Ecosystem Monitoring Program
BPA Project Number:  2003-007-00
CR-225870
Performance/Budget Period: October 1, 2012 – September 30, 2013

Technical Contact/Project Lead:  Catherine Corbett
Lower Columbia Estuary Partnership
811 SW Naito Parkway, Suite 410
Portland, Oregon  97204
Phone: (503) 226-1565 Ext. 240
Fax:  (503) 226-1580
corbett@lcrep.org

Contracting Contact: Tom Argent
Lower Columbia River Estuary Partnership
811 SW Naito Parkway, Suite 410
Portland, Oregon  97204
Phone: (503) 226-1565 Ext. 242
Fax:  (503) 226-1580
argent@lcrep.org

BPA Project Managers:  
Russell Scranton (FY12)
KEWR-4, Bonneville Power Administration
905 NE 11th Avenue
Portland, Oregon  97208
Phone:  503-230-4412
rwscranton@bpa.gov

Anne Creason (FY13)
KEWL-4, Bonneville Power Administration
905 NE 11th Avenue
Portland, Oregon  97208
Phone:  503-230-3859
amcreason@bpa.gov

SUMMARY
The Ecosystem Monitoring Program is an integrated status and trends program. The overall objectives of this Program is to track trends in the overall condition of the lower river, provide a suite of reference sites for use as end points in the region’s restoration actions, and place results of findings into the context with the larger ecosystem. As this Program is funded by the NPCC/BPA, a primary goal of this program is to collect key information on ecological conditions for a range of habitats in the lower river characteristic of those used by out migrating juvenile salmon and provide information towards implementation of the 2008 FCRPS BiOp. Information collected describes synoptic conditions and changes over time in vegetated floodplain habitats and the opportunity, capacity and realized function (Simenstad and Cordell 2000) they afford juvenile salmonids. These habitats are the targets of regional restoration efforts, which makes this Program integral for understanding the success of the regional habitat restoration program. The results of this program provide information on ambient environmental conditions and insight into the cumulative effects of existing and new management actions and anthropogenic impacts as they occur.

The Program specifically collects status and trends data on the following:
• salmonid occurrence, diet, condition and residency at shallow water and vegetated sites in the mainstem and tributary confluences;
• habitat structure, including physical, biological and chemical properties of these habitats;
• food web characteristics, including primary and secondary productivity at these habitats and in the mainstem lower river and
• provides information allowing other researchers to assess the biogeochemistry of tidal freshwater region of the lower river to the biogeochemistry of the estuary, which is key in tracking ocean acidification and climate change impacts on estuary habitat capacity.

Applications of Results to Management - The Program has provided key information on a suite of 51 reference sites across the lower river. These sites will be used as end points for restoration projects and used in combination with the AEMR Program data described below. Data collected through this Program on vegetation, elevation and hydrologic patterns from these sites have been used to create regionally specific restoration design considerations for use by restoration practitioners in designing more successful restoration actions. Patterns include 5 vegetation zones and 3-4 hydrologic zones and elevation tolerance of the invasive species, reed canarygrass. Data collected through this Program have also documented preferential use of regions of the lower river by different salmonid ESUs.    

Past Results - From fiscal years 2004 through 2011, with funding from NPCC/BPA, the Ecosystem Monitoring Program has accomplished the following major tasks: 1) developed a statistically valid, ecosystem-based monitoring plan for the estuary (focusing on juvenile salmon habitats); 2) developed and published a hierarchical estuarine ecosystem classification system (CREEC) in which to base sampling designs and habitat restoration strategies; 3) mapped over 19,000 acres of high and medium priority shallow water bathymetry gaps; 4) mapped land cover of the lower river floodplain in 2000 and 2010; 5) collected water chemistry data and juvenile salmonids to support the creation of 3 models related to salmonid uptake, transport, and ecological risk of toxic contaminants; 6) collected habitat structure data at 28 sites and comprehensively monitored 22 sites throughout the lower river for habitat structure; salmon occurrence, diet, condition, stock, and growth; prey availability and preference, providing in some areas the only contemporary juvenile salmon use data available; 7) initiated the characterization of the salmon food web at 4 sites representing the estuarine-tidal freshwater gradient; 8) collected abiotic environmental/water column condition data at 1-4 sites annually and 9) provided technical assistance to the USACE in creation of a terrain model of the lower river, resulting in a seamless bathymetry/topography map which will be invaluable in mapping salmon habitat opportunity in combination with river flow data.  

In addition, NPCC/BPA funding  provides leverage that allowed the Estuary Partnership to accomplish these additional estuary RME-related activities: 1) convened 5 technical workshops for researchers and managers on topics of interest such as land cover, bathymetry, toxic contaminants, and restoration; 2) provided monitoring coordination for entities involved in monitoring the lower river, exemplified by the estuary RME coordination meeting in spring 2010, 2011 and 2012 involving NMFS, PNNL, CREST, USACE, BPA, LCRFB and others; 3) compiled information and presented overviews of on-going monitoring activities at various events, including the Estuary and Ocean Subgroup, EPA Toxics Reduction Working Group; and regional and national conferences; 4) played a key role in efforts supporting regional monitoring coordination, including Pacific Northwest Aquatic Monitoring Partnership’s Integrated Status and Trends Monitoring group, an inventory of on-going effectiveness monitoring at restoration sites, and refinements to standardized protocols for restoration effectiveness monitoring; 5) acted as a central clearinghouse for GIS data while developing mapping website to house monitoring data collected in estuary; 6) supported on-going regional toxic contaminants reduction efforts, such as preparing the State of the River Report, presenting monitoring information at the workshops, developing a basin-wide contaminant monitoring strategy with EPA's Toxics Reduction Workgroup, and supporting the institution of an Oregon Drug Take Back Program; 7) presented monitoring efforts at several regional and national conferences, including the Coastal and Estuarine Research Federation and National Conference on Ecosystem Restoration; 8) chaired an all day session on monitoring and restoration efforts in Pacific Northwest estuaries at the 2009 Coastal and Estuarine Research Federation conference with co-chairs, PNNL and South Slough National Estuarine Research Reserve and 9) participated in regional forums, such as Pacific Estuarine Research Federation (PERS), NANOOS, American Fisheries Society, and Pacific Joint Venture, to share information and coordinate RME and restoration efforts. Information exchanged and gained and networking with other researchers doing related work during these events provide invaluable insight and guidance for future RME and restoration efforts in the lower river.

Current Work - The Estuary Partnership is currently developing an estuarine condition index to provide a framework for illustrating and reporting ecosystem conditions, how they are changing over time other information gleaned from the Program and management implications to the public, scientists and managers. This indicator system will use the US Environmental Protection Agency’s Biological Condition Gradient (BCG) framework (Davies and Jackson 2006).As this indicator system and numeric management targets are developed, they will be integrated into the Greater Ecosystem Restoration Program, including the monitoring design of the Ecosystem Monitoring Program.

BACKGROUND
Since 1991, 13 different evolutionarily significant units (ESUs) of anadromous salmonids that reproduce in the Columbia River basin have been listed as threatened or endangered under the Endangered Species Act (ESA) of the United States. These include steelhead (Oncorhynchus mykiss), chum salmon (O. keta), Chinook salmon (O. tshawytscha), lower Columbia River coho salmon (O. kisutch), and sockeye salmon (O. nerka) populations that spawn from the upper Snake River basin to tributaries of the lower river below Bonneville Dam. NMFS uses 4 viable salmonid population (VSP) performance criteria to define the viability status of salmonids: abundance, productivity, spatial structure, and diversity; all 4 of these VSP criteria are critical to salmon recovery and are interrelated (Fresh et al., 2005). NMFS recommends that the lower Columbia River and estuary contributes to the viability and persistence of all anadromous salmonid populations within the Columbia River Basin in the following ways: 1) the amount of estuarine habitat that is accessible affects the abundance and productivity of a population; 2) the distribution, connectivity, number, sizes, and shapes of estuarine habitats affect both the life history diversity and the spatial structure of a population; and 3) attributes of estuarine habitats (e.g., temperature and salinity regimes, food web interactions) affect diversity and productivity of populations (Fresh et al., 2005). Diverse habitats and the expression of life history strategies based on use of these habitats are directly linked to salmon population viability (i.e., persistence) over long time scales (McElhany et al., 2000). The Independent Scientific Review Panel (ISRP) for the Northwest Power Conservation Council (NPCC) concluded that estuary and ocean dynamics help control salmon productivity (Beamish and Bouillon, 1993; Beamish et al., 1999) and salmon biodiversity (including the diversity of life history strategies) helps reduce impacts from changing ocean and other conditions (ISG, 2000). Hence, changes to the estuarine ecosystem such as degradation and loss of estuarine habitat, can directly alter salmonid population viability.

Estuaries in general are presumed to offer 3 advantages to juvenile salmon in their transition from freshwater to saltwater environments: 1) a productive feeding area capable of sustaining increased growth rates; 2) a temporary refuge from marine predators; and 3) a physiological transition zone where fish can gradually acclimate to saltwater (Simenstad et al., 1982; Thorpe, 1994). All anadromous salmon and steelhead populations within the Columbia River Basin utilize the estuary as a critical migration corridor. In addition, research has well documented that Chinook salmon, especially subyearlings, and other salmon such as chum and coho to a lesser degree, can rear extensively in shallow water and vegetated habitats within the estuary, including tidal channels, tributary confluence and nearshore areas (e.g., Bottom et al., 2005; Fresh et al., 2005; Good et al., 2005; Fresh et al., 2006; Bottom et al., 2007; Roegner et al., 2008; Casillas, 2009). Subyearling migrants that enter the estuary as fry or fingerlings, or “ocean-type” salmon, exhibit a wide range of residence periods depending on the species, from days to weeks (chum) to several months (Chinook) (Thorpe, 1994). Juvenile salmon may occur in the estuary all year, as different species, size classes, and life history types continually move downstream and enter tidal waters from multiple upstream sources (Bottom et al., 2005). Peak estuarine migration periods vary among and within species, suggesting that different life history strategies may provide a mechanism for partitioning limited estuarine habitats (Myers and Horton 1982). In the Columbia River estuary, subyearling Chinook salmon are most abundant from March through September but are present all year (Rich, 1920; McCabe et al., 1986).

Because of the increasing awareness of the importance of the Columbia River estuary within salmonid life cycles, protection and restoration of important salmonid habitats within the estuary has been identified as a priority for salmon recovery. In addition, in life stage risk and sensitivity modeling, Kareiva et al. (2000) and McClure et al. (2003) found that to recover salmonid populations in the Columbia River Basin additional actions above and beyond passage improvements at the Federal Hydropower System dams were needed and that the life stages for rearing in the river, estuary and ocean were sensitive to disturbances (cited in Fresh et al., 2005). Kareiva et al. (2000) concluded that the maximum potential to contribute to anadromous salmonid recovery was associated with these life stages (Fresh et al., 2005). The questions of how much restoration will be necessary or which types of restoration are most beneficial for recovery within the estuary still exist.

The challenges of identifying, designing, implementing, and evaluating recovery actions in the estuary are significant, in part because managers know relatively little about the region and salmon habitat use patterns within it (Fresh et al., 2005). Recent past and ongoing RME efforts such as this project and the NMFS and PNNL projects funded by the USACE through the Anadromous Fish Evaluation Program: 1) “Estuarine Habitat and Juvenile Salmon: Current and Historical Linkages in the Lower Columbia River and Estuary 2002-2008”, 2) “Multi-Scale Action Effectiveness Research in the Lower Columbia River and Estuary” and 3) “Evaluation of Life History Diversity, Habitat Connectivity, and Survival Benefits Associated with Habitat Restoration Actions in the Lower Columbia River and Estuary” continue to expand our knowledge base. But many of our decisions are still based on conceptual ideas or assumptions (Fresh et al., 2005). In addition, the lower river is among the most heavily modified portions of the Columbia Basin (Thomas, 1983) due to the long history of coastal development and the cumulative effects of flow regulation, channel maintenance, habitat modification, and other changes upriver which have altered sediment transport, floodplain inundation patterns, and salinity regimes in the system (Simenstad et al., 1992; Weitkamp, 1994). Since the mid 1800s, these and other changes have decreased the amount of some types of wetland habitats in this region by as much as 70% from historical levels (LCREP 1999; LCEP 2012).

The Lower Columbia Estuary Partnership (Estuary Partnership) will implement elements of its Ecosystem Monitoring Program to provide information on salmonids and their habitat in the LCRE and address data management needs. This project builds on our previous projects under Bonneville Power Administration funding that created and began an ecosystem based monitoring program focused on improving the survival of juvenile salmonids through the LCRE. This project will continue to comprehensively assess habitat, fish, food web and abiotic conditions in the lower river, focusing on shallow water and vegetated habitats used extensively by juvenile salmonids for rearing and refugia.

This statement of work describes the work elements, deliverables, and costs for Ecosystem Monitoring Project (EMP) efforts that will be implemented from October 1, 2012 to September 30, 2013.

REVIEW OF PRIOR WORK

For previous contracts (2004-2011), please see past annual reports.

During October 1, 2011 through September 30, 2012, PNNL, NOAA Fisheries, USGS, OHSU, and CREST monitored habitat, abiotic environmental conditions, food web resources, and salmonids at six “fixed” sites in the lower Columbia River (Campbell Slough in Reach F, Franz Lake in Reach H, Whites Island in Reach C, Baker Bay in Reach A and Secret River and Welch Island in Reach B) (USGS collected food web and abiotic conditions at the first four sites only due to cost considerations). In addition, PNNL monitored vegetation (vegetation species, elevation, peak macrophyte biomass and water stage) and NOAA monitored fish (salmon, salmon prey and foodweb resources) at 3 “status” located at Reed Island, Lemon Island and Washougal/Camas in Reach G. For the first time, NOAA Fisheries also began fall fish sampling at all sites and installed a pit tag array at the Campbell Slough site to assess residency.

Additionally, OHSU installed and operated a Center for Coastal Margin Observation and Prediction (CMOP) LOBO (Land Ocean Biogeochemical Observatory) Platform in the tidal freshwater section of the LCRE for the first time. This new station will provide a high resolution, long term record of key water quality parameters for the assessment of primary production and the factors affecting the productivity of the  entire mainstem lower Columbia River from Bonneville Dam to the coastal ocean. By filling an important spatial data gap (there are no similar stations above Beaver Army Terminal), it will allow the Estuary Partnership to place the findings at the habitat monitoring sites into context with water quality of the mainstem Columbia River. It will also allow the Estuary Partnership to more fully integrate our research of on-going and projected worsening of ocean acidification, warming water temperatures and decreasing dissolved oxygen concentrations associated with climate change into the annual analyses and reporting completed under the EMP. Through this project, researchers will track and routinely report results of the following:
1. Seasonal primary production,  biomass and taxonomic classification for the lower river from Bonneville to the coast
2. Sources and variability of dissolved organic carbon, turbidity and nutrients in tidal freshwater and estuarine sections of lower river
3. Water temperatures,, conductivity, and dissolved oxygen levels in tidal freshwater and estuarine sections of lower river
This information will be key to understanding primary production throughout the lower river and instream processes controlling production and their influences on the dissolved oxygen levels found in the estuary, plume and outer continental shelf of Oregon and Washington.  

Finally, the action effectiveness monitoring program was transferred from the Habitat Restoration Program contract (2003-11-00) to the EMP contract during this contract year. The 2008 Draft Biological Opinion includes a Reasonable and Prudent Alternative (RPA) to “evaluate the effects of selected individual habitat restoration actions at project sites relative to reference sites and evaluate post-restoration trajectories based on project-specific goals and objectives” (RPA 60, Appendix A, NMFS, 2008). Since summer 2008 the Estuary Partnership and partners have implemented action effectiveness monitoring that addresses this RPA based on recommendations from the plan for “Research, Monitoring, and Evaluation for the Federal Columbia River Estuary Program” (Johnson et. al 2008). The Estuary Partnership, with input from the Estuary and Oceanic Subgroup (EOS) and Science Work Group, identified 4 pilot sites (Mirror Lake, Sandy River Delta, Scappoose Bottomlands, and Fort Clatsop). Sites were chosen to represent different restoration activities (culvert enhancement to improve fish passage; large wood installation; revegetation and cattle exclusion; and culvert removal for tidal reconnection), different habitats (bottomland forest, riparian forest, emergent wetland, and brackish wetland), and different geographic reaches of the river (reaches H, G, F, and A, ranging from tidal freshwater in reach H, the Columbia River Gorge, to saltwater intrusion in reach A, Astoria area). Action effectiveness monitoring partners are implementing the Roegner et al. (2009) protocols, which were designed for estuary-wide action effectiveness research, and are collecting data on parameters such as water quality, sediment accretion, channel cross-sections, vegetation cover, vegetation planting success, salmon, and salmon prey. During this contract period, action effectiveness monitoring continued at three of these sites. The Scappoose Bottomlands site was not be repeated this year because of access issues with the private landowner. Also, NOAA Fisheries installed a pit tag array at the Horsetail Creek restoration site for baseline data collection; construction at this site is planned for summer 2013.

WORK ELEMENTS FOR OCTOBER 1, 2012 TO SEPTEMBER 30, 2013
During the upcoming contract period, PNNL, NOAA Fisheries, USGS, OHSU, and CREST will implement the FY2013 monitoring work. In FY 2013 PNNL, NOAA Fisheries, and USGS will collect co-located data at six “fixed” stations:
1. Campbell Slough, which has been monitored yearly since 2007 to assess inter-annual variation in wetland habitat conditions and salmonid presence and abundance;
2. Franz Lake (monitored in 2008, 2009, 2011 and 2012)
3. Whites Island (monitored since 2009)
4. Baker Bay (monitored since 2011)
5. Secret River (monitored since 2012) and
6. Welch Island (monitored since 2012).
In 2012 PNNL will collect data on wetland vegetation species, elevation, peak macrophyte biomass, and water stage at the 6 fixed sites. NOAA Fisheries will monitor salmon, salmon prey and foodweb resources (i.e., zooplankton), at these sites to provide information on juvenile salmon use of the vegetated and shallow water habitats of the lower Columbia River. NOAA Fisheries will process salmon samples for stock, growth rates, stomach contents, and fish condition and send zooplankton samples to OHSU for processing and identification. USGS will collect data at four of the four “fixed” sites (1-4 above) to characterize the foodweb resources supporting juvenile salmonids, specifically primary productivity, and deploy probes to monitor the water column for parameters relevant to salmonids (e.g., temperature and dissolved oxygen). USGS will send phytoplankton samples to OHSU and macroinvertebrate benthic cores to CREST for processing and taxonomic identification. NOAA will continue to operate and maintain a pit tag array at Campbell Slough to assess salmon residency in LCRE floodplain habitats. Additionally, OHSU will continue to maintain the CMOP LOBO Platform in the tidal freshwater section of the LCRE for another year. The Estuary Partnership Science Work Group will review the data on a periodic basis and recommend possible research studies to address key questions as they arise.

With partial funding from this contract, the Estuary Partnership is currently developing an estuarine condition index to provide a framework for illustrating and reporting ecosystem conditions, how they are changing over time other information gleaned from the Program and management implications to the public, scientists and managers. This indicator system will use the US Environmental Protection Agency’s Biological Condition Gradient (BCG) framework. In spring 2012 the Estuary Partnership’s Science Work Group (SWG) established the following process for developing the estuary indicator system using the BCG framework:
1. Identify goal, objective, actions and assessment questions of interest to resource managers. (Completed by SWG; March 27, 2012)
2. Describe “minimally disturbed” LCRE, identify ecosystem attributes for protection or restoration. (Completed by April 4-5 workshop participants)
3. Define the key ecological needs of attributes and quantifiable targets for ecosystem attributes (Initiated by April 4-5 workshop participants; Continued work by Indicator Steering Committee and Focus Groups for Individual Attributes; Anticipated to be completed in fall 2012)
4. Determine core indicators and metrics (Initiated by April 4-5 workshop participants; Continued work by Indicator Steering Committee and Focus Groups for Individual Attributes; Anticipated to be completed in fall 2012)
5. Determine population of interest (using Columbia River Estuary Ecosystem Classification) for each core indicator and minimum number of sites (Future Work by SWG, Indicator Steering Committee; Anticipated to be completed in fall 2012)
6. Determine what specifically we measure (metrics), frequency of sampling and sampling period (Future Work by SWG, Indicator Steering Committee; Anticipated to be completed in fall/winter 2012)
7. Establish analysis methods, quality control and data management (Future Work by SWG, Indicator Steering Committee; Anticipated to be completed in fall/winter 2012)
8. Match available funding and projects to list of core indicators (Future Work by SWG, Indicator Steering Committee)
a. Define roles and responsibilities for collection of individual metrics, quality control and data management
b. Incorporate results from other estuary RME into index as relevant
9. Develop decision support tools, incorporate targets and monitoring results into management activities of lower river (Estuary Partnership staff, SWG, Indicator Steering Committee)
10. Monitor and provide results, provide periodic updates to stakeholders (Ecosystem Monitoring Program, AFEP research projects, other programs as applicable)
11. Provide recommendations for diagnostic /BACI studies to better understand uncertainties, variability and reasons behind trends/results (SWG, SRWG, CREC)
12. Update to reflect new findings and emerging issues as necessary.
As this indicator system and numeric management targets are developed, they will be integrated into the monitoring design of the Ecosystem Monitoring Program. The Estuary Partnership will contract to develop a refined monitoring design for the EMP. The contracted statistician will combine the ISTM tool developed through PNAMP, and overlay it with the population of interest from the Columbia River Ecosystem Classification (i.e., Ecosystem Complex or Catena). The intent is to develop a spatially balanced design (GRTS design), including a stratified, random selection of core and distributed (panel) sampling locations. In FY2014 and subsequent years, the Estuary Partnership will implement results from the refined monitoring design with a TBD number and location of sampling sites.

In addition to coordinating activities and on the ground work relevant to Estuary Partnership’s EMP, we will coordinate with the Pacific Northwest Aquatic Monitoring Program (PNAMP), Estuary Ocean Subgroup (EOS), researchers for the USACE Anadromous Fish Enhancement Program (AFEP), and the states’ recovery programs to ensure coordination, build monitoring efficiencies, and to increase the consistency of monitoring and sampling protocols used in the LCRE. We will also participate in the AFEP work to build a central RME database for the LCRE so that our data is accessible and usable to interested parties.

2012-2013 OBJECTIVES FOR THE ECOSYSTEM MONITORING PROGRAM INCLUDE:
1. Monitor habitat, abiotic environmental conditions, food web resources, and salmonids at 6 “fixed” sites and, if funding permits, up to 3 “status” sites within tidally influenced wetlands within TBD reach(es) of the LCRE
2. Coordinate on-going monitoring efforts in the LCRE with partners through facilitating annual estuary RME coordination meetings and the Science Work Group and participating in PNAMP
3. Continue maintenance and data collection at the CMOP LOBO Platform in the tidal freshwater section of the LCRE as well as annual reporting of food web conditions within the entire mainstem LCRE
4. Continue developing an estuarine condition index. Using the core indicators from this index, we will also develop a revised sampling design using the ISTM master sample tool from PNAMP and the Columbia River Estuary Ecosystem Classification
5. Evaluate the effects of selected individual habitat restoration actions at project sites relative to reference sites and evaluate post-restoration trajectories based on project-specific goals and objectives
6. Develop an Annual Report detailing the results of Objectives 1-5.