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Malheur River Basin TMDL and WQMP

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Water Quality Report Malheur River Basin Total Maximum Daily Load (TMDL) and Water Quality Management Plan (WQMP) September 2010 Last Updated: 09/2010 DEQ 10-WQ-023 This report prepared by: Oregon Department of Environmental Quality 811 SW 6th Avenue Portland, OR 97204 1-800-452-4011 www.oregon.gov/deq Primary Authors: John Dadoly and Ryan Michie For more information contact: John Dadoly, Basin Coordinator 700 SE Emigrant Avenue, Suite 330 Pendleton, OR 97801 (541) 278-4616 [email protected] Cheryll Hutchens-Woods, Water Quality Manager Oregon Department of Environmental Quality 700 SE Emigrant Avenue, Suite 330 Pendleton, OR 97801 (541) 278-4619 [email protected] Eugene Foster, Manager of Watershed Management Section Oregon Department of Environmental Quality 811 SW 6th Avenue Portland, OR 97204 (503) 229-5325 [email protected] Malheur River Basin TMDL September 2010 Table of Contents Executive Summary Chapter 1 Introduction Chapter 2 Scope of TMDL Chapter 3 Basin Assessment Chapter 4 Pollutant Sources Chapter 5 Summary of Current and Past Pollution Control Efforts Chapter 6 Dissolved Oxygen, Chlorophyll a, pH, and Phosphorus Chapter 7 Bacteria Chapter 8 Pesticides Chapter 9 Temperature Water Quality Management Plan Appendix A Bacteria TMDL Technical Information Appendix B Temperature TMDL Technical Data Appendix C Baseline Beneficial Use Status of the Malheur River Basin Appendix D Quality Assurance Project Plan/Sample & Analysis Plan: Malheur River Basin TMDL Nutrient Water Quality Study for TMDL Development – 2006 Appendix E Chlorophyll Data Regression Analysis OREGON DEPARTMENT OF ENVIRONMENTAL QUALITY i Malheur River Basin TMDL September 2010 Acknowledgements Data analysis: Jim Bloom John Dadoly Shannon Hubler Ryan Michie Dan Turner Data collection: Aaron Borisenko Paula Moon-Butzin Greg Coffeen Doug Drake Allen Hamel Larry Marxer Sarah Miller Contributors: Bureau of Land Management, Burns, District Bureau of Land Management, Vale, District Bureau of Reclamation, Pacific NW Region Burns Paiute Tribe Harney County Soil and Water Conservation District Idaho Power Company Malheur County Soil and Water Conservation District Malheur Experiment Station Malheur County Extension Office Malheur National Forest Malheur Watershed Council Oregon Department of Agriculture Oregon Department of Fish and Wildlife Owyhee Irrigation District Owyhee Watershed Council U.S. EPA Region 10 OREGON DEPARTMENT OF ENVIRONMENTAL QUALITY ii Malheur River Basin TMDL September 2010 Executive Summary The Malheur River is located in southeast Oregon. It is a tributary of the Snake River, which forms the border between Oregon and Idaho. This report describes DEQ’s requirements and strategy to reduce pollution in the Malheur River and its tributaries, as well as nearby small streams which drain directly into the Snake River in the nearby Middle Snake-Payette subbasin. The Malheur River Basin TMDL applies to all perennial and intermittent streams in the Malheur River Basin and the Middle Snake-Payette subbasin. A number of streams in the Malheur River Basin and Middle Snake-Payette Subbasin are listed as “water quality limited” for dissolved oxygen, chlorophyll a, bacteria, toxics (the pesticides DDT and Dieldrin), and temperature. The Malheur River Basin/Middle Snake-Payette Subbasin TMDLs address the violation of standards for three water quality parameters: chlorophyll a (a product of excessive algae growth due to phosphorus loading), bacteria and temperature. The following table summarizes the completed TMDL count for the Malheur River Basin and Middle Snake-Payette Subbasin using DEQ and EPA counting methods: Malheur River Basin, Middle Snake-Payette Subbasin TMDL count Parameter 303(d) listings DEQ TMDLs EPA TMDLs Chlorophyll a 3 3 3 DDT 1 Not addressed Not addressed Dieldrin 1 Not addressed Not addressed Dissolved Oxygen 1 delisted delisted E. coli 3 3 2 (1 duplicate listing) Fecal Coliform 8 7 (1 delisted) 6 (1 duplicate listing, 1 delisted) Temperature 21 21 21 Total 38 34 32 During development of the TMDL, two unlisted stream segments were identified that do not meet E.coli water quality criteria (Malheur River RM 129-170, Bully Creek RM 0-15.9), and two unlisted stream segments (Malheur River RM 67-123, North Fork Malheur RM 0-18) were identified for not meeting temperature criteria. These water quality impairments were addressed by the TMDL, but are not included in the table of TMDLs show above. Dissolved Oxygen and Chlorophyll Waterbodies in the Malheur River Basin were listed as water quality limited due to failure to meet applicable dissolved oxygen, and chlorophyll a water quality criteria. These factors indicate high levels algae growth. The dissolved oxygen 303(d) listing includes the mainstem Malheur River from its mouth to its headwaters in Logan Valley (RM 0-186.1). The chlorophyll a listings include the lower Malheur River (RM 0-67), lower Willow Creek (RM 0-27.4), and lower Bully Creek (RM 0-12.8). The dissolved oxygen listing occurs all year, while the chlorophyll a listings are for the Summer season only. Detailed review of monitoring data and applicable water quality criteria performed during TMDL development indicate that despite high nutrient concentrations and eutrophic conditions, applicable dissolved oxygen criteria are actually being met throughout the year. The Malheur River had been listed for low dissolved oxygen because past data analysis did not account for the use of Warm-Water dissolved oxygen criteria in the lower Malheur River Basin. This standard allows for the lower dissolved oxygen concentrations found in warmer water. Based on the analysis of available dissolved oxygen data, it is recommended that the entire Malheur River from RM 0 to RM 186.1 be removed from the DEQ dissolved oxygen 303(d) list. Review of chlorophyll a data performed during TMDL development also indicate that chlorophyll a criteria are being met the vast majority of the time during the critical Summer period in the Malheur River and OREGON DEPARTMENT OF ENVIRONMENTAL QUALITY iii Malheur River Basin TMDL September 2010 tributaries. The historic data used for the chlorophyll a 303(d) listings were not corrected for the presence of dead algal matter and led to the conclusion that chlorophyll a criteria were being exceeded. Significant diurnal dissolved oxygen concentration and pH swings indicate that eutrophic conditions occur in the Lower Malheur River and tributaries as well as downstream in the Snake River. These conditions are likely caused by high phosphorus concentrations which encourage algae growth. It was determined that phosphorus is a good surrogate parameter for chlorophyll and that efforts to reduce phosphorus will reduce chlorophyll a concentrations further and address the few instances where chlorophyll a concentrations exceed the seasonal water quality standard. Controlling phosphorus loading is also strongly related to control of sediment loading due to its affinity to bind to fine soil particles. The Malheur River was allocated a phosphorus load to the Snake River based on a total phosphorus concentration of 0.07 mg/l in the 2004 Snake River-Hells Canyon TMDL. Allocations within the Malheur River basin are based on this concentration limit. Bacteria Waterbodies in the Malheur River Basin are water quality limited due to fecal coliform bacteria concentrations which limit water contact recreation (such as wading, swimming and fishing) and other beneficial uses. Identified waterbodies of concern include the Upper Malheur River, Lower Malheur River, Lower Willow Creek, portions of Bully Creek, and the lower North Fork Malheur River. Portions of Shepherd Gulch and South Fork Jacobsen Gulch in the adjacent Middle Snake-Payette Subbasin are also included on the 303(d) list for fecal coliform bacteria. The 303(d) listings for bacteria occur in the summer period, with the exception of Willow Creek, which is listed all year. Analysis of the bacteria data conducted during development of the TMDL indicate that bacteria criteria are exceeded in Willow Creek, Bully Creek, the Malheur River, and the North Fork Malheur River year round, with reduced impacts during the non-irrigation season of late fall through early spring. Fecal coliform bacteria sources may include wildlife, livestock waste, failing residential septic systems, waste water treatment plant malfunctions, rural residential runoff and urban runoff. There are no permitted point sources of bacteria in the basin, and the generally sparse residential development restricts potential septic and non-permitted point sources to localized areas. Confined Animal Feeding Operations (CAFOs) are considered to be point sources which are not allowed to discharge to waters of the state. CAFOs were given a zero allocation in this TMDL. The major developed areas of the basin such as Ontario and Vale do not discharge waste water to any Malheur River Basin surface waterbodies (Ontario discharges to the Snake River in winter) and there are no plans to do so in the future, therefore no reserve capacity was allocated. Fecal coliform bacteria loading in the Malheur River Basin appear to be dominated by non-point sources. Nonpoint source pollution comes from diffuse sources such as livestock, wildlife, and urban runoff. Stream flow based allocations have been developed for nonpoint sources and apply year-round. The highest reductions in bacteria loading are needed in the lower Malheur River and its tributaries, Bully Creek and Willow Creek. Temperature Temperature
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