Beamer, E., Henderson, R., Ruff, C. and Wolf, K., 2017. Juvenile Chinook Salmon Utilization of Habitat Associated with the Fisher Slough Restoration Project, 2009 – 2015. Skagit River System Cooperative, La Conner, WA. pp. 75.

The Fisher Slough Restoration Project, located in the south fork Skagit River tidal delta near the town of Conway, is intended to help recover the six populations of wild Chinook salmon present within the Skagit River and its natal estuary. The restoration project was phased in three parts. Project Element 1, completed in 2009 was to improve fish passage and tidal inundation to areas upstream of the floodgate and to protect adjacent farmland from flooding by replacing an existing floodgate with a new floodgate within Fisher Slough at the Pioneer Highway crossing. Project Element 2 removed a fish passage barrier and relocated and updated drainage infrastructure that was preventing implementation of the final restoration Project Element. Project Element 3, completed in 2011, was a dike setback in order to allow more area to be inundated by tidal and freshwater hydrology, increasing fish carrying capacity, and to provide floodwater storage. The juvenile Chinook salmon monitoring results related to Project Elements 1 and 3 are presented in this report for all years of monitoring: 2009 – 2013, and 2015. Now with six years of monitoring data and all restoration elements complete, we answer five key questions in this report:
1. Did tidal habitat area increase following dike setback restoration at Fisher Slough? (Chapter 3)
2. Does restoration at Fisher Slough influence water temperature and dissolved oxygen? (Chapter 4)
3. Is juvenile Chinook salmon presence within Fisher Slough influenced by variable local environmental conditions, such as water temperature, dissolved oxygen, depth, and velocity? (Chapter 5)
4. How did floodgate operation vary over the juvenile Chinook salmon monitoring period for all years? (Chapter 6)
5. Did the dike setback restoration and floodgate operation influence juvenile Chinook salmon abundance, density, and size? (Chapter 7)
The restoration of freshwater tidal marsh habitat extent and connectivity within Fisher Slough as a result of the dike setback in combination with current floodgate operation provided significant benefits to fingerling Chinook salmon rearing in the Skagit River estuary. In addition to creating 45.9 acres of additional juvenile rearing habitat, the combined effects of the dike setback and current floodgate operation significantly changed the seasonal dynamics of dissolved oxygen and water temperature in a way that provided benefits to estuarine resident Chinook utilizing the full 55.7 acres of habitat on the site. Dike setback increased water temperature in both magnitude of seasonal maximum and spatial variation upstream of the floodgate in a way that likely allowed mobile juvenile Chinook to maximize growth during the spring and early summer months. We detected an order of magnitude (10×) increase in habitat use by juvenile Chinook salmon in Fisher Slough upstream of the floodgate, consistent with habitat use observed at other reference sites throughout the Skagit tidal delta. This increase is predominantly associated with the dike setback and current operation of the floodgate to allow fish passage during slack and flood stages of the tide cycle. The combination of dike setback and current floodgate operation translated to an increase in the smolt carrying capacity of Fisher Slough by 21,823 estuary rearing Chinook salmon smolts per year based on all years of monitoring after dike setback.