Thunder Bay North Harbour Fish Community and Habitat Synthesis December 21, 2012 Prepared for: Environment Canada Prepared by: Dr. Robert F. Foster Thunder Bay North Harbour Fish Community and Habitat Synthesis Executive Summary Existing fisheries and habitat reports, mapping, underwater video, and geospatial data were reviewed for the Thunder Bay North Harbour Area of Concern on Lake Superior near the community of Thunder Bay, Ontario. This review provides supporting documentation that will be used to identify appropriate mitigation for the Contaminated Sediment Management Area (CSMA) adjacent to the Cascades Fine Paper mill. A list of 55 species of fish that have been confirmed from the Thunder Bay Harbour and adjacent Lake Superior and tributaries was compiled, including 43 that have been confirmed in the Thunder Bay North Harbour (TBNH) study area from the mouth of the Current River north to the Cascade Fine Paper mill. Additional undocumented species may use TBNH study area given the relatively limited fisheries assessment that has been conducted there and the fact that 89 fish species are known to occur within the Lake Superior basin. Underwater video and sediment ponar grabs indicate that the TBNH study area is comprised of soft sediments, primarily fine sands and silts, with some clay. Coarser sands, limited patches of cobble, and some rip rap are found in a narrow nearshore band along the shoreline, but represents a small fraction of the TBNH study area (likely <5%). Available data indicate that gravel, cobble, and other coarse substrates are predominately limited to the Far‐field area, away from the CSMA. The substrate of the CSMA is predominately pulp fibre of over 1 m depth near the shoreline, with thinner deposits farther out. Approximately 29 ha of the TBNH study area have sparse to dense aquatic macrophytes dominated by the Canada waterweed, with some water milfoil and pondweeds. There are no submergents immediately adjacent to the Cascades mill where pulp depth is greater than 1 m, but the outer portion of the CSMA has dense beds of submergents, perhaps in response to increased nutrient availability. Available video footage suggest that submergents are sparser farther afield from the mill, with 70% of submergents in the TBNH study area on silt substrates in 2‐5 m water depth. The CSMA likely provides spawning habitat for yellow perch and small fish species that have adhesive eggs and may spawn over submergents (e.g., sticklebacks); unvegetated deep pulp deposits within the CSMA are less likely to be suitable spawning habitat. The CSMA appears to provide nursery habitat for young‐of‐the‐year (YOY) and/or juvenile longnose sucker, white sucker, and walleye that spawn in the nearby Current River. In particular, the CSMA could potentially provide important nursery habitat for a Thunder Bay Area of Concern walleye population, which is part of a Great Lakes rehabilitation effort. The CSMA also provides nursery habitat for yellow perch and small fish species such as spottail shiners, ninespine sticklebacks Northern Bioscience ii Thunder Bay North Harbour Fish Community and Habitat Synthesis and sculpins that spawn in or near the CSMA. These submergents support invertebrates that are prey for YOY and adult fish, and provide cover for fish of all ages. The CSMA also provides habitat for adult walleye, longnose and white suckers, northern pike, and yellow perch, as well as for a number of cyprinid and other small fish species. The significance of the CSMA as fish habitat is difficult to determine given the limited data for the CSMA and the surrounding TBNH. However, no fish surveys have been conducted in the CSMA since mill closure in 2009, and this may affect fish use in the area if they had formerly been attracted to the warmer water temperatures at the outfall. Additional fish and habitat surveys (e.g., submergents) are recommended to provide a more complete understanding of the significance of the CSMA relative to fish habitat elsewhere in the TBNH study area. The remediation of area without submerged aquatic vegetation could potentially ameliorate its value as fish habitat. Cover Photo: Thunder Bay North Harbour from near Port Arthur Shipyards (GoogleMap image) Northern Bioscience iii Thunder Bay North Harbour Fish Community and Habitat Synthesis Contents Executive Summary ..........................................................................................................................ii List of Figures ................................................................................................................................... v List of Tables ................................................................................................................................... vi List of Appendices ........................................................................................................................... vi 1 Introduction ............................................................................................................................ 1 1.1 Thunder Bay Area of Concern ...................................................................................... 1 1.2 The Current Study ......................................................................................................... 2 2 Aquatic Environment .............................................................................................................. 4 2.1 Water Depth ................................................................................................................. 4 2.2 Exposure / Fetch / Currents .......................................................................................... 6 2.3 Water Clarity and Quality ............................................................................................. 7 2.4 Substrate ....................................................................................................................... 8 2.4.1 Near‐field (CSMA) ..................................................................................................... 9 2.4.2 Mid‐field .................................................................................................................. 13 2.4.3 Far‐field ................................................................................................................... 15 2.5 Contaminants ............................................................................................................. 17 2.5.1 Benthic Invertebrates ............................................................................................. 17 2.5.2 Impacts on Fish ....................................................................................................... 19 2.6 Aquatic Vegetation ..................................................................................................... 23 2.6.1 Distribution and Abundance ................................................................................... 23 2.6.2 Species Composition ............................................................................................... 24 3 Fish Community .................................................................................................................... 27 3.1 Species at Risk ............................................................................................................. 33 4 Fish Habitat ........................................................................................................................... 34 4.1 Spawning Habitat........................................................................................................ 34 4.1.1 Yellow Perch ............................................................................................................ 35 4.1.2 Northern Pike .......................................................................................................... 35 4.1.3 Lake Trout ............................................................................................................... 35 4.1.4 Lake Whitefish and Lake Herring ............................................................................ 36 4.1.5 River‐Spawning Species .......................................................................................... 36 4.1.6 Other Fish Species ................................................................................................... 37 4.2 Nursery Habitat .......................................................................................................... 37 4.3 Adult Habitat .............................................................................................................. 38 4.4 Summary of Fish Habitat ............................................................................................ 44 5 Assessment of Significance of Fish Habitat .......................................................................... 46 6 Data Gaps and Recommendations ....................................................................................... 52 7 Literature Cited ..................................................................................................................... 53 Northern Bioscience iv Thunder Bay North Harbour Fish Community and Habitat Synthesis List of Figures Figure 1. Map of Thunder Bay Harbour Area of Concern. ............................................................. 1 Figure 2. Detail of Thunder Bay North Harbour study area and Contaminated Sediment Management Area ................................................................................................................