Technical Appendix 3 Water Quality Analysis TABLE OF CONTENTS WATER QUALITY ................................................................ 3-1 INTRODUCTION ................................................................. 3-1 EXISTING WATER QUALITY ...................................................... 3-1 Water Quality Standards ...................................................... 3-1 Evaluation of Data Quality .................................................... 3-3 Historic Water Quality Conditions .............................................. 3-4 Pine River .......................................................... 3-5 Navajo Reservoir ..................................................... 3-5 Animas River ........................................................ 3-5 Florida River ........................................................ 3-9 LaPlata River ........................................................ 3-9 Mancos River ........................................................ 3-9 San Juan River ....................................................... 3-9 Groundwater ....................................................... 3-12 WATER QUALITY IMPACT ANALYSIS ............................................ 3-16 Methodology .............................................................. 3-16 Introduction ........................................................ 3-16 Approach .......................................................... 3-16 Sites with Water Quality Measurements .................................. 3-19 Streamflow Data from the San Juan River Hydrology Model .................. 3-26 Calculation Process for Water Quality Changes ............................ 3-26 Significance Criteria ................................................. 3-31 Impacts from Refined Alternative 4 ............................................ 3-31 Construction Related Impacts .......................................... 3-31 Ridges Basin Reservoir ......................................... 3-31 Durango Pumping Plant ........................................ 3-32 Navajo Nation Municipal Pipeline ................................ 3-32 Non-binding Conveyance Pipelines ............................... 3-32 Operation Related Impacts ............................................. 3-32 Pine River ................................................... 3-32 Navajo Reservoir ............................................. 3-32 Ridges Basin Reservoir ......................................... 3-33 Florida River ................................................. 3-44 Animas and Florida Rivers ...................................... 3-44 Colorado Segments of the Animas River .................... 3-45 New Mexico Segments of the Animas River .................. 3-48 LaPlata River ....................................................... 3-50 Mancos River ................................................ 3-53 San Juan River ............................................... 3-53 San Juan River between Bloomfield and Farmington, NM ....... 3-53 San Juan River between Farmington and Shiprock, NM ........ 3-58 San Juan River between Shiprock and Four Corners, NM ....... 3-60 i San Juan River between Four Corners, NM and Mexican Hat, UT .............................................. 3-60 Groundwater ................................................. 3-65 Refined Alternative 6 Impact Analysis ......................................... 3-65 Construction Related Impacts .......................................... 3-65 Pumping Plants (Animas near Durango, LaPlata, Mancos) ............. 3-65 Lemon Reservoir .............................................. 3-65 Horse Gulch Reservoir ......................................... 3-65 Navajo Nation Municipal Pipeline ................................ 3-66 Non-binding Conveyance Pipelines ............................... 3-66 Operation Related Impacts ...................................... 3-66 Navajo Dam ........................................... 3-66 Pine River ............................................ 3-66 Florida River .......................................... 3-66 Animas River .......................................... 3-66 LaPlata River .......................................... 3-67 Mancos River .......................................... 3-67 San Juan River ......................................... 3-68 Dolores River .......................................... 3-68 McElmo Creek ......................................... 3-68 Groundwater .......................................... 3-68 References ...................................................................... 3-69 Attachment 1 .................................................................... 3-70 Attachment 2 .................................................................... 3-76 Attachment 3 .................................................................... 3-85 ii LIST OF TABLES Table 3-1. The Chemical Parameters Regulated along River Reaches Potentially Affected by the Project ...................................................................... 3-3 Table 3-2. Historic Water Quality Measurements on the Pine River ......................... 3-6 Table 3-3. Historic Water Quality Measurements in the Navajo Reservoir .................... 3-7 Table 3-4. Historic Water Quality Measurements on the Animas River ....................... 3-8 Table 3-5. Historic Water Quality Measurements on the LaPlata River ...................... 3-10 Table 3-6. Historic Water Quality Measurements on the Mancos River ..................... 3-11 Table 3-7. Historic Water Quality Measurements on the San Juan River ..................... 3-13 Table 3-8. Trace Elements in LaPlata Basin Shallow Groundwater Samples Collected During 1992 ..................................................................... 3-15 Table 3-9. The Practical Quantitation Limit for the State Regulated Parameters ............... 3-18 Table 3-10. The Study Sites Selected with Historical Water Quality Measurements ............. 3-20 Table 3-11. The USGS Streamflow Gaging Stations Used in the Water Quality Analysis ........ 3-26 Table 3-12. The Names of Extracted Objects Used for Calculating Mass and Water Balances ..................................................................... 3-27 Table 3-13. Ridges Basin Reservoir - Historic Water Quality Measurements on the Animas River ..................................................................... 3-34 Table 3-14. Ridges Basin Reservoir - Chemical Equilibrium Simulation ...................... 3-35 Table 3-15. Initial Conditions for Three-Year Simulation of Reservoir with No Withdrawals ..................................................................... 3-36 Table 3-16. Summary of Simulation Results with No Reservoir Withdrawals .................. 3-37 Table 3-17. Summary of Simulated Water Quality Conditions in a Dry(1981), Average (1991) and Wet 1983) Year ............................................................ 3-38 Table 3-18. Mercury Content of Fish Collected in Farmington Reservoir ..................... 3-44 Table 3-19. Calculated Measurable Increases for Colorado Portion of the Animas River ......... 3-46 Table 3-20. Exceedence values for the Colorado Portion of the Animas River ................. 3-47 Table 3-21. Water Temperature Impacts of Ridges Basin Reservoir Releases Due to Project Operation ..................................................................... 3-48 Table 3-22. Calculated Measurable Increases for the New Mexico Portion of the Animas River ..................................................................... 3-49 Table 3-23. Exceedence values for the New Mexico Portion of the Animas River .............. 3-50 Table 3-24. Calculated Measurable Increases for the Lower LaPlata River .................... 3-51 Table 3-25. Exceedence values for the lower LaPlata River ................................ 3-52 Table 3-26. Calculated Measurable Increases for the Lower Mancos River .................... 3-54 Table 3-27. Exceedence Values for the Lower Mancos River .............................. 3-55 Table 3-28. Calculated Measurable Increases in water quality constituent concentration for the San Juan River at Farmington, NM ................................................. 3-56 Table 3-29. Exceedence values for the San Juan River between Bloomfield and Farmington, NM ..................................................................... 3-57 Table 3-30. Calculated Measurable Increases for the San Juan River Between Farmington and Shiprock, NM .......................................................... 3-58 Table 3-31. Exceedence Values for the San Juan River Between Farmington and Shiprock, NM ..................................................................... 3-59 Table 3-32. Calculated Measurable Increases for the San Juan River Between Shiprock, NM and Four Corners, NM ........................................................... 3-61 Table 3-33. Exceedence values for the San Juan River between Shiprock, NM and Four Corners, CO ..................................................................... 3-62 iii Table 3-34. Calculated Measurable Increases for the San Juan River Between Four Corners, NM and Mexican Hat, UT ....................................................... 3-63 Table 3-35. Exceedence values for the San Juan River between Four Corners, CO and Mexican Hat, UT ..................................................................... 3-64 LIST OF FIGURES Figure 3-1. State Water Quality Regulatory Stream Reaches ........................... 3-2 Figure 3-2.