i AQUATIC HABITAT IN THE SOMASS RIVER ESTUARY: A SELECTIVE REVIEW AND IMPLICATIONS TO CHINOOK SALMON I. K. Birtwell, M. E. Wright And P. Edgell JUNE 2014 i CITATION AND REPORT AVAILABILITY Birtwell, I.K., M.E. Wright, and P. Edgell. 2014. Aquatic habitat in the Somass River estuary: a selective review and implications to Chinook salmon. Prepared for Fisheries and Oceans Canada, Nanaimo; Alberni Valley Enhancement Association, BC. DFO CATNO 352934. 151p. Available online from the Department of Fisheries and Oceans publications database which is accessible through WAVES: http://waves-vagues.dfo-mpo.gc.ca/waves-vagues/ CATNO 352934 Aquatic habitat in the Somass River estuary: a selective review and implications Title to chinook salmon Responsibility Ian K. Birtwell, Margaret E. Wright, Phil Edgell Author Birtwell, I.K.; Wright, M.E.; Edgell, P. Canada. Dept. of Fisheries and Oceans. Pacific Region; Alberni Valley Corporate Author Enhancement Association Imprint Nanaimo, B.C. : Fisheries and Oceans Canada, 2014 Date 2014 Pagination 151 p. Notes "June 2014"; Available on the Internet m; b; f; Canada; British Columbia; Somass R.; Alberni Inlet; estuaries; Descriptors environmental degradation; habitat loss; forest industry; industrial wastes; hatcheries; life history Collection Codes DFO Species Name Oncorhynchus tshawytscha This report reviews some of the information concerning changes to habitat in the Somass River estuary and the consequences to juvenile Chinook salmon which temporarily reside there during migration to the Pacific Ocean. Since the early 1970s the progeny of juvenile Chinook salmon from adults that spawned in the Somass River system have been augmented by releases of larger-sized hatchery-reared fish. Differential survival to adulthood is a concern for the Abstract respective groups of fish, and the quality and sufficiency of estuarine habitat have been implicated as two potential causes. Accordingly, comments in this report are presented to assist in understanding how "wild" (river-origin mix of wild and hatchery-origin vs. hatchery-reared) juvenile Chinook salmon may interact with, and be influenced by, habitat in the Somass River estuary and the inherent challenges to their survival to adulthood. Language Eng Authors: Ian K. Birtwell, 4801 Ocean Trail, Bowser, BC, V0R 1G0 Margaret E. Wright, Resource Restoration, Fisheries and Oceans Canada, 1965 Island Diesel Way, Nanaimo, BC. V9S 5W8 Phil Edgell, Alberni Valley Enhancement Association, 9231 Faber Road, Port Alberni, BC. V9Y 9C3 1 PREFACE Industrial and urban development has occurred at the head of Alberni Inlet and now it is estimated that only 33.5% of the “natural” Somass River estuary exists. This has occurred despite concern being expressed over almost 70 years for protection of salmon which are dependent upon the estuary during part of their lives. The construction and modifications to the Port Alberni pulp mill in the estuary of the Somass River in the late 1940s - 1950s, associated shoreline urban development, the treatment and disposal of sewage and other wastes, and industrial use of the intertidal areas for log handling and storage etc., have all contributed to changes to habitat which aquatic organisms depend on and, consequently, some adverse effects would be expected. Decades ago the magnitude and extent of changes that were expected due to industrial and urban development were not fully understood, and it was predicted that the waters of Alberni Inlet would assimilate the demands upon them without unduly constraining ecological functions and impacting valuable salmon resources. Unfortunately, subsequent studies revealed that these expectations had not always been met and changes had occurred which impacted aquatic organisms, and especially so at the head of Alberni Inlet in the estuary of the Somass River where impairment of habitat was most obvious in the shallow and deepwater habitats. This report reviews some of the information concerning changes to habitat in the Somass River estuary and the consequences to juvenile Chinook salmon which temporarily reside there during migration to the Pacific Ocean. Since the early 1970s the progeny of juvenile Chinook salmon from adults that spawned in the Somass River system have been augmented by releases of larger-sized hatchery- reared fish. Differential survival to adulthood is a concern for the respective groups of fish, and the quality and sufficiency of estuarine habitat have been implicated as two potential causes. Accordingly, comments in this report are presented to assist in understanding how “wild” (river-origin mix of wild and hatchery-origin vs. hatchery- reared) juvenile Chinook salmon may interact with, and be influenced by, habitat in the Somass River estuary and the inherent challenges to their survival to adulthood. This review covers many topics but of necessity it has been selective and limited in scope and detail; some aspects are explained more fully to assist comprehension. Our deductions are a reflection of information reviewed and trust that they are accurate. Comments are provided on specific habitat issues that have been identified through studies of Alberni Inlet, and also the current circumstance. Information on the use of estuaries by juvenile Chinook salmon is anticipated to assist efforts to maintain and rehabilitate fish habitat in the Somass River estuary; it is hoped that the information will also aid in the development of co-ordinated projects in this regard. (Cover: Aerial photograph, Somass River estuary and Alberni Harbour; from BC Government, Victoria, BC.) 2 TABLE OF CONTENTS Page CITATION AND REPORT AVAILABILITY i PREFACE 1 TABLE OF CONTENTS 2 LIST OF TABLES 8 LIST OF FIGURES 8 SUMMARY 9 INTRODUCTION 15 BRIEF PERSPECTIVE 16 Pulp mill location, effluent discharge, water quality and concern for salmon 16 Effluent discharge and dissolved oxygen (DO) 16 Consideration for the wellbeing of salmon 17 Effluent dispersion and the settlement of particulate matter 18 Upper Alberni Inlet and Harbour flushing 19 Effluent dilution 19 Environmental concerns 20 1970s 20 1980s 20 1990s to present 21 LITERATURE REVIEW 22 IMPORTANCE OF ESTUARIES TO THE SURVIVAL OF SALMON 23 Estuarine diversity and benefits 23 Habitat sufficiency, quality and linkage to survival 24 PORT ALBERNI PULP AND PAPER MILL 25 Acute toxicity of pulp mill effluent 25 Laboratory tests 25 Mill effluent toxicity and hypoxic conditions 25 Toxicity compliance monitoring and environmental relevance 26 Sub-lethal bioassays 27 PME zone of influence 27 Deductions regarding the impact of pulp mill operations 28 3 TABLE OF CONTENTS (contd.) Page DISSOLVED OXYGEN 29 Effluent colour, photosynthesis and dissolved oxygen 29 General and specific considerations 31 What is an appropriate level of dissolved oxygen to safeguard aquatic resources, and especially salmon? 31 Effects of hypoxic conditions on the breathing rate of adult sockeye salmon 31 Effect of hypoxic conditions on the swim speed of salmon 32 Behavioural response of adult sockeye salmon to hypoxic conditions 32 Growth impairment of juvenile Chinook salmon due to hypoxic conditions 32 The dissolved oxygen level that does not impair function 33 Criteria for dissolved oxygen and the protection of fish 34 The adequacy of DO criteria for application in Alberni Inlet 34 Dissolved oxygen monitoring reports and their assessment 35 Halocline 37 Surface waters 37 Upper water layer 38 Lower water layer 38 Historical comparisons 39 Outfall area 40 Fibre mat 40 ADULT SALMON 41 Adult sockeye salmon migration and aquatic conditions in the Somass River estuary 41 Fisheries and Oceans (DFO) study 42 Hatfield Consultant’s study 42 Migration rates 44 Thermal history and exposure to hypoxic waters 44 Adult sockeye salmon migration and dissolved oxygen in Alberni Inlet 44 Continuing concern for migrating adult salmon 46 Laboratory studies 46 Exposure to hypoxic conditions 47 Laboratory derived results and their relevance to field studies 47 Performance of adult sockeye salmon under hypoxic and normoxic conditions and sub-lethal exposure to contaminants 47 Deductions 48 JUVENILE SALMON 48 Juvenile salmon movement into estuarine habitat 48 Willapa Bay, Washington 49 4 TABLE OF CONTENTS (contd.) Page Dungeness River, Washington 49 Water velocity 50 Cowichan River and estuary (water velocity and depth) 50 Water velocity, depth, and habitat 51 Campbell River and estuary 51 Reduced value of some habitats and their use 52 Water velocity and prey 52 Tidal factor and habitats occupied 53 Habitat Type and Connectivity 54 Skagit River, Washington 54 Importance of the vegetated riparian zone 55 Food production 55 Cover 55 Movement of juvenile salmonids in the Somass River estuary 56 Dispersion, displacement and carrying capacity 57 Displacement and dispersion 58 Skagit River estuary 58 Sarita River estuary Barkley Sound 58 Somass River and estuary 59 Carrying capacity 61 Skagit River and estuary 62 Fish densities and habitat type 62 Somass River and estuary 62 Investigations of juvenile salmon ecology in the Somass estuary 63 Survival and behaviour experiments 63 In-situ survival bioassays 63 In-situ behaviour experiments 65 Laboratory studies (behaviour of juvenile Chinook salmon and hypoxic conditions) 66 Fish capture in vertically-stratified near-shore habitat and water quality 67 Fish capture in the intertidal zone and water quality 68 Fish capture 1970/71 68 Fish capture 1975/76 69 Study design 69 “Wild” juvenile Chinook salmon 70 Length and weight 71 Growth 71 Duration of juvenile