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. ii 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. ....................................................................