TABLE OF CONTENTS
List of Figures ........vi
List of Tables ........vii
Supporting Agencies and groups........ viii
Contributors ........ix
Preface ........xi
FMESP Steering Committee........ xii

CHAPTER ONE: Fundy Marine Ecosystem Science Project: Science Overview (G.R. Daborn)
1.1 Introduction ........1
1.2 Geomorphology of the Bay of Fundy ........2
1.3 Dynamic Relationships ........2
1.4 History of Resource Use ........5
1.5 History of Research on the Bay of Fundy ........6
1.6 New Concerns ........7
1.7 New Initiatives ........9
1.8 References ........9

CHAPTER TWO: The Physical Environment of the Bay of Fundy
( G.R. Daborn, G. Fader, D.A. Greenberg and B.D. Petrie)
2.1 Physical Oceanographic Processes ........13
2.1.1 Introduction ........13
2.1.2 L'Etang Inlet Studies ........13
2.1.3 The Classification of Estuaries Project ........14
2.1.4 Historical Temperature-Salinity Observations ........14
2.1.5 Tidal Variations ........15
2.1.6 What has Changed Recently?........15
2.1.7 A new generation of numerical models ........29
2.1.8 Future work ........29
2.1.9 Conclusions ........30

2.2 Sedimentological Processes ........30
2.2.1 Sediments: intertidal and benthic ........30
2.2.1.1 Introduction ........30
2.2.1.2 Minas Basin studies ........31
2.2.1.3 Annapolis Basin studies ........33
2.2.1.4 Sediment issues ........33
2.2.2 Marine aggregate assessment and sediment transport ........34
2.2.2.1 Mineral development agreement project ........34
2.2.2.2 Scots Bay Sand Wave Field ........34
2.2.2.3 Resource potential ........34
2.2.2.4 Multibeam bathymetry........35
2.2.2.5 Margaretsville Dunefield ........35
2.2.2.6 Seabed erosion ........35
2.2.2.7 Bottom fishing impacts ........37
2.2.2.8 Sediment transport ........37
2.2.2.9 Future research ........37
2.3 References........38

CHAPTER THREE: The Chemical Environment of the Bay of Fundy
(P.G. Wells, K. Ellis, D. Johnston P.D. Keizer and J.L Martin, P. Yeats)
3.1 Introduction ........41
3.2 The water column and water quality ........41
3.2.1 Inorganic nutrients ........41
3.2.2 Organic nutrients ........42
3.2.3 Nutrient dynamics ........42
3.2.4 Plant pigments and phytotoxins........ 43
3.2.5 Metals ........44
3.2.6 Radionuclides ........44
3.2.7 Organochlorines and organometals........ 47
3.2.8 Industrial, food processing and fish plant wastes ........48

3.3 Chemical contaminants in food chain and tissues
3.3.1 Introduction........48
3.3.2 Seston and plankton........ 49
3.3.3 Benthic invertebrates........ 49
3.3.4 Fish ........50
3.3.5 Seabirds ........52
3.3.6 Marine mammals ........53
3.3.6.1 Contaminants in harbour porpoises ........53
3.3.6.2 Contaminants in seals ........54
3.3.6.3 Contaminants in whales ........55
3.3.7 Ecological significance of contaminant burden in biota ........55
3.3.8 Conclusion and recommendations ........60
3.4 References ........60

CHAPTER FOUR: The Biological Environment of the Bay of Fundy
M. Brylinsky, M.D. Brown, G.R. Daborn, M. Dadswell, P.W. Hicklin, S.D. Kraus, W. Stobo and D.J. Wildish )
4.1 Introduction ........67
4.2 Primary production ........67
4.2.1 Introduction ........67
4.2.2 Phytoplankton ........68
4.2.3 Benthic microalgae ........69
4.2.4 Seaweeds ........69
4.2.5 Salt marsh ........70
4.3 Zooplankton ........71
4.3.1 Zooplankton surveys ........71
4.3.2 Zooplankton of the Bay of Fundy ........72
4.3.3 Zooplankton of the Minas Basin ........73
4.4 Benthos ........74
4.4.1 Subtidal........74
4.4.2 Benthic-pelagic coupling........75
4.4.3 Intertidal benthos ........76
4.4.4 Perspective on benthic biological research: 1983-95........ 78
4.5 Fish ........81

4.6 Birds ........83
4.6.1 Introduction ........83
4.6.2 Waterfowl ........84
4.6.3 Shorebirds ........91
4.6.4 Seaducks ........95
4.6.5 The seabirds of Machias Seal Island ........95

4.7 Marine Mammals ........96
4.7.1 Seals and seal issues in the Bay of Fundy ........96
4.7.1.1 Background ........96
4.7.1.2 Seal issues ........97
4.7.1.3 Information needs ........98
4.7.2 North Atlantic Right Whales in the Bay of Fundy........ 99
4.7.2.1 Introduction ........99
4.7.2.2 Designation of conservation areas ........100
4.7.2.3 Concerns ........101
4.7.2.4 New initiatives ........101
4.7.2.5 History of right whale research project in the Bay of Fundy ........102
4.8 References ........102

CHAPTER FIVE: Marine Resources of the Bay of Fundy (J.A.Percy)
5.1 Introduction ........111
5.2 Status of marine resources ........113
5.2.1 Pelagic fish........113
5.2.2 Demersal fish ........115
5.2.3 Diadromous fish........119
5.2.4 Invertebrates and marine plants ........122
5.2.5 Aggregate extraction ........130
5.3 Aquaculture ........131
5.3.1 Introduction ........131
5.3.2 Species in culture ........131
5.3.3 Possible environmental constraints to aquaculture ........133
5.3.4 Environmental impacts/resource use conflicts of aquaculture........135
5.4 References........137

CHAPTER SIX: Bay of Fundy Ecosystem Issues (J.A. Percy and P.G. Wells)
6.1 Introduction ........153
6.2 Environmental Issues........156
6.3 Scientific Questions Pertaining to Issues........164
6.4 References ........165

CHAPTER SEVEN: A Workshop Synthesis (J.A. Percy, P.G. Wells, A. Evans, and D.C. Gordon, Jr.)
7.1 Introduction ........167
7.2 Why a Bay of Fundy research initiative? ........167
7.3 A workshop overview ........169
7.3.1 Workshop synthesis ........169
7.3.2 Resource management and science ........170
7.3.3 Upper Bay and Lower Bay........171
7.3.3.1 Upper Bay Working Group ........172
7.3.3.2 Lower Bay Working Group........ 173
7.3.4 General information needs and research directions........ 175
7.3.4.1 Oceanography ........176
7.3.4.2 Geology/Sedimentology........177
7.3.4.3 Biology, ecology and resource management ........178
7.3.4.4 Research methodology and new initiatives........180
7.3.4.4.1 Use of existing data ........181
7.3.4.4.2 Monitoring ........182
7.3.4.4.3 Modelling ........183
7.3.4.4.4 New technologies ........184
7.3.4.4.5 Marine protected areas ........185
7.3.5 Sustaining the momentum ........185
7.3.5.1 Developing an action plan ........185
7.3.5.2 Fostering research........ 186
7.3.5.3 Coordination, communication and cooperation ........186
7.3.5.4 Involving communities and the public ........186
7.3.5.5 Fundy workshops ........187
7.4 Proposed action plan ........188
7.4.1 Immediate........ 188
7.4.2 Short-term ........189
7.4.3 Long-Term ........190
7.5 Concluding remarks ........190

APPENDICES
Appendix 1. Conceptual Models for use at FMESP Workshop ........192
Appendix 2. Workshop agenda........ 203
Appendix 3. Workshop participants ........205
Appendix 4. Project Bibliography ........209

LIST OF FIGURES
Figure 1 The Bay of Fundy and its principal subareas ........x
Figure 2.1 The entry for Annapolis Basin (from Gregory et al. 1993) ........16
Figure 2.2 The temperatures observed in the Bay of Fundy, where the solid line represents the monthly
mean temperature and the broken line ± 1 standard deviation (from Gregory et al. 1993) ........17
Figure 2.3 The monthly mean temperature and salinity in the inner (central) and outer Bay ........18
Figure 2.4 The monthly t in the inner (central) and outer Bay of Fundy ........19
Figure 2.5 The regions corresponding to the inner (central, area 55) and outer (area 54) Bay of Fundy
for the results shown in figures 2.3 and 2.4 ........20
Figure 2.6 The well mixed area (shaded) and stratified area of the Bay as determined by Garrett et al. (1978) ........21
Figure 2.7 The monthly average freshwater discharge into the Bay of Fundy from the major sources ........22
Figure 2.8 The annual discharge of the St. John River (1919-1993) and the five year running mean ........23
Figure 2.9 The differences from the annual average salinity and temperature at the surface and 90 m from
Prince 5 station from 1924-1994. The uniformity of the data from 0 and 90 m are consistent with the area
being tidally well mixed, except as seen in 1978 where the freshwater runoff in one month gave rise to the
strong anomaly difference noted in that year's average........ 24
Figure 2.10 The monthly mean geostrophic wind stresses from grid point 20 (44 48' N, 64 24' W
(Drinkwater and Pettipas 1993). x is resolved along 45 (positive to the NE) and y is resolved along
315 (positive to the NW) ........25
Figure 2.11 A typical finite element model grid showing how variable resolutionpermits better defining
of some regions while still including the influenceof distant regions in the same model. In this case interest
was focussed on Georges and Browns Banks ........26
Figure 2.12 A vertical slice from a finite element model illustrating the vertical structure of the tidal currents
on Georges Bank ........27
Figure 2.13 The paths traced by particles in the velocity field of Halifax Harbour M2 tidal and tidally driven
mean currents ........28
Figure 2.14 Shaded relief image of Margaretsville Dunefield ........36
Figure 3.1 Food chain dynamics model for a persistent chemical in the Bay of Fundy........ 56
Figure 3.2 PCB's in the Bay of Fundy present in water and sediment and accumulating in marine organisms
to higher concentrations ........58
Figure 3.3 PCB's present in water and sediments and accumulating in marine organisms to higher
concentrations in the Bay of Fundy compared with the St. Lawrence Estuary ........59
Figure 4.1 Coastal survey blocks: Grand Manan to Saint John, N.B. ........85
Figure 4.2 Coastal survey blocks: Saint John N.B. to Bridgetown, N.S.........85
Figure 4.3 Eider distribution in spring (March, April, May) ........86
Figure 4.4 Scoter distribution in spring (March, April, May)........86
Figure 4.5 Oldsquaw distribution in spring (March, April, May) ........87
Figure 4.6 Eider distribution in fall (September, October, November)........ 87
Figure 4.7 Scoter distribution in fall (September, October, November) ........88
Figure 4.8 Oldsquaw distribution in fall (September, October, November)........ 88
Figure 4.9 Eider distribution in winter (December, January, February)........ 89
Figure 4.10 Scoter distribution in winter (December, January, February)........ 89
Figure 4.11 Oldsquaw distribution in winter (December, January, February) ........90

LIST OF TABLES
Table 3.1 Data on PCB's in the Bay of Fundy marine ecosystem ........57
Table 4.1 Distribution of primary production in the Bay of Fundy ........68
Table 4.2 Themes of biennial benthic workshops held at St. Andrews Biological Station........ 79
Table 4.3 Human uses of the coastal zone ranked by need for seawater of high quality ........80
Table 4.4 Potential questions of importance relating to benthic biology in the Bay of Fundy ........81
Table 5.1 Marine resource species of the Bay of Fundy and their status ........112
Table 6.1 Bay of Fundy issues ........154