Environmental Controls on Clogging in Effluent-Dominated Waterways by Natalie Case A Thesis Presented in Partial Fulfillment of the Requirements for the Degree Master of Science Approved November 2012 by the Graduate Supervisory Committee: Juliet Stromberg, Chair Channah Rock Thomas Meixner ARIZONA STATE UNIVERSITY December 2012 ABSTRACT The Santa Cruz River, in southern Arizona, receives steady inputs of nutrient-enriched treated wastewater (effluent). Previous studies have documented reduced infiltration of surface water in the river. This disruption of hydrologic connectivity, or clogging, can have consequences for groundwater recharge, flows of wastewater in unwanted locations, and potentially even survivorship of floodplain riparian vegetation. Clogging can result from biotic processes (microbial or algal growth), abiotic processes (siltation of interstitial spaces), or both. Little is known about clogging in rivers and the environmental factors that regulate their dynamics, so natural field experiments along the Santa Cruz and San Pedro Rivers were used to answer: 1) Are there spatial patterns of hydraulic conductivity in the riverbed downstream from the effluent point- source? 2) Is there temporal variability in hydraulic conductivity and microbial abundance associated with flooding? 3) Are there environmental variables, such as nutrients or stream flow, related to differences in hydraulic conductivity and microbial abundance? To address these questions, a series of sites at increasing distance from two municipal effluent discharge points with differing water quality were selected on the Santa Cruz River and compared with non-effluent control reaches of the San Pedro River. Physical, chemical, and biological parameters were monitored over one year to capture seasonal changes and flood cycles. i An additional site on the Santa Cruz was established with the Bureau of Reclamation to determine the effects of drying on surface water infiltration. Results revealed trends of increasing conductivity with distance from the effluent discharge for both reaches. Conductivity on the low-nutrient reach was 1.4-3.1 times higher than the high-nutrient reach. Floods restored conductivity rates of the river banks, while in the absence of flooding, conductivity rates gradually declined to clogged conditions. Areas of low conductivity were associated with higher fine sediments and microbial counts, and lower nitrates. This study concludes that utilizing higher- quality effluent is sufficient to reduce clogging. However, even with improved water quality, the absence of scouring flows still leads to lower conductivity rates. Management strategies for effluent, riverbed groundwater recharge, and maintaining valued riparian corridors should include maintaining higher water quality and scouring flows. ii ACKNOWLEDGMENTS This work was sponsored by the Southwest Consortium for Environmental Research and Policy (SCERP) through a cooperative agreement with the U.S. Environmental Protection Agency, as well as the United States Bureau of Reclamation. I am grateful to all the people who helped me along the way, especially to my committee, Drs. Channah Rock, Tom Meixner, and Julie Stromberg for all the advice and help with troubleshooting. Kelley Riley provided training and use of lab space that was invaluable for the microbial methods. Sherri Sass of the Friends of the Santa Cruz River was always available for information on sites and historical data. Tom Colella, Cathy Kochert, and Marisa Masles at the Goldwater Environmental Lab helped me through nutrient analysis. Of course, none of this would have been possible without all the people that set aside time to help me with field and lab work - Meg White, Danika Setaro, Lane Butler, Amanda Suchy, Joe Monfeli, Michelle Perry, Tristan Dunton, Evan Balbona, Nick McLamb, Ray Leimkuehler, John Shasky, Kimberly Shaffer, Easton White, Kellie Elliott, and Chelsey Hull. The field work was tough, but always an adventure! For my lab mates that never had the pleasure of experiencing my field work, the crazy conversations iii made working in the lab fun. Also I thank Dr. John Nagy and Andrea Hazelton for taking time to look over my data and explain the statistics. Last but far from least, thanks to my family for always being supportive and encouraging. iv TABLE OF CONTENTS Page LIST OF TABLES ......................................................................................... vii LIST OF FIGURES ....................................................................................... ix CHAPTER 1. A search for Patterns and variables of riverbed clogging ...................... 1 Introduction .............................................................................. 1 Study Area And Experimental Design ..................................... 8 Methods ................................................................................. 12 Saturated hydraulic conductivity ................................... 12 Characterization of sediments and environmental variables ........................................................................ 14 Analysis ......................................................................... 17 Results ................................................................................... 17 Are there spatial patterns of hydraulic conductivity associated with effluent? ............................................... 18 Is there temporal variability in hydraulic conductivity and microbial abundance in response to flooding? ............. 19 Are there environmental variables, such as nutrients or stream flow, related to differences in hydraulic conductivity and microbial abundance? ........................ 21 v CHAPTER Page Discussion ............................................................................. 29 Are there spatial patterns of hydraulic conductivity associated with effluent? ............................................... 29 Is there temporal variability in hydraulic conductivity and microbial abundance in response to flooding? ............. 33 Are there environmental variables, such as nutrients or stream flow, related to differences in hydraulic conductivity and microbial abundance? ........................ 35 Conclusions ........................................................................... 40 2. BALANCING CLOGGING WITH ENHANCED RECHARGE .............. 65 Introduction ............................................................................ 65 Study Area ............................................................................. 67 Methods ................................................................................. 68 Hydrology ...................................................................... 68 Sediment characterization ............................................. 69 Water chemistry ............................................................ 71 Analysis ......................................................................... 72 Results ................................................................................... 73 vi Page Did hydraulic conductivity change over time with treatment? ..................................................................... 73 Did sediment biomass change over time with treatment? ....................................................................................... 74 Were there trends in physiochemical parameters? ...... 75 Discussion ............................................................................. 77 Did hydraulic conductivity change over time with treatment? ..................................................................... 77 Did sediment biomass change over time with treatment? ....................................................................................... 78 Were there trends in physiochemical parameters? ...... 81 Conclusions ........................................................................... 84 References ................................................................................................. 94 APPENDIX A HETEROTROPHIC PLATE COUNTS .............................................. 102 B HYDRAULIC CONDUCTIVITY OF SEDIMENTS BY DEPTH .......... 105 C HYDRAULIC CONDUCTIVITY BY MONTH ................................... 109 D SEDIMENT TEXTURE ANALYSIS .................................................. 115 vii LIST OF TABLES Table Page 1. Requirements for Class A+ and B effluent ...................................... 46 2. Spearman’s rho values measuring correlation between hydraulic conductivity, microbial counts, and environmental variables from the Santa Cruz and San Pedro Rivers .......................... 53 3. Pearson’s correlation coefficients for hydraulic conductivity, microbial counts, and fines on the Enhanced Recharge Project ......... 92 4. Water chemistry from the Enhanced Recharge Project .................. 93 viii LIST OF FIGURES Figure Page 1. Aerial view of tree die-off .................................................................. 42 2. Detail of clogging .............................................................................. 43 3. Conceptual model of clogging in an effluent-dominated waterway .. 44 4. Map of study sites on the Santa Cruz and San Pedro Rivers .......... 45 5. Examples of sediment cores ............................................................ 47 6. Hydraulic conductivity of Santa Cruz and San Pedro Rivers ........... 48 7. Stream discharge on the Lower Santa Cruz River during study period and 2 years prior .................................................................... 49 8. Stream discharge on the Upper Santa Cruz River during study period and 2 years prior .................................................................... 50 9. Stream discharge on the San Pedro River during study period and 95 years prior.......................................................................... 51 10. Heterotrophic plate counts from the Santa Cruz and San Pedro Rivers ...................................................................................... 52 11. Fine sediments concentrations on the Santa Cruz and San Pedro Rivers ..................................................................................... 54 12. Ammonia concentrations on the Santa Cruz and San Pedro Rivers ................................................................................................. 55 13. Nitrate-nitrite concentrations on the Santa Cruz and San Pedro Rivers ..................................................................................... 56 ix