Beamer, E., Shannahan, J., Wolf, K., Lowery, E. and Pflug, D., 2010. Freshwater Habitat Rearing Preferences for Stream Type Juvenile Chinook Salmon (Oncorhynchus tshwytscha) and Steelhead (O. mykiss) in the Skagit River Basin – Phase 1 Study Report. Skagit River System Cooperative, La Conner, WA. pp. 78.

This study is needed to better understand the causes of decline for two ESA listed
salmonid species that have at least a portion of their juvenile population exhibiting a
stream type life history: Chinook (Oncorhynchus tshawytscha) and steelhead (O. mykiss).
The study’s purpose is to identify seasonal and habitat type preferences in freshwater
habitat in the Skagit River basin by answering the following questions:
1. What habitat types are used by fish seasonally?
2. Where are fish located within the basin seasonally?
3. Where are habitats (by type) within the basin?
Habitat occupation by fish varies by season, due to environmental and ecological factors.
Carrying capacity and survival of fish can vary by habitat type and season so it is
important to know fish-habitat type associations (preferences) by season. By linking our
understanding of the fish (the answers to questions 1 and 2) to the location of habitat
types (the answer to question 3), we gain a spatial and temporal understanding of the
freshwater rearing period for stream type Chinook salmon and steelhead in the Skagit
River basin.
Our study is phased into two parts. Phase 1 of this study is designed to assess the
feasibility and statistical capabilities of our sampling design prior to implementing a
larger effort anticipated in Phase 2 of the study. The Phase 1 objectives include:
 Assemble a habitat database of the Skagit River basin in GIS;
 Use GIS data to select representative sampling reaches based on stratifying
factors of space, time of year, and habitat type;
 Collect pilot level fish observation data, including fish abundance and individual
size classes by species, to be used in statistical power analysis;
 Conduct statistical power analysis using pilot data; and
 Refine field methods for fish observation based on pilot fish data collection
experiences and relevant scientific literature on juvenile salmonid habitat
preferences and sampling methodologies.