Estuarine habitat in Puget Sound has declined dramatically since Euro-American settlement (Bortleson et al. 1980, Collins and Montgomery 2001).  In the Skagit delta approximately 60% of tidal emergent habitat has been lost and 94% of tidal scrub shrub habitat has been lost (Hood, unpublished data).  These areas provide critical habitat for a wide variety of fish and wildlife, including shorebirds, ducks, geese, swans, raptors, river otters, beaver, harbor seals, and many fish, most notably juvenile salmonids.  Of the salmonids, chinook are the most dependent on estuarine rearing habitat and Puget Sound Chinook are listed as threatened by the Endangered Species Act (64 Federal Register 14308, March 24 1999).

Dikes have isolated the Wiley Slough project area from the key processes of riverine and tidal flooding, thereby altering sediment transport and storage. These processes are crucial to forming and maintaining a variety of estuarine habitat conditions.  Construction of the Wiley Slough dikes, to drain and convert the project site to agricultural use, has resulted in direct loss of about 16 acres of tidal channel habitat and approximately 160 acres of intertidal marsh habitat.  However, there have been additional off-site impacts as a result of dike construction: 20 acres of intertidal channel habitat have been lost seaward of the dikes due to sediment deposition resulting from loss of tidal prism landward of the dikes (Hood 2004).  Additionally, the lower reach of Freshwater Slough has lost sinuosity and associated channel habitat diversity, probably due to loss of floodplain area via dike construction, which caused greater confinement of flood flows within Freshwater Slough (Hood 2004).  These off-site impacts from dike construction indicate that off-site areas will also likely respond to habitat restoration efforts that include significant dike removal.  Thus, habitat restoration and project monitoring require a landscape-scale perspective.

The project area is located in a transition zone between forested riverine tidal and estuarine emergent habitats.  However, vegetation has been significantly altered from historical conditions. The project area has been diked, drained and converted to agriculture, with cereal grains planted annually. Much of the natural forest, shrub, and herbaceous vegetation have been eliminated. Secondary forested areas exist along dikes and small berms adjacent to vestigial tidal channels.

All native anadromous fish and most native resident fish that would be expected to use the project site are currently excluded from the project site, as are other estuarine organisms dependent on tidal channel habitat. The site is extensively managed for put-and-take pheasant hunting and waterfowl (i.e., cereal grain is produced and seasonally flooded to attract and feed wintering waterfowl), but is also used by passerines.  Off-site (seaward of the dikes) impacts to fish and wildlife have occurred as a result of the loss of 20 acres of tidal channel habitat in lower Wiley Slough and the loss of channel sinuosity and associate habitat diversity in lower Freshwater Slough.  Fish and wildlife taxa likely to have been directly affected by loss of off-site habitat include salmon, bull trout, cutthroat trout, sturgeon (in pool habitat), shorebirds (feeding on sandbars), waterfowl (in channel habitat on low tides), and harbor seals.