlantic salmon by serving as a 

reservoir of ISAV. 

Recent studies in the United States and Canada indicate non-salmonids (i.e., gadids) can 

become infected with ISAV. Whether these species act as reservoirs in wild populations 

remains to be determined. Assays of non-salmonid fishes taken from pens containing 

ISA-diseased cultured Atlantic salmon resulted in isolation of virus from tissues of 

asymptomatic cod (MacLean et al. 2003). 

Results of recent studies conducted in Scotland and Canada indicate that ISAV exists at a 

low level in wild salmonids. ISAV has been found in Atlantic salmon aquaculture 

escapees (Olivier 2002; Raynard et al. 2001). There has been one case of wild salmon 

exhibiting ISA in Canada, but these wild fish were confined in a trapping facility with 

infected salmon of aquaculture origin. 

At the time of the listing of the DPS as endangered in December 2000 (65 FR 69459), 

some U.S. net-pen sites in Cobscook Bay, the location of Maine’s greatest concentration 

of salmon aquaculture pens, were within five km of Canada’s ISA positive sites, raising 

concerns about the potential for this disease to infect U.S. aquaculture and wild salmon 
1-62

stocks. Subsequent to the listing of the Gulf of Maine DPS of Atlantic salmon as 

endangered, the disease spread to U.S. aquaculture sites within Cobscook Bay. The first 

known case of ISA in Maine occurred in Cobscook Bay at a salmon aquaculture net-pen 

site. The infection probably occurred in 2000 and was confirmed in February 2001. By 

September 2001, 50% of the net-pen sites in Cobscook Bay were ISAV-infected or 

diseased. 

In January 2002, in an effort to control a catastrophic outbreak of ISA in Cobscook Bay, 

the Maine Department of Marine Resources (DMR), with the assistance of the U.S. 

Department of Agriculture’s Animal and Plant Health Inspection Service 

(USDA/APHIS), ordered the destruction of an estimated 1.5 million cultured salmon in 

the Bay. The industry was required to remove all fish from the Bay and a fallowing 

period, between sixty and ninety days, was imposed for the entire Bay in an attempt to 

eradicate the disease. The industry was also required to remove, clean and disinfect all 

the associated net-pens, barges and equipment at all the farms. The January 2002 order 

followed the voluntary removal by the aquaculture industry of nearly one million ISAinfected or exposed fish. In March 2002, ISA was also detected in an aquaculture facility 

in Passamaquoddy Bay. In response, the DMR issued an eradication order for the 

approximately 140,000 fish at the site. 

In response to the ISA outbreak in Cobscook Bay, Maine DMR implemented new fish 

health regulations. The new DMR rules include mandatory surveillance and reporting of 

all test results for ISAV in salmon culture facilities. Sites with confirmed presence of 

ISAV are automatically subject to a remedial action plan developed by the DMR in 

cooperation with the salmon growing industry. Under the new regulations, the movement 

of vessels and equipment is also restricted. Prior to the rule changes, surveillance was 

not mandatory and reporting was only required when a case of the disease was 

confirmed. 

The new rules require monthly sampling for all active finfish facilities in Cobscook Bay 

and quarterly testing for aquaculture facilities elsewhere in Maine. Reporting of results is 

mandatory and reports are provided to DMR. The DMR can require monthly testing for 

finfish facilities outside of Cobscook Bay if a positive case of ISAV is detected. The new 

rules expand DMR’s authority to take action at not only infected facilities, but also those 

exposed to ISAV. The rules require DMR to consult with all relevant state and federal 

entities with expertise in ISA control to keep ISA from spreading and prevent further 

outbreaks. 

In response to the ISA outbreaks, the Maine DMR, with assistance of the USDA/APHIS 

also implemented an ISA control and indemnity program for farm-raised salmon in the 

U.S. The funds provided by the USDA were used to help the State of Maine with 

epidemiology and surveillance, and to indemnify the industry for their losses due to ISA. 

Under the DMR rule, all salmon growers in Maine must participate in the program. The 

goal of this program is to control and contain the disease through rapid detection and 

depopulation of salmon that have been infected with or exposed to the ISA virus. 
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In Spring 2002, Maine DMR authorized the restocking of Cobscook Bay. The Bay had 

lain fallow since January 2002. This authorization followed USDA approval of the 

cleaning and disinfection of equipment and the fallowing period. Subsequent to 

approval, the aquaculture industry stocked 1.9 million smolts on seven farms in 

Cobscook Bay. The number of smolts stocked was 30% lower than the amount 

historically stocked in this area (DMR 2002). New husbandry standards have also been 

put in place as part of the ISA control program. These new standards are administered by 

DMR. 

The ISA control program initially divided Cobscook Bay into two management areas, a 

southern and a northern zone. The southern zone was stocked in even years beginning in 

Spring 2002. The northern zone was stocked only in odd years, beginning in Spring 

2003. Recently, USDA and Maine DMR have determined that the entire Cobscook Bay 

would be managed as a single area. DMR estimated that by there would be 

approximately 25% fewer fish in Cobscook Bay compared to previous levels. In addition, 

several conditions are required for each lot of smolts that are introduced into net-pens 

from freshwater hatcheries. All aquaculture facilities in Cobscook Bay are only 

permitted to raise a single-year class of fish. A minimum thirty-day fallowing period 

between production cycles is required. No more than 10% of the fish at a site may be 

carried over between production cycles and then only upon approval by DMR. This 

approval requires that no ISA is detected at the site during the production cycle, that 

general fish health is satisfactory, that fish are removed by September 1, and that there be 

a biweekly surveillance of the site by a fish health professional. Movement of fish 

between farms in the same zone requires a permit and verification that ISAV has not been 

detected at either site in the four weeks prior to movement. There will be no moving of 

fish between zones. In addition, farms, aquaculture vessels and processing plants are 

subject to routine third-party biosecurity audits. Despite these measures, additional cases 

of ISAV were detected at aquaculture sites in Cobscook Bay beginning in June 2003 and 

continuing in 2004. 

The DMR’s bay management program was developed following an evaluation of other 

bay management and ISA control programs in Canada, Ireland, Scotland and Norway. 

These nations have developed control programs intended to prevent further outbreaks of 

the disease. The DMR plans to codify bay management husbandry standards in a rule 

and establish other bay management areas where finfish leases are located. Successful 

sea lice management and control is a necessary component of bay area management as 

sea lice have been shown to retain the ISA virus after feeding on infected salmon 

(Nylund et al. 1993). 

During routine surveillance of all salmon culture sites in Maine, an apparently new strain 

of ISAV was detected in November 2003 at a site approximately 50 miles from Cobscook 

Bay. This was the first detection of ISAV at any site in Maine other than Cobscook Bay. 

The new strain did not cause disease in the cultured salmon and did not grow in the 

laboratory on various cell lines typically used in ISA isolation. Gene sequencing of this 

organism indicates it is more closely related to a Norwegian strain than the New 

Brunswick strain that has caused the mortalities in Cobscook Bay. Subsequently, this 
1-64

new strain has also been found in Cobscook Bay sites. Efforts are underway to sequence 

archived samples to determine the significance of the virus in the Cobscook Bay system. 

One potential mode of disease transmission is through biological sampling conducted by 

various state and federal agencies in DPS rivers. The development and implementation 

of disinfection and biosecurity protocols reduces the risk of a pathogen being moved 

from one location to another (G. Russell Danner, IF&W fish pathologist, personal 

communication 2004). Disinfection and biosecurity protocols, where not already in 

place, should be developed and implemented for all research and sampling activities 

taking place in rivers within the DPS (see page 4-63). 

2. Salmon Swimbladder Sarcoma (SSS) 

Salmon swimbladder sarcoma virus (SSSV) is a pathogen recently reported in North 

America. A similar (perhaps identical) virus was first reported from sub-adult farmed 

Atlantic salmon in Scotland in the 1970s (Duncan 1978; McKnight 1978). The disease 

has not been reported from Scotland since and the relationship between this and the 

Maine retrovirus has not been determined. 

The level of threat posed by SSSV is more difficult to assess than ISAV. In 1996, this 

retrovirus was detected in sub-adult salmon collected as parr from the Pleasant River for 

river-specific broodstock development. These fish were being held at the North 

Attleboro National Fish Hatchery (NANFH) in Massachusetts. Mortalities were first 

observed in 1997 and continued to occur in 1998. Necropsies revealed massive tumors in 

the swimbladder. The detection of the virus and the outbreak of disease resulted in a 

decision to destroy all captive broodstock for the Pleasant River. Pleasant River fish 

being held at a private hatchery in Deblois, Maine were also found to be positive for the 

virus, although no disease was present and no mortality occurred. As a precaution, all 

these fish were destroyed. The destruction of these broodstock significantly affected 

efforts to develop river-specific broodstock for the Pleasant River. 

No disease symptoms have ever been observed in wild populations or in the captive 

populations held in Maine. No fish at CBNFH have ever demonstrated symptoms of the 

disease in the seven years wild stocks have been held at that hatchery. 

It is not known if SSSV contributes to salmon mortality in natural conditions either 

directly through disease, indirectly through debilitation of immune system and resultant 

decrease in fitness and survival or if it has no substantial impact on survival in the wild. 

Assays done on Atlantic salmon adults and smolts from other Downeast DPS rivers 

revealed positive results in a small number of fish from the Machias, East Machias and 

Narraguagus rivers, although there were no signs of disease. These results indicate that 

the virus may be widespread at a low level in the environment. 
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D. PREDATION AND COMPETITION 

Predation would not be expected to threaten the continued existence of a healthy population. 

The threat of predation on endangered salmon is significant because of the very low numbers 

of adults returning to spawn and the increased population levels of some predators. Known 

predators of Atlantic salmon include marine mammals (e.g., seals, porpoises, dolphins), 

terrestrial mammals (e.g., otters, minks), birds, fish and sharks. Predation is a naturally 

occurring factor affecting salmon populations. Anthony (1994), the Atlantic Salmon Status 

Review (NMFS and FWS 1999) and Baum (1997) review the significant predators of 

Atlantic salmon and identify the various life stages of salmon they prey upon. 

Estimating predation rates is difficult because of the wide spatial and temporal distribution of 

Atlantic salmon at low densities and the large number and variety of potential predators. The 

final rule listing the DPS as endangered concludes that there are insufficient data at this time 

to show that predation threatens the continued existence of the DPS (65 FR 69459). 

Nonetheless, the threat from predation is significant because of low numbers of adult salmon. 

In addition to predation, the potential exists for interspecific competition between salmon and 

other species of fish including non-native species. Interspecific competition may result in 

adverse impacts to the DPS. Adverse effects of competition are exacerbated by the small 

size of the Atlantic salmon population. The introduction of non-native fish can endanger or 

threaten the continued existence of native species of fish (Lassuy 1999). For example, longterm stocking of non-native rainbow trout into streams in the Western U.S. has resulted in the 

widespread extinction of native trout populations through introgressive hybridization 

(Behnke and Zarn 1976; Leary et al. 1995). Introduced brown trout have replaced subspecies 

of cutthroat trout in large streams throughout the same region (Behnke 1992). 

1. Marine Mammals 

Since the passage of the Marine Mammal Protection Act (MMPA) in 1972, seal populations 

have increased in Maine. Five species of seals are found in the Gulf of Maine region: the 

harbor seal (Phoca vitulina), gray seal (Halichoeurs grypus), hooded seal (Cystophora 

cristata), harp seal (Phoca groenlandica) and ringed seal (Phoca hispida). Harbor seals and 

gray seals are the only seal species that have a year-round presence in Maine. Harp and 

hooded seal sightings and strandings have increased in recent years in New England (NMFS 

1996). The apparent increase in the number of harp and hooded seals is largely based on 

strandings and fishery bycatch data. These species are ice seals and usually occur in Maine 

from January to May. No systematic surveys document population trends of these two 

species in U.S. waters. Ringed seals are seldom observed in the Gulf of Maine (McAlpine et 

al. 1999; Lucas and McAlpine 2002). 

The growth of seal populations in Maine has led to speculation that declining salmon 

populations can be attributed, in part, to seal predation. Populations of both harbor and gray 

seals have grown since the early 1980s. Harbor seal populations along the coast of Maine 

have increased from 10,540 in 1981 to 30,990 in 1997; an average annual increase
1-66

of 4.2%. Similarly, the number of pups along the Maine coast has increased at an annual 

rate of 12.9% over the 1981-1997 period (Gilbert and Guldager 1998). Gray seal 

abundance is also increasing in the U.S. but the rate of increase is unknown (Waring et al. 

2000). In 1996, the estimated gray seal population in eastern Canada was 143,000 (Mohn 

and Bowen 1996). Gray seal populations in eastern Canada have experienced a 7.4% 

annual growth in the Gulf of St. Lawrence and a 12.6% increase at Sable Island (Hammill 

et al. 1998). Bowen et al. (2003) note that the numbers of gray seal pups on Sable Island, 

Canada, have been increasing at 12.8% since the early 1960s. Gray seal numbers in 

Maine increased from an estimated thirty animals in the early 1980s to between 500-

1,000 animals in 1993 (Waring et al. 2001). 

Seals are opportunistic feeders and will target both benthic and schooling pelagic fish 

species. Harbor seal prey include herring, alewife, capelin, clam, sand lance, cod, 

haddock, pollock, hake, ocean pout, flounder, squid and mackerel (Boulva and McLaren 

1979; Katona et al. 1993; Williams 1999). Payne and Seltzer (1989) found that in 

southern New England harbor seal scats collected in winter had a large fraction of 

sandlance otoliths. Gray seals feed primarily on squid, herring, hake and cod (Mansfield 

1988; Katona et al. 1993; USASAC 2000). Seal predation on salmonids has been 

documented in Europe and in the Pacific Northwest. Rae (1960, 1965, 1973) reported 

that seal predation on salmonids was significant around Scotland. These findings must be 

considered in light of the fact that these seals were caught in salmon nets. More recent 

studies employing improved dietary analysis techniques suggest that salmonids are of 

minor importance (NOAA AFSC 2001-04). 

There are only two documented cases of gray seal predation on Atlantic salmon in the 

Gulf of St. Lawrence (USASAC 2000). There have been no documented instances of 

Atlantic salmon being found in harbor seal stomachs in U.S. waters in the Western North 

Atlantic. The U.S. Atlantic Salmon Assessment Committee (USASAC) notes that if onehundred percent of the Atlantic salmon biomass in the Atlantic Ocean were consumed by 

harp seals29, Atlantic salmon would account for only 0.01 % of their annual diet. This 

illustrates the difficulty in documenting Atlantic salmon predation by seals (USASAC 

2000). 

During fish trapping operations in Maine, incidences of scarring and injury on adult 

Atlantic salmon have been observed. ASC staff records suggest that on the Penobscot 

River as many as 11% of adults entering the trap at the fishway have apparent seal bites 

(several hundred fish are examined each year) (MASCP 1997). Anglers and biologists 

have reported apparent seal bites on adult Atlantic salmon caught in Washington County 

rivers during the past twenty years. In 1986, members of the Two Rivers Salmon Club 

reported that 70% of the salmon caught in the East Machias River had seal bites (Baum 

1997). In Scotland, approximately 20% of returning salmon displayed predator damage 

(Thompson and Mackay 1999). The majority of the observed injuries were determined to 

be caused by odontocetes (primarily porpoises), not seals. These findings highlight the 

 

29 The Northwest Atlantic harp seal population is comprised of approximately 5.2 million animals. 

These seal populations consume approximately 3+ million tons of fish annually.
1-67

difficulty of using observed apparent predator damage in assessing the impact of different 

predators on salmon populations. Further, it is not possible to quantify the numbers of 

salmon that did not survive an attack. 

Evidence suggests that seal predation is not a function of population size, but rather is a 

function of habitat and individual rogue animals (NMFS 1996). For instance, Rae (1960, 

1965) found that seal attacks on salmon nets in Scotland were not related to population 

size. Seal attacks at river mouths are likely attributable to a few individuals that have 

learned how to catch salmon there (James Gilbert, University of Maine, personal 

communication). 

It has been suggested that expanding harp seal populations may indirectly impact salmon 

population abundance in the North Atlantic by their consumption of large amounts of 

capelin (Anthony 1994). The current available evidence on this impact is inconclusive. 

Capelin are a major prey item of Atlantic salmon off the coast of West Greenland and on 

the Canadian shelf (Hislop and Shelton 1993). Reddin and Carscadden (1982) conclude 

that an important biological link exists between salmon and capelin. Hislop and Shelton 

(1993) report that capelin comprised 72% of the diets of Atlantic salmon in West 

Greenland and 73% in Canada. They note, however, that Atlantic salmon, as 

opportunistic predators, are not very sensitive to interannual variation in the availability 

of any specific prey item. 

In Atlantic Canada, researchers have attempted to model the trophic impacts of seal 

predation on fish stocks (Stenson et al. 1997; Hammill and Stenson 2000). While 

estimates of consumption rates indicate that seals in Atlantic Canada do consume large 

quantities of fish, seal predation is only one of many sources of fish mortality. 

Estimating the relative impact of seal predation on fish stock abundance will not be 

possible until other sources of natural mortality are quantified (Hammill and Stenson 

2000). In order to fully assess the significance of this possible competition, a complete 

analysis of the food web in the Gulf of Maine and the Atlantic would be required. While 

multispecies predation models offer great potential to assess the impacts of predation, the 

data requirements make the use of such an approach unlikely in the near future (Hammill 

and Stenson 2000). 

2. Avian Predators 

The Services have concluded that avian predation poses a high level threat to the survival 

and recovery of the DPS. A number of bird species are known to prey on juvenile 

Atlantic salmon including the double-crested cormorant, mergansers, belted kingfisher, 

great black-backed gulls, gannets and owls. Among these, cormorants are often cited as a 

major predator contributing to declining salmon populations, although mergansers are 

also known to be significant predators. Avian predators of adult salmon include ospreys 

and eagles (NMFS 2000). 
1-68

i. Double-crested Cormorant 

Cormorants were extirpated from New England by the early European settlers (Baum 

1997) and did not begin to recolonize areas along the Maine coast until the 1920s (Krohn 

et al. 1995). In 1972, cormorants became a protected species under the Migratory Bird 

Treaty Act (MBTA). The MBTA regulates killing of protected birds and destruction of 

their nests and eggs. Cormorant populations increased rapidly through the mid-1980s 

(Krohn et al.1995). By the early 1990s, population growth had stabilized and there were 

an estimated 28,000 breeding pairs in 135 colonies in Maine (Krohn et al. 1994). In 1995, 

an aerial survey conducted by IFW biologists as part of an FWS funded colonial waterbird 

inventory recorded approximately 20,000 cormorant nests in 125 colonies in Maine. 

Several recent papers provide summaries of double-crested cormorant predation and its 

potential impact on Atlantic salmon populations in Maine (Blackwell and Krohn 1997; 

Blackwell et al. 1997; see also Baum 1997). Cormorants are highly opportunistic and 

voracious feeders that typically feed on mid-water schooling fish (Duffy 1995; Blackwell 

et al. 1997; Derby and Lovvorn 1997). They consume between 16-30% of their body 

weight of fish per day (Anthony 1994). In addition to Atlantic salmon, cormorants are 

known to feed on at least forty other species of fish (Baum 1997). 

Much of the published research reveals that cormorant predation on salmon is limited both 

temporally and spatially (Anthony 1994). Krohn et al. (1995) found that cormorant 

predation can reduce fish populations in localized feeding areas, including dams where 

migrating Atlantic salmon smolts can be congregated (Blackwell and Krohn 1997). 

Cormorants can consume large numbers of emigrating hatchery-reared salmon smolts 

during spring migration (Meister and Gramlich 1967; Kennedy and Greer 1988). The 

presence of manmade obstructions to passage, such as dams, weirs and fish traps, may 

exacerbate predation rates. 

Cormorant predation is reported to be generally higher on hatchery-reared than wild 

smolts (Anthony 1994; Baum 1997; NMFS 2000). There is little evidence, despite thirty 

years of study and the sampling of thousands of cormorant stomachs, of cormorant 

predation on wild Atlantic salmon smolts (Baum 1997). A number of factors may account 

for this observation, including method and timing of hatchery-reared smolt release, 

conspicuous external tags (i.e, carlin tags) on the backs of hatchery fish and behavioral 

differences between hatchery and wild smolts (i.e., predator avoidance behavior). Factors 

that likely serve to minimize cormorant predation on wild salmon smolts include predator 

avoidance behavior, the fact that smolts migrate primarily at night while cormorants 

forage primarily during the day and run timing (Baum 1997). 

Studies of cormorant predation conducted by the Atlantic Sea Run Salmon Commission 

(ASRSC; predecessor agency to ASC) and FWS (1972 to1982; 1986 to 1988) in the 

Penobscot River found predation rates of between 1-2% for hatchery smolts (Baum 1997). 

Meister and Gramlich (1967) studied salmon predation by cormorants in the Machias 

River estuary. The results of this study documented that cormorants consumed an 

estimated 8,000 tagged hatchery smolts during the period 1966-1967 in the Machias 

River. Predation rates on migrating hatchery-reared salmon smolts were found to be as
1-69

high as 13.4% in the Machias River (Meister and Gramlich 1967). This study suggests 

that cormorants can be significant predators of Atlantic salmon and may adversely affect 

the abundance of hatchery-reared salmon smolt in a river. More recently, Blackwell 

(1996) documented cormorant predation rates of up to 7% for hatchery-reared smolts in 

the Penobscot River. Much of the predation was observed in the headwater ponds of 

several hydropower dams (Blackwell 1996). 

ii. Mergansers 

Common and red-breasted mergansers are known to prey on juvenile Atlantic salmon. 

The common merganser preys on salmon parr in streams throughout the summer while 

the red-breasted merganser is a marine species that feeds more heavily on migrating 

smolts primarily in the spring (Anthony 1994). 

Studies in Canada found mergansers consumed more juvenile Atlantic salmon than did 

cormorants. White (1957) found that salmon parr were consistently the major food item 

of mergansers in the ten rivers in New Brunswick and the six rivers in Nova Scotia he 

studied. Elson (1975) concludes that smolt production was higher in the Maramichi River 

in Canada when mergansers were scarce. The DFO (1998) concludes that mergansers 

likely take substantial numbers of juvenile salmon in some maritime rivers (DFO 1998). 

The report notes that repeated experiments have failed to show that bird control increases 

juvenile salmon abundance (DFO 1998). 

Mergansers, like cormorants, are protected under the MBTA (16 USC Sec. 590q-1). 

Current state regulations permit hunting of this species. Hunters are permitted to shoot 

up to five mergansers per day (MIFW 2003). 

3. Piscine Predators and Competitors 

i. Freshwater 

Juvenile salmon are preyed on by a number of fish species. These include both native 

and non-native fish species. Native species include brook trout (Salvelinus fontinalis), 

American eel (Anguilla rostrata), chain pickerel (Esox niger) and landlocked salmon 

(Salmo salar sebago). Non-native species include smallmouth bass (Micropterus 

dolomieui), largemouth bass (Micropterus salmoides), brown trout (Salmo trutta), splake 

(hybrid cross of brook and lake trout), and rainbow trout (Oncorhynchus mykiss)(Godfrey 

1957; Warner 1972; Larsson 1985; Anthony 1994). 

The Services have concluded that predation and competition between Atlantic salmon 

and other non-native fish species poses a high level threat to the survival and recovery of 

the DPS. The introduction of non-native species of fish may adversely affect native 

species through predation, competition for food and available habitat, interbreeding and 

hybridization and the introduction of disease and parasites (Kohler and Courtenay 1986; 

ANS Task Force 1994; Lassuy 1999). Native species stocked outside their historic range 

are also a concern. Interactions between Atlantic salmon and non-salmonids, especially 
1-70

introduced species, are poorly understood. Most research on competition has focused on 

interactions between species of salmonids (Hearn 1987; Fausch 1988). Competitive 

interactions are often more harmful when they are between native and non-native species 

that have not co-evolved (Hearn 1987; Fausch 1988). The NRC (2004) concluded that 

non-native species that prey on salmon and compete with are potentially an important 

antrhopogenic threat to Atlantic salmon in Maine. 

Interspecific competition between Atlantic salmon and other salmonid species are 

dependent on a number of factors including the availability of food and habitat. 

Ecological interactions between salmonids can lead to increased mortality and decreased 

growth (Fausch and White 1986). Survival rates from eggs to the fry stage are affected 

by a number of factors (i.e., stream gradient, overwintering temperatures, water flows) 

including the level of predation and competition (Bley and Moring 1988). The growth 

rate of parr has been shown to be influenced by the level of competition and predation 

(Hearn 1987). 

The Maine IFW stocks a number of native and non-native salmonids into rivers, lakes 

and ponds within DPS river watersheds. In addition, many non-native species of fish 

have been introduced illegally in DPS river watersheds by individuals that wish to fish 

for these species. 

Chain pickerel (Esox niger) is native to the State of Maine. It was introduced into the 

Penobscot River watershed in 1819 and rapidly dispersed throughout the State including 

into DPS rivers (Baum 1997). Predation by pickerel on migrating Atlantic salmon smolts 

can be significant, particularly in lakes, ponds and other impoundments (Barr 1962; 

Warner 1972; Van den Ende 1993; Baum 1997). Barr (1962) found that 21% of the 

pickerel sampled in Beddington Lake on the Narraguagus River contained salmon smolts. 

Van den Ende (1993) found that Atlantic salmon are the most common prey item of chain 

pickerel in the Penobscot River. Nearly one-third of twenty-three pickerel captured in 

this study was found to contain Atlantic salmon. Maine IFW has removed the bag limit 

on chain pickerel on the five DPS rivers in Washington County to maximize harvest and 

reduce pickerel predation on Atlantic salmon. 

Smallmouth bass (Micropterus dolomieui) are known to prey on juvenile Atlantic 

salmon (Baum 1997). This species, first introduced into Maine waters in the 1860s, now 

occurs in all the DPS rivers with remnant populations of wild Atlantic salmon (MASCP 

1997; Baum 1997). Juvenile smallmouth bass are found consistently in the same habitat 

as juvenile Atlantic salmon. Interspecific competition between the two species could 

adversely affect Atlantic salmon. 

While smallmouth bass have been present in some DPS rivers for a number of decades 

(i.e., the Narraguagus and Machias), it has been introduced relatively recently to the 

Pleasant River. In the mid-1970s, this species was illegally introduced into Pleasant 

River Lake, a headwater lake of the Pleasant River. By 1995, smallmouth bass were 

found in the lower reaches of the river all the way to Columbia Falls at the head-of-tide 

(Scott 2002). Though little data has been published, smolt predation by smallmouth bass 
1-71

has been observed anecdotally and substantial levels of smolt predation by smallmouth 

bass have been observed in Pacific salmon populations (Rieman et al. 1991, Tabor et al. 

1993). The continued expansion and possible interactions between smallmouth bass and 

Atlantic salmon should be closely monitored. 

Van den Ende (1993) studied predation of Atlantic salmon smolts by smallmouth bass in 

the Penobscot River. Van den Ende (1993) did not document any consumption of smolts 

by smallmouth bass in the Penobscot River. Van den Ende concluded that smallmouth 

bass were probably not a major predator on Atlantic salmon smolts in the Penobscot 

River. His conclusions were based on a number of factors including: low feeding rates 

during the beginning of the smolt run30, morphological constraints (small mouth), 

differential habitat use by each species (smolts generally utilize areas of high current 

velocity; smallmouth bass prefer current edges and other low velocity areas), antipredator behavior of smolts and observed selection of small prey rather than large prey by 

smallmouth bass. 

The results of Van den Ende’s study, however, are limited because of the small number 

of smallmouth bass sampled (n=125) and the limited duration of the study (1-year). 

Furthermore, field sampling was conducted, by angling, in areas known to have relatively 

high smallmouth bass catch rates. Sampling sites were not selected according to the 

likelihood of encountering smallmouth bass actively consuming smolts, rather they were 

chosen based upon accessibility and previous capture success (Van den Ende 1993). 

Further, prey regurgitation among angled fish is common (West 2001) and likely much 

higher than with other sampling gear thus the results of dietary analyses on fish sampled 

by angling should be scrutinized very carefully. 

It is likely that smallmouth bass prey on salmon fry and parr, which are found in similar 

habitats as bass (Baum 1997). ASC electrofishing data from juvenile salmon rearing 

areas in DPS rivers indicate that smallmouth bass commonly occur in these areas at sizes 

capable of consuming juvenile Atlantic salmon (Ken Beland, ASC, personal 

communication). 

Largemouth bass (Micropterus salmoides) are present in the Sheepscot, Ducktrap and 

East Machias rivers. This species was introduced into Maine sometime during the early 

1900s although the exact date of introduction is not known. Largemouth bass are known 

to prey on salmon (Warner 1972, Anthony 1994). The potential level of predation on 

Atlantic salmon is currently unknown. There is currently no viable way to control these 

populations. 

Brown trout (Salmo trutta) are not indigenous to the waters of Maine. The first stocking 

of this species in Maine occurred in 1885 at Branch Lake, Ellsworth (Maine IFW 2001). 

Brown trout predation has been implicated in the decline of native salmonid populations 

 

30 Van den Ende (1993) found that smallmouth bass were inactive and did not feed at 5EC, 

responded to prey at 10EC and fed most actively at 15EC. By the time temperatures reach these 

levels, most salmon smolts have already migrated out of the river. 
1-72

in North America (Moyle 1976; Sharpe 1962; Alexander 1977; 1979; Taylor et al. 1984). 

Brown trout are known to eat large numbers of stocked Atlantic salmon fry (Maine ASC 

and Maine IFW 2002). Brown trout have been stocked into a number of headwater lakes 

within DPS river watersheds in Washington County including the East Machias and 

Machias watersheds (MASCP 1997). The Sheepscot River is the only salmon river 

within the DPS where brown trout have been captured during stream assessments 

(MASCP 1997)31. Stocked brown trout in the Sheepscot River have established a selfsustaining population. The potential exists for brown trout to prey on juvenile Atlantic 

salmon in the Sheepscot River. The Maine ASC has collected large brown trout (up to 

about 12”) in the vicinity of the head-tide dam and at other lower river sites. This reach 

of the Sheepscot River has the most continuous and highest quality spawning habitat in 

the entire river. In addition, the ASC has documented both juvenile and adult brown 

trout below Branch Pond on the West Branch of the Sheepscot River. The Maine IFW 

subsequently discontinued stocking of brown trout in Branch Pond in 2004. 

Brown trout are capable of hybridizing with other salmonids (Brown 1966; Schwartz 

1972, 1981; Dangel et al. 1973; Chevassus 1979; Taylor et al. 1984; Beall et al. 1997). 

Studies in Sweden (Nilsson 1965), Scotland (Hearn 1987), and Canada (Beland et al. 

1981, Beall et al. 1997) have documented brown trout/Atlantic salmon hybrids. One 

study that examined the incidence of hybrids in salmonid populations in Northern Spain 

and Southwestern France determined that significant proportions of salmonid populations 

were locally affected by hybridization. Hybridization was found to occur in the absence 

of conspecific males and due to the modification of spawning behavior by females (Beall 

et al. 1997). Hybridization has also been witnessed in the Connecticut River where 

salmon fry were stocked into a headwater tributary, where no adult salmon were present. 

The stream had a self-sustaining population of brown trout and enzyme electrophoresis 

later demonstrated the presence of one hybrid. Given that the maternal species was 

identified as a brown trout, it was concluded that the male parent had to have been a 

mature male Atlantic salmon parr (Gephard et al. 2000). Evidence also suggests that the 

number of hybrids increases with increasing population densities (Maine ASC and Maine 

IFW 2002). 

Brown trout and Atlantic salmon demonstrate similar spawning site preferences and 

spawn at about the same time in the fall. Evidence also suggests that brown trout females 

may prefer to spawn on existing redd sites. This creates the potential for superimposition 

of redds in spawning areas (Maine ASC and Maine IFW 2002). Interspecific competition 

between brown trout and Atlantic salmon also has the potential to negatively affect 

Atlantic salmon. Habitat use by Atlantic salmon has been found to be restricted through 

interspecific competition with brown trout that are more aggressive (Heggenes et al. 

1999; Kennedy et al. 1986; Hearn 1987; Fausch 1998). Furthermore, Harwood et al. 

(2001) determined that competition is not limited to the summer months, instead 

competition for food and resources observed during overwintering indicates potential 

 

31 The Maine IFW raises brown trout at the Palermo hatchery on the Sheepscot River for stocking 

purposes. Brown trout escaping from this hatchery contribute to resident populations of brown 

trout already established in the Sheepscot River.
1-73

affects on both the long-term and short-term growth of wild Atlantic salmon (Harwood et 

al. 2001). Also, at lower water temperatures, Atlantic salmon fry may compete less 

effectively than brown trout. However in Europe, Brown trout and Atlantic salmon are 

sympatric and habitat segregation allows them to remain genetically isolated (Hethagen 

1988; Hearn 1987). The extent of predation and competition between brown trout and 

Atlantic salmon has not been well documented in salmon rivers within the range of DPS. 

Splake (Salvelinus namaycush x Salvelinus fontinalis) is another potential predator and 

competitor of Atlantic salmon found in DPS rivers. In 1995, IFW stocked splake in 

seven lakes within the Sheepscot, Narraguagus, Pleasant and Machias river watersheds. 

In 2001, splake were stocked into Mopang Lake, Second Old Stream, Beddington Lake, 

Keeley Lake, Burntland Lake, Pleasant River Lake, Sheepscot River and Peaked 

Mountain Pond. Splake stocking has been successful only where an adequate volume of 

cool water (12-16oC) is available. Splake can drop down from lakes and ponds where 

they are stocked. The Maine IFW has documented numerous splake in the Sheepscot 

River below the stocking location of Sheepscot Lake. 

The potential exists for stocked splake to reach a size such that smolt predation becomes 

possible (Beland 2001). ASC and IFW biologists sampled splake in Beddington Lake 

(Narraguagus drainage) in 2001 and found one splake that had consumed an Atlantic 

salmon smolt (Ken Beland, ASC, Personal Communication). As a result, stocking of 

splake in Beddington Lake was terminated. Beddington Lake was the only Downeast 

splake stocking program on a mid-drainage lake that Atlantic salmon smolts migrate 

through. In other Downeast lakes, splake are stocked upstream of Atlantic salmon 

rearing habitats. 

Splake are non-reproductive in Maine waters. Therefore, future adverse interactions 

between splake and Atlantic salmon may be mitigated by termination of splake stocking. 

To date, neither splake reproduction nor naturally produced juveniles have been 

observed. Observations during the fall spawning period are ongoing and will continue. 

Little information is currently available to assess the level and significance of splake 

predation upon Atlantic salmon. 

Rainbow trout (Oncorhynchus mykiss) is native to the Western United States. Rainbow 

trout have been introduced into Maine through stocking for recreational fishing and for 

use in aquaculture operations. In terms of genetics, habitat, size, growth and life cycle, 

rainbow trout is the most similar species to the sea-run Atlantic salmon (Bley and 

Mooring 1988). 

Rainbow trout can be a significant competitor with Atlantic salmon. The potential for 

interactions between the two species exists as Atlantic salmon and rainbow trout exploit 

similar resources. Early life stages of the Atlantic salmon and rainbow trout are 

remarkably similar in habitat preferences, behavior and feeding (Bley and Mooring 

1988). In areas where Atlantic salmon and rainbow trout co-occur, significant niche 

overlap is expected. Under limiting circumstances, vigorous competition for resources is 

likely (Volpe et al. 2001). Interactions between Atlantic salmon and rainbow trout are 
1-74

most likely to occur during the juvenile life stages of these species (Gibson 1981). 

Interspecific competition during juvenile stages may be an important factor affecting 

growth and survival of Atlantic salmon (Fausch 1998). The potential also exists for 

Atlantic salmon redds to be superimposed by spring-spawning rainbow trout (Volpe et al. 

2001). 

Experiments done by Hearn and Kynard (1998) demonstrate that rainbow trout are better 

adapted to pools and habitats with low current velocities. In such habitats, rainbow trout 

are more aggressive and out-compete Atlantic salmon parr. These interspecific 

interactions may cause reductions in salmon populations. In a study done by Volpe et al 

(2001), rainbow trout performance was superior to Atlantic salmon. Should rainbow 

trout colonize freshwater habitats within DPS rivers through either intentional 

introduction or escapement from aquaculture facilities it could have adverse affects on 

wild salmon populations. Numerous reports (Bley and Moring 1988; Gibson 1981; 

Hearn and Kynard 1986; Volpe. et al. 2001) state that the potential exists for interspecific 

competition between the two species to have negative consequences for native Atlantic 

salmon. Currently rainbow trout are raised for aquaculture purposes at one site in 

Sheepscot Bay on the east side of Birch point. 

The Maine IFW does not currently stock rainbow trout in salmon rivers within the DPS. 

Private landowners with farm ponds may obtain rainbow trout or brook trout through the 

United States Department of Agriculture (USDA). The State requires a stocking permit 

for private ponds. On the basis of an informal intra-agency agreement between the ASC 

and IFW, IFW biologists deny permits for rainbow trout in DPS rivers, except in private 

ponds with no outlet streams (Ken Beland, ASC, personal communication). 

Brook trout (Salvelinus fontinalis) are indigenous to all Atlantic salmon rivers and have 

coevolved with Atlantic salmon. Once salmon eggs are deposited by the female, both 

brook trout and Atlantic salmon parr may feed on them (White 1939). Recent studies 

have documented brook trout feeding on large numbers of stocked Atlantic salmon fry 

(Maine ASC and Maine IFW 2002). 

Competition is most intense between juveniles of these species. While juvenile Atlantic 

salmon and brook trout are often found in the same stream, salmon are found 

predominately in riffles and trout in pools (Gibson 1973; Gibson 1981). This habitat 

partitioning (use of different habitat) during most of the growing season limits the 

opportunity for interaction between brook trout and juvenile salmon. Brook trout will 

out-compete Atlantic salmon in deep pools while Atlantic salmon will out-compete brook 

trout in riffles and flats (Gibson 1973; Gibson 1981). When Atlantic salmon fry do cooccur with brook trout fry, the growth of salmon is suppressed (Maine ASC and Maine 

IFW 2002). 

Landlocked salmon (Salmo salar sebago) are present in lakes within the Sheepscot, 

Narraguagus, Pleasant, Machias, East Machias and Dennys river watersheds. These 

populations were all introduced. In Maine, only the St. Croix, Union and Penobscot river 

drainages had native landlocked salmon (LLS) populations. Predation on juvenile 
1-75

salmon by adult landlocked salmon may occur either during periods of cool water 

temperatures before landlocked salmon move to nearby lakes or during periods of high 

flows when larger landlocked salmon might temporarily reside near nursery habitat 

(MASCP 1997). It is believed that the extent of predation of wild Atlantic salmon by 

landlocked salmon is relatively minor (MASCP 1997). Because sea-run and landlocked 

Atlantic salmon are the same species, direct competition for food and space is inevitable 

when the fish are in the same area (Maine ASC and Maine IFW 2002). The 

Meddybemps Lake outlet on the Dennys River is an area where competition between 

landlocked and sea-run Atlantic salmon could occur (Maine ASC and Maine IFW 2002). 

The Meddybemps Lake population of landlocked Atlantic salmon is stocked and natural 

spawning of landlocked salmon is known to occur. The success of this reproduction is 

not known but may result in hybridization, redd superimposition and ecological 

competition between juvenile life-stages. In addition, Sheepscot Lake has a selfsustaining population of landlocked salmon. ASC staff have documented adults and 

juvenile landlocked salmon below the Lake in the Sheepscot River. 

American eel (Anguilla rostrata) is commonly found in rivers within the range of the 

DPS. Eels are known to prey upon many fish species (Sinha and Jones 1967; Daniels 

1999). The potential exists for predation on fry, parr and smolts as juvenile Atlantic 

salmon habitat overlaps with eel habitat (Ken Beland, ASC, personal communication). 

There has been little directed research on predation of Atlantic salmon by eels. Baum 

(1997) and Godfrey (1957) report some eel predation on Atlantic salmon fry and parr. 

The remains of 429 salmon fry were once documented in one eel (Baum 1997). Sinha 

and Jones (1967) report unidentified salmonids in many eel stomachs. Larger eels are 

active piscivores, with eel foraging activity greatest in spring and early summer (Merry 

Gallagher, IFW, personal communication). During late summer sampling of juvenile 

salmon rearing habitats, ASC staff commonly encounter eels 20-70 cm in length, 

occasionally in abundance (Ken Beland, ASC, personal communication). Eels are not 

thought to pose a threat to adult salmon. 

ii. Estuarine and marine 

Smoltification occurs in the spring when juvenile salmon move downstream to the ocean. 

During their seaward migration, smolts enter estuaries and may not exit to the sea 

immediately (Fried et al. 1978; Danie et al. 1984). Extended residence in estuaries 

increases their vulnerability to predators including striped bass, cod, American pollock 

and whiting (Bley 1987; Carlin 1954; Bigelow and Schroeder 1953; Thurow 1966; Rae 

1966 and 1967; 1973; Hvidsten and Mokkelgjerd 1987; Hvidsten and Lund 1988; Barrett 

et al. 1990; Greenstreet et al. 1993, Massachusetts Cooperative Fish and Wildlife 

Research Unit, unpublished data). 

Atlantic salmon grow rapidly while in the ocean and increasing size reduces vulnerability 

to predators. Little is known about the predator-prey interactions involving salmon and 

piscine predators in the ocean, as documented below. 
1-76

Striped bass (Morone saxatilis) has been cited as a potentially significant predator of 

Atlantic salmon (MASCP 1997; Baum 1997; Beland et al. 2001). In a study on the 

Merrimack River, striped bass were found to prey on Atlantic salmon just below the 

Essex Dam (Blackwell and Juanes 1998). Blackwell and Juanes (1998) sampled stomach 

contents of 212 striped bass on the Merrimack River. This analysis revealed 32 

documented and 28 suspected salmon smolts in striped bass sampled. In 1998, 16 of 389 

striped bass stomachs analyzed contained salmon smolts. The difference between the 

two years may be explained by the timing and availability of river herring as an 

alternative prey species (USASAC 1999). Striped bass seem to be arriving in New 

England waters earlier in the spring and more fish may even be overwintering in New 

England (USASAC 1999). 

In Maine, striped bass populations have increased over the last ten years, extending their 

range into Downeast river estuaries. There is evidence that striped bass are now 

spawning in the Kennebec River and it is possible that spawning could expand to other 

northern river systems (USASAC 1999). The timing of the smolt migration (April-May) 

and the arrival of striped bass in Maine waters (May-June) may serve to minimize the 

potential for predator-prey interactions between these two species. Striped bass 

abundance in eastern Maine rivers is highly variable between years (Beland et al. 2001). 

Gadoid fishes such as cod and pollock are known to feed on post-smolts (Rae 1966, 

1967; Hvidsten and Mokkelgjerd 1987; Hvidsten and Lund 1988). Research on the food 

habits of thousands of cod in Newfoundland indicates that salmon is not a common prey 

item (DFO 1998). 

Benthic feeders, including shark, skate and ling prey on Atlantic salmon (Hislop and 

Shelton 1993). Wheeler and Gardner (1974) report that sharks are the most significant 

predator of adult Atlantic salmon in the marine environment. 

E. INADEQUACY OF EXISTING REGULATORY MECHANISMS 

A variety of state and federal statutes and regulations seek to address threats to Atlantic 

salmon and their habitat. These laws are complemented by international actions under 

NASCO, many interagency agreements and state-federal cooperative efforts. Existing 

regulatory mechanisms either lack the capacity or have not been implemented adequately 

to decrease or remove all threats to wild Atlantic salmon. 

The final rule listing the DPS identified two important concerns about existing 

regulations relating to salmon: 1) either they were inadequate or 2) were not being 

effectively implemented. Although there are still areas of concern, progress has been 

made (65 FR 69459). In order to protect DPS fish, Maine has closed all angling for 

Atlantic salmon, including catch and release. The State has developed a water use 

management plan for the Pleasant, Narraguagus rivers and Mopang Stream (a tributary of 

the Machias River). 
1-77

Regarding aquaculture, comprehensive solutions to minimize the threat of interaction 

between wild and aquaculture salmon are being implemented. The Services have worked 

extensively with the aquaculture industry, the State of Maine and the Army Corps of 

Engineers (ACOE) to eliminate the use of pure European strain and North 

American/European hybrids in marine cages. On June 19, 2003, the Maine DEP issued a 

general permit for salmon aquaculture under its delegated CWA authority. The DEP 

general permit includes conditions that will eliminate the use of non-North American 

strains of Atlantic salmon, improve containment measures, and require marking of 

salmon placed in net pens so that escapes, if they occur, can be traced. Similarly, the 

ACOE is proposing permit conditions that would eliminate European strain fish in sea 

cages, require marking, and would improve containment measures. On November 21, 

2003, NOAA Fisheries completed Section 7 consultation with the ACOE on the proposed 

permit modifications. The ACOE is currently in the process of issuing revised permits 

with the new conditions. Although importation of European milt is still allowed under 

state law, the progeny created from this milt could not be stocked in Maine waters under 

the existing state general permit and the proposed ACOE permit conditions. 

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. Recent improvements (e.g., installation of drum filter 

and screens) have been made at both of these hatcheries to help minimize escapement. 

Moreover, the industry has developed a hatchery management system that includes a 

Hazard Analysis Critical Control Point (HAACP)-based plan for each hatchery that 

follows the hatchery production cycle from arrival of eggs to smolt transport. The 

effectiveness of HAACP plans, filters, and screens in eliminating escapes from the two 

hatcheries has not yet been fully analyzed. Escapes of juvenile salmon from commercial 

hatcheries could still occur from catastrophic events (e.g., floods, icing of the water 

intake, and power outages). Escapement of juvenile aquaculture salmon from hatcheries 

into DPS river watersheds could negatively contribute to the status of the DPS, although 

with recent hatchery improvements, escape events are much less likely to occur. 

In addition to commercial aquaculture hatcheries private and public fish hatcheries exist 

on DPS rivers. Among these are the Palermo Hatchery on the Sheepscot River operated 

by the Maine IFW and the Columbia Falls Hatchery on the Pleasant River operated by 

the Downeast Salmon Federation (DSF). The Maine IFW raises brown trout at the 

Palermo hatchery on the Sheepscot River for stocking purposes. Brown trout escaping 

from this hatchery contribute to resident populations of brown trout already established in 

the Sheepscot river. Containment measures should be in place at all private and public 

hatcheries to prevent escapement from hatcheries into DPS river. 

Ocean harvest is still occurring off West Greenland and St. Pierre et Miquelon, though it 

is much reduced. One concern related to that harvest is the increased percentage of North 

American origin fish that comprise it. 
1-78

F. OTHER NATURAL AND ANTHROPOGENIC FACTORS AFFECTING 

THE SPECIES’ CONTINUED EXISTENCE 

1. Salmon Aquaculture 

The potential for interactions between wild Atlantic salmon and aquaculture escapees 

was key factors in the listing determination. Since the listing, much progress has been 

made to address the threats posed by salmon aquaculture to wild salmon populations. 

The Services have concluded, however, that the potential ecological interactions between 

wild and farmed raised salmon continues to be a high level threat to the conservation of 

the DPS. 

The Maine Atlantic salmon aquaculture industry is currently composed of seven 

companies with 41 lease sites, of which 14 are currently active, that cover approximately 

750 leased acres of water. There are approximately 200 active net pens covering a 

surface area of nearly 40 acres. The salmon aquaculture industry has grown rapidly over 

the last two decades in Maine. Annual Atlantic salmon aquaculture production in Maine 

increased from an estimated 20 mt in 1984 to a high of more than 16,400 mt. (>36 

million pounds) in 2000 (Honey et al. 1993: Baum 2001). From 2000 to 2001, annual 

production of Atlantic salmon in Maine decreased 28% to 26 million pounds (Sebastian 

Belle, Maine Aquaculture Association, personal communication). Numerous set backs, 

including disease and superchill, decreased production to15 million pounds in 2002 and 

13.2 million pounds in 2003. The number of farms actively rearing salmon has declined 

from 31 in 2001 to 14 in 2003. Most farms are concentrated in Cobscook Bay near 

Eastport, Maine but some are located in Machias Bay and as far south as Blue Hill Bay. 

The Maine industry is largely composed of international companies operating marine 

sites and hatcheries in both Canada and the United States. 

In Maine, pen-rearing salmon from smolt placement to harvest requires approximately 18 

months, yielding an average standing crop of about ten million salmon in two-year 

classes. Most salmon are harvested from October through March, although some salmon 

are harvested throughout the year. The aquaculture industry in Canada is approximately 

six times the size of the Maine industry, with production in 2003 totaling 73 million 

pounds. 

Until recently, five commercial freshwater hatcheries located in the U.S. largely 

supported the Maine industry and produced up to four million Atlantic salmon smolts 

annually. Heritage Salmon operated two hatcheries, Gardner Lake and Deblois, which 

produced 1.5 million smolts annually until the closure of the Deblois hatchery in the 

summer of 2002. The Deblois hatchery has been decommissioned and is no longer 

supporting the Maine Atlantic salmon farming industry. The Gardner Lake hatchery is 

on Chase Mill Stream, a tributary of the East Machias River, and the Deblois Hatchery (a 

state owned facility leased and operated by Heritage Salmon) is located on Beaver brook, 

a tributary to the Pleasant River. The other three hatcheries are located in the towns of 

Embden, Bingham and Oquossic and are in the Kennebec River drainage. Cooke 

Aquaculture, Inc. owns the hatcheries in Embden and Oquossic, each of which can 
1-79

annually produce up to 1 million smolts. A fire damaged the Embden hatchery in May 

2003, and its future is uncertain at this time. Stolt Sea Farm’s Bingham hatchery 

produces up to 1 million smolts annually, as well as housing adult brood stock. Both 

Cooke Aquaculture and Heritage Salmon own additional hatchery facilities in Canada, 

which produce juvenile salmon to support farm sites located in Maine. 

In previous years, Atlantic salmon broodstock lines used in aquaculture production 

included fish from the Penobscot River and the St. John River of North American origin 

and an industry strain from Scotland. The North American lines used in production today 

have been used since the mid-1980s. The Scottish strain was imported into the U.S. in 

the early 1990s and is composed primarily of Norwegian strains, often referred to as 

“Landcatch.” In 1991, the State of Maine (PL 1991 c381 sub section 2) prohibited the 

importation of non-North American fish and eggs but failed to restrict the importation of 

European milt. Some Maine industry companies continued to import salmon milt of 

European origin. The imported gametes from Europe were crossed with gametes from 

North America to produce a hybridized strain of Atlantic salmon referred to as the 

“Maine Strain.” Norwegian-origin milt (obtained from Icelandic sources) has been 

imported as recently as 1999. It is estimated that at least 50% of the production fish (fish 

destined for market or harvest) in Maine are either pure or hybridized Landcatch strains 

(Baum 2001). As noted (see page 1-20), a recent ruling issued by the United States 

District Court, District of Maine prohibits the use of European salmon by Atlantic 

Salmon of Maine and Stolt Sea Farm Inc. The other major salmon producer in Maine 

(Heritage Salmon) had previously agreed to not stock any non-North American salmon as 

part of a consent degree. Recent MEPDES permit requirements also prohibit Non-North 

American strain Atlantic salmon from being stocked into Maine waters for aquaculture 

use after July 31, 2004, with all Non-North American salmon needing to be removed 

from net pens prior to September 15, 2006. 

Interactions between wild Atlantic salmon and salmon aquaculture 

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). Escaped farmed salmon may adversely affect 

wild salmon through ecological and genetic effects. Escaped aquaculture salmon may 

interbreed with wild salmon, leading to disruption of local adaptations, threatening stock 

viability and decreasing recruitment, thereby leading to the extinction of wild salmon 

populations (Fleming et al. 2000; Utter et al. 1993; Verspoor 1997; Youngson and 

Verspoor 1998). Escaped aquaculture salmon may also transfer disease and/or parasites 

to wild salmon (Clifford 1997; Youngson et al. 1993; Webb et al. 1993; Windsor and 

Hutchinson 1990; Saunders 1991). Farm-raised Atlantic salmon have been documented 

in the wild (Bergan et al. 1991; Lura and Saegrov 1991; NASCO 1993; Hansen et al. 

1993; ICES-NASWG 1994; Skaala and Hindar 1997; Stokesbury and Lacroix 1997; 

USASAC 1999). 

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. 
1-80

Aquaculture escapees have been detected annually in Maine rivers since 199032. 

Aquaculture fish have been found in the Dennys, East Machias, Narraguagus, 

Pennamaquan, Penobscot and St. Croix rivers and Boyden and Hobart streams (Baum 

1991; USASAC 1996, 1997). In recent years, escaped aquaculture fish have accounted 

for 2% to 100% of the total salmon returns to some DPS rivers (NMFS and FWS 1999). 

Aquaculture salmon returning to Maine rivers can include mature males and females. 

The first sexually mature aquaculture salmon escapees were documented in 1996. In the 

St. Croix River, 5 of 17 escapees (30%) examined in September 1998 exhibited evidence 

of sexual maturation. In 1999, all three aquaculture escapees captured in the 

Narraguagus River were sexually mature (USASAC 2000). Of 45 captive reared fish 

examined from the St. Croix, Dennys, and Narraguagus rivers (1998-2000) ten females 

and eight males were mature, nine females and 16 males were immature, and maturity 

could not be determined for eight females and ten males (ASC unpublished data). 

It is currently not possible to assess the full extent of marine aquaculture escapees 

entering DPS rivers because 1) several DPS rivers have no counting or interception 

facilities, 2) most aquaculture fish are not currently marked (most aquaculture escapees 

are currently identified by physical characteristics, such as fin deformities and body 

shape and size and scale samples33, although recently some aquaculture fish have been 

marked with a fin clip) and 3) existing counting facilities do not operate year-round34. 

An accurate count of U.S. origin escapees is further confounded by the fact that some of 

the escapees detected in the DPS rivers may have come from nearby Canadian marine 

cages. Although progress has been made since 2003, comprehensive protective solutions 

to minimize the threat of interactions between wild and aquaculture salmon have not yet 

been fully implemented. 

In Maine, escapes of large numbers of aquaculture fish have occurred. In November 

2000, approximately 13,000 fish escaped from a net-pen near Eastport, Maine when a 

vessel transferring fish from one site to another accidentally hit one of the cages, tearing a 

hole in the pen. In December 2000, approximately 100,000 aquaculture salmon escaped 

in Machias Bay when a storm destroyed a steel cage. When the Services made the final 

listing decision, the threats posed by aquaculture practices in use at the time and the lack 

of progress in resolving those concerns were a major consideration. 

Seals are known to attack net-pens where farmed salmon are raised. These attacks may 

damage net-pens and result in the escape of farmed raised fish (Morris 1996; NMFS 

1996). For example, in Canada, it is estimated that minimally 61,600 fish escaped per 

year due to predator damage in New Brunswick between 1988 and 1998 (Jacobs and 

Terhune 2000). 

 

32 There were no documented aquaculture salmon detected in 2004. 

33 The use of scale characteristics (i.e., circuli patterns) and body morphology to identify escaped 

farmed salmon are well established techniques. The use of these techniques to identify 

aquaculture escapees is more problematic if fish have escaped early in their life cycle from 

freshwater hatcheries. 

34 Fish weirs are installed in late April to mid May, depending on river flow and ice conditions. 

Weirs are removed in mid- to late November depending on ice conditions. 
1-81

In Atlantic Canada, most aquaculture occurs in the lower Bay of Fundy, where there are 

an estimated sixty aquaculture facilities. These facilities are in close proximity to the 

DPS. Since the aquaculture industry began in the Canadian Maritimes in 1979, escapees 

have been documented in fourteen rivers in New Brunswick and Nova Scotia (DFO 

1998). Large scale escapes due to cage failure, storm events, anchor system failure, 

human error and vandalism have been documented in Canada (Fred Whorisky, Atlantic 

Salmon Federation (ASF), personal communication). NOAA (2004) funded an ASF 

research project through the Staltonstall-Kennedy grant program to provide additional 

information on escapes from Maritime Canada. The study is using radio tagged adult 

aquaculture fish reared at marine sites to track the migration pathways of released fish. 

Juvenile salmon of commercial hatchery-origin have been documented in DPS rivers in 

Maine. In 1999, 707 smolts were captured in a smolt trap on the Pleasant River during 

salmon population assessments. Of the fish collected, 31 had fin deformities and 

coloration and body form suggesting that they were of commercial hatchery-origin 

(USASAC 2000). The Deblois Hatchery is located upstream of the sampling site. Scale 

and tissue samples were collected for DNA analysis. Based on fin deformities, scale 

pattern analysis and genetic assignment tests, it was determined that approximately 20 to 

25% of the 1999 Pleasant River smolt run was of commercial hatchery origin. 

Subsequent electrofishing surveys were conducted within Beaver Meadow Brook at the 

outflow of the Deblois Hatchery. These surveys documented 87 salmon parr near the 

vicinity of the hatchery outflow. The hatchery is located at the upstream end of Beaver 

Meadow Brook, which does not have salmon habitat. The nearest reach of the Pleasant 

River is dead water habitat, unsuitable for spawning or rearing of salmon. Consequently, 

the Maine TAC concluded that hatchery-origin Atlantic salmon were escaping into the 

Pleasant River drainage from the Deblois Hatchery and that the escaped fish represent a 

threat to wild Atlantic salmon in the Pleasant River drainage (Maine TAC, 2000). As a 

result of these findings and recent cooperative efforts with state and federal agencies, 

Heritage Salmon upgraded the discharge system and developed a Containment 

Management System plan for the facility. Modifications included adding rotary drum 

filters to remove solids, a solids collection area and screened outlets from the hatchery. 

Having an established CMS plan in place and the additional secondary treatment of 

hatchery effluent should effectively eliminate escapes from the hatchery. 

Since 1989, annual population assessments conducted by ASC on Chase Mill Stream 

have resulted in the capture of suspected aquaculture-origin juvenile salmon in the 

vicinity of the Gardner Lake hatchery discharge. These fish had deformed fins and were 

typically larger than wild parr, characteristics associated with aquaculture fish. Until 

1999, no attempt was made to assess the origin of these fish. In October 1999, Chase 

Mill Stream was specifically electrofished in the vicinity of the hatchery outlet and, based 

on fin condition, twenty-eight suspected aquaculture origin salmon were collected 

(USASAC 2000). While the Gardner Lake hatchery is a likely source for these fish, the 

ASC captured large age-0+ and age-1+ parr with fin deformities in Chase Mill Stream as 

early as 1981, several years before that hatchery was constructed. ASC attributed the size 
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of some parr to the abundant food and stable temperatures that occur in this lake outlet. 

Although rare, ASC staff report that fin deformities among fish with wild scale growth 

patterns in Chase Mill Stream have been observed. In October 2004 the MEDEP issued a 

renewed discharge permit for the Gardner Lake hatchery. This permit requires a CMS 

plan with reporting and auditing requirements and prohibits the use of Non-North 

American Atlantic salmon strains. 

Ecological Effects 

Ecological interactions between farmed and wild salmon can occur through transfer of 

disease and parasites, competition for food and habitat, disturbance of reproductive 

habitat (i.e., redd superimposition) and increased predation. Ecological interactions 

between salmonids can lead to reduced reproductive success, increased mortality and 

decreased growth (Fausch and White 1986; Webb et al. 1991). 

Disease transfer and Parasites

Wild salmon may be vulnerable to exposure and infection with disease when passing in 

close proximity to infected aquaculture sites. The potential for disease transfer is a 

concern as both post-smolts and adult salmon migrate past aquaculture sites (DFO 1998; 

Crozier 1993; Skaala and Hindar 1997; Carr et al. 1997; Lura and Saegrov 1991). While 

fish pathogens exist in the wild, concentrations of individuals magnify the level of any 

pathogen present and the rate and extent of any resultant epizootic (Finlay and Falkow 

1989). The presence of the ISAV in the geographic range of the DPS and the existence 

of extensive concentrations of net-pens is a significant threat to the DPS. 

ISAV 

The outbreak of ISAV in Cobscook Bay (first detected in 2001) and the close proximity 

of high density fish farms to DPS rivers raises concerns about transference of this disease 

to wild salmon. Because a significant portion of endangered salmon must swim near 

U.S. net-pens in Cobscook Bay and Machias Bay, the establishment of ISA in and around 

U.S. net-pen sites and its presence in nearby Canadian aquaculture sites pose a risk to 

wild salmon. 

ISA poses a threat to both endangered wild and hatchery populations. The potential 

exists for infected escaped farmed salmon to spread disease to endangered salmon 

populations. There are no documented instances of this occurring except in one instance 

in Canada. In this instance wild fish held in a weir with aquaculture escapees were found 

to be positive for ISAV. In this instance, it is not clear if the wild fish were positive prior 

to the confinement with escaped farmed salmon. 

Sea Lice 

The potential exists for transfer of parasites between aquaculture facilities and wild 

salmon. The sea louse (Lepeophtheirus salmonis) is a small parasitic copepod found only 
1-83

on salmonids. It is one of the more common marine parasites of Atlantic salmon. Sea 

lice undergo a series of ten life stages, from egg to mobile, feeding adult (Johnson and 

Albright 1991). Sea lice normally die and fall off salmon within twenty-four hours of 

entry into freshwater (Baum 1997). 

Normally, the generally low numbers of sea lice typically found on wild salmon do not 

pose a health risk (Nolan et al.1999). Sea lice normally do not cause widespread 

mortality or severe pathological effects in Atlantic salmon (Wooten et al. 1982). While 

the prevalence of sea lice is often high on farmed salmon, the total number on individual 

fish is generally low (Wooten et al. 1982). However, a heavy burden of sea lice can kill 

an Atlantic salmon. Finstad et al. (2000) reports that a sea lice burden of eleven lice per 

fish is lethal to a juvenile salmon smolt of 15 g or less. In addition, as few as five adult 

sea lice can cause significant pathological damage to fish (Wooten et al. 1982). 

Sea lice may also be a vector of disease, including possibly ISA. An experimental study 

conducted in Norway by Nylund et al. (1993) concludes that sea lice on Atlantic salmon 

can function as a vector transmitting the ISAV. ISAV was shown to be present in the gut 

of the lice further substantiating this evidence. This study shows that the presence of just 

four infected sea lice can cause mortality to adult Atlantic salmon and that sea lice may 

transmit ISAV from one host to another (Nylund et al. 1993). 

Wild salmon are vulnerable to sea lice infestation originating from aquaculture facilities. 

In Norway, the level of sea lice infestation on wild fish in some areas where Atlantic 

salmon farming is concentrated has been found to be ten times greater than in areas 

where there are no salmon farms (NASCO 1993). Outmigrating salmon may acquire sea 

lice infestations if they migrate close to infected salmon aquaculture facilities. For adult 

salmon returning to their natal streams to spawn, the threat is likely lower because when 

fish enters freshwater sea lice die and fall off within twenty-four hours. 

It is difficult to estimate the population effects of sea lice infestations on seaward 

migrating wild Atlantic post-smolts. In Norway, surveys of emigrating post-smolt 

salmon found high numbers of sea lice on wild salmon migrating past salmon aquaculture 

sites. Minimum mortality rates for wild salmon smolts in this study were estimated at 

95% (Institute of Marine Research 2001). In 2001, NMFS researchers initiated research 

to sample outmigrating smolts in Penobscot Bay and the adjacent nearshore marine 

environment. So far, this research has not detected significant burdens of sea lice on 

North American fish. Penobscot Bay is not in the proximity of aquaculture marine net 

pens. Post-smolt trawling has not been conducted in Cobscook Bay where the 

aquaculture industry is currently concentrated. Sampling of salmon taken in the West 

Greenland fishery has found some fish carrying significant sea lice burdens - fish with 

fifty or more lice concentrated around the vent of the fish (Russell Brown, NMFS, 

personal communication). 

The aquaculture industry currently monitors for sea lice infestations and treats infected 

fish. Maine has coordinated bay wide pest management programs with Canada to more 

effectively control Sea Lice in Cobscook Bay (ISAV Program Standards 2002). The 
1-84

potential of sea lice to adversely affect the DPS and the role of salmon aquaculture sites 

as a reservoir for this parasite should be further investigated (see page 4-63). More 

investigation is needed, especially research regarding Calligus, which is another species 

of Sea Louse that is less host-specific, much more abundant, and has an unknown 

potential for transmission of disease. 

Competition

Competition for food and habitat has the potential to regulate salmon populations because 

carrying capacity of streams is limited for various life stages (White 1995). Competition 

may play an important role in regulating salmon population dynamics shortly after fry 

emerge from redds, when fry densities are at their highest (Hearn 1987). Because of 

artificial selection in the hatchery, farmed salmon are expected to be less fit than wild 

salmon; however, they may have competitive advantages at certain life stages (Gross 

1998). McGinnity et al. (1997) conducted a study to compare the performance of farmed 

and wild Atlantic salmon progeny in the Burrishoole River in western Ireland. The 

experiment found that the progeny of farmed fish grew faster and displaced native fish 

downstream. In Norway, Fleming et al. (1997) found that the progeny of escaped farmed 

salmon grew faster than the offspring of wild fish. In Ireland, Ferguson et al. (1997) 

found that farmed salmon displaced wild salmon into sub-optimal habitat where feeding 

rates were lower. Jonsson (1997) reports that the progeny of cultured salmon are 

generally more aggressive then wild salmon offspring. The results of theses studies 

suggest that aquaculture escapees and their progeny can outcompete wild salmon under 

certain conditions thereby adversely affecting wild Atlantic salmon populations. 

Escaped aquaculture fish may reduce the spawning success of wild salmon by digging up 

the redds of wild salmon (Lura and Saegrov 1991; Webb et al. 1991). Escaped farmed 

salmon have been documented to spawn later in the season than wild salmon (Lura and 

Saegrov 1991; Jonsson et al. 1991; Webb et al 1991; Jonsson 1997). This increases the 

potential for escaped farmed salmon to limit the success of wild spawners through redd 

superimposition (Webb et al 1991). The ASC has documented late-arriving aquaculture 

salmon in the Dennys River. These fish arrived after the normal wild spawning season. 

In addition, it has been speculated that salmon net-pens may aggregate predators (e.g., 

seals) of Atlantic salmon increasing the potential for predation of outmigrating wild postsmolts or returning sea-run adults. 

Genetic Effects 

Atlantic salmon populations at low levels, such as those in the Gulf of Maine DPS, are 

particularly vulnerable to genetic intrusion or other disturbance caused by escapees (DFO 

1998; Hutchings 1991; NRC 2002). These introgression events may be one of the most 

significant ways in which aquaculture salmon affect wild populations. While natural 
1-85

selection may be able to purge wild populations of maladaptive genetic traits, regularlyoccurring interaction between aquaculture fish and wild salmon makes this considerably 

less likely. Interactions between wild and aquaculture salmon may lead to decreased 

numbers of wild Atlantic salmon and, in the extreme, to extirpation of wild stock (Einum 

and Fleming 1997; Fleming and Einum 1997; Grant 1997; Saegrov et al. 1997). 

There is a positive relationship between the reproductive success of cultured fish and the 

time the fish has lived in nature before reaching sexual maturity (Jonsson 1997). 

Consequently, escapees from freshwater hatcheries may pose a larger genetic threat to 

wild populations than escapees from net-pens. Cases of chronic and large escapements 

from freshwater hatcheries in Maine have been documented (see above). 

Until recently, some ACOE permit holders continued to use European strains or hybrids 

despite their commitment not to do so when obtaining permits (i.e., many permit 

applications stated that no European strains or hybrids would be placed in cages)(see 

page 1-77). The Services had long expressed concern that the industry’s use of 

reproductively viable European strains (pure and hybrid) of Atlantic salmon within North 

America posed a threat to the DPS. Genetic studies demonstrate that there are significant 

differences between North American and European Atlantic salmon (NRC 2002, and the 

references therein). Breeding between genetically divergent populations may adversely 

affect natural populations (Utter et al. 1993; Verspoor 1997; Youngson and Verspoor 

1998; ISAB 2002). The introgression by non-North American stocks with endangered 

Atlantic salmon presents a substantial threat to the genetic integrity of North American 

stocks and threatens fitness through outbreeding depression. 

As noted, in May 2003, U.S. District Judge Gene Carter issued a ruling prohibiting the 

use of European salmon by Atlantic Salmon of Maine and Stolt Sea Farm Inc. The ruling 

was part of a lawsuit brought against the aquaculture industry under the Clean Water Act 

for operating without a NPDES permit as required under the Act. Heritage Salmon, the 

other major salmon producer in Maine, had already agreed to not stock any non-North 

American salmon as part of an earlier consent degree. Newly established MEPDES 

permit conditions include requirements for genetic testing and data submission to the 

Services to certify Atlantic salmon stocked in marine cages are of North American origin. 

In accordance with permit conditions effective July 31, 2004, it is prohibited to stock 

non-North American Atlantic salmon smolts into Maine waters and prior to September 

15, 2006 all non-North American salmon must be removed from net pens. 

There is evidence that escaped salmon of non-North American origin have spawned 

successfully in the wild with either native or other escaped aquaculture fish. In five of 

the six populations of DPS river broodstocks held at the CBNFH, parr collected from the 

wild had alleles and multilocus genotypes indicative of non-North American origin. 

These fish were culled out of the hatchery population. 

In addition to the threats identified above from current and past aquaculture practices, the 

potential use of transgenic salmonids in aquaculture poses additional unknown, but 

possibly significant, genetic and ecological risks to wild Atlantic salmon populations. 
1-86

Transgenic salmonids include fish species of the genus Salmo, Oncorhynchus or 

Salvelinus in the family Salmonidae that contain stably integrated recombinant DNA in 

all their cells. The “new” DNA typically contains a gene obtained from another 

species35. By 1989, production of fourteen species of transgenic fish had been reported 

(Kapuscinski and Hallerman 1990). Research and development efforts on transgenic 

forms of Atlantic salmon and rainbow trout are currently being directed toward their 

potential use for net-pen aquaculture. Research has focused on enhancement of growth 

and increased tolerance of low water temperature through the transfer of genetic material 

from cold-tolerant species, such as flounder. Transgenic fish have probably undergone 

severe “genetic bottlenecking” in their production. Thus, it is not possible to generically 

predict the impacts on Atlantic salmon if these transgenic fish were to escape into the 

wild. Any specific proposal to rear transgenic salmon must be evaluated to determine the 

potential impact on the listed population. 

Transgenic fish produced for culture in marine net-pens are bred to survive under nearly 

natural physical and chemical environmental conditions; thus, if they escape, it is likely 

that a portion of them will survive. The transmission of novel genes to wild fish could 

lead to physiological and behavioral changes and traits other than those targeted by the 

insert gene are likely to be affected (Kapuscinski and Hallerman 1990). Ecological 

effects are expected to be greatest where transgenic fish exhibit substantial altered 

performance. Such fish could destabilize or change aquatic ecosystems. Juvenile salmon 

of domesticated aquaculture strains have been shown to grow faster and be more 

aggressive than wild strains; they impact wild salmon through competition for food and 

space (Einum and Fleming 1997). It is reasonable to expect that genetically modified 

salmonids, possessing a greatly accelerated growth potential and occupying the same 

habitat as wild fish, could have a greater displacement impact on wild fish than nontransgenic domestic strains. Current MEPDES permit conditions prohibits the use of 

transgenic salmonids. 

2. Marine Survival 

Marine survival rates continue to be low for U.S. stocks of Atlantic salmon, impeding the 

recovery of the DPS. The current low marine survival rates remains a high level threat to 

the conservation of the DPS. Based on a review of twenty studies, reported survival rates 

of Atlantic salmon during the marine phase range from 0% to 20% (Bley and Moring 

1988). In the United States, return rates for hatchery stocked salmon were generally less 

than 1.5% for the Penobscot River from 1970 to 1998 (NMFS and FWS 1999). The most 

current estimates indicate that since 1990 return rates have been below 0.5% and in the 

most recent three years, below 0.2% (Russell Brown, NOAA Fisheries, personal 

communication). The return rates of wild salmon are usually higher than hatchery 

stocked salmon (Bley and Moring 1988; Friedland 1994). Preliminary estimates for the 

Narraguagus River indicate that total marine survival (emigrating smolt to returning 

adult) of DPS salmon are less than 2% (John Kocik, NOAA Fisheries, personal 

 

35 Transgenic organisms can also be called genetically modified organisms. Transgenic is usually 

used to refer to animals while genetically modified is usually used to refer to plants or 

microorganisms. 
1-87

communication). The number of naturally reproducing Atlantic salmon in DPS rivers is 

at a historic low, placing the DPS in danger of extinction. In 2004, only an estimated 60 

to 113 adult salmon returned to DPS rivers to spawn (USASAC 2003). 

The production potential and population dynamics of Atlantic salmon may be determined 

by year-to-year variability in oceanic natural mortality as well as the average level of 

natural mortality in the marine environment (NMFS and FWS 1999). On an interannual 

basis, marine survival rates can be more variable than freshwater survival rates (NMFS 

and FWS 1999). Reddin (1988) found that overall marine survival rates were typically 

higher (5.51%) than freshwater (1.67%). However, the variability in survival during the 

marine phase is approximately four times higher then during the freshwater phase of 

salmon’s life-history (Reddin 1988). Bley and Moring (1988) report that Atlantic salmon 

stocks that undertake longer migrations, such as those from DPS rivers, typically have 

lower marine survival. This hypothesis is consistent with an observed north to south 

gradient of decreasing marine survival rates. This theory is also consistent with typically 

high survival rates seen in several of the northern (Icelandic, Irish and Baltic) stocks of 

Atlantic salmon with limited migratory routes (Bley and Moring 1988). It is important to 

note that there is also a north-south trend of decreasing smolt-ages. This trend results in 

higher freshwater productivity in the southern extent of Atlantic salmon range that may 

offset the higher marine mortality. 

The factors affecting the survival of salmon during the marine phase of their life history 

are not well understood. Marine survival is determined by a combination of factors, 

including predation, starvation, disease/parasites, abiotic factors, and commercial 

fisheries. Based on the current level of knowledge of the marine ecology of Atlantic 

salmon, it is not possible to partition mortality into specific categories. 

Scientists have theorized that post-smolt survival accounts for a significant proportion of 

the variation in recruitment or return rate (i.e., total marine survival). It has been 

theorized that the transition from freshwater to the marine environment accounts for a 

high proportion of the total at-sea mortality. However, the factors responsible for 

reduced post-smolt survival are not well understood. Recent research on the effects of 

acid rain has shown that pulses of acidity can result in mortality in smolts during the 

transition from the freshwater to marine life phase of their life cycle (Magee et al. 2001, 

Rosseland et al. 2001)(see page 1-28). Survival can also be affected by exposure to 

endocrine disruptors that may also impair the smolts’ ability to successfully transition 

from the freshwater to the marine environment (Haines et al. 1990; Magee et al. 2001; 

Moore and Lower 2001). Migrating salmon smolts survival is also affected by predation 

and exposure to new disease pathogens and parasites. 

Sea surface temperature (SST) appears to be an important feature of the marine 

environment that affects Atlantic salmon survival. Survival appears to also be closely 

related to marine temperatures in the overwintering area, indicating that variation in the 

quality or quantity of food supply may play a significant role in survival (Friedland et al. 

1993; Reddin et al. 1993). Atlantic salmon are found in waters ranging from 3°C to 13°C 

(38°F to 56°F)(Baum 1997). The optimal water temperature range for Atlantic salmon is 
1-88

4°C to10°C (40°F to 46°F) waters, a temperature range thought to be ideal for growth 

(Saunders 1986). 

Saunders (1986) and Reddin and Shearer (1987) found that SST influenced Atlantic 

salmon marine distribution. Reddin and Shearer (1987) concluded that below-normal 

surface temperatures in the Labrador Sea over the winter were responsible for low 

catches in West Greenland in 1983 and 1984. Friedland et al. (1993) and Reddin et al. 

(1993) found that the pattern of stock production was related to the area of winter habitat 

available to North American post-smolts. The lack of a relationship for spring, summer 

and autumn suggests that habitat during these seasons may not be limiting. While these 

investigations have indicated the importance of SST to Atlantic salmon recruitment, the 

mechanisms responsible for reduced survival are still unknown. Mortality could arise 

from stress, starvation, predation, disease or other unknown mechanisms. The model 

used until recently to estimate the pre-fishery abundance (PFA) of non-maturing 1SW 

salmon available for harvest shows improving thermal habitat condition and predicts 

increased numbers of returning adults. The predicted increases in the number of 

returning adult Atlantic salmon have not occurred. 

Large scale oceanographic processes likely affect Atlantic salmon survival rates (Dunbar 

1993; Friedland 1994). Correlations have been found between SST and marine survival 

for Atlantic salmon (Scarnecchia 1984; Martin and Mitchell 1985; Scarnecchia et al. 

1989; Friedland et al 1993; Friedland et al 1996; Friedland 1998). The North Atlantic 

Oscillation (NAO) is one possible causal mechanism for this relationship. The NAO is 

responsible for variation of the pressure gradient over the North Atlantic and thus 

changes in weather patterns. A direct link has not been established between Atlantic 

salmon survival and the NAO. However, many other salmon species exhibit cyclic 

patterns of marine survival linked to large scale oceanographic processes. For example, 

marine survival of Pacific salmon species have been shown to vary with El Niño 

Southern Oscillation (ENSO) events (Johnson 1988; Beamish and Bouillon 1993; Francis 

and Hare 1994). 

Friedland et al. (1993) report that year-to-year variation in return rates of U.S. stocks, 

although at lower absolute levels, are generally synchronous with other Atlantic salmon 

stocks. Recent return rates have been decreasing for several North American Atlantic 

salmon stocks. The correlations between the survival rates of multiple stocks suggest that 

an important cause of mortality may act upon the stocks when they are mixed and 

utilizing a shared habitat. This observation suggests that although significant natural 

mortality may occur in the riverine and estuarine environment, it does not explain the 

patterning source of mortality observed in North American salmon stocks (Larsson 1985; 

Wood 1987; Hvidsten and Lund 1988; Magnhagen 1988). Friedland et al. (1993) found 

the survival rate for the Penobscot River stock was correlated to growth rates during the 

first winter at sea, suggesting that this period regulates annual recruitment. This 

observation suggests an association between growth rates and survival rates (NMFS and 

FWS 1999). In years of poor growth, a greater proportion of the stock died; when growth 

was better, so was survival (Friedland et al. 1993). 
1-89

The directed commercial fishery off the coasts of West Greenland and Canada was a 

major source of mortality from the 1960s to early 1990s. In Canada, all commercial 

fisheries are currently closed. In West Greenland, commercial fisheries have been 

greatly reduced by internationally negotiated quotas that are greatly reduced from past 

levels of exploitation (see page 1-56). As noted (see page 1-57), a small commercial 

fishery occurs off St. Pierre et Miquelon, a French territory off the coast of 

Newfoundland. Thus, ocean interception by fisheries has not been completely eliminated 

as a source of mortality to salmon of Maine origin. 

3. Hatcheries 

The conservation hatchery program is important in preserving individual and composite 

stocks until factors currently depressing overall survival rates and production problems 

can be addressed. As noted (see page 1-17), the first stocking of Atlantic salmon within 

the range of the Gulf of Maine DPS occurred in the early 1870s. In 1991, the current 

stocking program (see page 1-18) was initiated to supplement wild Atlantic salmon 

populations36. This is a river-specific program that stocks the progeny of salmon 

collected from DPS rivers into their river of origin (i.e., river-specific stocking). 

Broodstock from six of the eight DPS river populations (Dennys, East Machias, Machias, 

Pleasant, Narraguagus and Sheepscot rivers) are maintained at the CBNFH. In addition 

to river-specific stocking, these populations could be used to supplement any other rivers 

in the DPS range as needed by managers to foster the conservation of the DPS. Captive 

brood stock populations are maintained by annually collecting juveniles in the wild and 

rearing them to sexual maturity in the hatchery. Current hatchery management goals are 

intended to minimize risks to the natural genetic integrity of the wild stocks from 

selective pressures and inbreeding in the captive environment. 

Preservation of the genetic integrity of populations, and the genetic diversity within and 

among populations, is critical for the long-term fitness and viability of populations 

(Schonewald-Cox et al. 1983; Reed and Frankham 2003). An inherent risk associated 

with the broodstock and stocking program for the DPS is the risk of domestication (i.e., 

any change in the selection regime of a cultured population relative to that experienced 

by the natural population) and loss of genetic variability. 

The NRC (2004), in its recent review of Atlantic salmon in Maine, reviewed the current 

hatchery program. The NRC concluded: “The available information is not sufficient to 

conclude whether hatcheries in Maine can actually help to rehabilitate salmon 

populations, whether they might even be harming them, or whether other factors are 

affecting salmon so strongly that they overwhelm any good that hatcheries might do.” In 

its report, the NRC recommended that current hatchery practices should be evaluated in 

an adaptive management context to minimize potential genetic and ecological effects and 

to modify the program as appropriate (NRC 2004). In addition, the NRC report identifies 

 

36 Wild Atlantic salmon taken for hatchery rearing for broodstock purposes, and any captive progeny 

of these salmon, are included as part of the DPS. These river-specific hatchery fish are protected 

under the ESA, they will not be counted towards reclassification and delisting criteria (65 FR 

69459). 
1-90

an urgent need to understand the relative efficiency of stocking different life-stages. The 

stocking of different life-stages within DPS rivers provides the opportunity to evaluate 

the management advisability of this stocking strategy. The NRC Report also identifies 

the need for continued research and scientific guidance on the use of hatcheries in general 

as a salmon restoration tool. Consistent with the purpose of the recovery process under 

the ESA, the restoration of self-sustaining populations in the wild, hatchery 

supplementation will be reduced and ultimately discontinued when populations are 

recovered to secure levels. 

The Services and the ASC have conducted a structured analysis of the threats faced by 

the DPS including the risks associated with the river-specific hatchery program (see page 

1-93 Threats Assessment). The Services and ASC assessed various risks associated with 

the current hatchery program including (1) artificial selection/domestication (high); (2) 

conflicting stocking stages (e.g. stocking older life stages over younger life stages; low); 

(3) low effect population size (medium); (4) maintenance of broodstock at only one 

Location (medium). The results of the threats assessment concluded that the risk of 

artificial selection/domestication was high. The risk posed to the DPS from low effective 

population size and the maintenance of all broodstock at a single location was medium. 

And that stocking mixtures of different life history stages represented a low-level risk 

under current management schemes to reduce this risk. 

The Services agree with the NRC that there is a high priority need to monitor and 

evaluate the effectiveness and management advisability of river-specific stocking as a 

recovery strategy. In 1999, FWS expanded its Atlantic salmon genetic program. At the 

core of this expansion is genetic characterization of all fish intended for broodstock. The 

FWS, in cooperation with other federal and state agencies, is currently working to 

develop broodstock management plans for FWS Maine Hatchery Complex Program. 

While many of the elements of an effective broodstock plan are operationally in place, 

they are not well documented and the broodstock management plan will update and 

consolidate all the elements into one document. 

An important component of this plan is a Genetic Management Plan (GMP) that is 

needed to reduce several risks associated with captive breeding programs. These include 

1) genetic drift; 2) selection; 3) domestication; and 4) inbreeding. The GMP will 

evaluate the success of reducing these risks while maintaining discrete populations 

through within-river management of spawning, parr collection and other methods. The 

results of current genetic monitoring indicate that diversity within populations is being 

maintained. The GMP will assess whether crossing river-specific stocks may be 

necessary to offset any effects of inbreeding and/or otherwise be advantageous for 

recovery. 

4. Depleted Diadromous Fish Communities 

A structured assessment of the threats facing the DPS, found that depleted diadromous 

fish communities posed a high threat to the recovery of the DPS. As noted (see page 1-

14), rivers within the DPS once supported abundant populations of other native 
1-91

diadromous fish species including alewives, blueback herring, American shad, sea 

lamprey, anadromous rainbow smelt, Atlantic sturgeon, shortnose sturgeon and American 

eel. Atlantic salmon co-evolved with these and other aquatic organisms native to these 

rivers. As these fish completed their life cycles, they likely performed some important 

functions that may have been significant for Atlantic salmon to complete their life cycle. 

As discussed (see page 1-14) these other native fish species likely provided a number of 

important ecological functions including serving as an alternative prey base for predators, 

providing an important source of marine derived nutrients to the freshwater environment 

and habitat modification and enhancement. 

Many of these diadromous species have declined as dramatically as Atlantic salmon in 

recent years (Collette and Klein-MacPhee 2002). The absence of historical data for these 

species make it very difficult to assess the functions these fishes may have performed in a 

properly functioning ecosystem. Nonetheless it is likely that the absence of other 

populations of diadromous species of fish native to rivers within the DPS may be 

impeding the recovery of the DPS. Additional investigation of the role and importance of 

restoring other diadromous fish populations in the recovery of the DPS should be 

pursued. 

5. Climate Change 

The Services and ASC have concluded, based on an analysis various threats faced by the 

DPS, that climate change poses a high level threat to the conservation and recovery of the 

DPS. The Gulf of Maine DPS is at the southern end of the range. Riverine habitat 

occupied by the Gulf of Maine population segment of Atlantic salmon is unique in that it 

is at the southern extent of the North American range of Atlantic salmon (Saunders, 

1981; Baum, 1997). To survive at the extreme southern range, U.S. Atlantic salmon 

populations had to adapt to distinct physical and environmental conditions (Saunders, 

1981). In addition to the Gulf of Maine DPS, the Services determined that historic U.S. 

Atlantic salmon populations were comprised of at least two additional population 

segments: Long Island Sound (LIS) and Central New England (CNE). The LIS DPS and 

the CNE DPS were located to the south of the Gulf of Maine DPS. As detailed in the 

1999 Status Review, the Long Island Sound and the Central New England population 

segments have been extirpated. 

An examination of the effect of warming climate on fishery resources illustrates the 

challenges to fish on the southern end of their range. Climate models predict significant 

warming over the next century as the carbon dioxide content of the atmosphere increases 

(IPCC 2001). Records show that there have been periods of warming and cooling of the 

North Atlantic Ocean, but changes have not been uniform over all areas. Global warming 

can have an effect on sea temperatures, wind currents, fresh water input, and mixing of 

the ocean’s surface layer. 

Fish, being poikilotherms, maintain a body temperature almost identical to their 

surrounding environment. Thermal changes of just a few degrees Celsius can critically 

affect biological functions in salmonids. Impacts include such things as protein 
1-92

metabolism (McCarthy and Houlihan 1997; Somero and Hofmann 1997; and Reid et al., 

1998), response to aquatic contaminants (Reid et al., 1997), reproductive performance 

(Van Der Kraak and Pankhurst 1997), smolt development (McCormick et al. 1997), 

species distribution limits (McCarthy and Houlihan 1997; Keleher and Rahel, 1996; and 

Welch et al., 1998), and community structure of fish populations. It has been suggested 

that an overall increase in river water temperatures due to global warming may actually 

benefit certain fish populations due to greater growth opportunity. Increased 

opportunities for growth in the spring and summer could increase the percentage of fish 

that enter the upper size distribution of a population and smolt the following spring 

(Thorpe 1977; Thorpe et al., 1980; and Thorpe 1994). In addition, warmer rearing 

temperatures during the late winter and spring have been shown to advance the timing of 

the parr-smolt transformation in Atlantic salmon (Solbakken et al., 1994). There is, 

however, an optimal temperature range and a limit for growth after which salmon parr 

will stop feeding due to thermal stress. During this time, protein degradation and weight 

loss will increase with rising water temperature (McCarthy and Houlihan 1997). 

Research conducted by the U. S. Geological Survey, in cooperation with the Maine 

Atlantic Salmon Commission, indicate that the timing and magnitude of seasonal river 

flow, the occurrence and duration of river ice, and the seasonal water-content of coastal 

snow pack are showing systematic trends over time. Spring runoff has become earlier, 

water content in snow pack for March and April has decreased, and the duration of river 

ice has become shorter (Dudley and Hodgkins 2002). 

Recent data released by the Climate Monitoring Branch of the National Climatic Data 

Center show that the 2000-2001 winter was the warmest on record for the United States. 

The agency also reported that worldwide average temperatures for the last 100 years have 

increased. In addition, the 10 warmest individual years on record clustered in the 1990’s, 

indicating a global warming trend (IPCC 2001). 

Climate change is occurring and will undoubtedly have an effect on Atlantic salmon. As 

noted above, the Gulf of Maine DPS is at the southern extreme of Atlantic salmon’s 

range in North America. Atlantic salmon are highly sensitive to increased temperature, 

the Services have concluded that the effects of climate change could be significant. 

Therefore, climate change has been categorized as a high threat. The NRC (2004) 

concluded that some degree of climate warming or change in hydrologic regime could be 

tolerated if other problems affecting Atlantic salmon are reduced. In order to assess the 

effects of global climate change, very long-term temperature records of very high 

precision will be required. 

VII. THREATS ASSESSMENT 

The Gulf of Maine DPS of Atlantic salmon is extremely vulnerable due to the very low 

number of returning adults. Due to this small population size, the DPS is less able to 

withstand natural and anthropogenic factors that may affect its continued existence and 

recovery. These factors could range from genetic intrusions to catastrophic events. As 

populations within DPS rivers increase and recovery proceeds, the vulnerability of the 
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DPS will decrease37. As part of the recovery planning process, the threats facing the 

listed species have been assessed with regard to their geographic extent, severity, life 

stage affected and responsiveness to management. The more precisely threats can be 

assessed, the more refined and specific the recovery strategy can be, increasing the 

probability for successful recovery. 

A threats assessment should include consideration of both natural and anthropogenic 

threats that are the result of either intentional or unintentional actions. The current or 

potential impact of each threat on the DPS is affected by a variety factors including the 

geographic extent or magnitude of the threat (i.e., how many populations are impacted by 

the threat) and the specific life stage(s) affected. Generally, the greater the magnitude of 

a threat, the higher the concern over that specific threat. The later in the life cycle that a 

threat impacts the DPS, the greater the effect to the persistence and recovery of the DPS 

overall. For example, a threat that affects all populations in the DPS and affects returning 

adults would be assessed a higher risk than a threat affecting fry in only one population. 

In addition to the consideration of the geographic extent and life stage affected, a threats 

assessment should also evaluate the responsiveness of individual threats to management 

actions and the feasibility of implementing those actions. While there may be great 

concern over a particular threat to a species, if there are no effective measures that can be 

implemented to minimize or mitigate that threat, then abatement of this threat may not be 

a high priority recovery action. Based on the best available scientific information, 

actions specific to this threat may be limited to additional research and experimentation. 

The ability to implement management actions to address a threat and the likelihood that 

those actions will be effective are critical considerations when formulating a strategy for 

the recovery of a listed species. 

An assessment of threats must also recognize the interrelationship between various 

threats. There may be synergistic effects that must be taken into consideration. For 

example, while slightly lower dissolved oxygen (DO) may be tolerable for juvenile 

Atlantic salmon, in combination with elevated water temperatures it may result in more 

significant impacts, including mortality. Evaluation of individual threats in isolation may 

lead to an underestimate of their impact on Atlantic salmon. Attention needs to be paid 

to cumulative impacts of threats or interrelationships between threats in order to ensure 

an accurate assessment. Given the extremely low numbers of returning adult salmon to 

the Gulf of Maine DPS, priority should be given to those threats that alone, or in 

combination with other factors, pose a high risk to one or more life stages of Atlantic 

salmon. 

 

37 An important distinction exists between vulnerabilities and threats. A vulnerability is a weakness 

that can influence how various threats affect the resource. A threat is any circumstance or event 

with the potential to cause harm to the resource. Threats can come in a variety of forms, including 

those causing direct mortality of one or more life stages; indirect mortality through genetic, 

ecological or behavioral effects; impairing natural movement or life history functions; or 

degrading habitat. 
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As part of the Recovery Planning process, a two-day threats assessment workshop was 

held to assess the magnitude and severity of threats affecting the Gulf of Maine distinct 

population segment (DPS) of Atlantic salmon. The Services assembled a team of 

technical experts from ASC, NOAA Fisheries and FWS (Threats Assessment Group - 

TAG) to conduct a structured threats analysis. The TAG members represented many 

fields of expertise and are all actively engaged in Atlantic salmon management or science 

(See Appendix 5). The workshop participants reviewed the results of the Threats 

Assessment conducted as part of the development of the draft recovery plan. 

The Threats Assessment exercise was based on a three-step process (see Appendix 5). 

The first step of the threats assessment process was to assess the magnitude of the threat 

(i.e. what rivers are affected). The second step of the Threats Assessment exercise 

required the TAG to rank the severity of the threat at each life stage based on the threats 

assessment criteria. For simplicity, items were ranked on a scale of 0 to 4 to describe 

magnitude of threat to each different life stage. A life stage-specific threat severity of 

“negligible to no threat” was assigned a score of 0. An “unknown (uncertain)” severity 

received a score of 1, a “low” severity received a score of 2, a “moderate” severity a 3 

and a “high” severity a score of 4. In addition, each freshwater life stage (adult spawners, 

egg, fry, parr and smolt) was assigned a weight of 1 and the marine life stage was 

assigned a weight of 5. This was not a quantitative assessment but rather a structured 

categorical one that utilized classifications mutually determined by the TAG and 

represented by numbers for simplicity. While the full TAG assessed all classifications, 

when additional fields of expertise were needed (fish health and contaminants) that were 

not adequately represented on the TAG, additional experts were consulted. 

The third step in the threats assessment exercise was the development of the Threats 

Severity Index (TSI). The participants discussed a number of possible ways to calculate 

the TSI (e.g., a simple additive index, some type of weighted average). To calculate the 

TSI score, the life stage weighting was multiplied by its corresponding life stage-specific 

severity. These are summed across each threat and then multiplied by the numbers of 

rivers affected by the threat magnitude. The resulting TSI scores were then sorted and 

assigned a ranking of high, medium or low38. To determine the ranking, the sorted TSI 

scores were divided into thirds and the top third was assigned a ranking of high, the 

middle third was assigned medium and the lowest third was assigned a ranking of low. 

The TSI classifications were then carried over into the Implementation 

Schedule/Recovery Action priority template under the broad Threats/Recovery Actions. 

As part of the threats assessment, participants reviewed and discussed a number of broadbased issues related to description of threats and recovery actions raised by public and 

 

38 

Grouping TSI 

low < 95 

medium 95-140 

high >140 
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peer-review comments received on the draft recovery plan (See Appendix 7). The 

Workshop participants assessed the magnitude and severity of these threats/issues. 

In addition to the threats assessment, the TAG reviewed the Recovery Action priorities 

identified in the Implementation Schedule of the recovery plan. The goal of this review 

was twofold: (1) strengthen the linkage between the threats assessment and the Recovery 

Action prioritization; (2) review current recovery action priorities in light of any new or 

additional information available since the publication of the draft plan including the 

views/information provided in public comments received on the draft plan. As part of 

this analysis, the TAG assessed the implementation feasibility of Recovery Actions39. 

The purpose of this analysis was to highlight actions that would have both a high 

probability of mitigating specific threats and a high implementation feasibility. The 

participants identified whether the recovery actions were either research or management 

related. 

An evaluation of the geographic extent and life stage affected by threats, and the severity 

of these effects, resulted in the following threats being identified as high priority for 

action to reverse the decline of Atlantic salmon populations in the Gulf of Maine DPS: 

• Acidified water and associated aluminum toxicity which decrease juvenile 

survival 

• Aquaculture practices, which pose ecological and genetic risks 

• Avian Predation 

• Changing land use patterns (e.g., development, agriculture, forestry) 

• Climate Change 

• Depleted Diadromous Fish Communities 

• Incidental capture of adults and parr by recreational fishermen 

• Introduced fish species that compete or prey on Atlantic salmon 

• Low Marine Survival 

• Poaching of adults in DPS rivers 

• Recovery Hatchery Program (potential for artificial selection/domestication) 

• Sedimentation 

• Water extraction 

Acidified water and associated aluminum toxicity has been identified as potentially 

having severe effects on parr and smolts. For this reason, actions to address the source of 

acid rain and lowered bicarbonate buffering should be treated as priority implementation 

actions as well as mitigation measures that may ameliorate the impacts to parr and smolt. 

Increases in parr and smolt survival are critical in order to halt the decline and reverse the 

population trend. 

Aquaculture -- Commercial aquaculture of Atlantic salmon poses high risks to all life 

stages of Atlantic salmon through genetic, disease and ecological interactions. For this 

 

39 1 = Feasible (with adequate resources) 

2 = Possible (but with significant logistical, technical and/or legal obstacles) 

3 = Unfeasible 
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reason, actions to minimize the potential interaction between wild and farmed fish should 

continue to receive a high priority for implementation. 

Avian predators have the potential to cause direct mortality to various life stages of 

Atlantic salmon, including returning adults. Smolt outmigration occurs in a relatively 

narrow time window and along a narrow pathway exposing outmigrating smolts to 

predation by double-crested cormorants. Successful recovery is dependent on our ability 

to increase the numbers of outmigrating smolts and therefore actions to reduce 

vulnerability of smolts to predation by double-crested cormorants should be a high 

priority. 

Changing land-use patterns, particularly development, population growth and land 

conversion create a number of issues that may affect the DPS. For example population 

growth and development in Maine has accelerated in recent years, especially in the midcoast region. The Maine State Planning Office projects that the southern, mid-coast and 

Penobscot regions of Maine will continue to experience changes from current rural landuse to urban/suburban in the next several decades. This type of development will result 

in a variety of human activities that may affect salmon habitat. In particular construction 

of buildings, roads and road crossing and land clearing that can alter and disrupt the 

hydrological process in the system may result in a decline in water and habitat quality if 

not properly managed. 

In the Downeast region, forestry is the current dominant land use in the Dennys, East 

Machias, Machias, Pleasant and Narraguagus watersheds. In recent years, concerns have 

grown that large tracts of industrial forest lands are being subdivided and sold off into 

smaller tracts that will result in more aggressive harvest and development. The sale of 

this property has reportedly attracted liquidation timber harvesters and developers, known 

for intensive logging, followed quickly by subdivision and resale of property. This trend 

is projected to continue and will undoubtedly result in increased municipal water use 

demands. This change in land use patterns and resource demands will need to be 

managed in order to protect salmon and their habitat. 

Climate Change poses a high threat to the conservation and recovery of the DPS. The 

Gulf of Maine DPS is at the southern end of their range in North America. An 

examination of the effect of warming climate on fishery resources illustrates the 

challenges to fish on the southern end of their range. Climate models predict significant 

warming over the next century as the carbon dioxide content of the atmosphere increases. 

Records show that there have been periods of warming and cooling of the North Atlantic 

Ocean, but changes have not been uniform over all areas. Global warming can have an 

effect on sea temperatures, wind currents, fresh water input, and mixing of the ocean’s 

surface layer. The NRC (2004) concludes that any prolonged or significant warming of 

Maine’s climate would probably make the survival of Atlantic salmon in Maine more 

difficult due to a number of factors. Some degree of climate warming or change in the 

hydrologic regime could probably be tolerated if most other problems affecting the DPS 

were reduced (NRC 2004). 
1-97

Depleted Diadromous Fish Communities -- Other native diadromous fish populations 

have declined as dramatically as Atlantic salmon in recent years (Collette and Klein 

MacPhee 2002). Maine Atlantic salmon rivers historically supported abundant 

populations of other diadromous fish species including alewives, blueback herring, 

American shad, sea lamprey, anadromous rainbow smelt, Atlantic sturgeon, shortnose 

sturgeon, and American eel. Salmon co-evolved over time with these and other aquatic 

organisms native to these rivers. Large populations of clupeids, such as shad, alewife, 

and blueback herring, used these river systems as migratory corridors, spawning grounds, 

and juvenile nursery habitat. As these fish completed their life cycles, they likely 

performed some important functions that may help Atlantic salmon to complete their life 

cycle. Primarily, these functions may be classified under two broad categories: prey 

buffering and marine derived nutrient cycling. Existing records are not adequate to 

quantitatively assess the ecological functions that these other fishes may have performed 

in a properly functioning ecosystem and how the loss of these functions may be affecting 

the survival and recovery of the DPS. 

Incidental capture and poaching -- Direct mortality at various life stages of Atlantic 

salmon can significantly impede recovery of populations within DPS rivers, and actions 

to reduce mortality should receive a high priority in implementation. Sources of direct 

mortality of parr and returning adults include incidental capture by recreational 

fishermen, poaching and predation. For example, recreational fisheries for trout pose the 

greatest threat to parr. Any mortality of a returning adult has the most serious and 

immediate impact on the population, and therefore actions to prevent adult mortality by 

poaching should receive the highest priority. 

Introduced fish species -- Stocking of non-native fish species and land-locked salmon 

should be avoided in rivers within the DPS. Introduced fish species may compete and/or 

prey on Atlantic salmon. The introduction of non-native fish can endanger or threaten 

the continued existence of native species of fish. The potential exists for ecological 

interactions including predation and interspecific competition between salmon and other 

species of fish including non-native species. Interspecific competition may result in 

adverse impacts to the DPS. Adverse effects of these ecological interactions are 

exacerbated by the small size of the Atlantic salmon population. 

Low marine survival rates continue to be low for U.S. stocks of Atlantic salmon and is 

impeding the recovery of the DPS (see page 1-20). The most current estimates indicate 

that since 1990, return rates to the Penobscot River have been below 0.5% and in the 

most recent three years, below 0.2% (Russell Brown, NOAA Fisheries, personal 

communication). Preliminary estimates for the Narraguagus River indicate that total 

marine survival (emigrating smolt to returning adult) of DPS salmon are less than 2% 

(John Kocik, NOAA Fisheries, personal communication). The factors affecting the 

survival of salmon during the marine phase of their life history are not well understood. 

Recent research on the effects of acid rain has shown that pulses of acidity can result in 

mortality in smolts during the transition from the freshwater to marine life phase of their 

life cycle. The problem of mortality as smolts transition from freshwater to the ocean as 

post-smolts needs to be solved. If, as it seems likely, early mortality in estuaries and the 
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ocean is due in part to water chemistry, particularly acidification in freshwater, mitigation 

of this threat is an urgently needed action (NRC 2004). 

Large scale oceanographic processes also likely affect Atlantic salmon survival rates 

(Dunbar 1993; Friedland 1994). Sea surface temperature (SST) appears to be an 

important feature of the marine environment that affects Atlantic salmon survival. 

Correlation between the survival rates of multiple stocks suggest that an important cause 

of mortality may act upon the stocks when they are mixed and utilizing a shared habitat. 

Recovery Hatchery Program -- The conservation hatchery program is important in 

preserving individual and composite stocks until factors currently depressing overall 

survival rates and production problems can be addressed. An inherent risk associated 

with the broodstock and stocking program for the DPS is the risk of domestication (i.e., 

any change in the selection regime of a cultured population relative to that experienced 

by the natural population) and loss of genetic variability. The results of the threats 

assessment conducted as part of recovery plan development concluded that the risk of 

artificial selection/domestication is high. Current hatchery management goals are 

intended to minimize risks to the natural genetic integrity of the wild stocks from 

selective pressures and inbreeding in the captive environment. 

Sedimentation can impact salmon habitat in a number of ways. Sediment changes the 

physical structure of a river’s substrate, a critical factor in salmon survival. While a 

thorough assessment of habitat conditions has not been conducted, field evidence 

suggests that elevated levels of sediment have compromised spawning habitat along 

certain reaches in several DPS rivers. 

Water extraction -- Decreases in instream flows have the potential for high impacts to 

adult spawners, early freshwater life stages and parr. Water extractions have the potential 

to impede or prohibit access to spawning habitat, dewater redds, or reduce the quantity of 

habitat available for fry and parr. Interference with spawning or direct mortality of 

juveniles could have serious consequences for population recovery. 

In addition to the highest priority threats discussed above, moderate threats to adult 

spawners warrant attention for priority action due to the extremely low population 

numbers. Low dissolved oxygen due to excess nutrients from agriculture, sewage 

treatment, septic systems, processing/manufacturing facilities, and/or hatcheries has the 

potential to impact adult spawners. Elevated water temperatures due to land use 

practices, impoundment of free-flowing reaches of rivers, low flows, thermal discharges 

and/or decreased stream shading also has the potential to impact adult spawners. Impacts 

to adult spawners are also possible from obstructions to passage that may be caused by 

man-made barriers (e.g. dams, poorly designed roads and culverts) or natural barriers 

(e.g. geological falls, beaver dams and debris dams). Although these threats are not now 

categorized as high, the fact that they impact adult spawners justifies the elevation of 

concern such that actions to address these threats should be prioritized. 
1-99

In addition to the threats that are currently known to affect Atlantic salmon, there are 

factors that have the potential for significant adverse effects; however, the information 

needed to fully assess the severity of these factors is lacking. As such, additional 

research on the following factors is a critical recovery need: the effect of diseases and 

chemical contaminants on all life stages; the effect of marine mammal predation; and the 

effect of bycatch in U.S. commercial fisheries on adult spawners, smolts and in the 

marine environment. 

VIII. CURRENT CONSERVATION EFFORTS 

Atlantic salmon conservation and restoration efforts involving private citizens as well as 

state, federal, local and international organizations have been underway for more than 

150 years. Baum (1997) provides an excellent summary of historic restoration activities. 

The majority of these efforts is related to hatchery fish production and stocking activities. 

It has only been in the last two decades that a greater emphasis has been placed on the 

issue of quality, quantity and accessibility of Atlantic salmon habitat. The following 

section provides an overview of recent conservation efforts and accomplishments. Many 

of these are described in more detail in other sections of this plan. 

State of Maine Conservation Plan 

In 1997, the State of Maine established the Atlantic Salmon Conservation Plan for Seven 

Maine Rivers (MASCP). The MASCP (1997) provides the basis for many important ongoing Atlantic salmon conservation and recovery activities. This plan was developed 

with extensive participation of state and local agencies, industry, conservation groups and 

other stakeholders and with the input of NOAA Fisheries and FWS staff. This plan is 

administered by the Maine Atlantic Salmon Commission. The MASCP identifies 

fourteen goals for successful Atlantic salmon conservation (MASCP amendment). These 

goals fall under four major categories: fishery management, habitat protection, habitat 

enhancement and species protection. Key elements and factors addressed by the plan 

include: water quality and quantity, riparian habitat, fishing activities, predation, 

aquaculture, disease and stocking. The MASCP and progress reports on its 

implementation are important sources of information about recent and ongoing 

conservation efforts for the Gulf of Maine DPS of Atlantic salmon and can be accessed at 

ASC website (www.state.me.us/asa/). 

Many significant conservation efforts have been accomplished under the auspices of the 

MASCP. These include improving juvenile and adult salmon population assessment; 

construction of weirs and traps; mapping of spawning and nursery habitat and completion 

of riparian buffer methodology; habitat protection efforts including acquisition of riparian 

habitat, improvement of road crossings and evaluation of non-point source pollution; 

habitat enhancement activities including improving fish passage, water use management 

planning and upgrading road crossings, ditches and culverts; species protection efforts 

including work with the aquaculture industry and recreational fishing interests (MASC 

2000). Ongoing conservation activities that fall under the framework of the MASCP are 

detailed in other sections of this recovery plan. 
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This recovery plan builds on and expands recovery actions identified in the MASCP. 

The Services intend to maintain and expand ongoing collaborative recovery efforts 

implemented as part of the MASCP. The recovery program will build on and 

complement continuing conservation efforts identified in the MASCP. 

Other Ongoing Conservation Efforts 

Many public and private organizations and agencies have been involved in Atlantic 

salmon conservation. The Services recognize and acknowledge the ongoing efforts of 

these groups and accomplishments to date. Many of the ongoing efforts by these groups 

are outlined throughout the recovery plan. 

Several departments within Maine state government are involved in Atlantic salmon 

conservation. These include: Maine Atlantic Salmon Commission; Maine Department of 

Inland Fisheries & Wildlife; Maine Department of Environmental Protection; Maine 

Department of Agriculture, Food, and Rural Resources; Maine Department of 

Transportation; Maine Department of Conservation; Maine Forest Service, Maine 

Department of Marine Resources; Maine Land Use Regulation Commission; Maine State 

Planning Office. 

Federal agencies involved in Atlantic salmon conservation in Maine include: Army Corps 

of Engineers; National Marine Fisheries Service; USDA Natural Resource Conservation 

Service; United States Geological Survey (USGS); U.S. Environmental Protection 

Agency (EPA); and the U.S. Fish and Wildlife Service. 

The recovery process for endangered species incorporates all the elements of the ESA; 

regulatory protection, research, management and education and outreach. Regulatory 

actions, such as Section 7 consultations or Habitat Conservation Plans for a listed species, 

should be conducted in such a manner that furthers the recovery process. In addition to 

independent federal conservation efforts, many federal actions are cooperative and 

require collaborative efforts with the State of Maine and the many organizations acting to 

fulfill the goals of the MASCP. These efforts are discussed in more detail throughout the 

recovery plan. 

In addition to state and federal government initiatives, there are many private and public 

organizations involved in Atlantic salmon conservation efforts. These include: Atlantic 

Salmon Federation, Maine Council; Atlantic Salmon Unlimited; Cherryfield Foods Inc.; 

Coastal Mountain Land Trust; Cove Brook Watershed Council; Dennys River Watershed 

Council; Dennys River Sportsman’s Club; Downeast Rivers Coalition; Ducktrap 

Coalition; East Machias River Watershed Council; Eight Rivers Roundtable; Fish 

Friends; Fishing in Maine; Friends of the Kennebec; Kennebec County Soil & Water 

Conservation District; Knox/Lincoln County Soil & Water Conservation District; 

Machias River Watershed Council; Maine Rivers; Maine Environmental Research 

Institute; Maine Wild Blueberry Commission; Narraguagus River Watershed Council; 

Natural Resources Council of Maine; Northern Penobscot Salmon Club; Penobscot 
1-101

Riverkeepers; Pleasant River Watershed Council; Pleasant River Fish and Game 

Conservation Association; Pleasant River Hatchery; Project SHARE; Quoddy Regional 

Land Trust; Saco River Salmon Club; St. Croix International Waterway Commission; 

Sheepscot River Watershed Council; Sheepscot Valley Conservation Association; Trout 

Unlimited Maine Council; Trout Unlimited Merrymeeting Bay Chapter; University of 

Maine Cooperative Extension Service; Veazie Salmon Club; Waldo County Soil & Water 

Conservation District; Washington County Soil & Water Conservation District; Wild 

Salmon Resource Center; Wyman & Son Inc. The education and outreach section of the 

recovery plan includes a more detailed discussion of the ongoing efforts of the Watershed 

Councils. 

International Atlantic salmon conservation efforts are largely pursued through NASCO. 

Since the early 1990s, NASCO has drastically reduced harvest of Atlantic salmon on the 

high seas and from foreign fisheries. Ongoing efforts by NASCO are discussed in 

several of the following sections of this recovery plan. In addition, other groups involved 

in international Atlantic salmon issues include the North Atlantic Salmon Trust, the 

Atlantic Salmon Federation, Trout Unlimited, World Wildlife Fund, the Maine 

Aquaculture Association and other industry groups. 

Governance 

In Maine multiple agencies and organizations (e.g., state, federal, local, tribal, private) 

are involved, either directly or indirectly, in salmon conservation and recovery. The 

NRC (2004) provides a summary of the many groups involved in programs that influence 

human activities related to Atlantic salmon conservation. Given the number of agencies 

and other parties involved in salmon conservation, the potential exists for conflicting 

goals and mandates, overlapping management responsibility and gaps in authority 

between existing agencies and organizations. 

The NRC (2004) states that it was unable to assess the overall effectiveness and 

efficiency of efforts to which government agencies were contributing to the conservation 

and recovery of Atlantic salmon in Maine. The NRC recommended that a systematic 

assessment of the existing governance framework be conducted to evaluate whether this 

issue may be constraining the recovery of the DPS. 

The effectiveness of efforts to conserve and recover the DPS may have been affected by a 

failure to learn from policies and other initiatives (NRC 2004). One strategy for 

addressing this problem is to design policies based on the principles of adaptive 

management (NRC 2004)40. The Recovery Plan states that throughout all phases of 

recovery plan implementation, recovery actions will be designed as experiments, results 

will be monitored and future actions modified accordingly, following an adaptive 

management approach. 

 

40 Recovery actions and policies need to be designed as experiments so that their impacts can be 

monitored and results used to inform future recovery strategies and actions. 
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The Recovery Plan identifies a number of areas where existing governance related issues 

need to be addressed to ensure consistent and effective protection of Atlantic salmon in 

Maine. For example, the plan identifies discrepancies in existing permitting of water 

withdrawals in organized and unorganized townships that fall under the authority of 

LURC and DEP respectively (see page 1-27). Other areas where the plan identifies the 

need for greater coordination between existing agencies include, stocking programs, 

assessment and research, water quality monitoring, information dissemination, interagency communication and coordination 

The Atlantic Salmon Recovery Team will provide a forum that will serve as a clearing 

house for information on current activities related to salmon recovery. One of the 

primary responsibilities of the Atlantic Salmon Recovery Team’s Coordinating 

Committee is to ensure effective communication and coordination between the Recovery 

Team and other appropriate agencies and groups involved in salmon recovery and 

conservation (e.g., state and federal agencies, the Maine Technical Advisory Committee 

(TAC), the USASAC, local conservation organizations, industry). Through the 

preparation of an annual workplan and progress report, the Recovery Team will help 

identify areas where overlapping authority and conflicts in mandates may be impeding 

the efficacy of various recovery actions. 

The issue of continued and improved inter-agency coordination has been identified as an 

important need by a variety of agencies involved in salmon conservation. An example of 

inter-agency coordination at the state level is the annual meeting between Maine ASC 

and Maine IFW held to review existing stocking programs and assess the potential affects 

of these introductions on Atlantic salmon populations. At the federal level, FWS and 

NOAA Fisheries staff meets with the ACOE once every three weeks to screen permit 

applications. The purpose of these meetings is to identify projects that warrant Section 7 

consultation. At the state level, the Services also meet with Maine Department of 

Transportation (MDOT) once a month to discuss upcoming projects. MDOT reportedly 

does a good job identifying salmon concerns before a project gets to the permitting stage. 

Some MDOT do not undergo Section 7 consultation as there is no federal nexus (no 

federal highway funds or ACOE permit). In these cases, MDOT typically consults with 

the Maine ASC. 

The Services have developed a workload agreement at the regional level whereby 

responsibilities related to ESA implementation, particularly with regard to Section 7 and 

Section 10 are clearly delineated. Under this agreement, FWS is primarily responsible 

for activities and issues affecting the freshwater environment while NOAA Fisheries has 

assumed lead responsibility for activities within the estuarine and marine environment. 

The Services should review the current delineation of ESA responsibilities for the DPS to 

ensure effective and efficient implementation of activities necessary for the protection 

and recovery of the DPS. Joint jurisdiction of endangered species by NOAA and FWS 

creates an additional layer of bureaucracy that may result in delays in the implementation 

of recovery actions and adherence to other ESA mandates (e.g., permit review, permit 

issuance, recovery plan development). The Services will continue to review and assess 

the effectiveness of this workload division to ensure that it achieves the goal of efficient 
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allocation of existing resources and reduces unnecessary delays and duplication of 

efforts. 

Strong and effective local conservation organizations are important partners in recovery 

efforts. In 2004, the Eight Rivers Roundtable engaged the services of Demont & 

Associates, Inc., of Portland, Maine to assist in building local watershed capacity. 

Demont (2005) concluded that coordination of local conservation efforts by an umbrella 

organization could facilitate coordination between state, federal and various local 

organizations thereby strengthening the effectiveness of individual local councils. 

Demont (2005) concluded that in the long run, the existing definition and structure of the 

existing watershed councils may not be the most viable model for ensuring communitybased watershed management. For example, the councils have struggled to maintain 

active participation and secure funding for restoration activities (Demont 2005). An 

umbrella organization could provide a number of functions for local watershed 

organizations including: liaison with state and federal agencies; provide administrative 

support; provide organizational development and management; provide technical support; 

fund raising; advocacy for watershed-specific conservation programs and salmon 

recovery (Demont 2005). The report recommended that such an umbrella organization 

should be structured as a 501(C)3 organization, with bylaws and an elected board of 

directors (Demont 2005). It was further recommended that the Eight Rivers Roundtable 

is positioned to become a more active coordinating body for the watershed councils and a 

model for the development of other regional watershed bodies throughout the State 

(Demont 2005). 

River-specific Management Planning 

Based on an assessment of the threats to the survival and conservation of the species, the 

Recovery Plan identifies site-specific management actions for all the threats the Services 

have identified under Section 4(a)(1) of the ESA five-factor analysis. Section 4(f) of the 

ESA states that recovery plans, to the maximum extent practicable, must incorporate sitespecific management actions necessary for the survival and recovery of the species. 

Some of the threats identified are widespread and therefore the actions identified are 

applicable throughout the full range of the DPS. Other threats are present in only some 

of the watersheds and therefore the actions identified only apply in those specific 

watersheds. 

The Recovery Plan (see Implementation Schedule) establishes priorities for all recovery 

actions identified in the plan. These Recovery Action priorities (1, 2, 3)41 apply to the 

DPS as a whole, not a single river. Recovery Action priorities may change on different 

 

41 Priority 1 – Actions that must be taken to prevent extinction or to prevent the species from 

declining irreversibly 

Priority 2 – Actions that must be taken to prevent a significant decline in population/habitat 

quality or in other significant negative impact short of extinction 

Priority 3 - All other actions necessary to provide for full recovery of the species 
1-104

spatial or temporal scales. Recovery Actions may be higher priorities for individual 

rivers and populations then they are for the entire DPS. 

An assessment of the magnitude and severity of factors that may be affecting the 

conservation and recovery of Atlantic salmon reveals discrete issues exist for individual 

rivers within the DPS (see Threats Assessment). For example, the threat posed by acidity 

varies in geographic and seasonal patterns. Geographically, the DPS rivers located east 

of the Penobscot River have a lower pH than those located west of the Penobscot (Haines 

1981; Haines et al. 1990). Other examples include different land ownership patterns (i.e., 

multiple small landowners in Mid-Coast region vs. large landowners Downeast), road 

density, water use, introduced species and land development pressure. 

Implementation of the Recovery Plan may be facilitated by compiling a watershed or 

river-specific management plan that would include and highlight those threats and 

accompanying actions applicable within that particular area. River-specific plans could 

tailor recovery action implementation to specific watersheds to address different 

environmental conditions and land uses that exist in individual watersheds within the 

DPS. For example, land acquisition and conservation easements have been pursued on a 

number of DPS rivers. Within a particular watershed, an evaluation could be conducted 

to ensure that this type of land protection measures are pursued in areas that are 

threatened with serious, immediate development pressure, where the relationship between 

specific land use changes and habitat degradation is firmly established and where high 

value habitat is at risk. The reader should note that ongoing recovery implementation 

activities currently are responsive to the specific circumstances within individual 

watersheds (e.g., NPS surveys, nutrient management plans in the Sheepscot, liming 

project Downeast). 

Management plans for specific issues of concern have been developed, or are envisioned, 

for many of the rivers and watersheds within the DPS. For example, the Maine ASC has 

been working to develop river-specific fisheries management plans for individual DPS 

rivers. The State of Maine, working in cooperation with multiple public and private 

partners, has developed a water use management plan (WUMP) for the Narraguagus and 

Pleasant rivers and for Mopang Stream (a tributary to the Machias River) (MSPO 

2001)(see page 1-26). The WUMP was developed to address a specific issue (i.e., 

agricultural water use) that was a concern in these three rivers. In a number of instances, 

local conservation organizations have begun the process of developing river-specific 

management plans for specific issues. NPS management plans have been developed for 

the Narraguagus and Dennys River. These plans were developed by Project SHARE and 

the Narraguagus and Dennys river Watershed Councils (NRWC, DRWC) with support 

from a wide range of state, federal and local agencies. Project SHARE has initiated a 

program whereby river-specific water quality management plans will be developed for 

each of the eight DPS rivers (Project SHARE 2005). All these initiatives address discrete 

elements that comprehensive river-specific management plans should encompass. 

The NRC (2004) recommended that, over the long-term, some type of comprehensive 

decision-analysis approach should be utilized. The Services and the ASC continue to 
1-105

review available decision analysis techniques and consider the use of appropriate risk 

assessment tools in recovery implementation. 

The NRC (2004) recommendation related to the use of decision analysis stems in part 

from its stated view that great uncertainty exists regarding the causes of the decline of 

salmon populations in Maine and therefore what recovery actions are necessary to reverse 

the decline of the DPS. While the Services agree that uncertainty exists, the best 

available information clearly indicates several management approaches that have the 

potential to improve survival rates for Atlantic salmon at a number of life-stages (e.g., 

mitigation of low pH, habitat enhancement, predator control). These management 

strategies are based on the results of recent and ongoing research. As noted, the Services 

have already conducted a structured threat assessment in conjunction with the 

development of this Recovery Plan (see page 1-93). As noted, the assessment explicitly 

addressed the magnitude and severity of threats believed to be affecting the conservation 

and recovery of the species. When assessing the severity of various threats at individual 

life-stages uncertainty was explicitly addressed. 
2-1

PART TWO: RECOVERY STRATEGY 

The Gulf of Maine DPS continues to face a drastic population decline and severe threats 

to its persistence. Recovery actions must be implemented in a focused and strategic way 

to achieve the greatest benefits for recovery of the DPS. To accomplish this, two 

categories of actions will be high priority for the first phase of recovery plan 

implementation (i.e., the first five years): 

1) Implementation of the Priority 1 recovery actions (see Part Five: Implementation 

Schedule) that will reduce the severest threats (i.e., acidified water and associated 

aluminum toxicity, salmon aquaculture, avian predation, changing land use patterns, 

climate change, depleted diadromous fish communities, incidental capture by recreational 

fishermen, introduced fish species, low marine survival, poaching, recovery hatchery 

program, sedimentation and water extraction). 

2) Actions that address critical information needs. Actions include research to better 

understand threats and how best to address them. These threats include disease, chemical 

contaminants, acidified water, aluminum toxicity, predation, sedimentation, low marine 

survival and potential commercial fisheries bycatch. A population viability analysis 

(PVA)42 has been prepared for the eight rivers within the DPS known to still support wild 

salmon populations, and this, in combination with improved knowledge on threats, will 

help develop final reclassification and delisting criteria (see Part Three: Recovery Goal, 

Objectives and Criteria). Actions other than priority 1 recovery actions that can be 

initiated quickly and have the potential to significantly improve survival and reverse the 

decline of DPS populations. 

Presently a status review is underway to determine the relationship of large river systems 

to the DPS as currently delineated. This review will also determine the status of salmon 

populations within these large river systems, as well as any other additional salmon 

populations not presently within the geographic range of the DPS. Decisions regarding 

the status of these populations may have significant implications for the recovery 

strategy. 

Full recovery will encompass the full range of the DPS from the Kennebec to the St. 

Croix River. The initial focus of the recovery program, however, will be on the eight 

populations in the DPS that were extant at the time of the listing (see page 1-1). Without 

immediate action to conserve and protect these core populations and the remnant genetic 

variation they represent, long-term success and attainment of self-sustaining populations 

will be severely compromised. 

 

42 Population viability analysis (PVA) is a tool used to estimate the probability of persistence over 

time of given stock sizes. There are a wide range of modeling approaches used in PVA, from 

simple extrapolation of current trends to complex individual-based models. Whatever approach is 

taken, the purpose is the same, to predict the probability of the population persisting into the 

future. PVA is used to explore potential consequences of management actions in the light of 

uncertainty.
2-2

After the initial phase of recovery plan implementation is completed, efforts will focus on 

addressing remaining threats and information needs. Throughout all phases of recovery 

plan implementation, recovery actions will be designed as experiments, results will be 

monitored and future actions modified accordingly, following an adaptive management 

approach. In addition, the following principles will be used to bring focus to longer-term 

recovery efforts: 

1. Maintain and expand on-going collaborative conservation and recovery efforts. The 

recovery program will build on and complement continuing conservation efforts, most 

notably actions described in the 1997 Atlantic Salmon Conservation Plan for Seven 

Maine Rivers (MASCP). A number of multi-organizational groups (e.g., Project 

SHARE, Maine Technical Advisory Committee) are actively engaged in cooperative 

Atlantic salmon conservation activities. Local watershed councils, formed under the 

auspices of the MASCP, will also continue to play an important role in recovery activities 

in their respective DPS watersheds, particularly the planning and implementation of 

watershed-specific habitat protection and restoration, consistent with general habitat 

conservation actions outlined in this plan. Federal recovery efforts will strive to 

complement and enhance the expertise and commitment of this diverse group of 

agencies, organizations and interested parties, consistent with the principles of sound 

science and the mandates of the ESA. Recovery implementation will be coordinated with 

local Indian Tribes in accordance with Secretarial Order 3206. 

2. Utilize the river-specific hatchery populations as a temporary “bridge” through the 

present period of low returns of adult spawners, with the goal of attaining self-sustaining 

wild-spawning populations. While the recovery hatchery program serves an important 

role in preserving river-specific stocks until factors currently depressing survival rates 

and adult returns can be addressed, the purpose of the recovery process under the ESA is 

to restore self-sustaining populations in the wild. Thus, recovery of the Gulf of Maine 

DPS will require the recovery of secure wild-spawning Atlantic salmon populations that 

are able to live their entire lives and meet all of their requirements in the wild. The riverspecific hatchery fish are also listed and protected under the ESA and are also included as 

part of the DPS. However, these hatchery fish will not count toward a delisting until they 

have spawned naturally in the wild (65 FR 69459). 

Management of hatchery stocks outlined in this plan (as in the MASCP) is predicated on 

river-specific management, as Athe most scientifically prudent approach in order to 

protect any local adaptations, consistent with the long-established management for these 

rivers from ecological and evolutionary perspectives, river-specific stocking is currently 

viewed by the scientific community as the best available strategy to promote restoration 

of the resource.” (MASCP 1997). The current river-specific hatchery stocking program 

and efforts to prevent introgression of farmed fish into the wild salmon populations are 

both based on the goal of conserving the natural diversity of genetic traits of DPS stocks 

and maximizing the ability of these stocks to exploit their native habitat. These stocks 

have evolved over time in response to local conditions. Conservation of river-specific 

stocks reflects “evidence ... that restocking efforts are most likely to succeed when donor 

fish come from the river to be stocked” (MASCP 1997), and maximizes potential for 
2-3

retention of genetic traits needed to respond to long-term local environmental variation. 

This recovery plan supports that goal and also recognizes and strives to minimize risks to 

the natural genetic integrity of the wild stocks from selective pressures and inbreeding in 

the captive environment. In the event that significantly reduced genetic diversity or 

indications of inbreeding depression are observed in any river-specific population, 

carefully planned crossing of stocks during artificial propagation or via stocking may be 

required to increase population viability. Crossing of river-specific stocks within the 

GOM DPS would be an acceptable practice if it were deemed necessary and appropriate 

for recovery of the DPS. 

3. Restore, maintain, and ensure long-term protection of freshwater, estuarine, and 

marine habitats and natural processes in sufficient quantity and quality to support selfsustaining wild-spawning populations. Consistent with the central purpose of the ESA 

(section 2(b)): “to provide a means whereby the ecosystems upon which endangered 

species and threatened species may be conserved”), recovery efforts described in this 

plan are premised on the long-term protection and restoration of habitats for all stages of 

the Atlantic salmon life-cycle. This “ecosystem approach,” also reflected in the MASCP, 

recognizes the fundamental interdependence of aquatic, riparian, and upland habitats 

within DPS river watersheds. A variety of mechanisms, including (but not limited to) 

cooperative agreements, State and local land and water use regulations, habitat 

conservation plans (under Section 10 of the ESA), landowner incentive programs, 

conservation easements, and land acquisition may be employed to accomplish habitat 

restoration and protection. The ESA listing also recognizes the potential role of factors in 

the marine environment in the recent low adult returns. The Services are committed to 

prompt and appropriate response to any marine factors that may be identified and for 

which management is feasible. 

4. Seek long-term reductions in risks of disease transmission, genetic introgression, and 

ecological impacts from aquaculture-bred Atlantic salmon and non-indigenous fish 

species. Current low numbers render the DPS Atlantic salmon especially vulnerable to 

threats posed by aquaculture fish. Even when the DPS population attains numbers and 

distribution that satisfy the delisting criteria, however, the large numbers of farmed fish 

in hatcheries and marine cages within some DPS river watersheds will pose a substantial 

continuing risk to the persistence and integrity of the wild fish. Full recovery of the DPS 

will require long-term commitments to practices that minimize potential threats to the 

DPS from disease transmission, genetic introgression, and ecological impacts from 

farmed fish. Stocking of non-indigenous fish species poses risks due to predation and 

competition, and measures must be instituted to limit current and future stocking unless 

data indicates that a particular non-indigenous species does not pose a threat to Atlantic 

salmon. 

5. Employ appropriate and effective measures to reduce mortality of Gulf of Maine DPS 

Atlantic salmon due to international commercial fisheries, predation, and poaching until 

populations become self-sustaining. Atlantic salmon populations should be able to 

withstand natural predation rates and some controlled level of harvest. The current low 

number of Gulf of Maine DPS Atlantic salmon have elevated their vulnerability to even 
2-4

very small increments in mortality rates. Near-term recovery efforts, therefore, may 

include efforts to reduce predation-induced mortality, especially where human activities 

increase the salmon’s natural vulnerability to predation (e.g., by impeding salmon 

movements) or where predator populations are at historical high levels that are likely to 

pose a detriment to salmon survival and recovery. Likewise, efforts to minimize take due 

to poaching and harvest in international waters are warranted in light of the severely low 

current population numbers. Once populations have recovered to self-sustaining levels, 

the need for predator management should be reevaluated, along with the potential for the 

DPS to support carefully regulated sustainable harvest. 

6. Expand the distribution and increase the abundance of Atlantic salmon populations 

within the historic range of the DPS. The viability of the entire DPS is served by 

preventing formation of any further gaps in the range of the DPS and by restoring 

demographically and genetically secure diverse populations within many watersheds. 

Promoting recovery across rivers within the historic range of the DPS will help conserve 

the remaining genetic variability of populations, reduce the vulnerability of the DPS to 

catastrophic events and provide opportunities for research. Expanded distribution of 

Atlantic salmon stocks within the DPS could be achieved through natural recolonization 

or reintroduction, including the potential use of experimental population designations to 

reintroduce fish to other rivers within the geographic range of the DPS (see Section 

5.1.4). 
3-1

PART THREE: RECOVERY GOAL, OBJECTIVES AND CRITERIA 

The goal of the recovery program is removal of the Gulf of Maine DPS of Atlantic 

salmon from the Federal List of Endangered and Threatened Wildlife (50 CFR 17.11). 

Recovery will be achieved when conditions have been attained that allow self-sustaining 

populations to persist under minimal ongoing management and investment of resources. 

Achievement of recovery does not require the return of a species to all of its historic 

range, nor does it require attainment of full carrying capacity of available habitat if a 

smaller population is demonstrably secure. In order to achieve the goal of recovery, a 

stepwise approach will be adopted which first addresses the critically low number of 

adult Atlantic salmon returns then builds toward full recovery. Although the objectives 

are presented in a stepwise fashion, it is recognized that there is an inherent linkage 

among the objectives in that specific recovery actions will often help achieve all 

objectives. 

Development of Final Recovery Criteria 

The Atlantic salmon recovery planning process has involved considerable efforts to 

develop reclassification and delisting criteria. The Services and State partners have 

explored several approaches to establishing final demographic recovery criteria for the 

Gulf of Maine DPS of Atlantic salmon, but have concluded that all available methods are 

insufficient for purposes of this plan. As a result, the Services have concluded that it is 

not practicable at this time to establish final demographic criteria for reclassification and 

delisting criteria of the DPS. The reasons for this and the anticipated timeline necessary 

to develop such criteria are discussed below. 

The primary approach considered for establishing demographic reclassification and 

delisting criteria was the use of Conservation Spawning Escapement (CSE) targets43. 

While the increases in population abundance required to attain CSE targets for DPS 

rivers would reflect a healthier population than is currently present in the Gulf of Maine 

DPS, this method does not provide an indication of the probability of persistence (i.e., 

extinction risk) of the DPS. For example, CSE targets could substantially under or overrepresent the abundance of adult spawners needed to ensure a high probability of species 

persistence. In the first case, populations might remain highly vulnerable even at or 

above the theoretically attainable CSE. In the second case, recovery could be reached 

well before CSE targets are met. The size and distribution of the recovered population 

must be sufficient for the DPS to withstand natural environmental fluctuations. As a 

target, CSEs do not include consideration of the breadth of the genetic makeup of the 

species which is critical in order to conserve its adaptive capabilities, do not consider 

resiliency to ensure that the population can withstand stochastic events, and do not 

 

43 A CSE target is the number of returning adult spawners that will theoretically fully seed currently 

available juvenile rearing habitat. CSE is calculated using a number of factors, including average 

female fecundity, ratio of returning males to females, available freshwater habitat and target eggdeposition rates per unit of habitat needed to fully seed a river (Elson 1975).
3-2

consider redundancy in order to provide a margin of safety for the species to withstand 

catastrophic events. 

The Services also considered other potential approaches to establishing recovery criteria, 

including the use of criteria established by the World Conservation Union (IUCN 1994), 

and the use of a basic stock/recruitment curve and the concept of limit and target 

reference points similar to Canadian salmon management models44. The IUCN criteria 

are not species-specific and their application could result in delisting criteria that exceed 

the capacity of the habitat in the eight rivers, even taking into consideration all reasonable 

habitat restoration options. The limit and target reference point approach would require 

the use of a PVA model to define the stock/recruitment relationship for the DPS. This 

approach does not provide a measure of the long-term viability of the DPS and therefore 

was deemed to be insufficient for the development of recovery criteria. 

The Services and their State partners concluded, as a result of the unsuitability of the 

available approaches, that the development of final demographic recovery criteria would 

be facilitated by the use of a PVA model specific to the Gulf of Maine Atlantic salmon 

DPS. A life history PVA model has been developed for the eight rivers within the DPS 

still supporting wild salmon populations at the time of the listing. This model, which was 

developed by NOAA Fisheries, Northeast Fisheries Science Center (NEFSC) in 

cooperation with other state and federal partners, has undergone technical review45. A 

life history modeling approach was selected for the Gulf of Maine DPS due to the large 

amount of data available for the species. This approach has the benefit of higher 

biological realism but requires many more input parameters and distributions relative to 

simpler PVA models. Complex features of Atlantic salmon biology, such as anadromy, 

precocious parr, kelting and hatchery supplementation, are captured in the model. 

The Services will use the results of the PVA to assist in the development of final 

reclassification and delisting criteria for the DPS. A PVA is not a replacement for criteria 

based on threats, but can supplement them. The Services will integrate the existing PVA 

model with the comprehensive Viable Salmonid Populations (VSP)46 approach to 

determine appropriate final reclassification and delisting criteria. 

 

44 A limit reference point is a biological reference point, usually expressed in terms of spawning 

population numbers, that represents a threshold, below which a population is considered to be 

collapsing towards extinction. A target reference point is a biological reference point that is a 

desirable minimum population target to reach and maintain. 

45 The PVA model has been reviewed by internally as well as by a number of technical groups 

including the Maine TAC, the USASAC, ICES North Atlantic Salmon Working Group, NMFS 

NEFSC, NWFSC and the SWFSC. In May 2005, the PVA was presented in the peer-reviewed 

journal, Transactions of American Fisheries Society (see, Legault, C.M. 2005). Population 

Viability Analysis of Atlantic Salmon in Maine, USA. Transactions of the American Fisheries 

Society. 134(3):549-562).

46 McElhany et al. (2000) introduces the concept of viable salmonid populations (VSP). The VSP 

approach identifies attributes of viable salmonid populations and provides guidance on assessing 

the conservation status of Pacific salmonid populations and larger-scale salmonid groupings (i.e., 

Evolutionarily Significant Units (ESUs)). There are four parameters that are key to determining 

the viability of salmonid populations: abundance, population growth rate, population spatial 
3-3

Development of final objective, measurable reclassification and delisting criteria is not 

currently practicable for several reasons. The principle reason (as discussed above) is 

that currently available methods considered do not encompass and integrate the 

fundamental attributes of viable salmonid populations articulated by the VSP approach. 

The deficiencies of the available methods underscore the fundamental questions and 

attributes that the Services must identify (e.g., abundance, spatial distribution, diversity, 

population growth rate) to establish final recovery criteria. Progress to 

identify/incorporate these specific attributes has not been accomplished yet as limited 

resources have been focused on the stabilization criteria and preserving the 8 core 

populations known to have persisted in the DPS. 

Atlantic salmon recovery criteria will focus on achieving population levels consistent 

with their probability to avoid extinction, rather than a general rule of thumb for salmon 

production. The integration of the VSP approach with the results of the PVA will require 

scientists and managers to address the complex issues of 1) the role of vacant habitat; 2) 

mixing of stocks with current geographic juxtaposition of populations and other 

scenarios; and 3) the current and future habitat quality, quantity, and locations. The 

Services will develop these criteria through scientific and management panels that will 

outline appropriate risk levels and develop a case study of likely scenarios for recovery. 

The panels may utilize structured decision making to facilitate the development of these 

criteria. The Services anticipate that the consideration of VSP attributes and parameters 

will be an integral element in developing recovery criteria for the DPS. The goal will be 

to develop a complete set of objective and measurable criteria from which decisions 

relating to reclassification and delisting may be made. Such criteria must be based on the 

best available science that can be identified. The proposed final reclassification and 

delisting criteria will be reviewed by the scientific community and disseminated for 

formal public comment prior to final approval by the Services. As illustrated by the steps 

identified above, a collaborative process will be used to develop the final criteria that will 

be inclusive of knowledgeable experts and interested and potentially affected 

stakeholders. The Services are committed to the development of final reclassification 

and delisting criteria within three years of the finalization of this recovery plan, including 

technical, peer and formal public review of the criteria. 

Objective 1: Immediately halt the decline of the DPS and demonstrate a persistent 

increase in population abundance such that the overall probability of long-term survival is 

increased. 

As stated earlier, it is not practicable to establish a measurable criterion at this time with 

existing population assessment methodologies. In addition, the resources needed to 

develop long-term demographic criteria have thus far been directed toward identifying 

the measures needed to meet the more immediate aim of reversing population declines; 

upon approval of this plan, these resources will be redirected toward identifying the 

measures needed for full recovery. 

 structure and diversity. 
3-4

The initial focus of the recovery program will be on the 8 rivers within the DPS with 

extant populations at the time of the listing. To maintain a viable population for 

recovery, the first step is reversing these trends and conserving these extant populations. 

Without immediate action to conserve and protect these core populations and the remnant 

genetic variation they represent, long-term success and attainment of self-sustaining 

populations will be severely compromised. To achieve this first objective, the following 

criteria must be met: 

Criterion 1. Atlantic salmon are perpetuated in at least the eight rivers within the Gulf 

of Maine DPS that had extant populations at the time of listing; and 

Criterion 2. The replacement rate (5-year geometric mean) of adult salmon within DPS 

rivers is greater than 1.047. 

Criterion 1 recognizes that conserving the relatively broad geographic distribution in the 

extant populations is important for the reasons outlined in the Recovery Strategy. 

Achievement of this criterion may require stocking in rivers that are not stocked currently 

to enhance the demographic survival probabilities. Criterion 2 provides an objective 

measure of progress towards recovery, showing that the decline has been halted. The 

replacement rate describes the rate at which each subsequent generation, or cohort, 

replaces the previous one (NMFS 1995). The replacement rate will be calculated based 

on returning DPS adults. The 5-year time period represents the general time needed for 

an adult spawner’s offspring to complete its life cycle and return as an adult spawner. 

Progress towards achieving criterion 2 above will be annually assessed using available 

information on adult returns. 

Although the criteria are based on numbers and distribution of fish, they encompass 

evaluation of threat reduction. Success in increasing adult returns for the DPS to a level 

such that the five-year geometric mean is greater than 1.0 is dependent on, and reflective 

of, our ability to adequately address threats to the Gulf of Maine DPS, as described in the 

Threats Assessment (see pages 1-66 to1-68). 

The purpose of the recovery process under the ESA is to restore self-sustaining 

populations in the wild. Recovery of the Gulf of Maine DPS will require the recovery of 

secure wild-spawning Atlantic salmon populations that are able to live their entire lives 

and meet all of their requirements in the wild. The river-specific hatchery fish are 

included in the DPS and protected under the ESA, but only naturally-spawned adult 

spawners that have spent their life-cycle in the wild will be counted towards 

reclassification and delisting criteria (65 FR 69459). Once Objective 1 has been 

achieved, recovery actions necessary to achieve the second and third objectives of the 

recovery program will be concurrently implemented. 

 

47 As noted, Replacement rates of adult salmon in the Narraguagus River for the years 1996 to 2002 

all averaged less than 1.0, with the lowest value of 0.2 occurring in 2002. Population assessments 

on the DPS by USASAC show a current 5-year geometric mean replacement rate of 0.54 

(USASAC 2004, http://www.nefsc.noaa.gov/USASAC/).
3-5

Objective 2: Achieve the conditions necessary for the establishment of self-sustaining 

populations. 

Objective 3: Ensure that threats have been diminished such that the self-sustaining 

populations will remain viable over the long-term future. Objectives 2 and 3 relate to 

conditions necessary for reclassification and delisting discussed below. 

Preliminary Reclassification and Delisting Criteria 

In order to reclassify the Gulf of Maine DPS of Atlantic salmon from endangered to 

threatened, the Services must determine that the species’ abundance, survival, and 

distribution, taken together with the ESA listing factors, no longer render the species “in 

danger of extinction throughout all or a significant portion of its range.” Removal of 

ESA protection (i.e., delisting) requires demonstration that the threats that occurred at the 

time of listing have been removed or sufficiently reduced so the Gulf of Maine DPS of 

Atlantic salmon is no longer “likely to become an endangered species within the 

foreseeable future throughout all or a significant portion of its range.” Any new factors 

identified since listing must also be addressed in this analysis to ensure that the species 

no longer requires protection as a threatened or endangered species. 

The ESA requires that recovery plans, to the maximum extent practicable, incorporate 

objective, measurable criteria which, when met, would result in a determination in 

accordance with the provisions of the ESA that the species be removed from the Federal 

List of Endangered and Threatened Wildlife and Plants (50 CFR 17.11 and 17.12). The 

recovery criteria constitute the standards upon which the decision to reclassify or delist a 

species will be based. As discussed further below, final demographic (e.g., abundance 

and distribution) and threats-based recovery criteria are in the process of development. 

While this plan establishes some objective, measurable criteria specific to both 

population demographics and threat abatement, the Services have concluded that it is not 

practicable to provide measurable criteria for all demographic and threat based factors at 

this time. Therefore, qualitative delisting and reclassification criteria are provided as 

indicated in these instances. The reasons why it is not practicable to provide objective, 

measurable criteria for all delisting factors are discussed below. The actions necessary to 

be able to develop final criteria, within three years of this plan being finalized, are 

identified in this section. 

The delisting and reclassification criteria presented below include measurable and 

objective criteria. They include a component that measures population numbers and 

trends as well as components addressing threats to the species, including those identified 

under the five factor analysis conducted when the species was listed under the ESA. It is 

possible to determine if one has met these criteria or not by examining the population 

trends, the success of threat abatement and/or the extent of implementation of mitigation 

measures. 

When the final demographic recovery criteria (e.g. total population size, population 

structure and geographic distribution) are developed, those for delisting will differ from 
3-6

the criteria for reclassifying the DPS as threatened. This difference in demographic 

criteria will reflect the fact that a threatened population is still protected by the ESA, 

whereas a delisted population is not. A higher degree of confidence in the continued 

viability of the DPS is required, based on population demographics and the control of 

threats (as indicated below), before delisting it and completely removing the protections 

of the ESA. 

As noted, the Services deferred a decision whether the Gulf of Maine DPS range included 

the mainstem of the Penobscot River and its tributaries above the former site of the 

Bangor dam (65 FR 69459). Presently a status review is underway to determine the 

relationship of large river systems (e.g., Penobscot, Kennebec) to the DPS as currently 

delineated. This review will also determine the status of current salmon populations 

within these large river systems, as well as any other additional salmon populations 

present outside the geographic range of the DPS. Decisions regarding the relationship 

and status of these populations may have significant implications for the development of 

final recovery criteria. 

While the following criteria give a road map to the types of criteria that are necessary for 

recovery they do not, at this time, give the Services the ultimate targets for 

reclassification or delisting. Therefore, the Services do not believe that Atlantic salmon 

can be reconsidered for reclassification or delisting based on the available science until 

additional criteria are developed that address the threats and the population demographics 

in a more measurable way or there is a change in information that warrants 

reconsideration of the DPS. 

The integration of the VSP approach with PVA results will require scientists and 

managers to address complex population-level and habitat-related issues. It will also 

involve the use of expert panels to outline appropriate risk levels and develop alternative 

scenarios for recovery. The resultant criteria will be reviewed by the scientific 

community and disseminated for public comment prior to final approval by the Services. 

Development of measurable demographic criteria should be completed within three years 

of recovery plan approval. 

Preliminary Reclassification Criteria 

In order to consider reclassification, the first recovery objective (see above) will have 

been met, which is to immediately halt the decline of the DPS and demonstrate a 

persistent increase in population abundance such that the overall probability of long-term 

survival is increased. As described above, this recovery objective is meant to address the 

current situation of critically low numbers of adult Atlantic salmon returns. Once 

Objective 1 (including criterion 1 and 2) has been met, the following criteria would also 

need to be met for reclassification. 
3-7

A. Population Demographics 

In order to reclassify the Gulf of Maine DPS of Atlantic salmon from endangered to 

threatened, the DPS’ demographics must be consistent with a stable or increasing wild 

population not in danger of extinction. 

1. Population demographics, including but not limited to total population size, 

population structure and geographic distribution, as informed by modeling results, 

indicate that the DPS is not in danger of extinction throughout all or a significant 

portion of its range; and 

2. Atlantic salmon populations in the DPS are stable or increasing, as measured by 

the replacement rate (5-year geometric mean) of adult salmon within DPS rivers 

(see Recovery Objective section and footnote for more information on replacement 

rates). 

B. Control of Threats 

It is imperative that threats to the species be controlled prior to reclassification. This 

includes all threats identified at the time of listing, as well as any new factors identified 

since listing. Factors cited in the determination of endangered status for Atlantic salmon 

were disease; aquacultural practices; inadequate regulation of water withdrawals, disease, 

and aqauculture; and low marine survival (65 FR 69479, see page 1-20). Preliminary 

criteria have also been provided to address several other current or potential threats 

including acidification of freshwater habitats, depleted diadromous fish communities, 

direct and indirect marine harvest, incidental capture and poaching, competition with nonindigenous fish, hatchery supplementation, sedimentation, avian predation. 

In order to reclassify the Gulf of Maine DPS from endangered to threatened, the following 

threats-based criteria must be met through any regulatory or other means, including use of 

mechanisms available under the ESA. 

1. Acidification of freshwater habitats: Mechanisms are in place to ensure that pH is 

maintained at levels that provide suitable habitat quality and quantity for all life 

stages of Atlantic salmon within DPS rivers and tributaries. 

The Gulf of Maine DPS does not have chronically low pH levels, but does experience 

episodic events resulting in depressed pHs. Research is ongoing to understand the spatial 

and temporal extent of these events and their effect on the DPS. The Recovery Plan 

identifies the actions necessary to determine what levels of pH are suitable for the survival 

and conservation of the DPS. The Services will use the results of ongoing research to 

determine and establish suitable pH levels necessary for the survial and conservation of 

the DPS. The levels will serve as objective and measurable criteria. 

2. Aquaculture: 

a. There is no stocking of reproductively viable non-North American strains 

of Atlantic salmon in marine cages in Maine. 
3-8

b. Aquaculture facilities (freshwater and marine) have established a fully 

functional containment management systems (CMS) designed, 

constructed, and operated so as to prevent the accidental or consequential 

escape of fish to open water. 

c. All farmed raised fish in Maine are marked 

In November, 2003, NOAA Fisheries issued a Biological Opinion (BO) on the proposed 

modification of existing ACOE permits authorizing the installation and maintenance of 

aquaculture fish pens within the State of Maine. The BO establishes reasonable and 

prudent measures and associated terms and conditions specific to 2a) and 2b) above. 

These provide the objective and measurable standards by which the attainment of this 

criterion will be evaluated. 

3. Avian predation: Active management (e.g., non-lethal and lethal deterrence) 

results in a statistically significant reduction in predation by double-crested 

cormorants on migrating Atlantic salmon smolts . 

Predation would not be expected to threaten the continued existence of a healthy 

population. The threat of predation on endangered salmon is significant because of the 

very low numbers of adults returning to spawn and the increased population levels of 

some predators. The Services have concluded that double-crested cormorant predation 

has the potential to cause direct mortality to various life stages of Atlantic salmon, 

including returning adults. An adaptive management program is underway to determine 

if implementation of avian predator control will assist in the recovery and should be 

continued and expanded. Smolt outmigration occurs in a relatively narrow time window 

and along a narrow pathway exposing outmigrating smolts to predation by double-crested 

cormorants. 

4. Depleted diadromous fish communities: Diadromous fish species that co-evolved 

with salmon are restored to the watersheds in order to serve as predator buffers 

and contribute marine derived nutrients to the ecosystem. 

Other native diadromous fish populations have declined as dramatically as Atlantic 

salmon in recent years. The Services have concluded that the depletion of diadromous 

fish communities that have co-evolved with Atlantic salmon poses a threat to recovery 

efforts for Atlantic salmon (see page 1-91). However, the information is not currently 

available to identify which species, and at what levels, are essential to a fully functioning 

ecosystem and the recovery of the DPS. The Recovery Plan identifies actions necessary 

to define the role and function(s) that other diadromous fish species provide essential to 

the recovery of self-sustaining wild Atlantic salmon populations. These actions will 

provide the information necessary to establish objective and measurable delisting and 

reclassification criteria to determine the level of abatement of this threat. With this 

additional knowledge, the Services will be able to identify those species that are essential 

to the survival and recovery of the DPS. 
3-9

5. Direct and indirect marine harvest: Domestic and international regulatory 

mechanisms are in place that will prevent adverse effects to the long-term 

viability of the DPS from marine harvest. 

The International Council for the Exploration of the Sea (ICES) Advisory Committee on 

Fishery Management annually estimates the pre-fishery abundance (PFA) of nonmaturing 1SW salmon available for harvest, accounting for natural mortality. The 

required conservation escapement limits (CSE) for homewaters are subtracted from the 

PFA. If there is any surplus, 40% is allocated to West Greenland. This science-based 

allocation is fully protective of homewater stocks and its continuation is essential to the 

recovery of the species. The NASCO uses the ICES advice on catch and management 

options48 for Atlantic salmon fisheries to make science-based management decisions for 

this fishery. The ICES advice to NASCO for 2005, as it has been in recent years, was that 

catch should approach or reach zero. 

6. Disease: Disease detection and response plans for existing and newly discovered 

fish diseases are in place and fully implemented at all federal, state and private 

aquaculture facilities (freshwater and marine). 

Rapid detection and response to known and emerging diseases will minimize the risk of 

exposure and transmission to wild salmon stocks. Disinfection Protocol and/or 

Biosecurity plans for all field equipment and sampling gear should be established by all 

agencies (including IF&W and DMR) with personnel working in DPS waters to minimize 

the inadvertent spread of fish pathogens and other aquatic invasive species. 

7. Incidental capture and poaching: Regulatory mechanisms are in place and 

enforced to assure that angling for other species and poaching of salmon will not 

adversely affect the long-term viability of the DPS. 

For reclassification purposes, the level of mortality Atlantic salmon caused by incidental 

capture or poaching, in combination with other sources of mortality, must be sufficiently 

low such that the population is stable or increasing as measured by the replacement rate. 

It is not currently practicable to determine what level of mortality is sufficiently 

protective of the DPS. The analysis of this risk is dependent on the availability of final 

demographic criteria. 

In the meantime, the effect of incidental take will be analyzed through section 7 and/or 

section 10 processes. Any take authorized through these processes will not jeopardize the 

species (in full consideration of all other take occurring). 

8. Introduced fish species including non-indigenous species: 

 

48 Catch options are calculated using probability of attaining spawning escapement targets of 

between 25% and 50%. In 2002, the available catch surplus at the risk neutral (50% probability) 

was approximately 50,600 fish (ICES 2002). Below the risk averse probability value of 30%, 

there were no salmon surplus to conservation escapement limits (ICES 2002).
3-10

a. Stocking of non-indigenous fish species is prohibited within the DPS 

range. 

Exemptions to this prohibition could be authorized if a risk analysis demonstrated that the 

proposed stocking was not likely to adversely affect the long-term viability of the DPS. 

b. All stocking authorized under 6.a) above is accompanied by an ongoing 

monitoring program to detect and assess any adverse impacts to the DPS. 

9. Recovery hatchery program: A broodstock and conservation hatchery plan is in 

place and being implemented for the conservation hatchery program component 

of the recovery effort. Evaluation of the role and effectiveness of the 

conservation hatchery program demonstrates its ability to contribute to the 

recovery of the DPS. 

Hatcheries have been used in Maine to attempt to increase the populations of salmon 

since the 1870s. The NRC recommended that current hatchery practices should be 

evaluated in an adaptive management context to minimize potential genetic and 

ecological effects and to modify the program as appropriate (NRC 2004). To minimize 

the potential genetic and ecological threat posed by the hatchery program, the FWS, in 

cooperation with other federal and state agencies, is currently working to develop 

broodstock management plans for the FWS Maine Hatchery Complex Program. While 

many of the elements of an effective broodstock plan are operational, they are not well 

documented and the broodstock management plan will update and consolidate all the 

elements into one document. 

An effective broodstock plan must comprehensively cover seven elements: 1) collection 

of broodstock, 2) broodstock screening (e.g. culling and selection), 3) broodstock 

composition (e.g., captive, wild collections, backup sources), 4) mating strategies, 5) 

hatchery logistics (e.g., capacity, physical limitations), 6) production schedules, 7) 

demographic expectations/projections. An important component of this plan is a Genetic 

Management Plan (GMP) that is needed to reduce several risks associated with captive 

breeding programs (e.g., genetic drift; selection; domestication; inbreeding). 

10. Sedimentation: Long-term mechanisms (e.g., regulatory and non-regulatory) are 

in place to ensure Atlantic salmon habitat is not adversely affected by 

sedimentation. 

Preliminary evidence suggests that substrate embeddedness of between 45-50% results in 

reductions of production rates for juvenile Atlantic salmon. For activities within Gulf of 

Maine DPS watersheds, BMPs must be utilized to ensure that sedimentation does not 

result in embeddedness equal to or greater than 45% in spawning and rearing habitat. 

This number will be refined and modified as additional information becomes available. 
3-11

11. Water withdrawals: Long-term mechanisms are in place to effectively manage 

existing and new water withdrawals, to prevent water withdrawals from adversely 

affecting the long-term viability of the DPS. 

The flow requirements of juvenile Atlantic salmon have been assessed in only some of 

the rivers within the DPS. The Recovery Plan identifies the actions necessary to 

determine what water and flow levels are necessary to maintain suitable habitat quality 

and quantity for all life stages of Atlantic salmon throughout the DPS. The levels will 

serve as objective and measurable criteria. 

Preliminary Delisting Criteria 

A. Population Demographics 

1. Population demographics, including but not limited to total population size, 

population structure and geographic distribution, as informed by modeling results, 

indicate that the DPS is not likely to become an endangered species in the foreseeable 

future throughout all or a significant portion of its range; and 

2. Atlantic salmon populations in the DPS are stable or increasing, as measured by 

the replacement rate (5-year geometric mean) of adult salmon within DPS rivers (see 

Recovery Objective section and footnote for more information on replacement rates). 

3. Atlantic salmon populations in the DPS are not dependent on hatchery stocking. 

In order to delist the Gulf of Maine DPS of Atlantic salmon the Services must determine 

that self-sustaining wild Atlantic salmon populations are capable of completing their 

lifecycle in the absence of hatchery supplementation. The Services may conclude after 

delisting that hatchery supplementation for other purposes (e.g., recreational fishery) is 

warranted. However, the contribution of returning wild adult Atlantic salmon spawning 

in the wild must be sufficient to support a self-sustaining DPS without hatchery 

supplementation. The contribution of wild salmon versus hatchery reared salmon will be 

measured and monitored by currently available methods (e.g., genetics, tagging). 

B. Control of Threats 

To delist the Gulf of Maine DPS of Atlantic salmon, the same threats as those described 

under “Preliminary Downlisting Criteria” will have to be controlled. Because a delisted 

population would no longer receive protection under the ESA, it is imperative that threats 

to the continued viability of the DPS be controlled by means other than mechanisms 

available under the ESA (e.g., federal, state or local management mechanisms, treaties) 

before delisting could occur. It is also important to note that population augmentation 

through the hatchery program may increase a species’ population numbers while a threat 

continues. That is why for delisting purposes, the criteria include a requirement that the 

species not be dependent on hatchery stocking. 
3-12

1. Acidification of freshwater habitats: Mechanisms are in place to ensure that pH is 

maintained at levels that provide suitable habitat quality and quantity for all life 

stages of Atlantic salmon within DPS rivers and tributaries. 

The Gulf of Maine DPS does not have chronically low pH levels, but does experience 

episodic events resulting in depressed pHs. Research is ongoing to understand the spatial 

and temporal extent of these events and their effect on the DPS. The Recovery Plan 

identifies the actions necessary to determine what levels of pH are suitable for the 

survival and conservation of the DPS. The Services will use the results of ongoing 

research to determine and establish suitable pH levels necessary for the survival and 

conservation of the DPS. The levels will serve as objective and measurable criteria. 

2. Aquaculture: 

a. There is no stocking of reproductively viable non-North American strains 

of Atlantic salmon. 

b. Aquaculture facilities (freshwater and marine) have established a fully 

functional containment management systems (CMS) designed, 

constructed, and operated so as to prevent the accidental or consequential 

escape of fish to open water. 

c. All farmed raised fish in Maine are marked 

In November 2003, NOAA Fisheries issued a Biological Opinion (BO) on the proposed 

modification of existing ACOE permits authorizing the installation and maintenance of 

aquaculture fish pens within the State of Maine. The BO establishes reasonable and 

prudent measures and associated terms and conditions specific to 2a) and 2b) above. 

These provide the objective and measurable standards by which the attainment of this 

criterion will be evaluated. 

3. Avian predation: Active management (e.g., non-lethal and lethal deterrence) 

results in a statistically significant reduction in predation by double-crested 

cormorants on migrating Atlantic salmon smolts that will assist in recovery. 

Predation would not be expected to threaten the continued existence of a healthy 

population. The threat of predation on endangered salmon is significant because of the 

very low numbers of adults returning to spawn and the increased population levels of 

some predators. The Services have concluded that double-crested cormorant predation 

has the potential to cause direct mortality to various life stages of Atlantic salmon, 

including returning adults. An adaptive management program is underway to determine 

if implementation of avian predator control will assist in the recovery and should be 

continued and expanded. Smolt outmigration occurs in a relatively narrow time window 

and along a narrow pathway exposing outmigrating smolts to predation by double-crested 

cormorants. 

4. Depleted diadromous fish communities: Diadromous fish species that co-evolved 

with salmon are restored to the watersheds in order to serve as predator buffers 

and contribute marine derived nutrients to the ecosystem. 
3-13

Other native diadromous fish populations have declined as dramatically as Atlantic 

salmon in recent years. The Services have concluded that the depletion of diadromous 

fish communities that have co-evolved with Atlantic salmon poses a threat to recovery 

efforts for Atlantic salmon (see page 1-91). However, the information is not currently 

available to identify which species, and at what levels, are essential to a fully functioning 

ecosystem and the recovery of the DPS. The Recovery Plan identifies actions necessary 

to define the role and function(s) that other diadromous fish species provide essential to 

the recovery of self-sustaining wild Atlantic salmon populations. These actions will 

provide the information necessary to establish objective and measurable delisting and 

reclassification criteria to determine the level of abatement of this threat. With this 

additional knowledge, the Services will be able to identify those species that are essential 

to the survival and recovery of the DPS. 

5. Direct and indirect marine harvest: Domestic and international regulatory 

mechanisms are in place that will prevent adverse effects to the long-term 

viability of the DPS from marine harvest. 

The International Council for the Exploration of the Sea (ICES) Advisory Committee on 

Fishery Management, annually estimates the pre-fishery abundance (PFA) of nonmaturing 1SW salmon available for harvest, accounting for natural mortality. The 

required conservation escapement limits (CSE) for homewaters are subtracted from the 

PFA. If there is any surplus, 40% is allocated to West Greenland. This science-based 

allocation is fully protective of homewater stocks and its continuation is essential to the 

recovery of the species. The NASCO uses the ICES advice on catch and management 

options49 for Atlantic salmon fisheries to make science-based management decisions for 

this fishery. The ICES advice to NASCO for 2005, as it has been in recent years, was 

that catch should approach or reach zero. 

6. Disease: Disease detection and response plans for existing and newly discovered 

fish diseases are in place and fully implemented at all federal, state and private 

aquaculture facilities (freshwater and marine). 

Rapid detection and response to known and emerging diseases will minimize the risk of 

exposure and transmission to wild salmon stocks. Disinfection Protocol and/or 

Biosecurity plans for all field equipment and sampling gear should be established by all 

agencies (including IF&W and DMR) with personnel working in DPS waters to minimize 

the inadvertent spread of fish pathogens and other aquatic invasive species. 

7. Incidental capture and poaching: Regulatory mechanisms are in place and 

enforced to assure that angling for other species and poaching of salmon will not 

adversely affect the long-term viability of the DPS. 

 

49 Catch options are calculated using probability of attaining spawning escapement targets of 

between 25% and 50%. In 2002, the available catch surplus at the risk neutral (50% probability) 

was approximately 50,600 fish (ICES 2002). Below the risk averse probability value of 30%, 

there were no salmon surplus to conservation escapement limits (ICES 2002).
3-14

For delisting to occur, exisitng state regulation and enforcement without the additional 

protection of the ESA must be determined to be sufficient to allow recovery to continue. 

It is not currently practicable to determine what level of mortality due to incidental 

capture and poaching that can be sustained by a recovered DPS. The analysis of this risk 

is dependent on the availability of final demographic criteria. 

8. Introduced fish species including non-indigenous species: 

a. Stocking of non-indigenous fish species is prohibited. 

Exemptions to this prohibition could be authorized if a risk analysis demonstrated that the 

proposed stocking was not likely to adversely affect the long-term viability of the DPS. 

b. All stocking authorized under 6.a) above is accompanied by an ongoing 

monitoring program to detect and assess any adverse impacts to the DPS. 

9. Sedimentation: Long-term mechanisms (e.g., regulatory and non-regulatory) are 

in place to ensure Atlantic salmon habitat is not adversely affected by 

sedimentation. 

Preliminary evidence suggests that substrate embeddedness of between 45-50% results in 

reductions of production rates for juvenile Atlantic salmon. For activities within Gulf of 

Maine DPS watersheds, BMPs must be utilized to ensure that sedimentation does not 

result in embeddedness equal to or greater than 45% in spawning and rearing habitat. 

This number will be refined and modified as additional information becomes available. 

10. Water withdrawals: Long-term mechanisms are in place to effectively manage 

existing and new water withdrawals, to prevent water withdrawals from adversely 

affecting the long-term viability of the DPS. 

The flow requirements of juvenile Atlantic salmon have been assessed in only some of 

the rivers within the DPS. The Recovery Plan identifies the actions necessary to 

determine what water and flow levels are necessary to maintain suitable habitat quality 

and quantity for all life stages of Atlantic salmon throughout the DPS. The levels will 

serve as objective and measurable criteria. 
4-1

PART FOUR: RECOVERY PROGRAM 

A. RECOVERY ACTION OUTLINE 

1. Protect and restore freshwater and estuarine habitats 

1.1 Protect hydrologic conditions to ensure instream flows (volume, velocity, depth, 

temperature) adequate for Atlantic salmon 

1.1.1 Determine instream flow requirements for Atlantic salmon in additional 

DPS rivers 

1.1.1A Conduct IFIM studies on additional DPS rivers to determine flow 

requirements of juveniles 

1.1.1B Determine flow requirements of adult Atlantic salmon in DPS 

rivers 

1.1.2 Monitor surface and groundwater hydrology for DPS rivers 

1.1.2A Continue analyses of historical flow data for salmon rivers within 

the DPS to assess changes over time or hydrologic differences 

between the rivers that may affect salmon recovery efforts. 

1.1.2B Maintain existing USGS stream gauges on DPS rivers 

1.1.2C Develop and implement an effective flow monitoring program in 

addition to gauge-sites to monitor stream flow and discharge data 

at points along rivers 

1.1.2D Monitor and assess the potential for groundwater withdrawals to 

impact stream flow and cold water discharges 

1.1.3 Assess the impact of current water withdrawals on instream flows and 

Atlantic salmon and monitor future water use and demand 

1.1.3A Implement the Downeast Salmon Rivers Water Use Management 

Plan (WUMP) for the Pleasant and Narraguagus rivers and 

Mopang Stream 

1.1.3B Determine the effects of current irrigation withdrawals by all 

growers in the watersheds on flow and Atlantic salmon 

1.1.3C Assess and monitor other agricultural water use needs and 

demands within DPS river watersheds 

1.1.3D Develop water use management plans for other DPS rivers 

1.1.3E Continue periodic assessments of irrigation methods and water 

demands and their potential effects on hydrology and Atlantic 

salmon habitat 

1.1.4 Ensure that water withdrawals do not adversely affect Atlantic salmon 

1.1.4A Ensure that water withdrawal permit requirements protect stream 

flows required for the recovery and conservation of Atlantic 

salmon 

1.1.4B Issue and enforce all appropriate permits for water withdrawals 

1.1.5 Evaluate the effect instream water management may have on the 

hydrologic conditions of individual watersheds and Atlantic salmon 

habitat 
4-2

1.1.5A Conduct an inventory and assessment of the ability of dams in DPS 

watersheds to regulate flow 

1.1.5B Review current water management for the dams and develop an 

assessment of the effect of regulation on a watershed’s hydrology 

and thus Atlantic salmon habitat 

1.2 Ensure water quality to support healthy and productive salmon populations 

1.2.1 Review existing water quality standards for each river within the range of 

the DPS to determine adequacy to meet needs of Atlantic salmon 

1.2.2 Identify and mitigate water quality threats to Atlantic salmon within the 

DPS 

1.2.2A Evaluate the impacts of acid rain on juvenile Atlantic salmon 

survival in DPS rivers 

1.2.2B Identify available management measures and techniques to 

mitigate the potential impacts of acid rain on the DPS. 

Experimentally evaluate stream acidification mitigation techniques 

in a natural river system within the DPS 

1.2.2C Identify point sources of airborne pollutants contributing to acid 

precipitation that may be adversely affecting the DPS and reduce 

to levels that will not adversely affect or jeopardize the recovery of 

the DPS 

1.2.2D Model the impact of air and water quality issues, especially acid 

precipitation, on productivity of salmon in DPS rivers 

1.2.2E Evaluate current agricultural practices such as soil acidity 

management practices to determine whether they may affect pH 

levels in DPS rivers 

1.2.2F Evaluate the biological effects of low pH and aluminum and its 

toxicity on Atlantic salmon 

1.2.2G Sample resident fish from all DPS rivers and analyze them for 

tissue residues and bio-chemical factors indicative of exposure to 

endocrine disrupting chemicals. 

1.2.2H Evaluate the chronic and acute effects of agricultural chemicals on 

Atlantic salmon and how they may impact salmon recovery efforts 

1.2.2I Identify and consider appropriate management measures and 

techniques to mitigate the potential impacts of agricultural 

chemicals and other contaminants on the DPS 

1.2.2J Evaluate the link between pesticides and endocrine disruption 

1.2.2K Conduct research on the mechanisms of non-pesticide 

organochlorines exposure, uptake and effect in rivers where these 

contaminants are known to occur including, the Dennys below the 

Superfund site 

1.2.2L Continue State program to replace overboard discharges (OBDs) 

1.2.3 Develop and implement a water quality monitoring program for DPS 

rivers 
4-3

1.2.3A Implement a comprehensive and integrated long-term water 

chemistry monitoring program on all DPS rivers 

1.2.3B Implement a comprehensive and integrated long-term water quality 

monitoring program on all DPS rivers 

1.2.3C Monitor water temperatures in the vicinity of blueberry process 

water discharge sites on the Machias and Narraguagus rivers to 

assess the potential impact on Atlantic salmon 

1.2.4 Prepare and implement plans to reduce pollution 

1.2.4A Prepare and implement NPS pollution reduction plans for DPS 

rivers 

1.2.4B Evaluate the impacts of sedimentation on habitat quantity and 

quality including relationship between substrate embeddedness and 

habitat productivity in DPS rivers. 

1.2.4C Prepare and implement point source (PS) pollution reduction plans 

for DPS rivers 

1.2.4D Fully implement EPA aquaculture wastewater and effluent 

discharge regulations 

1.2.4E Continue monitoring of the remediation efforts at the Eastern 

Surplus Superfund site in Meddybemps 

1.2.4F Address any ground water problems at the Smith junkyard on the 

Dennys River and restore the site 

1.3 Ensure timely passage for each life-stage, including connectivity of spawning and 

nursery habitats, downstream passage for smolts and upstream passage for 

returning spawners 

1.3.1 Assess fish passage at dams, fishways and weirs currently in place and 

repair or improve as needed 

1.3.1A Repair or remove the Coopers Mill Dam to improve fish passage 

around the dam 

1.3.1B Evaluate the need to repair the existing fishway at Saco Falls 

1.3.2 Identify and improve culverts or other road crossings that impede salmon 

passage 

1.3.3 Identify and manage natural debris jams (including beaver dams) that 

impede salmon passage 

1.3.4 Condition permits for activities within the estuaries of DPS rivers so as to 

minimize potential effects on migration of juveniles and adults 

1.4 Secure long term protections for freshwater and estuarine habitats 

1.4.1 Ensure long-term protection of riparian habitat 

1.4.1A Provide long-term protection for riparian buffers through fee 

acquisition, conservation easements, conservation and 

management agreements, and other appropriate tools 

1.4.1B Promote the adoption and use of BMPs by landowners and 

compliance with these voluntary standards 

1.4.1C Identify riparian zone activities (e.g., harvest practices, ATVs, 

development etc.) and evaluate impacts on Atlantic salmon 
4-4

1.4.1D Evaluate current state and local land use regulations to determine 

adequacy of existing measures protecting riparian habitat and 

instream improve if appropriate 

1.4.1E Enhance protection of riparian areas where necessary through 

expanded enforcement and modifications to the Natural Resource 

Protection Act, Forest Practices Act, LURC Zoning standards, 

and/or Municipal Shoreland Zoning 

1.4.2 Protect estuarine habitat used by Atlantic salmon 

1.4.2A Evaluate the potential for activities in estuaries to adversely affect 

Atlantic salmon 

1.4.2B Condition permits for activities within the estuaries of DPS rivers 

so as to minimize potential effects on Atlantic salmon 

1.5 Restore degraded stream and estuarine salmon habitat 

1.5.1 Create regional hydraulic geometry curves and a reference reach database 

1.5.2 Identify, catalogue and prioritize habitat restoration needs 

1.5.2A Identify, catalogue and prioritize habitat restoration needs in DPS 

rivers 

1.5.2B Identify, catalogue and prioritize habitat restoration needs in 

estuarine habitat of DPS rivers 

1.5.3 Conduct high priority restoration projects 

1.5.4 Evaluate the potential of stream flow augmentation as a recovery tool to 

help meet Atlantic salmon flow needs and increase juvenile production 

and survival 

1.5.5 Evaluate the ecological role and importance of restoring other diadromous 

fish populations 

2. Minimize potential for take in freshwater, estuarine, and marine fisheries 

2.1 Prevent Directed Take of Atlantic salmon 

2.1.1 Maintain and enforce the closure of the directed sport fishery for Atlantic 

salmon 

2.1.2 Maintain current FMP that restricts directed harvest of Atlantic salmon in 

U.S. estuarine and marine waters 

2.1.3 Continue international efforts to reduce threats from commercial fisheries 

outside of U.S. jurisdiction 

2.1.3A Participate in international salmon management with the goal of 

ensuring any quotas set are based on the best available scientific 

data and provide adequate protection of U.S. stocks 

2.1.3B Continue U.S. participation in the international sampling program 

at West Greenland 

2.1.3C Continue efforts to implement a biological sampling program at St. 

Pierre et Miquelon to determine the origin of Atlantic salmon 

captured in this fishery 

2.2 Avoid bycatch of Atlantic salmon 

2.2.1 Monitor, assess and develop methods to avoid bycatch in recreational and 

commercial freshwater fisheries 
4-5

2.2.1A Assess the level of incidental take of Atlantic salmon by 

recreational anglers. 

2.2.1B Prohibit all recreational fishing in select areas utilized by Atlantic 

salmon as holding areas where salmon may be taken as bycatch or 

poached 

2.2.1C Develop a Section 10(a)(1)(B) habitat conservation plan for 

recreational fishing permitted by the State that may incidentally 

take Atlantic salmon 

2.2.1D Continue to monitor commercial freshwater fisheries where the 

potential for incidental take of Atlantic salmon exists 

2.2.2 Monitor, assess and develop methods to avoid bycatch in other estuarine 

or marine fisheries under U.S. jurisdiction 

2.2.2A Assess the potential risk for incidental take of Atlantic salmon in 

marine and estuarine fisheries 

2.2.2B Develop appropriate management strategies and regulatory 

measures to avoid bycatch of Atlantic salmon in estuarine and 

marine fisheries where significant potential for bycatch has been 

identified 

2.2.2C Increase observer coverage in the midwater trawl herring fishery to 

improve the ability to assess the potential for Atlantic salmon 

bycatch in the herring fishery. 

3. Reduce predation and competition on all life-stages of Atlantic salmon 

3.1 Assess impacts of predation on wild and hatchery-reared river-specific salmon 

populations and develop methods for reducing adverse affects from predation 

3.1.1 Evaluate salmon population management practices, habitat features and 

water management practices that may exacerbate predation rates 

3.1.1A Identify and catalogue locations that restrict passage and/or 

concentrate salmon and thereby increase the vulnerability of 

salmon to predation 

3.1.1B Review existing salmon population management practices to 

determine if they increase the vulnerability of juvenile salmon to 

cormorant predation 

3.1.1C Document and monitor the presence and abundance of potential 

salmon predators at natural and man-made concentration sites 

3.1.1D Assess the potential of land and water use practices to exacerbate 

predation rates 

3.1.2 Implement integrated management of cormorants to reduce predation on 

Atlantic salmon 

3.1.2A Evaluate the potential of cormorant predation to adversely affect 

the recovery of the DPS. 

3.1.2B Identify specific cormorant colonies within the DPS that may 

inflict significant levels of depredation on DPS salmon populations 

and implement appropriate experimental management measures 
4-6

3.1.2C Evaluate the potential of conserving and restoring runs of 

anadromous forage species to provide a buffer against predation on 

salmon 

3.1.3 Evaluate the need for integrated management of seals to reduce predation 

on Atlantic salmon 

3.1.3A Evaluate the effect of seal predation on the recovery of the DPS 

3.1.3B Document and monitor the presence and abundance of seals at 

natural and man-made concentration sites 

3.1.3C Conduct research to determine the role of net pen sites in seal 

aggregation and salmon predation 

3.1.3D Evaluate the potential of alternative research techniques and food 

habit sampling methodologies to help assess seal predation on 

Atlantic salmon 

3.1.3E Develop and implement appropriate management measures to 

mitigate the impact of documented seal predation on wild salmon 

populations 

3.1.4 Assess potential effects of other predators 

3.2 Reduce predation and competition between Atlantic salmon and other freshwater 

fish species 

3.2.1 Review and monitor potential impacts of existing stocking programs for 

other fish 

3.2.1A Review existing stocking programs and assess the potential 

impacts of these introductions on Atlantic salmon populations and 

ways to minimize potential adverse affects 

3.2.1B Monitor potential adverse interactions of existing stocking 

programs for freshwater salmonids in Atlantic salmon river 

drainages and fully assess the potential impacts of these programs 

on the DPS 

3.2.1C Suspend stocking of brown trout immediately in all DPS rivers 

until the potential impacts of these introductions can be fully 

assessed 

3.2.1D Monitor potential adverse interactions of existing stocking 

programs for freshwater salmonids (i.e., splake, landlocked 

salmon, brook trout) in headwater lakes of DPS rivers to determine 

the potential impacts of these programs on the DPS 

3.2.1E Develop a Section 10(a)(1)(B) habitat conservation plan for 

existing stocking programs if warranted 

3.2.2 Monitor populations of introduced non-salmonid species and implement 

management controls when appropriate and feasible 

4. Reduce risks from commercial aquaculture operations 

4.1 Improve containment at existing and future marine sites 

4.1A Evaluate new aquaculture lease and permit applications to ensure that net 

pens and equipment are adequate for site location and potential storm 

impact 
4-7

4.1B Develop fully functional containment management systems for the 

containment of farmed salmon at marine sites. 

4.1C Develop and implement integrated loss control plans for all salmon 

aquaculture facilities 

4.1D Develop and maintain an inventory tracking system for all marine 

aquaculture facilities 

4.1E Assess, document and monitor damage caused by seal predation that may 

lead to the escapement of farmed salmon into the environment 

4.2 Minimize the effects of escaped farmed salmon 

4.2.1 Develop and implement contingency measures in case of accidental 

release of farmed fish 

4.2.2 Maintain existing weirs on DPS rivers and establish additional sites as 

needed 

4.2.2A Maintain existing weirs on DPS rivers to minimize aquaculture 

escapees spawning, enable data collection and collect broodstock 

4.2.2B Construct weirs on DPS rivers, including the East Machias and 

Machias rivers, where necessary to exclude aquaculture escapees, 

enable data collection and collect broodstock 

4.2.3 Mark all farmed salmon prior to placement into marine net-pens 

4.2.4 Discontinue the culture of non-North American salmon 

4.2.5 Prohibit the placement into marine net-pens of reproductively viable 

transgenic salmon 

4.2.6 Continue research into developing strains of aquaculture fish that cannot 

interbreed with wild fish 

4.3 Minimize risks of disease and parasite transmission from farmed fish in marine 

pens to wild fish 

4.3.1 Minimize risk of disease transmission 

4.3.1A Develop and implement a comprehensive disease management 

plan that includes siting and standard operational procedures to 

minimize outbreaks of ISA. 

4.3.1B Develop and implement comprehensive integrated bay 

management plans that include coordination of stocking densities, 

harvesting and fallowing and disease treatment and management 

4.3.1C Revise federal import regulations (Title 50) to include the ISA 

virus 

4.3.1D Maintain and update existing fish health guidelines and protocols 

as necessary, to control the introduction of new pathogens and 

continue to provide protection from disease 

4.3.1E Expand the FWS Wild Fish Health Survey to include all DPS 

rivers 

4.3.1F Implement biosecurity and disinfection protocol for all research 

and assessment activities being conducted in rivers within the DPS 

4.3.2 Conduct research on endemic and exotic salmonid pathogens to reduce the 

potential of disease transfer from farmed fish to wild Atlantic salmon 
4-8

4.3.2A Determine the modes of transmission of the ISA virus 

4.3.2B Continue to investigate the role of wild fish species as potential 

reservoirs and vectors of ISA 

4.3.2C Initiate screening and long-term monitoring of resident and 

migratory fish in aquaculture production bays for endemic and 

exotic salmonid pathogens. 

4.3.2D Continue active research programs on immunization of farmed fish 

4.3.2E Develop an effective diagnostic technique for the SSS virus and 

determine the distribution of SSS virus within the geographic 

range of the DPS 

4.3.3 Reduce the potential for sea lice outbreaks in farmed and wild salmon 

populations 

4.3.3A Investigate the potential of sea lice to adversely affect the DPS and 

the role of salmon aquaculture sites as a reservoir for this parasite 

4.3.3B Regularly test and report sea lice burdens at individual net-pen 

facilities. 

4.3.3C Continue treatment for sea lice at aquaculture facilities 

4.4 Reduce risk of juvenile escapement from freshwater aquaculture facilities into 

DPS rivers 

4.4.1 Ensure containment at existing and future freshwater aquaculture facilities 

accessible to DPS rivers 

4.4.1A Develop and operate fully functional containment management 

systems for the containment of farmed salmon at freshwater 

hatchery sites. 

4.4.1B Develop integrated loss control plans for all salmon aquaculture 

hatchery facilities and conduct independent audits of freshwater 

hatcheries once loss control plans are in place 

4.4.1C Develop and maintain an inventory tracking system that facilitates 

the accurate tracking of total numbers of salmon smolts being 

produced by the hatchery 

4.4.2 Develop contingency plans to reduce adverse impacts if containment 

measures fail 

5. Supplement wild populations with hatchery-reared DPS salmon 

5.1 Stock cultured fish in natal rivers to supplement contributions of wild-spawned 

fish 

5.1.1 Maintain river-specific hatchery broodstock and continue to stock cultured 

fish in natal rivers 

5.1.1A Continue operation of federal fish rearing facilities needed for 

recovery of the DPS, including maintenance of river-specific 

broodstock 

5.1.1B Continue stocking cultured fish to supplement wild salmon 

populations 

5.1.2 Monitor and evaluate the current stocking program 

5.1.3 Evaluate and implement, as appropriate, new stocking strategies 
4-9

5.1.3A Evaluate the role of alternate stocking strategies to supplement 

wild salmon populations 

5.1.3B Continue to assess and evaluate the results of the adult stocking 

program 

5.1.3C Evaluate the role of streamside incubation facilities to supplement 

wild salmon populations 

5.1.4 Evaluate the potential role of reintroduction in the recovery of the DPS 

5.1.4A Evaluate the need to re-establish populations of Atlantic salmon in 

rivers within the DPS’s historic range from which river 

populations have been extirpated 

5.1.4B Evaluate whether the use of experimental populations will 

facilitate the recovery of the GOM DPS of Atlantic salmon 

5.2 Maintain fish health practices to minimize potential introduction of disease to 

hatchery stocks and transmission to wild populations 

5.2.1 Continue fish culture management practices at federal hatcheries to 

minimize the potential for disease 

5.2.2 Continue fish health surveillance efforts and implementation of fish health 

practices at federal hatcheries 

5.2.3 Continue research on fish health issues, detection and prevention 

5.2.3A Conduct research on ISA and SSS detection and prevention 

5.2.3B Conduct research on other pathogens to identify potential threats to 

the DPS 

5.2.3C Initiate screening and long-term monitoring of resident fish species 

in DPS rivers for endemic and exotic salmonid pathogens 

5.3 Maintain practices to prevent escapement from federal hatcheries 

5.3A Develop and implement procedures at federal hatcheries to identify 

potential escape sources and implement the appropriate modifications 

5.3B Implement discharge and effluent management protocols for all hatcheries 

with the goal of controlling and minimizing release of juveniles 

6. Conserve the genetic integrity of the DPS 

6.1 Ensure that culture and stocking programs conserve the genetic integrity of the 

DPS 

6.1.1 Develop broodstock management plans, including brood fish collection, 

genetic management and program evaluation protocols 

6.1.2 Continue to genetically characterize and screen all brood fish and to track 

parentage of all fish produced 

6.2 Ensure that management plans consider and avoid negative genetic effects of 

management actions 

6.3 Explore methods for long-term preservation of gametes and genes for future use 

6.4 Monitor genetic diversity, including parentage of smolts and returning adults 

7. Assess stock status of key life stages 

7.1 Assess abundance and survival of Atlantic salmon at key freshwater and marine 

life-stages 

7.1.1 Monitor adult returns and spawning escapement 
4-10

7.1.1A Monitor adult returns at existing fishways and weirs 

7.1.1B Construct weirs on the East Machias and Machias rivers to monitor 

adult returns 

7.1.1C Conduct intensive redd counts on all DPS rivers to index spawning 

escapement 

7.1.1D Continue development of DPS-level estimates of spawning 

escapement 

7.1.1E Develop accurate extrapolation methods to estimate abundance in 

areas where traditional redd counts are not feasible or practical 

7.1.2 Conduct basinwide assessment of large parr abundance and biological 

characteristics 

7.1.2A Continue basinwide assessment of large parr abundance and 

measurement of biological characteristics in the Narraguagus and 

Dennys river systems 

7.1.2B Expand assessments of large parr abundance to a third DPS river 

7.1.2C Establish 6-10 index sites to assess large parr abundance and 

biological characteristics in the remaining DPS rivers 

7.1.3 Conduct quantitative assessments of Atlantic salmon smolt production 

7.1.4 Monitor estuarine and coastal survival, ecology, and distribution of smolts 

using telemetry and surface trawling 

7.1.4A Continue telemetry studies of smolt migration from the Dennys 

and Narraguagus rivers 

7.1.4B Expand spatial coverage of detection arrays to better assess 

movements of post-smolts in the Gulf of Maine and the Bay of 

Fundy 

7.1.4C Continue post-smolt surface trawling assessment programs and 

expand the temporal and spatial extent of coverage 

7.1.5 Continue to participate and contribute to international cooperative research 

and assessment efforts to improve our understanding of salmon at sea 

7.1.6 Continue to develop and apply population viability analysis model 

8. Promote salmon recovery through increased public and government awareness 

8.1 Develop a comprehensive Education and Outreach Program for the Gulf of Maine 

DPS of Atlantic salmon 

8.1A Develop a comprehensive Education and Outreach Plan for the Gulf of 

Maine DPS of Atlantic salmon 

8.1B Continue efforts to educate anglers on the difference between trout and 

juvenile salmon 

8.1C Develop updated educational programs for schools 

8.1D Evaluate use of public display of salmon as outreach tool 

8.2 Maintain, and if necessary increase, coordination/communications between 

government and local agencies on issues pertaining to Atlantic salmon recovery 

9. Assess effectiveness of recovery actions and revise as appropriate 

9.1 Appoint a Recovery Team to coordinate implementation of recovery plan 

objectives 
4-11

9.2 Review implementation of Recovery Plan tasks annually and assess need for 

revisions, including changes in priorities 

9.2A Conduct an annual review of the implementation schedule 

9.2B Complete an annual progress report on completion of recovery actions 

9.3 Complete necessary addenda, updates and revisions to the Recovery Plan 
4-12

B. RECOVERY ACTION NARRATIVE 

The recovery actions outlined below reflect the best scientific and commercial information 

currently available. Following the narrative description of each recovery action and sub-action is 

a list of recovery actions items needed for salmon recovery. A thorough discussion of each 

proposed action can be found within the text of the appropriate recovery action or sub-action. 

The action items are intended to make proposed actions more readily identifiable to readers of 

this recovery plan. Estimated time and cost required, task priority and those responsible for 

carrying out each recovery action are identified in the Implementation Schedule (see pages 5-1 to 

5-11). A comprehensive list of all threats and the corresponding recovery actions follows at the 

end of the recovery plan in Appendix 1. 

Following recovery plan approval and subsequent implementation, the Services and the State of 

Maine will monitor recovery action implementation. The effectiveness of various recovery 

measures will be assessed and appropriate modifications implemented to accelerate progress 

towards the recovery goal. While many factors can confound efforts to evaluate the effects of 

discrete actions on wild populations, carefully designed monitoring is key to assessing and 

improving the effectiveness of recovery actions. Habitat improvement, predator management, 

stocking of hatchery-raised fish and efforts to reduce threats from commercial aquaculture are all 

appropriate subjects for monitoring and evaluation. Results of this type of monitoring will be 

considered during annual reviews of recovery plan implementation (under task 9) to assure 

timely adjustment of ongoing efforts and priorities. All recommended recovery actions should 

incorporate monitoring and evaluation to assess their effectiveness in furthering the recovery of 

the DPS. The results of research tasks described below will be used to evaluate and refine other 

recovery actions. The response of populations to recovery measures will be used to revise 

research priorities. 

The Services intend to maintain and expand ongoing collaborative conservation efforts 

conducted under the auspices of the Maine Atlantic Salmon Conservation Plan. 

1. Protect and restore freshwater and estuarine habitats 

Atlantic salmon habitat is comprised of several interrelated features. They include stream 

structure, substrate material, water flow, riparian cover and water chemistry. The following 

recovery actions are necessary to restore or protect one or more critical features of Atlantic 

salmon habitat. 

1.1 Protect hydrologic conditions to ensure instream flows (volume, velocity, 

depth, temperature) adequate for Atlantic salmon 

The rivers within the range of the DPS have inherent hydrologic differences. For example, there 

are significant groundwater sources within the Narraguagus River watershed but not in the 

Machias, East Machias and Dennys watersheds (MSPO 2001). In addition, each of the DPS 

river watersheds has different land usage patterns. The five DPS river watersheds in eastern 
4-13

Maine are dominated by forestry and agriculture, including blueberry production. The Ducktrap 

and Sheepscot river watersheds have a greater proportion of agricultural land, including 

numerous dairy farms. Dams are found on some of the DPS rivers, particularly near the 

headwaters. For example, the flow of the Dennys River has historically been managed to 

enhance salmon habitat using releases from a headwater dam located at the outlet of 

Meddybemps Lake. The annual flow cycle for DPS rivers includes the following general 

seasonal trends: 

• peak flows in April in response to snow-melt and spring runoff 

• decreasing flows from the spring runoff through late August 

• lowest flows from late July to mid September 

• increasing flows in response to typical fall rains (October-December) 

• decreased runoff in January and February, when most precipitation remains on the 

ground as snow 

Figure 11 illustrates annual flow patterns in four of the DPS rivers as relative flow (mean 

monthly flow expressed as a proportion of the mean annual flow). Peak runoff occurs in April in 

all four rivers with a mean April discharge that is nearly 2.5 times the annual mean except in the 

Sheepscot River, where relative flows are somewhat higher. Summer flows in all of these rivers 

fall to well under half the mean annual flow, with August and September flows in the Sheepscot 

River at about twenty percent of the mean annual flow. The Dennys River has the highest 

summer flow in relation to the annual mean. Relative flows increase through the fall and peak at 

1.3 times the mean in December, except for the Dennys River that has a somewhat lower relative 

flow. January and February flows in all four rivers are, on average, very close to the mean 

annual flow. 

The potential impacts of hydrologic manipulation for irrigation was identified as a primary threat 

to the DPS in the final listing determination (see page 1-20; 65 FR 69459; NMFS and FWS 

1999; MASCP 1997). The potential for water withdrawal to adversely affect the adequacy of 

instream flows for Atlantic salmon (volume, velocity, depth and temperature) should be assessed 

and continuously monitored. 

Currently available techniques to assess and monitor the impacts of water withdrawals on 

Atlantic salmon include: standard setting method (FWS instream flow policy-aquatic based 

flow), incremental flow instream studies (IFIM), Habitat Suitability Index (HSI) models, stream 

gage data, low flow studies, stream flow analysis conducted as part of Maine’s water use 

management planning (WUMP) initiative and precipitation and rainfall data. 

Standard setting techniques, including FWS’ New England Flow Policy, use historical flow 

records to establish protective flows. The FWS uses the median August flow (often estimated to 

be 0.5 cfs/sq.mi. of drainage area in the absence of actual long-term gaging records - USFWS 

New England aquatic base flow study 1981). This is commonly referred to as the Aquatic Base 

Flow (ABF). Similarly, FWS uses a standard fall/winter flow to protect spawning adults and 

overwintering eggs and larvae. 
4-14

Instream flow incremental methodology (IFIM) studies utilize morphological characteristics of 

the stream channel in representative river reaches to predict the availability of habitat at various 

water levels. IFIM studies have been conducted for Mopang Stream (a major tributary of the 

Machias River), Narraguagus, Pleasant and Dennys rivers (see page 1-26). Within an IFIM 

study, only variables related to the channel morphology and discharge (depth, velocity, cover, 

substrate embeddedness) are used. ABF or other standard setting techniques can be pro-rated 

based on drainage area, and applied over a wider geographic area than IFIM. 

Habitat Suitability Index (HSI)50 models are used within the IFIM study to evaluate salmon 

habitat at the reaches where hydraulic modeling was done for various flow regimes (e.g., low, 

medium, high). HSI models were developed as part of the FWS’ Habitat Evaluation Procedures 

(HEP). HSI models cannot be used independently, they require data from the stream reaches 

being evaluated. HSI models include habitat quality assessments for water quality variables 

(temp, pH, turbidity) that are not used in classic IFIM studies. HEP evaluations are typically 

conducted for habitats other than rivers and streams (e.g., wetlands). IFIM techniques are the 

 

50 HSI models are developed based on a number of relevant factors including water quality and observed 

densities of juveniles. Habitat is ranked on a 0 (unsuitable) to 1(optimally suitable) scale. HSI models can 

be used as a hypothesis of species-habitat interactions and are based on the assumption that high quality 

habitat is correlated with a high carrying capacity.

0.0

0.5

1.0

1.5

2.0

2.5

3.0

May June July Aug Sep Oct Nov Dec Jan Feb Mar Apr

Relative Flow

Narraguagus

Machias

Dennys

Sheepscot

Figure 11: Mean monthly flows for the Narraguagus, Machias, Dennys and Sheepscot rivers, normalized as 

relative flow. Relative flow is the mean monthly flow expressed as a proportion of the mean annual flow for 

each river (QM/QA). Mean monthly flow data are USGS flow statistics from 1949-2000 (Narraguagus), 1949-

1977 (Machias), 1955-1998 (Dennys) and 1939-2000 (Sheepscot).
4-15

more commonly used approach for evaluating the relationship between habitat and changing 

flows. The results of IFIM and HSI studies help establish the relationship between stream flow 

and habitat availability. 

Stream gages provide real time stream flow data. Stream gages can be used to determine when 

stream flow is nearing levels inadequate for Atlantic salmon if the gages are located in stream 

reaches where IFIM studies have been conducted. Stream flow conditions can only be assessed 

directly for habitat near stream gages. If stream gages are used to evaluate the effect of 

irrigation, the distance between the withdrawal reach/point and the stream gage must be known. 

The USGS, in cooperation with ASC, the Maine Geological Survey (MGS; a bureau within the 

Maine Department of Conservation) and the Aroostook County Water and Soil Management 

Board, has recently completed two multi-year studies of low-flow characteristics of streams in 

eastern and northern Maine (Lombard et al. 2003). The purpose of the study was to develop 

regression equations that can be used to estimate low-flow statistics at any ungaged location. 

The regional low-flow criteria for aquatic habitat currently in use may not be applicable to 

streams in specific areas of Maine. The low-flow data collection by USGS/MGS helps build the 

database on historic flows from which long-term averages can be obtained and applied. 

Management and effective utilization of water resources could be improved if more accurate, 

locally-based, low-flow estimation techniques were available (USGS 2002). 

As part of the State of Maine’s WUMP initiative, Horsley and Witten (H & W), a private 

consulting firm, was retained by the ACOE to model the likely impacts of water withdrawals on 

Atlantic salmon habitat. The H&W model provides estimates for baseflow and total flow in the 

watershed basins covered by the WUMP. The results of the H&W model were used by the 

WUMP advisory group to help develop the hierarchical water use strategy for water withdrawal 

recommended by the WUMP (see below). 

An evaluation of currently available hydrologic data should be conducted to ensure the data 

currently being collected is adequate to assess and monitor the potential impacts of water 

withdrawals on the DPS. This analysis should include consideration of what additional data are 

needed to ensure effective monitoring and management of water withdrawal impacts on Atlantic 

salmon. 

1.1.1 Determine instream flow requirements for Atlantic salmon in additional DPS 

rivers 

The flow requirements of Atlantic salmon need to be determined for all DPS rivers. Instream 

flow requirements for juvenile Atlantic salmon have been determined for rivers where IFIM 

studies were undertaken. The State of Maine, through the WUMP initiative, conducted IFIM 

studies to evaluate the effects of low, medium and high flow discharge periods on availability of 

juvenile habitat. Using IFIM, the flow requirements of juvenile Atlantic salmon have been 

assessed in the Narraguagus and Pleasant rivers and Mopang Stream as part of the WUMP 

(MSPO 2001). In addition, ASC completed an IFIM study for the Dennys River in 2002. The 
4-16

report will be used to help manage river flows to protect salmon habitat. IFIM studies may need 

to be conducted on additional rivers within the DPS. Conducting IFIM studies in additional DPS 

rivers will allow researchers to determine flow requirements for juvenile Atlantic salmon in these 

rivers. Conducting additional IFIM studies will help establish flows protective of Atlantic 

salmon needs, particularly if done in connection with proposed permits (i.e., site-specific). 

The information collected through these studies will assist in determining both Atlantic salmon 

flow requirements and natural hydrographic conditions for DPS rivers. Knowing Atlantic 

salmon flow requirements will enable managers to set water withdrawal permit requirements that 

are protective of Atlantic salmon (see below). This information is also an integral component of 

determining the effect of water withdrawal on flows in DPS rivers. 

The effect of alternative flow regimes on adult habitat currently cannot be assessed through IFIM 

studies. The available data are for juvenile rearing habitat. There are no HSI models for adults 

to be used in an IFIM study. There are general ways to model the effect of discharge on adult 

passage and holding zones. The need to conduct studies to determine flow requirements of adult 

Atlantic salmon in DPS rivers should be evaluated. 

Recovery Actions: 

1.1.1A Conduct IFIM studies on additional DPS rivers to determine flow 

requirements of juvenile Atlantic salmon 

1.1.1B Determine flow requirements of adult Atlantic salmon in DPS rivers 

1.1.2 Monitor surface and groundwater hydrology for DPS rivers 

Surface and groundwater hydrology should be analyzed and monitored for all DPS river 

watersheds with the DPS. The collection of hydrological and habitat/flow data is needed to 

assist in recovery and conservation efforts. The USGS has collected flow data at locations on 

many of the DPS rivers for different periods of record. The most extensive and up-to-date data 

are for sites on the Narraguagus, Machias, Dennys and Sheepscot rivers. Some data are also 

available for the East Machias and Pleasant rivers. Analyses of these flow data are ongoing and 

should be continued to assess and enable detection of changes over time or hydrologic 

differences between the rivers that may affect salmon recovery efforts. Several analyses have 

been completed (see Nielsen 1999; Dudley and Nielsen 2000; Lombard et al. 2003; Dudley 

2004). For example, analyses of these data by the USGS document an earlier spring runoff in 

recent years (Dudley and Hodgkins 2002). 

The USGS maintains stream gages on several of the DPS rivers. Stream gages provide important 

data about hydrological conditions. The USGS stream gages on the Narraguagus, Pleasant, 

Machias, Sheepscot, Dennys and Ducktrap rivers should continue to be maintained. These gages 

are needed to determine whether minimum flow requirements are being met. Monitoring data 

should be compiled in a single database. These data should be compiled in a timely manner to 
4-17

facilitate assessment of stream flow conditions. The need for a stream gage on the East Machias 

River should be evaluated. 

An effective flow monitoring strategy should be developed and implemented. This flowmonitoring program should include river specific monitoring plans to assess stream discharge 

data at points along the rivers in addition to gage-sites. A quality control plan should be 

developed and implemented to assure standard methods for data collection and reporting at all 

monitoring sites. In addition to providing hydrological information, gage data can help 

managers monitoring water withdrawal permits to determine if conditions are being met. 

Groundwater monitoring programs should be developed and implemented for all DPS river 

watersheds. As irrigation shifts to groundwater sources and ponds that are hydrologically distant 

from riverine surface waters the effects are more subtle and may be spatially and temporally 

distant from the withdrawal. While there are data on stream discharge, well levels, irrigation 

withdrawals and rainfall at a variety of locations throughout the DPS river basins Downeast, 

there are no analyses that link these monitoring points together to help determine if and how 

stream discharge may be affected by irrigation. Without that analysis the effect on habitat cannot 

be evaluated. Groundwater monitoring data should be archived in a central database accessible 

to state and federal managers. 

Currently, LURC requires permits for groundwater withdrawals. Permits should require impact 

assessments (well tests) and monitoring to avoid adverse effects on nearby surface waters. 

Groundwater monitoring programs should focus on aquifer connectivity. Shifts in irrigation 

techniques by wild blueberry growers from direct withdrawals from rivers to wells makes 

groundwater withdrawal an important consideration when collecting hydrological information in 

the DPS. The potential for groundwater withdrawals to impact stream flow and cold water 

discharges should be evaluated and monitored. 

Recovery Actions: 

1.1.2A Continue analyses of historical flow data for DPS rivers to assess changes 

over time or hydrologic differences between the rivers that may affect 

salmon recovery efforts 

1.1.2B Maintain existing USGS stream gages on DPS rivers 

1.1.2C Develop and implement an effective flow monitoring program in addition 

to gage-sites to monitor stream flow and discharge data at points along 

rivers 

1.1.2D Monitor and assess the potential for groundwater withdrawals to impact 

stream flow and cold water discharges 
4-18

1.1.3 Assess the impact of current water withdrawals on instream flows and on 

Atlantic salmon and monitor future water use and demand 

The threat of insufficient water in DPS rivers is significant and may be exacerbated by water 

withdrawals in summer months when natural flow conditions are already low. Irrigation is the 

most common use of water withdrawn from DPS river watersheds. Excessive withdrawal of 

water directly from rivers or from groundwater connected to rivers has the potential to adversely 

affect Atlantic salmon. The effect of water withdrawals on Atlantic salmon should be 

continually assessed and monitored. Water use and demand should also be monitored. 

The State of Maine has developed a water use management plan (WUMP)51 for the Narraguagus 

and Pleasant rivers and for Mopang Stream (MSPO 2001)(see page 1-26). Current demand for 

irrigation water by large wild blueberry growers is estimated in the WUMP for the three river 

basins covered by the plan. While there are too many factors involved to project future water 

demand with any confidence, it is likely that irrigation in the Pleasant, Narraguagus and Mopang 

river basins will increase. The WUMP should be fully implemented. The effectiveness of the 

WUMP in ensuring that water withdrawals are adequately managed and protective of Atlantic 

salmon should be continually monitored and evaluated. 

As noted, the WUMP provides estimated water demand for large wild blueberry growers within 

the river basins covered by the plan. Limited data are available on the current irrigation water 

demand of small and medium sized wild blueberry growers. In order to effectively manage and 

minimize adverse affects on Atlantic salmon and their habitat, total water demand should be 

assessed for all users. The State of Maine should prepare an annual report on current and 

projected water withdrawals each year as part of efforts to monitor and assess all water 

withdrawals within the three river basins addressed by the WUMP. 

While there is currently little or no water withdrawn from rivers outside the three covered by the 

WUMP (with the possible exception of the Sheepscot) this could change over time. Water 

management plans for other watersheds should be developed. These plans should be a means to 

assess current water use and demand and estimate effects on salmon and salmon habitat. 

Consideration should be given to balance the needs of water users with natural resources, 

including salmon. Water management plans should include information on natural hydrological 

conditions and trends in those conditions, current water demand projected growth and proposed 

means to manage for sustainable water withdrawals. As noted, population growth and 

development in Maine has accelerated in recent years, especially in the mid-coast region. This 

trend will undoubtedly result in changes in land use patterns and resource demands, including 

water use that will need to be managed in order to protect salmon and their habitat. 

 

51 As noted (page 20) the WUMP identifies a hierarchy of water supply alternatives and ranks these 

alternatives based on an assessment of potential threats each poses to Atlantic salmon habitat. Based on 

this assessment, the WUMP recommends utilizing groundwater sources first, followed by water storage 

options. Under the WUMP, surface water withdrawal is the least preferable alternative. The WUMP relies 

primarily on non-regulatory voluntary actions of water users in carrying out irrigation strategies intended to 

minimize potential impacts on instream flows. 
4-19

The State of Maine has recently enacted legislation (LD 1488) that requires the Maine DEP to 

work with state, regional and local agencies to develop water use policies that protect the 

environment from excessive drawdown of water sources during low flow periods. This bill 

requires annual water use reporting beginning in December 2003. The bill also directs the Maine 

Board of Environmental Protection to establish water use standards protective of instream flows 

needed by aquatic life by January 2005. This bill should be fully implemented. 

Recovery Actions: 

1.1.3A Implement the Downeast Salmon Rivers Water Use Management Plan 

(WUMP) for the Pleasant and Narraguagus rivers and Mopang Stream 

1.1.3B Determine the effects of current irrigation withdrawals by all growers on 

flow and Atlantic salmon 

1.1.3C Assess and monitor other agricultural water use needs and demands within 

DPS river watersheds 

1.1.3D Develop water use management plans for other DPS rivers 

1.1.3E Continue periodic assessments of irrigation methods and water demands 

and their potential effects on hydrology and Atlantic salmon habitat 

1.1.4 Ensure that water withdrawals do not adversely affect Atlantic salmon 

Water withdrawal permits should be conditioned so that they are protective of Atlantic salmon 

habitat52. Permitees should not be authorized to withdraw water to a level where flow is below 

what is needed by Atlantic salmon. In rivers where IFIM studies have been completed, the 

information to set protective permit requirements is available. Some blueberry producers have 

voluntarily agreed to cease withdrawals when flows drop below a critical level identified by 

IFIM studies. The results of IFIM studies should be incorporated in state/federal permits and 

monitored for compliance. 

Water withdrawal permits are issued by LURC in unorganized territories. In organized 

townships, Maine DEP has the authority to issue water withdrawal permits but does not currently 

do so. This results in unregulated water withdrawals in areas under DEP’s jurisdiction. Maine 

DEP should issue water withdrawal permits with requirements protective of Atlantic salmon. 

Water withdrawal permits issued by LURC require that water withdrawal reports be submitted 

weekly. LURC should review these reports as they are submitted in order to detect any 

violations. All water withdrawal permits should require a monitoring/reporting component. 

 

52 Existing water withdrawal permits issued by LURC and the ACOE for wild blueberry growers use the 

FWS ABF flows.
4-20

Recovery Actions: 

1.1.4A Ensure that water withdrawal permit requirements protect stream flows 

required for the recovery and conservation of Atlantic salmon 

1.1.4B Issue and enforce all appropriate permits for water withdrawals 

1.1.5 Evaluate the effect instream water management may have on the hydrologic 

conditions of individual watersheds and Atlantic salmon habitat 

As discussed (see page 1-27), impoundments used to regulate instream flow affect the hydrologic 

conditions of DPS rivers. Several DPS rivers have small dams on lakes and ponds within the 

drainage used to manipulate river flows. The effect that these impoundments have on the 

hydrologic conditions of individual watersheds and Atlantic salmon habitat should be evaluated 

Recovery Actions: 

1.1.5A Conduct an inventory and assessment of the ability of dams in DPS 

watersheds to regulate flow 

1.1.5B Review current water management for the dams and develop an 

assessment of the effect of regulation on a watershed’s hydrology and thus 

Atlantic salmon habitat. 

1.2 Ensure water quality to support healthy and productive salmon populations 

The ranges of water quality parameters that impact Atlantic salmon mortality and behavior are 

generally known (see Part One). 

1.2.1 Review existing water quality standards for each river within the range of 

the DPS to determine adequacy to meet needs of Atlantic salmon 

Existing water quality standards should be reviewed for each river within the range of the DPS to 

determine their adequacy to meet the needs of Atlantic salmon. The Maine DEP currently 

classifies all streams (third order and higher) according to coliform bacterial levels, aquatic life 

criteria and dissolved oxygen levels required to support biological functions (e.g., fish 

spawning). Aquatic life criteria are numeric measures of the diversity and abundance of benthic 

macroinvertebrate communities. In addition to numeric criteria there are provisions that apply to 

existing and designated uses and prohibitions against “anti-degradation”. Existing Maine water 

quality regulations also specify criteria for discharges that alter pH, temperature and nutrient 

levels. All DPS salmon rivers maintain AA ratings, the State’s highest water quality 

classification. The Sheepscot River meets the AA rating but did not attain satisfactory standards 

for bacteria and dissolved oxygen levels due to non-point source pollution. 
4-21

The State of Maine does not have regulatory water quality standards specific to Atlantic salmon, 

with the exception of the provisions pertaining to designated uses and anti-degradation. The 

adequacy of current water quality standards as they relate to Atlantic salmon needs should be 

assessed. The need to develop standards (e.g., temperature, dissolved oxygen, turbidity, pH, 

alkalinity, nutrients and other important parameters) specific to Atlantic salmon requirements 

should be evaluated. 

1.2.2 Identify and mitigate water quality threats to Atlantic salmon within the DPS 

Research is needed on water quality threats such as the threat posed by non-pesticide 

organochlorines, other chlorine compounds, the link between pesticides and endocrine disruption 

and the link between acid deposition and toxic levels of aluminum. Acidification and endocrine 

disruption are two of the most significant water quality threats to Atlantic salmon in Maine 

(Maine TAC 2002). Research should include the following water quality issues: 

• acid rain’s effect on juvenile Atlantic salmon 

• toxicity of low pH and aluminum 

• agricultural practices and pH 

• pesticides and endocrine disruption links 

• chronic and acute effect of agrochemical 

Stream acidification due to acid rain has a high likelihood of adversely affecting the recovery of 

Atlantic salmon in at least some Maine rivers (Maine TAC 2002). Acidification potentially 

affects the DPS through effects on parr/smolt transformation and smolt adaptation to seawater 

(see page 1-28). The impacts of acid rain on juvenile Atlantic salmon survival in DPS rivers 

should be evaluated. The best available data indicates that a risk to Atlantic salmon recovery is 

present (Maine TAC 2002). The Narraguagus, Pleasant, Machias, East Machias and Dennys 

rivers are the most vulnerable to acidification (Maine TAC 2002). Acidification of Maine 

Atlantic salmon rivers has been periodically investigated since the 1980s. Current data 

collection efforts are inadequate to fully characterize the risks. The TAC water quality 

committee recommended an intensive long-term water chemistry monitoring program on 

representative rivers. The measurement of water chemistry parameters is necessary to interpret 

the implications of changes in acidity on Atlantic salmon (Maine TAC 2002). 

Potential opportunities to mitigate the effects of stream acidification should be identified. 

Various methods have been successful in the U.S., Canada and Norway. Available methods to 

mitigate acid rain require adding carbonate materials to the river or watershed. These mitigation 

techniques have been used in Canada to restore Atlantic salmon rivers. Lacroix (1996) applied 

crushed limestone to a small acidified brook in eastern Canada to assess the efficacy of this 

technique to mitigate the impacts acid rain on Atlantic salmon populations. Lacroix reported a 

lasting small increase in pH in the limed section of the brook and downstream over eight years 

(Lacroix 1996). Lacroix (1996) found that Atlantic salmon consistently dug more redds in the 

limed section of the brook. He found that age-0 salmon and brook trout densities were always 

greater in the limed sections of the stream versus the unlimed portion. Lacroix suggested that, 
4-22

alternatively, this preference might be due to the physical enhancement of spawning habitat 

rather than decreased acidity. 

Most acid mitigation methods are expensive (such as the addition of lime to the entire watershed 

to increase the buffering capacity of the soils) or require that structures be built in streams 

(limestone infiltration beds). There are some low cost and low-tech approaches, such as the use 

of shells (such as mussel or clam shells from local seafood industries) in headwater streams. The 

shells decompose by physical and biological processes and increase pH buffering capacity and 

ambient calcium concentrations. The use of these techniques should be evaluated in Maine. The 

Services should work with ASC to identify a potential site to evaluate the mitigation of acid rain 

on Atlantic salmon populations. These mitigation techniques are short term solutions; the 

addition of carbonate to headwaters or to watershed soils only treats the symptoms of acid rain. 

Control of air pollution is necessary to reduce the impacts of acid rain on the DPS. Available air 

and water quality data should be reviewed and sources of airborne pollutants, such as sulfur and 

nitrogen dioxides, identified. The impact of acid precipitation on the productivity of salmon in 

DPS rivers should be modeled. The Services should consult with the EPA to ensure all measures 

necessary to reduce sources of acid rain to levels that do not adversely affect the DPS are 

initiated. 

In addition to acid precipitation, other human activities have the potential to alter the pH of DPS 

rivers and their tributaries. For example, the Maine Cooperative Extension recommends to wild 

blueberry growers the addition of sulfur to reduce soil pH if it is not within desired range of pH 

4.3-4.8 (see page 1-30). Conversely, if the soil is too acidic growers are advised to use lime. 

Either of these practices can affect surface water pH. The available data suggests that soil 

acidity might also have a role in governing pH in streams (Mark Whiting, Maine DEP, personal 

communication). The potential effect of soil pH adjustments on stream water pH should be 

evaluated. The extent of the use of these practices by wild blueberry growers should be assessed. 

The ASC and FWS should work with the Maine Cooperative Extension Service to ascertain the 

extent to which this practice is employed by local landowners and monitor its potential to affect 

pH in adjacent salmon streams the DPS. Prior to modifications of soil acidity within DPS river 

watersheds, blueberry growers should notify appropriate state and federal agencies to enable 

appropriate monitoring of the potential impacts on the pH of adjacent streams. 

Laboratory and field studies have demonstrated that low pH leaches aluminum and increases its 

toxicity to fish (see page 1-31). More study is needed on the biological effects of low pH and 

aluminum, particularly how it affects critical life stages such as smolts. Research is also needed 

on the synergistic effects of water chemistry parameters (pH, dissolved organic carbon, river 

discharge, water temperature, alkalinity), particularly the seasonal variation and influence of 

precipitation. This research will help in understanding the dynamics of pH/aluminum toxicity. 

The effects of chemical contaminants on the DPS need further study. Based on the results of this 

research, strategies should be developed to mitigate and minimize any harmful effects from these 
4-23

contaminants. Some of these chemicals (e.g., propiconozol, hexazinone and methoxychlor) are 

known to be estrogen mimics that may disrupt the normal physiology of Atlantic salmon. 

Endocrine disruption is a new field of study and many pesticides have not been studied. In 

addition, research has often focused on the active ingredient in the pesticide formulation. Some 

of the inert ingredients, including spreaders and emulsifiers (e.g., nonylphenols and phthalates) 

used in chemical formulations as carriers are now known to have endocrine effects. Because 

they are generally water soluble, these chemicals may get into the DPS rivers more readily than 

the active ingredient (Mark Whiting, Maine DEP, personal communication). More testing is 

needed of the effects of whole formula applications on fish. In addition, more sampling is 

needed to assess the occurrence of additional carrier compounds in DPS rivers. 

Endocrine disrupting chemicals have been detected in DPS rivers. Given the occurrence of 

known endocrine disrupting chemicals in Maine Atlantic salmon rivers, these chemicals have a 

high probability of adversely affecting Atlantic salmon recovery (Maine TAC 2002). While 

there are not sufficient water quality data to ascertain the extent of exposure of Atlantic salmon 

in Maine rivers and the potential affects these chemicals may have on the recovery of the DPS, 

the available evidence suggests that this issue may be important in recovery efforts (Maine TAC 

2002). Increased joint monitoring by Maine DEP, Maine BPC and other agencies is needed to 

accurately detect levels of pesticides in DPS river watersheds and to determine transport 

mechanisms, fate and toxicity. 

Research is also needed to understand the chronic and acute effects of pesticides on Atlantic 

salmon. Water quality monitoring has documented that hexazinone persists in the Narraguagus 

River at all times of the year and may come from contaminated groundwater. The other 

Downeast DPS rivers may have similar chronic hexazinone contamination. Resident fish from 

all DPS rivers should be sampled and analyzed for tissue residues and bio-chemical factors 

indicative of exposure to endocrine disrupting chemicals. Based on these results, additional 

investigations should be conducted. 

Other agricultural chemicals may be present at low levels following typical application periods 

or after stormwater runoff events. The Board of Pesticides Control (BPC) and DEP are 

collaborating to assess the importance of pesticide drift in transporting trace amounts of 

pesticides into the DPS rivers. Initial results from 2001 suggest that pesticides are quickly 

diluted and transported away by stream currents (Mark Whiting, Maine DEP, personal 

communication). These results need to be confirmed by more quantitative and longterm 

monitoring. Water quality monitoring should document temporal and spatial patterns of 

agricultural chemical contamination in the DPS rivers (see below). Additional research is 

needed to identify which chemicals have physiological effects and how these effects may impact 

salmon recovery efforts, including the link between pesticides and endocrine disruption. 

The Maine Cooperative Extension Service is developing Best Management Practices to help 

reduce spray drift from blueberry fields. The establishment of vegetated buffers could greatly 

reduce pesticide drift and bank erosion. This is recommended by draft BMP’s for spray 
4-24

applications, but there are currently no regulatory requirements or BMP standards for such 

buffers. The DEP should monitor and assess the efficacy of existing BMPs. DEP staff should 

work with blueberry growers and spray applicators prior to spraying to help ensure BMPs are 

employed to reduce spray drift. Cherryfield Foods, Inc., the largest of the wild blueberry 

growers in Downeast Maine, is planting evergreen buffers between blueberry fields and adjacent 

areas. The State should consider providing more assistance to blueberry growers to help them 

with environmental compliance issues. 

Maine Department of Transportation (MDOT) does not use herbicides for the control of roadside 

brush in the Downeast DPS rivers. This policy should be implemented in the other salmon river 

watersheds as well. 

Non-pesticide organochlorines have been identified as a potential threat to Atlantic salmon 

(Maine TAC 2002). These compounds include furans, dioxins and planar polychlorinated 

biphenyls (PCBs). In the DPS, non-pesticide organochlorines are known to be present in the 

Dennys Rivers below the Dennys River Eastern Surplus Superfund (DRESS) site (see page 4-

28). Further research on the mechanisms of exposure, uptake and effect of non-pesticide 

organochlorines on Atlantic salmon should be undertaken (Maine TAC 2002)(see page 1-38). 

Moore and Waring (1996, 2001) documented the effect of several pesticides on Atlantic salmon 

olfactory capabilities. The effects of chlorine compounds on salmon olfactory senses and 

homing behavior is currently unknown and should be studied (Maine TAC 2002). While the 

potential effects of chlorine compounds on Atlantic salmon are unknown, the density of 

overboard discharges (OBD)53 in Cherryfield on the Narraguagus River, is a matter of concern to 

salmon recovery efforts in this watershed (Maine TAC 2002). OBDs use chlorine tablets 

(calcium hypochlorite) in the chlorinator unit. There are thirty-seven OBD units in Cherryfield. 

OBDs in rivers other than the Narraguagus should also be assessed to determine the extent and 

level of threat to the DPS. 

Since 1987, the construction of new OBDs has been prohibited in Maine. In 1990, the Maine 

OBD program was initiated by the State legislature (38 MRSA Section 411-A) to help fund 

replacement systems that would eliminate OBDs in certain areas. Currently, the focus of the 

replacement program is in shellfish areas that would be open to shellfishing if the OBDs were 

removed. Maine DEP is responsible for annually inspecting all OBD systems and generating a 

priority list for replacement. In addition to DEP, the Farmers Home Administration and the 

Maine State Housing Authority can provide grants or low interest loans to towns or community 

groups for replacement of OBDs. This program to replace OBDs with less environmentally 

harmful wastewater treatment systems should be continued. 

 

53 An overboard discharge (OBD) is an alternative wastewater treatment system for sites where municipal 

sewer connection is not possible and where a traditional septic system is not feasible. The simplest kind of 

overboard discharge (OBD) is a holding tank with a chlorinator for the overflow pipe (Maine TAC 2002).
4-25

Recovery Actions: 

1.2.2A Evaluate the impacts of acid rain on juvenile Atlantic salmon survival in 

DPS rivers 

1.2.2B Identify available management measures and techniques to mitigate the 

potential impacts of acid rain on the DPS. Experimentally evaluate stream 

acidification mitigation techniques in a natural river system within the 

range of the DPS 

1.2.2C Identify point sources of airborne pollutants contributing to acid 

precipitation that may be adversely affecting the DPS and reduce to levels 

that will not adversely affect or jeopardize the recovery of the DPS 

1.2.2D Model the impact of air and water quality issues, especially acid 

precipitation, on productivity of salmon in DPS rivers 

1.2.2E Evaluate current agricultural practices such as soil acidity management 

practices to determine whether they may affect pH levels in DPS rivers 

1.2.2F Evaluate the biological effects of low pH and aluminum and its toxicity on 

Atlantic salmon 

1.2.2G Sample resident fish from all DPS rivers and analyze them for tissue 

residues and bio-chemical factors indicative of exposure to endocrine 

disrupting chemicals 

1.2.2H Evaluate the chronic and acute effects of agricultural chemicals on 

Atlantic salmon and how they may impact salmon recovery efforts 

1.2.2I Identify and consider appropriate management measures and techniques to 

mitigate the potential impacts of agricultural chemicals and other 

contaminants on the DPS 

1.2.2J Evaluate the link between pesticides and endocrine disruption 

1.2.2K Conduct research on the mechanisms of non-pesticide organochlorines 

exposure, uptake and effect in rivers where these contaminants are known 

to occur including, the Dennys below the Superfund site 

1.2.2L Continue State program to replace OBDs 
4-26

1.2.3 Develop and implement a water quality monitoring program for DPS rivers 

A comprehensive and integrated long-term water chemistry monitoring program on all DPS 

rivers should be initiated. The water quality of the main stems of the DPS rivers is well 

characterized. Historically, water quality data have been collected by several state and federal 

agencies throughout the range of the DPS. Water temperature measurements have been the most 

common type of data collected. Extensive pH and alkalinity data have also been collected in 

some of the DPS river watersheds as part of various research and monitoring programs. These 

data have been collected using different methodologies and dissimilar quality control and quality 

assurance procedures. Historical water quality data lack adequate temporal and spatial coverage 

to document significant trends in water chemistry or biological activity. The Maine DEP has 

compiled the available historic water quality data for the DPS rivers and is managing the 

information. These data should be reviewed for consistency and quality, assembled into a 

comprehensive computer-searchable database and made available to resource managers and 

researchers. 

Since 1999, the DEP has coordinated a water quality monitoring program for each of the eight 

salmon rivers (MASC 2000). The current program monitors temperature, dissolved oxygen, 

turbidity, pH, alkalinity, macroinvertebrates, nutrients and a suite of agricultural chemicals. 

These data provide an important baseline for understanding long-term water quality trends. 

Recent water quality sampling efforts have focused on monitoring stormwater runoff. Efforts 

have also focused on measuring water quality of tributaries and headwaters. These data are 

stored in a central database maintained by the DEP. 

The current water monitoring program should be reviewed to ensure that data collection is 

adequate to document and monitor regional patterns among the DPS river watersheds, intra-basin 

patterns (e.g., headwater to mouth), tributary-specific water quality (e.g., tributaries with poor or 

exceptional water quality), long-term trends and episodic events such as spring runoff and 

storms. DEP sampling locations should be geo-referenced using the interagency “River 

Kilometer” system. Periodic sampling of a limited set of parameters may be adequate for some 

water quality monitoring while comprehensive data collection at long-term index sites is required 

for other water quality monitoring issues. The current water quality monitoring should be 

continued. Where appropriate, water quality monitoring and data collection programs may be 

conducted by local conservation groups with technical support to ensure adherence to sampling 

and reporting protocols. 

The Downeast Rivers (Narraguagus, Pleasant, Machias, East Machias, Dennys) have an ongoing 

water temperature monitoring program instituted by the Maine ASC and FWS in the early 

1990’s. In addition, the Sheepscot and Ducktrap rivers, along with Cove Brook, have also had 

recent water temperature monitoring activity (generally late 1990’s to the present), much of 

which that has been carried out by local watershed councils. Many private conservation groups 

(e.g. Atlantic Salmon Federation), local watershed councils and Indian tribes (e.g. Penobscot 

Indian Nation) are carrying out monitoring programs of their own. 
4-27

The potential for water temperature elevation in the vicinity of blueberry processing water 

discharges has been identified as a water quality issue (see page 1-46). Water temperatures in 

the vicinity of such discharges should be monitored to assess the potential to adversely affect 

Atlantic salmon. 

The Water Resources Center at UM also conducts water quality research on the DPS rivers. The 

George Mitchell Center at UM is doing high-resolution studies of pH, aluminum and other 

chemical parameters using automated samplers (ISCO samplers). Water quality data from these 

studies should continue to be integrated into the Maine DEP database. 

Recovery Actions: 

1.2.3A Implement a comprehensive and integrated long-term water chemistry 

monitoring program on all DPS rivers 

1.2.3B Implement a comprehensive and integrated long-term water quality 

monitoring program on all DPS rivers 

1.2.3C Monitor water temperatures in the vicinity of blueberry process water 

discharge sites on the Machias and Narraguagus to assess the potential 

impact on Atlantic salmon 

1.2.4 Prepare and implement plans to reduce pollution 

Pollution problems in DPS rivers are generally not attributable to a single point source but are 

due to cumulative effects of many sources within individual watersheds (Maine TAC 2002). 

Water quality in the DPS rivers is generally good (see page 1-22). However, several non-point 

source and point source pollution problems exist. 

The Maine DEP has identified numerous non-point sources of pollution as well as unlicensed 

discharges (e.g., septic systems) within DPS river watersheds. Local groups (i.e., watershed 

councils, Project SHARE), with the assistance of state and federal biologists, have also 

completed non-point source assessments on most of the DPS rivers including the Narraguagus, 

Pleasant, Sheepscot, Dennys, Machias and Ducktrap rivers. The watershed councils NPS 

assessments have focused on identifying sources that could have a direct effect on critical salmon 

spawning or nursery areas. Plans should be developed and implemented to reduce these threats. 

For example, the Narraguagus River Watershed Council has developed a comprehensive 

watershed management plan to address NPS pollution within this watershed. This management 

plan is based on the results of the NPS survey the watershed council conducted of the 

Narraguagus River. Several other watershed councils are considering preparing similar plans to 

address NPS problems within their respective watersheds. State and federal agencies should 

work with local groups to help develop and implement watershed management plans for DPS 
4-28

rivers. State and federal agencies should provide technical assistance to local groups in the 

planning, design and implementation of projects to remediate NPS pollution. 

The Maine DEP has provided financial assistance to local groups for projects to reduce NPS 

pollution through the Section 319 grant program of the Clean Water Act (CWA). Section 319 of 

the CWA provides states, territories and tribes with grants to implement NPS pollution controls 

described in approved state NPS pollution management programs. Section 319 grants support a 

wide variety of activities including technical and financial assistance, training, demonstration 

projects and monitoring to assess the success of specific NPS pollution mitigation projects. 

As noted (see page 1-40), sediment can impact salmon habitat in a number of ways including 

substrate embeddedness, diminished habitat complexity and stream channel alteration. Ongoing 

research conducted by the ASC has begun to investigate the level of NPS related substrate 

embeddedness and habitat productivity in several DPS rivers. Estimates of embeddedness can be 

used to assess habitat degradation or identify stream reaches that may benefit from habitat 

restoration (Atkinson and Mackey 2004). This research should be continued and the results be 

used to catalogue degraded habitat and prioritize habitat restoration needs. 

The EPA has delegated authority to the State of Maine to administer the CWA NPDES program, 

including responsibility for issuing federal national wastewater discharge permits. All future 

permits for discharges from aquaculture facilities will be issued by the Maine DEP. The 

Services consulted with EPA on the effect of the delegation of the NPDES program on the DPS. 

The Services’ concerns included the accidental release of farmed Atlantic salmon. 

The permit conditions proposed by the State of Maine will require facilities to limit the use of 

certain chemicals and develop standards that will reduce the nutrient pollutant load; including a 

reduction of phosphorous discharge by up to 90%. The new permit conditions set forth by the 

State will be based on the State’s water classification standards set by Maine DEP (Maine TAC 

2002). 

Until recently, EPA has not administered discharge limitations and standards for commercial, 

state and federal aquaculture operations. Wastewater and effluent discharges from aquaculture 

facilities can adversely affect freshwater, estuarine and marine environments. In August 2004, 

EPA established effluent limitations guidelines for concentrated aquatic animal production 

facilities including commercial and public aquaculture facilities. These standards are intended to 

reconcile inconsistencies between state regulatory agencies and reduce nutrient loading and 

adverse water quality impacts due to wastewater and effluent discharge from aquaculture 

operations (69 FR 51892). These regulations should be fully implemented. 

Hazardous waste sites (i.e., landfills, junkyards, superfund sites) pose a potential threat to water 

quality within the DPS. The DEP and the watershed councils are planning on sampling surface 

water near landfills in the Cove Brook, Narraguagus and Machias river watersheds in 2002. The 

Dennys River Eastern Surplus Superfund (DRESS) site in Meddybemps and nearby Smith 

junkyard threaten water quality in the Dennys River. PCBs have been found in the Dennys River 
4-29

below the DRESS site in Meddybemps (Mierzykowski and Carr 1998). The Superfund site is in 

the latter stages of remediation. These remediation efforts should continue to be monitored. 

Hazardous waste material remains on-site nearby at the Smith junkyard despite significant fines 

and regulatory efforts to clean up the site. Federal, state and local governments should 

cooperatively work to permanently close the junkyard, address any groundwater problems and 

restore this severely degraded site. 

Recovery Actions: 

1.2.4A Prepare and implement NPS pollution reduction plans for DPS rivers 

1.2.4B Evaluate the impacts of sedimentation on habitat quantity and quality 

including relationship between substrate embeddedness and habitat 

productivity in DPS rivers. 

1.2.4C Prepare and implement point source pollution reduction plans for DPS 

rivers 

1.2.4D Fully implement EPA aquaculture wastewater and effluent discharge 

regulations 

1.2.4E Continue monitoring of the remediation efforts at the Eastern Surplus 

Superfund site in Meddybemps 

1.2.4F Address any groundwater problems at the Smith junkyard on the Dennys 

River and restore the site 

1.3 Ensure timely passage for each life-stage, including connectivity of spawning 

and nursery habitats, downstream passage for smolts and upstream passage 

for returning spawners 

Historically, man-made dams were a major cause of the decline of Atlantic salmon runs in Maine 

(Baum 1997). Most man-made obstructions to fish passage on DPS rivers have been removed or 

breached and no longer restrict salmon migration. The Services have concluded that manmade 

obstructions to passage is not a high level threat to the survival and conservation of the DPS. 

Dams that obstruct passage of salmon do, however, exist on several rivers within the range of the 

DPS that no longer support wild salmon populations. The role of vacant habitat within the range 

of the DPS will be evaluated in the context of the development of final recovery criteria for the 

DPS (see page 3-13). 
4-30

1.3.1 Assess fish passage at dams, fishways and weirs currently in place and repair 

or improve as needed 

The Coopers Mills Dam on the Sheepscot River intermittently restricts access to Atlantic salmon 

spawning and rearing habitat. Improving fish passage at Coopers Mills Dam will reconnect 

habitats and help assure accessibility to spawning and rearing habitats. The IFW, DMR and the 

Town of Whitefield (which owns the dam) should repair the dam and improve fish passage 

around the dam or remove the dam. 

The Stillwater Dam on the Narraguagus River is equipped with a fishway. Fishways are also 

present at some natural obstructions within the DPS. At Saco Falls on the Pleasant River, a 

fishway exists that was constructed to improve existing fish passage above the natural falls. 

With salmon runs in the Pleasant River being in critical condition, every effort should be made to 

maximize the opportunity for spawning escapement within the river. ASC should evaluate the 

need to repair the existing fishway at Saco Falls to improve upstream passage for salmon in order 

to ensure that salmon have access to upstream habitat. Repairs were slated to begin in Fall 2002 

but have not yet been completed. 

The efficiency of existing fishways on DPS rivers has not been well documented (Baum et al. 

1992). The ASC, in cooperation with the state and federal agencies should assess the adequacy 

of existing fishways to provide up- and downstream passage for Atlantic salmon. Where 

necessary, fishways should be repaired and maintained. 

The potential for weirs to restrict fish passage should be assessed. Little is known about the 

potential of weirs to delay adult salmon migration. Weirs may potentially deter salmon from 

continuing upstream or critically delay migration. Weirs may also increase the risk of predation 

on migrating salmon. Investigations into these issues should be conducted. 

Recovery Actions: 

1.3.1A Repair or remove the Coopers Mill Dam to improve fish passage 

1.3.1B Evaluate the need to repair the existing fishway at Saco Falls 

1.3.2 Identify and improve culverts or other road crossings that impede salmon 

passage 

In addition to dams, poorly designed culverts and bridges can restrict salmon migration. These 

structures can act as barriers to passage for salmon of varying lifestages by altering natural flow 

regimes and affecting water depth and velocity. 
4-31

1.3.3 Identify and manage natural debris jams (including beaver dams) that 

impede salmon passage 

Beaver dams and debris blockages can impede salmon passage and restrict access to spawning 

and rearing habitat. Currently, biologists and volunteers remove debris jams on DPS rivers and 

tributaries as time permits. The ASC and FWS should continue to identify areas where beaver 

dams impede passage to spawning habitat and work with the watershed councils to breach dams 

in these areas during the spawning migration. Breaching efforts are generally focused on 

impassable obstructions located downstream of spawning habitat (MASCP 1997). Breaching 

efforts should be timed to ensure that returning adult salmon are able to access spawning habitat. 

Current breaching activities appear sufficient to ensure adequate passage for current adult 

returns. Precautions should be taken to minimize potential negative ecosystem impacts to habitat 

and juvenile salmon when breaching these obstructions (e.g., sedimentation, increased turbidity). 

The Dennys River Watershed Council has developed a plan to control beaver populations to 

enhance salmon habitat within Venture Brook. Dams will be breached and the recovery of 

salmon habitat within the stream will be monitored. As part of the project, an ecological 

assessment of the watershed was conducted including mapping existing habitat and documenting 

stream flow conditions. The results of this project should be monitored to determine the impact 

of beaver dam removal and beaver control on the improvement of habitat and Atlantic salmon 

recovery. The project could be expanded to three areas (one each on an important salmon 

tributary to the Machias, Pleasant, and Narraguagus rivers). Suitable salmon habitat in Venture 

Brook is limited -- different tributaries containing substantial amounts of salmon rearing habitat 

should be selected for study. 

Debris jams can also impede salmon passage. Some debris jams are a result of human 

disturbances that result in the build up of large woody debris, whereas other debris jams are part 

of the natural processes that occur in river corridors. The ASC should continue to monitor debris 

jams and oversee their removal if necessary to provide access to spawning habitat. 

1.3.4 Condition permits for activities within the estuaries of DPS rivers so as to 

minimize potential effects on migration of juveniles and adults 

Dredging, construction of drainage systems and construction of culverts and bridges all have the 

potential to adversely affect Atlantic salmon in estuaries. These activities can result in increased 

sedimentation, suspension of toxic chemicals or other compounds present in sediments and 

changes to natural flow regimes (see page 1-40). These changes can disrupt the migration of 

juvenile and adult Atlantic salmon by creating physical, thermal and sediment migration barriers. 

Permits for these activities and other activities in estuaries that have the potential to affect the 

migration of Atlantic salmon should be conditioned to minimize the impact on migration. 
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1.4 Secure long term protections for freshwater and estuarine habitats 

Long-term protections for freshwater and estuarine habitats includes protecting of the riparian 

zone as well as ensuring adequate water quality and quantity in the DPS river watersheds. Water 

quality and quantity are addressed in sections 1.1, 1.2, and 1.3. 

1.4.1 Ensure long-term protection of riparian habitat 

Vegetated riparian buffer zones should be established and maintained by using the most 

appropriate tool(s) for each specific situation. Partnerships among private landowners; state, 

federal, local, and Tribal governments; watershed councils and others will be key to 

implementing this action. Available tools include, conservation and management agreements, 

conservation easements, fee acquisitions, state and local land and water use regulations, 

voluntary BMPs, and other mechanisms to secure long-term protections of riparian and 

freshwater habitat and ensure that riparian functions are maintained into the future to support 

recovering salmon populations. 

Vegetated riparian buffers provide shade, regulate temperature and stream flow, protect water 

quality and act as a source of woody debris and organic matter (Kleinschmidt 1999). Vegetated 

riparian buffers provide a number of functions important for maintaining salmon habitat. 

Naturally vegetated riparian buffer zones are critical to maintain the health of adjacent aquatic 

systems. Establishing and maintaining riparian buffers is a critical means of protecting Atlantic 

salmon habitat. Significant disturbances that alter riparian habitat adjacent to salmon rivers can 

result in degradation of salmon habitat (Kleinschmidt 1999). Activities that have the potential to 

degrade instream habitat include timber harvesting, road construction, agriculture and 

development (Moring and Finlayson 1996). 

In 1998, the Maine State Planning Office (MSPO) prepared a methodology to determine 

minimum buffer widths to protect Atlantic salmon habitat. Otherwise known as the 

“Kleinschmidt Methodology” the study developed criteria to evaluate a host of physical 

characteristics of a given riparian zone and calculate a buffer width that is protective of the 

adjacent instream habitat. Depending upon slopes, soils, surface conditions, vegetative cover 

and tree canopy, an undisturbed protective buffer can be anywhere from 75 to 300 feet from the 

mean high water mark. This methodology establishes a scientific basis for determining riparian 

buffers adequate to protect Atlantic salmon habitat. This methodology is a tool that can be used 

to establish site-specific protective riparian buffers adjacent to important spawning and rearing 

habitat in cooperation with willing landowners. 

The majority of riparian lands along DPS rivers and streams are in private ownership. Many 

landowners in DPS river watersheds rely on agricultural, forestry and livestock activities for their 

livelihood. It is critical that the Services, state and federal agencies, local government and local 

conservation organizations work with private landowners to provide information about salmon 

recovery efforts and protect riparian and freshwater habitat. A watershed-wide risk assessment 
4-33

would be a valuable tool to determine a comprehensive, big picture understanding of the need to 

protect habitat through the use of riparian buffers. 

In Maine, both voluntary guidelines and regulatory measures exist to minimize potential adverse 

impacts to the aquatic environment and Atlantic salmon from activities within the riparian zone. 

These include local best management practices, shoreland ordinances, conservation easements, 

land acquisitions for the purpose of conservation protection and regulatory measures. Efforts to 

institute long-term protections for riparian and freshwater habitat should be continued. 

The State of Maine and the timber industry have implemented regulatory and voluntary measures 

to minimize the impacts of activities within the riparian zone, including streamside harvesting, 

stream crossings, haul roads and erosion control techniques. 

International Paper (IP) 54 had instituted voluntary forest management standards that include 

limitations on timber harvest within riparian buffer zones. The measures establish variable 

riparian buffers dependent on the stream reach (1st and 2nd order streams - 100 foot buffer; 3rd 

order streams - 330 foot buffer; 4th and 5th order streams - 660 foot buffers). These measures 

include no cutting within 25 feet of water and no more than 30% of timber removed over ten 

years within the riparian zone. 

The MFS has developed BMPs to minimize the impact of logging activities in the riparian zone 

on instream habitat. These BMPs are intended to reduce sediment and pollution inputs into 

bodies of water. Implementation of BMP recommendations is voluntary. BMPs have been 

adopted by many landowners and the timber industry. International Paper, for example, has 

BMPs that are implemented on all their lands in Downeast Maine. The MFS has produced a 

booklet on all their BMPs and this is used as guidance for all MFS projects and services. The 

application of sound riparian forest management and BMPs should continue to be encouraged. 

The MFS should continue to evaluate and monitor compliance with voluntary standards and 

adoption and use of BMPs by landowners55. The effectiveness of these practices and programs 

should be improved where needed. Forestry practices and their impacts should continue to be 

monitored to determine risk levels, identify threats and remediate impacts to Atlantic salmon and 

their habitat. 

Local organizations and the State of Maine have worked with landowners over the past several 

years to secure long-term protection of riparian and adjacent instream habitat through 

 

54 As noted, in November 2004, International Paper sold its Maine and New Hampshire forestlands, totaling 

approximately 1.1 million acres, to GMO Renewable Resources, LLC, (GMORR) a private forest 

investment management company. The new landowner plans on keeping the land in the Sustainable 

Forestry Initiative (SFI) certification program. 

55 MFS is mandated to evaluate and monitor the use of forestry BMPs in timber harvesting operations to 

protect water quality (PL 1997 § 648). In 2003, MFS inspected over 3500 timber harvest operations 

statewide to evaluate the use and effectiveness of BMPs. MFS found 7% of the inspections found 

insufficient us eof BMPs to protect water quality. In contrast, a similar study in 1995 found only a 47% 

BMP use. 
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conservation easements and direct fee acquisition of riparian habitat along DPS rivers. 

Conservation easements to protect Atlantic salmon habitat have been secured on most salmon 

rivers within the DPS. Existing conservation easements contain specific standards designed to 

preserve canopy, protect cold water inputs and encourage natural stream structure. 

Conservation easements typically establish an undisturbed buffer by restricting certain activities 

from occurring in the riparian zone. Landowners may continue to use their property but agree to 

certain conditions designed to protect the functions and values provided by riparian buffers. 

Conservation easements are held by either a qualified state agency or land trust which is 

responsible for upholding the terms of the easement. If the land is sold, the restrictions run with 

the deed and continue to benefit the stream and its corridor. Securing appropriate conservation 

easements should continue to be pursued as a means of providing long-term protection to habitat 

within the riparian zones of DPS rivers. 

Land acquisition is another method available to ensure long-term protection of riparian habitat. 

To date, ASC and several local conservation organizations including the Quoddy Regional Land 

Trust, the Downeast Rivers Land Trust, the Sheepscot Valley Conservation Association and the 

Coastal Mountains Land Trust have acquired riparian property that provides significant 

protection to instream habitat. Existing land acquisition efforts serve as potential models for 

protecting the long term viability of habitat on other DPS rivers. 

In addition to voluntary BMPs, several laws regulate land use in the riparian zone. The Maine 

Shoreland Zoning Act regulates land use within 250 feet of rivers with watersheds of at least 25 

square miles in drainage area. Where clearing of vegetation and timber harvesting are permitted, 

selective cutting of not more than 40% of the trees four inches or more in diameter in any tenyear period is allowed provided a well-distributed stand of trees and other natural vegetation 

remains. This statute also establishes protective standards for significant river segments 

including parts of the East Machias, Pleasant, Machias and Narraguagus rivers. These standards 

establish buffer zones around significant river segments that must be applied by each 

municipality to principle structures, new road construction and new gravel pits. Unorganized 

territories fall under LURC’s jurisdiction. LURC has also established standards for clearing of 

vegetation and timber harvesting within the shoreland zone of rivers, streams, lakes and ponds. 

Current state and local land use regulations should be evaluated to determine the adequacy of 

existing measures protecting riparian habitat. Where necessary, existing measures regulating 

activities within the riparian zone should be strengthened including monitoring and enforcement. 

In addition to regulatory measures, programs to promote better land use practices by local 

landowners should be continued and expanded. 

Recovery Actions: 

1.4.1A Provide long-term protection for riparian buffers through fee acquisition, 

conservation easements, conservation and management agreements, and 

other appropriate tools 
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1.4.1B Promote the adoption and use of BMPs by landowners and compliance 

with these voluntary standards 

1.4.1C Identify riparian zone activities (e.g., harvest practices, ATVs, 

development etc.) and evaluate impacts on Atlantic salmon 

1.4.1D Evaluate current state and local land use regulations to determine 

adequacy of existing measures protecting riparian habitat and instream 

improve if appropriate 

1.4.1E Enhance protection of riparian areas where necessary through expanded 

enforcement and modifications to the Natural Resource Protection Act, 

Forest Practices Act, LURC Zoning standards, and/or Municipal 

Shoreland Zoning 

1.4.2 Protect estuarine habitat used by Atlantic salmon 

Activities that have the potential to adversely affect Atlantic salmon should be evaluated and 

potential adverse impacts minimized. Estuarine habitat is used by both outmigrating Atlantic 

salmon smolts and returning adult Atlantic salmon. Atlantic salmon smolts are particularly 

sensitive during their transition to saltwater. Adult salmon are known to hold in estuaries during 

periods of low-flow in rivers. 

Permits for activities in estuaries should be conditioned to minimize any adverse affects on 

Atlantic salmon and their habitat. Numerous activities can contribute to degradation of estuarine 

habitat. Activities that have the potential to disturb the estuarine environment include dredging, 

construction of culverts and bridges, construction of drainage systems and coastal zone 

development. Activities in estuaries can result in increased sedimentation, suspension of toxic 

chemicals or other compounds present in sediments, nutrient loading, changes to natural flow 

regimes and general habitat loss and degradation. Permit conditions should include time of year 

restrictions, methodology, monitoring and reporting protocols. 

Dredging has the potential to adversely affect estuarine habitat in a number of ways (see page 1-

40). To minimize the effects on Atlantic salmon, all dredging and/or construction activities in 

DPS river estuaries should be conducted in such a manner as to minimize the potential to 

adversely affect Atlantic salmon. Environmental parameters should be monitored throughout 

projects so that the rate and manner of activity can be adjusted to ensure minimum impacts on 

the estuarine environment. 

Recovery Actions: 

1.4.2A Evaluate the potential for activities in estuaries to adversely affect Atlantic 

salmon 
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1.4.2B Condition permits for activities within the estuaries of DPS rivers so as to 

minimize potential effects on Atlantic salmon 

1.5 Restore degraded stream and estuarine salmon habitat 

Many historical land and water use activities have altered, and in some cases destroyed, the 

habitat needed by Atlantic salmon for spawning, growth and migration (see page 1-21). There 

are many habitat restoration needs and opportunities within the DPS. These include stream 

channel restoration, enhancement of fish passage, riparian habitat restoration, bank stabilization, 

culvert repair and improved stream crossings. The Services should work with ASC and other 

organizations to identify, coordinate and implement necessary stream restoration activities. 

Habitat restoration opportunities in DPS rivers should be identified, catalogued and prioritized. 

Restoration projects should be implemented to restore degraded habitat and maximize production 

of juvenile salmon in Maine rivers. 

The ASC and FWS have surveyed Atlantic salmon habitat in all DPS river watersheds within the 

DPS. These data provide a substantial baseline inventory of current habitat in these watersheds. 

Further surveys are needed to assess how much habitat was available historically and to assess 

other elements of habitat suitability such as temperature, pH shading, and additional physical 

habitat parameters (e.g., substrate embeddedness). The existing physical habitat data should be 

integrated with habitat suitability data (Stanley and Trial 1995). 

Currently NOAA Fisheries researchers are working on a model that will enable the estimation of 

Atlantic salmon habitat within rivers for which stream surveys have not been conducted. The 

model predicts potential habitat/historic habitat within a watershed. The model incorporates 

stream gradient, valley slope, channel confinement (the ratio of valley width to channel width) 

and riparian vegetation land cover type within 100 m of the river as inputs in the model. 

The model is a landscape predictive model. The model evaluates the shape of the land to 

determine areas which may provide habitat if other factors are addressed. The landscape 

predictive model may be able to provide estimates of not only habitat quantity but also estimated 

quality. Because understanding the quality of existing habitat is an essential component of 

recovery efforts, efforts should be continued to use this model for this application. 

1.5.1 Create regional hydraulic geometry curves and a reference reach database 

The FWS, ASC, Maine DOC and USGS are conducting stream assessments in order to establish 

a regional curve for all Maine rivers. Regional curves relate the dimensions (width, depth, cross 

sectional area, velocity) of streams at bankfull discharge56 to drainage area. This information is 

 

56 The bankfull discharge is the “discharge at which channel maintenance is the most effective, that is, the 

discharge at which moving sediment, forming or removing bars, forming or changing bends and meanders 

and generally doing work that results in the average morphologic characteristics of channels” (Dunne and 

Leopold 1978). 
4-37

needed so hydrologists and biologists can evaluate modified stream channels and design 

appropriate stream channel restoration projects. While general physical characteristics of good 

juvenile Atlantic salmon habitat are understood, less information is available on the processes 

that maintain stable channels in Maine rivers. These geomorphologic processes, including 

sediment transport and deposit, are critical to maintaining stable and productive fish habitat (Hill 

et al. 1991; Leopold et al. 1992; McBain and Thrush 1997). A reference reach database will 

allow the identification of degraded and altered stream channels by determining the 

characteristics of a naturally stable stream in a particular watershed. Without regional curves, 

degraded stream channels are less likely to be successfully restored as high quality salmon 

habitat. Efforts to develop regional curves should be continued and completed. 

1.5.2 Identify, catalogue and prioritize habitat restoration needs 

Throughout the U.S., Canada and Europe, stream channel restoration and habitat enhancement 

projects have been implemented to restore damaged habitats to more natural conditions and 

recreate historic geographical and hydrological systems. Available stream restoration techniques 

include soft engineering and other techniques that have been used to restore stream flow, bank 

stabilization and channel reconstruction. 

Many restoration opportunities exist within the DPS river watersheds. Efforts to identify these 

opportunities are underway by state, federal and local organizations. The Services should work 

with these organizations to identify, catalogue and prioritize habitat restoration needs within DPS 

river watersheds. 

Habitat restoration needs within the DPS river watersheds and estuaries should be assessed, 

catalogued and prioritized to identify degraded habitat and restoration opportunities. These may 

include obstruction to fish passage or habitat quality problems that can be addressed to enhance 

the survival of Atlantic salmon within estuaries. Potential concerns include poorly constructed 

culverts that restrict fish passage and/or create sedimentation and other water quality issues (see 

section 1.3). 

Local conservation organizations are often uniquely qualified to identify habitat problems and 

restoration opportunities. These organizations’ knowledge of local conditions and communities 

makes them important partners in identifying and implementing habitat restoration opportunities. 

Locally initiated actions for watershed protection and management are often more widely 

accepted and more effective than regulatory intervention. The watershed councils should 

continue to work in collaboration with landowners, local governments, state and federal 

agencies, businesses and non-profit organizations to identify and, where appropriate, implement 

salmon habitat protection and restoration projects. 

Recovery Actions: 

1.5.2A Identify, catalogue and prioritize habitat restoration needs in DPS rivers 
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1.5.2B Identify, catalogue and prioritize habitat restoration needs in estuarine 

habitat of DPS rivers 

1.5.3 Conduct high priority restoration projects 

Based on the preceding identification and prioritization of habitat restoration needs, the Services 

in cooperation with state, federal and local organizations, should conduct high priority 

restoration projects. Many restoration activities are currently being implemented by state, 

federal and local organizations. For example, local watershed councils have focused their efforts 

on the restoration of degraded riparian areas. In the Sheepscot, Pleasant and East Machias river 

watersheds, volunteers have planted trees to stabilize soils and provide shade. Volunteers have 

also corrected improper road ditching problems and replaced road culverts at road crossings to 

reduce sedimentation and mitigate chronic erosion problems. On the Narraguagus and Machias 

rivers, two bridges have been built to provide ATVs an alternative to driving through streams. 

1.5.4 Evaluate the potential of stream flow augmentation as a recovery tool to help 

meet Atlantic salmon flow needs and increase juvenile production and 

survival 

The potential of flow augmentation to increase juvenile salmon survival and production should 

be evaluated. Augmenting winter flows has been shown to increase parr populations and 

improve pre-smolt survival (Hvidsten and Ugedal 1991; Hvidsten 1993). Flow augmentation 

was found to increase parr populations in Barrows Stream in the East Machias River drainage 

(Havey 1974). Augmenting summer flows increased parr populations in several case studies in 

Canada (Ruggles 1988) and Maine (Havey 1974). Flows in the Dennys River have been 

augmented with water released from Meddybemps Lake. 

1.5.5 Evaluate the ecological role and importance of restoring other diadromous 

fish populations 

As discussed (see page 1-14), Maine Atlantic salmon rivers historically supported abundant 

populations of other native diadromous fish species including alewives, blueback herring, 

American shad, sea lamprey, anadromous rainbow smelt, Atlantic sturgeon, shortnose sturgeon 

and American eel. As these fish completed their life cycles, they likely performed important 

ecological functions that may have been important to Atlantic salmon in completing their life 

cycle. Primarily, these functions may be categorized under three broad categories: prey 

buffering, marine derived nutrient cycling and habitat modification and enhancement. 

Many of these diadromous species have declined as dramatically as Atlantic salmon in recent 

years (Collette and Klein-MacPhee 2002). The absence of historical data for these species make 

it very difficult to assess the functions these fishes may have performed in a properly functioning 

ecosystem. Nonetheless it is likely that the absence of other populations of diadromous species 

of fish native to rivers within the DPS may be impeding the recovery of the DPS. Additional 
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investigation of the role and importance of restoring other diadromous fish populations in the 

recovery of the DPS should be pursued. 

2. Minimize potential for take in freshwater, estuarine, and marine fisheries 

2.1 Prevent Directed Take of Atlantic salmon 

The intentional capture of Atlantic salmon is a violation of the ESA’s Section 9 prohibition 

against “take” of Gulf of Maine DPS Atlantic salmon (65 FR 69479, 50 CFR 17.21). Under the 

ESA, the term “take” means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or 

collect, or to attempt to engage in any such conduct. 

2.1.1 Maintain and enforce the closure of the directed sport fishery for Atlantic 

salmon 

In December 1999, the State of Maine adopted regulations prohibiting all angling for Atlantic 

salmon year round in Maine (12 MRSA § 9907). Under these regulations, it is unlawful to angle, 

take or possess any Atlantic salmon from all Maine waters (including coastal waters). This ban 

remains in effect. The closure in freshwater is enforced by the Maine Warden Service under the 

Maine IFW. The Maine Marine Patrol, under the Maine DMR, has jurisdiction over tidal waters, 

including coastal estuaries. The State should maintain and enforce the closure of the directed 

sport fishery for Atlantic salmon. It is believed that poaching activity occurs in Maine rivers (see 

page 1-35). Given the low numbers of returning adult salmon, any poaching is a significant 

threat. NOAA Fisheries and FWS each have a federal agent in Maine responsible for enforcing 

the provisions of the ESA. Continued enforcement efforts and adequate penalties are essential to 

help minimize the threat of poaching. 

2.1.2 Maintain current FMP that restricts directed harvest of Atlantic salmon in 

U.S. estuarine and marine waters 

Current regulations in place under the Atlantic salmon FMP that prohibit the direct harvest and 

possession of Atlantic salmon in the U.S. EEZ should be maintained (see page 1-52). The FMP 

was intended to safeguard U.S. Atlantic salmon, protect the U.S. investment in the state-federal 

restoration program and strengthen the U.S. position in international negotiations. 

2.1.3 Continue international efforts to reduce threats from commercial fisheries 

outside of U.S. jurisdiction 

Historically, a major source of Atlantic salmon mortality in the marine environment was the 

directed commercial fishery off the western Greenland and Canadian coasts (see pages 1-56 to1-

57)57. These commercial fisheries have been greatly reduced but not completely eliminated as a 

 

57 Piscine and mammalian predation is another source of mortality on Atlantic salmon during the marine 

phase of this species life history. Recovery actions necessary to mitigate adverse impacts from predation to 

the recovery of the DPS are discussed below, pages 4-44 – 4-53.
4-40

source of mortality to Maine Atlantic salmon. The North American component of this mixed 

stock fishery58 likely includes a high proportion of Canadian-origin salmon and a low proportion 

of U.S. salmon. Maine-origin salmon, including DPS salmon, are likely taken in low numbers in 

this fishery. 

The NASCO is the international organization responsible for the management of Atlantic salmon 

in the North Atlantic Ocean. The NASCO pursues its goals by controlling the exploitation of 

Atlantic salmon by member nations. The NASCO consists of a Council and three regional 

Commissions: the North American (NAC), West Greenland and the Northeast Atlantic 

Commissions. The U.S. participates in the management activities of both the North American 

and West Greenland Commissions, as well as in the deliberations of the full Council. The U.S. 

participates in these international forums to manage the commercial harvest of Atlantic salmon at 

levels that ensure that adequate numbers of Atlantic salmon are available to meet conservation 

spawning escapement targets. The goal of these efforts is to ensure adequate escapement of 

Atlantic salmon to recover U.S. Atlantic salmon populations. The U.S. should continue to 

advocate for the precautionary, scientifically-based management of Atlantic salmon stocks 

through the NASCO process. 

The NASCO is advised on catch and management options59 for Atlantic salmon fisheries by the 

International Council for the Exploration of the Sea (ICES) Advisory Committee on Fishery 

Management. This management advice is based upon estimates of the pre-fishery abundance 

(PFA) of non-maturing 1SW salmon available for harvest, accounting for natural mortality and 

conservation escapement limits. The ICES advice to NASCO for 2002, as it has been in recent 

years, was that catch should approach or reach zero (ICES 2002). 

In August 2002, the Greenland Home Rule Government and the Organization of Hunters and 

Fishermen in Greenland (KNAPK) jointly agreed to suspend all commercial fishing for Atlantic 

salmon within Greenland territorial waters. This agreement is renewable annually for up to five 

years and results in suspension of the commercial fishery for Atlantic salmon in Greenland. As 

noted (see page 1-56), the internal use fishery is not included in the agreement. The agreement 

was negotiated by the North Atlantic Salmon Fund, the Atlantic Salmon Federation and the 

National Fish and Wildlife Foundation. 

U.S. participation in the international sampling program of the West Greenland fishery should be 

continued. Because the ocean intercept fisheries for Atlantic salmon are mixed-stock, it is 

important to know what proportion of this catch is U.S. origin fish and if possible, what 

proportion is DPS fish. One way to get this data is to sample catch from these international 

fisheries. Efforts by NOAA Fisheries have led to increased sampling of Atlantic salmon 

 

58 Atlantic salmon are harvested when stocks originating from different countries are intermixed in the marine 

environment.

59 Catch options are calculated using probability of attaining spawning escapement targets of between 25% 

and 50%. In 2002, the available catch surplus at the risk neutral (50% probability) was approximately 

50,600 fish (ICES 2002). Below the risk averse probability value of 30%, there were no salmon surplus to 

conservation escapement limits (ICES 2002).
4-41

captured in the West Greenland fishery in recent years. The goal of this research is to estimate 

stock specific removal rates of the fishery and to improve our understanding of the impacts of the 

fishery on U.S. Atlantic salmon populations. Large-scale marking of Penobscot River origin 

Atlantic salmon (~170,000 marked smolts released annually) provides a method to assess West 

Greenland fishery impacts on Maine origin, although not listed, Atlantic salmon. While almost 

half of the Greenland commercial landings were examined for marks in 2001, only one marked 

Penobscot fish was detected, indicating that interception of Penobscot River origin fish occurs, 

but likely at low levels. 

A small commercial Atlantic salmon fishery occurs off St. Pierre et Miquelon and lands 

approximately 2-3 mt/year. There is great interest by the U.S. and Canada in sampling this catch 

to gain more information on stock composition. The NMFS, working through the U.S. State 

Department, has sought to establish a sampling program in St. Pierre et Miquelon similar to the 

one being conducted in West Greenland. Efforts should be continued to establish a sampling 

program to determine the level of take and potential impact this fishery may have on the 

continued persistence and recovery of the Gulf of Maine DPS. 

Recovery Actions: 

2.1.3A Participate in international salmon management with the goal of ensuring 

any quotas set are based on the best available scientific data and provide 

adequate protection of U.S. stocks 

2.1.3B Continue U.S. participation in the international sampling program at West 

Greenland 

2.1.3C Continue efforts to implement a biological sampling program at St. Pierre 

et Miquelon to determine the origin of Atlantic salmon captured in this 

fishery 

2.2 Avoid bycatch of Atlantic salmon 

The incidental capture of Atlantic salmon is a violation of the ESA’s Section 9 prohibition 

against “take” of Gulf of Maine DPS Atlantic salmon (65 FR 69479, 50 CFR 17.21). Incidental 

take is defined as take that is incidental to, and not the purpose of, carrying out an otherwise 

lawful activity. 

The Services have concluded that the potential incidental capture of Atlantic salmon by 

recreational anglers targeting other fish species poses a high level threat to the DPS. Juvenile 

and adult Atlantic salmon may be incidentally taken as bycatch by state permitted recreational 

anglers fishing for other freshwater game fish species such as brown trout, brook trout and 

landlocked salmon (see page 1-52). There are recreational fisheries for marine species of fish 

(e.g., striped bass and American shad) that also take place in estuaries and in freshwater in DPS 
4-42

rivers. In marine and estuarine waters60, these fisheries do not require that anglers have a 

license, they are regulated with size and bag limits. These fisheries generally fall under the 

jurisdiction of Maine DMR. These fisheries have the potential to incidentally capture DPS 

Atlantic salmon. There is currently no process in place to assess the number of Atlantic salmon 

caught as recreational bycatch or to estimate the mortality associated with this take (LWRC 

1999). 

2.2.1 Monitor, assess and develop methods to avoid bycatch in recreational and 

commercial freshwater fisheries 

The State should assess the level of incidental take of Atlantic salmon in recreational fisheries 

through appropriate methods such as creel surveys, spot checks and voluntary reporting by 

anglers. Information should be collected on both the level of effort and amount of take. If 

necessary, additional measures should be considered to minimize this threat including gear 

restrictions (i.e., barbless hooks) and time and area closures to minimize the potential for the 

incidental take of Atlantic salmon. 

The State has implemented a number of regulatory measures designed to minimize the potential 

for the incidental take of Atlantic salmon (see page 1-52). These measures include minimum 

size limits and seasonal restrictions. The State should review existing regulatory measures to 

assess their effectiveness in minimizing the incidental capture and injury associated with 

recreational angling in DPS rivers. 

Given the extremely low Atlantic salmon population levels, the harvest (incidental or intentional) 

of any Atlantic salmon may adversely affect the DPS. Any measurable bycatch mortality could 

be high enough to cause harm to these populations (Maine TAC 1998). Deliberate targeting of 

Atlantic salmon by some anglers poses a serious threat to the recovery of Atlantic salmon 

populations and the DPS as a whole. The Services should work with the Maine IFW to close 

select cold water adult Atlantic salmon holding areas to all fishing where Atlantic salmon may be 

taken as bycatch or poached. All fishing should be prohibited in all highly utilized cold water 

holding areas until such time as wild Atlantic salmon populations have recovered sufficiently to 

withstand possible adverse impacts associated with incidental take by recreational anglers. 

Under section 10(a)(1)(B) of the ESA, non-federal entities may apply for permits from the 

Services to take ESA-listed species if such taking is incidental to, and not the purpose of, the 

carrying out of an otherwise lawful activity. The Services should work with the State to develop 

a Section 10(a)(1)(B) conservation plan for recreational fishing permitted by the State. This plan 

should institute a reporting and monitoring program to better estimate incidental take of Atlantic 

salmon in recreational fisheries. This plan should assess the risk of incidental take and its 

impacts on the recovery of the DPS. This plan should identify specific measures that will be 

taken to minimize the potential for incidental take of Atlantic salmon by recreational anglers. 

Under the ESA, the permit shall be issued if: (1) the taking will be incidental; (2) the applicant 

 

60 There is a license required to take striped bass above the head of tide (i.e., in freshwater).
4-43

will, to the maximum extent practicable, minimize and mitigate the impacts of such taking; (3) 

the applicant will ensure that adequate funding for the conservation plan will be provided; (4) the 

taking will not appreciably reduce the likelihood of the survival and recovery of the species in 

the wild; and (5) any other measures that the Services may require as being necessary or 

appropriate will be met. 

The ASC and IFW have developed materials to aid anglers in identifying juvenile Atlantic 

salmon. These programs should be continued and expanded to minimize the threat of take 

associated with recreational fisheries. 

The State should continue to monitor other commercial freshwater fisheries in order to ensure 

these fisheries do not incidentally take DPS salmon. Small scale commercial fisheries for 

species other than salmon are conducted in some DPS rivers. These fisheries may have the 

potential to incidentally take endangered salmon. Maine DMR staff monitor the elver fishery to 

assess potential bycatch of other species of fish including Atlantic salmon (see page 1-55). In 

recent years no incidental bycatch of either juvenile or adult Atlantic salmon has been observed 

or documented in elver nets. IFW and DMR permit alewife harvest by towns and/or individuals 

in some of the DPS rivers. The alewife fishery should also be evaluated and monitored. 

Recovery Actions: 

2.2.1A Assess the level of incidental take of Atlantic salmon by recreational 

anglers 

2.2.1B Prohibit all recreational fishing in select areas utilized by Atlantic salmon 

as holding areas to all fishing where Atlantic salmon may be taken as 

bycatch or poached 

2.2.1C Develop a Section 10(a)(1)(B) habitat conservation plan for recreational 

fishing permitted by the State that may incidentally take Atlantic salmon 

2.2.1D Continue to monitor commercial freshwater fisheries where the potential 

for incidental take of Atlantic salmon exists 

2.2.2 Monitor, assess and develop methods to avoid bycatch in other estuarine or 

marine fisheries under U.S. jurisdiction 

The potential exists for juvenile and adult Atlantic salmon to be incidentally taken as bycatch in 

commercial and recreational fisheries targeting other marine and estuarine species (see page 1-

54). The NMFS should work with the State of Maine and the NEFMC to develop research 

programs necessary to assess this threat. Based on the results of these assessments, appropriate 

management strategies and regulatory measures to avoid bycatch of Atlantic salmon in estuarine 

and marine fisheries should be developed and implemented. Based on the potential spatial and 

temporal overlap of the midwater trawl herring fishery and post-smolt outmigration, observer 
4-44

coverage should be increased in the fleet in order to improve the ability to assess the potential for 

Atlantic salmon bycatch to occur in the herring fishery. 

Recovery Actions: 

2.2.2A Assess the potential risk for incidental take of Atlantic salmon in marine 

and estuarine fisheries 

2.2.2B Develop appropriate management strategies and regulatory measures to 

avoid bycatch of Atlantic salmon in estuarine and marine fisheries where 

significant potential for bycatch is identified 

2.2.2C Increase observer coverage in the midwater trawl herring fishery to 

improve the ability to assess the potential for Atlantic salmon bycatch in 

the herring fishery. 

3. Reduce predation and competition on all life-stages of Atlantic salmon 

Atlantic salmon are preyed upon by numerous species of mammals, birds and fish (see pages 1-

65 to1-76). Predation would not be expected to threaten the continued existence of healthy 

populations. The threat of predation is significant today because of small salmon populations 

and the increased populations of some predators. 

3.1 Assess impacts of predation on wild and hatchery-reared river-specific 

salmon populations and develop methods for reducing adverse affects from 

predation 

Predation rates and the impact on the DPS are difficult to estimate and assess because of the 

wide spatial and temporal distribution of Atlantic salmon and the large number of potential 

predators. The development and implementation of management measures to minimize potential 

impacts of predation on the DPS requires a clear understanding of the nature and extent of the 

threat. Known and potential predators should be ranked relative to their impact on the DPS. 

This information should be used to direct further research and assessment activities. 

3.1.1 Evaluate salmon population management practices, habitat features and 

water management practices that may exacerbate predation rates 

There are a number of factors that can exacerbate predation rates on Atlantic salmon. These 

include salmon population management practices, natural and man-made concentration sites and 

land and water management practices that affect the vulnerability of Atlantic salmon to 

predation. Based on the results of the following recommended research and assessment tasks, 

appropriate management measures to reduce documented impacts of predation on the DPS 

should be developed and implemented. 
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Habitat features 

Habitat features that may increase the vulnerability of salmon to predation should be identified 

and catalogued. These features include natural and man-made obstructions that may restrict 

passage and/or concentrate salmon (see page 1-49). These obstructions include falls, beaver and 

debris dams and man-made dams. Information from this assessment should be used to develop 

management strategies to minimize predation and remediate passage problems where possible. 

Studies in the Pacific Northwest have shown that pinniped (sea lions and seals) predation, 

especially at areas of restricted passage, can adversely affect small salmonid populations and 

impede recovery (NMFS 1999a). Similarly, juvenile salmon are especially vulnerable to 

cormorant predation when they are concentrated during downstream passage at man-made 

structures (dams) and natural obstructions. 

Salmon management practices 

Current salmon population management practices should be reviewed to determine whether 

modifications are necessary to help minimize the vulnerability of juvenile salmon to predation. 

There are a number of management practices that may increase the vulnerability of hatcheryreared salmon smolts to predation including method and timing of smolt stocking and tagging 

methods. Hatchery-reared smolts often show decreased predator avoidance behavior compared 

to wild smolts. These behavioral differences may contribute to increased predation. Ongoing 

studies by NMFS NWFSC indicate that predator avoidance conditioning can increase the 

survival of smolts stocked into the wild. Modifications to hatchery practices to condition fish to 

increase predator avoidance behavior should be evaluated. 

The installation and operation of weirs and fish traps are other examples of salmon management 

practices that might increase the vulnerability of salmon to predation. The potential for these 

structures to increase predation rates of Atlantic salmon should be assessed. The presence of 

potential salmon predators within the vicinity of weirs and fish traps should be systematically 

monitored to determine whether these facilities may concentrate potential salmon predators. 

Land and water use management practices 

There are a number of land and water management practices that may exacerbate predation rates. 

Excess sedimentation can lead to loss of habitat and filling of pools. The loss of shelter in 

interstitial gravel and cobble spaces due to filling by sediment can result in increased predation 

(Cordone and Kelley 1961; Bjornn et al. 1974, Waters 1995)(see page 1-41). Dams and 

improperly functioning fishways may obstruct fish passage and concentrate juvenile and adult 

salmon, thus making them more susceptible to predation. Water withdrawals can change basic 

sediment transport functions and result in stream channel changes. Water withdrawals also have 

the potential to expose or reduce salmon habitat thereby restricting salmon movement and/or 

concentrating fish in pools and other holding areas. This could increase their vulnerability to 

predation. 
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Recovery Actions: 

3.1.1A Identify and catalogue locations that restrict passage and/or concentrate 

salmon and thereby increase the vulnerability of salmon to predation 

3.1.1B Review existing salmon population management practices to determine if 

they increase the vulnerability of juvenile salmon to cormorant predation 

3.1.1C Document and monitor the presence and abundance of potential salmon 

predators at natural and man-made concentration sites 

3.1.1D Assess the potential of land and water use practices to exacerbate 

predation rates 

3.1.2 Implement integrated management of cormorants to reduce predation on 

Atlantic salmon 

Integrated cormorant management61 should be implemented to reduce predation on Atlantic 

salmon. Cormorant predation on Atlantic salmon in Maine has been well-studied (see page 1-

69). It is known that cormorants prey on hatchery smolts. Cormorant predation is generally 

higher on hatchery-reared than wild smolts (Blackwell 1996; Anthony 1994; Baum 1997; NMFS 

2000). The potential for cormorant predation to adversely affect the recovery of the DPS should 

be further evaluated. More information is needed on the impacts of predation on hatchery-reared 

salmon smolts. Studies should identify specific cormorant colonies that may inflict significant 

levels of depredation on salmon populations within the DPS. 

Management measures to reduce cormorant predation on hatchery-reared Atlantic salmon smolts 

should be evaluated and implemented if appropriate. Potential measures include modifications 

of man-made structures that slow or impede passage (e.g., fishways, weirs and traps) and the use 

of non-lethal deterrence and/or selective lethal removal of cormorants at locations where they are 

observed to be significant salmon predators. 

Lethal control of cormorants is currently subject to depredation permits that may be issued by 

FWS under the Migratory Bird Treaty Act62. The FWS may issue depredation permits 

authorizing lethal control of cormorants, their eggs, and/or nests, particularly in situations where 

 

61 Integrated predator management involves a management approach that emphasizes monitoring and 

adaptive management. Integrated predator management plans should: identify and prioritize management 

areas; clearly define goals; identify areas of limited or no predator control for comparison; work with state 

and local authorities; review plan annually and change/amend as needed; outline specific priorities and 

tasks.

62 In November 2001, FWS released a draft Environmental Impact Statement (EIS) and management plan for the doublecrested cormorants. The draft EIS explores additional alternatives for managing cormorants throughout the contiguous 

United States.
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the need for cormorant control is recognized in a state or federal conservation plan for a sensitive 

species, including endangered species. 

If there are specific reaches or areas on DPS rivers where cormorant predation is adversely 

affecting the recovery of salmon populations, the birds responsible for the depredation should be 

targeted for removal. Implementation of specific cormorant management activities should 

include monitoring to assess their effectiveness and allow for appropriate modification of 

management protocols. 

The restoration of runs of other forage species such as alewife (Alosa pseudoharengus), shad 

(Alosa sapidissima) and blueback herring (Alosa aestivalis) is one method to mitigate the effects 

of predation on Atlantic salmon, particularly cormorant predation. Alewife restoration may be 

particularly beneficial for Atlantic salmon as the time of migration for these two species 

coincides. The potential for restoration of these runs to help reduce predation on Atlantic salmon 

should be evaluated. Alewives and shad can serve as buffer species that will dilute the effect of 

predation on Atlantic salmon. 

In addition, recovery efforts that aid fish species such as alewives and shad will be beneficial to 

Atlantic salmon recovery as well. Restoring the natural runs of these anadromous fish will 

require removal of barriers to fish passage or the addition of fishways and enhancement of 

stream and river health (i.e., water of sufficient quantity and quality). Current restoration efforts 

for these anadromous species occur under the jurisdiction of the Maine DMR Stock 

Enhancement Program. Efforts include control of fishing effort, construction of fish passage at 

dams, fish stocking and improvements to water quality and habitat including wetlands, spawning 

grounds and nursery areas. 

Recovery Actions: 

3.1.2A Evaluate the potential of cormorant predation to adversely affect the 

recovery of the DPS 

3.1.2B Identify specific cormorant colonies within the DPS that may inflict 

significant levels of depredation on DPS salmon populations and 

implement appropriate experimental management measures 

3.1.2C Promote the conservation and restoration runs of anadromous forage 

species to provide a buffer against predation on salmon 

3.1.3 Evaluate the need for integrated management of seals to reduce predation on 

Atlantic salmon 

The extent of seal predation on wild Atlantic salmon in Maine and the impact on the recovery of 

the DPS has not been adequately assessed and documented. Additional investigation is needed 

to assess whether seal predation may adversely affect the DPS. 
4-48

Salmon may be more vulnerable to seal predation in areas where salmon are concentrated. Sitespecific investigations of seal predation on DPS Atlantic salmon populations are needed. The 

presence and abundance of seals at natural and man-made concentration sites (dams, weirs, falls, 

fishways) should be systematically monitored and documented. These studies should evaluate 

the spatial and temporal presence of seals in these areas. 

Similarly, salmon aquaculture net-pens may play a role in aggregating seals and increasing the 

potential for predation on both outmigrating post-smolts and returning adults. Based on the 

available data, although somewhat minimal, it seems that net-pens do not aggregate seals 

(Nelson 2004). This potential threat should be investigated in conjunction with research to 

assess seal attacks on net-pens and implementation of deterrence measures. 

The NMFS and ASC should evaluate available predation study techniques to determine their 

utility to document seal predation on Atlantic salmon. One method to assess seal predation is to 

examine and quantify the composition of seal diets. The examination of gastrointestinal tracts of 

seals is one method of quantifying prey consumption rates. This type of approach is difficult due 

to the wide spatial and temporal distribution of Atlantic salmon at low densities and the fact that 

seals are opportunistic feeders. Furthermore, this type of study requires the lethal take of seals. 

The Marine Mammal Protection Act (MMPA) strictly limits the conditions under which marine 

mammals may by taken63. 

Opportunistic stomach content analysis (e.g., seals taken incidentally in commercial fisheries, 

seals entrained in power plant coolant water intakes) of seal’s food habits provides another 

potential opportunity to study seal predation on Atlantic salmon. Stomach samples collected 

from harbor seals incidentally taken in Gulf of Maine sink gillnet fisheries during the period 

1991-1997 have been analyzed (Williams 1999). Additional stomachs are archived at the NMFS 

NEFSC Laboratory in Woods Hole. Additional stomach content analysis should be conducted if 

appropriate. 

Alternatives to conventional diet sampling techniques, including scat analysis and fatty acid 

signature analysis, stable isotope analysis, crittercams should be evaluated. Fatty acid signature 

analysis can allow researchers to identify individual prey species. Fatty acids are formed when 

fats are broken down during digestion and are incorporated into the blubber of marine mammals. 

By taking a blubber sample from a predator, researchers may be able to identify specific prey 

species as certain fatty acids are unique to individual prey species. 

Scat analysis has been used to study pinniped food habits. Prey identification is determined by 

analyses of prey hard parts such as otoliths, fish bones, gill rakers and cartilaginous parts 

recovered from seal scats. In the Pacific Northwest, researchers found that adult salmon 

accounted for 6% (percent frequency of occurrence in scats) of harbor seals diets and juvenile 

salmon accounted for 19% (Browne et al. in NMFS 2003). Variation in ingestion and digestion 

 

63 Under the MMPA take means “to harrass, hunt, capture or attempt to hunt, capture, or kill any marine 

mammal.”
4-49

of identifiable hard parts makes it difficult to quantify the total contribution of salmon in 

pinniped diets (NMFS 1999). Scats are difficult to collect on rocky ledges (typical harbor seal 

and grey seal habitat along the Maine coast). Some samples were collected in Summer 2001 

(Jim Gilbert, UM, personal communication). 

Harbor seal food habit studies that rely on bony parts are likely to underestimate the take of adult 

salmon. Generally, harbor seals eat small fish (20-30 cm) that can be swallowed whole. Seal 

predation on adult salmon at aquaculture pen sites and elsewhere however is characterized by 

bites from the belly of the fish, and no bones large enough to withstand digestion are consumed. 

Stable isotope analysis (Smith, et al., 1997) is showing more promise for identification of food to 

species, and genetic analyses of hard parts found in scats may be a precursor to identification of 

soft tissues from stomachs (Orr, et al., 2004, Purcell, et al., 2004). 

Predator tags are another promising new research tool to assess predation on juvenile Atlantic 

salmon. Efforts are ongoing to develop a telemetry tag that will enable researchers to detect 

predation on stocked smolts. These efforts should be continued. 

Scarring and injury (including apparent claw and tooth abrasions) indicative of marine mammal 

predation have been observed on adult Atlantic salmon during fish trapping operations in Maine 

(see page 1-66). The ASC should continue efforts to develop a standardized catalogue of these 

wounds to verify and document seal related injury. These data may enable ASC to assess 

possible predation trends. 

Some individuals and organizations have advocated that lethal seal control programs should be 

implemented in Maine to control seal populations. This is due to the perception that seal 

predation is in part responsible for the severely depressed status of wild salmon populations. 

There is insufficient data on the extent and impact of pinniped predation on the recovery of the 

DPS to recommend the lethal take of individual seals. Predator culling program may not have 

direct benefits on specific prey stocks and may not result in increased fish populations (United 

Nations Environment Program (UNEP) 1999). 

The MMPA prohibits the take of all marine mammals except under strictly defined conditions. 

Any management measures to mitigate marine mammal predation must conform with the 

requirements of the MMPA. Section 104(c) of the MMPA grants authority for the issuance of 

permits to conduct scientific research that includes non-lethal take of marine mammals. Under 

the MMPA, permits may not be issued for research involving the lethal take of marine mammals 

unless it can be demonstrated by an applicant that a non-lethal method of conducting the research 

is not feasible. Additional data are needed before any management measure involving lethal take 

should be considered or recommended. 
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Section 120 of the MMPA is the only potential authority for intentional lethal taking64 of seals. 

Lethal take is limited under this provision to individually identifiable pinnipeds and includes 

many related requirements. 

Based on the results of the preceding recommended research programs, appropriate management 

measures should be developed and implemented to mitigate the impact of documented seal 

predation on wild salmon populations. 

Recovery Actions: 

3.1.3A Evaluate the effect of seal predation on the recovery of the DPS 

3.1.3B Document and monitor the presence and abundance of seals at natural and 

man-made concentration sites 

3.1.3C Conduct research to determine the role of net-pen sites in seal aggregation 

and salmon predation 

3.1.3D Evaluate the potential of alternative research techniques and food habit 

sampling methodologies to help assess seal predation on Atlantic salmon 

3.1.3E Develop and implement appropriate management measures to mitigate the 

impact of documented seal predation on wild salmon populations 

3.1.4 Assess potential effects of other predators 

The role of other potential predators of Atlantic salmon to adversely affect the recovery of the 

species should be evaluated. These other predators include mustelids (e.g. otters and mink), 

gulls, pelagic birds (e.g., gannets), marine fish (e.g., cod), sharks, estuarine fish (e.g. striped 

bass) and other marine mammals (dolphins, porpoises, whales). Based on the results of these 

evaluations, appropriate management measures should be considered and implemented. 

 

64 Section 109(h)(1) of the MMPA provides an exception to the takings prohibitions for any federal, state, or local 

government official or employee, or a person designated under section 112(c), in the course of his or her duties, for 

taking marine mammals in a humane manner if the taking is for the nonlethal removal of nuisance animals. If the State 

determined that predation on Atlantic salmon is a "nuisance", then section 109(h) gives them authority to use non-lethal 

taking without any other permit or authorization requirements. It is important to note that there would probably be 

some constraints on such an approach - such as confining it to specific areas. NMFS and the State of Washington used 

this authority to remove and hold in temporary captivity sea lions that were adversely affecting steelhead runs at the 

Ballard Locks in Seattle Washington. Nonlethal deterrent methods, such as hazing and acoustic barriers, were also 

used.
4-51

3.2 Reduce predation and competition between Atlantic salmon and other 

freshwater fish species 

The introduction of non-native fish species into aquatic ecosystems can adversely affect native 

fish species through competition for food and available habitat, predation, interbreeding and 

hybridization and the introduction of disease and parasites (see page 1-69). 

3.2.1 Review and monitor potential impacts of existing stocking programs for 

other fish 

The Maine IFW stocks brown trout65, splake, landlocked salmon and brook trout in rivers and 

lakes within DPS river watersheds in order to enhance recreational fishing opportunities for the 

public. The NRC (2004) recommended that the stocking of non-native species, including brown 

trout, small- and largemouth bass and landlocked salmon, into DPS rivers be avoided. All 

existing stocking programs should be evaluated to assess the potential impacts of these 

introductions on Atlantic salmon populations. Methods to minimize potential adverse affects of 

these stocking programs should be evaluated. 

Stocking of freshwater salmonids in Atlantic salmon river watersheds should be evaluated to 

fully assess the potential adverse impacts of these programs on the DPS. Program evaluation 

should include an assessment of the proximity of stocking sites to Atlantic salmon habitat and 

the potential for direct interactions to occur. Environmental parameters such as temperature and 

habitat that influence the potential for adverse impacts of the stocking program on the recovery 

of the DPS should also be assessed. Plans to monitor potential adverse effects of stocking 

programs should be developed and implemented. Given the severely depressed status of wild 

salmon populations, and the particular concern for the adverse effects of brown trout, stocking of 

this species should be suspended in all DPS river watersheds until the potential impacts of these 

introductions can be fully assessed. 

The stocking of non-native and native species into headwater lakes of DPS rivers should also be 

evaluated immediately to determine the potential impacts of these programs on the DPS. The 

potential for adverse interspecific competition between other salmonid species (e.g., splake, 

landlocked salmon and brook trout) stocked in headwater lakes of DPS rivers within the DPS is 

thought to be low (Ken Beland, ASC, personal communication). Because most of these lakes are 

glacial oligotrophic or mesotrophic lakes with small outlet streams, there is more spatial 

segregation of fisheries than might be the case for lakes a river flows through in the case of 

riverine fish management and stocking programs. In addition, many of the headwater lakes are 

well separated from areas with documented Atlantic salmon reproduction or juvenile rearing 

habitat reducing the potential for interactions (Ken Beland, ASC, personal communication). 

Landlocked salmon stocked into headwater lakes are found in riverine habitat below these lakes 

in a number of the DPS rivers. Existing data should be reviewed to determine the extent of 

 

65 As noted (page 51), brown trout are raised at the Palermo hatchery on the Sheepscot River for stocking 

purposes.
4-52

landlocked salmon distribution within DPS rivers. Based on the results of this review, stocking 

programs should be modified or suspended if they increase the potential for adverse interactions 

with wild anadromous Atlantic salmon. The ASC and IFW should continue to monitor the 

distribution of landlocked salmon in DPS river wtaresheds. This can be accomplished under 

existing monitoring programs. 

In June 2002, the IFW and ASC signed an MOA to guide the management and stocking of fish 

in Atlantic salmon rivers in order to minimize any potential impacts of stocking on Atlantic 

salmon. Under the MOA, biologists from ASC and IFW are to meet annually to review existing 

stocking programs and assess the potential affects of these introductions on Atlantic salmon 

populations. ASC and IFW staff have met annually since 2001 to discuss and review stocking 

and data collection plans and resolve concerns about potential interspecific conflicts. 

In addition to potential adverse ecological impacts, stocking of game fish into rivers supporting 

wild salmon may increase the potential for incidental take of Atlantic salmon by anglers 

targeting these species. The Services should work with the State of Maine to assess the need to 

develop a Section 10(a)(1)(B) permit for existing stocking programs, and if appropriate, assist in 

the development of such a permit. On the West Coast, NMFS has worked with states to develop 

habitat conservation plans under Section 10(a)(1)(B) of the ESA for stocking programs that had 

the potential to adversely affect listed Pacific salmon66. Under the ESA, Section 7 consultations 

provide another means to develop responsible alternatives to the potential impacts stocking may 

have on Atlantic salmon. NMFS has also conducted Section 7 consultations on the West Coast 

for federal stocking programs for species such as trout that might interact with listed salmon and 

result in take. 

Recovery Actions: 

3.2.1A Review existing stocking programs and assess the potential impacts of 

these introductions on Atlantic salmon populations and ways to minimize 

potential adverse affects 

3.2.1B Monitor potential adverse interactions of existing stocking programs for 

freshwater salmonids in Atlantic salmon river drainages and fully assess 

the potential impacts of these programs on the DPS 

3.2.1C Suspend stocking of brown trout immediately in all DPS rivers until the 

potential impacts of these introductions can be fully assessed 

 

66 In some cases, NOAA-Fisheries has tried to eliminate or dramatically reduce stocking programs that were 

thought to cause adverse ecological or genetic impacts. In other cases, mitigation has been required. For 

example in California, striped bass are stocked into the Sacramento and San Joaquin rivers and delta. 

Striped bass eat juvenile salmon. The NOAA-Fisheries worked with the State of California to develop an 

ESA Section 10 permit to address the incidental take of listed salmon caused by this stocking program.
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3.2.1D Monitor potential adverse interactions of existing stocking programs for 

freshwater salmonids (i.e., splake, landlocked salmon, brook trout) in 

headwater lakes of DPS rivers to determine the potential impacts of these 

programs on the DPS 

3.2.1E Develop a Section 10(a)(1)(B) habitat conservation plan for existing 

stocking programs and, if warranted and implement 

3.2.2 Monitor populations of introduced non-salmonid species and implement 

management controls when appropriate and feasible 

The ASC and IFW should continue to monitor populations of introduced species such as 

smallmouth bass and largemouth bass and implement management controls when appropriate 

and feasible. The State should continue to enforce laws regulating the introduction of fish 

species to water bodies within the State. Violations of these laws should be prosecuted and 

appropriate fines and penalties imposed. Maine IFW has removed the size and bag limit on 

smallmouth bass in the Pleasant and Dennys Rivers and is in the process of extending this 

regulation to Old Stream, New Stream, and Northern Stream. Selected headwater lakes in the 

Machias and East Machias watersheds are managed for quality sized bass. The IFW has 

proposed a no minimum length/bag limit on bass and pickerel in the main stem of the Sheepscot 

from the Route 105 Bridge to the head of tide and on the West Branch from Branch Pond to the 

confluence with the Main stem. 

4. Reduce risks from commercial aquaculture operations 

Potential interactions between wild Atlantic salmon and salmon aquaculture represent a 

significant threat to the continued existence of the DPS (65 FR 69459; NMFS and FWS 

1999)(see pages 1-78 to1-86). There is substantial documentation that escaped farmed salmon 

can adversely affect wild salmon populations through ecological, genetic and disease related 

effects (Fleming et al. 2000; DFO 1998; Clifford et al.1997; Skaala and Hindar; Carr et al. 1997; 

Crozier 1993; Youngson et al. 1993; Lura and Saegrov 1991; Saunders 1991; Windsor and 

Hutchinson 1990). 

The following recovery actions are necessary to minimize the threats posed by the U.S. salmon 

aquaculture industry to the Gulf of Maine DPS of Atlantic salmon. These actions include 

measures to minimize the likelihood of incidental take or harm from the accidental release of 

aquaculture salmon as well as measures needed to minimize the threat of disease and parasites to 

the DPS. 

4.1 Improve containment at existing and future marine sites 

In January 2001, the EPA delegated authority to the State of Maine to administer the CWA, 

National Pollutant Discharge Elimination System (NPDES) program67. An MEPDES general 

 

67 The EPA retains oversight of this program. 
4-54

permit for Atlantic salmon aquaculture was finalized in 2003 and includes special conditions for 

protection of endangered Atlantic salmon. These conditions focused on finfish aquaculture 

operations in four primary areas: (1) fish husbandry and culture; (2) loss prevention through 

audited containment practices; (3) marking cultured fish to identify the origin of escapes; and (4) 

use of only North American strains of Atlantic salmon. 

As part of these new MEPDES permit requirements, all Atlantic salmon aquaculture facilities are 

required to use a fully functional marine containment management system (CMS) designed, 

constructed and operated to effectively achieve zero escapement of fish from the facility. All 

cages should be designed appropriately and mooring systems should be adequately designed, 

deployed and maintained. All aquaculture facilities should maintain permanent records of their 

containment systems to track cage history, the types of cages on each site, date of manufacture, 

date of installation, modifications and repairs and inspections. These records are available to the 

Services upon request. 

Siting and equipment are also very important parts of the permit requirements issued from DMR 

and the ACOE. For an aquaculture facility, an applicant must conduct a baseline assessment68 of 

the site and demonstrate that the leased area is suitable for establishing net pen salmon farming. 

The applicant must demonstrate the equipment (i.e., moorings, and cages) proposed for use at the 

site is suitable to withstand environmental conditions typical of the area. This evaluation is 

needed to minimize the risk of catastrophic loss at a site due to net-pen failure during times such 

as extreme tides, wind, icing or a storm event. 

Presumably, many of the threats (i.e., disease and/or parasite transfer, ecological interactions) to 

endangered salmon posed by aquaculture could be reduced by placing marine cages at greater 

distances from DPS rivers. Establishing a buffer between DPS rivers and marine cages may 

reduce the potential for diseases and parasites to be transferred to wild salmon migrating past 

marine cages from the river to the ocean or upon return. In addition, locating marine net-pens 

further from DPS rivers could reduce the likelihood of farmed fish imprinting on odors from the 

river and homing to that river in the event of an escape. Unfortunately, the areas suitable for 

marine cage culture with existing technology largely coincide with areas used by wild fish. 

While some countries have established “aquaculture free” zones for the protection of wild fish, 

establishing such zones in Maine would be difficult and at this point have been determined not to 

be necessary for recovery of the DPS. 

In 2001, the National Fish and Wildlife Foundation (NFWF) provided a $500,000 grant to the 

Maine Aquaculture Association (MMA) designed to help the aquaculture industry address 

containment concerns and develop a marking program (see below). Under the NFWF grant, an 

advisory committee and two working groups were established. The working groups include a 

 

68 The baseline assessment of a proposed facility is also necessary to document potential future impacts to 

water quality or the benthic environment. Flushing must be adequate to minimize the potential for 

degradation of the site. The DMR conducts routine benthic monitoring of on-site environmental conditions 

in proximity to marine net-pen sites under the Finfish Aquaculture Monitoring Program (FAMP). This 

program is necessary to ensure that aquaculture operations do not degrade the environment. 
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marking working group and a containment working group. The containment working group 

addressed containment at both marine sites and at freshwater hatcheries. The containment 

groups used the Hazard Analysis Critical Control Point (HACCP) approach to identify and 

implement BMPs at critical control points. The containment working groups have developed a 

generic HACCP plan that now serves as the framework for site-specific plans at every facility (as 

now required by MEDPES permits). The marking working group is evaluating various marking 

techniques that would allow assessment of containment measures. 

To assist in the development an integrated CMS program for the Maine salmon farming industry, 

some marine and hatchery facilities participated in a trial audit period to refine the essential 

components of an effective containment program. Since the inception of the CMS program 

(2003), all active hatcheries and marine farm sites have been audited through an interagency 

collaborative process involving DMR, DEP and NMFS personnel. 

All salmon aquaculture facilities are required to develop an integrated CMS plan for the facility. 

The CMS plan should consist of management and auditing methods to describe or address the 

following: inventory control procedures, predator control procedures, escape response 

procedures, unusual event management, severe weather procedures and training. The plan 

should include a schedule for preventative maintenance and inspection of the facility’s 

containment systems. The CMS should address all the steps involved in the commercial 

culturing process and the potential for losses at each of these points should be identified through 

a hazard analysis. The CMS should include a facility specific list of critical control points (CCP) 

where escapes could potentially occur. Each CCP should address the following to minimize the 

risk of escapement: specific location, control mechanisms, critical limits, monitoring procedures, 

appropriate corrective actions, verification procedures that define adequate CCP monitoring and 

a defined record keeping system. The facility shall report any known or suspected escapes of 

more than 50 fish with an average weight of 2 Kg each or more within 24 hrs to the appropriate 

personnel immediately. The CMS will be audited at least once per year and within 30 days of a 

reportable escape to evaluate the efficacy of containment measures in place and compliance with 

monitoring critical limits and taking appropriate corrective actions in accordance with best 

management practices specified in the CMS plan. Any equipment failure or other losses should 

trigger a corrective action needed to immediately stabilize the situation; upon further evaluation 

of these measures, any deficiencies noted should be corrected immediately to prevent further 

loss. 

All salmon aquaculture facilities are required to develop and maintain an inventory tracking 

system that allows clear, accurate inventory tracking of all size classes (i.e. average weight and 

age) of Atlantic salmon, including documentation of mortality events and any escapes. Each 

facility should have an inventory tracking system as a means to track all fish on site. The 

inventory tracking system should account for how many fish are stocked at the site originally, 

how many are harvested for sale, and, if that number differs, where the losses are accounted for. 

Mortalities should also be recorded and accounted for. Inventory measures should include 

marking of all fish before they are stocked into marine net-pens. Marks should be permanent 

and identify the fish to its facility of origin. This information should be provided to the 
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appropriate permitting agencies (e.g., ACOE and DEP) electronically on a monthly and per-pen 

basis, clearly identifying the total number of fish, number of smolts transferred, fish harvested, 

mortalities and escapes. This information, along with the containment audit results, will assist in 

evaluating the effectiveness of the containment management system. 

Permitting agencies should provide an annual report to the Services. The report should include: 

species authorized and presently cultured; number of fish produced; information on stocking 

(i.e., number, size, age) and harvesting (i.e., number, size, age); current equipment used; number 

of aquaculture fish accidentally released and how; presence of ISAV and disease treatments 

implemented; and the incidence of predator attacks. This report should also include documented 

mortality and the number of unaccounted fish. 

In addition to containment failures caused by mechanical or human error, seal attacks on net-pen 

sites may result in damage to nets and allow farmed salmon to escape. The interactions of seals 

and net-pens should be documented and monitored. The NMFS is working with researchers at 

UM to investigate some of these issues. Nelson (2004) examined the nature and frequency of 

seal predation at aquaculture facilities and whether the severity of seal predation was related to 

the proximity of seal haul-out sites at net pens. Neslon found that the further away that a net pen 

site was located the less likely it was to experience seal predation. Nelson (2004) concluded that 

aquaculture sites located further than 4.75 – 5 km away from a seal haul out site were at a 

substantially reduced level of risk for seal predation. 

In 1996, NMFS, under the auspices of Section 120(h) of the MMPA, established a task force to 

examine the problem of seals interacting with aquaculture resources in the Gulf of Maine and 

recommend measures to mitigate the interactions (NMFS 1996). The Task Force’s report 

discusses a number of regulatory, technological and financial issues related to the development 

of measures to minimize these interactions. These included net design, deterrence measures, 

research and interagency and international cooperation needs. These recommendations should 

be reviewed and fully implemented as appropriate. Section 101(a)(4) of the MMPA was 

established for the protection of self, public property and private property. Individuals can take 

necessary nonlethal steps to protect their property provided the animal is not injured or killed. 

Killing marine mammals to protect fishing gear or catch, including aquaculture, is prohibited by 

section 118(a)(5) and 101(a)(4) of the MMPA69. 

Recovery Actions: 

4.1A Evaluate new aquaculture lease and permit applications to ensure that netpens and equipment are adequate for site location and potential storm 

impact. 

 

69 Prior to the 1994 amendments, the MMPA authorized fishermen, including aquaculture operators, to use 

injurious or lethal force to prevent mammals from damaging gear or catch. 
4-57

4.1B Develop fully functional containment management systems for the 

containment of farmed salmon at marine sites. 

4.1C Develop and implement Containment Management System plans for all 

salmon aquaculture facilities 

4.1D Develop and maintain an inventory tracking system for all aquaculture 

facilities 

4.1E Assess, document and monitor damage caused by seal predation that may 

lead to the escapement of farmed salmon into the environment 

4.2 Minimize the effects of escaped farmed salmon 

As noted, escaped farmed salmon may adversely affect wild salmon through ecological, genetic 

and disease effects (see page 1-79). The Atlantic salmon industry in Maine is concentrated in 

Cobscook Bay in Washington County (see page 1-78). Five of the DPS rivers (Dennys, East 

Machias, Machias, Narraguagus and Pleasant rivers) are in close proximity to marine cages. The 

Dennys River is most likely to be impacted by escapees from marine cages due to the high 

density of cages in Cobscook Bay and Passamaquoddy Bay (Canada). All DPS river populations 

are at a heightened risk due to low numbers of wild adult returns. In the Pleasant and East 

Machias river watersheds, this threat has been exacerbated by the escape of juvenile salmon from 

commercial freshwater hatcheries in these watersheds (see page 1-81). 

4.2.1 Develop and implement contingency measures in case of accidental release of 

farmed fish 

All aquaculture facilities should develop contingency plans in case of an accidental release of 

farmed salmon. In developing site-specific Containment Management System plans, facilities 

should identify what methods of recapture of escaped fish are appropriate for their facility and 

surrounding waters. Recapture of escaped farmed salmon present a number of difficulties 

including unknown dispersal rates of escaped salmon and possible accidental take (seasonally) of 

DPS salmon. The potential risk for the accidental capture of wild DPS fish would need to be 

evaluated for each recapture method and procedure. All necessary equipment and permits should 

be acquired in advance of an event actually occurring. Contingency measures should include 

immediate notification of state and federal authorities if loss or escape of farmed salmon occurs. 

In addition federal and state biologists should develop contingency plans for the recapture of 

escaped farmed salmon in estuarine and freshwater habitats. 

4.2.2 Maintain existing weirs on DPS rivers and establish additional sites as 

needed 

Information on escaped farmed salmon provides a measure of the success of aquaculture 

containment systems. Seasonal fish weirs can help reduce opportunities for aquaculture escapees 
4-58

to interact with wild salmon in DPS rivers. Seasonal weirs, while deployed (from late April, 

early May to mid- to late November), reduce the likelihood that aquaculture escapees will enter 

DPS rivers, thereby reducing the potential for interbreeding and habitat competition between 

farmed salmon and wild salmon. 

Fish weirs perform several important functions for the recovery of the DPS including exclusion 

of aquaculture escapees from DPS rivers and assessment of wild populations. Weirs enable 

biologists to examine migrating adults and deny aquaculture escapees passage upstream to 

spawning sites. In addition to helping exclude escaped aquaculture salmon, weirs enable ASC to 

collect valuable data such as the numbers, source and condition of returning adults. This 

information is used to monitor the abundance of wild stocks and properly manage the 

populations (see Section 7). 

Accurate screening of fish at weirs is essential. Screening involves observation of phenotype 

including body-shape and existence of fin deformities along with scale reading used to age fish 

and determine their origin (i.e., wild or farmed). Two types of errors are possible, aquaculture 

fish can be allowed upstream and potentially spawn, or DPS fish can be prevented from 

migrating upstream. Both types of screening errors can be minimized through the use of 

accurate screening protocols, such as the ones developed by ASC and marking of aquaculture 

fish. Accurate screening protocols will increase the ability to correctly identify salmon collected 

at weirs. Screening protocols must balance the necessity of minimizing mortality and handling 

of fish at the weirs with reducing the potential for screening errors. 

The construction, operation and maintenance of weirs on the Dennys, East Machias, Machias, 

Pleasant and Narraguagus rivers has been an important component of the efforts to conserve and 

restore wild Atlantic salmon in Maine (MASCP 1997). Seasonal trapping facilities are located 

on the Narraguagus, Pleasant and Dennys rivers. Plans to construct a weir on the East Machias 

River have been delayed due to local concerns and denial of a permit by the Town of East 

Machias to construct the weir. Weirs should be constructed with state-of-the-art technology and 

operate continuously from ice out to ice in and effectively without hindering the passage of wild 

Atlantic salmon. The need to construct a weir or fish trap on the Machias River should be 

evaluated. Bad Little Falls, located at the mouth of the Machias River, may serve as a natural 

barrier to aquaculture fish. As previously noted (see page 1-51), concrete defectors were built to 

provide eddies and resting areas for salmon moving upstream through the gorge at Bad Little 

Falls in order to facilitate upstream fish passage. 

Recovery Actions: 

4.2.2A Maintain existing weirs on DPS rivers to minimize aquaculture escapees 

spawning, enable data collection and collect broodstock 

4.2.2B Construct weirs on DPS rivers, including the East Machias and Machias 

rivers, where necessary to exclude aquaculture escapees, enable data 

collection and collect broodstock 
4-59

4.2.3 Mark all farmed salmon prior to placement into marine net-pens 

The marking of aquaculture fish will assist biologists to accurately screen fish captured at weirs. 

Marking of aquaculture fish will help minimize handling and mortality of wild salmon at the 

weirs and reduce the potential for screening errors (see above). Quick and positive identification 

at the weir is critical to allow wild fish to be passed upstream and aquaculture escapees to be 

denied passage upstream. 

Each farmed Atlantic salmon should carry a mark to identify its facility of origin. Fish should be 

marked before being stocked into a net-pen. Marks should be permanent and, if internal, the tag 

should be detectable visually or by means of a mechanical or electronic device (e.g., fish should 

not have to be killed to detect tag). Marks should be detectable with minimum handling of fish. 

Salmon are often trapped at very high water temperatures (>22oC) which is stressful for the fish. 

Prior to stocking, the mark should be filed with the appropriate permitting agencies and a record 

of the marks maintained by the aquaculture company. Such a mark will help identify escaped 

fish at weirs and other sorting sites. This will facilitate the identification and correction of 

containment failure. 

The marking of aquaculture fish should be coordinated with Canadian authorities and the 

Canadian aquaculture industry if possible. Such discussions could occur under the auspices of 

the North American Committee (NAC) of NASCO to which the U.S. and Canada are members. 

As noted, in 2001, the National Fish and Wildlife Foundation (NFWF) provided a $500,000 

grant to the Maine Aquaculture Association (MMA) designed to help the aquaculture industry 

address containment concerns and develop an effective marking program. Under the NFWF 

grant, an advisory committee and two working groups were established. The working groups 

include a marking/tagging working group and a containment working group. The marking 

working group is currently evaluating various marking techniques that would allow assessment 

of containment measures. 

In accordance with MEPDES permit conditions fish introduced into net pens must be marked to 

designate their origin so that in the event they escape or are released from a marine facility they 

may be identified. Timelines are established for achieving several levels of mark specificity, 

however the specific marking technique or strategy is not specified. All marks, however, must 

be approved by the MEDEP before use. 

4.2.4 Discontinue the culture of non-North American salmon 

The use of reproductively viable non-North American Atlantic salmon stocks by the aquaculture 

industry should be discontinued immediately at all aquaculture facilities70. Non-North American 

stock is defined as any Atlantic salmon (Salmo salar) that contains genetic material derived 

 

70 According to MEDEP permits, no further stocking of NNA salmon will be permitted after July 31, 2004 

and all NNA salmon out of pens by Sept. 15, 2006. 
4-60

partially (hybrids) or entirely (purebreds) from any Atlantic salmon stocks of non-North 

American heritage, regardless of the number of generations that have passed since the initial 

introduction of the non-North American genetic material. 

Genetic analysis demonstrates that North American and European Atlantic salmon are 

genetically distinct (NRC 2002, and references therein). Interbreeding between an escaped 

Atlantic salmon of European-origin and a DPS fish could lead to the introduction of non-native 

genetic material that is not adapted to DPS river populations. 

4.2.5 Prohibit the placement into marine net-pens of reproductively viable 

transgenic salmon 

The use of reproductively viable transgenic salmonids should be prohibited within the DPS at all 

aquaculture facilities where an escapement may result in potential interactions with wild Atlantic 

salmon until a full risk assessment is conducted. Transgenic salmonids are defined as species of 

the genera Salmo, Oncorhynchus and Salvelinus of the family Salmonidae that contain within 

their DNA copies of novel genetic constructs introduced through recombinant DNA technology 

using genetic material derived from a species different than the recipient. The consequences of 

potential interbreeding between an escaped transgenic salmonid and a wild Atlantic salmon 

could be significant. The MEPDES permits prohibit the use of transgenic salmon. 

4.2.6 Continue research into developing strains of aquaculture fish that cannot 

interbreed with wild fish 

One potential means to reduce the genetic threat of interbreeding between wild and domesticated 

salmon is to develop and raise fish incapable of successfully reproducing. The effectiveness of 

methods to sterilize Atlantic salmon varies greatly (i.e., sterilization is not always successful). 

This should be considered when assessing whether the use of sterilized fish will minimize the 

risk of interbreeding between wild and farmed fish. 

Experiments have been conducted in rearing sterile triploid71 Atlantic salmon for use in 

commercial culture in order to reduce the potential for genetic interaction with wild stock. While 

growth and survival in freshwater has been demonstrated to be comparable to diploid strains, 

mortality during the transition to marine cages has been higher and deformities among triploids 

remain a major concern (O’Flynn et al. 1997). An evaluation of the use of sterile triploid 

Atlantic salmon was undertaken from 1994-1998 by the Marine Laboratory in Aberdeen, 

Scotland. Performance trials in Ireland and Norway demonstrated that triploids grew similarly 

and survived as well as diploids in freshwater. In sea water, triploids grew similarly to diploids 

but suffered higher losses in half of the trials (The Salmon Research Agency of Ireland 

Incorporated 1998; Marine Laboratory Aberdeen 1998). 

 

71 Triploid refers to having three copies of each chromosome rather than the normal two copies (i.e., diploid).
4-61

The United States Department of Agriculture (USDA) has initiated a breeding program to assist 

in the development of suitable North American strains of Atlantic salmon for use in aquaculture. 

Recent work on different genetic strains underway at the Huntsman Marine Science Center 

(HMSC) in St. Andrews, Canada has produced some promising results. Researchers at the 

HMSC and USDA facility are working with sterile triploid salmon of the “Cascade” strain, 

believed to be of Gaspé Peninsula origin. These fish have reportedly performed well in seawater 

for growth and survival (Fred Whorisky, ASF, personal communication). These fish may be a 

feasible alternative to reproductively viable strains of domesticated Atlantic salmon now used by 

the aquaculture industry. Continued research in this field is encouraged. It is also important to 

note that while triploidy may be effective in preventing interbreeding between escapees and wild 

fish, sterile escapees may still disrupt the breeding of wild fish and compete for food and habitat. 

4.3 Minimize risks of disease and parasite transmission from farmed fish in 

marine pens to wild fish 

Atlantic salmon are susceptible to a number of diseases that can result in direct or indirect 

mortality (see pages 1-58 to1-65). 

4.3.1 Minimize risk of disease transmission 

All aquaculture facilities should develop and adhere to stringent pathogen monitoring protocols 

to minimize the risk of disease transmission from farmed salmon to wild Atlantic salmon 

including those required by the Maine DMR and USDA APHIS ISAV programs. Monitoring 

results should be provided to the Services. 

All aquaculture facilities should develop remedial action plans in the case of a confirmed case of 

ISA. Copies of these plans should be provided to the Services. Site-specific remedial action 

plans should be fully and immediately implemented when necessary. 

The USDA APHIS, at the invitation of the Maine DMR, has taken the lead in developing 

standard operational procedures designed to minimize potential outbreaks of ISA. Proposed 

management measures to reduce the current biomass loading of Cobscook Bay include reducing 

stocking densities and alternate year stocking in different management zones. Single generation 

management can reduce the risk of disease transfer between year classes. These measures were 

implemented by DMR for Cobscook Bay in 2002. 

The discharge of processing wastes and therapeutic compounds not approved by FDA or EPA 

should be prohibited. All aquaculture facilities should implement strict controls preventing the 

discharge of blood and other potential infectious material. 

Integrated single bay management plans can help reduce the disease risk posed to wild fish from 

farmed Atlantic salmon. Under such a management plan, all the growers within a bay coordinate 

stocking densities, disease treatments, fallowing and harvesting of fish. Coordination among 

growers within a bay has benefits both to the commercial industry and to wild fish. This method 
4-62

can reduce the risk that aquaculture operation will result in a degradation to the environment or 

other resources within the bay. The development of such plans should be encouraged where 

commercial sites are already in operation and should be a requirement before any cages are 

placed in an unoccupied bay. 

The U.S. salmon aquaculture industry and regulatory agencies should develop comprehensive 

bay management plans for all areas used by the Maine salmon farming industry. The plans 

should include, but not be limited to: 

• a concise description of the bay/area in terms of physical characteristics, history, 

aquaculture operations, future potential/carrying capacity, potential user conflicts and 

problems 

• integration of codes of practice for current aquaculture operations and translation of those 

codes to the specific circumstances of each bay or coastal region 

• a development plan for any future aquaculture activities in the bay 

• address other resource use and activities in the bay including culture of species other than 

salmon. 

The development and implementation of bay management plans will need to be coordinated with 

Canadian authorities and the aquaculture industry72 if disease risks are to be effectively 

minimized. 

Other protocols and guidelines (e.g., AFS/FHS, NESFH, NASCO, see page 1-40) also exist to 

help minimize the risk of disease transmission to wild fish. These should continue to be 

enforced. Federal import regulations (Title 50) currently apply only to a limited number of 

pathogens. This regulation should be revised to include the ISA virus and other salmonid 

pathogens that may be identified in the future. The NESFH guidelines and the NASCO 

protocols should be maintained and updated to continue to provide protection from diseases that 

are especially lethal and difficult to control, such as IHN which is currently limited to salmonids 

found west of the Rocky Mountains, and non-marine VHS which occurs in European and other 

countries. Appropriately, these pathogens, along with ISA virus, are addressed as exotic diseases 

of regulatory concern by the Maine Department of Marine Resources Salmonid Fish Health 

Inspection Regulations. 

The FWS established the National Wild Fish Health Survey (Survey) and its associated database 

in 1997 to determine the national distribution of disease associated fish pathogens. In 1999, due 

to the realization of this disease’s threat to wild salmon, ISA virus (and its established, 

standardized laboratory procedures for detection) was added to the Survey as a Pathogen of 

Regional Concern. Through the Survey, cooperating resource agencies have and continue to 

provide health samples from fish collected from the DPS rivers. 

 

72 As noted (see page 1-59), most aquaculture in Atlantic Canada occurs in the lower Bay of Fundy, where there are an 

estimated 60 facilities. There are a large number of aquaculture sites on the Canadian side of Cobscook and 

Passamoquoddy Bays, where they have the potential to affect U.S. aquaculture sites in these bays.
4-63

Research is also needed on the migration patterns of early post-smolts in the Maine coastal area 

to better understand the relationship of migration to net-pen locations and the extent to which 

wild fish may be vulnerable to exposure to ISA. 

As discussed (see page 1-64), another potential mode of disease transmission is through 

biological sampling conducted by various state and federal agencies in DPS rivers. The 

development and implementation of disinfection and biosecurity protocols reduces the risk of a 

pathogen being moved from one location to another (G. Russell Danner, IF&W fish pathologist, 

personal communication 2004). Disinfection and biosecurity protocols, where not already in 

place, should be developed and implemented for all research and sampling activities taking place 

in rivers within the DPS. 

Recovery Actions: 

4.3.1A Develop and implement a comprehensive disease management plan that 

includes siting and standard operational procedures to minimize outbreaks 

of ISA. This plan should also include procedures for identifying, 

reporting and controlling outbreaks 

4.3.1B Develop and implement comprehensive integrated bay management plans 

that include coordination of stocking densities, harvesting and fallowing 

and disease treatment and management 

4.3.1C Revise federal import regulations (Title 50) to include the ISA virus 

4.3.1D Maintain and update existing fish health guidelines and protocols as 

necessary, to control the introduction of new pathogens and continue to 

provide protection from disease 

4.3.1E Expand the FWS Wild Fish Health Survey to include DPS rivers 

4.3.1F Implement biosecurity and disinfection protocol for all research and 

assessment activities being conducted in rivers within the DPS 

4.3.2 Conduct research on endemic and exotic salmonid pathogens to reduce the 

potential of disease transfer from farmed fish to wild Atlantic salmon 

Research on the ISA virus should be continued, including the role of other fish species (both 

domesticated and wild) and sea lice as potential reservoirs and vectors of ISAV. The survey of 

diseases in free ranging marine and anadromous fish is important to understand the role of other 

species as potential vectors and to evaluate the potential for cross-species transfer of disease. 

Resident and migratory fish species in aquaculture production bays should be monitored for 

endemic and exotic salmonid pathogens. 
4-64

Research is also needed to better understand the potential for wild salmon to contract the virus 

from infected net-pen sites. Research on detection and prevention of salmonid diseases should 

continue. 

In laboratory studies, rainbow trout and brown trout have been shown to be asymptomatic 

carriers of ISAV that can transmit the virus to salmon by co-habitation (Nylund and Jakobsen 

1995; Nylund et al. 1995; Nylund et al. 1997) (see page 1-61). The expansion of marine rainbow 

trout culture should be prohibited until the Maine Fish Health Technical Committee, state and 

federal biologists have evaluated the disease risk posed by the culture of salmonid species other 

than Atlantic salmon. 

Vaccination technology for Atlantic salmon diseases, including ISAV, should continue to be 

improved. More effective vaccines and efficient delivery techniques may help reduce the 

potential for breakouts in net-pens and reduce the potential for this disease to adversely affect the 

DPS. The potential to vaccinate Atlantic salmon against other salmonid pathogens should also 

be investigated and current vaccination programs should be continued. 

The presence of SSSV in the DPS was cited as a listing factor for the DPS. The current 

distribution of this virus within the DPS should be determined. The potential for this disease to 

affect net-pens and adversely affect the DPS should also be investigated. 

Recovery Actions: 

4.3.2A Determine the modes of transmission of the ISA virus 

4.3.2B Continue to investigate the role of sea lice and wild fish species as 

potential reservoirs and vectors of ISA 

4.3.2C Initiate screening and long-term monitoring of resident and migratory fish 

in aquaculture production bays for endemic and exotic salmonid 

pathogens 

4.3.2D Continue active research programs on immunization of farmed fish 

4.3.2E Develop an effective diagnostic technique for the SSS virus and determine 

the distribution of SSS virus within the geographic range of the DPS 

4.3.3 Reduce the potential for sea lice outbreaks in farmed and wild salmon 

populations 

The potential of sea lice to adversely affect the DPS and the role of salmon aquaculture sites as a 

reservoir for this parasite should be investigated. Wild salmon are vulnerable to sea lice 

infestation originating from aquaculture facilities (see page 1-84). Ongoing sampling of 

outmigrating salmon smolts in Penobscot Bay and the adjacent nearshore marine environment 
4-65

has not detected significant sea lice burdens on outmigrating Atlantic salmon (see page 1-83).73

Aquaculture facilities should regularly test and report sea lice burdens at net-pen facilities. 

Acceptable sea lice burden guidelines should be established based upon the best available 

information. 

The aquaculture industry currently monitors for sea lice infestations and treats infected fish. The 

Maine aquaculture industry uses emamectin benzoate (brand name SLICE) to treat sea lice as 

part of an FDA trial to test the effectiveness and safety of this new animal drug. Because farm 

raised salmon are classified as a food-producing animal, drugs must also be tested for safety to 

human consumers. The first step in this process is the Investigational New Animal Drug 

exemption (INAD) (United States Food and Drug Administration (FDA) website). SLICE is 

used in Maine under an INAD exemption (U Maine website). SLICE is administered to Atlantic 

salmon orally as an in-feed treatment, eliminating the mass discharge of therapeutant into the 

ocean as with the previously used sea lice treatment, cypermethrin (brand name Excis)74. SLICE 

treatment prevents recruitment of new lice for ten weeks which can allow the cycle of 

reproduction to be broken (Stone et al. 2000). This treatment could be especially promising if 

used strategically in a whole bay or system. Since sea lice have been implicated in the 

transmission of ISAV, control of lice is important to the industry and recovery efforts. 

A number of preventative measures can be taken to minimize the potential for sea lice 

originating from salmon aquaculture facilities to adversely affect wild Atlantic salmon. Single 

bay management has been effective in helping to reduce the frequency and extent of sea lice 

outbreaks. Among these management techniques are fallowing, single year class stocking, 

density and siting (see page 4-61). 

Recovery Actions: 

4.3.3A Investigate the potential of sea lice to adversely affect the DPS and the 

role of salmon aquaculture sites as a reservoir for this parasite 

4.3.3B Regularly test and report sea lice burdens at individual net-pen facilities 

4.3.3C Continue treatment for sea lice at aquaculture facilities 

 

73 As noted (see page 1-83), Penobscot Bay is not in the proximity of aquaculture marine net pens. Postsmolt trawling has not been conducted in Cobscook Bay where the aquaculture industry is currently 

concentrated. Sampling of salmon taken in the West Greenland fishery has found some fish carrying 

significant sea lice burdens - fish with fifty or more lice concentrated around the vent of the fish (Russell 

Brown, NMFS, personal communication). 

74 Previously, the aquaculture industry in Maine used Excis to treat sea lice. The treatment process includes 

placing a tarpaulin under the net-pen and drawing the net upwards reducing the volume of water the fish 

are held in. This reduces the amount of chemical needed to reach the desired concentration for effective 

treatment. After the appropriate treatment duration the tarpaulin is removed. This treatment methodology 

results in the release of cypermethrin into the waters surrounding the pens (Milewski 2000). Cypermethrin 

is no longer used by the aquaculture industry in Maine. 
4-66

4.4 Reduce risk of juvenile escapement from freshwater aquaculture facilities 

into DPS rivers 

Juvenile escapees from freshwater aquaculture hatcheries may pose a larger threat to wild 

populations than escapees from net-pen sites (see page 1-85). A relationship between the 

reproductive success of cultured fish and the time the fish has lived in the wild before reaching 

sexual maturity has been demonstrated (Jonsson 1997). 

Until recently, five freshwater hatcheries in the United States provided smolts to the salmon 

aquaculture industry for stocking into marine net-pens. Two of these commercial hatcheries 

were operated on two of the DPS rivers (see page 1-78). Juvenile salmon of aquaculture 

hatchery origin have been documented in DPS rivers in Maine (see page 1-81). 

4.4.1 Ensure containment at existing and future freshwater aquaculture facilities 

accessible to DPS rivers 

The DEP is currently in the process of renewing the discharge permits for all freshwater 

hatcheries in Maine, including those used by the aquaculture industry. In October 2004, DEP 

issued a new permit to the Gardner Lake hatchery, requiring a fully functional CMS plan with 

escape reporting requirements. Furthermore, because it directly discharges to a DPS river 

(Chase Mills Stream, a tributary of the East Machias River) this hatchery is prohibited from 

possessing any non-North American salmon. 

All salmon aquaculture hatcheries should develop an integrated loss control plan for the facility. 

The plan should include a schedule for preventative maintenance and inspection of the facility’s 

containment system. The loss control plan should address contingency escape recovery 

protocols and facility husbandry practices. Husbandry practices include fish transfer procedures 

during grading and stocking. This plan should include all the steps involved in the commercial 

culturing process. An acceptable site-specific plan must include a facility specific list of CCPs 

where escapes have been determined to potentially occur. The potential for losses at each of 

these points should be identified and steps taken to minimize the risk of escapement. 

Freshwater aquaculture facilities are required to have annual audits to evaluate the adequacy of 

containment measures and compliance with best management measures. Any losses should 

trigger an evaluation of containment measures and any deficiencies should be corrected 

promptly. All aquaculture facilities should maintain permanent records of their containment 

systems to track the integrity of barriers, modifications, repairs and inspection of the facilities 

containment system. Records should be maintained on all containment systems and be made 

available to regulators upon request. 

All salmon aquaculture hatcheries should develop and maintain an inventory tracking system that 

allows clear, accurate inventory tracking of all size classes (i.e. average weight and age) of 

Atlantic salmon, including documentation of any escapes. The information should be provided 

to the Services on request, clearly identifying the total number of fish reared, number of smolts 
4-67

transferred and probable escapes. This information along with the audit results will assist with 

evaluating the effectiveness of the containment management systems. 

Recovery Actions: 

4.4.1A Develop and operate fully functional containment management systems 

for the containment of farmed salmon at freshwater hatchery sites 

4.4.1B Develop integrated loss control plans for all salmon aquaculture hatchery 

facilities 

4.4.1C Develop and maintain an inventory tracking system that facilitates the 

accurate tracking of total numbers of salmon smolts being produced by the 

hatchery 

4.4.2 Develop contingency plans to reduce adverse impacts if containment 

measures fail 

The potential for failure of containment measures at freshwater facilities needs to be anticipated 

and appropriate contingency measures developed. A contingency plan should be prepared so 

that measures can be implemented promptly in the event of catastrophic failure. The 

Containment Management System plans developed for each facility should include emergency 

response procedures designed to minimize escapes from the facility in the event the final 

containment barrier is compromised. 

5. Supplement wild populations with hatchery-reared DPS salmon 

In 1991, based on the recommendation of the Maine TAC, the current river-specific stocking 

program was initiated (see page 1-18). The river-specific stocking program stocks fish as fry as 

the primary management strategy to recover the DPS. Fry stocking minimizes the time that fish 

are held in captivity and reduces the opportunity for hatchery selection. 

5.1 Stock cultured fish in natal rivers to supplement contributions of wildspawned fish 

The numbers of fry stocked into a specific river are determined by ASC and approved by the 

TAC annually based on the available habitat and the amount of habitat not used for spawning the 

previous fall (i.e., the extent of underused habitat). 

The use of smolts (retaining fry in the hatchery until ready to migrate to sea as smolts) for 

stocking has been initiated on an experimental basis for the Dennys River. The advantage of 

using smolts is that the numbers of fish stocked is not limited by habitat capacity (as it is with 

fry) because smolts spend little time in the river before seaward migration. The disadvantages 

include (a) the need for significantly greater hatchery facility, staff and budgetary resources 
4-68

relative to fry production and distribution; (b) increased potential for hatchery selection to 

negatively affect genetic diversity; (c) less effective imprinting and resultant higher adult 

straying rate; and (d) reduced fitness in the wild as a result of conditioning to the hatchery 

environment (e.g., naivete relative to predator avoidance and foraging). A smolt stocking 

program in the Pleasant River has also been initiated. 

5.1.1 Maintain river-specific hatchery broodstock and continue to stock cultured 

fish in natal rivers 

River-specific broodstock should continue to be maintained at federal fish rearing facilities. 

Broodstock from six of the eight DPS river populations (Dennys, East Machias, Machias, 

Pleasant, Narraguagus and Sheepscot rivers) are maintained at the CBNFH. A broodstock 

program was not developed for the Ducktrap River and Cove Brook. The captive broodstock 

serve multiple purposes. They (a) provide a reservoir of diverse genetic material from the DPS 

to protect from catastrophic losses in the wild; (b) support river-specific stocking strategy to 

enhance juvenile population abundance; and (c) increase the effective spawning population size 

(Ne) of each DPS river population and the overall DPS to minimize loss of genetic diversity 

(genetic bottlenecks) associated with very small populations. 

Captive brood stock populations are maintained by annually collecting juveniles in the wild and 

rearing them to sexual maturity in the hatchery. Brood stock are genetically characterized prior 

to reaching sexual maturity to help guide hatchery spawning operations and insure siblings or 

closely related individuals are not mated, which would result in inbreeding and loss of diversity 

and fitness. Genetic characterization also allows discrimination of wild from hatchery-origin 

fish, thus enabling evaluation of stocking success. 

Hatchery-reared river-specific Atlantic salmon should continue to be stocked into DPS rivers to 

aid recovery of wild salmon populations. All federal fish rearing facilities needed for recovery 

of the DPS should continue to be operated. 

Recovery Actions: 

5.1.1A Continue operation of federal fish rearing facilities needed for recovery of 

the DPS, including maintenance of river-specific broodstock 

5.1.1B Continue stocking cultured fish to supplement wild salmon populations 

5.1.2 Monitor and evaluate the current stocking program 

The Services and ASC should continue to monitor and evaluate the current river-specific 

stocking program. The effectiveness and management advisability of river-specific stocking as a 

recovery strategy should be continuously reviewed and evaluated. The NRC (2004) concluded 

that there has not been an adequate assessment of whether returning stocked salmon contribute 

offspring to the next generation. The Services and ASC should also review the need for alternate 
4-69

stocking strategies (see below). The advisability of using smolts should continue to be evaluated 

as rearing facilities are expanded for possible smolt propagation. The need for a back-up 

hatchery facility, in addition to CBNFH, should be considered. Such a facility would provide an 

additional source of broodstock in case of a catastrophic event at CBNFH. 

5.1.3 Evaluate and implement, as appropriate, new stocking strategies 

New stocking strategies (i.e., alternate life-stage stocking, stream-side hatchery boxes, satellite 

hatcheries) should be evaluated in an effort to improve the survival of hatchery-reared Atlantic 

salmon after release. The appropriateness of stocking other life stages (parr, smolts, adults) 

should continue to be evaluated. The NRC (2004) concluded that there is an urgent need to 

understand the relative efficiency of the stocking of different life-stages of salmon in terms of 

adult returns and their reproductive success. 

The stocking of different life-stages within DPS rivers provides the opportunity to evaluate the 

management advisability of this stocking strategy. Since 2001, smolts and parr (byproducts of 

the smolt stocking program) have been stocked into the Dennys River as part of ongoing salmon 

research. A smolt stocking program has been initiated for the Pleasant River. As part of this 

program, parr were stocked into the Pleasant River beginning in Fall 2002. Smolt stocking begin 

in the Spring 2003. Fry stocking will continue in other DPS rivers providing the opportunity to 

compare the success of these alternate life-stage stocking programs. The evaluation of these 

alternate life-stage stocking program is critical for promoting recovery of the DPS and should be 

continued. These evaluations also provide the opportunity to evaluate the relative survival and 

return rates of stocking different life-stages. 

In 1997, the Services, the State of Maine and representatives of, at the time, the three largest 

salmon aquaculture companies (Atlantic Salmon of Maine, Heritage Salmon, Maine Aquafoods) 

implemented a cooperative program to preserve and rebuild endangered Atlantic salmon 

populations in Maine. The aquaculture industry raised river-specific Atlantic salmon for select 

rivers from eggs provided by the CBNFH to mature adults. Adults were stocked into the 

Dennys, Machias and St. Croix rivers. The objectives of this program were to 1) evaluate the 

feasibility of using river-specific marine-reared adult salmon to stock rivers and for these adults 

to successfully reproduce in their natal river, 2) as a gene banking program to protect against the 

loss of genetic material from these three populations in the event of a cataclysmic event at 

CBNFH, and 3) involve the industry in the restoration program. 

The initial results of the program were mixed. In 2000, a number of redds were constructed but 

no fry were collected during subsequent sampling of the redds. Based on the 2000 results, 

stocking logistics were modified for 2001. In 2002, researchers sampled redds on the Dennys 

and St. Croix rivers to capture emergent fry to evaluate the viability of the progeny. On the 

Dennys River, only nine fry were captured in fry traps, with an additional 43 being collected in 

rotary screw traps. On the St. Croix River, twelve redds were sampled at three sites. 

Researchers collected 8,000 fry at one site, with numbers being lower at the other two locations 

sampled. 
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The evaluation of the adult stocking program includes a number of projects to assess its potential 

to help rebuild and recover Atlantic salmon populations in historic habitat in Maine. Because 

this is a relatively novel technique, assessment and monitoring of the success of this program in 

producing Atlantic salmon is important and should be continued. 

The use of streamside incubation facilities is another stocking strategy that may enhance survival 

as well as add insurance against catastrophic losses due to hatchery accidents. Streamside 

hatchery projects offer a unique opportunity to involve the local public in the stocking program. 

Streamside incubation facilities would utilize river-specific water sources allowing for the 

evaluation of this factor. The potential use of streamside incubation facilities to enhance the 

effectiveness of juvenile stocking practices should be evaluated. 

Recovery Actions: 

5.1.3A Evaluate the role of alternate stocking strategies to supplement wild 

salmon populations 

5.1.3B Continue to assess and evaluate the results of the adult stocking program 

5.1.3D Evaluate the role of streamside incubation facilities to supplement wild 

salmon populations 

5.1.4 Evaluate the potential role of reintroduction in the recovery of the DPS 

The reintroduction of Atlantic salmon to streams and rivers within the DPS’s geographic range 

(see page 1-1) from which the species has been extirpated should be evaluated to determine the 

need to re-establish additional populations to recover the DPS. The PVA (see page 3-12) can be 

utilized to help explore relationships between the probability of persistence of existing 

populations and the role of the extirpated populations in the viability of the DPS. The PVA 

results will help inform management decisions regarding whether there is a need to re-establish 

populations into formerly occupied rivers and streams outside those currently known to have 

persisted. If reintroduction projects are proposed, all necessary environmental reviews will be 

conducted and the public will be provided an opportunity to review any such proposal at an early 

stage 

The eight DPS rivers known to still support wild populations of Atlantic salmon provide a 

relatively small potential carrying capacity when compared to the Penobscot and Kennebec 

rivers75. Table 2 provides estimates of habitat units76 present in river within the geographic 

range of the DPS. (see Table 2). In addition to the eight DPS rivers known to still support wild 

 

75 The total combined conservation spawning escapement (CSE) targets for these eight populations is 1482 

fish. 

76 One habitat unit = 100 m2

. 
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salmon populations, there are a number of small coastal rivers within the geographic range of the 

DPS from which wild salmon populations have been extirpated (Beland 1984; Baum et al. 1995). 

These small coastal river systems support additional unoccupied juvenile production habitat 

The estimated amount of habitat for the eight rivers within the range of the DPS known too still 

support wild salmon populations is 22,425 habitat units. The estimated amount of habitat found 

in small coastal rivers within the geographic range of the DPS from which wild salmon 

populations are believed to have been extirpated is approximately 24,688 habitat units77. 

One potential mechanism to facilitate reintroduction of salmon populations is the designation of 

experimental populations as provided for under Section 10(j) of the ESA. Establishment of 

experimental populations has the potential to contribute to recovery of the DPS in a number of 

ways. Examples of potential contributions include: 

• Providing opportunities for research on environmental factors that may be limiting 

survival at various life stages without risk to the remnant populations in the eight rivers 

(e.g., stocking strategies; impacts of contaminants - acidification of rivers, pesticides, 

habitat restoration techniques) 

• Serving as a hedge against catastrophic events (e.g., disease) that might threaten the riverspecific populations of endangered salmon currently maintained at the CBNFH 

• Decreasing the vulnerability of the DPS to extinction by increasing overall numbers of 

fish in the wild, at least in the short-term, while wild populations remain extremely low. 

Section 10(j) of the ESA authorizes the establishment of experimental populations to facilitate 

the recovery of endangered and threatened species. An experimental population is defined as 

Aan introduced and/or designated population (including any off-spring arising solely therefrom) 

that has been so designated in accordance with the procedures of this subpart but only when and 

at such times as the population is wholly separate geographically from non-experimental 

populations of the same species” (49 FR 33894). 

Experimental populations are classified as either “essential” or “nonessential.” An experimental 

population “whose loss would be likely to appreciably reduce the likelihood of the survival of 

the species in the wild” is classified as “essential” (49 FR 33894). All other experimental 

populations are classified as “nonessential” (49 FR 33894). The essential/nonessential 

classification influences how Section 7 of the ESA is applied to experimental populations. 

 

77 As noted, the Services have deferred a decision whether to include the mainstem of the Penobscot River 

and its tributaries above the former site of the Bangor dam pending further analysis (see page 1-3). 
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Table 2: Atlantic salmon habitat within the range of the Gulf of Maine DPS and other Maine Rivers78

Drainage Total Habitat Units 

Pennamaquan River 52 

Dennys River 2,152 

Grand Manan Channel Coastal79 3,674 

East Machias River 3,006 

Machias River 6,156 

Chandler River 167 

Roque Bluffs Coastal80 1,641 

Pleasant River 1,220 

Narraguagus River 6,014 

Tunk Stream 625 

Mt Desert Coastal 1805 

Union River 2594 

Kennduskeag 559 

Cove Brook 235 

Marsh Stream 3,490 

Passagassawaukeag River 331 

Ducktrap River 845 

Western Penobscot Bay Coastal 1,613 

Sheepscot River 2,797 

Central Maine Coastal (CMC)81 7,412 

Cobbosseecontee Stream 170 

Togus Stream 380 

Bond Brook 175 

 

Penobscot River 114,453 

Kennebec River 77,209 

Androscoggin River 46,472 

 

78 Estimates of habitat abundance are derived from stream survey data and a watershed area to habitat regression methodology developed 

by the NEFSC. 79 Grand Manan Channel Coastal includes Orange River and Hobart and Boyden streams 80 Roques Bluff Coastal includes Indian River 81 CMC Rivers: St. Georges, Medomak and Pemaquid rivers 
4-73

Essential experimental populations are treated as threatened species and subject to protection 

under both 7(a)(1) and 7(a)(2) of the ESA. Federal agencies are therefore required to engage in 

consultations with the Services to ensure their actions are not likely to jeopardize the continued 

existence of the species. Because essential experimental populations are treated as threatened 

species under the ESA, which allows the Services to establish special regulations in a 4(d) rule. 

The Services may use discretion as to the nature of the protective regulations and may exempt 

experimental populations from protection against any or all prohibited acts outlined in section 

9(1)(a). 

Nonessential experimental populations are treated as a species proposed for listing and are only 

subject to protection under 7(a)(4). Section 7(a)(4) requires federal agencies to conference with 

the Services when a proposed action is likely to jeopardize the continued existence of a species 

proposed for listing. 

Designation of an experimental population requires consideration of the following issues (50 

CFR 17.81(b): 

• Possible adverse effects on remnant populations as a result of removal of individuals or 

eggs 

• The likelihood that such an experimental population will become established and survive 

in the foreseeable future 

• The relative effects that the establishment of an experimental population will have on the 

recovery of the species 

• The extent to which the introduced population may be affected by existing or anticipated 

federal or state actions or private activities within or adjacent to the experimental 

population area. 

A process for periodic review and evaluation of the success or failure of the release and the 

effect of the release on the conservation and recovery of the species is also required. The 

Services must consult with appropriate state fish and wildlife agencies, local governmental 

entities, affected federal agencies and affected private landowners in developing and 

implementing experimental population rules. 

Production of Atlantic salmon in the river-specific hatchery program, in accordance with the 

broodstock collection, spawning, rearing and stocking protocols, results in unavoidable “surplus” 

broodstock production. Surplus is defined here as broodstock in excess of the biological 

carrying capacity of the native watershed of the broodstock. The Craig Brook NFH produces fry 

in excess of current stocking density demands for the DPS rivers. Both the broodstock and their 

offspring are afforded full protection under the ESA, therefore the Services are responsible for 

the disposition of “surplus” broodstock pursuant to the Interagency Policy Regarding Controlled 

Propagation of Species Listed under the ESA (65 FR 56916). Utilizing surplus hatchery 

products (e.g., surplus broodstock, eggs, fry) to re-establish populations where they are currently 

extirpated is consistent with the Services’ mandate to properly manage propagated species and 

recover the DPS. 
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The Services should evaluate whether the use of experimental populations will facilitate the 

recovery of the DPS. As part of this evaluation, the Services should consider criteria to identify 

candidate rivers for establishing re-introduced populations. In 2002, at the direction of the 

Signatories (ASC, NMFS, FWS), the TAC evaluated appropriate use and potential expansion 

beyond the rivers of origin for the Signatories. This document provides a rigorous examination 

of the technical merits of utilizing existing hatchery products that exceed current stocking 

density targets. This evaluation identified and prioritized potential rivers that could be 

candidates for utilization of these bonus fish. 

Recovery Actions: 

5.1.4A Evaluate the need to re-establish populations of Atlantic salmon in rivers 

within the DPS’s historic range from which river populations have been 

extirpated 

5.1.4B Evaluate whether the use of experimental populations will facilitate the 

recovery of the GOM DPS of Atlantic salmon 

5.2 Maintain Fish Health Practices to Minimize Potential Introduction of Disease 

to Hatchery Stocks and transmission to Wild Populations 

The FWS should continue to rigorously implement fish health practices to minimize potential 

introduction of disease to hatchery stocks and transmission to wild populations. FWS’s fish 

health practices to minimize disease threats and impacts on both captive and wild populations 

can be organized into three categories: fish culture management, health surveillance and 

research. 

5.2.1 Continue fish culture management practices at federal hatcheries to 

minimize the potential for disease 

Isolation of broodstock populations from each other at CBNFH is a key element in reducing 

disease risks. When fish captured from the wild are received at the facility, they are immediately 

isolated from other broodstocks and from different year classes of the same brood stock for a 

minimum of one year. This physical isolation includes use of separate equipment, separate water 

(filtered and disinfected with ultra-violet radiation) and strict sanitary practices, as outlined in the 

CBNFH Standard Fish Husbandry Procedures for Biosecurity, Best Management Plan for ISA 

virus and the Best Management Plan for SSS virus. 

5.2.2 Continue fish health surveillance efforts and implementation of fish health 

practices at federal hatcheries 

Brood fish collected from the wild are non-lethally screened for bacterial pathogens and ISAV 

upon arrival at the facility. All broodstock mortalities are tested for parasites, bacteria and 
4-75

viruses of concern (as well as any presently unknown pathogens or parasites). Fish are also 

sampled for vertically transmitted (from parent to offspring) pathogens at the time of spawning 

to reduce the risk of stocking diseased fish. Sampling is done in compliance with FWS Fish 

Health Policy, the New England Salmonid Health Guidelines and the IFW’s Salmonid Fish 

Health Inspection Regulations. In compliance with these policies, fry are inspected for 

replicating viral agents prior to release in the wild. All results from recent screenings have been 

negative. 

During a recent typical twelve-month period of fish health surveillance at CBNFH, sampling 

consisted of 210 mortalities monitored (representing 2.1% to 8.6% of the captive populations 

they originated from); ovarian fluids from 586 mature females (all of the listed stocks spawned 

and 148 Penobscot fish); 180 non-lethal bacterial (vent) cultures from recently captured wild 

young (future broodstock); and 420 lethal samples including fry from all river systems and adult 

Penobscot fish. During this period, Reverse Transcription Polymerase Chain Reaction (RTPCR) screening resulted in one ISA positive Penobscot River sea-run salmon. Follow-up cell 

culture did not confirm the initial result. During this same period, screening results for all other 

diseases of concern were negative. 

5.2.3 Continue research on fish health issues, detection and prevention 

The standard ISAV assay of cell culture using the Atlantic salmon head-kidney (SHK-1) cell line 

continues to be used for broodstock management purposes, but the 28-day time requirement is 

often too long to allow timely fish health management. In addition, the Lamar Fish Health 

Center (LFHC) is using RT-PCR for detection of ISAV and has begun using the Atlantic salmon 

kidney (ASK) cell line for ISAV assay, along with the OIE approved SHK-1 cell line. The ASK 

cells respond well and show effects of infection sooner than the SHK-1 cells. 

The laboratory has participated in quality assurance and quality control exercises to evaluate 

detection methodologies for ISAV with NMFS, the University of Maine, USDA-APHIS, DFOCanada and a private fish health diagnostic lab in Maine. Sample type (e.g., blood versus tissue), 

laboratory assay (PCR versus cell culture) and tissue transport medium (HBSS versus PBS) are 

parameters investigated through the use of blind samples consisting of presumed negative fish as 

well as experimental fish inoculated with ISAV. 

The Cornell University College of Veterinary Medicine has continued research on SSSV. It has 

mapped the entire genome of this retrovirus developed a PCR assay and completed an antibodybased (ELISA) assay for detection. The Lamar Fish Health Center has cooperated with the 

Olympia (Washington) Fish Health Center and USGS-BRD (Biological Resource Division) 

Seattle Science Center to coordinate testing of Penobscot Atlantic salmon for ISAV 

susceptibility with Pacific salmon investigations. The FWS should continue to support work on 

fish health issues, such as ISA and SSS detection and prevention through its Lamar Fish Health 

Center. 
4-76

Research on other potential pathogens is also needed to better understand the threat of disease to 

the DPS. Efforts to prevent outbreaks of furunculosis in hatcheries should continue as well as 

research into methods of transmission and prevention of other fungal infection. Ongoing 

research on bacterial cold-water disease (CWD) caused by the bacterium Flavobacterium 

psychrophila, should be continued. Ongoing studies at the USGS Leetown Science Center have 

shown that this bacterium is associated with peduncle lesions, skin ulcers, fin erosions, 

neurological symptoms and skeletal deformities. This bacterium has been shown to be vertically 

transmitted from carrier adults to offspring via eggs. The bacteria influence egg quality and 

early life stage survival. The threat from CWD is potentially serious if the bacteria are vertically 

transmitted from broodstock to eggs and to fry in the hatchery. Research on the use of 

antibiotics and other methods to prevent outbreaks of this disease should be continued. 

Resident fish species within DPS rivers should be monitored for endemic and exotic salmonid 

pathogens. This monitoring program should annually screen multi-species samples in each DPS 

river. 

Recovery Actions: 

5.2.3A Conduct research on ISAV and SSSV detection and prevention 

5.2.3B Conduct research on other pathogens to identify potential threats to the 

DPS 

5.2.3C Initiate screening and long-term monitoring of resident fish species in DPS 

rivers for endemic and exotic salmonid pathogens 

5.3 Maintain practices to prevent escapement from federal hatcheries 

The CBNFH and the GLNFH are dedicated solely to Atlantic salmon production. The potential 

exists for juveniles to escape from these facilities into rivers within the geographic range of the 

DPS (e.g., the lower Penobscot and Union river drainages where the hatcheries are located). 

Escapees and any resultant adults could be confused with wild salmon and confound surveys and 

research data related to wild salmon recovery. The risks of hatchery escapes can be minimized 

by performing annual inspections of each hatchery to identify possible sources of escape, with 

particular attention paid to discharge and effluent sites. If necessary, remedial actions should be 

taken to remedy any containment failures. Discharge and effluent management protocols should 

be implemented to minimize the release of juveniles. 

Recovery Actions: 

5.3A Develop and implement procedures at federal hatcheries to identify 

potential escape sources and implement the appropriate modifications 
4-77

5.3B Implement discharge and effluent management protocols for all federal 

hatcheries with the goal of controlling and minimizing release of juveniles 

6. Conserve the genetic integrity of the DPS 

Preservation of the genetic integrity of populations, and management of diversity within and 

among populations, is critical for the long-term fitness and viability of populations (e.g., 

Schonewald-Cox et al. 1983; Reed and Frankham 2003). As such, one of the goals of the Gulf 

of Maine DPS recovery program is to maintain the genetic integrity of wild and captive 

populations and prevent detrimental losses of genetic diversity that may result from management 

actions or lack of actions. 

6.1 Ensure that culture and stocking programs conserve the genetic integrity of 

the DPS 

In recognition of the fact that comprehensive genetic and trait data are needed to implement 

biologically sound management actions, the FWS expanded its Atlantic salmon genetic program 

in 1999. At the core of this expansion is genetic characterization of all fish intended for 

broodstock. In 2002, in collaboration with the University of Maine, FWS began trait monitoring 

of captive river-specific broodstock. This combination of genetic screening and trait monitoring 

offers unprecedented abilities to evaluate many components of broodstock management and 

population health. 

6.1.1 Develop broodstock management plans, including brood fish collection, 

genetic management and program evaluation protocols 

The FWS, in cooperation with other federal and state agencies, should develop broodstock 

management plans for FWS Maine Hatchery Complex program. An effective broodstock plan 

must comprehensively cover seven elements: 1) collection of broodstock, 2) broodstock 

screening (e.g. culling and selection), 3) broodstock composition (e.g., captive, wild collections, 

backup sources), 4) mating strategies, 5) hatchery logistics (e.g., capacity, physical limitations), 

6) production schedules, 7) demographic expectations/projections. While many of these 

elements are already operationally in place, they should be consolidated and updated in one 

guiding document. 

6.1.2 Continue to genetically characterize and screen all brood fish and to track 

parentage of all fish produced 

As part of ongoing broodstock management, FWS should continue to genetically characterize 

and screen all broodstock. This will help ensure avoidance of mating closely-related fish (i.e., 

minimize inbreeding), avoidance of using foreign fish (e.g., aquaculture escapees) as broodstock 

and maximization of genetic diversity of hatchery-produced fish. The genetic characterization 

will also allow the production of genetically “marked” offspring that can be distinguished from 

each other, and from naturally-produced fish. 
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In addition to monitoring of neutral genetic variation, monitoring of heritable trait variation is 

important because trait variation relates more directly to features that influence the performance 

of fish in the wild. Long-term monitoring of trait variation is needed to effectively evaluate 

deleterious or positive trends in trait means and diversity. 

6.2 Ensure that management plans consider and avoid negative genetic effects of 

management actions and promote preservation of adaptive variation 

Many of the management actions associated with recovery of the DPS may present genetic 

hazards. As management plans are developed and revised, these hazards should be explicitly 

identified and avoidance measures enacted. The broodstock and stocking program for the DPS is 

an especially important area of consideration because of the inherent hazards of domestication 

(i.e., any change in the selection regime of a cultured population relative to that experienced by 

the natural population) and loss of adaptive genetic variability. As the number of returning wild 

and hatchery-origin adults changes through time, the broodstock stocking program for the DPS 

must maintain and update the appropriate genetic management plans. Genetic Management 

Plans (GMPs) will focus on goals to reduce 1) genetic drift; 2) unintentional selection; 3) 

domestication; and 4) inbreeding. 

6.3 Explore methods for long-term preservation of gametes and genes for future 

use 

The long-term preservation of gametes is one measure that could help maintain the genetic 

diversity within the DPS by serving as a gene bank in case of gamete shortages or a catastrophic 

population loss. At present, techniques for preservation of fish eggs are lacking, but 

cryopreservation of sperm is a viable technique that is an integral part of propagation programs 

for other endangered salmon species. Further consideration should be given to the application of 

this technology to the recovery of the DPS. 

6.4 Monitor genetic diversity, including important trait variation and parentage 

of smolts and returning adults 

Genetic monitoring of salmon from the DPS rivers is needed to ensure that adaptive diversity is 

maintained and protected. In addition, monitoring will help assess the effects of management 

actions and provide information to assist recovery such as which fish stockings were effective, 

which adults spawned successfully and whether Atlantic salmon stocked in DPS rivers perform, 

or behave differently compared to naturally-spawned fish. 

7. Assess stock status of key life stages 

More than a century of restoration efforts for Maine Atlantic salmon and international interest in 

the conservation of wild Atlantic salmon have produced a rich and valuable body of scientific 

literature to help guide recovery efforts for the Gulf of Maine DPS. This information is useful 

for initiating and planning recovery activities. No universal formula for recovery of wild 
4-79

salmonid populations exists. There are significant gaps in our understanding of the factors that 

continue to depress populations and the actions needed to achieve recovery both across the DPS 

and in specific DPS rivers. One weakness of U.S. Atlantic salmon recovery efforts to date has 

been the lack of quantitative information to evaluate management actions. Long time-series of 

hatchery stocking, adult returns to traps and catch data do exist. The state and federal 

management agencies responsible for collecting these data are in the process of consolidating 

information and building electronic databases that will facilitate comprehensive analyses of these 

data. When historical data are consolidated in databases, historical management practices in 

Maine should be re-assessed using modern analytical approaches. Recovery efforts for the DPS 

should use the available comprehensive scientific literature to inform management decisions and 

actions. 

An adaptive management approach is needed that integrates actions to reduce threats to Atlantic 

salmon and their habitat with ongoing assessment and research activities. All population 

monitoring and scientific investigations must include an assessment component. An appropriate 

level of assessment will help inform management decisions and ensure that these decisions are 

based on the best available and most current scientific information. Ongoing assessment will 

allow for evaluation of management actions as well as the integration of new ideas and 

management directions (Smith and Walters 1981; Milliman et al. 1987; Walters et al. 1993). 

Such an approach requires that assessment and research be intensive and that it continually and 

thoroughly evaluates the results of ongoing actions. This will allow modifications to activities to 

improve the effectiveness of the overall recovery effort. The Services believe that the scientific 

investigations described below will provide information for refinement of recovery actions 

described in other sections of this plan. Likewise, evaluation of the results of these scientific 

investigations and other recovery actions may suggest the need for additional research tasks or 

revision of priorities accorded to research tasks specified below. 

As noted (see page 1-57), concerns exist about potential mortality associated with research and 

monitoring activities. The Services will continue assess the benefits and risks of research and 

avoid and minimize any potential adverse effects of research and monitoring activities through 

stringent sampling and handling protocols. The Services will consider the impacts, both direct 

and cumulative, of ongoing and proposed research permitted under Section 10(a)(1)(A) permits 

and will seek to avoid and minimize any potential adverse effect. The Services will ensure that 

all research and monitoring conducted in habitat containing DPS fish is done so in accordance 

with the requirements of the ESA. The Services will continue to work to develop and implement 

non-invasive means of conducting research and data collection necessary to monitor and assess 

the status and trends of the DPS. 

7.1 Assess abundance and survival of Atlantic salmon at key freshwater and 

marine life-stages 

The relative abundance of Atlantic salmon populations can be monitored by assessment of 

annual abundance at one life history stage such as adult returns or escapement as indexed by redd 
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counts. However, the conservation of Maine Atlantic salmon populations requires assessments 

of stage-specific survival for all life stages. This information is needed to understand where and 

when mortality is occurring and if this mortality is within the expected normal ranges reported 

for the species. Equally important is the fact that stage-specific data provide information on 

potential population bottlenecks that might be addressed through adaptive management actions. 

Assessing production of Atlantic salmon parr, smolts, returning adults and spawning escapement 

of adult Atlantic salmon are key elements of evaluating the population dynamics of Atlantic 

salmon. DPS Atlantic salmon generally live in freshwater for two years and saltwater for two 

years and use discrete habitats within these ecosystems (tributaries, rivers, estuaries, coastal 

waters and high seas). Focusing assessment work on the transition between these habitats and 

ecosystems is vital in determining where population growth could be inhibited. In addition, there 

is some variability in duration of Atlantic salmon’s freshwater and marine residency. Therefore, 

it is important to age Atlantic salmon to facilitate both age-structured as well as stage-specific 

assessments of mortality rates. This approach will result in data that can be used to continually 

assess the potential factors impeding or enhancing the recovery of DPS populations. Stagespecific production and mortality rates should be investigated further. 

The data collected from assessments outlined below can provide a critical link between 

freshwater and marine stages across the Gulf of Maine DPS. Collection of these data will 

provide additional future benefits by enabling researchers to characterize the health of DPS 

populations compared to historic levels and biological expectations of carrying capacities; to 

characterize the age distribution of populations, reconstruct the growth histories and compare 

them to the population growth histories; and identify critical bottlenecks or factors that may be 

related to survival within the freshwater and marine environment. 

Based on stage-specific population assessments (see below), mortality rates can be partitioned to 

individual life stages. These data, however, do not reveal the underlying causes of mortality. 

This information should be used to direct research needed to identify factors contributing to 

mortality at each freshwater and marine life-stage. In order for Atlantic salmon recovery efforts 

to be successful, sources of stage-specific mortality need to be identified. 

While no one particular habitat issue is likely causing the decline in freshwater production, the 

cumulative impacts of multiple threats may be affecting survival due to habitat degradation and 

direct mortality. Results of studies on the Narraguagus and Pleasant rivers demonstrate that full 

freshwater production is not being achieved despite fry stocking efforts. These results suggest 

that a factor, or factors, within the rivers may be negatively impacting freshwater habitat for 

Atlantic salmon. 

Low survival rates in the marine environment are also hindering Atlantic salmon recovery 

efforts. As in the freshwater habitat, stage-specific mortality in the marine environment is most 

likely due to the cumulative effect of a number of factors. Poor adaptation of smolts to the 

marine environment has been cited as a potential cause of low marine survival. Oceanographic 

perturbations, including changes in temperature and salinity, may also be contributing factors to 
4-81

low marine survival. Increases in predators and declines in food source, such as capelin, are 

other potential sources of mortality. Assessment of these factors may allow development of 

corrective actions and the implementation of appropriate recovery actions. 

At current levels of abundance, it is difficult to categorize any threat to the species and its habitat 

as negligible. Although it is difficult to isolate and evaluate the impact of individual habitat 

issues, the available information indicates that cumulative impacts from habitat degradation 

issues (e.g., sedimentation, substrate embeddedness, acidification, endocrine disrupting 

chemicals) pose a threat to Atlantic salmon stocks. Stream acidification and chronic exposure to 

chemical residues that act as endocrine disruptors are two threats that may be contributing to 

mortality of Atlantic salmon in freshwater. In addition, low overwinter survival may also be 

hindering recovery efforts. This issue needs further investigation. The relationship between 

these factors and freshwater production and survival of Atlantic salmon needs to be studied in 

detail so that cause and effect connections can be determined or ruled out. Corrective actions 

can then be implemented as appropriate to enhance recovery. 

7.1.1 Monitor adult returns and spawning escapement 

Estimating adult returns and spawning escapement to DPS rivers is essential to assess the status 

of wild salmon populations within the DPS82. These estimates form the basis of population 

assessments that provide information on the effectiveness of recovery measures and help inform 

management decisions. Since these assessments document abundance during the least abundant 

stage of their life history, they provide a vital measurement of stock status and health. 

Estimates of adult salmon returns can be made based on fish trap or weir counts. Weirs and traps 

currently provide the most accurate assessment tool because they provide actual counts of 

returns. Weirs enable ASC biologists to collect data on numbers, origin and condition of 

returning adults. Biological samples such as scales can be collected to determine the agestructure of returning adults. This information is used for annual stock assessment to measure 

progress in meeting escapement goals. It is also used for management purposes to determine 

each river’s annual stocking requirements and stocking locations. 

Weirs are currently in place on the Dennys and Pleasant rivers and there is a fish trapping facility 

at the Stillwater Dam on the Narraguagus River. Adult Atlantic salmon returns should continue 

to be monitored at weirs and fishways to obtain accurate counts of returning adult salmon. As 

new designs and procedures become available, biologists should evaluate these opportunities for 

their potential to increase counting accuracy, maximize data collected and minimize stress to 

returning salmon. The need for weirs on the East Machias and Machias rivers should be 

evaluated (see page 4-58). 

 

82 Adult returns are defined as the number of pre-spawning Atlantic salmon returning to their natal river. 

Spawning escapement is the number of adults that actually survive to spawn (late October to early 

November) after they return to their natal river (May to October).
4-82

Using weirs to assess adult returns has risks (blocking passage, delaying migration, possible 

adult mortality). Before weirs are installed in additional rivers, risks should be fully assessed in 

comparison to the risk of aquaculture escapes to the river system. Weirs and fishways should be 

constantly monitored to ensure that impacts on the population are minimized while collecting 

biological data. 

Estimates of spawners on rivers without weirs or traps are based on redds counts, which can be 

compared with numbers of returns to weirs/traps using a return-redd model (USASAC 2001). 

The NMFS and ASC developed a model relating redd counts to estimates of adult salmon 

abundance that has been in use since 2000. The relationship between redd counts and adult 

abundance is derived from assessments of adult returns and redd counts conducted on the 

Narraguagus River using data from 1991-2000. Using this model, managers can estimate both 

the total returns to the river as well as use redd counts directly to evaluate spawning activity 

within a watershed. 

Since these redd counts index escapement directly, they provide information on the natural 

spawning activity of both naturally-reared and stocked returns. The ASC conducts annual late 

fall GPS mapping of redds in the eight rivers; this data is then referenced to a GIS river kilometer 

network and archived in a digital database to provide estimates of habitat utilization as well as 

return estimates for the rivers without weirs/traps. This positional data on all redds and redd 

clusters can be used to minimize interactions between naturally-spawned and fry-stocked 

juveniles. This level of spatial management provides opportunities that allow fry stocking to 

enhance the populations while minimizing interactions to improve survival of naturally-spawned 

fish. Ongoing efforts to refine this model and develop additional reference points on other DPS 

rivers to improve the model’s accuracy should be continued. 

Recovery Actions: 

7.1.1A Monitor adult returns at existing fishways and weirs 

7.1.1B Construct weirs on the East Machias and Machias rivers to monitor adult 

returns 

7.1.1C Conduct intensive redd counts on all DPS rivers to index spawning 

escapement 

7.1.1D Continue development of DPS-level estimates of spawning escapement 

7.1.1E Develop accurate extrapolation methods to estimate abundance in areas 

where traditional redd counts are not feasible or practical 
4-83

7.1.2 Conduct basinwide assessment of large parr abundance and biological 

characteristics 

Since 1947, ASC and its predecessors have been evaluating large parr (fish > 110 mm total 

length) production at various index sites in many Maine rivers. Electrofishing surveys of fish in 

these rivers during August and September can provide information on the abundance and 

size/age structure of Atlantic salmon juveniles in the rivers. The indices of large parr are 

particularly useful because most of these fish are nearing the end of utilization of freshwater 

nursery habitat and will be headed to sea the following spring. Historic data are being compiled 

by ASC and entered into electronic databases. These index data provide a historic record of the 

production of juvenile Atlantic salmon in discrete stream reaches over time. 

Assessments of large parr are a primary tool for assessment of the freshwater productivity of 

each river. Since 1991, ASC and NMFS have estimated parr production in the Narraguagus 

River through intensive stream surveys (Beland and Dube 1999). These surveys cover various 

types of Atlantic salmon habitat from headwaters to lower reaches of the river. With these data, 

biologists can estimate large parr abundance for the entire river. This type of assessment is time 

intensive as up to 10% of the watershed may need to be sampled. With these data biologists can 

evaluate areas that over- or under-produce large parr and determine the variability in basin-wide 

production on an annual basis. As these data become available, mechanisms that limit the 

production of salmon can be assessed, identified and mitigated to increase juvenile production. 

Assessment of large parr abundance at such an intensive level as conducted in the Narraguagus 

River may not be needed for all populations in the Gulf of Maine DPS but increased monitoring 

of large parr abundance would be useful in all rivers. The addition of intensive basinwide 

estimates of large parr at the extremes of the current distribution of wild salmon populations 

within the range of the DPS would benefit assessment of inter-river variability in production. 

The ASC has established a second intensive sampling program on the Dennys River. Large parr 

assessments in the Narraguagus and Dennys rivers should be continued and the potential for the 

Sheepscot River to be a third location should be evaluated. It would be useful to establish an 

additional six to ten representative sites on other rivers to better understand the relative 

abundance of large parr and provide data to cross reference index-sampled rivers with those 

being more intensively surveyed. These data would be useful for tracking of management 

actions such as stocking as well as to assess effects of abiotic factors such as drought, winter 

severity and floods. 

Recovery Actions: 

7.1.2A Continue basinwide assessment of large parr abundance and measurement 

of biological characteristics in the Narraguagus and Dennys river systems 

7.1.2B Expand assessments of large parr abundance to a third DPS river 
4-84

7.1.2C Establish six to ten index sites to assess large parr abundance and 

biological characteristics in remaining DPS rivers 

7.1.3 Conduct quantitative assessments of Atlantic salmon smolt production 

In addition to large parr assessments, NMFS and ASC monitor the emigration of smolts. This 

includes the timing of migration and biological sampling. Since 1996, the abundance of smolts 

in the Narraguagus River has been estimated (Kocik et al. 1999). Smolts are captured either with 

rotary-screw smolt traps (RST) or with experimental weir-based smolt traps (WBST). Smolt 

assessments provide an opportunity to collect scale samples for aging, tissue samples for genetic 

studies and gill biopsies for physiological measures. Additionally, smolt trapping in the lower 

reaches of river systems provides an opportunity for tagging, telemetry and other related projects 

aimed at improving the understanding of the estuarine and marine ecology of Atlantic salmon. 

By comparing smolt population data and large parr population data, biologists can determine 

overwinter survival from large parr to smolt stage. Data from the Narraguagus River has shown 

that even in years with a substantial increase in parr production (>125%), smolt production has 

remained relatively stable (~2% increase). Total freshwater production could potentially be 

increased if mechanisms for these differences can be identified. 

Survival from the parr to the smolt stage in Maine was previously estimated to range from 30% 

to 70% (Bley and Moring 1988; Baum 1997). Survival estimates in the Narraguagus River for 

all years studied are substantially lower than the previously reported estimates for Maine (Bley 

1987; Bley and Moring 1988; Baum 1997; Kocik et al. 1999). Kocik (1999) calculated that parr 

to smolt survival in the Narraguagus River was less than 30%. Because smolt assessments in the 

Narraguagus River suggest that production is well below the estimated capacity, it appears that 

low overwinter survival may be impeding the recovery of this population. 

Similar assessments have been initiated on the Pleasant River (1999) and the Sheepscot River 

(2001) to determine if recent pre-smolt and marine survival estimates on the Narraguagus River 

are representative of other DPS rivers. The juxtaposition of rearing habitat and smolt trapping 

sites in both the Pleasant and Sheepscot rivers is such that only an index of smolt emigration can 

be obtained. These data have shown that the population of naturally-reared smolts is declining in 

the Pleasant River and is very low in the Sheepscot River. Modeling efforts are underway to 

improve estimates of smolt abundance in these two index rivers to allow more quantitative 

assessments of production. Assessment of smolt abundance in an additional river system would 

be useful for better understanding the total smolt production across the rivers of the DPS and the 

utility of single or multiple rivers as indices for the entire stock complex. 

7.1.4 Monitor estuarine and coastal survival, ecology, and distribution of smolts 

using telemetry and surface trawling 

The emigration of Atlantic salmon smolts from Gulf of Maine rivers occurs from April through 

June. During this transition, fish experience physiological changes (i.e., smoltification) and 
4-85

encounter new predators upon entering the estuarine and marine environments. Relatively little 

is known about the behavior of Atlantic salmon during the smolt-post-smolt transition and their 

migration through coastal waters of the Gulf of Maine. A major obstacle to the study of Atlantic 

salmon in the marine environment has been the relatively low density of salmon over the 

extended geographic range in the ocean (Hislop and Shelton 1993). Two relatively new 

assessment and research tools, ultrasonic telemetry and surface trawling, are now available to 

monitor fish during this transitional stage in estuarine and marine environments even when fish 

are relatively scarce. 

Ultrasonic telemetry is an effective way to monitor the migration of these fish through this 

transition and can provide estimates of mortality as fish pass through discrete ecological zones: 

riverine, estuarine, nearshore and Gulf of Maine. Ultrasonic tracking studies conducted in Maine 

estuaries, the Gulf of Maine and the Bay of Fundy have provided indications of migration 

pathways and some information concerning zone-specific mortality. 

Ultrasonic tracking studies of Atlantic salmon smolts within the Gulf of Maine have been 

conducted on both wild and hatchery-reared fish during the period from 1996-1999 and in 2001 

for hatchery stocked smolts. The goal of this research is to determine the early migration route 

through nearshore waters of the Gulf of Maine and to estimate survival rates of both wild and 

hatchery-reared fish. Pilot studies were conducted on the Narraguagus River in 1996 and from 

1997 to 1999. During this time, about 100 wild smolts were monitored to assess their progress 

migrating to the Gulf of Maine. These studies will be expanded seaward from 2002 through 

2005 to determine the initial direction of migration of smolts relative to the Maine Coastal 

Current. 

In 2001, NMFS biologists initiated a five-year study to monitor the early marine migration of 

ultrasonically tagged hatchery-reared Atlantic salmon smolts within the Dennys River and 

Cobscook Bay. Through a partnership with the Canadian DFO, existing U.S. and Canadian 

electronic tracking arrays were integrated to track the movement of smolts exiting the Bay of 

Fundy and entering the Gulf of Maine. Researchers monitored the within-river movements, 

downstream passage success and early marine migration patterns of these tagged smolts. While 

these studies are still in progress, preliminary results suggest substantial numbers of smolts die 

relatively soon after leaving the riverine environment. These findings highlight the need to 

identify the mechanisms responsible for mortality as smolts enter saltwater. 

Also in 2001, NMFS initiated a multi-year surface-trawling program to sample U.S. Atlantic 

salmon post-smolts in Penobscot Bay and nearshore waters of the Gulf of Maine. The goal of 

the program is to improve current understanding of factors affecting growth and survival and the 

nearshore migration patterns of Atlantic salmon post-smolts. During this survey, hatchery and 

wild post-smolts of Penobscot River origin were targeted83. This research has the potential to 

provide important information concerning sources of lethal and sub-lethal mortality. In addition, 

 

83 Two lower Penobscot Bay stocks (Cove Brook and the Ducktrap River) are currently listed under the ESA. 

Given the estimated smolt production in these systems relative to the Penobscot River, the probability that 

significant numbers of smolts from these rivers were captured is minimal.
4-86

this research may provide new information concerning early marine survival of Atlantic salmon. 

This program is part of a multinational effort to improve the understanding of post-smolt ecology 

through a coordinated NASCO research program. 

Results from the 2001 survey indicated that greater than 97% of captured smolts were age 1+ 

hatchery smolts originating from the Penobscot River. The continuation of this assessment 

program will improve the understanding of the ecology of post-smolts. This program should be 

expanded to include more offshore sampling stations, thereby gaining additional information 

about the migration patterns and survival of post-smolts as they leave freshwater and begin their 

ocean migration. 

Recovery Actions: 

7.1.4A Continue telemetry studies of smolt migration from the Dennys (hatchery 

fish) and Narraguagus (wild fish) rivers 

7.1.4B Expand spatial coverage of detection arrays to better assess movements of 

post-smolts in the Gulf of Maine and the Bay of Fundy 

7.1.4C Continue post-smolt surface trawling assessment programs and expand the 

temporal and spatial extent of coverage 

7.1.5 Continue to participate and contribute to international cooperative research 

and assessment efforts to improve our understanding of salmon at sea 

While the marine life history of Atlantic salmon is poorly understood, there has been substantial 

progress in understanding the marine ecology and population dynamics of Atlantic salmon 

during the past decade. Progress has been made in our understanding of growth, survival and 

migration patterns of salmon while in the ocean. Central to this progress has been the work of 

assessment committees such as the U.S. Atlantic Salmon Assessment Committee (USASAC), the 

ICES Working and Study Groups (the North American Salmon Study Group (ICES-NASSG) 

and the North Atlantic Salmon Working Group (ICES-NASWG)(Windsor and Hutchinson 

1994). The U.S. should continue to participate in international scientific organizations and 

forums to identify threats to Atlantic salmon in the marine environment. 

International research programs should be pursued as part of efforts to identify threats to marine 

life stages. NASCO provides a framework for coordinated marine research. NASCO has 

established an international research fund to promote coordination of research efforts among 

members. For example, the post-smolt research initiated in 2001 (see above) is part of a 

multinational effort involving Canadian, Norwegian and Scottish efforts to improve our 

understanding of post-smolt ecology through a coordinated NASCO research program. 
4-87

7.1.6 Develop and apply population viability analysis model 

Computerized population viability models are valuable tools that can help managers understand 

the dynamics of species. Such models can be especially useful for species with many life stages 

that are subject to a large number of highly variable environmental factors, such as Atlantic 

salmon. Models can help managers evaluate the relative benefits of alternative management 

actions. While the reliability of such models is dependent on the accuracy of data inputs, 

population models can help identify which data exert the most influence on model outputs (i.e., 

sensitivity analysis), thereby assisting prioritization of data collection needs. Sound application 

of modeling results requires testing of model predictions against empirical data and logical 

expectations. 

In the spring of 2001, biologists from the Services and ASC initiated efforts to develop a 

population viability analysis (PVA) for the DPS. Like most population viability models, this tool 

is a dynamic model that will change over time as new information becomes available. This 

model will provide information needed to estimate the relative effects of various threats, 

environmental factors and potential recovery actions on the DPS and its probability of 

persistence. For example, population viability modeling may reveal relationships between 

population size and probability of persistence, including adequacy of target populations to 

withstand variable cycles in marine survival. The Services and ASC should continue to develop 

a PVA specific to the DPS and apply the results of this model. 

8 Promote salmon recovery through increased public and government 

awareness 

8.1 Develop a comprehensive Education and Outreach Program for the Gulf of 

Maine DPS of Atlantic salmon 

Education and outreach programs are a critical component of successful conservation and 

recovery plans. Public information and outreach programs help build public support and a strong 

constituency for Atlantic salmon recovery and conservation in Maine. Efforts to increase and 

improve public awareness of Atlantic salmon conservation should continue through media, 

educational material, public forums and workshops, demonstration projects and technical 

assistance. Virtually all successful conservation programs include education and public outreach 

programs. Public awareness is important to the success of Atlantic salmon recovery efforts in 

Maine. 

Education and outreach programs inform the general public and interested parties, such as land 

owners, business and industry, state and local government about the Atlantic salmon recovery 

process. Education and information campaigns help promote Atlantic salmon as an important 

national resource and encourage individual and group involvement in the recovery process. 

A comprehensive and coordinated Education and Outreach Plan for the Gulf of Maine DPS of 

Atlantic salmon should be developed. This plan should include a strategy to coordinate the 
4-88

efforts of federal, state and local organizations currently involved in education and outreach 

programs. The plan should identify target audiences, review existing programs and materials, 

evaluate the role of public display of Atlantic salmon, identify education and outreach needs, 

identify responsibilities and costs and develop strategies for dissemination of information and 

materials. 

Numerous education and outreach programs are ongoing and should be reviewed to help identify 

outreach needs and refine programs as necessary. The plan should consider identified education 

and outreach needs, some of which are discussed below. 

State and federal agencies should provide technical support to landowners for conservation 

measures that are needed to recover and conserve the DPS. The majority of riparian lands along 

DPS rivers and streams are in private ownership. Many landowners in DPS river watersheds rely 

on agricultural, forestry and livestock activities for their livelihood. It is critical that the 

Services, state and federal agencies, local government and local conservation organizations work 

with these landowners to provide information about salmon recovery efforts. 

Members of the outdoor sporting community, such as recreational anglers and recreational 

vehicle riders are an important audience to inform on how their activities may affect salmon 

recovery. The Maine Department of Conservation (DOC) has taken steps to establish ATV clubs 

and educate recreational riders on responsible practices that minimize the impacts that ATV’s 

have on land and water resources. Efforts by ASC, IFW and ASF to make anglers aware of the 

difference between trout and young salmon should continue in order to minimize the potential 

take of juvenile salmon. 

There is a need to update and develop new Atlantic salmon education and outreach materials. 

These materials are needed to reach new target audiences, take advantage of advancing media, 

and stimulate continuing public interest and awareness. In addition, all materials should be kept 

current regarding the status of the species and recovery efforts. Efforts to increase and improve 

public awareness of Atlantic salmon conservation should continue through media, educational 

material, public forums and workshops, demonstration projects and technical assistance. 

Updated educational programs for schools should be developed. These should build upon 

existing curriculum materials while updating them. The updated classroom materials should also 

extend beyond elementary schools, where current efforts are focused. 

Strong and effective local conservation organizations are important partners in recovery efforts. 

Local watershed groups need adequate technical support and training to effectively identify and 

prioritize conservation and restoration projects. Local organizations help promote public 

awareness, salmon recovery and conservation at the local watershed level. Several of the 

organizations currently involved in education and outreach efforts are outlined in Appendix 5. 

While there are numerous local organizations already involved in education and outreach 

activities, a coordinated network for distribution of information and education materials should 
4-89

be developed. This will allow information sharing between groups as well as a more coordinated 

effort to distribute relevant information and direct efforts to the appropriate audiences. 

Recovery Actions: 

8.1A Develop a comprehensive Education and Outreach Plan for the Gulf of 

Maine DPS of Atlantic salmon 

8.1B Continue efforts to educate anglers on the difference between trout and 

juvenile salmon 

8.1C Develop updated educational programs for schools 

8.1D Evaluate the role of public display of salmon as an outreach tool 

8.2 Maintain, and if necessary increase, coordination/communications between 

government and local agencies on issues pertaining to Atlantic salmon 

recovery 

Federal and state agencies and local governments should continue to work cooperatively to 

recover the DPS. Where necessary, interagency communication and coordination should be 

strengthened. Existing coordination and communication mechanisms between federal and state 

agencies and local conservation organizations and other constituency groups should be reviewed 

and strengthened as necessary. 

There are many organizations and groups involved in the protection and recovery of Atlantic 

salmon. Ensuring inter-organizational coordination and communication mechanisms are in place 

will increase the effectiveness and efficiency of these groups. Coordination of local conservation 

efforts by an umbrella organization could coordinate communications between various local 

organizations and strengthen the effectiveness of member organizations through the power of 

combined resources (See Demont 2005). 

Existing communication networks and other mechanisms for exchanging research results and 

highlighting recovery actions should also be maintained and expanded as appropriate. The 

Maine Atlantic Salmon Technical Advisory Committee and the Maine Atlantic Salmon 

Commission are two important entities involved in research and management of Atlantic salmon 

in Maine. The Services should continue to work closely with the ASC and the Maine TAC to 

coordinate recovery efforts. 
4-90

9. Assess effectiveness of recovery actions and revise as appropriate 

Regular and rigorous monitoring and evaluation are critical to an effective and efficient recovery 

program for any endangered or threatened species. Monitoring assures that recovery efforts are 

being implemented in a timely fashion, that effectiveness of those efforts is continually assessed 

and that appropriate changes are made to maximize conservation of the species. To this end, 

several types of reviews are necessary. 

9.1 Appoint a Recovery Implementation Team to coordinate implementation of 

recovery plan objectives 

A Recovery Implementation Team should be appointed (by the Services) to coordinate 

implementation of recovery actions, and to assess and integrate ongoing recovery efforts. The 

Implementation Team should consist of individuals with experience in Atlantic salmon 

conservation and familiarity with issues affecting Atlantic salmon recovery. Within the overall 

team structure, a coordinating committee will be appointed who will handle team logistics and 

organizational matters. The coordinating committee will include a representative of the Maine 

ASC, NMFS and FWS. The Recovery Team will work in concert with other technical and 

management groups involved in the recovery effort, including the Maine TAC. The coordinating 

committee and Recovery Team proper will convene periodic meetings to aid in coordination of 

recovery efforts and implementation of recovery actions. The coordinating committee and 

Recovery Team will also be responsible for monitoring recovery progress and updating the 

recovery plan to reflect new scientific findings, current status of the population, improved 

understanding of factors affecting recovery, and completion of recovery actions and objectives. 

9.2 Review implementation of Recovery Plan tasks annually and assess need for 

revisions, including changes in priorities 

The Recovery Implementation Team should meet at least annually to review ongoing recovery 

efforts and implementation of recovery actions. The Implementation Schedule (see pages 5-1 to 

5-11) lists and prioritizes tasks that are necessary to achieve recovery. This schedule should be 

reviewed annually to assess what efforts have been implemented to date. Not all tasks are of 

equal priority and it is not expected that every task will be implemented every year. Many tasks 

will require ongoing implementation, although the type and intensity of activity may change over 

time. Annual reviews provide important opportunities to identify any gaps in ongoing efforts 

and improve coordination among all agencies, organizations and other partners. 

The ESA mandates that a progress report on the status of efforts to develop and implement 

recovery plans and the status of the species. This progress report should include actions taken by 

NMFS, FWS, other federal agencies, state and local governments and other organizations that 

affect the recovery of the species. This information will be compiled into the report sent to the 

Congress on the status of efforts to develop and implement recovery plans. These reports will 

also be made available to the public. 
4-91

Recovery Actions: 

9.2A Conduct an annual review of the implementation schedule 

9.2B Complete an annual progress report on completion of recovery actions 

9.3 Complete necessary addenda, updates and revisions to the Recovery Plan 

Once the recovery plan has final approval, efforts should continue to be made to ensure that all 

information in the recovery plan is relevant and up to date. As new information on threats, 

actions, the biology of the species and results of research becomes available, changes to the 

recovery plan may be necessary. Three types of recovery plan changes are possible: addenda, 

updates and revisions. 

An addendum can be added to a plan after the final plan has been approved. Types of addenda 

can range from implementation strategies or participation plans to more minor attachments of 

data. Most addenda will be minor additions and would not require public review or comment. 

Recovery plan updates also involve relatively minor changes. An update may identify specific 

actions that have been initiated or will be initiated since the plan was completed, as well as 

changes in species status or background information that do not alter the overall direction of the 

recovery effort. Updates will be completed by the lead biologist for the species or the recovery 

team. An update represents a minor change to the recovery plan and does not require public 

review or comment. 

A recovery plan revision is a substantial rewrite of at least a portion of a recovery plan and is 

usually required when there are major changes to be made. A revision may be required when 

new threats to the species are identified, when research identifies new life history traits that have 

significant recovery ramifications or when the current plan is not achieving its objectives. 

Revisions of recovery plans represent a major change to the recovery plan and should include 

public review and comment. 
5-1

PART FIVE: IMPLEMENTATION SCHEDULE 

The following Implementation Schedule outlines actions and estimated time frames for 

the Atlantic salmon recovery program, with a focus on the next three fiscal years84. The 

schedule is a guide for meeting the recovery objective and criteria discussed in Part Three 

of this plan. It indicates task priorities, task descriptions and numbers, task duration, 

agencies and other parties responsible for implementing the tasks and estimated costs. 

The reader should consult the recovery action table and/or the appropriate section of the 

recovery plan for the full description of the site specific management actions planned for 

implementation. This implementation schedule will be updated as recovery actions are 

accomplished or as otherwise dictated. 

Key to Task Priority Numbers (Column 1) 

PRIORITY TYPE OF TASK 

1 Actions that must be taken to prevent extinction or to prevent the species from 

declining irreversibly 

2 Actions that must be taken to prevent a significant decline in population/habitat 

quality or other significant negative impact short of extinction 

3 All other actions necessary to provide for full recovery of the species 

Total Estimated Cost of Recovery: The total cost of recovery is undeterminable at this 

time. It is impossible to estimate the cost of recovery for the DPS. The species continues 

to decline and its status is precarious. Even when we achieve a complete reversal of 

downward trends and population growth, it is not possible to estimate the cost of 

recovery of the DPS. 

Despite ongoing efforts to arrest and reverse the decline of the DPS adult salmon returns 

to DPS rivers remain at historic lows (an estimated 60 to 113 adult returns in 2004). 

The initial focus of the recovery program will be on the 8 rivers within the DPS with 

extant populations at the time of the listing. The initial goal of recovery efforts is to 

immediately halt the decline of the DPS and demonstrate a persistent increase in 

population abundance such that the overall probability of long-term survival is increased. 

Research is ongoing to help identify the causes for the species continued decline and 

identify appropriate measures to mitigate threats and recover the DPS. Pending the 

results of the recommended research it is not yet possible to identify recovery actions and 

strategies to mitigate the threats. Specific research needs, including estimated times and 

costs, are identified in Part 4 of this plan and prioritized in the implementation schedule. 

In the face of this continued uncertainty of the overall causes of the species decline it is 

 

84 Consistent with NMFS Recovery Planning Guidance the implementation schedule provides cost 

estimates for three years. 
5-2

not possible to identify all recovery actions that may be necessary to recover the DPS and 

therefore be able to estimate costs for full recovery of the DPS. 

The Services have concluded that it is not practicable at this time to establish final 

demographic criteria for reclassification and delisting of the DPS. The Recovery Plan 

does, however, contain both preliminary demographic and threat reduction recovery 

criteria. The first objective of the plan is to halt the decline of the DPS and demonstrate a 

persistent increase in population abundance trends such that the overall probability of 

long-term survival is increased. In the absence of final measurable and objective criteria 

it is not possible at this time to provide a full estimate of the cost of achieving the 

conditions that will constitute a secure and recovered DPS. 

The Implementation Schedule, however, does contain cost estimates for individual tasks. 

The total estimated minimum cost of recovery actions identified for year 1 to year 3 is 

$36.6 million. 

Estimated Date of Recovery: It is impossible to estimate the date of recovery for the 

DPS. The species continues to decline and its status is precarious. Even when we 

achieve a complete reversal of downward trends and population growth, it is not possible 

to estimate the date of recovery of the DPS. 

Key to Responsible Agencies (column 5) 

ACOE Army Corps of Engineers (U.S.) 

ASC Atlantic Salmon Commission (Maine) 

ASF Atlantic Salmon Federation 

ASMFC Atlantic States Marine Fisheries Commission 

BPC Board of Pesticide Control (Maine) 

BPL Bureau of Parks and Lands (Maine) 

DAFRR Department of Agriculture, Food and Rural Resources (Maine) 

DEP Department of Environmental Protection (Maine) 

DMR Department of Marine Resources (Maine) 

FWS U.S. Fish and Wildlife Service 

ICES International Council for the Exploration of the Sea 

IFW Inland Fisheries and Wildlife, Department of (Maine) 

Industry Forest industry, blueberry and other agricultural industries, aquaculture industry 

LURC Land Use Regulatory Commission (Maine) 

LWRC Land and Water Resources Council (Maine) 
5-3

MDEP Maine Department of Environmental Protection 

MDOC Maine Department of Conservation 

MDOT Maine Department of Transportation 

MFS Maine Forest Service 

MGS Maine Geological Survey 

MSPO Maine State Planning Office 

MWBC Maine Wild Blueberry Commission 

NASCO North Atlantic Salmon Conservation Organization (international) 

NEFHC New England Fish Health Committee 

NEFMC New England Fishery Management Council 

NFWF National Fish and Wildlife Foundation 

NGO Non-governmental organizations (e.g., ASF, DSF Watershed Councils, TU, 

Local Land Trusts, Project SHARE) 

NOAA National Oceanographic and Atmospheric Administration 

NRCS Natural Resource Conservation Service 

TAC Technical Advisory Committee 

UM University of Maine 

USDA U.S. Department of Agriculture (APHIS) 

U.S. EPA U.S. Environmental Protection Agency 

USGS U.S. Geological Survey 

WCSWD Washington County Soil and Water Conservation District 

WGNAS Working Group on North Atlantic Salmon 
IMPLEMENTATION SCHEDULE

ATLANTIC SALMON RECOVERY PLAN

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

1 1.1.2C

Develop and implement an effective flow monitoring program in addition to gage-sites to monitor stream flow and discharge data at points along rivers. 

Long-term FWS USGS MGS, DEP, LURC

92K 92K 92K

1 1.1.2D Monitor and assess the potential for groundwater withdrawals to impact stream flow and cold water discharges Long-term FWS USGS DAFRR MGS DEP LURC Industry 100K 100K 100K 

1 1.1.3B Determine the effects of current irrigation withdrawals by all growers in the watersheds on flow and Atlantic salmon Long-term USGS FWS DAFRR MGS, DEP, LURC Industry 100K 100k 100K

1 1.1.4A

Ensure that water withdrawal permit requirements protect stream flows required for the recovery and conservation of Atlantic salmon.

Long-term FWS ASC, DEP, LURC 

DAFRR Industry 45K 45K 45K

1 1.1.4B Issue and enforce all appropriate permits for water withdrawals Long-term ACOE FWS DEP, LURC DAFRR Industry 10K 10K 10K 

1 1.2.2A Evaluate the impacts of acid rain on juvenile Atlantic salmon survival in DPS rivers 3 years USGS, NMFS EPA ASC, DEP, UM, NGOs 75K 75K 75K

1 1.2.2B 

Identify available management measures and techniques to mitigate the potential impacts of acid rain on the DPS. Experimentally evaluate stream acidification mitigation techniques in a natural river system within the range of the DPS 

3 years NMFS FWS 

USGS

ASC, DEP, NGOs

250K 120K 120K

1 1.2.2C 

Identify point sources of airborne pollutants contributing to acid precipitation that may be adversely affecting the DPS and reduce to levels that will not adversely affect or jeopardize the recovery of the DPS

4 years EPA FWS 

NMFS

DEP 

25K 25K

1 1.2.2F Evaluate the biological effects of low pH and aluminum and its toxicity on Atlantic salmon 3 years USGS EPA FWS NMFS DEP UM 75K 75K 75K

1 1.2.2J Evaluate the link between pesticides and endocrine disruption 3 years USGS EPA FWS NMFS DEP, UM, BPC 75K 75K 75K

1 1.2.2G 

Sample resident fish from all DPS rivers and analyze them for tissue residues and bio-chemical factors indicative of exposure to endocrine disrupting chemicals. 

3 years EPA NMFS 

FWS

ASC, DEP

45K 45K 45K 

1 1.2.3A Implement a comprehensive and integrated long-term water chemistry monitoring program on all DPS rivers 1 year FWS EPA DEP, UM, ASC, NGOs 100K 100K 100K 

1 1.2.4B 

Evaluate the impacts of sedimentation on habitat quantity and quality including relationship between substrate embeddedness and habitat productivity in DPS rivers.

NMFS, FWS, USGS

ASC NGOs 

1 1.4.1C Identify riparian zone activities (e.g., harvest practices, ATVs, development etc.) and evaluate impacts on Atlantic salmon Long-term MFS Industry ASC NGOs 25K 

1 1.5.1 

Create regional hydraulic geometry curves and a reference reach database 3 years FWS ASC

75K 75K

1 1.5.3 Conduct high priority restoration projects Long-term NRCS ASC MFS MDOT NGOs 300K 

1 1.5.5 Evaluate the ecological role and importance of restoring other diadromous fish populations 

Lead Agency Estimated Cost

5-4
IMPLEMENTATION SCHEDULE

ATLANTIC SALMON RECOVERY PLAN

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

1 2.1.1 Maintain and enforce the closure of the directed sport fishery for Atlantic salmon Long-term NMFS FWS IFW, DMR 20K 20K 20K

1 2.1.2 

Maintain current FMP that restricts directed harvest of Atlantic salmon in U.S. estuarine and marine waters

Long-term NMFS NEFMC 

1 2.1.3A 

Participate in international salmon management with the goal of ensuring any quotas set are based on the best available scientific data and provide adequate protection of US stocks

Long-term NMFS ASC

30K 30K 30K

1 2.2.1B

Prohibit all recreational fishing in select areas utilized by Atlantic salmon as holding areas to all fishing where Atlantic salmon may be taken as bycatch or poached

Long-term IFW, ASC 

1 2.2.1C 

Develop a Section 10(a)(1)(B) habitat conservation plan for recreational fishing permitted by the State that may incidentally take Atlantic salmon

2 years FWS IFW ASC

50K 50K

1 3.1.2C 

Evaluate the potential of conserving and restoring runs of anadromous forage species to provide a buffer against predation on salmon and other ecological benefits

Long-term FWS NMFS ASC IFW DMR

100K

1 3.2.1A 

Review existing stocking programs and assess the potential impacts of these introductions on Atlantic salmon populations and ways to minimize potential adverse affects

1 year NMFS FWS ASC IFW

5K 5K 5K

1 3.2.1B 

Monitor potential adverse interactions of existing stocking programs for freshwater salmonids in Atlantic salmon river drainages and fully assess the potential impacts of these programs on the DPS

1 year NMFS FWS ASC IFW

20K 20K 20K

1 3.2.1E Develop a Section 10(a)(1)(B) habitat conservation plan for existing stocking programs and, if warranted and implement 1 year FWS ASC IFW 50K 

1 3.2.2 Monitor populations of introduced non-salmonid species and implement management controls when appropriate and feasible Long-term FWS ASC IFW 30K 30K 30K 

1 4.1B Develop fully functional containment management systems for the containment of farmed salmon at marine sites. Long-term ACOE NMFS FWS Industry, DMR 

1 4.1C 

Develop and implement integrated loss control plans for all salmon aquaculture facilities

Long-term ACOE NMFS 

FWS

DMR Industry 

1 4.3.1A 

Develop and implement a comprehensive disease management plan that includes siting and standard operational procedures to minimize outbreaks of ISA. 

Long-term USDA NMFS 

FWS ACOE

Industry DMR NASCO

200K

1 4.3.2A Determine the modes of transmission of the ISA virus 3 years USDA NMFS FWS DMR Industry 

1 4.3.2B Continue to investigate the role of wild fish species as potential reservoirs and vectors of ISA 3 years NMFS USDA DMR Industry 120K 120K 

1 4.4.1B 

Develop integrated loss control plans for all salmon aquaculture hatchery facilities. Conduct independent audits of freshwater hatcheries once loss control plans are in place

Long-term ACOE NMFS 

FWS

Industry DEP DMR 

1 5.1.1A 

Continue operation of federal fish rearing facilities needed for recovery of the DPS, including maintenance of river-specific broodstock

Long-term FWS

725K 750K 785K

5-5
IMPLEMENTATION SCHEDULE

ATLANTIC SALMON RECOVERY PLAN

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

1 5.1.1B Continue stocking cultured fish to supplement wild salmon populations Long-term FWS ASC, TAC 60K 63K 66K

1 5.1.2 

Monitor and evaluate the current stocking program Long-term NMFS FWS ASC, TAC

150K 150K 150K

1 5.1.3A Evaluate the role of alternate stocking strategies to supplement wild salmon populations 5 years NMFS FWS ASC, TAC, Industry 50K 50K 50K 

1 5.1.4A Evaluate the need to re-establish populations of Atlantic salmon in extripated rivers within the DPS 5 years NMFS FWS ASC, TAC 1 5.1.4B Establish experimental populations to assist in the recovery of the GOM DPS of Atlantic salmon NMFS FWS ASC, TAC 120K 120K1 5.2.1 Continue fish culture management practices at federal hatcheries to minimize the potential for disease Long-term FWS 

1 5.2.2 Continue fish health surveillance efforts and implementation of fish health practices at federal hatcheries Long-term FWS 20K 20K 20K

1 5.2.3A Conduct research on ISA and SSS detection and prevention 3 years NMFS FWS, USGS ASC 50K 50K 50K 

1 6.1.1 Update brood stock management plans, including brood fish collection, genetic management and program evaluation 1 year FWS ASC, Maine TAC 1 6.1.2 Continue to genetically characterize and screen all brood fish and to track parentage of all fish produced Long-term FWS ASC 60K 60K 60K

1 6.2 Ensure that management plans consider and avoid negative genetic effects of management actions Long-term FWS NMFS ASC 1 6.4 Monitor genetic diversity, including parentage of smolts and returning adults Long-term FWS ASC 30K 30K 30K

1 7.1.1A Monitor adult returns at existing fishways and weirs Long-term ASC 60K 60K 60K

1 7.1.1B 

Construct weirs on the East Machias and Machias rivers to monitor adult returns

2 years FWS NMFS ASC 

1 7.1.1C Conduct intensive redd counts on all DPS rivers to index spawning 

escapement

Long-term ASC 10K 10K 10K 

1 7.1.2A 

Continue basinwide assessment of large parr abundance and measurement of biological characteristics in the Narraguagus and Dennys river systems 

Long-term NMFS ASC

100K 100K 100K

1 7.1.3 Conduct quantitative assessments of Atlantic salmon smolt production Long-term NMFS ASC 250K 250K 250K 

1 7.1.4A Continue telemetry studies of smolt migration from the Dennys and Narraguagus rivers 3 years NMFS ASC 100K 100K 100K 

1 7.1.4C Continue post-smolt surface trawling assessment programs and expand the temporal and spatial extent of coverage 3 years NMFS 283K 283K 283K

1 7.1.5 

Continue to participate and contribute to international cooperative research and assessment efforts to improve our understanding of salmon at sea

Long-term NMFS FWS ASC

150K 150K 150K

1 8.2

Maintain, and if necessary increase, coordination/communications between government and local agencies on issues pertaining to Atlantic salmon recovery

Long-term NMFS FWS ASC 

5-6
IMPLEMENTATION SCHEDULE

ATLANTIC SALMON RECOVERY PLAN

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

2 1.1.1A

Conduct IFIM studies on additional DPS rivers to determine flow requirements of juveniles

3 years USGS, FWS, 

NMFS

ASC

75K 75K 

2 1.1.1B Determine flow requirements of adult Atlantic salmon in DPS rivers 5 years USGS, FWS, NMFS ASC 

2 1.1.2A 

Continue analyses of historical flow data for DPS rivers to assess changes over time or hydrologic differences between the rivers that may affect salmon recovery efforts.

1 year USGS MGS

20K Cost TBD

2 1.1.2B Maintain existing USGS stream gages on DPS rivers Long-term USGS MGS ASC 120K 120K 120K 

2 1.1.3A

Implement the Downeast Salmon Rivers Water Use Management Plan (WUMP) for the Pleasant and Narraguagus rivers and Mopang Stream

5 years USGS FWS 

NRCS

DAFRR, Industry ASC, DEP, LURC 1M 1M 1M

2 1.1.3D

Develop water use management plans for other DPS rivers 3 years FWS DAFRR, Industry 

LURC DEP MSPO NGOs

250K

2 1.1.3E

Continue periodic assessments of irrigation methods and water demands and their potential effects on hydrology and Atlantic salmon habitat

Long-term NRCS DAFRR DEP LURC 

Industry 20K

2 1.1.5B

Review current water management for the dams and develop an assessment of the effect of regulation on a watershed’s hydrology and thus Atlantic salmon habitat

2 1.2.2D Model the impact on air and water quality issues, especially acid precipitation, on productivity of salmon in DPS rivers 2 years EPA FWS NMFS DEP UM ASC 45K 45K

2 1.2.2E 

Evaluate current agricultural practices such as soil acidity management practices to determine whether they may affect pH levels in DPS rivers 

3 years FWS, NRCS Industry, MDOC 

MWBC

2 1.2.2I 

Identify and consider appropriate management measures and techniques to mitigate the potential impacts of agricultural chemicals and other contaminants on the DPS

Duration TBD FWS EPA DEP BPC MDA MDOC

Industry

2 1.2.2H 

Evaluate the chronic and acute effects of agricultural chemicals on Atlantic salmon and how they may impact salmon recovery efforts

3 years FWS NMFS BPC, DEP, ASC

75K 75K 75K

2 1.2.2K

Conduct research on the mechanisms of non-pesticide organochlorines exposure, uptake and effect in rivers where these contaminants are known to occur including, the Dennys below the Eastern Surplus Superfund site

3 years EPA USGS 

FWS

DEP UM 

25K 25K

2 1.2.2L 

Continue State program to replace OBDs 3 years DEP 

2 1.2.3B Implement a comprehensive and integrated long-term water quality monitoring program on all DPS rivers 

2 1.2.4A Prepare and implement NPS pollution reduction plans for DPS rivers 3 years FWS NMFS EPA ASC DEP MFS SWCD NGOs 100K 100K 100K 

5-7
IMPLEMENTATION SCHEDULE

ATLANTIC SALMON RECOVERY PLAN

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

2 1.2.4C 

Prepare and implement Point Source pollution reduction plans for DPS rivers 2 year EPA DEP

32K Y3 Costs TB

2 1.2.4E Continue monitoring of the remediation efforts at the Eastern Surplus Superfund site in Meddybemps periodic EPA DEP 15K 15K 

2 1.2.4F Address any ground water problems at the Smith junkyard on the Dennys River and restore the site Duration TBD EPA DEP 2 1.3.1A Repair or remove the Coopers Mill Dam to improve fish passage around the dam 1 year FWS ASC IFW DMR Local Gov 65K

2 1.3.2 Identify and improve culverts or other road crossings that impede salmon 

passage

Long-term FWS NRCS 

NMFS

ASC MFS MDOT NGOs Industry 75K 75K 

2 1.3.4 

Condition permits for activities within the estuaries of DPS rivers so as to minimize potential effects on migration of juveniles and adults 

Long-term ACOE ASC 

45K 45K 

2 1.4.1A 

Provide long-term protection for riparian buffers through fee acquisition, conservation easements, conservation and management agreements, and other appropriate tools

Long-term NRCS FWS LURC MFS Industry 

ASC NGOs 5 Million 5 Million 5 Million

2 1.4.1B Promote the adoption and use of BMPs by landowners and compliance with these voluntary standards Long-term MFS landowners NGOs 25K 25K 

2 1.4.1D 

Evaluate current state and local land use regulations to determine adequacy of existing measures protecting riparian habitat and instream improve if appropriate

2 year NRCS FWS ASC LURC MSPO 

MFS DAFRR 25K 25K

2 1.4.1E

Enhance protection of riparian areas where necessary through expanded enforcement and modifications to the Natural Resource Protection Act, Forest Practices Act, LURC Zoning standards, and/or Municipal Shoreland Zoning

Long-term LURC 

2 1.4.2A Evaluate the potential for activities in estuaries to adversely affect Atlantic salmon Long-term NMFS FWS ACOE Exisitng resources Exisitng resources Existing resources

2 1.4.2B Condition permits for activities within the estuaries of DPS rivers so as to minimize potential effects on Atlantic salmon Long-term NMFS FWS ACOE Exisitng resources Exisitng resources Existing resources

2 1.5.4 

Evaluate the potential of stream flow augmentation as a recovery tool to help meet Atlantic salmon flow needs and increase juvenile production and survival

1 year FWS ASC MGS

60K 60K

2 2.1.3B Continue US participation in the international sampling program at West Greenland Long-term NMFS 30K 30K 30K

2 2.1.3C 

Continue efforts to implement a biological sampling program at St. Pierre et Miquelon to determine the origin of Atlantic salmon captured in this fishery

Long-term NMFS USDOS 

Intnl. Partners 70K

2 2.2.1A Assess the level of incidental take of Atlantic salmon by recreational anglers. Long-term FWS IFW ASC 25K 10K 

2 2.2.1D Continue to monitor commercial freshwater fisheries where the potential for incidental take of Atlantic salmon exists Long-term DMR ASC IFW 2 2.2.2A Assess the potential risk for incidental take of Atlantic salmon in marine and estuarine fisheries 3 years NMFS DMR ASC 45K 45K 45K 

5-8
IMPLEMENTATION SCHEDULE

ATLANTIC SALMON RECOVERY PLAN

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

2 2.2.2B 

Develop appropriate management strategies and regulatory measures to avoid bycatch of Atlantic salmon in estuarine and marine fisheries where significant potential for bycatch has been identified 

Duration TBD NMFS DMR, ASC 

2

2.2.2C Increase observer coverage in the midwater trawl herring fishery to improve 

the ability to assess the potential for Atlantic salmon bycatch in the herring fishery.

NMFS NEFMC DMR 

2 3.1.1A 

Identify and catalogue locations that restrict passage and/or concentrate salmon and thereby increase the vulnerability of salmon to predation

1 year FWS NMFS ASC IFW DMR 

20K

2 3.1.1B 

Review existing salmon population management practices to determine if they increase the vulnerability of juvenile salmon to cormorant predation 

3 year FWS ASC UM

25K 25K 25K

2 3.1.1C Document and monitor the presence and abundance of potential salmon predators at natural and man-made concentration sites 3 years FWS NMFS ASC UM 25K 25K

2 3.1.2A Evaluate the potential of cormorant predation to adversely affect the recovery of the DPS 3 years FWS NMFS ASC IFW 25K 25K

2 3.1.2B 

Identify specific cormorant colonies within the DPS that may inflict significant levels of depredation on DPS salmon populations and implement appropriate experimental management measures

4 years FWS NMFS ASC

20K 20K 20K

2 3.1.3A Evaluate the effect of seal predation on the recovery of the DPS Duration TBD FWS NMFS ASC 

2 3.1.3B Document and monitor the presence and abundance of seals at natural and man-made concentration sites 3 years NMFS FWS ASC UM 25K 25K 

2 3.1.3C Conduct research to determine the role of net pen sites in seal aggregation and salmon predation 3 years NMFS FWS ASC UM 25K 25K 

2 3.1.3D 

Evaluate the potential of alternative research techniques and food habit sampling methodologies to help assess seal predation on Atlantic salmon

3 years NMFS ASC UM

35K

2 3.1.3E 

Develop and implement appropriate management measures to mitigate the impact of documented seal predation on wild salmon populations

Duration TBD NMFS FWS ASC 

2 3.1.4 Assess potential effects of other predators 3 years NMFS FWS ASC, UM 2 3.2.1C 

Suspend stocking of brown trout immediately in all DPS rivers until the potential impacts of these introductions can be fully assessed 

IFW ASC 

2 3.2.1D 

Monitor potential adverse interactions of existing stocking programs for freshwater salmonids (i.e., splake, landlocked salmon, brook trout) in headwater lakes of DPS rivers to determine the potential impacts of these programs on the DPS

1 year NMFS FWS IFW ASC

30K 30K 30K

2 4.1A 

Evaluate new aquaculture lease and permit applications to ensure that net pens and equipment are adequate for site location and potential storm impact.

Long-term ACOE NMFS 

FWS

DMR ASC 

30K 30K

5-9
IMPLEMENTATION SCHEDULE

ATLANTIC SALMON RECOVERY PLAN

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

2 4.1D Develop and maintain an inventory tracking system for all marine aquaculture facilities Long-term NMFS ACOE FWS DMR Industry 2 4.1E 

Assess, document and monitor damage caused by seal predation that may lead to the escapement of farmed salmon into the environment

3 years NMFS Industry, UM, DMR

15K 15K

2 4.2.1 Develop and implement contingency measures in case of accidental release of farmed fish Long-term NMFS ACOE FWS ASC Industry 10K 2K 2K 

2 4.2.2A Maintain existing weirs on DPS rivers to minimize aquaculture escapees spawning, enable data collection and collect broodstock Long-term NMFS FWS ASC Industry 132K 264K 264K 

2 4.2.2B 

Construct weirs on DPS rivers, including the East Machias and Machias rivers, where necessary to exclude aquaculture escapees, enable data collection and collect broodstock

Long-term NMFS FWS ASC Industry

831K

2 4.2.3 Mark all farmed salmon prior to placement into marine net-pens Long-term Industry 100K 100K 100K 

2 4.2.4 Discontinue the culture of non-North American salmon 5 years ACOE NMFS FWS Industry 

2 4.2.5 Prohibit the placement into marine net-pens of reproductively viable transgenic salmon ACOE NMFS FWS DMR Industry 

2 4.3.1B 

Develop and implement comprehensive integrated bay management plans that include coordination of stocking densities, harvesting and fallowing and disease treatment and management

3 years USDA NMFS 

FWS ACOE

DMR Industry NGOs ASC

50K 50K 50K

2 4.3.1C Revise federal import regulations (Title 50) to include the ISA virus 1 year FWS 10K

2 4.3.1D 

Maintain and update existing fish health guidelines and protocols as necessary, to control the introduction of new pathogens and continue to provide protection from disease

Long-term NMFS FWS ASC DMR 

2 4.3.1E Expand the FWS Wild Fish Health Survey to include DPS rivers Long-term FWS ASC 20K 20K 20K 

2 4.3.1F

Implement biosecurity and disinfection protocol for all research and assessment activities being conducted in rivers within the DPS

NMFS FWS EPA USGS

ASC DMR IFW 

2 4.3.2C 

Initiate screening and long-term monitoring of resident and migratory fish in aquaculture production bays for endemic and exotic salmonid pathogens. 

Long-term NMFS Industry DMR

120K 120K 120K

2 4.3.2D Continue active research programs on immunization of farmed fish 3 years USDA FWS Industry DMR 

2 4.3.3A 

Investigate the potential of sea lice to adversely affect the DPS and the role of salmon aquaculture sites as a reservoir for this parasite 

3 year NMFS ACOE 

FWS

Industry DMR 

2 4.3.3B Regularly test and report sea lice burdens at individual net-pen facilities. Long-term Industry, DMR 2 4.3.3C Continue treatment for sea lice at aquaculture facilities Long-term USDA Industry DMR UM 2 4.4.1A 

Develop and operate fully functional containment management systems for the containment of farmed salmon at freshwater hatchery sites.

Long-term Industry DEP IFW 

5-10
IMPLEMENTATION SCHEDULE

ATLANTIC SALMON RECOVERY PLAN

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

2 4.4.1C 

Develop and maintain an inventory tracking system that facilitates the accurate tracking of total numbers of salmon smolts being produced by the hatchery

Long-term ACOE NMFS 

FWS

Industry DEP DMR

30K 30K

2 4.4.2 Develop contingency plans to reduce adverse impacts if containment measures fail 2 years Industry DEP 

2 5.1.3B Continue to assess and evaluate the results of the adult stocking program 2 years NMFS ASC, TAC2 5.1.3C Evaluate the role of streamside incubation facilities to supplement wild salmon populations 5 years NMFS FWS ASC, TAC 40K 40K 40K 

2 5.2.3B Conduct research on other pathogens to identify potential threats to the DPS NMFS FWS ASC 15K 

2 5.2.3C Initiate screening and long-term monitoring of resident fish species in DPS rivers for endemic and exotic salmonid pathogens Long-term NMFS FWS ASC 20K 20K 20K 

2 5.3A 

Develop and implement procedures at federal hatcheries to identify potential escape sources and implement the appropriate modifications

Long-term FWS See Action 

5.3A

2 5.3B 

Implement discharge and effluent management protocols for all federal hatcheries with the goal of controlling and minimizing release of juveniles

2 year FWS EPA DEP

20K Y3 Costs TB

2 6.3 Explore methods for long-term preservation of gametes and genes for future use (e.g., cryopreservation) 3 year FWS, NMFS, USGS ASC UM 15K 30K 

2 7.1.1D 

Continue development of DPS-level estimates of spawning escapement Long-term NMFS ASC, TAC 

2 7.1.1E Develop accurate extrapolation methods to estimate abundance in areas where traditional redd counts are not feasible or practical 2 year NMFS ASC, TAC 

2 7.1.2B Expand assessments of large parr abundance to a third DPS river Long-term NMFS ASC, TAC 50K 50K 

2 7.1.2C Establish 6-10 index sites to assess large parr abundance and biological characteristics in the remaining DPS rivers 2 years NMFS ASC, TAC 50K 50K 

2 7.1.4B 

Expand spatial coverage of detection arrays to better assess movements of post-smolts in the Gulf of Maine and the Bay of Fundy

3 years NMFS ASC

283K 283K

2 7.1.6 Develop and apply population viability analysis model 1 year NMFS FWS ASC 25K 

2 8.1A Develop and implement a comprehensive Education and Outreach Plan for the Gulf of Maine DPS of Atlantic salmon Long-term NMFS FWS ASC 75K 75K 

2 8.1B Continue efforts to educate anglers on the difference between trout and juvenile salmon Long-term NMFS FWS ASC IFW DMR 15K 15K 

2 9.4

Continue to evaluate Atlantic salmon populations in other rivers within the range of the DPS and the appropriateness of their protection under the ESA

5 years NMFS FWS ASC

25K 25K

3 1.1.3C Assess and monitor other agricultural water use needs and demands within DPS river watersheds Long-term NRCS LURC DEP 30K 30K 

5-11
IMPLEMENTATION SCHEDULE

ATLANTIC SALMON RECOVERY PLAN

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

3 1.1.5A

Review current water management for the dams and develop an assessment of the effect of regulation on a watershed’s hydrology and thus Atlantic salmon habitat.

3 1.2.1

Review existing water quality standards for each river within the DPS to determine adequacy to meet the needs of Atlantic salmon 

1 year FWS ASC DEP 

3K

3 1.2.3C 

Monitor water temperatures in the vicinity of blueberry process water discharge sites on the Machias and Narraguagus rivers to assess the potential impact on Atlantic salmon

Long-term FWS USGS DEP NGOs Industry

10K

3 1.2.4D Fully implement EPA aquaculture wastewater and effluent discharge regulations Duration TBD EPA FWS DEP 3 1.3.1B Evaluate the need to repair the existing fishway at Saco Falls 1 year ASC 50K 

3 1.3.3 Identify and manage natural debris jams (including beaver dams) that impede salmon passage Long-term FWS ASC NGOs 5K 5K 

3 1.5.2A Identify, catalogue and prioritize habitat restoration needs in DPS rivers 2 years FWS NMFS ASC NGOs 32K 

3 1.5.2B Identify, catalogue and prioritize habitat restoration needs in estuarine habitat of DPS rivers 2 years FWS NMFS ASC NGOs 32K3 3.1.1D Assess the potential of land and water use practices to exacerbate predation 

rates

2 years FWS NMFS ASC 25K 

3 4.2.6 Continue research into developing strains of aquaculture fish that cannot interbreed with wild Atlantic salmon Duration TBD Industry UM 75K3 4.3.2E 

Develop an effective diagnostic technique for the SSS virus and determine the distribution of SSS virus within the geographic range of the DPS 

3 years USWFS NMFS Cornell U. ASC

25K

3 8.1C 

Develop updated educational programs for schools Long-term NMFS FWS ASC

10K

3 8.1D Evaluate the role of public display of salmon as an outreach tool 1 year NMFS FWS3 9.1 Appoint a Recovery Implementation Team to coordinate implementation of recovery plan objectives NMFS FWS ASC 

3 9.2A Conduct an annual review of the implementation schedule Long-term NMFS FWS ASC, TAC 5K 5K 

3 9.2B Complete a biennial progress report on completion of recovery tasks Long-term NMFS FWS ASC 5K 5K 

3 9.3

Complete necessary addenda, updates and revisions to the Recovery Plan Long-term NMFS FWS ASC 

5-12
6-1

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ME. 

Ainley, D.G. 1984. Comorants Family Phalacrocoracidae. Pages 92-101 in D. Haley ed. 

Seabirds of the eastern North Pacific and Arctic waters. Pacific Search Press, 

Seattle. 214 p. 

Alexander, G. R. 1977. Consumption of small trout by large predatory brown trout in the 

North Branch of the Au Sable River, Michigan. Michigan Department of Natural 

Resources, Fisheries Research Report 1855:1-26. 

Alexander, G. R. 1979. Predators of fish in coldwater streams. Pages 153-170 in H. 

Clepper, ed. Predator-prey systems in fisheries management. Sport Fishing 

Institute, Washington, D.C. 

Allin, L.C. and R.W. Judd. 1995. Creating Maine’s resource economy. Pages 262-288 in 

Judd, R.W., E.A. Churchill and J.W. Eastman editors. Maine: The Pine Tree State 

from Prehistory to Present. Orono ME: University of Maine Press. 

Ambrose, H.E., M.A. Wilzbach, and K.W. Cummins. 2004. Periphyton response to 

increased light and salmon carcass introduction in northern California streams. 

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Anthony, V. C. 1994. The significance of predation on Atlantic salmon. Pages 240-284 

in New England Atlantic salmon management conference. National Marine 

Fisheries Service, Woods Hole, MA. 

Aquatic Nuisance Species (ANS) Task Force. 1994. Intentional introductions policy 

review, findings, conclusions, and recommendations of the intentional 

introductions policy review, report to Congress, March 1994. 

Arter, B.S. 2004. Sheepscot River Water Quality Strategic Plan: A Guide for Coordinated 

Water Quality Monitoring Efforts on an Atlantic Salmon Watershed in Maine. 

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ASA (Atlantic Salmon Authority). 1998. 1997 Endangered species project report B 

annual report number 4. ASA, Bangor, Maine. 

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report. NOAA Grant NA17FL1157. Bangor ME: Maine Atlantic Salmon 

Commission. 
6-2

Atkins, C. G. 1874. On the salmon of eastern North America, and its artificial culture. 

Pages 227-335 in United States Commision of Fish and Fisheries Report of the 

Commissioner for 1872 and 1873, part II. Washington. 

Atkinson, E.J., G. Mackey, and J. Trial. 2004. Substrate embeddedness and juvenile 

Atlantic salmon (Salmo salar) habitat in the Narraguagus River. Unpublished 

report. 

Atkinson, E. J. and Mackey, G. 2005. Survey of Substrate Embeddedness. Maine 

Atlantic Salmon Commission: Atlantic Salmon Freshwater Assessments and 

Research Semi-Annual Project Report. Prepared for NOAA-Fisheries. 

Gloucester, MA. 

Bakshtansky, E.L., I.A.. Barybina, and V.D. Nesterov. 1976. Changes in the intensity of 

downstream migration of Atlantic salmon smolts according to abiotic conditions. 

International Council for the Exploration of the Sea. 1-9. 

Barr, L. M. 1962. A life history of the chain pickerel, Esox niger Lesueur, in Beddington 

Lake, Maine. Master's thesis. University of Maine, Orono. 

Barrett, R. T., N. Røv, J. Loen, and W. A. Montevecchi. 1990. Diets of shags 

Phalacrocorax aristotelis and cormorants P. carbo in Norway and possible 

implications for gadoid stock recruitment. Marine Ecology Progress Series 66: 

205-218. 

Barton, BA. 1977. Short-term effects of highway construction on the limnology of a 

small stream in southern Ontario. Freshwater Biology 7: 99-108. 

Baum, E. T. 1997. Maine Atlantic Salmon: A National Treasure. Atlantic Salmon 

Unlimited. 224 pp. 

Baum, E. T. Division of Fisheries and Oceans (DFO). 1998. History and description of 

the Atlantic salmon aquaulture industry of Maine. Canadian Stock Assessment 

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Baum, E.T. 2001. US/Ireland cooperative program on salmon aquaculture industry. Final 

Report. 34 pp. 

Baum E.T., R.M. Jordan. 1982. The Narraguagus River, an Atlantic salmon river 

management report. Atlantic Sea Run Salmon Commission. Bangor, Maine. 

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42-47. 
7-1

APPENDIX 1: LISTING FACTORS (THREATS) AND RECOVERY TASKS 

LISTING FACTORS/RECOVERY ACTIONS 

Listing Factor* Threat Recovery Actions 

A Water Use 

1.1.1A; 1.1.1B; 1.1.2A; 1.1.2B; 1.1.2C; 1.1.2D; 

1.1.3A; 1.1.3B; 1.1.3C; 1.1.3D; 1.1.3E; 1.1.4A; 

1.1.4B; 1.1.5A; 1.1.5B 

A Water Quality 

1.2.1; 1.2.2L; 1.2.3A; 1.2.4C; 1.2.4D; 1.2.4E 

A Acidified Water and Aluminum 

1.2.2A; 1.2.2B; 1.2.2C; 1.2.2D; 1.2.2E; 1.2.2F; 

1.2.3A 

A Pesticides, other contaminants 

and endocrine disruption 

1.2.2G; 1.2.2H; 1.2.2I; 1.2.2J; 1.2.2K; 1.2.3A; 1.2.4F 

A Sedimentation 

1.2.4A; 1.2.4B; 1.3.4 

A Excess Nutrients 

1.2.3A; 1.2.4A; 1.2.4C 

A Elevated Water Temperatures 

1.2.3A; 1.2.3B; 1.2.3C 

A Obstruction to Passage 

1.3.1; 1.3.1A; 1.3.1B; 1.3.2; 1.3.3; 1.3.4; 1.1.5A; 

1.1.5B 

A Manmade Barriers 

1.3.1; 1.3.1A; 1.3.1B; 1.3.2 

A Natural Barriers 

1.3.3; 1.3.4 

A Habitat Protection 

1.4.1A; 1.4.1B; 1.4.1C; 1.4.1D; 1.4.1E; 1.4.2A; 

1.4.2B 

A Ecosystem Function and Habitat 

Restoration 

1.5.1; 1.5.2A; 1.5.2B; 1.5.3; 1.5.4; 1.5.5 

B Commercial and Recreational 

Fisheries 

2.1.1; 2.1.2; 2.1.3A; 2.1.3B; 2.1.3C; 2.2.1A; 2.2.1B; 

2.2.1C; 2.2.1D; 2.2.2A; 2.2.2B; 2.2.2C 

B US Fisheries 

2.1.1; 2.1.2; 2.1.3A; 2.1.3B; 2.1.3C; 2.2.1A; 2.2.1B; 

2.2.1C; 2.2.1D; 2.2.2A; 2.2.2B; 2.2.2C 
7-2

Listing Factor* Threat Recovery Actions 

B Canadian Fisheries 

2.1.3; 2.1.3A 

B West Greenland Fishery 2.1.3A; 2.1.3B 

B St. Pierre et Miquelon 2.1.3C 

C Disease 

4.3.1A; 4.3.1B; 4.3.1C; 4.3.1D; 4.3.1E; 4.3.1F; 

4.3.2A; 4.3.2B; 4.3.2C; 4.3.2D; 4.3.1E; 4.3.3A; 

4.3.3B; 4.3.3C; 5.2.1; 5.2.2; 5.2.3A; 5.2.3B; 5.2.3C 

C Infectious Salmon Anemia (ISA) 

4.3.1A; 4.3.1B; 4.3.1C; 4.3.1D; 4.3.1E; 4.3.1F; 

4.3.2A; 4.3.2B; 4.3.2C; 4.3.2D; 4.3.3A; 4.3.3B; 

4.3.3C; 5.2.1; 5.2.3A; 5.2.3 

C Salmon Swimbladder Sarcoma 

(SSS) 

4.3.1D; 4.3.1E; 4.3.1F; 4.3.2C; 4.3.2E; 5.2.1; 5.2.3A; 

5.2.3 

D Predation 

3.1.1A; 3.1.1B; 3.1.1C; 3.1.1D; 3.1.2A; 3.1.2B; 

3.1.2C; 3.1.3A; 3.1.3B; 3.1.3C; 3.1.3D; 3.1.3E; 

3.1.4; 3.2.1A; 3.2.1B; 3.2.1C; 3.2.1D; 3.2.1E; 3.2.2 

D Marine Mammals 

3.3.1A; 3.1.1C; 3.1.1D; 3.1.2C; 3.1.3A; 3.1.3B; 

3.1.3C; 3.1.3D; 3.1.3E 

D Avian Predators 

3.1.1A; 3.1.1B; 3.1.1C; 3.1.1D; 3.1.2A; 3.1.2B; 

3.1.2C 

D Double-crested Cormorants 

3.1.1B; 3.1.1C; 3.1.1D; 3.1.2A; 3.1.2B; 3.1.2C 

D Mergansers 

3.1.2C; 3.1.4 

D 

Piscine Predators and 

Competitors 

3.1.2C; 3.1.4; 3.2.1A; 3.2.1B; 3.2.1C; 3.2.1D; 

3.2.1E; 3.2.2 

D Freshwater 

3.1.2C; 3.2.1A; 3.2.1B; 3.2.1C; 3.2.1D; 3.2.1E; 3.2.2 

D Estuarine and Marine 

3.1.2C; 3.1.4 

E Water withdrawals 

1.1.1A; 1.1.1B; 1.1.2A; 1.1.2B; 1.12C; 1.1.2D; 

1.1.2E; 1.1.3A; 1.1.3B; 1.1.3C; 1.1.3D; 1.1.3E; 

1.1.4A; 1.1.4B 

E Disease 

4.3.1A; 4.3.1B; 4.3.1C; 4.3.1D; 4.3.1E;4.3.2A; 

4.3.2B; 4.3.2C; 4.3.2D; 4.3.1E; 4.3.3A; 4.3.3B; 

4.3.3C 
7-3

Listing Factor* Threat Recovery Actions 

E Aquaculture 

4.1A; 4.1B; 4.1C; 4.1D; 4.1E; 4.2.1; 4.2.2A; 4.2.2B; 

4.2.3 ;4.2.4; 4.2.5; 4.2.6; 4.3.1A; 4.3.1B; 4.3.1C; 

4.3.1D; 4.3.1E; 4.3.1F; 4.3.2A; 4.3.2B; 4.3.2C; 

4.3.2D; 4.3.2E; 4.3.3A; 4.3.3B; 4.3.3C; 4.4.1A; 

4.4.1B; 4.4.1C; 4.4.2 

F Salmon Aquaculture 

4.1A; 4.1B; 4.1C; 4.1D; 4.1E; 4.2.1; 4.2.2A; 4.2.2B; 

4.2.3; 4.2.4; 4.2.5; 4.2.6; 4.3.1A; 4.3.1B; 4.3.1C; 

4.3.1D; 4.3.1E; 4.3.1F; 4.3.2A; 4.3.2B; 4.3.2C; 

4.3.2D; 4.3.2E; 4.3.3A; 4.3.3B; 4.3.3C; 4.4.1A; 

4.4.1B; 4.4.1C; 4.4.2 

F Marine Survival 

2.1.3A; 2.1.3B; 2.1.3C; 2.2.1A; 2.2.1C; 2.2.2A; 

2.2.2B; 2.2.2C; 3.1.3A; 3.1.3B; 3.1.3C; 3.1.3D; 

3.1.3E; 3.1.4; 4.3.3A; 4.3.3B; 4.3.3C; 7.1.4A; 

7.1.4B; 7.1.4C; 7.1.5 

F Low abundance and survival 

 

5.1.1A; 5.1.1B; 5.1.2; 5.1.3A; 5.1.3B; 5.1.3C; 

5.1.4A; 5.1.4B; 5.1.4C; 5.3A; 5.3B 

F Conserve genetic integrity 

6.1.1; 6.1.2; 6.2; 6.3; 6.4 

 

Population assessments 

7.1.1A; 7.1.1B; 7.1.1C; 7.1.1D; 7.1.1E; 7.1.2A; 

7.1.2B; 7.1.2C; 7.1.3; 7.1.4A; 7.1.4B; 7.1.4C; 7.1.5; 

7.1.6 

 

Education and Outreach 

8.1A; 8.1B; 8.1C; 8.2 

 

Assess recovery program 

9.1; 9.2A; 9.2B; 9.3 

*Listing Factors: 

A. Causes of Present or Threatened Destruction, Modification or Curtailment of Habitat or Range 

B. Overutilization for Commercial, Recreational, Scientific, or Educational Purposes 

C. Disease 

D. Predation and Competition 

E. Inadequacy of Existing Regulatory Mechanisms 

F. Other Natural and Manmade Factors Affecting the Species Continued Existence
8-1

APPENDIX 2: REGULATORY PROTECTIONS 

Maine Laws and Regulations 

Department of Conservation 

Land Use Regulation Law, 12 MRSA §§ 681-689 

Forest Practices Act, 12 MRSA §§ 8867-8869 

Forest Products Refuse Act, 38 MRSA § 417 

Tree Growth Tax Law, 36 MRSA § 578 

Department of Marine Resources 

Fishways Laws, 12 MRSA §§ 6121-6125 

Commercial and Sport Fishing Limits, 12 MRSA § 6553 

Importation, Leases, Research 12 MRSA §§ 6071(4), 6072, 6078 

Fish Health, 12 MRSA § 7202 

Maine Department of Inland Fisheries and Wildlife 

Fish Hatcheries Laws, 12 MRSA §§ 7611-7674 

Fishways and Dams Laws, 12 MRSA §§ 7701-A to 7702 

Atlantic Salmon Laws, 12 MRSA §§ 9901-9907 

Maine Department of Environmental Protection 

Maine Rivers Laws, 12 MRSA §§ 401-407 

Water Quality Laws, 38 MRSA §§ 361-372, 401-424, 451-452, 464-470, 571 

Mandatory Shoreland Zoning Act, 38 MRSA §§ 435-449, 436-A, 437, 438-A, 439-A -

441, 443-A -449 

Natural Resources Protection Act, 38 MRSA §§ 480-A to 480-U 

Site Location of Development Law, 38 MRSA §§ 481 to 490-J 

Maine Waterway Development and Conservation Act, 38 MRSA §§ 630-637, 640 

Maine Dam Registration, Abandonment, and Water Level Act, 38 MRSA §§ 815-818, 

830-843 

Oil and Hazardous Materials, 38 MRSA §§ 543-550 

Nutrient Management Act, 7 MRSA §§ 4201-4214 

Wastewater Discharge Law, 38 MRSA § 413 

Atlantic Salmon Authority 

Enabling Legislation, 12 MRSA §§ 9901-9906 

Atlantic Salmon Angling Prohibition, 12 MRSA § 9907 

Maine Department of Agriculture Food and Rural Resources 

The Right to Farm Law, 17 MRSA §§ 2805 

Board of Pesticide Control Laws, 7 MRSA §§ 601-625 and 22 MRSA § 1471 A-X 

Manure Handling and Spreading Laws, 38 MRSA §§ 2701-B, 417-A 
8-2

Federal Laws and Regulations 

Endangered Species Act of 1973, 16 USC 1531 et seq. 

Fishery Conservation and Management Act of 1976, 16 USC 1801 et seq. 

Fish and Wildlife Coordination Act, 16 USC 661 

Federal Power Act, 16 USC 791a 

Federal Water Pollution Control Act, 33 USC 1251 

Fish and Wildlife Act of 1956, 16 USC 742a 

Federal Aid in Fish Restoration Act, 16 USC 777 

Anadromous Fish Conservation Act, 16 USC 757 

National Environmental Policy Act, 42 USC 4321 

Rivers and Harbor Act of 1899 (33 USC sec. 403). 
9-1

APPENDIX 3: ESTABLISHED EDUCATION AND OUTREACH PROGRAMS AND 

GROUPS IN MAINE 

Project SHARE 

In 1994, project SHARE (Salmon Habitat and River Enhancement), was established to provide a 

forum to protect and enhance Atlantic salmon habitat in the five Downeast Maine salmon rivers 

(Narraguagus, Pleasant, Machias, East Machias and Dennys rivers). Project SHARE provides 

educational and outreach services through bi-monthly forums on salmon related issues; 

coordinating public meetings and educational sessions; and assisting local watershed groups in 

fund raising and capacity building. 

Atlantic Salmon Federation and the Maine Council 

In 1992, the Atlantic Salmon Federation and their affiliate, the Maine Council of the Atlantic 

Salmon Federation, began sponsoring the “Fish Friends” program. Fish Friends provided 

Atlantic Salmon egg incubators to many schools in Maine and other New England states, as well 

as in New Brunswick and Nova Scotia. In 1995, Craig Brook National Fish Hatchery (CBNFH) 

joined in partnership with the Maine Council and extended the program into high schools in 

several central and eastern Maine communities where wild Atlantic salmon populations still 

exist. The CBNFH has supplied Atlantic salmon eggs for Maine schools and one business site in 

the Bangor region each year. The “Fish Friends” and “Salmon-in-Schools” programs educate 

thousand of students each year about Atlantic salmon, their habitat and the general ecology of 

watershed ecosystem ecosystems. The ASF has also developed educational materials designed 

to promote catch and release, fish identification (trout vs. young salmon for example) and raise 

public awareness. 

The Ducktrap Coalition 

In 1995, the Ducktrap Coalition, the watershed council for the Ducktrap River, was established. 

The Coalition established an education committee that has conducted a number of outreach 

programs. Programs include a newsletter sent to all residents of the watershed; press releases 

about the projects conducted by the Coalition; development of a watershed curriculum for 

elementary school students; placement of the Fish Friends salmon nursery aquaria in schools and 

forest management workshops. The Coalition also holds public events called “Ducktrap 

Celebrations” to invite the public to meet the Coalition members and learn about conservation 

efforts in the Ducktrap River watershed. 

The Eight Watershed Councils 

In 1997, the State of Maine published the MASCP. The Plan called for establishing watershed 

councils85 on the seven rivers known to support wild salmon populations. The charge of the 

 

85 Current watershed councils include, Dennys River Watershed Council, East Machias River Watershed 

Council, Machias River Watershed Council, Pleasant River Watershed Council, Narraguagus River 
9-2

watershed councils was to help guide salmon conservation activities specific to each individual 

watershed. Watershed councils are involved in numerous public information and educational 

activities including organizing and facilitating public forums and workshops and establishing and 

maintaining informational kiosks. In 2000, a watershed council was established on Cove Brook 

independent of the State Conservation Plan, though carrying out similar activities. 

The Wild Salmon Resource Center 

In 1991, the Wild Salmon Resource Center was established as an educational and outreach center 

to help increase public awareness and knowledge about wild Atlantic salmon in Maine. The 

Center has organized public field trips and helped develop a K-12 ecology/watershed curriculum 

utilizing Atlantic salmon biology and conservation issues. 

Soil and Water Conservation Districts: 

The Soil and Water Conservation Districts (SWCD) play an important role in Atlantic salmon 

outreach and education efforts. The SWCD provide professional resources to local volunteer 

groups, businesses and, local, state and federal governments. 

The SWCD outreach efforts include hosting workshops on land and water conservation measures 

to minimize the impacts from irrigation and pesticide use, identifying and remediating nonpoint 

source pollution problems and educating land owners on forest and agriculture BMPs. The 

SWCD also provide technical expertise in conducting watershed assessments and surveys, assist 

state agencies with water quality planning and monitoring and coordinate community based 

restoration and river cleanup efforts. 

State Fisheries Agencies 

The ASC and IFW have developed catch and release brochures and identification pamphlets that 

are distributed as wallet inserts to recreational anglers and are included in fishing regulations 

handbooks. The identification pamphlets provide information on characteristics that distinguish 

juvenile salmon from other salmonids, such as brook trout and brown trout. 

National Marine Fisheries Service 

NMFS has provided funding to the watershed councils and the Downeast Salmon Federation to 

develop education programs and establish kiosks that provide information to the public on 

Atlantic salmon life history and ongoing salmon protection efforts. The NMFS has also 

 Watershed Council, the Ducktrap River Watershed Coalition, Cove Brook Watershed Council and the 

Sheepscot River Watershed Council. In addition, the Ducktrap Coalition is coordinated with the Coastal 

Mountains Land Trust, an active land trust whose mission is to establish a system of conservation lands in 

the Western Penobscot Bay region. The Downeast Salmon Federation is another local organization 

involved Atlantic salmon recovery efforts in Downeast Maine. This organization coordinates the Downeast 

Rivers Coalition, which in turn provides supports the five Downeast watershed councils.
9-3

provided funding for the operation of the Wild Salmon Resource Center in Columbia Falls. The 

NMFS maintains a website (http://www.nero.nmfs.gov/atsalmon/) that provides information on 

the issues related to the recovery and conservation of Maine’s wild Atlantic salmon populations. 

In 2002, NMFS hired an education and outreach coordinator to focus on Atlantic salmon issues. 

The coordinator will focus on promoting and educating the public about efforts to enhance 

Atlantic salmon populations. The coordinator will also assist watershed councils and promote 

cooperative efforts implemented to protect, enhance or restore Atlantic salmon populations. 

The US Fish and Wildlife Service 

The newly reconstructed Craig Brook National Fish Hatchery in East Orland, Maine contains an 

outreach and education center. This facility includes the Atlantic Salmon Museum and a nature 

trail. The education and outreach center is open to school groups and the public. The center 

helps raise public awareness of Atlantic salmon conservation and recovery efforts. In addition, 

the new Craig Brook facility provides meeting facilities for federal, state, tribal, nongovernmental agencies and organizations, groups and individuals engaged in Atlantic salmon 

issues and projects. 

Other Ongoing Outreach and Education Efforts 

Members of the outdoor sporting community, such as recreational anglers and recreational 

vehicle riders are an important audience to inform on how their activities may affect salmon 

recovery. The Maine Department of Conservation (DOC) has taken steps to establish ATV clubs 

and educate recreational riders on responsible practices that minimize the impacts that ATV’s 

have on land and water resources. There has also been considerable efforts by ASC, IFW and 

ASF to make anglers aware of the difference between trout and young salmon to minimize the 

potential take of juvenile salmon. 
10-1

APPENDIX 4: GLOSSARY OF TERMS 

0+ parr: Parr that are less than one year old. 

1SW: a salmon that has passed one December 31st since becoming a smolt. 

2SW: a salmon that has passed two December 31st’ssince becoming a smolt. 

3SW: a salmon that has passed three December 31st’ since becoming a smolt. 

Adaptive management: Adaptive management is a systematic process for continually improving 

management policies and practices by learning from the outcomes of management actions. 

Adaptive management requires the rigorous combination of management, research and 

monitoring to gain critical knowledge currently lacking. 

Alevins: the period after hatching when the salmon feeds only on the yolk sac. Alevins are 

buried within the substrate of the stream bottom. This is the same stage known as “sac fry.” 

Allele: One member of a pair or series of genes that occupy a specific position on a specific 

chromosome. 

Anadromous: a term to describe fish that are hatched and reared in freshwater, migrate to salt 

water and then migrate back to freshwater to spawn. 

Benthic: Relating to or occurring near the bottom of the ocean. 

Black salmon: an adult salmon that has already spawned and is still found in the freshwater 

reaches of the river between November of the year of spawning until the salmon returns to sea 

the following year. Also known as kelt. 

Bright salmon: a salmon that has entered its natal stream upon return from the sea. 

Broodstock: Mature fish held in a hatchery for breeding purposes 

Conservation spawning escapement: Number of returning adults needed to fully use the 

spawning habitat 

Distinct Population Segment (DPS): Defined by the ESA as a population segment that is 

“discrete”, “that is, it is to some extent separated from the remainder of the species, and is 

“significant,” biologically and ecologically. 

Effective population size: the number of individuals in a population contributing directly to the 

gene pool 
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Endocrine: the system of chemical communications within an organism, including hormones 

and other regulatory mechanisms. 

Epizootic: a disease affecting a large number of animals within a geographic area at the same 

time. 

Escaped Salmon: spent part or all of their life cycle undergoing artificial propagation and 

originate from accidental or unplanned releases into the wild. 

Exclusive economic zone (EEZ): area extending up to 200 nautical miles from the US coastline. 

Eyed egg: the stage from the appearance of faint eyes until hatching. 

Fry: the stage between alevin and parr; fish are actively feeding and living in their natal stream. 

Genetic bottle necking: a significant reduction in genetic diversity due to a sudden decrease in 

population size 

Grilse: a 1SW salmon that has matured after one winter at sea. This term applies to salmon that 

have returned to their natal river. 

Heterozygosity: having different alleles at one or more corresponding chromosomal loci. 

Homozygosity: having the same alleles at a particular gene locus on homologous chromosomes. 

Kelt: this term is synonymous with black salmon. 

Landlocked salmon: non-anadromous Atlantic salmon; i.e., these fish do not migrate away from 

the rivers upon maturity. 

MSW salmon: multi-sea winter salmon have matured after two or more winters at sea. 

Native Salmon: wild salmon that are members of a population with no known effects from 

intentional or accidental releases 

Naturalized Salmon: salmon that have spent their entire life cycle in the wild and originate from 

parents, one or both of which were not wild or native salmon 

Nonpoint source pollution: NPS pollution is caused by rainfall or snowmelt moving over and 

through the ground. As the runoff moves, it picks up and carries away pollutants, finally 

depositing them into aquatic environments (e.g., rivers, lakes, wetlands) 

Osmoregulation: the process by which the balance of water and salt is regulated. 
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Parr: juvenile salmon before smoltification; parr are characterized by 8-11 vertical, darkpigmented bars (known as “parr marks”) on silvery sides. 

Pathogen: a disease causing agent, such as a bacteria or virus. 

Pelagic: Relating to or occurring in the open ocean 

Point source pollution: pollutants that come from a concentrated originating point, such as a 

sewer line or a factory. 

Post-smolt: the life stage during the first year of life at sea, from July 1 to December 31 of the 

year the salmon left the river as a smolt. 

Precocious parr: an Atlantic salmon that becomes sexually mature in freshwater without ever 

going to sea. 

Pre-smolt: parr that have began the smoltification process. 

Redd: nest where female salmon lay their eggs. Typically covered with gravel. 

Repeat spawners: adult salmon found in freshwater on its second (or more) spawning migration. 

Riparian: relating to or located on the banks of a river or stream 

Sac-fry: also known as alevin. 

Salmon: any adult salmon after the post-smolt stage. 

Salmonid: fish belonging to the family Salmonidae including salmon and trout. 

Smolt: juvenile salmon that have completed the smoltification process. Smolts are silverycolored and can survive the transition from fresh to salt water. This stage describes juvenile 

salmon during its active migration to sea in the spring. 

Smoltification: the process by which parr change into smolt. This includes osmoregulatory 

changes which allow the fish to survive in salt water. 

Spawning escapement: number of mature salmon that successfully return to their rivers of origin 

to spawn. 

Splake: hybrid of a female lake trout and a male brook trout 

Stock: a species or unit of a species that is a race, a population or a subpopulation generally 

defined for management purposes. 
10-4

Straying: describes fish that spawn in a stream other than the one they were hatched in. 

Stocked Salmon: salmon that have had artificial spawning or rearing techniques applied at some 

point in their life cycle and/or originate from intentional releases to the wild. 

Transgenic fish: a genetically modified fish into which additional genes have been inserted 

Triploid: having three copies of each chromosome, rather than the normal two copies. 

Weir: a structure across a river channel which obstructs the free passage of fish and is used for 

the purpose of taking or facilitating the taking of fish. 

Wild Salmon: salmon that have spent their entire life cycle in the wild and originate from parents 

which were also spawned and continuously lived in the wild. 
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APPENDIX 5: GULF OF MAINE DPS OF ATLANTIC SALMON THREATS 

ASSESSMENT 

Threats Assessment Workshop 

December 3 & 4, 2004, Portland Maine

Workshop Participants 

Melissa Halsted (ASC) 

Pat Keliher (ASC) 

Joan Trial (ASC) 

Meredith Bartron (FWS) 

Carl Burger (FWS) 

Wende Mahaney (FWS) 

Steve Mierzykowski (FWS) 

Jed Wright (FWS) 

Jessica Anthony (NOAA) 

John Kocik (NOAA) 

Mark Minton (NOAA) 

Rory Saunders (NOAA) 

Tim Sheehan (NOAA) 

Severity Index 

0 = negligible to no threat 

1 = Unknown (Uncertain) 

2 = low 

3 = moderate 

4 = high 
Threats Assessment 

Worksheet

Current Severity at Each Lifestage

Threat Source MAGNITUDE # of Rivers 

weighting 1 1 1 1 1 5

Adult 

Spawners

egg

fry

Parr

Smolt

Marine

A. PRESENT (includes historic) OR THREATENED DESTRUCTION, MODIFICATION OR CURTAILMENT OF HABITAT OR RANGE

Water Use

Instream Management 4,5,6,7,8 5 4 4 4 4 3 0 

Extraction 1,2,3,4,5,6,7,8 8 4 4 4 4 2 0 

Water Quality

Acidified water and aluminum 4,5,6,7,8 5 3 4 4 4 4 4 

Chemical Contaminants 1,2,3,4,5,6,7,8 8 3 3 3 3 3 0 

Physical Habitat Alteration

Sedimentation 1,2,3,4,5,6,7,8 8 3 4 3 4 2 2 

Excess Anthropogenic Nutrients 1,3 2 3 2 2 3 2 0 

Elevated Water Temperatures 1,2,3,4,5,6,7,8 8 4 2 3 3 0 0 

Lifestage

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Threats Assessment 

Worksheet

Threat Source MAGNITUDE # of Rivers 

weighting 1 1 1 1 1 5

Adult 

Spawners

egg

fry

Parr

Smolt

Marine

Lifestage

Obstruction to Passage

Manmade Barriers

1,2,3,4,5,6,7,8 8 4 0 2 3 3 0 

Natural Barriers 1,2,3,4,5,6,7,8 8 3 0 2 2 2 0 

B. OVERUTILIZATION FOR COMMERCIAL, RECREATIONAL, SCIENTIFIC OR EDUCATIONAL PURPOSES

U.S. Commercial Fisheries

1,2,3,4,5,6,7,8 8 2 0 0 0 0 1 

U.S. Recreational Fisheries 

1,2,3,4,5,6,7,8 8 3 0 0 2 2 3 

Canadian Fisheries (All) 1,2,3,4,5,6,7,8 8 0 0 0 0 0 2 

West Greenland Fishery 1,2,3,4,5,6,7,8 8 0 0 0 0 0 3 

St. Pierre et Miquelon Fishery

1,2,3,4,5,6,7,8 8 0 0 0 0 0 1 

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Threats Assessment 

Worksheet

Threat Source MAGNITUDE # of Rivers 

weighting 1 1 1 1 1 5

Adult 

Spawners

egg

fry

Parr

Smolt

Marine

Lifestage

Scientific Research 1,2,3,4,5,6,7,8 8 4 0 0 2 2 0 

C. Predation, Disease, and Competition

Cold Water Disease 1,4,6,7,8 5 0 3 4 1 1 0 

Infectious Salmon Anemia (ISA)

1,2,3,4,5,6,7,8 

(4,5,6,7 to lesser 

extent) 8 2 0 0 0 2 2 

Salmon Swimbladder Sarcoma (SSS) 1,4,5,6,7 5 2 1 1 1 1 2 

Marine Mammals

1,2,3,4,5,6,7,8 8 0 0 0 0 0 3 

Avian Predators 1,2,3,4,5,6,7,8 8 2 0 0 3 3 2 

Piscine Predators and Competitors

Introduced 1,2,3,4,5,6,7,8 8 4 3 4 4 4 0 Native 1,2,3,4,5,6,7,8 8 0 0 2 2 0 0 

Marine 1,2,3,4,5,6,7,8 8 0 0 0 0 2 2 

D. INADEQUACY OF EXISTING REGULATORY MECHANISMS (Water Withdrawal, Aquaculture, other)

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Threats Assessment 

Worksheet

Threat Source MAGNITUDE # of Rivers 

weighting 1 1 1 1 1 5

Adult 

Spawners

egg

fry

Parr

Smolt

Marine

Lifestage

E. OTHER NATURAL AND ANTHROPOGENIC FACTORS AFFECTING THE SPECIES’ CONTINUED EXISTENCE

Salmon Aquaculture

Genetic Introgression w/ aquaculture escapees 1,2,3,4,5,6,7,8 8 3 1 1 3 1 1 

Ecological/ Disease 1,2,3,4,5,6,7,8 8 4 4 3 3 3 2 

Hatchery Program

Genetic Introgression 1,4,5,6,7,8 6 4 2 2 2 2 2 

Overrepresentation from excess broodstock 1,4,5,6,7,8 6 4 4 0 0 0 0 

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Threats Assessment 

Worksheet

Threat Source MAGNITUDE # of Rivers 

weighting 1 1 1 1 1 5

Adult 

Spawners

egg

fry

Parr

Smolt

Marine

Lifestage

Artificial Selection/ Domestication 1,4,5,6,7,8 6 4 4 4 4 4 4 

Conflicting Stocking Stages 1,4,5,6,7,8 6 0 0 3 3 3 0 Low Effect Population Size 1,4,5,6,7,8 6 4 2 2 2 2 2 

Restriction of Broodstock to One Location 1,4,5,6,7,8 6 4 4 4 4 4 0 

Other Hatchery Programs (Palermo) 1 1 434440 Poaching 1,2,3,4,5,6,7,8 8 4 0 0 2 2 2 

Depleted Diadromous Fish Communities 1,2,3,4,5,6,7,8 8 2 2 3 3 3 3 Marine Survival 1,2,3,4,5,6,7,8 8 0 0 0 0 0 4 Land Use (development, agri, forestry etc.) 1,2,3,4,5,6,7,8 8 4 4 4 4 4 0 Climate Change 1,2,3,4,5,6,7,8 8 4 4 4 4 4 4 

11-6
12-1

APPENDIX 6: RESPONSE TO PUBLIC AND PEER-REVIEW COMMENTS 

Recovery Plan for the Gulf of Maine 

Distinct Population Segment of Atlantic Salmon 

Response to Public and Peer-Review Comments 

In June 2004, the Services distributed a draft recovery plan for the Gulf of Maine distinct 

population segment (DPS) of Atlantic salmon for public review and comment. During the 90-

day public comment period the Services held two formal public hearings as well as numerous 

meetings and briefings with federal, state, local and private stakeholders to discuss the recovery 

plan. 

The Services received comments from a wide range of stakeholders and interested parties 

including state, federal and local government agencies, local stakeholder groups, NGOs, industry 

and private citizens. The comments received ranged from endorsements of the plan to 

disagreement with specific as well as general elements contained in the plan. Many of the 

comments received provided technical corrections and additional information for the Service’s 

consideration in the preparation of a final plan. 

The Maine ASC coordinated the review of the draft plan by state agencies. The State agencies 

involved in the Plan review were the ASC, DMR, IFW, DEP, DAFRR, BPC, DOC, BPL, MFS, 

MGS, DOT and SPO. 

In addition to public review, the recovery plan underwent peer-review. The Services and the 

state identified and contacted 27 peer reviewers with specific technical and other relevant 

expertise, requesting review and comments on the draft recovery plan. These individuals were 

asked to review relevant sections of the plan for technical accuracy and completeness. The peerreviewers were also asked to identify any specific issues or information that the Services should 

consider in the preparation of a final draft plan. The Services received 8 responses from the 

individuals contacted. 

In conjunction with efforts to prepare a final recovery plan, the Services and the Maine ASC 

conducted a two-day Threats Assessment Workshop in December 2004. The public and peer 

review comments received during the public comment period were explicitly considered by 

workshop participants. In addition, the Services reviewed and considered the recommendations 

of the recent National Research Council’s (NRC) report (see NRC 2004). The results of this 

workshop were incorporated into the final recovery plan. 

The public and peer review comments received during the public comment period have been 

fully considered in the preparation of this recovery plan. In response to comments received the 

Services have made revisions to the draft plan as appropriate. In addition, the Services have 

reviewed and considered the recommendations of the recent NRC (2004) report on Atlantic 
12-2

Salmon in Maine and incorporated the recommendations as appropriate. 

Comment 1: Threats Assessment 

A number of comments were submitted questioning the relationship between the threats 

assessment and the text related to those identified threats and/or their priorities in the 

implementation table. It was suggested that better documentation of the risk assessment method 

used to identify the top threats would be instructive for the reader. Others commented that some 

of the threats were more applicable to some watersheds and not to others. Finally, some 

questioned the estimates of costs in the Implementation Schedule and the State of Maine 

suggested that they could assist the federal Services, with the assistance of the Recovery Team, 

to refine these estimates. 

Response: A workshop was held with state and federal agency experts to conduct a threats 

assessment. The purpose of this workshop was to address the concerns submitted by the public 

with the goal of expanding the section of the recovery plan to include an explanation of the 

process utilized and factors considered in conducting the threats assessment. Another goal was 

to attempt to link the threats assessment to the implementation schedule and to ensure 

consistency in addressing threats throughout the body of the recovery plan. The final plan 

includes a revised threat assessment that was the product of the workshop mentioned above. 

Comment 2: Water Use 

Some comments recommended that the plan take a broader approach to addressing water use 

related to hydrologic manipulation of river flow. Others stated that the terms “excessive or 

unregulated withdrawals” were not accurate or instructive and stated that the Plan did not 

adequately acknowledge the existing state regulatory programs that are in place to guard against 

threats to habitat due to water withdrawal. It was suggested that too much emphasis was placed 

on water withdrawal in the plan and that the plan should focus on a solution based approach as 

agreed to by private and public, State and Federal partners in the Downeast Rivers Water Use 

Management Plan (WUMP) developed under the State Atlantic Salmon Conservation Plan 

instead of focusing on water-use permitting. 

The Downeast Salmon Federation (DSF) states that the draft plan should specifically state that 

the Water Use Management Plan (WUMP) is not comprehensive enough to truly deserve the 

name. DSF states that a reader of the recovery plan unfamiliar with the WUMP might conclude 

that these “plans” address cumulative as well as individual withdrawals. DSF comments that the 

WUMP actually addresses only those withdrawals made by the larger industry users and does not 

do a thorough or precautionary job of planning or managing water use in these watersheds. 

Lastly, DSF states that the documents referred to as the WUMP provide a basis from which to 

move forward, but are sorely lacking in addressing the impact of the full range of irrigators 

within these watersheds. 

Response: The Recovery Plan endorses the implementation of the WUMP as an important 

recovery action for the DPS. The Services agree with the comment that the practical threat of 

water use is much less today than it was in 1995 when the State Conservation Plan was being 
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developed. As explained in the Plan, the WUMP is a significant accomplishment and provides 

an excellent foundation as a planning document. In order for it to be effective as a tool for the 

protection and recovery of Atlantic salmon, however, the WUMP needs to be endorsed by the 

state regulatory agencies and consistently applied in the State of Maine in both organized and 

unorganized territories. While voluntary compliance with the WUMP by growers may be 

reducing the practical threat of water withdrawals to salmon and their habitat today, it does not 

provide security into the future that this threat will remain reduced. 

Comment 3: Forestry

Some comments were submitted concurring with the conclusion in the draft plan that current 

timber harvesting activities do not represent a significant threat under current management 

measures and harvest practices. Other commenters questioned the basis for this conclusion. 

They cited the following potential impacts from forest practices: sedimentation, thermal loading, 

altering water chemistry, altering hydrology and limiting large woody debris. Other commenters 

raised concern that changes in land ownership could lead to increased harvesting and impacts to 

Atlantic salmon and their habitat. One comment requested that the Services review the state 

laws that govern forest management and timber harvesting and another comment specifically 

stated that the State of Maine’s Forest Practices Act provides little protection to smaller order 

streams. In addition, some stated that there was little to no enforcement of existing forest laws 

and regulations. Some commenters contend that the draft plan does not adequately describe the 

forestry issue. DSF states that forestry practices impact watershed productivity particularly 

when first order streams do not receive adequate protection from cutting activities. These 

commenters state that these streams receive the least protection under current law and the least 

emphasis under current conservation easement strategies and as a result these water bodies are 

experiencing the most abuse and neglect. 

Response: In the recovery plan we acknowledge that forestry practices can negatively impact 

Atlantic salmon habitat. Due to state laws and best management practices (BMPs), widespread 

problems with forestry practices have not been documented. These impacts can occur, however, 

and in some cases the protective measures currently in place are best management practices that 

are not regulatory in nature. In general, landowners are required to protect water quality and to 

utilize best management practices to ensure that water quality is not negatively impacted by 

harvesting. The BMPs are not prescriptive in nature, however, and instead require what is 

necessary to achieve the outcome of preventing negative impacts to water quality. Foresters are 

provided with a range of BMPs and training in those techniques, but the ultimate decision of 

what specific techniques to apply is left to their discretion in light of the site specific 

circumstances. We acknowledge that land ownership is changing in Downeast Maine and we 

cannot take for granted the excellent relationship we have had with landowners in the past who 

have voluntarily adopted protective measures for Atlantic salmon. Efforts to work with new 

landowners are ongoing and Project SHARE has been very instrumental in this effort. It will be 

important during implementation of the recovery plan for the Services to continue to work with 

landowners and the Maine Forest Service to ensure that salmon habitat is not negatively 

impacted by forestry practices. 
12-4

Comment 4: Land Acquisition & Riparian Buffers 

Some suggested land acquisition and conservation easements should be pursued in areas that are 

threatened with serious, immediate, development pressure, where the relationship between 

specific land use changes and habitat degradation is firmly established and where high value 

habitat is at risk. Others argued that the case for riparian buffer protection is based on the 

presumed impacts of sedimentation, removal of shade and associated increases in stream 

temperature, alteration of natural processes that create large woody debris, low DO from nutrient 

enrichment, runoff of chemical contaminants from agricultural and silvicultural lands. These 

individuals state that there is little documentation of existing problems. 

Response: The available scientific literature provides a strong basis for the need for a riparian 

buffer zone to prevent adverse impacts to water quality. The major focus in recovery planning 

and implementation is to ensure that buffers are adequate to prevent impacts to water quality. If 

receiving waters are not impacted by sediment, nutrients, chemicals, and sufficient vegetation 

remains to prevent increases in water temperature then Atlantic salmon habitat should be 

protected. Purchasing all of the land in the riparian habitat in the Gulf of Maine DPS of Atlantic 

salmon is not possible and is not necessary for salmon protection and recovery. Our focus is, 

therefore, on ensuring that regulations and best management practices to protect water quality are 

fully implemented and evaluated. Where opportunities present themselves, the purchase of land 

and conservation easements has been and likely will continue to be an important tool in the effort 

to protect important riparian areas adjacent to salmon habitat. 

Comment 5: Aquaculture 

Comments were provided stating that some of the section in the draft plan on aquaculture was 

outdated and requesting that the final recovery plan acknowledge progress made to address the 

threat of aquaculture. Other comments identified areas where actions to address the threat from 

aquaculture needed to be strengthened and specifically cited disease management, the 

establishment of aquaculture free-zones and bay management planning. 

Response: We have updated the section in the recovery plan related to aquaculture. As noted in 

the comments, the Services have been working with the aquaculture industry and the State of 

Maine for a number of years to implement measures to minimize the potential for aquaculture 

practices to negatively impact Atlantic salmon and their habitat. As correctly noted in the 

comments, significant progress has been made recently to incorporate a number of these 

protective measures in permit conditions. Aquaculture free-zones have been considered, but not 

implemented due to the lack of adequate sites sufficiently removed from the Gulf of Maine DPS. 

Bay management planning is an excellent tool for ensuring that aquaculture practices are well 

coordinated and that cumulative impacts are identified and assessed. We have included a 

discussion on bay management in the final recovery plan. 

Comment 6: Habitat Quality and Restoration 

Comments were submitted stating that the recovery plan needed to identify habitat as a limiting 

factor to Atlantic salmon throughout Maine and placing habitat restoration as a top priority. One 

comment stated that poor large parr survival indicated that habitat in the rivers may be marginal 
12-5

and that greater emphasis should be placed on investigating this further. Comments suggested 

that a greater emphasis needed to be placed on restoring the structure and function of these 

rivers. Another comment recommended that the size and scale of riparian buffer zones needs to 

be carefully assessed to determine if they are adequate to meet the needs of Atlantic salmon and 

the rest of the ecosystem. 

Response: The plan does identify habitat quality as a significant threat to the recovery of 

Atlantic salmon. As explained in the plan, assessment activities have documented significant 

mortality occurring during the last winter large parr are in the river and also as smolts are 

migrating out of the river. These research findings indicate that there are problems with habitat 

quality. Research and management efforts are now concentrated on specifically identifying 

limiting factors in the freshwater, estuarine and marine environments. Examples include 

assessment of embeddedness and substrate permeability and its relationship to productivity and 

consideration of a pilot liming study to evaluate the benefits of buffering the river as smolts 

migrate into saltwater. In addition, the final recovery plan discusses the need to investigate the 

potential role of diminished habitat complexity in the conservation of the DPS. 

Comment 7: Ecosystem Restoration 

Comments recommended that the plan needed to go further in incorporating an ecosystem 

approach to recovering the DPS and should consider rivers as entire systems. One comment 

stated that non-native species should not be stocked into rivers within the DPS and another 

recommended pursing the restoration of alewives. Other comments stated that to restore salmon 

we need to restore the other species with which it co-evolved over the years. 

Response: The goal of the Endangered Species Act is to conserve the ecosystems upon which 

endangered and threatened species depend. The plan acknowledges that recovery of endangered 

Atlantic salmon depends on recovery of the rivers, estuaries and marine environment. Recovery 

includes restoration of other diadromous species which provide important benefits to Atlantic 

salmon including serving as predator buffers and contributing marine derived nutrients to the 

ecosystem. 

Comment 8: Changing land-use patterns 

A comment recommended that changing land use patterns (i.e., development and sprawl) needs 

to be addressed more thoroughly in the plan. It was also suggested that habitat protection needs 

to be guided by an ecosystem management approach that looks at what is happening across the 

landscape. One comment stated that if the long term effects of historical land use and impacts 

from current land use are not addressed rapidly and aggressively we will not see the restoration 

of self-sustaining Atlantic salmon populations in Maine. 

Response: The recovery plan focuses on threats to Atlantic salmon habitat so the impacts of 

changing land use patterns are addressed in a variety of sections. As noted in the comment, 

development can impact Atlantic salmon habitat by contributing sediments, chemicals and 

nutrients and increasing water temperature. Land use changes will continue to be monitored 

during implementation of the recovery plan with a focus on how those changes increase impacts 
12-6

to salmon habitat. 

Comment 9: Stakeholder and community involvement 

Comments stated that the plan does not identify many areas where non-agency organizations and 

stakeholders are involved and recommended that the plan identify more ways to include 

stakeholders and the local knowledge that these individuals and groups possess. Another 

comment stated that the Watershed Councils are essential for salmon recovery and must have the 

backing of state and federal agencies involved in salmon restoration. It further suggested that the 

“Implementation Schedule” should include funding to support the full time staff needed to keep 

the Watershed Councils functioning as an effective component of salmon restoration efforts. 

Response: The recovery plan acknowledges the critical role that local citizens and organizations 

have and will continue to play in recovery of Atlantic salmon. These individuals serve as the 

eyes and ears in these watersheds and are frequently the first to identify specific habitat problems 

that need to be addressed and opportunities for habitat enhancement. The implementation 

schedule identifies the actions at the local level and the funding estimated to be necessary to 

carry out those activities. Included in these estimates would be the personnel resources needed 

to carry out these tasks. 

Comment 10: Hatcheries 

A number of comments were submitted on the existing hatchery program. One comment 

suggested that the plan identify the need to assess whether hatchery-reared fish, which are 

essentially land-locked, are capable of transitioning to saltwater water. Another comment 

suggested that there should not be a “broodstock retirement” program as currently exists and that 

instead these brood fish should be producing progeny for other rivers to establish experimental 

populations. It was suggested that stocking of additional streams might provide a surprising 

result in terms of a few returning adults and perhaps a catch and release fishery at some point in 

the future which could go a long way toward rebuilding popular support for the recovery 

program as a whole. 

Response: The recovery plan supports the recommendation from the NRC report that the 

hatchery program should be reviewed. The issues identified above, including the source of the 

fish taken into the hatchery, the use of spent broodstock, life stage to be stocked, and evaluation 

of hatchery products should all be included in a review as recommended in the final recovery 

plan. The recovery plan also includes a recommendation to evaluate additional stocking in other 

rivers within the DPS. 

Comment 11: West Greenland Fishery 

A comment suggested that the management and establishment of commercial quotas should not 

be left solely up to NASCO and stated that NASCO failed to follow ICES advice to adopt the 

zero quota for the WGF in 2001 and 2002. It suggested that the plan recommend a continued 

suspension of a commercial fishery for Atlantic salmon until such time as rivers within the 

United States have self-sustaining populations. It further recommended that the recovery plan 

explicitly support the existing 5-year Greenland Conservation agreement and call for the 
12-7

continued elimination of the West Greenland Fishery as a priority recovery action. 

Response: NASCO is the international organization created with the purpose of international 

coordination and cooperation for Atlantic salmon conservation and management. It is the forum 

for the Untied States to engage Denmark, on behalf of Greenland, in discussions on management 

of Atlantic salmon fisheries. The recovery plan identifies the commercial catch of Atlantic 

salmon off the coast of Greenland as a threat to the recovery of the Gulf of Maine DPS. The 

model utilized by ICES to provide management advice to NASCO estimates pre-fishery 

abundance off Greenland and subtracts the spawning escapement needs for all the rivers 

represented in that mixed stock and then allocates a portion of the remainder to the Greenland 

fishery. While this, in theory, offers adequate protection to all stocks contributing to the mixed 

stock off Greenland, some stocks may be disproportionately affected by the fishery. For 

instance, if Canadian and Northern European stocks recovery more quickly than U.S. and 

Southern European stocks then the pre-fishery abundance may increase enough to allow for a 

commercial harvest off Greenland yet the stocks in the southern portion of the range may still be 

significantly lower than spawning escapement goals. Continued involvement in the international 

management forum and involvement of conservation organizations is necessary to ensure 

adequate protection of U.S. stocks. 

Comment 12: Penobscot and Other Large Rivers 

Several commenters stated that the Recovery Plan does not adequately address the relationship 

and importance of the Penobscot to the listed rivers. These comments stated that this is a serious 

omission in the draft recovery plan. The recovery plan’s failure to adequately recognize the 

importance of the Penobscot to the listed rivers is a serious omission and needs to be rectified in 

the final plan. Likewise, the plan needs to look at the role of Maine’s other large salmon rivers, 

particularly those within the geographic range of the DPS, i.e., the Kennebec, Androscoggin and 

St. Croix rivers, as well as the Saco River. 

Response: The recovery plan is for the listed entity – the Gulf of Maine DPS of Atlantic salmon 

that was listed in 2000. At the time of the listing, the mainstem Penobscot River was excluded 

from the Gulf of Maine DPS due to outstanding data and analysis. The plan properly focuses on 

the threats to Atlantic salmon and their habitat as listed and identifies actions necessary to avoid 

or minimize those threats in the future. 

Comment 13: Acid Rain 

A comment offered support for efforts to mitigate the effects of acid rain on the DPS, but stated 

that the draft plan does not place adequate emphasis on mitigating the underlying causes of acid 

rain. The comment recommended that the Services place a high priority on consulting with the 

EPA on identifying point sources of air pollution contributing to acid rain. 

Response: The available information on acid deposition in Maine indicates that, as a result of 

air pollution regulations, acid deposition is decreasing. The current problems appear to be 

caused by the removal of buffering capacity in these rivers over time which now allows acid 

pulses to cause effects to Atlantic salmon. The mitigation effort appears to be necessary to 
12-8

provide buffering capacity until such time as the habitat recovers from the years of significant 

acid rain deposition and leaching of buffering capacity from the watersheds. 

Comment 14: Elevated Water Temperature 

A comment stated that the draft recovery plan does not adequately discuss the threat of elevated 

water temperature. 

Response: There is no question in the literature as to the negative effects of high temperature. 

The best available data seems to show a significant number of days when the temperature goes 

above the thresholds for feeding and survival. The draft recovery plan identifies elevated water 

temperature as a threat to Atlantic salmon. As noted in the comment, temperatures have been 

recorded at levels higher than that preferred and sometimes even tolerable for salmon. The 

recovery plan also identifies activities that can cause increased water temperature including 

removal of vegetation in the riparian zone and water withdrawals. 

Comment 15: Education 

A comment stated that education is an essential component to species or population restoration 

and will require substantial investment and commitment on the part of all of the players in this 

recovery. The commenter stated that the recovery plan’s implementation schedule lacks funding 

and commitment for education. 

Response: The Recovery Plan states that education and outreach programs are a critical 

component of successful conservation and recovery plans. The Recovery Plan states that public 

information and outreach programs help build public support and a strong constituency for 

Atlantic salmon recovery and conservation in Maine. The Recovery Plan recommends that 

efforts to increase and improve public awareness of Atlantic salmon conservation should 

continue through media, educational material, public forums and workshops, demonstration 

projects and technical assistance. The Recovery Plan notes that virtually all successful 

conservation programs include education and public outreach programs. Public awareness is 

important to the success of Atlantic salmon recovery efforts in Maine. 

The Recovery Plan states that education and outreach programs inform the general public and 

interested parties, such as land owners, business and industry, state and local government about 

the Atlantic salmon recovery process. Education and information campaigns help promote 

Atlantic salmon as an important national resource and encourage individual and group 

involvement in the recovery process. The Recovery Plan recommends that a comprehensive and 

coordinated Education and Outreach Plan for the Gulf of Maine DPS of Atlantic salmon should 

be developed. This plan should include a strategy to coordinate the efforts of federal, state and 

local organizations currently involved in education and outreach programs. The plan should 

identify target audiences, review existing programs and materials, evaluate the role of public 

display of Atlantic salmon, identify education and outreach needs, identify responsibilities and 

costs and develop strategies for dissemination of information and materials. 
12-9

Comment 16: Governance 

A comment suggested that the plan should include a discussion on governance and referenced 

the NRC report which also suggested that this issue should be investigated. The comment 

suggested that the Services should pull language from the NRC report and the comments 

received to help create this new section. The DSF suggests a review of the literature on the topic 

of natural resource “co–management” and referenced lobster fisheries co-management in Maine 

as one example of an alternative and reasonably successful structure that should be reviewed. 

Response: The Recovery Plan recommends that federal and state agencies and local 

governments should continue to work cooperatively to recover the DPS. Where necessary, 

interagency communication and coordination should be strengthened. Existing coordination and 

communication mechanisms between federal and state agencies and local conservation 

organizations and other constituency groups should be reviewed and strengthened. The Plan 

acknowledges that there are many organizations and groups involved in the protection and 

recovery of Atlantic salmon. Ensuring inter-organizational coordination and communication 

mechanisms are in place will increase the effectiveness and efficiency of these groups. The 

implementation schedule in the recovery plan identifies responsible entities for each of the 

recovery plan actions. There are a number of organizations, agencies, individuals and industries 

involved in Atlantic salmon protection and recovery as noted in the NRC report. By assigning 

responsibility appropriately for carrying out activities, the plan describes roles for each of these 

groups in recovery implementation. The recovery plan implementation team will also coordinate 

actions and help reduce the potential for overlap. The Recovery Plan has been revised to include 

an expanded discussion of the issue of governance as it relates to the recovery of the DPS. The 

Services agree that the complexity of the multiple state, federal, local and private groups 

involved in salmon recovery or related activities presents specific challenges that must be 

addressed if recovery is to be successful. 

Comment 17: River-specific recovery planning

Several comments stated that the recovery plan did not address recovery action at a river-specific 

scale. These individual state that the plan does not make any attempt to address individual 

rivers, identify unique threats to salmon in each and describe actions necessary to address each 

threat. In addition, the comments state that the threats identified in the plan are not the most 

important in all watersheds. 

Response: The Recovery Plan considers threats to the DPS at a river-specific scale and 

discusses regional differences that exist between various watersheds and regions in Maine. The 

Recovery Plan identifies site-specific management actions for all the threats the Services have 

identified under Section 4(a)(1) of the ESA five-factor analysis. The Services acknowledge that 

the Recovery Plan does not present comprehensive river specific recovery strategies for each of 

the rivers still known to support wild salmon populations. The Services agree that recovery 

implementation may be further facilitated by the development of watershed or river-specific 

management plans that would include and highlight those threats and accompanying actions 

applicable within that particular area. The Recovery Plan acknowledges ongoing recovery 

implementation activities that are currently responsive to the specific circumstances within 
12-10

individual watersheds (e.g., NPS surveys, nutrient management plans in the Sheepscot, liming 

project Downeast). Management plans for specific issues of concern have been developed, or 

are envisioned, for many of the rivers and watersheds within the DPS. For example, the Maine 

ASC has been working to develop river-specific fisheries management plans for individual DPS 

rivers. The State of Maine, working in cooperation with multiple public and private partners, has 

developed a water use management plan (WUMP) for the Narraguagus and Pleasant rivers and 

for Mopang Stream (a tributary to the Machias River) The WUMP was developed to address a 

specific issue (i.e., agricultural water use) that was a concern in these three rivers. In a number 

of instances, local conservation organizations have begun the process of developing riverspecific management plans for specific issues. 

Comment 18: Pesticides

The Services received a number of comments related to pesticides. Comments provided by the 

State of Maine questioned the factual basis of statements in the draft plan that drift of hexazinone 

from aerial applications has been documented. The State stated that it had no documentation of 

hexazinone drift in its records. The DSF commented that the plan did not adequately present the 

extent of pesticide use and the threat to the DPS posed by DPS by this activity. The Services 

received comments that the threat from pesticides warrants consultation between the Services 

and the EPA on the effects of pesticide registration on the DPS. This commenter stated that 

pesticides should not be used until this consultation has taken place. Further, these comments 

stated the view that the recovery plan does not place a high enough priority on measures to 

control pesticide use. Lastly, the comments stated that no pesticides can be discharged into DPS 

waters without a CWA, NPDES permit. 

Response: The Services have revised the recovery plan based on public comments received. An 

assessment of the magnitude and severity of the threat posed to the survival and recovery of the 

DPS by chemical contaminants resulted in the conclusion that pesticides currently are not a highlevel threat to the DPS recovery. The recovery plan identifies a number of recovery actions 

related to continued monitoring of any threat to the DPS related to pesticides. Should water 

quality or other data indicate that pesticides applied in accordance with approved labeling 

instructions may be adversely affecting the DPS, the Services will consult with the U.S. 

Environmental Protection Agency (EPA) to address any potential impact to the DPS. 
13-1

APPENDIX 7: PUBLIC AND PEER REVIEW COMMENTS 

The Services received comments from a wide range of stakeholders and interested parties 

including state, federal and local government agencies, local stakeholder groups, NGOs, industry 

and private citizens. The comments received ranged from endorsements of the plan to 

disagreement with specific as well as general elements contained in the plan. Many of the 

comments received provided technical corrections and additional information for the Service’s 

consideration in the preparation of a final plan. The Maine ASC coordinated the review of the 

draft plan by state agencies. The State agencies involved in the Plan review were the ASC, 

DMR, IFW, DEP, DAFRR, BPC, DOC, BPL, MFS, MGS, DOT and SPO. 

In addition to public review, the recovery plan underwent peer-review. The Services and the 

state identified and contacted 27 peer reviewers with specific technical and other relevant 

expertise, requesting review and comments on the draft recovery plan. These individuals were 

asked to review relevant sections of the plan for technical accuracy and completeness. The peerreviewers were also asked to identify any specific issues or information that the Services should 

consider in the preparation of a final draft plan. The Services received 8 responses from the 

individuals contacted. 

Complete copies of the public and peer-review comments received by the Services are available 

on request from: 

NMFS 

Attn: Mark Minton, 

Atlantic Salmon Recovery Plan Coordinator 

One Blackburn Drive 

Gloucester, MA 01930 

(978)-281-9328 x6534 

email: Mark.Minton@noaa.gov
APPENDIX 8

RECOVERY ACTIONS

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

2 1.1.1A

Conduct IFIM studies on additional DPS rivers to determine flow requirements of juveniles

3 years USGS, FWS, 

NMFS

ASC

75K 75K 

2 1.1.1B Determine flow requirements of adult Atlantic salmon in DPS rivers 5 years USGS, FWS, NMFS ASC 

2 1.1.2A 

Continue analyses of historical flow data for DPS rivers to assess changes over time or hydrologic differences between the rivers that may affect salmon recovery efforts.

1 year USGS MGS

20K Cost TBD

2 1.1.2B Maintain existing USGS stream gages on DPS rivers Long-term USGS MGS ASC 120K 120K 120K 

1 1.1.2C

Develop and implement an effective flow monitoring program in addition to gage-sites to monitor stream flow and discharge data at points along rivers. 

Long-term FWS USGS MGS, DEP, LURC

92K 92K 92K

1 1.1.2D Monitor and assess the potential for groundwater withdrawals to impact stream flow and cold water discharges Long-term FWS USGS DAFRR MGS DEP LURC Industry 100K 100K 100K 

2 1.1.3A

Implement the Downeast Salmon Rivers Water Use Management Plan (WUMP) for the Pleasant and Narraguagus rivers and Mopang Stream

5 years USGS FWS 

NRCS

DAFRR, Industry ASC, DEP, LURC 1M 1M 1M

1 1.1.3B Determine the effects of current irrigation withdrawals by all growers in the watersheds on flow and Atlantic salmon Long-term USGS FWS DAFRR MGS, DEP, LURC Industry 100K 100k 100K

3 1.1.3C Assess and monitor other agricultural water use needs and demands within DPS river watersheds Long-term NRCS LURC DEP 30K 30K 

2 1.1.3D

Develop water use management plans for other DPS rivers 3 years FWS DAFRR, Industry 

LURC DEP MSPO NGOs

250K

2 1.1.3E

Continue periodic assessments of irrigation methods and water demands and their potential effects on hydrology and Atlantic salmon habitat

Long-term NRCS DAFRR DEP LURC 

Industry 20K

1 1.1.4A

Ensure that water withdrawal permit requirements protect stream flows required for the recovery and conservation of Atlantic salmon.

Long-term FWS ASC, DEP, LURC 

DAFRR Industry 45K 45K 45K

1 1.1.4B Issue and enforce all appropriate permits for water withdrawals Long-term ACOE FWS DEP, LURC DAFRR Industry 10K 10K 10K 

2 1.1.5B

Review current water management for the dams and develop an assessment of the effect of regulation on a watershed’s hydrology and thus Atlantic salmon habitat

3 1.1.5A

Review current water management for the dams and develop an assessment of the effect of regulation on a watershed’s hydrology and thus Atlantic salmon habitat.

3 1.2.1

Review existing water quality standards for each river within the DPS to determine adequacy to meet the needs of Atlantic salmon 

1 year FWS ASC DEP 

3K

1 1.2.2A Evaluate the impacts of acid rain on juvenile Atlantic salmon survival in DPS rivers 3 years USGS, NMFS EPA ASC, DEP, UM, NGOs 75K 75K 75K

Lead Agency Estimated Cost

14-1
APPENDIX 8

RECOVERY ACTIONS

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

1 1.2.2B 

Identify available management measures and techniques to mitigate the potential impacts of acid rain on the DPS. Experimentally evaluate stream acidification mitigation techniques in a natural river system within the range of the DPS 

3 years NMFS FWS 

USGS

ASC, DEP, NGOs

250K 120K 120K

1 1.2.2C 

Identify point sources of airborne pollutants contributing to acid precipitation that may be adversely affecting the DPS and reduce to levels that will not adversely affect or jeopardize the recovery of the DPS

4 years EPA FWS 

NMFS

DEP 

25K 25K

2 1.2.2D Model the impact on air and water quality issues, especially acid precipitation, on productivity of salmon in DPS rivers 2 years EPA FWS NMFS DEP UM ASC 45K 45K

2 1.2.2E 

Evaluate current agricultural practices such as soil acidity management practices to determine whether they may affect pH levels in DPS rivers 

3 years FWS, NRCS Industry, MDOC 

MWBC

1 1.2.2F Evaluate the biological effects of low pH and aluminum and its toxicity on Atlantic salmon 3 years USGS EPA FWS NMFS DEP UM 75K 75K 75K

2 1.2.2I 

Identify and consider appropriate management measures and techniques to mitigate the potential impacts of agricultural chemicals and other contaminants on the DPS

Duration TBD FWS EPA DEP BPC MDA MDOC

Industry

1 1.2.2J Evaluate the link between pesticides and endocrine disruption 3 years USGS EPA FWS NMFS DEP, UM, BPC 75K 75K 75K

2 1.2.2H 

Evaluate the chronic and acute effects of agricultural chemicals on Atlantic salmon and how they may impact salmon recovery efforts

3 years FWS NMFS BPC, DEP, ASC

75K 75K 75K

2 1.2.2K

Conduct research on the mechanisms of non-pesticide organochlorines exposure, uptake and effect in rivers where these contaminants are known to occur including, the Dennys below the Eastern Surplus Superfund site

3 years EPA USGS 

FWS

DEP UM 

25K 25K

1 1.2.2G 

Sample resident fish from all DPS rivers and analyze them for tissue residues and bio-chemical factors indicative of exposure to endocrine disrupting chemicals. 

3 years EPA NMFS 

FWS

ASC, DEP

45K 45K 45K 

2 1.2.2L 

Continue State program to replace OBDs 3 years DEP 

1 1.2.3A Implement a comprehensive and integrated long-term water chemistry monitoring program on all DPS rivers 1 year FWS EPA DEP, UM, ASC, NGOs 100K 100K 100K 

2 1.2.3B Implement a comprehensive and integrated long-term water quality monitoring program on all DPS rivers 

3 1.2.3C 

Monitor water temperatures in the vicinity of blueberry process water discharge sites on the Machias and Narraguagus rivers to assess the potential impact on Atlantic salmon

Long-term FWS USGS DEP NGOs Industry

10K

1 1.2.4B 

Evaluate the impacts of sedimentation on habitat quantity and quality including relationship between substrate embeddedness and habitat productivity in DPS rivers.

NMFS, FWS, USGS

ASC NGOs 

14-2
APPENDIX 8

RECOVERY ACTIONS

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

2 1.2.4A Prepare and implement NPS pollution reduction plans for DPS rivers 3 years FWS NMFS EPA ASC DEP MFS SWCD NGOs 100K 100K 100K 

2 1.2.4C 

Prepare and implement Point Source pollution reduction plans for DPS rivers 2 year EPA DEP

32K Y3 Costs TB

3 1.2.4D Fully implement EPA aquaculture wastewater and effluent discharge regulations Duration TBD EPA FWS DEP 2 1.2.4E Continue monitoring of the remediation efforts at the Eastern Surplus Superfund site in Meddybemps periodic EPA DEP 15K 15K 

2 1.2.4F Address any ground water problems at the Smith junkyard on the Dennys River and restore the site Duration TBD EPA DEP 2 1.3.1A Repair or remove the Coopers Mill Dam to improve fish passage around the dam 1 year FWS ASC IFW DMR Local Gov 65K

3 1.3.1B Evaluate the need to repair the existing fishway at Saco Falls 1 year ASC 50K 

2 1.3.2 Identify and improve culverts or other road crossings that impede salmon 

passage

Long-term FWS NRCS 

NMFS

ASC MFS MDOT NGOs Industry 75K 75K 

3 1.3.3 Identify and manage natural debris jams (including beaver dams) that impede salmon passage Long-term FWS ASC NGOs 5K 5K 

2 1.3.4 

Condition permits for activities within the estuaries of DPS rivers so as to minimize potential effects on migration of juveniles and adults 

Long-term ACOE ASC 

45K 45K 

2 1.4.1A 

Provide long-term protection for riparian buffers through fee acquisition, conservation easements, conservation and management agreements, and other appropriate tools

Long-term NRCS FWS LURC MFS Industry 

ASC NGOs 5 Million 5 Million 5 Million

2 1.4.1B Promote the adoption and use of BMPs by landowners and compliance with these voluntary standards Long-term MFS landowners NGOs 25K 25K 

1 1.4.1C Identify riparian zone activities (e.g., harvest practices, ATVs, development etc.) and evaluate impacts on Atlantic salmon Long-term MFS Industry ASC NGOs 25K 

2 1.4.1D 

Evaluate current state and local land use regulations to determine adequacy of existing measures protecting riparian habitat and instream improve if appropriate

2 year NRCS FWS ASC LURC MSPO 

MFS DAFRR 25K 25K

2 1.4.1E

Enhance protection of riparian areas where necessary through expanded enforcement and modifications to the Natural Resource Protection Act, Forest Practices Act, LURC Zoning standards, and/or Municipal Shoreland Zoning

Long-term LURC 

2 1.4.2A Evaluate the potential for activities in estuaries to adversely affect Atlantic salmon Long-term NMFS FWS ACOE 45K 45K 45K2 1.4.2B Condition permits for activities within the estuaries of DPS rivers so as to minimize potential effects on Atlantic salmon Long-term NMFS FWS ACOE 45K 45K 45K1 1.5.1 

Create regional hydraulic geometry curves and a reference reach database 3 years FWS ASC

75K 75K

3 1.5.2A Identify, catalogue and prioritize habitat restoration needs in DPS rivers 2 years FWS NMFS ASC NGOs 32K 

14-3
APPENDIX 8

RECOVERY ACTIONS

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

3 1.5.2B Identify, catalogue and prioritize habitat restoration needs in estuarine habitat of DPS rivers 2 years FWS NMFS ASC NGOs 32K

1 1.5.3 Conduct high priority restoration projects Long-term NRCS ASC MFS MDOT NGOs 300K 

1 1.5.5 Evaluate the ecological role and importance of restoring other diadromous fish populations 

2 1.5.4 

Evaluate the potential of stream flow augmentation as a recovery tool to help meet Atlantic salmon flow needs and increase juvenile production and survival

1 year FWS ASC MGS

60K 60K

1 2.1.1 Maintain and enforce the closure of the directed sport fishery for Atlantic salmon Long-term NMFS FWS IFW, DMR 20K 20K 20K

1 2.1.2 

Maintain current FMP that restricts directed harvest of Atlantic salmon in U.S. estuarine and marine waters

Long-term NMFS NEFMC 

1 2.1.3A 

Participate in international salmon management with the goal of ensuring any quotas set are based on the best available scientific data and provide adequate protection of US stocks

Long-term NMFS ASC

30K 30K 30K

2 2.1.3B Continue US participation in the international sampling program at West Greenland Long-term NMFS 30K 30K 30K

2 2.1.3C 

Continue efforts to implement a biological sampling program at St. Pierre et Miquelon to determine the origin of Atlantic salmon captured in this fishery

Long-term NMFS USDOS 

Intnl. Partners 70K

2 2.2.1A Assess the level of incidental take of Atlantic salmon by recreational anglers. Long-term FWS IFW ASC 25K 10K 

1 2.2.1B

Prohibit all recreational fishing in select areas utilized by Atlantic salmon as holding areas to all fishing where Atlantic salmon may be taken as bycatch or poached

Long-term IFW, ASC 

1 2.2.1C 

Develop a Section 10(a)(1)(B) habitat conservation plan for recreational fishing permitted by the State that may incidentally take Atlantic salmon

2 years FWS IFW ASC

50K 50K

2 2.2.1D Continue to monitor commercial freshwater fisheries where the potential for incidental take of Atlantic salmon exists Long-term DMR ASC IFW 2 2.2.2A Assess the potential risk for incidental take of Atlantic salmon in marine and estuarine fisheries 3 years NMFS DMR ASC 45K 45K 45K 

2 2.2.2B 

Develop appropriate management strategies and regulatory measures to avoid bycatch of Atlantic salmon in estuarine and marine fisheries where significant potential for bycatch has been identified 

Duration TBD NMFS DMR, ASC 

2

2.2.2C Increase observer coverage in the midwater trawl herring fishery to improve 

the ability to assess the potential for Atlantic salmon bycatch in the herring fishery.

NMFS NEFMC DMR 

2 3.1.1A 

Identify and catalogue locations that restrict passage and/or concentrate salmon and thereby increase the vulnerability of salmon to predation

1 year FWS NMFS ASC IFW DMR 

20K

14-4
APPENDIX 8

RECOVERY ACTIONS

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

2 3.1.1B 

Review existing salmon population management practices to determine if they increase the vulnerability of juvenile salmon to cormorant predation 

3 year FWS ASC UM

25K 25K 25K

2 3.1.1C Document and monitor the presence and abundance of potential salmon predators at natural and man-made concentration sites 3 years FWS NMFS ASC UM 25K 25K

3 3.1.1D Assess the potential of land and water use practices to exacerbate predation 

rates

2 years FWS NMFS ASC 25K 

2 3.1.2A Evaluate the potential of cormorant predation to adversely affect the recovery of the DPS 3 years FWS NMFS ASC IFW 25K 25K

2 3.1.2B 

Identify specific cormorant colonies within the DPS that may inflict significant levels of depredation on DPS salmon populations and implement appropriate experimental management measures

4 years FWS NMFS ASC

20K 20K 20K

1 3.1.2C 

Evaluate the potential of conserving and restoring runs of anadromous forage species to provide a buffer against predation on salmon and other ecological benefits

Long-term FWS NMFS ASC IFW DMR

100K

2 3.1.3A Evaluate the effect of seal predation on the recovery of the DPS Duration TBD FWS NMFS ASC 

2 3.1.3B Document and monitor the presence and abundance of seals at natural and man-made concentration sites 3 years NMFS FWS ASC UM 25K 25K 

2 3.1.3C Conduct research to determine the role of net pen sites in seal aggregation and salmon predation 3 years NMFS FWS ASC UM 25K 25K 

2 3.1.3D 

Evaluate the potential of alternative research techniques and food habit sampling methodologies to help assess seal predation on Atlantic salmon

3 years NMFS ASC UM

35K

2 3.1.3E 

Develop and implement appropriate management measures to mitigate the impact of documented seal predation on wild salmon populations

Duration TBD NMFS FWS ASC 

2 3.1.4 Assess potential effects of other predators 3 years NMFS FWS ASC, UM 1 3.2.1A 

Review existing stocking programs and assess the potential impacts of these introductions on Atlantic salmon populations and ways to minimize potential adverse affects

1 year NMFS FWS ASC IFW

5K 5K 5K

1 3.2.1B 

Monitor potential adverse interactions of existing stocking programs for freshwater salmonids in Atlantic salmon river drainages and fully assess the potential impacts of these programs on the DPS

1 year NMFS FWS ASC IFW

20K 20K 20K

2 3.2.1C 

Suspend stocking of brown trout immediately in all DPS rivers until the potential impacts of these introductions can be fully assessed 

IFW ASC 

2 3.2.1D 

Monitor potential adverse interactions of existing stocking programs for freshwater salmonids (i.e., splake, landlocked salmon, brook trout) in headwater lakes of DPS rivers to determine the potential impacts of these programs on the DPS

1 year NMFS FWS IFW ASC

30K 30K 30K

1 3.2.1E Develop a Section 10(a)(1)(B) habitat conservation plan for existing stocking programs and, if warranted and implement 1 year FWS ASC IFW 50K 

14-5
APPENDIX 8

RECOVERY ACTIONS

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

1 3.2.2 Monitor populations of introduced non-salmonid species and implement management controls when appropriate and feasible Long-term FWS ASC IFW 30K 30K 30K 

2 4.1A 

Evaluate new aquaculture lease and permit applications to ensure that net pens and equipment are adequate for site location and potential storm impact.

Long-term ACOE NMFS 

FWS

DMR ASC 

30K 30K

1 4.1B Develop fully functional containment management systems for the containment of farmed salmon at marine sites. Long-term ACOE NMFS FWS Industry, DMR 

1 4.1C 

Develop and implement integrated loss control plans for all salmon aquaculture facilities

Long-term ACOE NMFS 

FWS

DMR Industry 

2 4.1D Develop and maintain an inventory tracking system for all marine aquaculture facilities Long-term NMFS ACOE FWS DMR Industry 2 4.1E 

Assess, document and monitor damage caused by seal predation that may lead to the escapement of farmed salmon into the environment

3 years NMFS Industry, UM, DMR

15K 15K

2 4.2.1 Develop and implement contingency measures in case of accidental release of farmed fish Long-term NMFS ACOE FWS ASC Industry 10K 2K 2K 

2 4.2.2A Maintain existing weirs on DPS rivers to minimize aquaculture escapees spawning, enable data collection and collect broodstock Long-term NMFS FWS ASC Industry 132K 264K 264K 

2 4.2.2B 

Construct weirs on DPS rivers, including the East Machias and Machias rivers, where necessary to exclude aquaculture escapees, enable data collection and collect broodstock

Long-term NMFS FWS ASC Industry

831K

2 4.2.3 Mark all farmed salmon prior to placement into marine net-pens Long-term Industry 100K 100K 100K 

2 4.2.4 Discontinue the culture of non-North American salmon 5 years ACOE NMFS FWS Industry 

2 4.2.5 Prohibit the placement into marine net-pens of reproductively viable transgenic salmon ACOE NMFS FWS DMR Industry 

3 4.2.6 Continue research into developing strains of aquaculture fish that cannot interbreed with wild Atlantic salmon Duration TBD Industry UM 75K

1 4.3.1A 

Develop and implement a comprehensive disease management plan that includes siting and standard operational procedures to minimize outbreaks of ISA. 

Long-term USDA NMFS 

FWS ACOE

Industry DMR NASCO

200K

2 4.3.1B 

Develop and implement comprehensive integrated bay management plans that include coordination of stocking densities, harvesting and fallowing and disease treatment and management

3 years USDA NMFS 

FWS ACOE

DMR Industry NGOs ASC

50K 50K 50K

2 4.3.1C Revise federal import regulations (Title 50) to include the ISA virus 1 year FWS 10K

2 4.3.1D 

Maintain and update existing fish health guidelines and protocols as necessary, to control the introduction of new pathogens and continue to provide protection from disease

Long-term NMFS FWS ASC DMR 

2 4.3.1E Expand the FWS Wild Fish Health Survey to include DPS rivers Long-term FWS ASC 20K 20K 20K 

2 4.3.1F

Implement biosecurity and disinfection protocol for all research and assessment activities being conducted in rivers within the DPS

NMFS FWS EPA USGS

ASC DMR IFW 

14-6
APPENDIX 8

RECOVERY ACTIONS

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

1 4.3.2A Determine the modes of transmission of the ISA virus 3 years USDA NMFS FWS DMR Industry 

1 4.3.2B Continue to investigate the role of wild fish species as potential reservoirs and vectors of ISA 3 years NMFS USDA DMR Industry 120K 120K 

2 4.3.2C 

Initiate screening and long-term monitoring of resident and migratory fish in aquaculture production bays for endemic and exotic salmonid pathogens. 

Long-term NMFS Industry DMR

120K 120K 120K

2 4.3.2D Continue active research programs on immunization of farmed fish 3 years USDA FWS Industry DMR 

3 4.3.2E 

Develop an effective diagnostic technique for the SSS virus and determine the distribution of SSS virus within the geographic range of the DPS 

3 years USWFS NMFS Cornell U. ASC

25K

2 4.3.3A 

Investigate the potential of sea lice to adversely affect the DPS and the role of salmon aquaculture sites as a reservoir for this parasite 

3 year NMFS ACOE 

FWS

Industry DMR 

2 4.3.3B Regularly test and report sea lice burdens at individual net-pen facilities. Long-term Industry, DMR 2 4.3.3C Continue treatment for sea lice at aquaculture facilities Long-term USDA Industry DMR UM 2 4.4.1A 

Develop and operate fully functional containment management systems for the containment of farmed salmon at freshwater hatchery sites.

Long-term Industry DEP IFW 

1 4.4.1B 

Develop integrated loss control plans for all salmon aquaculture hatchery facilities. Conduct independent audits of freshwater hatcheries once loss control plans are in place

Long-term ACOE NMFS 

FWS

Industry DEP DMR 

2 4.4.1C 

Develop and maintain an inventory tracking system that facilitates the accurate tracking of total numbers of salmon smolts being produced by the hatchery

Long-term ACOE NMFS 

FWS

Industry DEP DMR

30K 30K

2 4.4.2 Develop contingency plans to reduce adverse impacts if containment measures fail 2 years Industry DEP 

1 5.1.1A 

Continue operation of federal fish rearing facilities needed for recovery of the DPS, including maintenance of river-specific broodstock

Long-term FWS

725K 750K 785K

1 5.1.1B Continue stocking cultured fish to supplement wild salmon populations Long-term FWS ASC, TAC 60K 63K 66K

1 5.1.2 

Monitor and evaluate the current stocking program Long-term NMFS FWS ASC, TAC

150K 150K 150K

1 5.1.3A Evaluate the role of alternate stocking strategies to supplement wild salmon populations 5 years NMFS FWS ASC, TAC, Industry 50K 50K 50K 

2 5.1.3B Continue to assess and evaluate the results of the adult stocking program 2 years NMFS ASC, TAC2 5.1.3C Evaluate the role of streamside incubation facilities to supplement wild salmon populations 5 years NMFS FWS ASC, TAC 40K 40K 40K 

1 5.1.4A Evaluate the need to re-establish populations of Atlantic salmon in extripated rivers within the DPS 5 years NMFS FWS ASC, TAC 

14-7
APPENDIX 8

RECOVERY ACTIONS

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

1 5.1.4B Establish experimental populations to assist in the recovery of the GOM DPS of Atlantic salmon NMFS FWS ASC, TAC 120K 120K1 5.2.1 Continue fish culture management practices at federal hatcheries to minimize the potential for disease Long-term FWS 

1 5.2.2 Continue fish health surveillance efforts and implementation of fish health practices at federal hatcheries Long-term FWS 20K 20K 20K

1 5.2.3A Conduct research on ISA and SSS detection and prevention 3 years NMFS FWS, USGS ASC 50K 50K 50K 

2 5.2.3B Conduct research on other pathogens to identify potential threats to the DPS NMFS FWS ASC 15K 

2 5.2.3C Initiate screening and long-term monitoring of resident fish species in DPS rivers for endemic and exotic salmonid pathogens Long-term NMFS FWS ASC 20K 20K 20K 

2 5.3A 

Develop and implement procedures at federal hatcheries to identify potential escape sources and implement the appropriate modifications

Long-term FWS See Action 

5.3A

2 5.3B 

Implement discharge and effluent management protocols for all federal hatcheries with the goal of controlling and minimizing release of juveniles

2 year FWS EPA DEP

20K Y3 Costs TB

1 6.1.1 Update brood stock management plans, including brood fish collection, genetic management and program evaluation 1 year FWS ASC, Maine TAC 1 6.1.2 Continue to genetically characterize and screen all brood fish and to track parentage of all fish produced Long-term FWS ASC 60K 60K 60K

1 6.2 Ensure that management plans consider and avoid negative genetic effects of management actions Long-term FWS NMFS ASC 2 6.3 Explore methods for long-term preservation of gametes and genes for future use (e.g., cryopreservation) 3 year FWS, NMFS, USGS ASC UM 15K 30K 

1 6.4 Monitor genetic diversity, including parentage of smolts and returning adults Long-term FWS ASC 30K 30K 30K

1 7.1.1A Monitor adult returns at existing fishways and weirs Long-term ASC 60K 60K 60K

1 7.1.1B 

Construct weirs on the East Machias and Machias rivers to monitor adult returns

2 years FWS NMFS ASC 

1 7.1.1C Conduct intensive redd counts on all DPS rivers to index spawning 

escapement

Long-term ASC 10K 10K 10K 

2 7.1.1D 

Continue development of DPS-level estimates of spawning escapement Long-term NMFS ASC, TAC 

2 7.1.1E Develop accurate extrapolation methods to estimate abundance in areas where traditional redd counts are not feasible or practical 2 year NMFS ASC, TAC 

1 7.1.2A 

Continue basinwide assessment of large parr abundance and measurement of biological characteristics in the Narraguagus and Dennys river systems 

Long-term NMFS ASC

100K 100K 100K

2 7.1.2B Expand assessments of large parr abundance to a third DPS river Long-term NMFS ASC, TAC 50K 50K 

2 7.1.2C Establish 6-10 index sites to assess large parr abundance and biological characteristics in the remaining DPS rivers 2 years NMFS ASC, TAC 50K 50K 

14-8
APPENDIX 8

RECOVERY ACTIONS

Priority Task Task Description Duration Federal State & Other Year 1 Year 2 Year 3 

Lead Agency Estimated Cost

1 7.1.3 Conduct quantitative assessments of Atlantic salmon smolt production Long-term NMFS ASC 250K 250K 250K 

1 7.1.4A Continue telemetry studies of smolt migration from the Dennys and Narraguagus rivers 3 years NMFS ASC 100K 100K 100K 

2 7.1.4B 

Expand spatial coverage of detection arrays to better assess movements of post-smolts in the Gulf of Maine and the Bay of Fundy

3 years NMFS ASC

283K 283K

1 7.1.4C Continue post-smolt surface trawling assessment programs and expand the temporal and spatial extent of coverage 3 years NMFS 283K 283K 283K

1 7.1.5 

Continue to participate and contribute to international cooperative research and assessment efforts to improve our understanding of salmon at sea

Long-term NMFS FWS ASC

150K 150K 150K

2 7.1.6 Develop and apply population viability analysis model 1 year NMFS FWS ASC 25K 

2 8.1A Develop and implement a comprehensive Education and Outreach Plan for the Gulf of Maine DPS of Atlantic salmon Long-term NMFS FWS ASC 75K 75K 

2 8.1B Continue efforts to educate anglers on the difference between trout and juvenile salmon Long-term NMFS FWS ASC IFW DMR 15K 15K 

3 8.1C 

Develop updated educational programs for schools Long-term NMFS FWS ASC

10K

3 8.1D Evaluate the role of public display of salmon as an outreach tool 1 year NMFS FWS1 8.2

Maintain, and if necessary increase, coordination/communications between government and local agencies on issues pertaining to Atlantic salmon recovery

Long-term NMFS FWS ASC 

3 9.1 Appoint a Recovery Implementation Team to coordinate implementation of recovery plan objectives NMFS FWS ASC 

3 9.2A Conduct an annual review of the implementation schedule Long-term NMFS FWS ASC, TAC 5K 5K 

3 9.2B Complete a biennial progress report on completion of recovery tasks Long-term NMFS FWS ASC 5K 5K 

3 9.3

Complete necessary addenda, updates and revisions to the Recovery Plan Long-term NMFS FWS ASC 

2 9.4

Continue to evaluate Atlantic salmon populations in other rivers within the range of the DPS and the appropriateness of their protection under the ESA

5 years NMFS FWS ASC

25K 25K

14-9