The contract supports two major monitoring programs: 1) our Ecosystem Monitoring Program is an integrated status and trends program that focuses on tracking temporal trends in conditions juvenile salmon and steelhead encounter as they outmigrate in the lower river, providing a suite of reference sites for use as end points in our restoration actions, and placing results of research and action effectiveness into the context with the larger ecosystem and 2) our Action Effectiveness Monitoring Program which focuses on providing information on all restoration actions in the lower river. The latter program’s objectives are to assess whether restoration actions are meeting partners’ goals or whether future actions are necessary; allows us to assess the impacts and ecological uplift restoration actions are providing; identifies which actions are working best; and improve the efficacy of our restoration actions. The two programs are inherently intertwined with ... several of the Ecosystem Monitoring Program sites serving as reference sites for restoration project sites that are funded under multiple BPA projects:
•    Columbia Land Trust (CLT) - #2011-007-00,
•    Columbia River Estuary Study Taskforce (CREST)- #2010-004-00,
•    Cowlitz Indian Tribe (CIT) - 2012-015-00, and
•    Washington Department of Fish and Wildlife (WDFW) -2010–070–00).
These partners collect basic pre- and post-construction action effectiveness data at their restoration sites. This project allows us to collect more intensive data at a select subset of restoration sites and coordinate the data collection, analyses, management, and reporting of these partners’ monitoring data. Critically, this project also allows us to continue to fill information gaps, improve our knowledge of the lower Columbia River and its role in supporting juvenile salmonids, and track changes to ecosystem structure and function under a shifting climate.

Ecosystem Monitoring Program
Anthropogenic impacts since the 1880s have greatly reduced the quantity and quality of native habitats available for aquatic species such as salmon and steelhead in the lower Columbia River.  Continued implementation of this NPCC/BPA project overcomes a lack of sustained research and monitoring in the estuary. This NPCC/BPA project supports two major monitoring programs that are critical in supporting the ecosystem restoration program in the lower Columbia River, including the Corps" & BPA’s Columbia Estuary Ecosystem Restoration Program (CEERP).

The first is the Lower Columbia Estuary Partnership (LCEP) Ecosystem Monitoring Program (EMP), an integrated status and trends program for the lower Columbia River and estuary. The study area extends from the mouth of the estuary to the Bonneville Dam. The program is designed to provide an inventory of the different types of habitats within the lower river; track trends in the overall condition of these habitats and the ecosystem; provide a suite of reference sites for use as end points in the region’s habitat restoration actions, and place findings from management actions into context with the larger ecosystem. The Program is a collaborative effort with NOAA National Marine Fisheries Service (NOAA Fisheries), University of Washington (UW), Oregon Health & Science University (OHSU), and Columbia River Estuary Study Taskforce (CREST).

There presently are 5 EMP trend sites, distributed along the estuarine-tidal freshwater gradient so as to be representative of gradient conditions: 1) Ilwaco Slough in Reach A (2010-2023), 2) Welch Island in Reach B (2010-2023), 3) Whites Island in Reach C (2009-2023), 4) Campbell Slough in the Reach F (2005–2023), and 5) Franz Lake in Reach H (2008-2009, 2011-2023). Habitat structure and hydrology data collection began in 2005, fish data collection began in 2007, fish prey data collection began in 2007, and mainstem water quality data and food web data collection began in 2010.  Data collection includes:
•    Salmonid occurrence, composition, growth, diet, condition and residency
•    Habitat structure, including physical, biological and chemical properties of habitats
•    Food web characteristics, including rates and composition of primary and secondary productivity, abiotic conditions controlling productivity at floodplain habitats and in the mainstem lower river, and role in juvenile salmon diets
•    Biogeochemistry of tidal freshwater region of the lower river for comparison to EMP sites and the biogeochemistry of the estuary, key for assessing hypoxia, ocean acidification and climate change impacts.

Between 2010 through 2017, there was a 6th trend site at Secret River in Reach B. Because of safety concerns with site conditions for fish sampling, we dropped sampling at the Secret River site in 2014 and began testing key uncertainties in lieu of this: 1) how far do upper Columbia River juvenile salmon go up tidal tributaries and 2) does timing of fish sampling within a tidal cycle influence catch? In 2015, we sampled for fish community within tidal reaches of two tributaries (lower Lewis and Grays Rivers). In 2016 and 2017 we tested the timing of sampling during tidal cycles a three EMP sites. Starting in 2018 we complete a one-time, synoptic sampling of fish at some of the Action Effectiveness Monitoring (AEM) sites to assess whether fish are using the restored sites (see AEM section below). We also began monitoring detritus and plant C:N:Liginin content at Whites, Welch, and Franz Lake to better assess role and contributions of different plant species in juvenile salmon food web. We also annually sample habitat conditions at Cunningham Lake, a reference site for multiple restoration sites on Sauvie Island.

Applications of Results to Management – funded under BPA’s Columbia River Estuary Ecosystem Restoration Program (CEERP), a primary goal of the EMP 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 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 make the program integral for understanding the success of the regional habitat restoration program. The results of the EMP 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 EMP has provided key information on a suite of reference sites across the lower river. These sites are used as end points for restoration projects and used in combination with the AEM Program data described below. Data collected through the EMP 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 identified the marsh elevation tolerance of the invasive species, reed canarygrass. Data collected through the EMP have also documented differences in the use of the lower river by different salmonid ESUs, and we are now just beginning to understand the juvenile Chinook salmon food web through data collected under the EMP.  Data are used for completing templates/applications for project evaluation by the Expert Regional Technical Group and LCEP Project Review Committee. They are used to inform ecological function models to inform and improve restoration design and within the AEM Program to provide a comparison of conditions within the larger ecosystem to conditions we find at restoration sites.  

Importance of the EMP
•    Integrated assessment allowing the development of an estuarine indicator system – NOAA has documented that juvenile salmon growth and condition at ocean entry is a predictor of early ocean survival. EMP researchers are developing an indicator system of ecological conditions that can be used to predict juvenile salmon growth and survival while within the lower river. We are using the California Current Integrated Ecosystem Assessment and the indicator dashboard as a template.    
•    Status and trends monitoring of estuary ecosystem condition–– without the EMP, we would only understand conditions at individual restoration sites for a snapshot in time. Without an understanding of the conditions in the mainstem or across the lower river ecosystem, we could not assess the performance or benefits of restoration actions (e.g., EMP data provide a comparison with AEM data)
•    Provides basic information on how the estuary functions – despite our growing body of understanding gathered through this and prior USACE-funded research, there is a continued paucity of research and monitoring in the lower river that limits our basic understanding
•    Provides an inventory of habitats across the estuary-river continuum –and the important role they play within salmon and steelhead life cycles
•    Provides the only information on the inter-annual variability of species composition and condition, habitat structure, instream conditions, and foodweb resources
•    Only systemic mainstem water quality monitoring station above Beaver Army Terminal Center.  OHSU’s Coastal Margin Observation and Prediction (CMOP) station was installed and is now maintained through this program. Our collaboration provides not only the data but our ability to tie into research by OHSU and the Northwest Association of Networked Ocean Observing Systems (NANOOS). The CMOP station is important for modeling and predicting mainstem conditions for the Columbia River Treaty. It is the only monitoring above Beaver Army Terminal and below Bonneville that tracks mainstem biogeochemical water quality conditions.
•    Results are used for identifying, designing, and monitoring restoration projects – for example:
•    Findings on the elevation and inundation period where reed canarygrass thrives (invasive, nuisance species) are used in designing restoration projects by CREST, CLT, WDFW, LCEP, others to reduce its occurrence at restoration sites
•    Results from a focused study on the effects of invasive species (i.e., reed canarygrass) on macroinvertebrate community structure and macrodetrital production indicate the importance of preserving native wetland plant communities.  
•    Hydrologic characteristics of estuary regions are used to provide context for inundation anticipated at restoration sites by CLT, WDFW, LCEP, others
•    Sites are used as reference sites for restoration projects by CREST, CLT, WDFW, LCEP, others.
•    In-stream mainstem conditions used in determining if “greening of river” (macrodetritus versus plankton base of salmon foodweb) is correct and whether the system is nutrient-limited or nutrient-enriched
•    Data is used to track, predict, and understand the impacts of shifting climate conditions, such as warming temperatures and increased flooding from sea level rise and more frequent and intense storm events, on the ecology of the lower Columbia River

Past Results - From fiscal years 2004 through 2023, with funding from BPA, EMP partners have accomplished the following major tasks: 1) developed a statistically valid, ecosystem-based monitoring plan for the estuary; 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 three 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 and salmon occurrence, diet, condition, stock, growth, prey availability, and preference; 7) characterized the salmon food web at six “trend” sites representing the estuarine-tidal freshwater gradient; 8) collected abiotic environmental/water column condition data at trend sites annually; 9) installed and maintained a CMOP Land Ocean Biogeochemical Observatory (LOBO) platform above the Willamette River confluence with the Columbia to better understand drivers of biogeochemistry of mainstem versus off-channel site conditions; 10) 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; 11) provided results for a comparison of macroinvertebrate prey availability, plant biomass, and detrital production at sites dominated by the invasive reed canarygrass versus sites dominated by native vegetation; 12) produced two syntheses of EMP data – one focusing on reporting trends in habitat structure; fish composition, condition, growth rate and prey consumption, and the second focusing on the juvenile salmon food web dynamics and inter-annual variability of the metrics collected under this program; 13) created a conceptual model and overview description of the juvenile Chinook salmon food web within the lower river; 14) began developing an index of estuarine water conditions to provide context for conditions juvenile salmon and steelhead experience as they outmigrate and for results of analyses (e.g., “typical” high, low, and normal freshet conditions); 15) provided results on the success of restoration projects across the lower river based on water surface elevation, water temperature and periodicity of these conditions to the USACE Synthesis Memorandum #2; 16) presented our results and climate adaptation measures to our Science Work Group and a series of local and regional conferences and workshops; 17) facilitated biennial Columbia River Estuary Conferences (CREC) and provided 3-4 presentations at each; 18) coordinated on-going effectiveness monitoring at restoration sites, including providing QA/QC of partners’ data, data management, data analysis and reporting; and 19) provided (and coordinated that of partners) periodic refinements to standardized protocols for restoration effectiveness monitoring.

In addition, NPCC/BPA funding  is leveraged to allow LCEP to accomplish many RME-related coordination activities: 1) convening technical workshops for researchers and managers on topics of interest such as land cover, bathymetry, toxic contaminants, and restoration; 2) convening biennial CRECs; 3) providing RME coordination for entities working in the lower river, namely NMFS, PNNL, CREST, USACE, BPA, LCRFB, ODFW, OHSU and others; 4) supported other regional monitoring coordination efforts, including Pacific Northwest Aquatic Monitoring Partnership; 5) acted as a central clearinghouse for GIS and monitoring data while developing mapping website to house 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; 7) presented monitoring efforts at several regional and national conferences, including the Coastal and Estuarine Research Federation, American Fisheries Society, and CRECs; and 8) participated in regional forums, such as the Northwest Power and Conservation Council’s Ocean Forum, Pacific Estuarine Research Federation (PERS), NANOOS, American Fisheries Society, and Pacific Joint Venture, to share information and coordinate RME and restoration efforts. Information exchanged during these events allows coordination and leveraging of research results and provides invaluable insight and guidance for future RME and restoration efforts in the lower river.

Current EMP Work - Schott & Associates and CREST previously assisted LCEP staff in collecting data on wetland vegetation species, elevation, macrophyte biomass, and water stage at the six trend sites (including Cunningham Lake). NOAA Fisheries monitored salmon and salmon prey, and collect food web resources at five of these sites to provide information on juvenile salmon use of the vegetated and shallow water habitats of the lower Columbia River. NOAA Fisheries processed salmon samples for stock, growth rates, stomach contents, and fish condition and send zooplankton samples to OHSU for processing and identification. OHSU collected food web data at the same five sites to characterize conditions supporting juvenile salmonids, specifically rate and composition of primary and secondary productivity, abiotic conditions that limit productivity, and stable isotope analysis of salmon tissue and mucous. OHSU sent benthic cores to UW for processing and taxonomic identification. NOAA sent samples from macroinvertebrate tows and juvenile salmon stomach contents to UW for processing and taxonomic identification. NOAA installed and maintained a PIT tag array at Campbell Slough to assess salmon residency in floodplain habitats. Additionally, OHSU maintained the CMOP LOBO Platform in the tidal freshwater section of the lower river to track water column salmon habitat conditions. OHSU reported on 1) seasonal primary production biomass and taxonomy for lower river from Bonneville to plume; 2) sources of dissolved organic carbon, turbidity and nutrients in tidal freshwater and estuarine sections of lower river; and 3) water temperatures, pH, dissolved oxygen levels in tidal freshwater and estuarine (except pH) sections of lower river. LCEP's Science Work Group reviewed the data on a periodic basis to recommend possible research studies to address key questions as they arise. We initiated preparation of a series of manuscripts for refereed journals for data collected through summer 2019; however only one of these has been finalized and submitted.  

Action Effectiveness Monitoring Program
The AEM program was transferred from the Habitat Restoration Program contract (2003-11-00) to this contract in 2013. The AEM Program provides information about the efficacy of restoration actions, allows the quantification of change in ecosystem condition resulting from specific restoration actions, and helps determine if restoration actions are meeting project sponsors objectives and goals. Between 2007-2013 the Estuary Partnership and partners implemented a pilot action effectiveness monitoring program 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 four 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; re-vegetation 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). AEM partners collected data using a suite of standardized sampling protocols in Roegner et al. (2007), and metrics such as water quality, sediment accretion, channel cross-sections, vegetation cover, vegetation planting success, salmon presence/absence, and salmon prey. AEM occurred at these sites from 2007-2013, except for the Scappoose Bottomlands site, which was not repeated in 2013 as a result of access issues with the private landowner. In 2009, researchers from PNNL, Estuary Partnership, NOAA, USACE and CREST, compiled AEM data from multiple restoration sites in a pilot meta-analysis for the USACE Cumulative Effects of Restoration project.  

The development of “Protocols for Monitoring Habitat Restoration Projects in the Lower Columbia River and Estuary” (Roegner et al. 2009) in 2007 and revised in 2009 provided a framework for the when, where, why, and how of AEM. The standardization of monitoring metrics and sampling protocols across sites and partners allows the ecological impact of restoration actions to be compared across the landscape and through time to help determine the cumulative effects of restoration efforts. Many of the authors of Roegner et al. (2007, 2009) work on the EMP and designed the protocols so that the data collected under AEM are comparable with data collected under the EMP. The Estuary Partnership facilitated the training of partners on these methods, including annual Science Work Group meetings to discuss results and lessons learned. To promote access to the protocols and sharing, the Estuary Partnership also added the Roegner et al. protocols to www.monitoringmethods.org.  

The pilot AEM Program from 2007-2013 demonstrated the need for 1) improvements in monitoring metrics; 2) a site prioritization strategy; 3) an increase in the number of sites monitored; 4) improved data management, analysis and reporting; and 5) a standardized timeline for pre- and post-restoration construction monitoring.  Based on lessons learned, the Estuary Partnership with BPA, USACE, and PNNL developed “A Programmatic Plan for Restoration Action Effectiveness Monitoring and Research (AEMR) in the Lower Columbia River and Estuary” (Johnson et al. 2013) to improve and standardize sampling metrics and timelines; create different levels of monitoring efforts (Standard [Level 3], Core [Level 2], and Intensive [Level 1]); designate how these levels will be determined by site; and identify protocols for data management, analyses, and reporting.  
  
In 2013, the Estuary Partnership began implementing the new programmatic AEM plan. The Estuary Partnership, BPA, and US Army Corps of Engineers (USACE), used the programmatic AEM prioritization process in Johnson et al. (2013) to identify four sites (Kandoll Farm Phase 2 [pre construction], Steamboat Slough [pre construction], Sauvie Island North Unit [pre construction], and Dibblee Point [post construction]) for Level 2 monitoring in 2013. Also, NOAA Fisheries installed a pit tag array at the Horsetail Creek restoration site for Level 1 baseline data collection in 2013; construction at this site occurred in summer 2013. The pit tag array continued collecting post construction AEM data through 2020, and the equipment was removed in 2021.

We collect pre- and post-construction Level 2 AEM data at an average of 4-6 restoration sites per year depending on level of effort needed (see annual reports for list of sites monitored). Along with these restoration sites, nearby reference or control sites were identified and monitored to create a pair of sites to ensure the requirements for a Before After Reference Impact (BARI/BACI) statistical design were met. AEM monitoring at restoration and reference, control sites included characterizing vegetation, sampling macroinvertebrate communities, and collecting channel cross sections and was preformed prior to restoration actions to capture pre-restoration ecological conditions. All AEM data collection was conducted using the Roegner et al. (2009) protocols, as updated in 2019 and 2020.

In addition to Level 2 monitoring, LCEP coordinates with project sponsors collecting Level 3 AEM to support standardized protocols in sampling design and metrics are being used (water elevation, water temperature, sediment accretion, and photo points) at all restoration sites receiving BPA funding. This coordination role included hosting a 2-day workshop with project sponsors in 2014 and hosting annual meetings to present results from the previous year’s AEM. We also compile and QA/QC Level 3 data. Starting in 2022, we have uploaded Level 3 data into Tableau for supporting the sharing, analyses and reporting of AEM data.

In 2017-2018, the Estuary Partnership analyzed and reported pre- and post- construction water temperature and surface elevation data for Level 3 AEM sites for the USACE’s 2018 CEERP Synthesis Memorandum. A subset of results was also presented at the 2018 CREC and at a March Science Work Group meeting.

Current AEM work-LCEP built upon previous AEM efforts by continuing the collection of Level 2 AEM data at three to six sites, which are identified by the AEM Steering Committee (BPA, USACE, and NOAA). LCEP conducted synoptic fish collection at a subset of AEM sites (i.e., Year 5 Level 2 AEM sites) to establish the presence/absence of salmonid species and if they are using the restored sites. LCEP also coordinated with Level 3 data collection efforts of restoration project sponsors, including working with monitoring partners to update the suite of standardized monitoring protocols. LCEP compiled, and performs quality checks of Level 3 data, and starting in 2022 uploads them to Tableau on behalf of monitoring partners. LCEP analyzes Level 2 data and provides results to BPA in an annual report and at the annual Science Work Group meeting.

In addition to on-the-ground data collection work relevant and coordinating activities of lower Columbia partners to the EMP and AEM, LCEP participates in the Northwest Power and Conservation Council Ocean Subgroup, PNAMP, and other BPA or Northwest Power and Conservation Council meetings as needed.

2024-2025 OBJECTIVES FOR THE ECOSYSTEM and ACTION EFFECTIVENESS MONITORING PROGRAMS INCLUDE:
1.    Convene a regular Science Forum of restoration and research partners to discuss ongoing monitoring efforts in relation to critical uncertainties for the CEERP. Forum members will collaboratively discuss methods of addressing uncertainties with the limited budget for data collection under the CEERP.
2.     Monitor habitat, abiotic environmental conditions, food web resources, and salmonids at “trend” sites within tidally influenced wetlands of the lower Columbia River.
3.    Continue maintenance and data collection at the CMOP LOBO Platform in the tidal freshwater section of the lower Columbia River as well as annual reporting of food web conditions within the entire mainstem lower Columbia River.
4.    Collect AEM data at LCEP restoration sites and provide support to partners for their collection of pre- and post- construction AEM data at BPA-funded restoration sites, as funding and time allows.
5.    Support AEM data management with project sponsors (CREST, CLT, Cowlitz Indian Tribe, WDFW), including providing quality assurance checks upon request and as funding and time allows.
6.    Prepare multiple manuscripts of the data collected through this contract and submit to refereed journals.
7.    Continue to research and expand methods and utility for reporting results of the data collected through this contract including through the use of Tableau software, database programs, and/or hybrid systems.  
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