Ecosystem Monitoring Program
BPA Project Number:  2003-007-00
CR- 349316
Performance/Budget Period: October 1, 2021 – September 30, 2022

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
ccorbett@estuarypartnership.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
targent@estuarypartnership.org

BPA Project Manager:  Siena Lopez-Johnston
KEWL-4, Bonneville Power Administration
905 NE 11th Avenue
Portland, Oregon  97208
Phone:  (503) 230-3859
smlopez@bpa.gov

SUMMARY

The contract supports two major monitoring programs: 1) our Ecosystem Monitoring Program is an integrated status and trends program that focuses on tracking trends in the overall condition of 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 sites serving as reference sites for restoration project sites. Both programs are essential for answering key uncertainties about how the lower river functions and understanding ecosystem conditions, how they are changing, and how management actions (e.g., habitat restoration) are improving conditions in the lower river.

Ecosystem Monitoring Program
The Lower Columbia Estuary Partnership (Estuary Partnership) Ecosystem Monitoring Program (EMP) is an integrated status and trends program for the lower Columbia River. 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).

The program was created in 2004 to address the previous lack of research and monitoring within the tidal freshwater section of the lower river (Reaches C-H), resulting in little basic understanding of habitats, fish use, and food web dynamics in this region. At first, the Estuary Partnership and its monitoring partners focused on gaining an understanding of the spatial variability of habitats and fish use (or “status”) across the lower river. From 2004-2012, three to four “status” sites were sampled. We used the eight Hydrogeomorphic Reaches (A-H), identified in the Columbia River Estuary Ecosystem Classification (CREEC) developed through this project in its early years, as the basis for stratifying our sampling. We rotated the “status” sites around the lower river to an unsampled reach each year. In 2007 we initiated a “trend” (or fixed) site to begin understanding the inter-annual variability of conditions. In 2009 we began switching the focus of our sampling to the temporal variability of habitats, fish use, and food web dynamics by adding a growing number of “trend” sites and reducing the number of “status” sites. By 2013, the transition was complete with 6 trend sites. The focus of the EMP is on minimally disturbed tidally influenced emergent wetland sites within off channel sloughs, representative of end points for the majority of restoration efforts within the lower river.

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 (2010-2020), 2) Welch Island in Reach B (2010-2020), 3) Whites Island in Reach C (2009-2020), 4) Campbell Slough in the Reach F (2005–2020), and 5) Franz Lake in Reach H (2008-2009, 2011-2020). 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 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 Action Effectiveness Monitoring (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 Estuary Partnership 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 this Program and its Future
•    Status and trends monitoring of estuary ecosystem condition–tracks inter-annual variability and unusual ecological conditions such as those in 2015 associated with “the blob” and the unusual warm/dry summer (perhaps repeated in 2021?). Without this program we can only understand conditions at individual restoration sites and cannot roll-up AEM data and assess benefits of restoration actions without an understanding of what’s also going on across the estuary
•    Only consistent monitoring of habitat conditions and fish use in lower river – there is a continued paucity of research and monitoring in the lower river that limits our basic understanding
•    Provides the only “long-term” dataset of fish use across tidal freshwater sections – ranging 7-14 years; previous studies were temporally or spatially limited
•    Provides an inventory of habitats and only information on inter-annual variability of habitat, instream conditions, food web resources and fish use - and the important role they play within salmon and steelhead life cycles
•    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, Estuary Partnership, 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.  
•    Fish use data are used for ERTG templates by CREST, CLT, WDFW, Estuary Partnership, others and scoring of SBUs by ERTG
•    Hydrologic characteristics of estuary regions are used to provide context for inundation anticipated at restoration sites by CLT, WDFW, Estuary Partnership, others
•    Sites are used as reference sites for restoration projects by CREST, CLT, WDFW, Estuary Partnership, others. We have done comparisons of reference site conditions with restoration sites action effectiveness data (completed in 2012)
•    In stream mainstem conditions used in determining if “greening of river” (macrodetritus versus plankton base of salmon foodweb) is correct and whether system is nutrient limited or nutrient enriched

Past Results - From fiscal years 2004 through 2021, with funding from NPCC/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 offchannel 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 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 the Estuary Partnership 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 Columbia River Estuary Conferences; 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 Columbia River Estuary Conferences; 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 - In 2022 Schmidt & Associates and CREST will assist Estuary Partnership staff in collecting data on wetland vegetation species, elevation, macrophyte biomass, and water stage at the six trend sites (including Cunningham Lake). NOAA Fisheries will monitor 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 will process salmon samples for stock, growth rates, stomach contents, and fish condition and send zooplankton samples to OHSU for processing and identification. OHSU will collect 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 will send benthic cores to UW for processing and taxonomic identification. NOAA will send samples from macroinvertebrate tows and juvenile salmon stomach contents to UW for processing and taxonomic identification. NOAA will continue to operate and maintain a PIT tag array at Campbell Slough to assess salmon residency in floodplain habitats. Additionally, OHSU will continue to maintain the CMOP LOBO Platform in the tidal freshwater section of the lower river for another year. Through this project, CMOP researchers will track and report 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. 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. We will produce a series of manuscripts for refereed journals for data collected through summer 2019.  

Action Effectiveness Monitoring Program
The Action Effectiveness Monitoring program (AEM) 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. In 2014, we collected Level 2 AEM data at five sites (Kandoll Farm Phase 2 [post construction]; Sauvie Island North Unit Phases 1 and 2 [post and pre construction respectively]; Wallacut Slough [pre construction]; Sandy River Delta [post construction]). In 2015, we collected Level 2 AEMR data at four sites (Wallooskee-Youngs [pre], La Center Bottoms [pre], Steamboat Slough [post], Sauvie Island North Unit 2 [post]). In 2016 and 2017, we collected post construction data at Kandoll Farm Ph 2, Sauvie Island North Unit Ph 1 and 2 respectively, Sandy River Delta and La Center Bottoms, Steamboat Slough, Dibblee Point and Wallacut Slough; and we collected pre construction data at Flight’s End. In 2018, we collected post construction Level 2 AEMR data at five restoration sites (Wallooskee-Youngs; Kandoll Farm; La Center; Flight’s End; and Sauvie Island North Unit Phase 1. In 2019 we collected Level 2 at Wallacut Slough, Steamboat Slough, Sauvie Island North Unit, and Steigerwald restoration sites. In 2020 we collected Level 2 at Wallooskee-Youngs, La Center, Flight’s End restoration sites. In 2021, we collected data at JR Polensky, Steigerwald, Wallacut, and Ruby Lake. 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. This results in a total of 8-10 sites per year. 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, the Estuary Partnership coordinates project sponsors collecting Level 3 AEM to ensure 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, working with them to develop site sampling plans for each site, and hosting annual meetings to present results from previous year’s AEM.

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

Current AEM work-The Estuary Partnership continues to build upon previous AEM efforts by continuing the collection of Level 2 AEM data at four to six sites, which are identified by the AEM Steering Committee (Estuary Partnership, BPA and USACE). The Estuary Partnership will conduct 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 determine what stocks of fish are using the restored sites. The Estuary Partnership will also continue coordinating Level 3 data collection efforts of restoration project sponsors, including undertaking field quality assurance audits. The Estuary Partnership compiles, and quality checks all Level 3 data, and houses the data pending the completion of regional monitoring database. The Estuary Partnership analyzes all Level 2 data and provides results to BPA in an annual report. A subset of the Level 3 data is included within this report as well. In addition to data management and analysis, the Estuary Partnership coordinates the clarification or updating of monitoring protocols.

In addition to on-the-ground data collection work relevant and coordinating activities of lower Columbia partners to the EMP and AEM, we will participate in the Northwest Power and Conservation Council Ocean Subgroup, PNAMP, and other BPA or Northwest Power and Conservation Council meetings as needed. We will also participate in the completion of a centralized database for the lower Columbia allowing the data to be properly managed and accessible to interested partners.

2021-2022 OBJECTIVES FOR THE ECOSYSTEM and ACTION EFFECTIVENESS MONITORING PROGRAMS INCLUDE:
1.    Monitor habitat, abiotic environmental conditions, food web resources, and salmonids at “trend” sites within tidally influenced wetlands of the lower Columbia River.
2.    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.
3.    Collect pre- and post- construction Level 2 AEM data at priority restoration sites, identified in spring 2021 by the AEM Steering Committee, and, as funding allows, expand collection (pre-construction) to new priority restoration sites.
4.    Coordinate Level 3 AEM data collection and management with project sponsors (CREST, CLT, Cowlitz Indian Tribe, WDFW), including field quality assurance audits.
5.    Develop Annual Reports detailing methods, results, and recommendations.
6.    Continue to identify methods of collaborating sampling, data analyses, and reporting with USACE-funded RME researchers.