LAKE ONTARIO FISH COMMUNITIES AND FISHERIES: 2012 ANNUAL REPORT OF THE LAKE ONTARIO MANAGEMENT UNIT LAKE ONTARIO FISH COMMUNITIES AND FISHERIES: 2012 ANNUAL REPORT OF THE LAKE ONTARIO MANAGEMENT UNIT Prepared for the Great Lakes Fishery Commission 2013 Lower Lakes Committee Meetings Niagara Falls, NY USA March 26-28, 2013 © 2013, Queen’s Printer for Ontario Printed in Picton, Ontario, Canada March 2013 Report ISSN 1201-8449 Please cite this report as follows: Ontario Ministry of Natural Resources. 2013. Lake Ontario Fish Communities and Fisheries: 2012 Annual Report of the Lake Ontario Management Unit. Ontario Ministry of Natural Resources, Picton, Ontario, Canada. Report available on the following website: http://www.glfc.org/lakecom/loc/mgmt_unit/index.html TABLE OF CONTENTS Foreword ............................................................................................................................................ v 1. Status of Major Species 1.1 Chinook Salmon ................................................................................................................... 1 1.2 Rainbow Trout ...................................................................................................................... 1 1.3 Atlantic Salmon .................................................................................................................... 1 1.4 Lake Trout ............................................................................................................................ 1 1.5 Lake Whitefish ..................................................................................................................... 1 1.6 Lake Herring (Cisco) ............................................................................................................ 2 1.7 Northern Pike ....................................................................................................................... 2 1.8 Muskellunge ......................................................................................................................... 2 1.9 American Eel ........................................................................................................................ 2 1.10 Smallmouth Bass ................................................................................................................ 2 1.11 Largemouth Bass ................................................................................................................ 2 1.12 Panfish ................................................................................................................................ 3 1.13 Yellow Perch ...................................................................................................................... 3 1.14 Walleye ............................................................................................................................... 3 1.15 Prey Fish ............................................................................................................................. 3 1.16 Round Goby ....................................................................................................................... 3 2. Index Fishing Projects 2.1 Ganaraska Fishway Rainbow Trout Assessment.................................................................. 4 2.2 Eastern Lake Ontario and Bay of Quinte Fish Community Index Gill Netting ................... 6 2.3 Eastern Lake Ontario and Bay of Quinte Fish Community Index Trawling ...................... 22 2.4 Lake Ontario Nearshore Community Index Netting .......................................................... 36 2.5 Lake-wide Hydroacoustic Assessment of Prey Fish .......................................................... 43 2.6 St. Lawrence River Fish Community Index Netting—Lake St. Francis ............................ 45 2.7 Credit River Chinook Assessment ...................................................................................... 48 2.8 Juvenile Atlantic Salmon Parr Survey ................................................................................ 49 2.9 Credit River Atlantic Salmon Smolt Survey ..................................................................... 51 2.10 Credit River Fishway Atlantic Salmon Assessment ........................................................ 54 3. Recreational Fishery Surveys 3.1 Western Lake Ontario Boat Angling Fishery ..................................................................... 57 3.2 Chinook Salmon Mark and Tag Monitoring ...................................................................... 60 3.3 Lake Ontario Volunteer Angler Diary Program ................................................................. 62 3.4 Credit River Angling Survey .............................................................................................. 65 3.5 Bay of Quinte Open-water Angling Survey ....................................................................... 68 3.6 Bay of Quinte Volunteer Walleye Angler Diary Program ................................................. 72 4. Commercial Fishery 4.1 Quota and Harvest Summary.............................................................................................. 76 4.2 Lake Whitefish Commercial Catch Sampling .................................................................... 87 4.3 Lake Herring Commercial Catch Sampling ....................................................................... 89 5. Age and Growth Summary .................................................................................................. 90 6. Contaminant Monitoring ..................................................................................................... 91 7. Stocking Program ................................................................................................................... 92 8. Biodiversity and Species Rehabilitation 8.1 Introduction ...................................................................................................................... 103 8.2 Atlantic Salmon Restoration ............................................................................................ 103 8.3 American Eel Restoration ............................................................................................... 106 8.4 Deepwater Cisco Restoration ........................................................................................... 109 8.5 Lake Trout Restoration ..................................................................................................... 110 9. Management Planning 9.1 Fisheries Management Zone 20 Council (FMZ20) .......................................................... 111 9.2 Lake Ontario and St. Lawrence River Commercial Fishing Liaison Committee ............. 111 9.3 Fisheries Management Plans ............................................................................................ 111 10. Research Activities 10.1 Project Quinte ................................................................................................................. 113 10.2 Linking Nearshore to Offshore Production in Lake Ontario .......................................... 113 10.3 Bilge and Live Wells – Possible Refuges for Aquatic Invasive Species? ...................... 114 10.4 Compendium of Research on Aquatic Invasive Species in Ontario ............................... 115 10.5 Do all Lake Ontario Salmonid Species Behave Similarly? ............................................ 115 10.6 Assessing Fish Health in Lake Ontario using Morphological, Biochemical, and Nutritional Metrics ............................................................................................................ 117 10.7 Assessing Methods for Monitoring Northern Pike and Muskrats in Relation to Water Levels Regulation ................................................................................................... 118 11. Partnerships 11.1 St. Lawrence River Seine Netting Survey and Muskellunge Nursery Site Identification ..................................................................................................................... 119 11.2 Nearshore Fish Community Index Netting—Hamilton Harbour and Toronto Waterfront ......................................................................................................................... 121 11.3 Warings Creek Brook Trout Rehabilitation ................................................................... 121 12. Staff 2012 ................................................................................................................................ 123 13. Operational Field and Lab Schedule 2012.............................................................. 125 14. Primary Publications 2012 ............................................................................................. 126 v Lake Ontario Fish Communities and Fisheries: 2012 Annual Report of the Lake Ontario Management Unit Foreword The Lake Ontario Management Unit (LOMU) is pleased to release its Annual Report of assessment and management activities carried out during 2012. Lake Ontario fisheries are managed by MNR in partnership with New York State within the Lake Ontario Committee under the Great Lakes Fishery Commission. Lake Ontario Fish Community Objectives provide bi-national fisheries management direction to protect and restore native species and to maintain sustainable fisheries. Our many partners include: New York Department of Environmental Conservation, Canadian Department of Fisheries and Oceans, the U.S. Fish and