For salmonids, high water temperature and low dissolved oxygen are the main water quality problems. High temperatures can lower dissolved oxygen, impair the immune system of salmon, and give non-native warmwater species a competitive edge over native salmonids. The Stillaguamish watershed, as defined by WRIA 5 boundaries, includes 22 miles of marine shoreline. This is less than one percent of the total nearshore habitat contained within the 19 watersheds of Puget Sound. Generally speaking, the nearshore habitat associated with the Stillaguamish is in relatively good condition when compared to the urbanized nearshore areas of Puget Sound.
Residential development is the primary threat.
There are currently no measures in place to ensure that the nearshore areas remain in tact. Returning adult salmon also use nearshore habitats. Cordgrass invasions eliminate native salt marsh vegetation, displace native plants and animals, raise the elevation of the estuary substrate, and lead to an increase in flooding. The eventual consequence of Spartina growing in estuarine environments is the removal of intertidal acreage to salt marsh at and above Mean Ordinary High Water. The Stillaguamish estuary provides habitat for juvenile salmon to make a physiological transition between freshwater and saltwater environments and for adult salmon to transition between saltwater and freshwater.