Greene, C., Beamer, E. and Anderson, J., 2016. Skagit River Estuary Intensively Monitored Watershed Annual Report. Northwest Fisheries Science Center, Seattle, WA. pp. 25.

Chinook salmon are well known for utilizing natal river tidal deltas, non-natal pocket estuaries (nearshore lagoons and marshes), and other estuarine habitats for rearing during outmigration (Reimers 1973, Healey 1980, Beamer et al. 2003). Several studies have linked population responses to availability of estuary habitat, either by examining return rates of groups of fish given access to different habitat zones (Levings et al. 1989) or by comparing survival rates of fish from populations with varying levels of estuary habitat degradation (Magnuson & Hilborn 2003). These studies support the hypothesis that estuarine habitat is vital for juvenile Chinook salmon. However, these necessarily coarse-scale studies do not address the potential for large-scale estuarine habitat restoration to benefit salmon population productivity and life history diversity.
Rather than adopt hypotheses regarding the importance of estuarine habitat to Chinook salmon populations from the limited studies conducted in other river systems, the Skagit co-managers developed and implemented a research plan to determine the role the Skagit estuary might play in recovering wild Skagit Chinook salmon. Results from the Skagit studies are summarized in Beamer et al. (2005) and include elements relating to: estuary habitat use by juvenile Chinook salmon, juvenile Chinook life history variation, estuary habitat loss, and Chinook marine survival by life history type. In summary, the research led to the following conclusions:
1. All six wild Skagit Chinook salmon stocks include delta rearing and fry migrant life history types in their populations. These life history types currently rear in Skagit delta and pocket estuary habitats.
2. Skagit delta and pocket estuary habitats are much smaller and more fragmented than historically. Therefore, rearing opportunity of estuarine rearing Chinook salmon has been greatly reduced. Restoration opportunities exist at both historic delta and pocket estuary sites.
3. At contemporary Chinook salmon population levels, current delta habitat conditions are limiting the number and size of juvenile Chinook salmon rearing in delta habitat. Otolith data indicate that delta residence is important for the success of juvenile Chinook salmon surviving later in their life cycle. Restoration of delta habitat should increase capacity for delta rearing Chinook salmon.
4. At contemporary Chinook salmon population levels, limitations in current delta habitat conditions are displacing juvenile Chinook salmon from delta habitat to Skagit Bay habitat and forcing a change in their life history type from delta rearing to fry migrants. Literature values show that fry migrant survival is much lower than for delta rearing individuals.
5. Some fry migrant Chinook salmon rear and take refuge in pocket estuaries. Restoration of pocket estuary habitat can be a strategy to partially mitigate delta density dependence and improve survival of naturally occurring fry migrants.
6. Differences in habitat connectivity influence juvenile Chinook salmon abundance in both delta and pocket estuary habitats, indicating that habitat fragmentation, in addition to habitat loss, has been detrimental to Skagit Chinook populations. Restoration of connectivity should be a component of Skagit Chinook salmon population recovery planning.
7. Large-scale climatic processes influence marine survival. In the past 30 years we have observed two different climate regimes; average marine survival between regimes has varied by a factor of three. Skagit Chinook salmon population recovery planning must consider possible shifts in marine survival and ensure population recovery is achieved under a variety of conditions, including the worst-case scenario.