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Fecal Indicator Bacteria and Source Identification in the Pajaro River Watershed, Santa Clara County

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Fecal Indicator Bacteria and Source Identification in the Pajaro River Watershed, Santa Clara County Fecal Indicator Bacteria and Source Identification in the Pajaro River Watershed, Santa Clara County 1 2 3 4 1: Potential source animals upstream of WAT on Llagas Creek. 2: Swallow nests under an overpass crossing at Uvas Creek. 3: Animal tracks on bank of Llagas Creek upstream of MON. 4: K. Mann sampling at the Pajaro River. Environmental Planning Unit (#247) Santa Clara Valley Water District Safe Clean Water Project B2 December 2017 Prepared by B. Tu, K. Mann and E. Wilkinson Reviewed by B. Calhoun Table of Contents Executive Summary ....................................................................................................................................... 1 Introduction and Background ....................................................................................................................... 2 Introduction .............................................................................................................................................. 2 Regulatory Background ............................................................................................................................. 2 Pathogens in Water Bodies and Fecal Indicator Bacteria ......................................................................... 2 Regulatory Recommendations for Fecal Indicator Bacteria ..................................................................... 4 Frequency of Recommended Testing for Fecal Indicator Bacteria ........................................................... 5 Land Use and Fecal Indicating Bacteria Sources within the Pajaro River Watershed .............................. 5 Microbial Source Tracking ......................................................................................................................... 7 Methods ........................................................................................................................................................ 8 Sampling Design ........................................................................................................................................ 8 Sampling Sites ........................................................................................................................................... 8 Sample Collection ................................................................................................................................... 11 Sample Analysis ....................................................................................................................................... 11 Sampling Conditions ............................................................................................................................... 12 Results ......................................................................................................................................................... 13 Discussion.................................................................................................................................................... 19 2015 vs. 2016 Approach.......................................................................................................................... 19 Site Level Analysis ................................................................................................................................... 20 Sub-watershed Level Analysis ................................................................................................................. 33 Water Leaving Santa Clara County.......................................................................................................... 35 Conclusion and Recommendations ............................................................................................................ 35 Conclusion ............................................................................................................................................... 35 Recommendations .................................................................................................................................. 36 References .................................................................................................................................................. 38 Appendices .................................................................................................................................................. 39 Appendix A: 2015 FIB and MST Results .................................................................................................. 40 Appendix B: 2015 Water Quality Data .................................................................................................... 41 Appendix C: 2016 FIB and MST Results ................................................................................................... 43 Appendix D: 2016 Water Quality Data .................................................................................................... 46 List of Figures Figure 1. Fecal Indicator Bacteria relationship hierarchy ............................................................................. 3 Figure 2. Land use types surrounding waterways of the Pajaro River Watershed in Santa Clara County ... 6 Figure 3. Sites identified for pathogen sampling in the Pajaro Watershed portion of South Santa Clara County. ........................................................................................................................................................ 10 Figure 4. 2015 E. coli Results. ...................................................................................................................... 15 Figure 5. 2016 E. coli Results. ...................................................................................................................... 15 Figure 6. 2015 Enterococci Results. ............................................................................................................ 16 Figure 7. 2016 Enterococci Results. ............................................................................................................ 16 Figure 8. 2015 Microbial Source Tracking Results ...................................................................................... 17 Figure 9. 2016 Microbial Source Tracking Results. .................................................................................... 18 Figure 10. Sheep observed on a property upstream of OAK ...................................................................... 21 Figure 11. Fenced cattle observed upstream of WAT. ............................................................................... 23 Figure 12. Warning signs indicating deer upstream of WAT ...................................................................... 23 Figure 13. Dog tracks observed adjacent to Llagas Creek upstream of site MON...................................... 25 Figure 14. Swallow nests observed under a bridge at LLA ......................................................................... 28 Figure 15. Sampling at SBC.......................................................................................................................... 30 Figure 16. Disposed bags of Animal Carcasses ........................................................................................... 31 List of Tables Table 1. CCRWQCB Basin Plan Requirements. Values are given as Most Probable Number (MPN) of colony forming units of fecal coliforms, based on the logarithmic mean of a minimum of 5 samples collected over a 30-day period. .................................................................................................................... 4 Table 2. U.S. EPA Recommended Testing, 2012. Duration and Frequency for Primary Contact: ................ 5 Table 3. Coordinates and description of sites identified for pathogen sampling in the Pajaro Watershed, South Santa Clara County. ............................................................................................................................ 8 Table 4: March 2016 Precipitation Events .................................................................................................. 12 Table 5. 2015 Fecal Indicator Bacteria Results – Geometric Mean and Statistical Threshold Value Recommendation 1 ..................................................................................................................................... 13 Table 6. 2016 Fecal Indicator Bacteria Results – Geometric Mean and Statistical Threshold Value Recommendation 1 ..................................................................................................................................... 14 Table 7: Locations and Dates for Tested Coyote Scat ................................................................................. 19 Executive Summary Past sampling conducted by the Central Coast Regional Water Quality Control Board (CCRWQCB) and related programs has shown that fecal indicator bacteria (FIB) in the Pajaro River Watershed often exceed Basin Plan Objectives and EPA recommended thresholds. FIB presence in water is used to indicate recent fecal contamination of water, and assess illness risks for those that come in to contact with the water. Illness risks vary based on the level of FIB present, as well as the extent of bodily contact with the water. A Total Maximum Daily Load (TMDL) has been initiated for fecal coliform bacteria in multiple waterways of the Pajaro River Watershed. The City of Gilroy, City of Morgan Hill, and County of Santa Clara implemented a regional pathogen indicator sampling
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