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Lower Willamette Cold Water Refuge Interpretation Study

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Lower Willamette Cold Water Refuge Interpretation Study Department of Environmental Quality regon Environmental Solutions Division 700 NE Multnomah Street, Suite 600 Kate Brown, Governor Portland, OR 97232 (503) 229-5696 FAX(503)229-5675 TIY711 March 18, 2020 Kim Kratz Assistant Regional Administrator Oregon and Washington Coastal Office National Marine Fisheries Service 1201 Northeast Lloyd Boulevard, Suite 1100 Portland, OR 97232 RE: Submittal of Cold-Water Refuge Report for the Lower Willamette River to Address RP A Dear Mr. Kratz, The Oregon Department of Environmental Quality is pleased to submit the attached Lower Willamette River Cold Water Refuge Report. This report is submitted to satisfy a reasonable and prudent alternative (RP A) from the 2015 National Marine Fisheries Service Biological Opinion on the U.S. EPA approval of Oregon's 2003 water temperature standards for the Lower Willamette migration corridor. The RPA addresses the jeopardy decision for threatened and endangered Upper Willamette and Lower Columbia River Chinook salmon (Oncorhynchus tshawytscha), and Upper Willamette and Lower Columbia River steelhead trout (Oncorhynchus mykiss) identified in the Biological Opinion. The purpose of this RPA is to interpret the cold-water refuge (CWR) narrative provision in order to allow for implementation of the criterion through DEQ' s Clean Water Act authorities. The lower 50 miles of the Willamette River is designated a salmon and steelhead migration corridor for purposes of Oregon's water temperature standard. The CWR study identifies the source, location, and levels of use of CWR habitat available to adult and juvenile life stages of these populations, with emphasis on the support of migrating adult salmon and steelhead. The Oregon DEQ agreed to develop the cold-water refuge study, with oversight from the U.S. EPA and NMFS, for the lower 50 miles of the Willamette River. The study evaluates whether there is sufficient cold-water refuge to support the listed salmon and steelhead populations, and therefore, whether the narrative criterion is being met. The study also identifies data gaps and uncertainties. Finally, the report recommends that the existing cold-water refuge habitat within the designated migration corridor be protected through regulatory or voluntary actions. In order to complete this study, DEQ convened and consulted with an external scientific panel of experts from federal, state, local, and academic institutions with experience in cold-water refuge identification or salmon and steelhead biology and conservation specific to the Willamette River. This included biologists from ODFW, NMFS, USGS, U.S. EPA, U.S. FWS, the University ofldaho, Oregon State University, and the City of Portland. This study reflects the best data and scientific expertise available for documenting cold-water habitat availability and use by salmon and steelhead for this reach of the Willamette River. If you have questions regarding this submittal or would like additional information, please contact me or have your staff contact Debra Sturdevant, Water Quality Standards Program Lead, at 503-299-5384. Sincerely, ) 0 AA AA ;},ii ,1 lJJ_.. ~ ;;';;'J['' uP Water Quality Program Deputy Administrator Cc: Anne Mullan, NOAA-NMFS Mark Liverman, NOAA-NMFS John Palmer, U.S. EPA Hanh Shaw, U.S. EPA Rochelle Labiosa, U.S. EPA Connie Dou, ODEQ Enclosure: Lower Willamette River Cold Water Refuge Study Lower Willamette River Cold-Water Refuge Narrative Criterion Interpretation Study Submitted to: NOAA –– National Marine Fisheries Service By: Oregon Department of Environmental Quality – Division of Water Quality Standards and Assessment March 2020 Water Quality Standards and Assessment 700 NE Multnomah St. Suite 600 Portland, OR 97232 Phone: 503-229-5696 800-452-4011 Fax: 503-229-5850 Contact: Debra Sturdevant or James McConaghie www.oregon.gov/DEQ DEQ is a leader in restoring, maintaining and enhancing the quality of Oregon’s air, land and water. 1 This report prepared by: Department of Environmental Quality 700 NE Multnomah Street, Suite 600 Portland, OR 97232 1-800-452-4011 www.oregon.gov/deq Contacts: James McConaghie, PhD [email protected] 503-229-5619 Debra Sturdevant, Program Lead [email protected] 503-229-6691 2 DEQ can provide documents in an alternate format or in a language other than English upon request. Call DEQ at 800-452-4011 or email [email protected]. 3 About This Document This document contains results and conclusions from analysis of data to apply Oregon’s cold water refugia narrative criterion in the migration corridor reach of the Willamette River. This is to satisfy the Reasonable and Prudent Alternative (RPA) in the National Marine Fisheries Services Endangered Species Act Biological Opinion on the Environmental Protection Agency's Proposed Approval of Certain Oregon Water Quality Standards Including Temperature and Intergravel Dissolved Oxygen (2015). 4 Acknowledgements DEQ appreciates the significant contributions from the following individuals and institutions in the preparation of this document: Melissa Brown and Julia Bond, City of Portland Bureau of Environmental Services and Krista Jones, USGS Oregon Water Science Center – for providing valuable water temperature datasets that were critical for identifying cold-water sources in the lower Willamette River. Stanley Gregory, Oregon State University and Thomas Friesen, Oregon Department of Wildlife – for access to unpublished datasets on fish presence, abundance, and behavior in the lower Willamette River. The Oregon Department of Fish and Wildlife and Pacific General Electric for providing raw data from their databases of daily fish passage counts. Peter Leinenbach, U.S. EPA for NorWeST modeling of tributary water temperatures in the Willamette Basin. And Matthew Keefer, University of Idaho, for access to unpublished datasets and draft reports, and his multiple thoughtful reviews of this work, which greatly improved the scientific robustness of the report. 5 Table of contents Executive summary ..................................................................................................................................... 15 Introduction ......................................................................................................................................... 19 Objectives of the cold-water refuge study .................................................................................. 19 Project scope ............................................................................................................................... 19 External Coordination ................................................................................................................. 20 Background ......................................................................................................................................... 23 Objectives of this section: ........................................................................................................... 23 Regulatory history ....................................................................................................................... 23 Biology and ecology of CWR use ............................................................................................... 31 Thermal impacts on migrating salmon and steelhead ............................................................. 31 Existing cold-water refuge for adult Chinook and steelhead in the lower Willamette River.............. 38 Chapter outline ............................................................................................................................ 38 Temperature for the lower Willamette main stem and major tributaries .................................... 41 Tributary scale CWR .................................................................................................................. 46 CWR associated with in-channel geomorphologic features ....................................................... 72 Summary of results identifying geomorphic cold water features ............................................... 82 CWR identification conclusions ................................................................................................. 83 Adult salmon and steelhead migration patterns and CWR use ........................................................... 87 Chapter outline ............................................................................................................................ 87 Migration patterns of Willamette River Chinook salmon and steelhead .................................... 89 Fish passage counts ..................................................................................................................... 92 Thermal exposure to temperatures above biological thresholds under different temperature conditions .............................................................................................................................................. 112 Evidence of refuge use by migrating Adult salmon and steelhead ........................................... 122 Summary and conclusions on CWR use ................................................................................... 134 Adult UWR winter steelhead .................................................................................................... 137 Adult LCR fall Chinook ............................................................................................................ 138 Adult LCR winter steelhead .....................................................................................................
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