SAN JUAN RIVER BASIN RECOVERY IMPLEMENTATION PROGRAM DETAILED REACH STUDY 2009 DRAFT FINAL REPORT prepared by Ron Bliesner Keller-Bliesner Engineering, LLC 78 East Center Logan, Utah 84321 (435) 753-5651 Ernesto De La Hoz Paul Holden BIO-WEST, Inc. Logan, Utah 84321 and Vince Lamarra Ecosystems Research Institute 975 South Highway 89-91 Logan, Utah 84321 (435) 752-2580 May 06, 2010 TABLE OF CONTENTS LIST OF FIGURES.......................................................................................................... II LIST OF TABLES .......................................................................................................... III EXECUTIVE SUMMARY ................................................................................................ 1 DETAILED REACH ............................................................................................................... 1 SMALL-BODIED MONITORING HABITAT SELECTION ....................................................... 2 NON-NATIVE REMOVAL AND ADULT MONITORING HABITAT ASSOCIATION ................ 2 Findings from Analysis of Combined GPS Data .............................................................. 2 Findings from Analysis of Large Bodied Monitoring Data ................................................ 3 LARVAL RAZORBACK SUCKER HABITAT USE AND AVAILABILITY ................................. 3 CHAPTER 1: INTRODUCTION ...................................................................................... 4 SAN JUAN RIVER STUDY AREA ......................................................................................... 5 CHAPTER 2: DETAILED REACH FISH SURVEY (2007-2009) ..................................... 7 INTRODUCTION ................................................................................................................... 7 METHODS ............................................................................................................................ 7 Data Analysis ................................................................................................................. 9 RESULTS ........................................................................................................................... 10 Habitat Utilization ..........................................................................................................10 Capture per Unit of Effort ...............................................................................................15 Colorado Pikeminnow Population Estimate ...................................................................20 Habitat Selection Analysis .............................................................................................20 Habitat Availability .........................................................................................................27 Other SJRIP Studies .....................................................................................................33 Physical Characteristics ................................................................................................36 DISCUSSION ...................................................................................................................... 37 CHAPTER 3: HABITAT ASSOCIATION OF COLORADO PIKEMINNOW AND RAZORBACK SUCKER ............................................................................................... 40 INTRODUCTION ................................................................................................................. 40 METHODS .......................................................................................................................... 40 Detailed Reach ..............................................................................................................40 Large Bodied and Non-native Removal .........................................................................41 Larval Fish Study ...........................................................................................................42 RESULTS ........................................................................................................................... 42 Detailed Reach Analysis ................................................................................................42 Non-Native Removal and Large-Bodied Monitoring Razorback Sucker and Colorado Pikeminnow Habitat Association ........................................................................51 Larval Razorback Sucker Habitat Association ...............................................................53 DISCUSSION ...................................................................................................................... 57 Detailed Reach Habitat Association ...............................................................................57 Non-Native Removal and Large-Bodied Monitoring Razorback Sucker and Colorado Pikeminnow Habitat Association ........................................................................57 Larval Razorback Sucker Habitat Association ...............................................................58 REFERENCES .............................................................................................................. 59 APPENDIX A ............................................................................................................... 61 DETAILED REACH STUDY Page i 2009 DRAFT FINAL REPORT April 1, 2010 LIST OF FIGURES Figure 1.01. San Juan Basin location map showing geomorphic reaches ................................ 6 Figure 2.01. Length frequency distribution for Colorado pikeminnow captured in DR82, DR131, and DR137 during the detailed reach study (2007-2009). ..................... 12 Figure 2.02. Habitat use by Colorado pikeminnow. Proportion of pikeminnow captured by habitat type (All reaches and years combined). .................................................. 12 Figure 2.03. Habitat use by the complete fish assemblage. Proportion of fish captured by habitat type (All reaches and years combined). .................................................. 15 Figure 2.04. Colorado pikeminnow CPUE during surveys conducted in DR 82, DR131, and DR 137 during March and August of 2007,2008, and 2009 . NS indicates reach not sampled. ...................................................................................................... 18 Figure 2.05. CPUE for Colorado pikeminnow, all fishes , all native fishes, and all nonnative fishes during surveys conducted along DR 82, DR131, and DR 137 during March and August of 2007, 2008, and 2009. NS indicates reach not sampled. ............. 21 Figure 2.06. CPUE for Colorado pikeminnow, flannelmouth sucker, bluehead sucker, and speckled dace during surveys conducted in DR 82, DR131, and DR 137 during March and August of 2007,2008, and 2009. NS indicates reach not sampled. ... 22 Figure 2.07. CPUE for Colorado pikeminnow, channel catfish, red shiner, and fathead minnow during surveys conducted in DR 82, DR131, and DR 137 during March and August of 2007, 2008, and 2009. NS indicates reach not sampled. ................... 23 Figure 2.08. Scatter plot of mean velocity and depth for all samples and for those withColorado pikeminnow. Red markers indicate captures on pikeminnow with TL < 100 mm. Blue markers indicate captures of pikeminnow with TL > 100 mm.36 Figure 3.01. Graphical representation of seined areas, buffers and intersection with habitat mapping used in habitat association analysis ..................................................... 41 Figure 3.02. Colorado pikeminnow capture locations in DR 82, March 2008 and 2009. ......... 49 Figure 3.03. Colorado pikeminnow capture locations in DR 82, August 2007 - 2009 ............. 49 Figure 3.04. Colorado pikeminnow capture locations in DR 137, March 2008 and 2009. ....... 50 Figure 3.05. Colorado pikeminnow capture locations in DR 82, August 2007 - 2009. ............ 50 Figure 3.06. 2009 San Juan River Flow at Four Corners, New Mexico and Larval fish sampling dates. .................................................................................................. 56 DETAILED REACH STUDY Page ii 2009 DRAFT FINAL REPORT April 1, 2010 LIST OF TABLES Table 2.01. Summary of habitat use by Colorado pikeminnow along DR 82, DR 131, and DR137 (total pikeminnow captured): 2007-2009 ................................................ 11 Table 2.02. Summary of overall fish habitat use along DR82, DR131, DR137 (Total fish captured):2007-2009 .......................................................................................... 13 Table 2.03. Total fish captured by habitat type. All reaches combined (2007-2009) .............. 14 Table 2.04. Number of fish captured by species during March and August 2009. ................. 16 Table 2.05. Sample frequency (number of seine hauls by habitat) during surveys along DR82, DR131, and DR137 in the San Juan River (2007-2009). ......................... 17 Table 2.06. CPUE Summary (number of fish/area sampled m2): 2007-2009 ........................ 19 Table 2.07. Summary of population estimates for Colorado pikeminnow based on mark- recapture data collected during detailed reach fish surveys along DR82, DR131, and DR137 of the San Juan River: 2007-2009. .................................................. 24 Table 2.08. Summary of Colorado pikeminnow habitat selection by year, month, and reach*. (2007-2009). ...................................................................................................... 25 Table 2.09. Summary of habitat selection ratios for Colorado