Protocols for Monitoring Habitat Restoration Projects in the Lower Columbia River and Estuaryiii AbstractThis document describes a set of protocols developed by the National Marine Fisheries Service of the National Oceanographic and Atmospheric Administration, Pacific Northwest National Laboratory, and the Columbia River Estuary Study Taskforce with the support of the U.S. Army Corps of Engineers. These protocols are designed for researchers and managers monitoring the effectiveness of actions to restore degraded wetland habitat in the lower Columbia River and estuary (CRE). The intent is to promote a standard set of monitoring protocols to assess and compare habitat restoration projects in the region.The goal of many restoration activities in the CRE is to repair the connectivity and function of wetland habitats, and thereby to allow juvenile salmon to regain benefit from these important rearing and refuge areas. To do this effectively, researchers and managers require the means to 1) evaluate the results of individual restoration activities, 2) compare results among projects, and 3) determine the long-term and cumulative effects of habitat restoration on the overall estuary ecosystem. To help achieve this, we have developed a standardized set of monitoring protocols. We limited the number of metrics to a proposed "core" set and selected measurement methods that are straightforward and economical to use. By "core," we mean an optimum suite of metrics that can adequately detail the results of restoration, depending on the goals of the restoration action and financial and logistical limitations of comprehensively monitoring ecological change over extended temporal and spatial scales. We selected core metrics based on the following criteria: 1) correspond to commonly held restoration project goals; 2) are applicable to all sites; 3) characterize controlling factors, ecosystem structure, and ecosystem function; 4) are relevant to both present and future investigations; and 5) are practical in terms of level of effort.In this document, we summarize the types of restoration strategies being planned and implemented in the CRE. We then propose a set of metrics and statistical design for restoration monitoring activities based on commonly shared ecological goals. Finally, we provide specific protocols for this set of estuary monitoring metrics. Monitoring protocols are provided for hydrology (water surface elevation); water quality (temperature, salinity); elevation (topography); landscape features (remote sensing); plant community (composition and cover); vegetation plantings (success); and fish community (species, temporal presence, size/age structure).

The research presented in this report is part of the regional habitat restoration program in the lower Columbia River and estuary (LCRE). As part of this program, we have established a suite of reference sites to help meet the goal of understanding and restoring wetland habitat. The data collected at these reference sites from 2005 through the present were analyzed in this study to meet two primary objectives: 1) to inform restoration planning and design by quantifying the ecological and hydrological conditions necessary for development of wetland plant communities and tidal channel networks and 2) to evaluate the effectiveness of wetland restoration actions in the LCRE by comparing restoration and reference site monitoring data. In this report, we present the results of the analysis of 51 reference wetland sites, focusing on the elevation, sediment, and inundation ranges required by native tidal wetland vegetation. We describe critical factors influencing existing wetland patterns in the LCRE, including the vegetation assemblages present, the elevation ranges at which they occur, and the inundation dynamics that result in their current distribution. Finally, we present how these data can be used to evaluate restoration action effectiveness. v Executive Summary vi Hydro-Vegetation Zones Shallow-water vegetation assemblages show distinct differences along the gradient between the mouth of the river and the upstream end of the estuary at Bonneville Lock and Dam. There are three zones based on species richness; the central region (rkm 50 to rkm 150) has the greatest number of species, and the upper and lower ends of the estuary have lower numbers of species. These three species richness zones can be characterized hydrodynamically as tidal-dominated, mixed tidal and riverdominated, and river-dominated, moving from the mouth of the Columbia River to Bonneville Dam. We hypothesize that fewer vegetation species are physiologically adapted to the extreme inundation in the upper end of the estuary, and, likewise, few are adapted to the tidal variability and salinity in the lower estuary. The fact that the mixed zone contains the greatest number of species suggests that the natural ecological disturbance regime may be lower there, and there may be a larger species pool adapted for these conditions in this zone. This intermediate disturbance hypothesis has been used in many ecosystems to describe the conditions that result in higher species diversity. Further examination of the hydrologic gradient revealed that the estuary can be divided further into five zones, driven primarily by salinity intrusion at the lower end and stronger fluvial flooding influence at the upper end. The breaks for these zones occur at approximately rkm 40, 104, 136, and 181. These breaks are preliminary and should be refined with additional data in areas of sparse sites and with other hydrologic analyses currently under way. The five hydro-vegetation zones developed from this analysis provide a means of determining the ranges of controlling factors ...

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In 2006, the Portland District of the U.S. Army Corps of Engineers (USACE) contracted with the Pacific Northwest National Laboratory (PNNL) to conduct three studies using acoustic telemetry to estimate detection probabilities and survival of juvenile Chinook salmon at three hydropower projects on the lower Columbia River. The primary goals were to estimate detection and survival probabilities based on sampling with Juvenile Salmon Acoustic Telemetry System (JSATS) equipment, assess the feasibility of using JSATS for survival studies, and estimate sample sizes needed to obtain a desired level of precision in future studies. Tagging We conducted acoustic-telemetry survival studies on yearling and sub-yearling Chinook salmon at John Day Dam (JDA), The Dalles Dam (TDA), and Bonneville Dam (BON). We surgically implanted 2,501 yearling Chinook salmon in spring and 2,502 sub-yearling Chinook salmon in summer with passive integrated transponder (PIT) and JSATS acoustic tags. Fish were collected and tagged at the John Day Dam Smolt Monitoring Facility (SMF), and unintentional tagging mortality averaged 0.6% in spring and 0.7% in summer. Tagging seasons encompassed the peaks of the spring and summer runs of juvenile Chinook salmon. The spring tagging season was from May 13 to June 6, 2006, and targeted the yearling Chinook run, which peaked between May 20 and June 1, 2006. A 95-mm minimum length limitation on tagging did not restrict the lengths of fish that could be tagged in the spring, and the length frequencies of tagged and untagged yearling Chinook salmon in the juvenile bypass system (JBS) samples were very similar. The summer tagging season was from June 11 to July 13, 2006, and targeted the subyearling Chinook run, which peaked around July 1. The 95-mm minimum tagging length effectively eliminated about 23% of the run-of-river sub-yearlings from the sample because they were too small to tag without increasing tagging mortality. Tagging must include 80 to 100 mm subyearlings to be fully representative of the runof-river population at JDA in summer. All fish tagged in this study and released at or below JDA were implanted with JSATS tags that transmitted a coded signal transmitting once every 5 seconds (5 s tags) that were expected to last about 30 days, and fish that were released into the Snake River by other studies were implanted with tags that transmitted once every 10 s. We conducted a tag-life study using 100 10 s tags and 100 5 s tags randomly sampled from lots allocated to survival studies. The tag-life study verified that most tags lasted about as long as expected. All 10-s tags sampled from lots of tags implanted in Snake River fish lasted at least 57 days relative to an expected 55 days, and all the 5-s tags exceeded the expected 30-day life by about 5 days. No tag-life correction was needed or used for the 2006 survival studies in spring or summer because over 99% of tagged fish exited the study area before tags expired. Tag life and survivorship curves are presented in Appendix A.

This report should be cited as follows:Weiland, MA, GR Ploskey, JS Hughes, Z Deng, T Fu, J Kim, GE Johnson, GW Batten, ES Fischer, F Khan, SA Zimmerman, DM Faber, KM Carter, JW Boyd, RL Townsend, JR Skalski, TJ Monter, AW Cushing, MM Meyer. 2011. Acoustic Telemetry Evaluation of Juvenile Salmonid Passage and Survival Proportions at John Day Dam, 2009. PNNL-20766. Draft report submitted by the Pacific Northwest National Laboratory to the U.S. Army Corps of Engineers, Portland District, Portland, Oregon.iii PrefaceThe study reported herein was funded as part of the Anadromous Fish Evaluation Program, which is managed by the U.S. Army Corps of Engineers (USACE). The Anadromous Fish Evaluation Program study code is SPE-P-08-03: Studies of Surface Spill at John Day Dam. The study was led by the Pacific Northwest National Laboratory (PNNL) for the USACE Portland District. The USACE technical leads were Robert Wertheimer, Sean Tackley, and Brad Eppard. The PNNL study project manager was Mark Weiland (509 427-5923). The data are archived at PNNL offices in North Bonneville, Washington.v Executive SummaryImproving the survival rate of juvenile salmonids migrating downstream through the Federal Columbia River Power System (FCRPS) continues to be a high priority for the USACE and the region. Many of these fish are from populations listed as threatened or endangered under the Endangered Species Act. Increasing survival rates is necessary to ensure sustainable salmon populations in the future and meet performance standards set forth in the 2008 Biological Opinion (BiOp) and 2008 Columbia Basin Fish Accords on operation of the FCRPS. The BiOp mandates that a 96% and 93% survival rate be achieved for spring and summer downstream migrating juvenile salmonids, respectively. At John Day Dam (JDA), the Portland District is evaluating the provision of surface-flow outlets (SFOs) as a means to increase fish-passage efficiency and in turn increase the fish-passage survival rate by reducing turbine passage of juvenile salmonids. The goal of the study reported here was to provide fish-passage and survival data necessary to evaluate the performance of the prototype SFO, called a top-spill weir (TSW), and the dam as a whole relative to the performance standards in the BiOp. The Portland District and regional fisheries managers will use the data to adaptively manage the configuration and operation of JDA to maximize the survival rate for juvenile salmonids. This is the report of research for the acoustic telemetry evaluation of juvenile salmonids during 2009 at JDA. The study was conducted by the Pacific Northwest National Laboratory and the University of Washington for the U.S. Army Corps of Engineers (USACE) Portland District. S.1 ObjectivesThe overall purpose of the acoustic-telemetry study at JDA during 2009 was to determine the best configuration and operation for JDA prior to conducting BiOp performance standard tests. The primary objective was to determine the best operation between 30% and 40% spill treatments. Route-specific, J...