Beamer, E., Henderson, R. and Wolf, K., 2011. Juvenile Salmon, Estuarine, and Freshwater Fish Utilization of Habitat Associated with the Fisher Slough Restoration Project in 2010. Skagit River System Cooperative, La Conner, WA. pp. 72.

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. We report monitoring results
related to Project Element 1 (of three), which replaces an existing floodgate with a new
floodgate. The goal of Project Element 1 is to improve fish passage and tidal inundation
to areas upstream of the floodgate and to protect adjacent farmland from flooding. Data
collected in 2009 represent baseline values of fish utilization before floodgate
replacement. Data collected in 2010 (reported in this document) represent post-Project
Element 1 values: those collected after the 2009 floodgate replacement.
The new Fisher Slough floodgate, during the monitoring period covered by this report,
was operated according to management periods outlined in its hydraulic permit.
Upstream juvenile salmon fry and parr passage opportunity was estimated to be adequate
for 90% of the time of the last four weeks of the Spring Salmon Migration Management
Period (May). Data were not reliable in earlier time periods to estimate fish passage
opportunity for the entire Spring Salmon Migration Management Period.
In 2010, we found 16 different species of fish in the study area, including six different
salmonids and other freshwater and estuarine species. In contrast to results from 2009,
more wild juvenile Chinook salmon were found at sites downstream of the floodgate than
at sites upstream, suggesting that floodgate replacement resulted in a decrease in
upstream juvenile salmon passage. Due to unreliable data to estimate fish passage
opportunity in earlier time periods of the Spring Salmon Migration Management Period,
we have no real explanation as to how the new floodgate design, or its operation in 2010,
may have influenced fish passage opportunity. For this reason, we recommend another
year of monitoring for Project Element 1 of the restoration project before there are
complicating treatment influences from later restoration (e.g., Project Element 3 – dike
setback). Monitoring would need to include appropriate and complete floodgate
measurements related to fish passage.
We used selected environmental variables to improve understanding of the juvenile
Chinook salmon density trends independent of fish passage opportunity at the floodgate.
We concluded that salinity, water depth, substrate, and water velocity are not likely
influencing juvenile Chinook salmon use between sites up- and downstream of the
floodgate. We found that site differences in vegetation may influence juvenile Chinook
salmon use between sites up- and downstream of the floodgate. We found that dissolved
oxygen levels in Fisher Slough upstream of the floodgate may be lower than ideal for
juvenile salmon rearing and for migration requirements upstream of the floodgate during
daytime in June or later in summer. Water temperature appears to be a factor contributing
to juvenile Chinook salmon timing at the end of the monitoring period (late July and
August), but this factor was generally found to be influencing sites up- and downstream
of the floodgate equally.