ti LOWER CIENEGA CREEK RESTORATION EVALUATION PROJECT: An Investigation into Developing Quantitative Methods for Assessing Stream Channel Physical Condition Funded by the Arizona Water Protection Fund Grant # 90-068 WPF by Lin Lawson and Hans Huth November 2003 Arizona Department of Environmental Quality Southern Regional Office Tucson, Arizona ADEQ Report #EQR0303 The "Old Timer" on the title page is a cottonwood we found in the Upper Basin of Cienega Creek near primary control point #2. The cadastral location of the tree is T19S R17E S15 dac (7.5 minute topographic map Spring Water Canyon, Ariz., 1981). The photo was taken from the terrace on the west side of the creek looking east. The base of the tree sits about ten feet below the top of the terrace and next to a barbed wire fence. Photo was taken at sunset on 18 June 2001 by Hans Huth with a Nikon digital camera. ABSTRACT This project was funded by the Arizona Water Protection Fund to evaluate a 10-mile reach in the Lower Basin of Cienega Creek, in southeast Arizona, for potential stream stabilization projects, and to develop and test quantitative techniques for assessing the physical condition of stream channels. A land survey of the geomorphology of the stream channel in the Upper and Lower Basins was conducted during the period December 2000 through April 2002. Two samples sites were located in each of the basins from which water quality, macroinvertebrate, and diatom samples were retrieved. One of the two sites in the Upper Basin was chosen as the reference condition to which the two sites in the Lower Basin were compared. Differences in water quality between the two basins are likely due to exposed marine sedimentary rocks in the Lower Basin. Macroinvertebrate and habitat assessment data revealed that habitat complexity was significantly less at the Lower Basin sites. Diatom taxa and abundance were correlated with water quality but not habitat complexity. The land survey showed that ephemeral and perennial reaches of the creek responded to the same hydrological processes. A local watershed area/cross-section area curve was constructed from over sixty cross-sections measured along the creek. Ephemeral cross-sections plotted closely to the regression line, which had a high correlation coefficient. The local curve was congruent with two regional curves, indicating its consistency with regional hydrological processes. These results gave validity for combining morphological data from both ephemeral and perennial reaches for streambed morphological analyses. Streambed feature analysis revealed morphological differences between the two basins. A Linear Habitat Complexity Index, developed from survey data, isolated a least impaired reference reach in the Upper Basin. A comparison of the reference reach to the channel in the Lower Basin showed the channel in the Lower Basin to be dominated by runs with few pools or riffles, indicative of an unstable channel. A pool facet slope analysis revealed that pools in the Lower Basin have shallow slopes, indicative of shallow pools. Pool facet slopes in the Lower Basin were significantly different than pool facet slopes in the reference reach. Reach slope departure analysis identified twenty-one ephemeral tributaries contributing sediment to the Lower Basin channel. Four of the contributors have supplied massive amounts of sediment to the lower channel. Several quantitative techniques for assessing the physical state of stream channels were developed and successfully employed to evaluate the morphological data collected during the project. These techniques will require further testing on streams throughout the state. It was concluded that the additions of sediment to the Lower Basin channel have been long in duration and massive in extent throughout its entire length, and any stream stabilization projects constructed in the near future would be without merit. The presence of the sediment and several active headcuts indicate an unstable channel, not conducive to long-term successful restoration projects. A series of recommendations are made to federal, state, and county agencies, and private land- holders for watershed management and improvement actions. PREFACE "It is not the critic who counts; not the man who points out how the strong man stumbles, or where the doer of deeds could have done them better. The credit belongs to the man who is actually in the arena, whose face is marred by dust and sweat and blood; who strives valiantly; who errs, and comes short again and again, because there is no effort without error and shortcoming; but who does actually strive to do the deeds; who knows the great enthusiasms, the great devotions; who spends himself in a worthy cause; who at best knows in the end the triumph of high achievement, and who at the worst, if he fails, at least fails while daring greatly, so that his place shall never be with those cold and timid souls who know neither victory and defeat." Theodore Roosevelt, address at the Sorbonne, Paris, France, April 23, 1910. TABLE OF CONTENTS Page FIGURES ii TABLES iii MAPS iv INTRODUCTION 1 STUDY AREA AND BACKGROUND 3 METHODS 5 Sampling Sites and Sampling Frequency 5 Sample Collection 5 Water Quality Procedures Discharge Measurement 6 Macroinvertebrate Collection Procedure 6 Diatom Collection Procedure 7 Bank Loss Procedure 7 Geomorphology Survey Procedure 7 RESULTS AND DISCUSSION 10 Water Quality 10 Results 10 Biological 16 Diatom Results 16 Benthic Macroinvertebrate Results 20 Geomorphology 25 Comparison of Ephemeral and Perennial Stream Channels 25 Bank Erosion as an Indicator of Excessive Sediment 27 Pool Facet Slope as an Indicator of Excessive Sediment 29 Streambed Feature Index as an Indicator of Excessive Sediment 32 Slope Deflection Analysis for Identifying Sediment Sources 35 Estimated Sediment Loads to Cienega Creek from Tributaries 66 SUMMARY AND CONCLUSIONS 67 RECOMMENDATIONS 70 LITERATURE CITED 72 ACKNOWLEDGEMENTS 73 APPENDIX TABLE OF CONTENTS 75 FIGURES Page Figure 1. Primary Control Point Distribution and Sample Site Locations for the Cienega Creek Basin 9 Figure 2. Conceptualization of Structural Components Producing Intermittent Flow in Lower Cienega Creek, Pima County, Arizona 15 Figure 3. Non-Metric Multidimensional Scaling Ordination Plot of Diatom Communities 17 Figure 4. Dendogram of Hierarchical Clustering of Water Quality Data from Four Sample Sites 21 Figtire 5. Dendogram of Hierarchical Clustering of Habitat Data from Four Sample Sites 22 Figure 6. MDS of Bray-Curtis Similarities from Log+1 Transformed Species Data and Water Quality Data and Untransformed Physical Data 23 Figure 7. Cienega Creek and Regional Curves Showing Cross-sectional Area as a Function of Watershed Area 25 Figure 8. Map of the Cienega Creek Basin Showing Locations of Primary Control Points and BM sites 28 Figure 9. Comparison of Reference Reach Facet Slopes to Lower Basin Facet Slopes 29 Figure 10 Box-and-Whiskers Plot of Pool Facet Slopes 30 Figure 11. Pool Facet Slope Distribution of Lower Basin Data Set 30 Figure 12. Pool Facet Slope Distribution of Reference Data Set 30 Figure 13. Results of First Exploratory Analysis to Identify a Reference Reach in the Upper Basin 34 Figure 14. Linear Habitat Complexity Index Applied to Reference Reach 35 Figure 15. Linear Habitat Complexity Index Applied to Lower Basin Channel 35 Figure 16. Longitudinal Profile of Streambed from CP17 to CP 19 38 Figure 17. Longitudinal Profile of Streambed from CP19 to CP20 41 Figure 18. Longitudinal Profile of Streambed from CP20 to CP21 46 Figure 19. Longitudinal Profile of Streambed from CP21 to CP22 54 Figure 20. Longitudinal Profile of Streambed from CP22 to CP23 55 Figure 21. Longitudinal Profile of Streambed from CP23 to CP24 61 TABLES Page Table I. Chemical Results for Nutrients 11 Table 2. Chemical Results for Metals , 11 Table 3. Chemical Results for Inorganics 12 Table 4. Field Data 13 Table 5. Summary of Results for the Kruskai-Wallis Test to Examine the Differences in Water Quality Parameters Among Sites 14 Table 6. Percent Similarity Matrix of Diatoms at Four Sample Sites with Replicates 17 Table 7. Correlation Analysis on Diatom Abundance and Selected Environmental Variables 18 Table 8. Summary of Macroinvertebrate Results with Arizona Index of Biological Integrity Rating 20 Table 9. Summary of Site Field Assessment for Physical Integrity 24 Table 10. Cienega Creek BEM Sites, Locations, and Potential Erosion Ratings 27 Table 11. Frequency Table of Pool Facet Slope Data from Lower Basin and Reference Reach 31 Table 12. Estimated Sediment Loads to Cienega Creek from Tributaries 66 MAPS Page Map 1. Cienega Creek Showing Beginning of Survey in the Lower Basin 37 Map 2. Cienega Creek Showing Next Downstream Reach from Map 1 42 Map 3. Cienega Creek Showing Next Downstream Reach from Map 2 45 Map 4. Cienega Creek Showing Next Downstream Reach from Map 3 53 Map 5. Cienega Creek Showing Next Downstream Reach from Map 4 62 iv INTRODUCTION The primary objective of the "Lower Cienega Creek Restoration Evaluation Project" was to gather environmental data, from which the streambed in the lower basin of the watershed could be evaluated for potential stream stabilization projects, and to develop and test quantitative techniques for assessing the physical condition of stream channels in Arizona. After several years of viewing portions of the creek, observations were made that excessive amounts of sediment were being stored in the channel, but it was unknown to what magnitude the ecosystem was being impaired by this pollutant. The sediment problem in Cienega Creek is not uncommon to the nation's streams and rivers. For several decades in the twentieth century, point source pollution was the focal point of pollution abatement to the nation's waters by the responsible federal and state agencies. After much success in lessening that problem, emphasis has now shifted to non-point source pollution. The single greatest non-point source pollutant to surface water resources in the United States is sediment (Ritchie, 1972; Oschwald, 1972; Downing, 1980; Lemley, 1982).