Biological Evaluation & EFH Assessment April 2013 PERMIT #WAS-026638 Biological Evaluation and Essential Fish Habitat Assessment for Issuance of NPDES Permit #WAS-026638 For Discharges from the Joint Base Lewis-McChord Municipal Separate Storm Sewer System (MS4) April 2013 Prepared by: US EPA Region 10 Office of Water and Watersheds 1 Biological Evaluation & EFH Assessment April 2013 PERMIT #WAS-026638 Table of Contents 1.0 INTRODUCTION ................................................................................................................................................ 5 2.0 DESCRIPTION OF THE ACTION AREA AND THE ACTION .................................................................................... 9 2.1 Action Area ................................................................................................................................................... 9 2.2 Purpose and Objectives................................................................................................................................ 9 2.2.1 Statutory Background of the NPDES Stormwater Permit Program ......................................................... 9 2.3 Description of the MS4 Owned and Operated By JBLM ............................................................................ 12 2.3.1 MS4 Characteristics and Associated Receiving Waters ......................................................................... 12 2.3.2 Description of the Permit’s Narrative Effluent Limitations ................................................................... 35 3.0 STATUS OF SPECIES, CRITICAL HABITAT and ESSENTIAL FISH HABITAT.......................................................... 45 3.1 Species List ................................................................................................................................................. 45 3.2 Species Which This Action Results in “No Effect” ...................................................................................... 46 3.3 Status of ESA Species and Critical Habitat in the Action Area .................................................................... 46 3.3.1 Puget Sound Chinook Salmon ............................................................................................................... 46 3.3.2 Puget Sound Steelhead Trout ................................................................................................................ 51 3.3.3 Bull Trout ............................................................................................................................................... 56 3.4 Essential Fish Habitat Potentially In the Action Area ................................................................................. 60 3.4.1 Habitat Requirements of Salmonids in Streams .................................................................................... 61 3.4.2 Habitat Requirements of Salmonids in the Marine Environments ........................................................ 62 4.0 ENVIRONMENTAL BASELINE ........................................................................................................................... 63 4.1 Description of the Environmental Baseline ................................................................................................ 63 4.1.1 Murray/Sequalitchew Watershed, including the Puget Sound Nearshore ........................................... 64 4.1.2 Clover Creek Watershed ........................................................................................................................ 70 4.2 Effectiveness of Stormwater Management BMPs ..................................................................................... 74 5.0 EFFECTS OF THE ACTION ................................................................................................................................ 76 5.1 Description of How the Environmental Baseline Would Be Affected ........................................................ 77 5.2 Water Bodies That May Be Affected by JBLM MS4 Discharges ................................................................. 77 5.2.1 Puget Sound Nearshore, in the Vicinity of the JBLM Canal Outfall ....................................................... 77 5.2.2 Clover Creek, from JBLM-McChord Field to Lake Steilacoom ................................................................ 81 5.2.3 Nisqually River and Muck Creek ............................................................................................................ 81 6.0 RELATED JBLM ACTIONS ................................................................................................................................. 82 7.0 CONCLUSION & SUMMARY EFFECT DETERMINATIONS FOR LISTED SPECIES, CRITICAL HABITAT & EFH ...... 83 7.1 ESA Effect Determinations ......................................................................................................................... 83 7.2 ESA Critical Habitat Effect Determinations ................................................................................................ 83 7.3 Essential Fish Habitat Determinations ....................................................................................................... 83 8.0 REFERENCES ................................................................................................................................................... 84 9.0 APPENDICES .................................................................................................................................................... 94 2 Biological Evaluation & EFH Assessment April 2013 PERMIT #WAS-026638 Cover Image Source: JBLM-DPW, 2012a. List of Tables Table 1. Surface Water Quality Standards/Beneficial Uses for Waters Within/Near JBLM Table 2. Outfall Inventory for JBLM-Main and JBLM-North Cantonment Areas Table 3. Oil-Water Separator Inventory for JBLM-Main and JBLM-North Cantonment Areas Table 4. Outfall Inventory for JBLM-McChord Field Cantonment Area Table 5. Oil-Water Separator Inventory for JBLM- McChord Field Cantonment Area Table 6. Summary of the JBLM MS4 Permit’s Narrative Effluent Limits Table 7. Summary of Expected Stormwater BMP Performance in Western WA List of Figures Figure 1. Action Area for EPA’s NPDES Permit for Discharges from the Municipal Separate Storm Sewer System (MS4) Operated by JBLM Figure 2. Joint Base Lewis-McChord and Surrounding Vicinity Figure 3. Locator Map for Cantonment Areas known as JBLM-Main and JBLM-North Figure 4. Graphic of Drainage Areas & Outfall Inventory- JBLM-Main & JBLM-North Figure 5. Overview Map of the JBLM-Main Area. Figure 6. Detail Map of the Northern Portion of the JBLM-Main & MS4 Outfall Locations Figure 7. Overview Map of the Southern Portion of the JBLM-Main Area Figure 8. Detail Map of the Southern Portion of JBLM-Main & Locations of MS4 Outfalls 02 and 03 Figure 9. Overview of Drainage Pathways & Locations of MS4 Outfalls 04 and 05 within JBLM-North Figure 10. Graphic of the Subbasin Drainage Basins within JBLM-North, and Locations of MS4 OF 04 and OF 05, into Puget Sound via the JBLM Canal Figure 11. Satellite Image Depicting the Point of Discharge of the JBLM Canal into Puget Sound Figure 12. Locator Map for the Area known as JBLM-McChord Field Figure 13. Overview Map of the JBLM-McChord Field Cantonment Area (including Residential Areas) Figure 14. Detail of JBLM-McChord Field (Airfield Subarea) Drainage Basins and MS4 Outfall Locations into Clover Creek Figure 15. Depiction of JBLM Training Areas, Indicating Land Use Designations Figure 16. Depiction of Road Network within JBLM Cantonment and Training Areas Figure 17. Action Area for EPA’s Permit for Discharges from the MS4 Owned/Operated by JBLM Figure 18. Puget Sound Chinook Distribution in the JBLM Cantonment and Training Areas Figure 19. Puget Sound Chinook Salmon Distribution within Chambers/Clover Creek Watershed Figure 20. Winter Steelhead Distribution in the JBLM Cantonment and Training Areas Figure 21. Summer Steelhead Distribution in the JBLM Cantonment and Training Areas Figure 22. Winter Steelhead Distribution Near the Action Area within Chambers/Clover Creek Watershed Figure 23. Murray/Sequalitchew Creek Watershed within the Action Area Figure 24. Diagram of Sequalitchew Lake Diversion Weir Figure 25. Map of Clover Creek Watershed Figure 26. In-stream Zinc Concentrations, Clover Creek Downstream of JBLM-McChord Field, at Fence Line Figure 27. In-stream Copper Concentrations, Clover Creek Downstream of JBLM-McChord Field at Fence Line 3 Biological Evaluation & EFH Assessment April 2013 PERMIT #WAS-026638 Acronyms AKART All Known Available and Reasonable Methods of Treatment, Prevention and Control ASDM 2008 Aviation Stormwater Design Manual BE Biological Evaluation B-IBI Benthic Index of Biological Integrity BMPs Best Management Practices CWA Clean Water Act CFR Code of Federal Regulations CFS Cubic Feet per Second DPS Distinct Population Status EFH Essential Fish Habitat EPA U.S. Environmental Protection Agency ESA Endangered Species Act ESU Evolutionarily Significant Unit FMP Fishery Management Plans FR Federal Register In/hr Inches per hour ID Identification Number JBLM Joint Base Lewis-McChord LID Low Impact Development MEP Maximum Extent Practicable MSFCMA Magnuson-Stevens Fishery Conservation and Management Act MSGP NPDES Multi-Sector General Permit for Stormwater Discharges Associated with Industrial Activities for Federal Operators in Washington State, Permit #WAR-05-000F MS4 Municipal Separate Storm Sewer System NMFS