Juvenile Chinook and Coho Salmon Habitats and Distribution in the Matanuska-Susitna Borough: 2016 December 2016

Juvenile Chinook and coho salmon habitats and distribution in the Matanuska-Susitna Borough: 2016 December 2016

For: By:

Matanuska-Susitna Borough: Fish and Jeffrey C. Davis, Gay A. Davis, and Sean Kinard Wildlife Commission P.O. Box 923, Talkeetna, AK 99676 Juvenile Chinook and coho salmon habitats December 2016

Acknowledgements. This project was completed with financial support from the Matanuska- Susitna Borough, Fish and Wildlife Commission. A large amount of data collection and date entry was conducted by Sean Kinard, Hannah Gould, and Caroline Graham.

Juvenile Chinook and coho salmon habitats December 2016

Contents 1.0 Introduction ...... 1 2.0 Methods...... 2 2.1 Sampling Locations ...... 2 2.2 Fish Sampling ...... 2 2.3 Water Quality ...... 4 2.4 Physical Habitat Surveys ...... 4 2.4.1 Reach-level habitat characteristics ...... 4 2.4.2 Trap-level habitat characteristics ...... 5 3.0 Results ...... 6 3.1 Stream Water Quality ...... 6 3.1.1 pH ...... 6 3.1.2 Specific Conductivity...... 6 3.1.3 Turbidity ...... 7 3.1.4 Temperature ...... 7 3.1.5 Dissolved Oxygen ...... 9 3.2 Physical Stream Characteristics ...... 9 3.2.1 Stream Flow Classification ...... 9 3.2.2 Large Woody Debris ...... 11 3.2.3 Discharge ...... 11 3.2.4 Riparian vegetation ...... 12 3.2.5 Substrata ...... 12 3.2.6 Stream Morphology ...... 15 3.2.7 Trap Habitat Data ...... 17 3.3 Fish Distribution and Abundance ...... 19 3.3.1 Coho salmon ...... 21 3.3.2 Chinook salmon ...... 25 3.3.3 Change in juvenile salmon abundance over time ...... 30 3.3.3 Resident Salmonids ...... 37 3.3.4 Resident non-salmonids ...... 39 4.0 Summary ...... 39 4.1 Objective 1 ...... 39

iii

Juvenile Chinook and coho salmon habitats December 2016

4.2 Objective 2 ...... 40 4.3 Objective 3 ...... 40 5.0 Literature Cited ...... 42

Figures

Figure 1. Specific conductivity of water in each stream during May 2016...... 7 Figure 2. Percent of days each stream daily maximum temperature exceeded 13°C and 15°C. .... 8 Figure 3. Average monthly degree days (sum of daily average values) for upland, wetland, and lake-stream systems for June, July, and August, 2015...... 8 Figure 4. Stream flow classification of all streams are plotted as proportions of the entire sampled reach, ordered by %riffle from greatest to lowest...... 9 Figure 5. Proportion of riffle and pool in streams containing a combined total of 30% or more in their stream flow classification...... 10 Figure 6. Stream flow classification displayed as a proportion of swift mesohabitats (riffle and run). Colors represent different stream types (blue = upland, yellow = wetland, green = lake- stream-complex)...... 10 Figure 7. Relative abundance of Large Woody Debris in each stream. Colors represent different stream types (blue = upland, yellow = wetland, green = lake-stream-complex)...... 11 Figure 8. Discharge (ft3/s) for each stream in June 2016 plotted on a logarithmic scale. Colors represent different stream types (blue = upland, yellow = wetland, green = lake-stream-complex)...... 12 Figure 9. Substrate size (mm) at 50% of the cumulative frequency distribution at each stream. Colors represent different stream types (blue = upland, yellow = wetland, green = lake-stream- complex)...... 14 Figure 10. Percent of substrates that were more than 20% embedded. Colors represent different stream types (blue = upland, yellow = wetland, green = lake-stream-complex)...... 14 Figure 11. Average stream slope for the four stream types. Error bars are one standard deviation...... 16 Figure 12. Average channel depth among the four stream types. Error bars are one standard deviation...... 16 Figure 13. Average width/depth ratio for the four stream classification types. Error bars are one standard deviation...... 17 Figure 14. Relative percent of juvenile Chinook and coho salmon, resident salmonids (Dolly Varden char, rainbow trout, whitefish), and other resident fish species to the total average CPUT...... 21 Figure 15. The frequency distribution of coho salmon fork lengths from all sites. Coho salmon with fork lengths under 70mm were considered age-0...... 23 Figure 16. The proportion (as a percentage) of age-0 and age-1+ coho salmon at each site. Age-0 coho were defined as having a fork length less than 70 mm...... 23 Figure 17. Median fork lengths of age-0 and age 1+ coho salmon. Age-0 coho were defined as being less than 70 mm...... 24 iv

Juvenile Chinook and coho salmon habitats December 2016

Figure 18. Average condition of coho salmon at each sample site...... 24 Figure 19. Juvenile coho salmon relative abundance as CPUT comparing large streams, small upland, small wetland, and lake-stream complexes...... 26 Figure 20. Medial fork lengths among stream types. Juvenile coho salmon < 70 mm were longer in lake-stream complexes compared to large streams. There were no differences in fork lengths of juvenile coho salmon > 69 mm among the other stream classification types...... 26 Figure 21. Average juvenile Chinook salmon CPUT at each surveyed site (Summer 2016)...... 27 Figure 22. The size frequency distribution of Chinook salmon fork lengths from all sample sites...... 27 Figure 23. Median fork lengths for Chinook salmon in streams with sample sizes greater than 10...... 28 Figure 24. Relationship between June cumulative degree days at a sampling reach and juvenile Chinook salmon fork lengths in early July...... 28 Figure 25. Average condition of Chinook salmon at each sample site...... 29 Figure 26. Juvenile Chinook salmon CPUT among stream classification types showing the abundance of these fish in large upland and large wetland stream compared to other stream classification types...... 30 Figure 27. Negative relationship between juvenile coho salmon and Chinook salmon...... 30 Figure 28. Relative abundance of juvenile coho and Chinook salmon in Moose Creek (Kroto Creek drainage), a large wetland stream, on three sampling dates. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 31 Figure 29. Relative abundance of juvenile coho and Chinook salmon in a small wetland stream in the Moose Creek drainage. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 32 Figure 30. Relative abundance of coho salmon in a small wetland stream in the Rabideux Creek drainage. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 32 Figure 31. Relative abundance of juvenile coho and Chinook salmon in a small upland stream in the Little Willow Creek drainage. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 33 Figure 32. Relative abundance of juvenile coho and Chinook salmon in a small upland stream in the Little Willow Creek drainage. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 33 Figure 33. Relative abundance of juvenile coho salmon and Chinook salmon in the Little Susitna River, a large upland stream, near the Church Road Bridge in 2010 and 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 34 Figure 34. Relative abundance of juvenile coho salmon and Chinook salmon in a small upland tributary to the Little Susitna River from 2008 through 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 34

Juvenile Chinook and coho salmon habitats December 2016

Figure 35. Relative abundance of juvenile coho salmon and Chinook salmon in a small upland tributary to the Little Susitna River from 2008 to 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 35 Figure 36. Relative abundance of juvenile coho salmon and Chinook salmon in Wasilla Creek, a small upland stream, from 2010 to 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 35 Figure 37. Relative abundance of juvenile coho salmon in Cottonwood Creek, a lake-stream system, from 2010 to 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 36 Figure 38. Relative abundance of coho salmon in Question Creek, and lake-stream system from 2013 to 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October)...... 36 Figure 39. Adult coho salmon return as a function of juvenile coho salmon relative abundance in Queer Creek, three years previously...... 37 Figure 40. Adult coho salmon return in the Little Susitna River as a function of juvenile coho salmon relative abundance in Colter Creek, a small upland tributary. Regression equation excludes adult return for 2012 (red point) which was low relative to the high juvenile coho salmon CPUT in 2009...... 37 Figure 41. Percent of CPUT at each site composed of juvenile Chinook and coho salmon and other resident salmonids (Dolly Varden char and rainbow trout)...... 38 Figure 42. Average CPUT of rainbow trout and Dolly Varden char from sampling reaches from streams classified as upland, wetland, or lake-stream systems. Error bars are one standard deviation...... 39

Tables

Table 1. Mat-Su Basin sites surveyed May-August 2016...... 3 Table 2. Water quality values for each stream measured in May of 2016...... 6 Table 3 Dominant bank-edge (0-3m) riparian vegetation for each stream...... 13 Table 4 Summary statistics for substrate size and embeddedness...... 13 Table 7. Stream morphology characteristics based on the average of 5 transects in each stream. The Stream type averages for these sites are presented at the bottom of the table...... 15 Table 5 Percent of traps at each sample site with substrate and cover type...... 18 Table 6 Summary statistics of depth and velocity data at trap locations in each stream...... 19 Table 8. The number fish, by species, captured during summer sampling in each stream...... 20 Table 9. Average Catch per Unit Trap (CPUT) for streams in the Mat-Su Basin...... 22

Juvenile Chinook and coho salmon habitats December 2016 ARRI

1.0 Introduction Maintaining healthy Pacific salmon populations and salmon fisheries is a priority for the Matanuska-Susitna Borough. In order to determine the best course of action necessary to maintain salmon healthy salmon populations, the Matanuska-Susitna Borough, Fish and Wildlife Commission, sponsored a study to identify and prioritize actions that support and maintain a salmon fishery within northern Cook Inlet and the Matanuska and Susitna River drainages. The result of this study is the Research Monitoring and Evaluation Plan for Upper Cook Inlet (RM&E Plan), (2015). The Mission of the RM&E Plan is to “develop a strategic action plan that encompasses the interests of partners and governing agencies in guiding funds towards research, monitoring and evaluation of projects selected to manage, protect and improve Mat-Su Borough salmon stocks for optimum benefits while maintaining biological productivity and diversity.” The RM&E plan focuses on three main areas: the status of salmon, salmon fisheries, and salmon ecosystems. This project has been developed to provide information toward addressing multiple issues and objectives identified in the RM&E Plan. One of the objectives under the status of salmon is to identify the significance of different rivers and streams based on the relative abundance by life stage or inferred by habitat. This project addresses this objective by measuring the relative abundance of juvenile Chinook and coho salmon among different stream types throughout the Mat-Su Borough. A second objective is to evaluate the effects of human development and activities on salmon production and trends. The RM&E plan recommends studies that describe important habitats for different life stages, and those that provide complete physical habitat surveys of representative areas, monitor index watersheds over time, monitor changes in habitat conditions in relation to habitat production. This project builds upon previous juvenile salmon monitoring efforts (Miller et al. 2011, Ramage et al. 2014, and Davis et al. 2015) by providing information on the significance of different streams for juvenile Chinook and coho salmon. Concomitant measures of physical habitat characteristics and site specific habitat preferences and habitat characterization along with information on habitat conditions among multiple streams can be used to infer broad scale patterns of juvenile salmon distribution. Whereas small scale habitat suitability can be used to identify important habitat characteristics within a stream classification type. The location of sampling sites in representative urban and undisturbed rural streams can be used to assess the effects of human development on juvenile Chinook and coho salmon rearing and overwintering. The project will describe important summer rearing habitats for juvenile Chinook and coho salmon and provide complete physical habitat surveys. The objectives of this study are: 1. Obtain measures of the relative abundance of juvenile salmon among multiple different stream types distributed throughout the Mat-Su Borough in 2016 and 2017,

Juvenile Chinook and coho salmon habitats December 2016 ARRI 2. Test for differences in juvenile salmon relative abundance and indices of growth over time, and among stream classification types, and 3. Test for relationships between juvenile salmon relative abundance and differences in habitat suitability, physical habitat, spawner abundance and egg survival, and water quality. This report summarizes 2016 data collection efforts and initial tests for differences in juvenile salmon relative abundance among stream classification types.

2.0 Methods

2.1 Sampling Locations This study was conducted at 17 sampling locations within the Susitna and Matanuska River drainages from May through September of 2016. Sampling locations were selected to represent common stream types found within these drainages; Large and small upland streams, large and small wetland or brown-water streams, and lake-stream systems (Table 1). All streams draining the Talkeetna Mountains on the east side of the Susitna River, that appear clear of organic staining, and of moderate to steep slopes were classified as upland streams. Streams were classified as wetland streams if they drain the lowlands west of the Susitna River, and appear to contain higher concentrations of organic acids giving them a stained or brown appearance. First or second order streams were classified as “small” and third or larger order streams were classified as “large”. Two small tributaries were sampled within the drainage of each large upland or wetland stream. Three sampling reaches were in streams influenced by lakes and were classified as “lake-stream systems.” Two streams, Cottonwood Creek (Wasilla) and Wasilla Creek are influenced by commercial development.

2.2 Fish Sampling Fish sampling was conducted in 100 or 200 m sampling reaches based on stream classification (large or small) and reach lengths. Reach lengths were 20 x channel width with a minimum length of 100 m. Fish sampling was conducted using the methods applied previously in similar studies (Miller et al 2011, Davis et al. 2015). Fish were sampled using Gee minnow traps (1/4 inch mesh, Memphis Net and Twine). Minnow traps were baited with commercial salmon roe (Alaska Bait Company) enclosed in perforated ‘whirl-pak’ bags. For sampling reach lengths > 150 m 20 traps were used for reach lengths < 150 m 10 traps were used. Traps were selectively placed in slower moving water and ideally protected by cover from overhanging banks or woody debris, if present. A minimum separation distance of approximately 10 m was maintained between traps. The traps were left to soak for 20 to 24 hours. Captured fish were transferred from the traps to plastic buckets filled with stream water. All juvenile salmonids, whitefish (Prosopium cylindraceum), burbot (Lota lota), and blackfish were identified to species and all salmon species (Onchorynchus sp.) and Dolly Varden (Salvelinus malma) were measured to fork length (FL). Within each site, the first 100 salmon of each species were weighed to the nearest 10-1 grams (OHAUS CS 200). Trautman (1973) was used to identify presmolt Pacific Salmon. Resident sculpin and stickleback were identified to genus. Each trap

Juvenile Chinook and coho salmon habitats December 2016 ARRI was evaluated separately providing 10 or 20 replicate catch per unit trap (CPUT) values for each sampling reach. Table 1. Mat-Su Basin sites surveyed May-August 2016.

Stream Latitude Longitude Classification Moose Creek (Petersville) 62.25426 -150.43332 Large Wetland Chijik Tributary 62.09567 -150.53697 Small Wetland Cottonwood Creek (Petersville) 62.20435 -150.47757 Small Wetland Rabideux Creek 62.18985 -150.21059 Large Wetland Sawmill Creek 62.24271 -150.25076 Small Wetland Queer Creek 62.19191 -150.21997 Small Wetland Little Willow Creek 61.80954 -150.09306 Large Upland Iron Creek South 61.83591 -149.84396 Small Upland Iron Creek North 61.83368 -149.82973 Small Upland Little Susitna River 61.64350 -149.52960 Large Upland Colter Creek 61.65395 -149.49934 Small Upland Swiftwater Creek 61.64923 -149.51299 Small Upland Question Creek 62.22188 -150.08810 Lake-Stream System Little Meadow Creek 61.57668 -149.72887 Lake-Stream System Cottonwood Creek (Wasilla) 61.57479 -149.41231 Lake-Stream System Moose Creek (Palmer) 61.67451 -149.03737 Large Upland Wasilla Creek 61.56713 -149.31400 Small Upland

Fish community metrics were calculated for each sampling reach to allow for comparisons among streams. Average catch per unit trap (CPUT) was calculated for each species and age class. CPUT averages were further used to calculate ratios of juvenile salmon to resident fish species. The median fork length was calculated for each species at each site with a sample size exceeding 10. Length frequency distributions were used to estimate coho salmon and Chinook salmon age classes. Only one age class of Chinook salmon were observed at all sites. If there was a distinct bimodal distribution at a sampling site, we used this to determine the maximum length for an age-0 coho salmon and recalculated the median, mode, and total number of fish that were considered age-0. If the distribution was not clearly bimodal, we defined age-0 coho salmon as being ≤ 70mm in fork length and age-1+ fish as being equal to or > 70 mm in fork length. Condition factor (C) was calculated for each fish with a recorded fork length and weight by following the following equation:

= 10000 𝑊𝑊 𝐶𝐶 � 3� ∗ Where weight (W) is in grams and fork length𝐿𝐿 (L) in millimeters.

Juvenile Chinook and coho salmon habitats December 2016 ARRI 2.3 Water Quality Stream water temperature was collected at each site with an Onset Pro V2 Data logger and recorded every 30 minutes from June 1 through ~September 20. Dissolved oxygen, pH, specific conductivity, temperature and turbidity were measured while deploying the temperature loggers in the month of May. Dissolved oxygen (mg/L and percent saturation) and temperature were measured using an YSI Pro ODO handheld meter. Specific conductivity (μS/cm), pH and temperature were measured using an YSI model 63 handheld meter. Turbidity (NTU) was measured using a LaMotte 2020we/wi meter.

2.4 Physical Habitat Surveys 2.4.1 Reach-level habitat characteristics Sampling reaches were initially scouted a distance of 400 meters from access points to determine the sinuosity, width, and general characteristics. Sampling reach length was determined by multiplying average stream width by 20. Minimum reach length was 100 m and maximum length 200 m. Reaches were at least 100 meters from roadways and road crossings. Stream discharge was measured and all flow mesohabitat types classified. Stream channel geomorphology, undercut banks, water surface and bed slope, substrate size distribution, and large woody debris (LWD) abundance was measured in each sampling reach. Riparian vegetation type was classified. Stream discharge was measured at each sampling reach in late May and in July during fish sampling. Water velocity (ft/s) was measured using a Swoffer Model 3000 current meter and stream discharge (cfs) calculated as the sum of component sections. Discharge in the Little Susitna River (USGS Gauge No. 15290000) and Moose Creek (Palmer) (USGS Gauge No. 15283700) were obtained from the USGS for the day of surveying and sampling. Stream flow types were classified after Hawkins (1993). Stream flow mesohabitat classification was applied to the dominant (>50% channel width) features in a given cross section. Stream flows were classified as one of four 4 mesohabitat classification types including pool, riffle, run, and glide. Pools were defined as having no measureable water surface slope due to a hydraulic control provided by the stream bed, water surface, or debris dam. Riffles were defined as a fast water habitat with turbulent, shallow flow over submerged or partially submerged gravel and cobble substrates. Runs were classified as a reach of homogeneous flow separating riffles and pools with a surface slope between 1%-3% slope and no outlet control. Glides were defined as a long homogeneous reach with a slope of 0.5%-1% slope and no outlet control. Mesohabitat areas were measured with a meter tape and slope was evaluated using and hand level and leveling rod. Stream cross-section and slope were measured at 5 transects evenly distributed through each sampling reach. The stream cross-section was determined by measuring the height from the ground or streambed to a measuring tape stretched approximately level across the channel. The measuring tape was secured above the slope break on both banks. Height to tape was measured using a leveling rod and water depth was measured when within the flowing channel (Davis et al. 2001). In order to correct for errors in the level of the tape used in each cross section, the difference between the heights at each water’s edge was used to generate a corrective linear equation which was applied to each individual cross section. A line was drawn between the 4

Juvenile Chinook and coho salmon habitats December 2016 ARRI wetted edges of each transect and a cross sectional area was calculated for each transect. Mean channel depth was calculated by dividing cross-section area by channel width. The undercut distance was measured at both water edges and averaged at each transect. Stream slope was determined by measuring the change in water surface and stream bed elevation between two riffles using a hand level and leveling rod. Substratum size distribution was determined by conducting Wolman pebble counts of 100 stones (Wolman 1954) as modified by Bevenger and King (1995). Particle median diameters were measured using a 1980 U.S Forest Service “gravel-meter” template containing predetermined particle sizes ranging from 2-mm to 360-mm. Percent embedded was determined for particles larger than 2-mm based on the proportion each stone was buried in fines based on visual inspection for primary productivity and biofilm lines. Visual and tactile estimates of size and embeddedness were used in areas not wadeable. All large woody debris (LWD) and debris dams were surveyed throughout each reach and a LWD index calculated. All woody debris (pieces 10 cm in diameter and 1 m in length or greater) and debris dams (three or more pieces) within the bankfull channel were counted and recorded in accordance with the USDA Forest Service General Technical Report 2001 (Davis et al. 2001). Once a total LWD score was obtained, all sites were corrected for reach length by determining the LWD Index per 100 m stream reach. Riparian vegetation was classified at each channel cross-section transect using the USFS Alaska Vegetation Classification System (Vireck et al. 1992). The length of each distinct vegetation community lateral to the stream channel on both banks was measured. Distances were obtained using an Opti-Logic LH-series Laser Rangefinder. The dominant riparian vegetation was defined as the most frequent riparian classification along the bank edge of each stream. 2.4.2 Trap-level habitat characteristics Water depth, velocity, substrate size, and sources of cover were measured at each minnow trap location. Depth and velocities were measured immediately upstream of a trap’s placement using a meter stick and a Swoffer Model 3000 current meter. The dominant substrate within 1.0 meters of the trap was recorded according to the following scheme: boulder (>256mm), cobble (64-256mm), gravel (2-64mm), sand (.1-1mm), and silt (<.1mm) (Gordon et al. 2004). If several substrates were present, a dominant and subdominant substrate were recorded. Any sources of cover within 0.5 meters of the trap location were recorded as LWD, shrubs, aquatic vegetation, and/or undercut banks. LWD was defined as pieces exceeding 1m in length and 10 cm in diameter. Shrub cover was defined as woody debris, trees or bushes whose branches were in or directly above the water. Aquatic vegetation included submergent and emergent macrophytes. Undercut banks were defined by a minimum undercut of 0.25 meters and the presence of exposed roots or shading from the bank.

Juvenile Chinook and coho salmon habitats December 2016 ARRI 3.0 Results

3.1 Stream Water Quality 3.1.1 pH Measures of pH during May tended to be acidic with values in most streams below 7.0. Stream water pH averaged 6.6 with a standard deviation of 0.57. Stream pH ranged from 5.58 in Wasilla Creek to 7.70 in Cottonwood Creek (Wasilla). Lake-stream complexes had the highest average pH of 7.48. Wetland streams tended to be more acidic than upland streams (Table 2). Table 2. Water quality values for each stream measured in May of 2016.

Stream Stream Type % Oxygen Dissolved saturation Oxygen Dissolved (mg/L) pH Conductivity (µS/cm) (°C) Temperature Turbidity (NTU) Moose Creek (Petersville) Wetland 106.40 12.13 6.50 63.55 9.65 1.85 Chijik Tributary Wetland 86.60 9.09 6.65 38.00 13.20 1.25 Cottonwood Creek (Petersville) Wetland 99.20 10.48 6.03 21.50 12.50 0.45 Rabideux Creek Wetland 107.20 11.37 6.98 80.90 12.70 1.08 Sawmill Creek Wetland 90.20 9.81 6.24 41.30 11.55 0.58 Queer Creek Wetland 101.90 10.15 6.07 15.80 15.50 0.50 Little Willow Creek Upland 100.70 11.43 5.79 29.10 9.70 3.53 Iron Creek South Upland 99.00 11.14 6.88 46.50 10.15 4.96 Iron Creek North Upland 98.20 11.35 6.51 52.90 8.95 2.12 Little Susitna Upland 99.30 12.49 6.87 70.55 7.27 3.25 Swiftwater Creek Upland 99.80 11.77 7.07 47.50 9.47 0.74 Colter Creek Upland 99.40 11.97 7.16 40.50 7.25 1.04 Question Creek Lake- 107.30 10.57 7.27 58.50 15.90 NA Stream Little Meadow Creek Lake- 95.90 10.39 7.13 168.40 11.80 0.82 Stream Cottonwood Creek (Wasilla) Lake- 102.90 9.72 7.70 248.20 17.93 1.05 Stream Moose Creek (Palmer) Upland 99.70 12.45 6.91 75.10 6.30 3.01 Wasilla Creek Upland 100.40 10.92 5.58 204.40 11.45 1.22

3.1.2 Specific Conductivity Specific conductivity among sampled sites averaged 76.63 µS/cm with a standard deviation of 66.19 µS/cm (Table 1). Specific conductivity ranged from 15.8 µS/cm in Queer Creek to 248.2 µS/cm in Cottonwood Creek (Wasilla). Lake-stream complexes tended to have higher conductivity (125.4 µS/cm) on average than upland (70.8 µS/cm) or wetland streams (61.4

Juvenile Chinook and coho salmon habitats December 2016 ARRI µS/cm) (Figure 2). Specific conductivity was considerably higher in the urban or semi urban streams, Wasilla Creek, Cottonwood Creek, and Little Meadow Creek than all other streams.

300.00

250.00

µS/cm) 200.00

150.00

100.00

Specific conductivity ( 50.00

0.00

Figure 1. Specific conductivity of water in each stream during May 2016.

3.1.3 Turbidity Stream water turbidity was low at all sampling sites during May 2016. The average turbidty of all sample sites was 1.7 NTU with a standard deviation of 1.3 NTU. Turbidity in each stream ranged from 0.45 in Cottonwood Creek (Petersville), a small wetland stream, to 4.96 in Iron Creek South, a small upland stream. Average spring turbidity was significantly higher (ANOVA p = 0.05) in upland streams at 2.5 NTU compared to wetland and lake-stream complexes at 0.95 NTU. 3.1.4 Temperature The average temperature of stream water of all sample sites in from point measures in late May, 2016, was 11.25 °C with a standard deviation of 3.19 °C (Table 2). Temperatures ranged from 6.3 °C in Moose Creek (Palmer) to 17.9 °C in Cottonwood Creek (Wasilla). Lake-stream complexes (16.92 °C) had higher water temperatures on average than wetland streams (12.41 °C) or upland streams (10.78 °C). Water temperatures were higher in wetland streams and lake-stream systems compared to upland streams. The portion of days maximum daily water temperature exceeded 13 and 15°C is shown in Figure 2. Upland streams had very few days were maximum water temperatures exceed 15°C. 7

Juvenile Chinook and coho salmon habitats December 2016 ARRI Wasilla Creek, Little Willow Creek and the South Fork of Iron Creek (a tributary to Little Willow Creek) are the warmest upland streams. Based on monthly cumulative degree days (sum of daily averages), lake-stream systems are warmer than wetland streams, which are warmer than upland streams (Figure 3). Average monthly degree days for these stream types are significantly different (ANOVA p <0.001).

120.00 Percent Days >13 C Percent of Days >15C 100.00

80.00

60.00

40.00

20.00

0.00

Figure 2. Percent of days each stream daily maximum temperature exceeded 13°C and 15°C.

800

700

600

500

400

300

Cumulative degree days 200

100

0 June July August

Upland Wetland Lake/Stream

Figure 3. Average monthly degree days (sum of daily average values) for upland, wetland, and lake-stream systems for June, July, and August, 2015.

Juvenile Chinook and coho salmon habitats December 2016 ARRI

3.1.5 Dissolved Oxygen Dissolved oxygen (DO) in streams averaged 11.01 mg/L with a standard deviation of 1.00 mg/L. The lowest DO concentration was 9.09 mg/L and was 86.6% saturated in Chijik Tributary. The highest DO concentration was 12.49 mg/L and was 99.3% saturated in the Little Susitna River. DO concentration and percent saturation tended to be higher in upland streams (11.69 mg/L) and lower in wetland streams (10.49 mg/L) and lake-stream complexes (10.15 mg/L).

3.2 Physical Stream Characteristics 3.2.1 Stream Flow Classification Riffle habitat dominated reaches in upland streams (included Question Creek, Swiftwater Creek, Colter Creek, Iron Creek North, Moose Creek (Palmer)) and Cottonwood Creek (Wasilla). Sites that contained mostly pool habitat were three wetland streams (Little Meadow Creek, Cottonwood Creek (Petersville), and Rabideux Creek) and one upland stream (Iron Creek South). Glide habitat was dominant in 2 wetland streams (Chijik Tributary and Sawmill Creek). Run habitat was dominant in larger streams (Little Willow Creek, the Little Susitna River, and Moose Creek (Petersville) (Figure 4). Most wetland streams contained larger proportions of slow (glide and pool) than swift (riffle and run) habitats. Most upland streams were composed of more than 66% Swift (run and riffle) habitats. Lake Stream Complexes and Cottonwood Creek (Petersville) contained roughly equal proportion of swift and slow habitats. (Figure 5 and 6).

100%

50% Porportion (%) 0%

Riffle Pool Run Glide

Figure 4. Stream flow classification of all streams are plotted as proportions of the entire sampled reach, ordered by % riffle from greatest to lowest.

Juvenile Chinook and coho salmon habitats December 2016 ARRI

Stream Flow Classification Pool/Riffle Ratios 100%

50%

Riffle Figure 5. Proportion of riffle and pool in streams containing a combined total of 30% or more in their stream flow classification.

% of Swift (Riffle + Run) Stream Flow Classification 100%

67%

33%

Figure 6. Stream flow classification displayed as a proportion of swift mesohabitats (riffle and run). Colors represent different stream types (blue = upland, yellow = wetland, green = lake- stream-complex).

Juvenile Chinook and coho salmon habitats December 2016 ARRI 3.2.2 Large Woody Debris The average LWDI/100 m was 408 with a standard deviation of 193 amongst streams. The values ranged from 106.25 in Rabideux Creek, a large wetland stream, to 876 in Question Creek a small lake-stream systems. There was no significant difference in the LWDI or pieces of large woody debris/100 m between wetland and upland streams, or between large streams, small upland streams, small wetland streams, or lake-stream systems.

Question Creek Cottonwood Creek (Wasilla) Moose Creek (Palmer) Queer Creek Cottonwood Creek (Petersville) Iron Creek South Swiftwater Creek Wasilla Creek Little Willow Creek Colter Creek Sawmill Creek Iron Creek North Little Susitna River Chijik Trib Moose Creek (Petersville) Meadow Creek Rabideux Creek 106 298 490 682 874 LWDI/100m

Figure 7. Relative abundance of Large Woody Debris in each stream. Colors represent different stream types (blue = upland, yellow = wetland, green = lake-stream-complex).

3.2.3 Discharge Stream discharge during late June to early July is shown in Figure 8. The median stream discharge was 9.26 ft3/s. Stream discharges ranged from 3.3 ft3/s in Chijik Tributary to 649 ft3/s in the Little Susitna River. Discharge was higher in large upland streams compared to large wetland streams.

Juvenile Chinook and coho salmon habitats December 2016 ARRI

Little Susitna 649 Little Willow Creek 296.51 Moose Creek (Palmer) 230 Moose Creek (Petersville) 45.33 Rabideux Creek 19.88 Wasilla Creek 18.97 Question creek 9.97 Cottonwood Creek (Wasilla) 9.53 Iron Creek South 9.26 Sawmill Creek 8.54 Swiftwater Creek 7.37 Little Meadow Creek 6.72 Iron Creek North 5.7 Queer Creek 5.36 Colter Creek 4.07 Cottonwood Creek (Petersville) 3.64 Chijik Trib 3.27 1 10 100 1000 Discharge (ft3/s)

Figure 8. Discharge (ft3/s) for each stream in June 2016 plotted on a logarithmic scale. Colors represent different stream types (blue = upland, yellow = wetland, green = lake-stream-complex).

3.2.4 Riparian vegetation

The most common riparian vegetation among sample sites was mesic herbaceous graminoid, but there were 9 different categories among the sample sites (Table 3). Riparian vegetation along upland was dominated by open or closed alder scrub and blue-joint grass (Calamagrostis canadensis). Sweet-gale also was common along wetland streams. 3.2.5 Substrata The substrate diameter at 50% of the distribution (D50) ranged from 27 mm in Little Meadow Creek to 57 mm in Moose Creek Palmer. The percent fines (particles < 2 mm) ranged from 0 to 24/%, and the proportion of substrate more than 20% embedded in fine sediment ranged from 28% in Little Meadow Creek to 88% in Moose Creek (Petersville). Iron Creek South, a small upland stream, had the highest percent fines (24%) and the smallest D25 (9 mm) (Table 4 and Figure 9). There were no significant differences in the D50, D25, or percent fines between wetland upland streams and wetland streams. Mean embeddedness was, 27.5 in upland streams and 47.2 in wetland streams, but means were not significantly different (t-test, p – 0.08). However, the average portion of substrate embedded more than 20% was greater in wetland streams, at 64.4 compared to 40.6 in upland streams (t-test, p = 0.04) (Figure 10).

Juvenile Chinook and coho salmon habitats December 2016 ARRI Table 3 Dominant bank-edge (0-3m) riparian vegetation for each stream.

Site Dominant Riparian Vegetation Moose Creek (Petersville) Mesic herbaceous graminoid / Open tall scrub Chijik Trib Wet herbaceous graminoid Cottonwood Creek (Petersville) Dry herbaceous forb Rabideux Creek Mesic herbaceous graminoid Sawmill Creek Open tall scrub Queer Creek Mesic herbaceous forb Little Willow Creek Closed tall scrub Iron Creek North Mesic herbaceous graminoid Iron Creek South Open tall scrub Little Susitna River Mesic herbaceous graminoid Swiftwater Creek Dry herbaceous forb Colter Creek Mesic herbaceous forb Question Creek Open low scrub Little Meadow Creek Herbaceous freshwater aquatic vegetation Cottonwood Creek (Wasilla) Open broadleaf forest Moose Creek (Palmer) Closed tall scrub Wasilla Creek Open low scrub

Table 4 Summary statistics for substrate size and embeddedness.

% <2 Mean D50, Size D25, Size % mm Embeddedness (mm) at (mm) at 25% Substrate (%) 50% of of >20% Stream distribution distribution Embedded Moose Creek (Petersville) 7.1 56 52 33 88.0 Chijik Tributary 16.9 63 92 13 82.4 Cottonwood Creek (Petersville) 5.2 33 44 27 50.5 Rabideux Creek 3.0 44 54 35 82.3 Sawmill Creek 1.0 31 65 32 49.5 Queer Creek 1.0 20 41 27 33.7 Question Creek 1.0 23 44 24 32.7 Little Willow River 3.0 33 31 23 41.7 Iron Creek North 1.0 20 60 34 29.6 Iron Creek South 24.0 39 91 9 65.3 Little Meadow Creek 7.0 19 27 17 28.3 Little Susitna River 0.0 25 39 27 35.4 Colter Creek 0.0 27 64 45 36.5 Swiftwater Creek 0.0 21 63 37 35.4 Moose Creek (Palmer) 2.0 32 98 57 53.6 Cottonwood Creek (Wasilla) 6.0 41 64 22.6 51.6 Wasilla Creek 4.0 43 47 26 63.2

Juvenile Chinook and coho salmon habitats December 2016 ARRI

Moose Creek (Palmer) Chijik Trib Iron Creek South Sawmill Creek Colter Creek Cottonwood Creek (Wasilla) Swiftwater Creek Iron Creek North Rabideux Creek Moose Creek (Petersvile) Wasilla Creek Cottonwood Creek (Petersvile) Question Creek Queer Creek Little Susitna River Little Willow River Little Meadow Creek 0 20 40 60 80 100 120 Substrate diameter (mm) at 50% of the distribution

Figure 9. Substrate size (mm) at 50% of the cumulative frequency distribution at each stream. Colors represent different stream types (blue = upland, yellow = wetland, green = lake-stream- complex).

Moose Creek (Petersvile) Chijik Trib Rabideux Creek Iron Creek South Wasilla Creek Moose Creek (Palmer) Cottonwood Creek (Wasilla) Cottonwood Creek (Petersville) Sawmill Creek Little Willow River Colter Creek Little Susitna River Swiftwater Creek Queer Creek Question Creek Iron Creek North Little Meadow Creek 0 10 20 30 40 50 60 70 80 90 % Substrate >20% Embeddedness

Figure 10. Percent of substrates that were more than 20% embedded. Colors represent different stream types (blue = upland, yellow = wetland, green = lake-stream-complex).

Juvenile Chinook and coho salmon habitats December 2016 ARRI 3.2.6 Stream Morphology Cross sectional stream area ranged from 0.49 (m2) in Colter Creek to 16.35 (m2) in the Little Susitna River (Table 7). The bed-slopes ranged from 0.001 in Moose Creek (Petersville) to 0.032 in Iron Creek South. Width/depth ratio ranged from a low to 7.51 in Chijik Tributary, a small wetland stream, to 60.5 in Little Meadow Creek. Bank undercut depths ranged from 0.01 (m) at Moose Creek (Palmer) to 0.16 (m) at Rabideux Creek. Channel cross-section area was largest in the large streams. There were no significant differences in channel cross-section area between the small upland, small wetland, and lake-stream systems. Large streams also had the lowest stream slopes at 0.19% (Figure 11). The average slope in small upland streams was over 2%, which was significantly steeper than all other stream types (ANOVA p < 0.001). Large steams also were significantly deeper (Figure 12). Average ratios of width to depth were significantly higher in the wider-shallower Lake-Stream systems, compared to small upland and small wetland streams (ANOVA, p = 0.02) (Figure 13). Table 5. Stream morphology characteristics based on the average of 5 transects in each stream. The Stream type averages for these sites are presented at the bottom of the table.

) 2

Ratio

Cross Section Area (m Section Cross Stream Bank Full Width (m) Undercut Bank (m) Slope Bank Height (m) Width/Depth Moose Creek (Petersville) 4.96 12.48 0.06 0.001 1.33 31.4 Chijik Tributary 1.12 2.90 0.12 0.008 1.06 7.51 Cottonwood Creek (Petersville) 1.02 4.15 0.14 0.009 0.93 16.9 Question Creek 0.95 6.39 0.11 0.012 0.71 42.9 Rabideux Creek 3.89 9.60 0.16 0.001 1.11 23.7 Sawmill Creek 1.38 5.18 0.12 0.011 0.91 19.5 Queer Creek 1.05 5.38 0.09 0.003 0.88 27.5 Little Willow Creek 14.33 18.40 0.02 0.004 1.82 23.6 Iron Creek North 0.59 3.10 0.15 0.022 1.07 16.2 Iron Creek South 1.01 3.59 0.07 0.032 1.08 12.8 Little Meadow Creek 2.12 11.32 0.02 0.007 0.61 60.5 Little Susitna River 16.35 24.94 0.03 0.001 2.38 38.0 Colter Creek 0.49 3.17 0.14 0.020 0.88 20.5 Swiftwater Creek 0.56 4.31 0.13 0.012 0.54 33.3 Moose Creek (Palmer) 3.06 10.90 0.01 0.007 0.99 38.8 Cottonwood Creek (Wasilla) 1.46 9.94 0.02 0.005 0.73 67.5 Wasilla Creek 1.35 6.63 0.12 0.005 0.92 32.5

Juvenile Chinook and coho salmon habitats December 2016 ARRI

3.50

3.00

2.50

2.00

1.50

1.00 Average slope (percent)

0.50

0.00 Large Streams Small Upland Small Wetland Lake/Stream

Figure 11. Average stream slope for the four stream types. Error bars are one standard deviation.

1.80

1.60

1.40

1.20

1.00

0.80

0.60 Average depth (m) 0.40

0.20

0.00 Large Streams Small Upland Small Wetland Lake/Stream

Figure 12. Average channel depth among the four stream types. Error bars are one standard deviation.

Juvenile Chinook and coho salmon habitats December 2016 ARRI

40.00

35.00

30.00

25.00

20.00

15.00 Average w/d ratio 10.00

5.00

0.00 Large Streams Small Upland Small Wetland Lake/Stream

Figure 13. Average width/depth ratio for the four stream classification types. Error bars are one standard deviation.

3.2.7 Trap Habitat Data Most traps were placed in stream margins with small substrates and woody cover. On average, substrates at trap locations were dominated by sand (30%), silt (28%), and gravel (24%). Traps usually had one or more source of cover; on average, cover sources around traps included shrubs (56%), undercut banks (40%), and/or LWD (35%)(Table 5). The average depth of trap locations ranged from 0.22 m in Question Creek to 0.47 m in Chijik Tributary and Moose Creek (Petersville). The average water velocity at traps in each stream ranged from 0.05 at Chijik Tributary to 0.45 at Colter Creek (Table 6). Relationships between fish distribution and abundance and small scale habitat criteria will be completed following the second year of data collection.

Juvenile Chinook and coho salmon habitats December 2016 ARRI Table 6 Percent of traps at each sample site with substrate and cover type.

Stream % Silt %Sand Gravel% % Cobble % Boulder % Shrub %UCB %LWD Macrophyte % Moose Creek (Petersville) 75 0 25 0 0 35 25 15 30

Chijik Trib 30 40 20 10 0 40 70 0 0

Cottonwood Creek (Petersville) 40 10 30 20 0 60 30 50 0

Rabideux Creek 15 0 60 25 0 20 70 15 20

Sawmill Creek 10 0 0 70 20 90 50 10 20

Queer Creek 0 10 80 10 0 70 40 20 20

Question Creek 0 30 40 30 0 80 50 60 0

Little Willow Creek 85 10 5 0 0 45 20 60 0

Iron Creek North 0 100 0 0 0 100 100 30 0

Iron Creek South 60 20 0 20 0 80 60 40 0

Little Meadow Creek 30 0 60 10 0 50 0 20 100

Little Susitna River 70 10 0 20 0 60 40 25 0

Colter Creek 0 70 10 20 0 120 30 20 0

Swiftwater Creek 0 80 10 10 0 40 10 50 0

Wasilla Creek 20 50 30 0 0 0 80 30 0

Moose Creek (Palmer) 5 70 5 20 0 35 5 65 0

Cottonwood Creek (Wasilla) 50 10 30 10 0 20 0 80 40

Juvenile Chinook and coho salmon habitats December 2016 ARRI Table 7 Summary statistics of depth and velocity data at trap locations in each stream.

Stream Depth Mean (m) Depth Median (m) Depth Std. Dev. (m) (ft/s) Mean Velocity Velocity Median (ft/s) Dev.Velocity Std. (ft/s) Moose Creek (Petersville) 0.47 0.46 0.22 0.11 0.06 0.14 Chijik Tributary 0.47 0.43 0.11 0.05 0.01 0.08 Cottonwood Creek (Petersville) 0.36 0.30 0.19 0.08 0.02 0.12 Rabideux Creek 0.45 0.44 0.12 0.23 0.05 0.35 Sawmill Creek 0.31 0.29 0.08 0.14 0.08 0.16 Queer Creek 0.36 0.36 0.12 0.10 0.01 0.18 Little Willow Creek 0.51 0.52 0.26 0.10 0.05 0.13 Iron Creek North 0.27 0.26 0.05 0.08 0.04 0.10 Iron Creek South 0.28 0.29 0.09 0.26 0.19 0.23 Little Susitna River 0.40 0.32 0.25 0.43 0.33 0.36 Colter Creek 0.25 0.22 0.10 0.45 0.38 0.26 Swiftwater Creek 0.32 0.28 0.18 0.12 0.04 0.19 Question Creek 0.22 0.23 0.04 0.29 0.30 0.25 Little Meadow Creek 0.24 0.25 0.04 0.11 0.02 0.15 Cottonwood Creek (Wasilla) 0.23 0.21 0.07 0.12 0.10 0.12 Moose Creek (Palmer) 0.25 0.24 0.07 0.26 0.22 0.19 Wasilla Creek 0.40 0.36 0.19 0.28 0.30 0.21

3.3 Fish Distribution and Abundance Summer sampling in 2016 resulted in a total catch of 3,631 fish from 17 streams in the Mat-Su Borough (Table 8). Fish species collected include coho salmon (Onchorynchus kisutch), Chinook salmon (O. tshawytscha), sockeye salmon (O. nerka), Dolly Varden (Salvelinus malma), rainbow trout (O. mykiss), burbot (Lota lota), round- whitefish (Prosopium cylindraceum), and Alaska blackfish (Dallia pectoralis). Sculpin and sticklebacks were not identified to species, but were recorded in catches. Juvenile coho salmon were the dominant fish species captured (1930 fish) and made up 53% of all fish captured (Figure 14). Juvenile Chinook salmon made up 26% (931 fish) of the total catch. Resident salmonids, Dolly Varden and rainbow trout made up 7% (158 fish) of the total fish species captured.

Juvenile Chinook and coho salmon habitats December 2016 ARRI Table 8. The number fish, by species, captured during summer sampling in each stream.

Stream # traps Alaska blackfish burbot Chinook salmon coho salmon Dolly Varden rainbow trout sculpin salmon sockeye stickleback whitefish Total Fish Moose Creek (Petersville) 20 5 199 96 1 2 303 Chijik Trib 10 54 106 160 Cottonwood 10 12 113 1 126 Creek (Petersville) Rabideux Creek 20 70 231 1 1 158 461 Sawmill Creek 20 4 80 4 2 3 93 Queer Creek 10 1 62 5 2 45 115 Little Willow Creek 20 1 95 146 24 266 Iron Creek North 10 41 2 7 50 Iron Creek South 9 68 5 3 76 Little Susitna 20 168 256 58 1 1 484 Colter Creek 10 12 139 21 1 173 Swiftwater Creek 10 1 95 37 1 134 Question Creek 20 156 14 1 18 1 190 Little Meadow 10 139 52 15 112 318 Creek Cottonwood Creek 10 1 19 3 2 12 37 (Wasilla) Moose Creek 20 361 51 20 6 1 439 (Palmer) Wasilla Creek 10 7 184 11 4 206 Grand Total 239 1 5 931 1930 149 99 60 1 454 1 3631 *One trap was damaged and rendered non-functioning between deployment and retrieval.

Juvenile Chinook and coho salmon habitats December 2016 ARRI

14% 7%

26%

53%

Resident salmonids Chinook salmon Coho Salmon Other resident fish

Figure 14. Relative percent of juvenile Chinook and coho salmon, resident salmonids (Dolly Varden char, rainbow trout, whitefish), and other resident fish species (sculpin and stickleback) to the total average CPUT.

3.3.1 Coho salmon Relative abundance, size, and condition Juvenile coho salmon were present in catches from all sampling reaches. Average juvenile coho CPUT ranged from 1.9 in Cottonwood Creek (Wasilla) to 18.4 in Wasilla Creek (Table 9). Juvenile coho salmon comprised over 50% of the juvenile salmon catch in all streams except Moose Creek (Palmer) and Moose Creek (Petersville), where more juvenile Chinook salmon were present than coho. The bimodal size frequency distribution for coho salmon indicates two or more age classes (Figure 15). The portion of coho by age class varied among streams. Age-0 coho salmon dominated the population in most streams; however, more age-1 than age-0 coho were captured in Iron Creek South, Chijik Tributary, and Question Creek (Figure 16). The mean fork length of age-0 coho was 53 mm with a standard deviation of 7mm, and the mean fork length of age-1+ coho salmon was 82 mm with a standard deviation of 10 mm. Median presumed age- 0 coho fork lengths in each stream ranged from 49 mm in Sawmill Creek to 59 m in Iron Creek South (Figure 17). The average condition factor for all coho salmon was 0.103g/mm3 with a standard deviation between streams of 0.004 g/mm3. The condition factors of coho from each stream ranged from 0.096 in Iron Creek North to 0.112 g/mm3 in Swiftwater creek. Condition was over 1.5 standard deviations above the mean in Wasilla Creek, Cottonwood Creek (Wasilla), and Swiftwater Creek (Figure 18).

Juvenile Chinook and coho salmon habitats December 2016 ARRI

Table 9. Average Catch per Unit Trap (CPUT) for streams in the Mat-Su Basin.

Stream Coho Chinook Sockeye Rainbow Trout Dolly Varden Burbot Whitefish Alaska blackfish Sculpin Stickleback Moose Creek (Petersville) 4.8 10.0 0.0 0.1 0.0 0.3 0.0 0.0 0.1 0.0 Chijik Tributary 5.4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 10.6 Cottonwood Creek 11.3 1.2 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.0 Rabideux Creek 11.6 3.5 0.0 0.1 0.0 0.0 0.0 0.0 0.1 7.9 Sawmill Creek 8.0 0.4 0.0 0.4 0.0 0.0 0.0 0.0 0.2 0.3 Queer Creek 6.2 0.1 0.0 0.5 0.0 0.0 0.0 0.0 0.2 4.5 Little Willow Creek 7.3 4.8 0.0 0.0 0.0 0.0 0.0 0.1 1.2 0.0 Iron Creek North 4.1 0.0 0.0 0.7 0.2 0.0 0.0 0.0 0.0 0.0 Iron Creek South 7.6 0.0 0.0 0.6 0.0 0.0 0.0 0.0 0.3 0.0 Little Susitna River 12.8 8.4 0.0 0.1 2.9 0.0 0.0 0.0 0.1 0.0 Colter Creek 13.9 1.2 0.0 0.0 2.1 0.0 0.0 0.0 0.1 0.0 Swiftwater Creek 9.5 0.1 0.0 0.0 3.7 0.0 0.0 0.0 0.1 0.0 Question Creek 15.6 0.0 0.1 1.4 0.0 0.0 0.1 0.0 0.0 1.8 Little Meadow Creek 13.9 0.0 0.0 5.2 0.0 0.0 0.0 0.0 1.5 11.2 Cottonwood Creek (Wasilla) 1.9 0.1 0.0 0.3 0.0 0.0 0.0 0.0 0.2 1.2 Moose Creek (near Palmer) 2.6 18.1 0.0 0.3 1.0 0.0 0.0 0.0 0.1 0.0 Wasilla Creek 18.4 0.7 0.0 0.0 1.1 0.0 0.0 0.0 0.4 0.0

Juvenile Chinook and coho salmon habitats December 2016 ARRI

10 Age-0 Age-1 8

4 Frequency (% Frequency total) of 2

Fork Length (mm) Figure 15. The frequency distribution of coho salmon fork lengths from all sites. Coho salmon with fork lengths ≤70 mm were considered age-0.

100%

50%

Age 0 Age 1+

Figure 16. The proportion (as a percentage) of age-0 and age-1+ coho salmon at each site. Age-0 coho were defined as having a fork length ≤ 70 mm.

Juvenile Chinook and coho salmon habitats December 2016 ARRI

100 90 80 70 60 50 40 30

Fork Length (mm) Length Fork 20 10 0

Age-0 Age-1+

. Figure 17. Median fork lengths of age-0 and age 1+ coho salmon. Age-0 coho were defined as being less than 70 mm.

0.115

0.11

0.105

0.1

0.095 Condition (g/mm^3) 0.09

0.085

Figure 18. Average condition of coho salmon at each sample site.

Juvenile Chinook and coho salmon habitats December 2016 ARRI Distribution and size among stream types The relative abundance of total juvenile coho salmon or coho salmon ≤ 70 mm did not differ among stream classification types. Average CPUT was similar between wetland, upland, and lake stream complex classification types at 9.5, 7.9, and 10.5, respectively. CPUT in lake-stream complexes was highly variable due to low CPUT (1.9) in Cottonwood Creek in Wasilla. Relative abundance also did not differ significantly when comparing large streams, with small upland and small wetland stream types (Figure 19). Median fork lengths of presumed age-0 and age-1 coho salmon also did not differ among wetland, upland, and lake stream complexes. However, median fork lengths did differ significantly for age-0 coho salmon with larger fish in lake-stream complexes (57.7 mm) compared to the large streams (50.3 mm) (Figure 20). 3.3.2 Chinook salmon Relative abundance, size, and condition Juvenile Chinook salmon were the second most abundant fish species and were present in 12 of the 17 streams sampled. Juvenile Chinook salmon were absent from catches in both Iron Creek sites, Chijik Tributary, Little Meadow Creek, and Question Creek. Among sites where juvenile Chinook salmon were present, CPUT ranged from 0.1 at Cottonwood Creek (Wasilla), Queer Creek, and Swiftwater Creek to 18.1 in Moose Creek (Palmer) (Figure 21). Chinook salmon were more abundant than coho in Moose Creek (Petersville) and Moose Creek (near Palmer). Juvenile Chinook salmon represented a single size class (Figure 22). The mean fork length of all Chinook salmon was 60 mm with a standard deviation of 6 mm. The median fork length of Chinook in each stream ranged from 56 mm in Moose Creek (Palmer) to 65 mm in Little Willow Creek. Although the highest median fork length was in an upland stream (Little Willow Creek) (Figure 23). There was a significant relationship between juvenile Chinook salmon fork lengths and water temperatures (Figure 24). Fork lengths were longer in the wetland streams (Moose Creek and Rabideux Creek) compared to the large clearwater streams (Little Susitna and Moose Creek near Sutton). The mean condition for juvenile Chinook salmon was 0.10 g/mm3 with a standard deviation of 0.006 g/mm3. Condition ranged from 0.090 g/mm3 in Cottonwood Creek (Petersville) to 0.167 g/mm3 in the Little Susitna River (Figure 25).

Juvenile Chinook and coho salmon habitats December 2016 ARRI

20 18 16 14 12 10 CPUT 8 6 4 2 0 Large Streams Small Upland Small Wetland Lake/Stream

Total coho salmon coho salmon < 70 mm

Figure 19. Juvenile coho salmon relative abundance as CPUT comparing large streams, small upland, small wetland, and lake-stream complexes.

100 90 80 70 60 50 40 30

Median fork length (mm) 20 10 0 Large Streams Small Upland Small Wetland Lake/Stream

coho salmon < 70 mm coho salmon >69 mm

Figure 20. Medial fork lengths among stream types. Juvenile coho salmon < 70 mm were longer in lake-stream complexes compared to large streams. There were no differences in fork lengths of juvenile coho salmon > 69 mm among the other stream classification types.

Juvenile Chinook and coho salmon habitats December 2016 ARRI

20.0 18.1

10.0 10.0 8.4 CPUT 4.8 3.5

0.7 1.2 1.2 0.0 0.0 0.0 0.0 0.0 0.1 0.1 0.1 0.4 0.0

Figure 21. Average juvenile Chinook salmon CPUT at each surveyed site (Summer 2016).

5 Frequency (% Frequency total) of

0 44 47 50 53 56 59 62 65 68 71 74 77 80 83 86 Fork Length (mm)

Figure 22. The size frequency distribution of Chinook salmon fork lengths from all sample sites.

Juvenile Chinook and coho salmon habitats December 2016 ARRI

68 66 64 62 60 58

Fork Length (mm) Length Fork 56 54 52 Moose Colter Creek Little Rabideux Cottonwood Moose Little Creek Susitna Creek Creek Creek Willow (Palmer) (Petersville) (Petersville) Creek

Figure 23. Median fork lengths for Chinook salmon in streams with sample sizes greater than 10.

65 y = 0.0259x + 52.457 64 R² = 0.4929 63 62 61

(mm) 60 59 58 57 56 Juvenile Chinook Median Fork Length Length Fork Median Chinook Juvenile 55 150.00 200.00 250.00 300.00 350.00 400.00 450.00 June Cumulaive Degree Days

Figure 24. Relationship between June cumulative degree days at a sampling reach and juvenile Chinook salmon fork lengths in early July.

Juvenile Chinook and coho salmon habitats December 2016 ARRI

0.11

0.1

0.09 Condition (g/mm^3)

0.08 Cottonwood Rabideux Moose Moose Little Colter Little Creek Creek Creek Creek Willow Creek Susitna (Petersville) (Palmer) (Petersville) Creek

Figure 25. Average condition of Chinook salmon at each sample site.

Distribution and size among stream types Chinook salmon relative abundance was different among some stream classification types. There was no significant difference in juvenile Chinook salmon relative abundance between upland and wetland stream classification type, with average CPUT of 4.2 and 2.5, respectively. Chinook salmon were absent from the stream reaches in the lake-stream systems sampled. Using only those drainages where juvenile Chinook salmon were present, Juvenile Chinook salmon abundance was significantly higher in the large mainstem streams compared to small wetland, or small upland tributaries to those streams (Figure 26). Juvenile Chinook salmon fork lengths; however, did not vary between wetland and upland streams or among large and small wetland and upland streams. Juvenile coho salmon were present in stream reaches where Chinook were present. However, in addition to the difference in relative abundance of Chinook salmon among stream classification types, their relative abundance also varied with the abundance of coho salmon. Juvenile Chinook salmon were more abundant at sites with low coho salmon abundance (Figure 27).

Juvenile Chinook and coho salmon habitats December 2016 ARRI

CPUT 6

0 Large Streams Small Upland Small Wetland Lake/Stream

Chinook salmon

Figure 26. Juvenile Chinook salmon CPUT among stream classification types showing the abundance of these fish in large upland and large wetland stream compared to other stream classification types.

20.0 18.0 16.0 14.0 12.0 y = -0.8459x + 13.865 R² = 0.4963 10.0 8.0 6.0

Juvenile CPUT Chinook Juvenile 4.0 2.0 0.0 0.0 5.0 10.0 15.0 20.0 Juvenile coho salmon CPUT

Figure 27. Negative relationship between juvenile coho salmon and Chinook salmon.

3.3.3 Change in juvenile salmon abundance over time Figures 28 through 38 show the relative abundance of juvenile coho and Chinook salmon from 2008 to 2016 at sampling reaches with available data. Relative abundance of juvenile salmon in

Juvenile Chinook and coho salmon habitats December 2016 ARRI most streams was highest in 2009. High relative abundance also was observed in 2008 and 2011. The lowest relative abundance was observed in 2013 in most upland streams, but not most wetland or lake-stream systems. The relative abundance of juvenile coho salmon has declined in two streams: Cottonwood Creek (Wasilla) an urban steam, and Queer Creek a small wetland stream. The relative abundance of juvenile coho salmon has declined significantly in Cottonwood Creek since 2010 and in Queer Creek since 2008. There is some indication that juvenile salmon relative abundance is related to adult returns. Juvenile coho salmon relative abundance in Queer Creek was related to adult coho salmon counts in the Deshka River three years later (Figure 39). However, a similar relationship was not observed in the Little Susitna River, primarily due to the low return in 2012 (Figure 40).

Moose Creek: Oilwell Road 30.0

25.0

20.0

15.0

10.0 Average CPUT

5.0

0.0

coho salmon Chinook salmon

Figure 28. Relative abundance of juvenile coho and Chinook salmon in Moose Creek (Kroto Creek drainage), a large wetland stream, on three sampling dates. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October).

Juvenile Chinook and coho salmon habitats December 2016 ARRI

Moose Creek Drainage: Chijik Tributary 30.0

25.0

20.0

15.0

10.0 Average CPUT

5.0

0.0

coho salmon Chinook salmon

Figure 29. Relative abundance of juvenile coho and Chinook salmon in a small wetland stream in the Moose Creek drainage. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October).

Rabideux Creek Drainage: Queer Creek 30.0

25.0

20.0

15.0

10.0 Average CPUT

5.0

0.0

coho salmon Chinook salmon

Figure 30. Relative abundance of coho salmon in a small wetland stream in the Rabideux Creek drainage. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October).

Juvenile Chinook and coho salmon habitats December 2016 ARRI

Little Willow Creek Drainage: Iron Creek North 30.0

25.0

20.0

15.0

10.0 Average CPUT

5.0

0.0

coho salmon Chinook salmon

Figure 31. Relative abundance of juvenile coho and Chinook salmon in a small upland stream in the Little Willow Creek drainage. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October).

Little Willow Creek Drainage: Iron Creek South 30.0

25.0

20.0

15.0

10.0 Average CPUT

5.0

0.0

coho salmon Chinook salmon

Figure 32. Relative abundance of juvenile coho and Chinook salmon in a small upland stream in the Little Willow Creek drainage. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October).

Juvenile Chinook and coho salmon habitats December 2016 ARRI

Little Susitna River at Church Road 30.0 25.0 20.0 15.0 10.0 Average CPUT 5.0 0.0

coho salmon Chinook salmon

Figure 33. Relative abundance of juvenile coho salmon and Chinook salmon in the Little Susitna River, a large upland stream, near the Church Road Bridge in 2010 and 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October).

Little Susitna Drainage: Swiftwater Creek 30.0

25.0

20.0

15.0

Average CPUT 10.0

5.0

0.0

coho salmon Chinook salmon

Figure 34. Relative abundance of juvenile coho salmon and Chinook salmon in a small upland tributary to the Little Susitna River from 2008 through 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October).

Juvenile Chinook and coho salmon habitats December 2016 ARRI

Little Susitna Drainage: Colter Creek 30.0

25.0

20.0

15.0

Average CPUT 10.0

5.0

0.0

Wasilla Creek: Parks Highway 30.0

25.0

20.0

15.0

Average CPUT 10.0

5.0

0.0

coho salmon Chinook salmon

Figure 36. Relative abundance of juvenile coho salmon and Chinook salmon in Wasilla Creek, a small upland stream, from 2010 to 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October).

Juvenile Chinook and coho salmon habitats December 2016 ARRI

Cottonwood Creek (Wasilla): Old Mat Road 30.0

25.0

20.0

15.0

10.0 Average CPUT

5.0

0.0

coho salmon Chinook salmon

Figure 37. Relative abundance of juvenile coho salmon in Cottonwood Creek, a lake-stream system, from 2010 to 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October).

Question Creek: Talkeetna Spur Road 30.0

25.0

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coho salmon Chinook salmon

Figure 38. Relative abundance of coho salmon in Question Creek, and lake-stream system from 2013 to 2016. S indicates samples collected in the summer (late June through August) and F indicates samples collected in the fall (September and October).

Juvenile Chinook and coho salmon habitats December 2016 ARRI

Rabideux drainage: Queer Creek 30000

y = 1073.5x - 2240.8 25000 R² = 0.6337 20000

15000

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5000 Deshka weir countyears3 later 0 5 7 9 11 13 15 17 19 21 Juvenile coho salmon CPUT

Figure 39. Adult coho salmon return as a function of juvenile coho salmon relative abundance in Queer Creek, three years previously.

Little Susitna drainage: Colter Creek 35000 y = 2139.5x + 3419.7 30000 R² = 0.8791 25000

20000

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10000 Adult coho return return coho Adult 5000

0 0 2 4 6 8 10 12 14 16 Juvenile coho CPUT

Figure 40. Adult coho salmon return in the Little Susitna River as a function of juvenile coho salmon relative abundance in Colter Creek, a small upland tributary. Regression equation excludes adult return for 2012 (red point) which was low relative to the high juvenile coho salmon CPUT in 2009.

3.3.3 Resident Salmonids A total of 249 resident salmonids (Dolly Varden char, rainbow trout, and a single round whitefish) were captured during the summer of 2016 which composed 7% of the total catch. 37

Juvenile Chinook and coho salmon habitats December 2016 ARRI Resident salmonids made up 28 to 5 percent of the total salmonids captured within a sampling reach (Figure 41). Rainbow trout were collected in eleven streams including Cottonwood Creek (Wasilla), both Iron Creek sites, Little Meadow Creek, Little Susitna River, Moose Creek (Palmer), Moose Creek (Petersville), Queer Creek, Question Creek, Rabideux Creek, and Sawmill Creek. The average rainbow trout CPUT ranged from 0.1 in Little Susitna River, Moose Creek (Petersville), and Rabideux Creek, to a maximum of 5.2 in Little Meadow Creek. Rainbow Trout were captured in all drainage systems except Wasilla Creek. Dolly Varden were present in six streams including Colter Creek, Swiftwater Creek, Little Susitna River, Moose Creek (Palmer), and both Iron Creek sites. The average Dolly Varden CPUT ranged from 0.2 in Iron Creek North to 3.7 in Swiftwater Creek. Dolly Varden were captured only in upland streams including Little Willow Creek, Little Susitna River, Moose Creek (Palmer), and Wasilla Creek. Dolly Varden and rainbow trout were not distributed equally among stream classification types sampled. Dolly Varden were captured only in sampling reaches located in upland streams. Rainbow trout were captured in upland streams, wetland streams, and lake-stream complexes, but were more significantly higher in catches from reaches in lake-stream complexes (Figure 42).

100%

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Juvenile Salmon Resident Salmonids

Figure 41. Percent of CPUT at each site composed of juvenile Chinook and coho salmon and other resident salmonids (Dolly Varden char and rainbow trout).

Juvenile Chinook and coho salmon habitats December 2016 ARRI

6.0

5.0

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0.0 Wetland Upland Lake/Stream

rainbow trout Dolly Varden

Figure 42. Average CPUT of rainbow trout and Dolly Varden char from sampling reaches from streams classified as upland, wetland, or lake-stream systems. Error bars are one standard deviation.

3.3.4 Resident non-salmonids A total of 515 resident non-salmonid fish (sculpins, sticklebacks, and a single Alaska blackfish) were captured comprising 14% of the total catch. A total of 60 sculpins were captured in fourteen streams. Their average CPUT was 0.3. The minimum CPUT was 0.05 in Little Susitna River, Moose Creek, and Rabideux Creek. The maximum CPUT was 1.5 in Little Meadow Creek. The median CPUT was 0.2 in Cottonwood Creek (Wasilla), Queer Creek, and Sawmill Creek. A total of 454 stickleback were captured in seven streams. The average CPUT was 5.4. The minimum CPUT was 0.3 at Sawmill Creek. The maximum CPUT was 11.2 at Little Meadow Creek. The median CPUT was 4.5 at Queer Creek.

4.0 Summary

4.1 Objective 1 The first study objective was to, obtain measures of the relative abundance of juvenile salmon among multiple different stream types in 2016 and 2017. This report summarizes the first year of data collection for 2016. Sampling was conducted in July at 17 sampling locations representing four different stream classification types and included streams sites with relatively dense urban development. Juvenile coho salmon were distributed among all sampling sites. Relative abundance as CPUT was variable among sites ranging from 2 to 18. Based on size frequency distribution there were at least 2 age classes present at all sampling locations; however, the portion of catch composed of age-0 fish varied among sites.

Juvenile Chinook and coho salmon habitats December 2016 ARRI Juvenile Chinook salmon were present in catches from 12 of the 17 sampling sites. Relative abundance as CPUT ranged from 0.1 to 18. Based on the size frequency distribution there was only one age class of juvenile Chinook salmon. Juvenile Chinook and coho salmon overlapped in their distribution; however, there is an indication of spatial segregation. At sites where both fish were present, their relative abundance was inversely proportional, with low juvenile coho CPUT at sites with high juvenile Chinook CPUT.

4.2 Objective 2 The second objective is to test for differences in juvenile salmon relative abundance and indices of growth over time, and among stream classification types. There was a large range in water quality and physical habitat characteristics among the sampling stream reaches. Stream classification types accounted for some of the differences in water quality and physical habitat characteristics. Stream slopes, water depths, substrate embeddedness, water temperatures, pH, and the portion of fast (riffle/run) to slow (pool/glide) varied by classification type. The differences in the relative abundance of coho salmon among sampling sites was not explained by differences in stream size or classification types investigated. There was no significant differences in the relative abundance of juvenile coho salmon as CPUT (total, those fish < 70 mm, and those fish > 69 mm) between large streams, small upland streams, wetland streams, and lake-stream systems. There were also no significant differences in the relative abundance of juvenile coho salmon between wetland and upland stream types. The relative abundance of juvenile Chinook salmon was significantly different among stream classification types. Juvenile Chinook salmon were more abundant in the large, 3rd order streams, compared to small upland or small wetland streams within the same drainages. Greater abundance of juvenile Chinook in large streams has been reported previously (Kirsch et al. 2014). In addition to the largest cross-section channel area, these streams had the lowest slopes, and were deeper than other stream types. However, there were no other water quality or physical habitat characteristics that distinguished these streams from other classification types. There was some indication that juvenile salmon growth rates were faster in warmer streams. The fork lengths of juvenile coho salmon were longest in the lake-stream systems which were the warmest of the four stream classification types. There also was a significant positive relationship between juvenile Chinook fork lengths and water temperatures.

4.3 Objective 3 The third objective is to test for relationships between juvenile salmon relative abundance and differences in habitat suitability, physical habitat, spawner abundance and egg survival, and water quality. This objective has only been partially addressed in this report. Small-scale habitat characteristics were measured at each trap location in 2016; however, habitat suitability criteria and indices will be developed with combined 2016 and 2017 results. Habitat suitability indices will be used to evaluate differences in CPUT among sampling sites and stream classification types.

Juvenile Chinook and coho salmon habitats December 2016 ARRI There were no significant relationships between salmon escapement and juvenile salmon relative abundance the following year. Additional variables including fall peak flows and minimum winter temperatures likely affect egg survival and influence the relationship between spawning adults and the relative abundance of juvenile salmon the following year. There is an indication at some sites that adult coho salmon escapement is related to juvenile salmon abundance. This relationship will be further evaluated by including the portion of returning adults that spent one or two years in fresh water and the relative abundance of age-0 and age-1+ juveniles.

Juvenile Chinook and coho salmon habitats December 2016 ARRI

5.0 Literature Cited Bevenger, G. S., and R. M. King. 1995. A pebble count procedure for assessing watershed cumulative effects. USDA Forest Service. Rocky Mountain Forest and Range Experiment Station. Fort Collins, CO. Research Paper RM-RP-319. Davis, J.C., G.A. Davis, A. Crabb, R. Burns, H. Ramage, and L. Jensen. 2015. Monitoring juvenile salmon and resident fish in the Matanuska-Susitna Basin: 2013-2014. Final Report for the Mat-Su Salmon Habitat Partnership and US Fish and Wildlife Service. Aquatic Restoration and Research Institute. Talkeetna, Alaska. Davis, J.C., G.W. Minshall, C.T. Robinson, and P. Landres. 2001. Monitoring wilderness stream ecosystems. Gen. Tech. Rep. RMRS-GTR-70. Ogden, UT: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 137p. Gordon, Nancy D., Brian L. Finlayson, and Thomas A. McMahon. Stream hydrology: an introduction for ecologists. John Wiley and Sons, 2004. Hawkins, Charles P., et al. "A hierarchical approach to classifying stream habitat features." Fisheries 18.6 (1993): 3-12. Kirsch, J.M. J.D. Buckwalter and D. J. Reed. 2014. Fish inventory and anadromous cataloging in the Susitna River, Matanuska River, and Knik River basins, 2003 and 2011. Alaska Department of Fish and Game, Fishery Data Series No. 14-04. Miller, E.M., J.C. Davis, and G.A. Davis. 2011. Monitoring juvenile salmon and resident fish with the Matanuska-Susitna Basin. Final Report for the Mat-Su Basin Salmon Habitat Partnership. Aquatic Restoration and Research Institute, Talkeetna, AK. Rantz, S. E., and others. 1982. Measurement and computation of streamflow--Volume 1. Measurement of stage and discharge. U.S. Geological Survey Water-Supply Paper 2175, 284p. Trautman, M.B. 1973. A guide to the collection and identification of presmolt Pacific salmon in Alaska with an illustrated key. NOAA Technical Memorandum NMFS ABFL-2. Seattle, WA. Viereck, L.A., Dyrness, C.T., Batten, A.R., Wenzlick, K.J. 1992. The Alaska vegetation classification. General Technical Report PNW-GTR-286. U.S. Department of Agriculture, Forest Service. Pacific Northwest Research Station, Portland, OR. 278 p. Wolman, M.G. 1954. A method of sampling coarse river bed material. Transactions of the American Geophysical Union 35:951-956.