Goal
In FY05, the goals of this estuary pilot monitoring study will be 1) to prepare for an FY06 study to determine presence through time of subyearling Chinook salmon at the Sandy River delta in the tidal freshwater reach of the Columbia River, and 2) to integrate pertinent results from other estuary monitoring studies.

Background
Subyearling fall Chinook salmon (Oncorhynchus tshawytscha) from endangered stocks in the Snake River migrate downstream through the lower Columbia River and estuary in summer and fall.  These fish are hypothesized to benefit from shallow-water habitats in the tidal freshwater reach of the lower river (River Miles 46-146) for feeding and refuge .  Accordingly, in its September 2004 draft Biological Opinion  on hydrosystem operations, NOAA Fisheries identified these lower Columbia River habitats as important to the continued existence of the Snake River evolutionarily significant unit.  Overall, however, little is known about presence of juvenile salmonids in shallow water habitats in the tidal freshwater reach of the lower river .  Furthermore, fish sampling as part of status and trends monitoring in the tidal freshwater reach is sparse, as opposed to the relatively intensive sampling for juvenile salmon in the estuary proper (RM 0-46).  Thus, there is a need for a comprehensive pilot program to address the gap for tidal freshwater fish sampling, especially for subyearling Chinook salmon, and to link this research with that elsewhere in the lower Columbia River and estuary.

The NOAA Fisheries' Biological Opinion and the Action Agencies' Updated Proposed Action  in 2004 specifically supported the habitat restoration effort currently underway at the Sandy River delta near Troutdale, Oregon (RM 122).  The Corps and BPA are planning to spend collectively approximately $2,000,000 on habitat restoration at the Sandy River delta.  One of the goals  of the Sandy River delta restoration project is to: "Restore 90 acres of native hardwood riparian forest and 20 acres of a seasonally wet slough in the Sandy River Delta to complete a 250-acre block of regionally scarce floodplain habitat."  Invasive species are being removed, trees are being planted in riparian zones, and a tidal slough channel and wetland areas are planned to be rehabilitated through removal of a blockage.  Action effectiveness monitoring will be necessary.  Although at this time there is some question about removal of the blockage for reasons unrelated to ecological restoration, baseline data on fish presence would be useful to evaluate the effectiveness of restoration whether the blockage is removed or not.  Regardless of its scope, one of the important outcomes of the restoration work at the Sandy River delta is expected to be increased foraging and refuge habitat for listed salmonids.  Therefore, the Sandy River delta would be a logical location to investigate the presence of subyearling Chinook salmon in shallow water habitat in the lower river.  

Ongoing research relevant to this pilot monitoring study is being performed under the following projects:
1) current and historic biophysical linkages conducted by NOAA Fisheries with funding from BPA and COE;
2) cumulative ecosystem effects of restoration conducted by PNNL and NOAA Fisheries with funding from COE;
3) juvenile salmonid survival in the estuary conducted by PNNL and NOAA Fisheries with funding from COE;
4) alternative smolt transportation (barging) conducted by PNNL and NOAA Fisheries with funding from COE;
5) habitat monitoring conducted by LCREP with funding from BPA; and
6) juvenile salmon stranding from ship traffic conducted by PNNL with funding from COE.  

The pilot monitoring study would complement, not duplicate, these efforts for several reasons.  First, the NOAA monitoring project is focused on juvenile salmon monitoring in the lower 46 river miles, not RM 46-146.  Second, the plan is for the cumulative effects project will be limited in the near term to only two freshwater sites on tributaries or Youngs and/or Grays bays.  Third, the survival and transportation studies will involve tagging (3,000 and 500 juvenile salmon, respectively) and releasing fish at Bonneville Dam.  Fourth, the LCREP project will be monitoring attributes of habitat in RM 46-146, but not juvenile salmon.  Fifth, the salmon stranding study is occurring specifically before and after the Columbia River Channel Improvements Project, not over the long-term.  Therefore, a pilot monitoring study for juvenile subyearling in the tidal freshwater reach of the Columbia River (RM 46-146) would integrate well with ongoing research.  This statement of work is for the first-year of a pilot monitoring study in the estuary.  

Implications
If juvenile subyearling salmon are present at the site, in subsequent years the project goal could be expanded to a) focus on subyearling salmon from the Snake River specifically , or other stocks of interest, and b) include other sampling locations of interest, and/or c) include more biological information such as prey items, growth rates, residence time, and fish community structure.  This latter information would greatly help understand the linkages between the salmonids and the habitats at the sites.

If juvenile subyearling salmon are not present at the site at any of the sampling locations, the implication is that habitat restoration activities in the tidal freshwater portion of the Columbia River may not benefit upriver salmon stocks.  The data from this study will have to be studied with data from other studies to attain the most comprehensive evaluation possible of the effects of tidal freshwater habitat restoration on upriver salmon stocks.