Velocity Distributions and Fish Use of Engineered Log Jams

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1 Velocity Distributions and Fish Use of Engineered Log Jams Sarah Wassmund 1, Edgar Verdin 2, Tom Glass 3, and Kelsi Lakey 4 Advisors: Cara Walter, M.S., Oregon State University; Desiree Tullos, Ph.D., Oregon State University; Matthew Cox, M.S., Oregon State University Abstract Wood in streams has a varied history. Currently, efforts and funds are being channeled into the placement of large woody debris (LWD) in streams in the Pacific Northwest, primarily for the benefits that it yields in terms of sediment stabilization and habitat creation. While the first of these, sediment stabilization, is relatively well understood, many questions remain regarding the exact mechanisms underlying the creation of habitat for aquatic species. While undoubtedly many factors are at play, such as cover, water temperature, and sediment type, changes to the velocity of the water likely have a significant role in determining habitat preferences among fish. This study aims to assess the velocity profiles of locations used by juvenile salmonids in two third order streams in Oregon s Coast Range, as well as to profile the bathymetry and flow characteristics of these streams in order to aid the development of future experimental channel investigations. Fish at the two sites were found to have mean horizontal velocity preferences of cm/s and cm/s, indicating a distinct preference within the study sites. 1 Department of Fisheries Biology, Humboldt State University, Arcata, CA Department of Civil and Environmental Engineering, Portland State University, Portland, OR Department of Biology, Whitman College, Walla Walla, WA School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164

2 1 Contents LIST OF FIGURES INTRODUCTION METHODS STUDY SITES... 4 Full channel jam... 4 Meander jam FIELD METHODS Velocity measurements Bathymetry surveys Salmonid observations Total Station surveys Particle counts ANALYTICAL METHODS Bathymetry and Velocity Corrections using ArcGIS Analysis of fish observations Velocity analysis RESULTS AND DISCUSSION FULL CHANNEL JAM Positioning of logs Stream Profiling Salmonid composition, orientation, and location Positioning of logs Stream profiling Salmonid composition, orientation, and location STUDY LIMITATIONS AND SOURCES OF ERROR CONCLUSIONS ACKNOWLEDGEMENTS REFERENCES APPENDIX I SEDIMENT PROFILING CROOKED CREEK CANAL CREEK APPENDIX II SALMONID OBSERVATION TABLES CROOKED CREEK CANAL CREEK... 30

3 2 List of Figures Figure 1. Approximate locations of the jams... 3 Figure 2. Location of the full channel jam on Canal Creek... 5 Figure 3. Location of the meander jam located on Crooked Creek Figure 4. Three dimensional visualization of the full channel jam..... Error! Bookmark not defined. Figure 5. Bathymetric profile of the full channel jam.... Error! Bookmark not defined. Figure 6. Contour plot of velocity data at the full channel jam Figure 7. Salmonid focal point observations at the full channel jam Figure 8. Distribution of coho length at the full channel jam Figure 9. Fish utilization of horizontal magnitude velocity at the full channel jam Figure 10. Fish utilization of total velocity magnitude plotted with total measureable velocity magnitude values at the full channel jam Figure 11. Fish utilization of vertical velocity at the full channel jam Figure 12. Three dimensional visualization of the meander jam Figure 13. Bathymetric profile of meander jam Figure 14. Contour plot of water velocity at meander jam Figure 15. Salmonid observations at the meander jam Figure 16. Distribution of coho length at the meander jam site Figure 17. Fish utilization of horizontal magnitude velocity at the meander jam site Figure 18. Fish utilization of vertical velocity at the meander jam site. FFPs were observed and correlated to the closest vertical velocity value measured in centimeters per second Figure 19. Fish utilization of total velocity magnitude vs. total measureable velocity values at the meander jam site Figure 20. Sample selection of FFPs and their associated water velocity vectors Figure 21. Histogram representation of the differences between the orientation of the fish and the inverse orientation of its ascribed velocity vector

4 3 1.0 Introduction The relationship between wood and streams in the Pacific Northwest has changed dramatically over time. Historically, wood was removed from streams for several reasons. For example, timber harvest along riparian zones dramatically decreased the amount of wood available to enter the streams. Splash damming, which coincided with forest harvest practices, further reduced the amount of wood in streams. The goal of splash damming was to transport logs from harvest sites to sawmills. The technique of splash damming involved building a dam in a stream to block a substantial amount of flow. Logs would be placed behind the dam and once enough water was accumulated, it would be opened and both the water and logs would flow downstream. To aid in the effectiveness of splash damming obstacles such as large boulders and other pieces of wood were removed from streams resulting in streams devoid of in-stream structure. From the 1950s to the 1980s, wood was also removed from streams for navigational purposes as well as for perceived benefits to fish passage and water quality (Burnett et. al., 2008). Current understanding is that large woody debris (LWD) in streams provides crucial habitat for fish species including salmonids (Bilby and Bisson 1998). In the 1980s researchers (e.g. Bisson et al. 1987) began studying wood and its benefits for creating salmonid habitat in streams. As part of wide-scale efforts to facilitate salmonid recovery, managers began adding wood to channels, often in the form of engineered log jams (ELJ) (Burnett et. al., 2008). Currently, wood placement into streams is one of the most common habitat restoration techniques in the Pacific Northwest (Katz et. al., 2007). Engineered log jams are placed in streams for several reasons, though primarily for fish habitat restoration and bank stabilization. Research on engineered log jams has been focused primarily on construction (Nagayama and Nakamura, 2009) rather than their effects on flow (e.g. He et al., 2009; Lacey and Millar, 2004) and the fish behavior (Kemp, 2010 and references within). The objectives of this study are to gain understanding on both a) how ELJs affect flow and b) how and which fish utilize the flow fields generated by ELJs. We selected both a full-channel ELJ and an engineered meander jam as survey sites to understand the flow conditions for different structure types. The ultimate goal of this project is to contribute information on how to better construct engineered log jams for both fish use and beneficial modification of channel hydraulics.

5 4 2.0 Methods 2.1 Study sites Both sites are located in the Alsea watershed of Oregon s Coast Range, east of the city of Corvallis (Error! Not a valid bookmark selfreference.). Sites were selected within the same hydrographic region to reduce effects of variability in geology, hydrology, and ecology. Full channel jam The full channel jam is located on Canal Creek, a third order tributary to the lower Alsea River at an elevation of 45 meters above mean sea level. The site itself is located at [44 21' "N, ' "W], approximately 22 kilometers southeast of the town of Waldport, OR and just downstream of Canal Creek s confluence with the East Fork of Canal Creek (Figure 2). All observations at the full channel jam were made in a stretch of stream of approximately 35 m length and between 4.6 m and 9.4 m width. The jam is located in a meander bend, and consists of seven primary logs, which span the channel to varying extents. Two of these logs (logs 3 and 4, see Figure 4) have created a small dam that retains sediment. A single large root wad (log 6) sits in the center of the channel downstream of the jam structure, oriented with the rootwad in the upstream/downstream direction. Figure 1. Approximate locations of meander jam (red), and the full channel jam (blue). The Alsea River watershed is shaded in green. At the full-channel jam, we observed rainbow trout (Oncorhynchus mykiss), coho salmon (Oncorhynchus kisutch), sculpin (family Cottidae), crayfish, and lamprey (order Petromyzontiformes). Cutthroat trout (Oncorhynchus clarkii) may also be present, though no adults

6 5 were observed within the site. Given the difficulty in distinguishing between juvenile O. mykiss and O. clarkii in the field, their presence could not be ruled out. Substrate at the full-channel jam is highly varied, characterized by sand and gravel in the upper section of the jam, and by silt and larger cobbles in the downstream section of the jam (Appendix I). Meander jam The meander jam is located on Crooked Creek, which is a third order stream in the headwaters of the Alsea River, at an elevation of 120 meters above mean sea level. The site is located at [44 25' "N, ' "W], approximately 5.4 km northeast of the town of Alsea and just downstream of Crooked Creek s confluence with Baker Creek (Figure 3). All observations were conducted within a stretch of stream approximately 13 m long, the width of which varied from 4.3 m to 7.2 m. The jam was installed in 2008 by The Freshwater Trust s StreamBank Program, and consists of six logs partially buried in the outside bank (river right, facing downstream) of a meander, in such a way that the root wads sit approximately in the center of the wetted channel. Four distinct pools are formed between the logs. Underneath the six buried logs, a fully submerged and half buried log longitudinally spans the length of the jam and supports the other six logs. The inside of the meander (river left) consists of a cobble bar. Directly downstream of the engineered structure is a naturally-occurring full-channel jam, which has created a small backwater pool. The beginning of the study site was designated to be immediately upstream of this pool. Figure 2. Full channel jam located on Canal Creek at the tip of the blue arrow. Oregon State Highway 34 lies about half a mile north of the shown site location. At this meander jam, we observed rainbow trout (Oncorhynchus mykiss), coho salmon (Oncorhynchus kisutch), chinook salmon (Oncorhynchus tshawytscha), sculpin (family Cottidae) and

7 6 crayfish. Like at the full channel jam, cutthroat trout (Oncorhynchus clarkii) may be present, though no adults were observed within the site. Substrate in the site consisted mostly of cobble, gravel, and coarse sands. The main channel is dominated by the medium cobble (D50 = mm), while the pools featured mainly sand and medium gravel (D50 = mm) (Appendix I). Figure 3. Meander jam site located on Crooked Creek at the tip of the red arrow. Oregon State Highway 34 runs from the upper right to lower left, following the north fork of the Alsea River. Note the town of Alsea in the lower left. 2.2 Field Methods All field observations at the meander jam were conducted between July 9, 2012 and July 24, 2012, and those at the full channel jam were conducted between July 31, 2012 and August 8, Data collection took place in five forms: velocity measurements, bathymetry measurements, fish observations, total station surveys, and particle counts of the bed material.

8 Velocity measurements Velocity measurements were taken using a Teledyne RD Instruments StreamPro Acoustic Doppler Current Profiler (ADCP). An ADCP measures stream velocity by pinging, or emitting acoustic signals, into the water below. The signals are reflected off of particles floating in the current, and are subsequently detected by the sensor/transducer unit. The velocity is calculated from the frequency shift which the acoustic signal undergoes when reflected. Each ping consists of four simultaneous signals, which are emitted at a frequency of 2MHz. The four beams all originate from a central head with four transducers, but each is oriented 20 degrees out from the vertical. Using the frequency shift from each, a space-averaged instantaneous three-dimensional velocity vector can be generated for each of a number of bins, or horizontal cross-sections in the stream. Velocity measurements were taken in accordance with the physical characteristics of the stream. At the meander jam, two streamwise transects were taken along the length of the thalweg, and each pool was surveyed as an individual transect. At the full channel jam, most surveys took place according to depth, resulting in a series of pool transects with depths greater than 0.25 meters. The sampling mechanism of the StreamPro has an inherent blanking distance - a minimum vertical distance from the transducer head that is necessary to take an accurate measurement - which disallows it from being used in water under a certain depth. Additionally, the StreamPro is not able to take measurements immediately adjacent to the bottom. To track its position relative to the start of the transect, the StreamPro employs a feature called bottom-track, whereby a special ping is emitted to detect the velocity of the bottom which, if the bottom is immobile, reflects the motion of the instrument itself. In combination with an internal compass, this feature allows the StreamPro to keep a log of its position. However, if the StreamPro at any time loses track of the bottom (which typically results from the transducer temporarily rising above the surface of the water), the accuracy and utility of the bottom-track feature is quickly reduced. In order to check for, and to some extent mitigate this, Total Station points were taken at the start and end points of each transect (see Total Station surveys) Bathymetry surveys Bathymetry data were collected using a combination of the ADCP s bottom-track feature and Total Station survey points. All ADCP-accessible (greater than 25 cm) sections of the wetted channel were surveyed. Total station based topographic data was taken on a 1x1 meter grid system throughout the wetted and non-wetted channel.

9 Salmonid observations Fish observations were conducted between 10:00 a.m. and 3:30 p.m. Following appropriate snorkel protocol (O Neal 2007), each observation consisted of finding and identifying an appropriate target fish, which was then observed for a period of five minutes to determine if it was demonstrating fidelity to a focal point. Focal points were defined as an area of approximately 10 cm diameter and fidelity necessitated spending 80% of the observation period within the designated area. If the fish met this qualification, the snorkeler recorded the species, length, distance from stream bed, and orientation of the fish. The position of the fish was then marked and surveyed using the Total Station (see Total Station surveys). At the meander jam, observations were conducted between July 10 and July 24, while those at the full channel jam were conducted between August 2 and August 8. Each snorkeler remained in her or his personally designated pools throughout the entire sample period, and there was no overlap between pools snorkeled in an attempt to minimize recount Total Station surveys Total Station surveys were conducted using a Nikon DTM-352 Total Station. All prominent features of the site were surveyed, including the tops of the ends of key member logs, the outer edges of root wads, the edges of the wetted channel, the vegetation line, locations of fish (when possible), locations of large cobbles and boulders, and the elevation of the water surface. The coordinate system for the site was established by consistently using two 2x2 stakes for the total station location and backsight for each site with GPS coordinates acquired with an RTK GPS and post-processed with OPUS Particle counts Facies were mapped at each site and 100-particle counts were collected, according to the Wolman (1954) method, within each unit. 2.3 Analytical Methods Bathymetry and Velocity Corrections using ArcGIS ADCP measurements were pre-processed and downloaded using WinRiverII as ASCII output text files. Using the MATLAB code AdMap2 (written communications, David S. Mueller, U.S.

10 9 Geological Survey, Office of Surface Water), the text files were used to create CSV files of Multi- Beam Bathymetry (MMB) and velocity for uploading into ArcMap and ArcScene. The processing of the velocity and bathymetry data in AdMap2 includes X, Y, Z. The velocity files included all the measureable velocity readings recorded by the ADCP s sensor. Part of the AdMap2 process required using a water surface elevation file to generate the XY-location and the water surface elevation at the start of every transect. The XY-locations were determined by first using the Total Station to record the starting and ending location of each transect, measured at the inner upper right corner of the ADCP float. By measuring the XY-distance between the sensor and the Total Station rod, the starting/ending location of the sensor was determined by calculating the necessary Easting (X) and Northing (Y) rod to sensor offsets using the following equations: Where, ( ) ( ) And TSx being the measured X distance from the rod to sensor. TSy being the measured Y distance from the rod to sensor. H being the heading of the ADCP float; which was measured using the internal compass of the ADCP and acquired from a Generic ASCII output file for the transect data in WinRiverII. ( ) The water surface elevation was then recorded at the nearest wetted channel bank and perpendicular to the flow at the sensor s location. The shallow depths at both creeks combined with the ADCP s water depth limitation caused the system to lose bottom track about once per transect. The loss in bottom track resulted in the ship track location jumping by a large (range of 0.5m to 80 m) distance. To correct the ship track shift, an XY-bathymetry displacement file was created using WinRiverII to locate the data points and the XY-displacement when bottom track was lost. The average expected displacement for the shifted data was calculated and subtracted from the shift distances to determine the offsets necessary to move shifted ensembles back to their true locations. The ending Total Station points for transects were then used to determine if any whole transect rotations were necessary to account for differences between true north and magnetic north, or for errors in the internal compass of the

11 10 ADCP when tracking its path. The corrected MMB and velocity files were then uploaded onto ArcScene for plotting Analysis of fish observations Fish locations, represented as fish focal points (FFPs), were imported into ArcScene10 along with the bathymetry, velocity and water surface elevations. Shape files were used to pair each individual FFP with the nearest velocity vector. This was performed in the 3D Analyst toolbar, under 3D features using the near 3D option. The FFP location shape file was the input feature and the velocity shape files were inserted into the near category. This analysis produced the x, y, and z coordinates of the closest velocity value to each specific FFP. The x, y, and z coordinates of the closest velocity vector were then populated in the attribute table of the FFP shape file in ArcScene10 or within the.dbf file. However this process produced only the x, y, and z coordinates of the specific velocity. In order to find the actual velocity values represented by the coordinates, the coordinates were inserted in the Microsoft Excel file that contained both the velocity coordinates and their respective velocity values. For each site a new file was created with both the velocity coordinates and the corresponding velocity values. Histograms were created to assess for velocity preferences among fish. Velocities in the horizontal plane were represented by a directionless magnitude value, while those in the vertical direction were bidirectional (ie. could be either positive or negative) Velocity analysis Files containing x, y, z coordinates with corresponding values for u, v and w velocities, respectively, were created in AdMap using the WinRiver data. These files also included horizontal magnitude (hmag) and vector magnitude (vmag, which combines u,v and w). Data were entered into ArcMap and then manually corrected for ship-track errors (See Section 2.3.1). These data files were combined into one large Excel file to include all ADCP transects for each site. This Excel file was then analyzed in MATLAB. U and V velocity data was averaged over depth at each ensemble location. The horizontal magnitude was then calculated from the U and V components. Each horizontal magnitude was paired with Easting and Northing GPS coordinates. 3.0 Results and Discussion

12 Full Channel Jam Positioning of logs The full channel jam at Canal Creek is comprised of seven primary logs (Figure 4). Log 2 sits on top of logs 1, 6, and 7. Log 1 sits on top of logs 4, 6 and 7. Logs 3 and 4 rest upon the channel bottom for the entirety of their length. Logs 6 and 7 extend beyond what appears to be the downstream extent in Figure 4, in such a way that both are completely above the water within the boundaries of the site. The upstream end of log 6 consists of a large root wad (volume = 1.35 m 3, including empty space within wad), which lies on the streambed. A deep (approximately 0.6 m) pool has been formed underneath logs 6 and 7, downstream of their intersection with logs 1 and 2 (Figure 5). Log 5 is partially submerged. Figure 4. Three dimensional visualization of the full channel jam. Note direction of flow, indicated by red arrows. Also note that though the figure depicts log 1 resting on top of log 2, log 2 actually rest on top of log 1 and then bends downward to place the far riverleft end of the log 2 below that of log 1. This bend in the log could not be depicted using our graphic system which assumes a linear connection between the measured ends of the logs, making the log intersection erroneous but the far end placements correct (in reality, log 2 rests upon log 1). Figure 5. Bathymetric profile of the full channel jam. Elevation is measured in meters above sea level. Note the direction of flow, from right to left, as indicated by the blue arrow. The wetted channel at the time of measurement.

13 Stream Profiling Logs 3 and 4 seem to have had the most significant impact on the bathymetry of the channel based on the locations of sediment retention; A large composite of small woody debris and sediment has accumulated on the upstream side of logs 3 and 4, diverting flow to river right. The majority of flow then passes around the river right ends of these two logs, through a narrow opening between their ends (which are rested upon a large boulder), and the bank. The channel upstream of the logs is dominated by sand (38%) and gravel (36%), though cobble (13%) and silt (8%) also feature prominently in the sediment composition (Appendix I Figure G). The adjacent bar is composed entirely of sand (73%) and gravel (27%) (Appendix I Figure F). Downstream of logs 3 and 4, the thalweg proceeds along river right, underneath logs 1 and 2, followed by 6 and 7. Silt dominates much of the area to river left of log 7 (Appendix I Figures I and J). A velocity contour map was created for surveyed regions of the stream (Figure 6). The highest velocities were measured in the thalweg and in isolated spots within pools, while the pools in the lower section of the jam were generally areas of lower velocity. Figure 6. Contour plot of velocity data at the full channel jam. Flow is directed to the left of the page as is indicated by box and arrow near the top right of the graph.

14 Salmonid composition, orientation, and location Salmonid species present at the full channel jam consisted primarily of Coho salmon (Oncorhynchus kisutch) (n=132). In addition, some adult Rainbow trout (Oncorhynchus mykiss) Figure 7. Salmonid focal point observations at the full channel jam. Individual fish focal points are indicated by red (Coho) and blue (trout) arrowheads. The orientation and size of the arrowheads reflect the orientation and length of the fish observed at each focal point within the stream mm, Figure 8), and trout ranged from 40 mm to 150 mm (n=8). were present (n=6), as were some trout juvenile (genus Oncorhynchus, species either mykiss or clarkii) (n=2) (Figure 7). Coho ranged from 20 mm to 80 mm in length (n=132, mean = Fish focal points (FFP) were often observed directly underneath or downstream of logs, such as the cluster underneath the log 1, 2, 6, 7 intersection (Figure 7). However, many FFPs were also observed in open shallow water with little cover, such as the riffle in the upstream section of the site (above logs 3 and 4). Number of Fish n= Oncorhynchus kisutch lengths mm Figure 8. Distribution of Coho length at the full channel jam. Note that the bin sizes are defined as 20-29, 30-39, etc. (ie. a fish 50 mm long will fall into the 50-60mm bar). 80 Frequency distribution analysis revealed a mean horizontal magnitude preference among FFPs of 34 cm/s (n=139, standard deviation=29 cm/s, Figure 9), and a mean vertical velocity preference of 0.0 cm/s (n=139, standard deviation=10.5 cm/s, Figure 10). This result is markedly higher than findings in previous studies (Beecher et al. 2002), which have determined that

15 Percent of Total Velocity Values n= juvenile Coho show an overall velocity preference of 3-6 cm/s. FFPs were observed and correlated to the closest total velocity magnitude values in centimeters per second (Figure 11). Total velocity magnitude values are calculated from combining the vectors of the u, v and w vector fields. The mean magnitude preference for the fish was 35 cm/s (n=139, standard deviation = 30 cm/s). The mean velocity magnitude of total measureable data was 36 cm/s (n=43,638, standard deviation=26 cm/s). It is important to note that there were other velocity values that were not measurable due to equipment limitations. The total velocity values represented in this graph are only the values that our equipment was able to measure. Flow areas within un-measureable stream zones appeared to be roughly the same in size for the full channel jam. Figure 9. Fish utilization of horizontal magnitude Velocity at the full channel jam. FFPs were observed and correlated to the closest horizontal magnitude velocity value measure in centimeters per second. Horizontal magnitude velocity values are calculated from combining the vectors of both the u and the v fields. One outlier value of was excluded from the graph and is attributed to a data collection error. 8 7 Fish Focal Point Velocities Total Measurable Velocities Total Velocity Magnitude (cm/s) Figure 11. Fish utilization of total velocity magnitude plotted with total measureable velocity magnitude values at the full channel jam. One outlier fish focal point velocity value of was excluded from the graph and is attributed to a data collection error Figure 10. Fish utilization of vertical velocity at the full channel jam. FFPs were observed and correlated to the closest vertical velocity value measured in centimeters per second.

16 Meander Jam Positioning of logs The meander jam at Crooked Creek is comprised of seven primary logs (Figure 12). Log 7 is completely submerged and lies along the length of the jam, partially buried in the streambed. All other logs (1-6) are buried in the bank of river right, and protrude out into the channel. Logs 1-6 all end in root wads, which are submerged to varying degrees in the stream at baseflow. These logs exist in pairs, each of which consists of a primary log resting on the channel bottom and a secondary log resting upon the first. Logs 2, 4, and 6 are primary logs that are oriented perpendicular to the flow and rest upon the channel bottom. Logs 1, 3, and 5 are their corresponding secondary logs that are oriented facing upstream (Figure 12). Figure 12. Three dimensional visualization of the meander jam. Note direction of flow, indicated by red arrows. Log 7 (not pictured) is submerged beneath logs 2, 4, and 6. Each log terminates at a root wad (not visualized), which lie approximately in the center of the channel Stream profiling The meander jam is composed of four distinct pools interspersed among the logs, and the thalweg, which flows approximately through the center of the wetted channel, immediately adjacent to the root wads of logs 2, 4, and 6 (on the right side of the log structure). The deepest points of the channel lie within the structure, and at the interface between the logs and the thalweg (Figure 13). Bed material within the pools is primarily comprised of gravel (60%) and sand (36%) (Appendix I Figure D). The thalweg substrate is characterized primarily by cobble (47%) and

17 16 gravel (43%) (Appendix I Figure C), while the bar contains mainly gravel (52%) and cobble (37%) (Appendix I Figure B). A velocity contour map was created for surveyed regions of the stream (Figure 14). The Figure 13. Bathymetric profile of meander jam. Elevation is measured in meters above sea level. Note the direction of flow, from top to bottom, as indicated by the blue arrow. The wetted channel at the time of measurement is indicated by the blue lines. highest velocities occurred in the thalweg and in perimeter of the uppermost pool, while the pools in the lower section of the jam generally experienced lower velocities. Figure 14. Contour plot of water velocity at meander jam. Flow is directed down the page and is indicated by box and arrow near the top of the graph. The four slow moving blue pockets are in the location of the four pools, where the faster moving red areas is the thalweg.

18 Number of Fish n= Salmonid composition, orientation, and location Salmonid species present at the meander jam consisted mainly of coho salmon (Oncorhynchus kisutch) (n=26), though some Chinook (Oncorhynchus tshawytscha) (n=5), and adult rainbow trout (Oncorhynchus mykiss) (n=3) were also observed (Figure 15). Two (n=2) juvenile trout were also observed (genus Oncorhynchus, species either mykiss or clarkii). Cumulatively, far fewer salmonids were observed at the meander jam site (n=36) than at the full channel jam (n=140). Coho ranged in size from 35 mm to 70 mm (n=26, mean=54 mm Figure 16), Chinook ranged from 30 mm to 50 mm (n=5), and trout ranged from 30 mm to 145 mm (n=5) Oncorhynchus kisutch lengths (mm) Figure 16. Distribution of Coho length at the meander jam site. Figure 15. Salmonid observations at the meander jam. Individual fish focal points are indicated by red (Coho), gold (Chinook), and blue (trout) arrowheads. The orientation and size of the arrowheads reflect the orientation and length of the fish observed at each focal point within the stream. The highest concentration of FFPs at the meander jam was located in the pool directly downstream from logs 5 and 6, where water flowed out from underneath log 6 into a relatively deep pool. Frequency distribution analysis revealed a mean horizontal magnitude preference among FFPs of 33 cm/s (n=34, standard deviation=17 cm/s, Figure 17), and a mean vertical velocity preference of 0 cm/s (n=34, standard deviation=9 cm/s, Figure 18). Interestingly, these findings are very consistent with the velocity preferences at the full channel jam, and as such are similarly higher than those found by Beecher et al. (2002). 80

19 Percent of Total Velocity Values n= FFPs were observed and correlated to the closest total velocity magnitude values (Figure 15). The mean vertical magnitude preference for the fish at the meander jam site was 35 cm/s (n=34, standard deviation = 16 cm/s). The mean total magnitude for the measurable velocity values was 46cm/s (n=5,395, standard deviation = 30 cm/s). Again, we note that other velocity values were not measurable in the channel due to equipment limitations. The total velocity Figure 17. Fish utilization of horizontal magnitude velocity at the meander jam site. FFPs were observed and correlated to the closest horizontal magnitude velocity values in centimeters per second. 12 Fish Focal Point Velocities Total Measureable Velocities Total Velocity Magnitude (cm/s) Figure 18. Fish utilization of vertical velocity at the meander jam site. FFPs were observed and correlated to the closest vertical velocity value measured in centimeters per second. Figure 19. Fish utilization of total velocity magnitude vs. total measureable velocity values at the meander jam site. values represented in this graph are thus only the values that our equipment was able to measure. 4.0 Study limitations and sources of error A number of error sources exist in the collection of the data included in this study. As discussed briefly in Section 2.2, the accurate positioning of the velocity vectors within the site depend entirely on the bottom-track function of the instrument. Given the difficulties encountered in the field in maintaining bottom track, and despite numerous hours of manual adjustments in ArcMap, it is likely that many of the velocity vectors do not accurately represent the locations to which they have been ascribed.

20 Frequency 19 In addition to the inaccuracies of the velocity data itself, the fish histogram plots likely also contain errors. The histograms were created on the premise that each FFP could be associated with a velocity vector describing the immediately surrounding water. In reality, owing to the relatively sparse velocity data, the vector ascribed to each FFP is often located a nonnegligible distance (often as much as cm) from the FFP itself (Figure 20). The reliability of the results is thus highly dependent on the length scale of the flow structures in the channel More Difference in orientation (in degrees) between fish and velocity vector Figure 21. Histogram representation of the differences between the orientation of the fish and the inverse orientation of its ascribed velocity vector. A difference of zero would indicate that the fish is swimming directly into the flow, while a difference of 180 indicates that the fish has its tail oriented directly upstream. Data taken from meander jam. Figure 20. Sample selection of FFPs and their associated water velocity vectors. Sample taken from lowermost pool in the meander jam site (see log numbers for orientation). Thin black lines connect each FFP (indicated by arrowheads) with its associated velocity vector (indicated by green arrows). The orientations of the FFPs represent the orientation of the observed fish in that location, and the orientation of the velocity vectors represent the direction of flow at that location. Note that this illustration depicts the entire water column, so FFPs may be at different depths (a fact that explains the two velocity vectors which seem to cross each other). We investigated the potential discrepancy between the water velocity vectors that have been ascribed to each FFP and the true velocity vector at each location. A histogram was created to compare the orientation of the fish with the inverse orientation of the ascribed velocity vector (Figure 21). Under the assumption that fish choose to minimize energy expenditure by choosing FFPs that are oriented into the flow (i.e. oriented in the upstream direction), the relatively even spread of this histogram can be taken as a suggestion that the velocity vectors are indeed

21 20 misrepresentative of the true velocity at the location of the FFP. A final consideration regarding the FFP/velocity analysis lies in the data collection method of the ADCP itself. As discussed in the methods section, each ensemble collected by the StreamPro represents a pyramid in the water column. The pyramids are divided into a number of horizontal slices ( bins ), within which a velocity measurement is taken at each of the four vertices. In our analysis, all four of these measurements are averaged to give one three-dimensional velocity measurement per bin, the coordinates of which lie directly below the transducer. Due to the pyramid shape of the ensemble, the volume of each bin increases from the surface of the water to the streambed. As a result of velocity averaging over a greater volume, the accuracy of the velocity measurement given for each bin could potentially decreases. 5.0 Conclusions In-stream flow characteristics can have a powerful value in predicting the locations of fish. Management tools, such as the Physical Habitat Simulation System (PHABSIM), monopolize on this premise as a means of making informed decisions regarding stream and riparian developments, such as the placement of engineered log jams (Beecher et al. 2011). For this reason, a thorough understanding of how fish of different species and sizes utilize flow is valuable. Keeping in mind the significant sources of error inherent to the data collection process of this study, we have tentative suggest a mean horizontal velocity preference among juvenile salmonids, particularly age 0+ coho salmon, of approximately 34 cm/s. This number is substantially higher than most previous studies conducted on the subject, which report a preferred velocity for these fish of 3-6 cm/s (Beecher et al. 2011), and less than 20 cm/s (Bisson et al. 1988). This low velocity preference has been well established (Bisson et al. 1988), as coho salmon are typically associated with slow moving, calm pools. We note possible explanations for the discrepancy between this and other studies. In our comparisons between the fish s preferred velocities and the total measured velocities in the stream, we show that, at the meander jam site, the fish seem to avoid the fastest flowing water in the site, which is in keeping with our qualitative observations (Figure 19). At the full channel jam site, however, fish appear to prefer nearly the exact velocity that is most abundant (Figure 11). Of course, the second case may be explained by the resolution of our velocity data, which may not be fine enough to detect true preferences among coho. The same may be true of the first site as well.

22 21 Additionally, we note that, in the datasets for both sites, we have included a small number of other species (and, consequently, larger fish), which likely do prefer higher velocities than coho. Nonetheless, it appears that the coho at our sites do indeed occupy focal points with a mean water velocity of ~34 cm/s. These results suggest the need for re-evaluating the coho s feeding strategy and habitat requirements in the regions around woody debris. For example, under such a scenario, coho may present a more active competitive presence to other species (such as trout) in the stream, which typically occupy higher velocities. Additional study of FFP velocities is necessary to verify our results. 6.0 Acknowledgements Foremost, we would like to thank our on-call, keeper-of-the-knowledge adviser Cara Walter. Cara, you are probably well aware of how little we would have accomplished this summer without you. Of course, we would also like to thank Desiree Tullos and Matt Cox for providing guidance and clarification in all aspects of the project. Finally, our gratitude too must be paid to Julia Jones, Tom Dietterich, and again Desiree Tullos and Matt Cox for their countless hours in pulling together the Ecosystem Informatics Summer Institute REU, under which this project was possible.

23 22 References Beecher H. A., Caldwell B. A., and S. B. DeMond Evaluation of Depth and Velocity Preferences of Juvenile Coho Salmon in Washington Streams. North American Journal of Fisheries Management 22, Bilby, R. E. and P. A. Bisson Function and distribution of large woody debris in Naiman RJ, Bilby RE, eds. River Ecology and Management: Lessons From the Pacific Coastal Ecoregion New York: Springer-Verlag. Bisson, P. A., Bilby, R. E., Bryant, M. D., Dolloff, C. A., Grette, G. B., House, R. A., Murphy, M.L., Koski, K.V., & Sedell, J.R.. (1987). Large woody debris in forested streams in the Pacific Northwest: past, present, and future. In E. O. Salo & T. W. Cundy (Eds.), Streamside management: forestry and fisheries interactions. University of Washington Press, Seattle: Burnett, K. M., G. R. Guillermo, and J. Behan A Pilot Test of Systematic Review Techniques: Evaluating Whether Wood Placements in Streams of the Pacific Northwest Affect Salmonid Abundance, Growth, Survival or Habitat Complexity. Document no ,The Institute for National Resources, Oregon. He, Z., Wu, W., & Shields, F. D. Jr Numerical analysis of effects of large wood structures on channel morphology and fish habitat suitability in a Southern US sandy creek. Ecohydrology, 2, Katz, S. L., Barnas, K., Hicks, R., Cowen, J., & Jenkinson, R Freshwater Habitat Restoration Actions in the Pacific Northwest: A Decade s Investment in Habitat Improvement. Restoration Ecology, 15(3), Kemp, P In-Channel Placement of Structure to Enhance Habitat Complexity and Connectivity for Stream-Dwelling Salmonids. In P. Kemp (Ed.),Salmonid Fisheries: Freshwater Habitat Management (pp ). Oxford, UK: Wiley-Blackwell. Lacey, R. W., & Millar, R. G Reach Scale Hydraulic Assessment of Instream Salmonid Habitat Restoration. Journal of the American Water Resources Association, 40(6), Mueller, David S., U.S. Geological Survey, Office of Surface Water, written communication Nagayama, S., & Nakamura, F Fish habitat rehabilitation using wood in the world. Landscape and Ecological Engineering, 6(2), O Neal, J Snorkel Surveys. In D. Johnson, B. Shrier, J. O Neal, J. Knutzen, X. Augerot, T. O Neil, T. Pearsons (eds.) Salmonid Field Protocols Handbook. American Fisheries Society.

24 23 Wolman, M. G A method of sampling coarse river-bed material. Transactions of the American Geophysical Union 35(6):

25 percent finer than 24 Appendix I Sediment profiling Crooked Creek Figure A. Locations of individually counted facies at the meander jam on Crooked Creek. Note that though the entire bar and thalweg were each counted separately, all pools were counted together and can be seen represented in Figure D below. cumulative % # of particles 100% 90% 80% 70% 60% 50% 8 40% 6 30% 20% 4 10% 2 0% particle size (mm) number of particles Sediment type Silt/clay 0% Sand 9% Gravel 52% Cobble 37% Boulder 1%. Figure B. Bar - Sediment distribution in the bar of the Crooked Creek meander jam.

26 percent finer than percent finer than 25 cumulative % # of particles 100% 90% 80% 70% 60% 50% 40% 30% 20% 5 10% 0% particle size (mm) number of particles Sediment type Silt/clay. 0% Sand 5% Gravel 43% Cobble 47% Boulder 3% Figure C. Thalweg - Sediment distribution in the thalweg of the Crooked Creek meander jam. cumulative % # of particles 100% 90% 80% 70% 60% 50% 40% 30% 10 20% 10% 5 0% particle size (mm) number of particles Sediment type Silt/clay 0% Sand 36% Gravel 60% Cobble 3% Boulder 0% Figure D. Pools - Sediment distribution in the pools of the Crooked Creek meander jam. Note that all pools were included within this count.

27 percent finer than 26 Canal Creek Figure E. Location of the individually counted facies at the full-channel jam on Canal Creek. cumulative % # of particles 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% particle size (mm) Figure F. Bar - Sediment distribution in the bar of the full channel jam, as indicated in Figure E number of particles Sediment type Silt/clay 0% Sand 73% Gravel 27% Cobble 0% Boulder 0%

28 percent finer than percent finer than 27 cumulative % # of particles 100% 45 90% 40 80% 35 70% 30 60% 25 50% 20 40% 30% 15 20% 10 10% 5 0% particle size (mm) number of particles Sediment type Silt/clay 8% Sand 38% Gravel 36% Cobble 13% Boulder 2% Bedrock 3% Figure G. Upstream thalweg - Sediment distribution within the channel of the full channel jam, upstream of the dam (logs 3 and 4) as indicated in Figure E. cumulative % # of particles 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% particle size (mm) number of particles Sediment type Silt/clay 26% Sand 35% Gravel 11% Cobble 11% Boulder 1% Bedrock 14% Figure H. Intermediate zone - Sediment distribution within the channel within the full channel jam, downstream of the dam (logs 3 and 4) in the Canal Creek full channel jam, as indicated in Figure E.

29 percent finer than percent finer than 28 cumulative % # of particles 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% particle size (mm) number of particles Sediment type Silt/clay 67% Sand 14% Gravel 6% Cobble 7% Boulder 2% Bedrock 4% Figure I. Mid river left - Sediment distribution within the channel within the mid river left zone of the full channel jam indicated in Figure E. cumulative % # of particles 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% particle size (mm) number of particles Sediment type Silt/clay 17% Sand 4% Gravel 12% Cobble 32% Boulder 25% Bedrock 10% Figure J. Lower river left Sediment distribution within the channel of the full channel jam, within the lower river left zone indication in Figure E.

30 29 Appendix II Salmonid observation tables Crooked Creek Species Length (m) Orientation (degrees) Distance from Streambed (m) TROUT CHINOOK COHO CHINOOK COHO TROUT COHO CHINOOK COHO COHO COHO COHO COHO COHO COHO COHO CHINOOK CHINOOK COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO TROUT TROUT TROUT

31 30 Canal Creek Species Length (m) Orientation (Degrees) Distance from streambed (m) COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO TROUT COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO

32 31 Species Length (m) Orientation (Degrees) Distance from streambed (m) COHO COHO COHO COHO COHO COHO COHO COHO TROUT COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO

33 32 Species Length (m) Orientation (Degrees) Distance from streambed (m) COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO COHO TROUT COHO COHO COHO COHO COHO COHO COHO COHO COHO TROUT COHO TROUT TROUT TROUT TROUT