Beamer, E., Henderson, R. and Wolf, K., 2013. Juvenile Salmon, Estuarine, and Freshwater Fish Utilization of Habitat Associated with the Fisher Slough Restoration Project in 2012. Skagit River System Cooperative, La Conner, WA. pp. 101.

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 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 resolved a drainage conflict preventing implementation of the final restoration Project Element. Project Element 3 was a dike setback in order to allow more of the agricultural area to be inundated by tidal and freshwater hydrology, increasing fish carrying capacity. The new tidal habitat area, following implementation of Project Element 3, increased from 9.8 acres to 55.7 acres. All three phases were completed before monitoring in 2012. The monitoring results related to Project Elements 1 and 3 are presented in this report.
The new Fisher Slough floodgate, during the 2012 monitoring period covered by this report, was operated according to management periods outlined in its hydraulic permit. Upstream juvenile salmon passage opportunity coincides with non-ebb tidal stage periods when floodgate doors are open and was estimated to occur 37.6% of the time during the 2012 fish monitoring period. This statistic varied little over the previous three years (2009 – 2011) of monitoring Fisher Slough’s floodgate, ranging between 45% and 47%.
In 2012, 19 different species of fish were found in the study area, including six different salmonids and other freshwater and estuarine species. Average monthly juvenile wild Chinook salmon density was higher upstream of the floodgate than downstream of the floodgate in 2012 (year 3 after replacement and year 1 after dike setback), but it is not significant at the 0.05 level. In contrast with the two previous years, an analysis of juvenile Chinook salmon density and landscape connectivity shows that values from Fisher Slough are within the normal pattern observed at all other Skagit River delta sites, suggesting there was no disruption at the site of the floodgate in 2012 after completion of dike setback restoration. Updated juvenile Chinook salmon carrying capacity predicted tidal habitat upstream of the floodgate has the capacity to support 38,773 or 23,935 tidal delta-rearing Chinook salmon smolts annually, depending on which landscape connectivity value is used. Juvenile wild Chinook salmon population size in tidal habitat of Fisher Slough upstream of the floodgate in 2012 was equivalent to the higher of the updated carrying capacity estimates.
Our limited statistical tests and graphical trends over four years of monitoring support two tentative conclusions: (1) The new floodgate alone did not influence juvenile wild Chinook salmon as hypothesized (i.e., juvenile wild Chinook salmon abundance would increase upstream of the floodgate after its replacement) in 2010 and 2011, and (2) juvenile Chinook salmon responded as hypothesized to dike setback restoration (along with the new floodgate) in 2012. Dike setback restoration was hypothesized to increase fish carrying capacity by increasing available habitat. Our best estimate of increased carrying capacity as a result of Fisher Slough restoration is 21,823 juvenile Chinook annually as of 2012. However this estimate only takes into consideration one year of post-restoration results and is subject to change as more information becomes available from future years of fish monitoring. The results could change based on: 1) how fish find the area each year (i.e., fluctuations in habitat connectivity) and 2) how channel/impounded areas change over time within the restoration project area.