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QUALITY ASSURANCE
PROJECT PLAN (QAPP)
For
Monitoring ecosystem response to restoration and climate change in the Snohomish River estuary.
Jan 2013
QAPP for Monitoring ecosystem response to restoration and climate change in the Snohomish River estuary.
Jan 2013
3
2. TABLE OF CONTENTS
1. APPROVAL OF QAPP: ...................................................................................................................... 2
2. TABLE OF CONTENTS .................................................................................................................... 3
3. PROJECT MANAGEMENT .............................................................................................................. 4
DISTRIBUTION LIST ........................................................................................................................... 4
PROJECT TASK/ORGANIZATION ..................................................................................................... 4
PROBLEM DEFINITION/BACKGROUND ......................................................................................... 4
PROJECT TASK DESCRIPTION.......................................................................................................... 5
DATA QUALITY OBJECTIVES AND MEASUREMENTS CRITERIA ............................................ 9
SPECIAL TRAINING AND CERTIFICATION ................................................................................. 10
DOCUMENTS AND RECORDS ......................................................................................................... 11
4. DATA GENERATION AND ACQUISITION ................................................................................. 12
SAMPLING PROCESS DESIGN (Experimental Design) ................................................................... 12
SAMPLING METHODOLOGY .......................................................................................................... 13
SAMPLE HANDLING AND CUSTODY ........................................................................................... 15
ANALYTICAL METHODS ................................................................................................................. 16
QUALITY CONTROL ......................................................................................................................... 16
INSTRUMENT/EQUIPMENT TESTING, INSPECTION AND MAINTENANCE .......................... 16
INSTRUMENT/EQUIPMENT CALIBRATION AND FREQUENCY .............................................. 16
INSPECTION/ACCEPTANCE OF CONSUMABLE SUPPLIES ...................................................... 16
NON-DIRECT MEASUREMENTS (SECONDARY DATA)............................................................. 17
DATA MANAGEMENT ...................................................................................................................... 17
5. ASSESSMENTS AND RESPONSE ACTIONS .............................................................................. 17
REPORTS TO MANAGEMENT .......................................................... Error! Bookmark not defined.
6. DATA VALIDATION AND USABILITY ...................................................................................... 18
VERIFICATION AND VALIDATION METHODS ........................................................................... 18
RECONCILIATION WITH USER REQUIREMENTS....................................................................... 18
7. REFERENCES .................................................................................................................................. 19
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3. PROJECT MANAGEMENT
DISTRIBUTION LIST
Copies of the completed/signed project plan and reports shall be distributed to:
Name Title Affiliation E-Mail Phone QAPP Report
Todd Zackey Principal
Investigator
Tulalip
Tribes
[email protected] 360-716-
4637
x x
Joshua Kubo Project
Manager
Tulalip
Tribes
[email protected] 360-716-
4638
x x
Dr. Casey Rice Co-PI NOAA [email protected] 425-347-
6935 x231
x x
Joshua Chamberlin Co-PI NOAA [email protected] 206-302-
2472
x x
Jason Hall Co-PI NOAA [email protected] 206-302-
1748
x x
Jason Schilling Co-PI Tulalip
Tribes
jschilling@tulaliptribes-
nsn.gov
360-716-
4611
x x
Tiffany Waters QA NWIFC [email protected] 360-528-
4318
x
Lisa Chang R10 QAM EPA [email protected] 206-553-
0226
x
PROJECT TASK/ORGANIZATION The following individuals comprised the project team with responsibilities for the design and
implementation of this project:
Todd Zackey, Principal Investigator, is the main point of contact and shall have the over-all
responsibility for the implementation of the project. He shall ensure that the project shall adhere to all
the objectives, protocols and timeline specifications of the EPA approved QAPP.
Joshua Kubo, Project Manager, will be responsible for project reporting, grant budget management, and
assuring all grant requirements are met.
Dr. Casimir Rice, Joshua Chamberlin, Jason Hall, Jason Schilling, Co-investigators, are responsible for
key components of the project. Dr. Rice and Joshua Chamberlin are responsible for fish sampling and
field coordination, Jason Hall is responsible for hydrology, and Jason Schilling is responsible for birds.
Ginna Grepo-Grove, Lisa Chang: The USEPA Quality Assurance Manager is Ginna Grepo-Grove. She
or her designee will review and approve the QAPP and subsequent addendums or amendments to the
QAPP submitted to the USEPA. NWIFC’s EPA Project Officer is Lisa Chang and she is responsible for
QAPP for Monitoring ecosystem response to restoration and climate change in the Snohomish River estuary.
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interfacing with NWIFC to oversee that the overall grant conditions are met in accordance with the
NWIFC EPA contract.
Tiffany Waters, Lucy Yanez: The NWIFC Puget Sound Recovery Project Coordinator is Tiffany Waters
and the Contracts Specialist is Lucy Yanez. NWIFC shall administer the EPA-sponsored grant sub-
award and shall be responsible for the oversight of the contract, ensuring that the goals and objectives of
the project are achieved. They will ensure that project deliverables are complete and of necessary quality
and that the project completion dates are met. They will interface with the USEPA regarding the status
of the approved project.
PROBLEM DEFINITION/BACKGROUND Protection and recovery of the Snohomish River estuary is a high priority for Tulalip Tribes
because the existence and persistence of salmon and other natural resources dependent on the estuary are
integral for the tribe to maintain its cultural identity and subsistence. For example, with several salmon
stocks (including wild Chinook, the most estuary dependent of all salmon) diminished throughout
Tulalip’s usual and accustomed fishing areas, significant investments in salmon recovery are necessary
to support tribal fisheries and Treaty Rights. High priority activities such as estuarine protection and
restoration are therefore a reserved treaty right and strongly supported by Tulalip and other Puget Sound
Tribes. In order to ensure the future of estuary-dependent components of the Tribes’ natural heritage,
scientific information is necessary to understand how the Snohomish estuary ecosystem works, how it
responds to anthropogenic stressors such as climate change, and whether actions intended to improve
ecological condition are effective. Extensive, estuary-wide monitoring efforts are a clear priority of the
Tulalip Tribes, and the proposed work addresses this need.
The Snohomish River estuary is the second largest in the Puget Sound and provides habitat for Chinook
and other salmonids (Snohomish Basin Salmon Recovery Forum 2005). These estuarine rearing and
migration areas are necessary in the transition from freshwater to the critically important first year at
sea. Similarly, estuaries provide vital habitat for a myriad of resident, migratory, and overwintering bird
populations (City of Everett 2001, Wentworth-Davis 2011). The massive loss and degradation of
juvenile salmonid habitat in the Snohomish estuary, as a result of modern human activities, was
identified in the Snohomish Basin Recovery Plan as the primary factor limiting Chinook salmon survival
in the basin (Snohomish River Basin Salmon Conservation Plan 2005). Additionally, degraded estuarine
habitat conditions combined with a changing climate and sea level rise have been identified as threats to
Puget Sound avian assemblages (Audubon 2009). Fortunately, the Snohomish estuary has high potential
for wild Chinook and avian recovery through restoration of estuarine wetlands, where over 1200 acres
have been restored or identified as potential restoration projects. Coupled with extensive restoration
actions is the need for ongoing monitoring throughout the estuary to track individual and cumulative
effectiveness of restoration projects, and to determine the condition of Snohomish estuarine habitats in
response to continuing anthropogenic stressors, including climate change. All ecosystem and salmon
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recovery planning efforts recognize the need for monitoring (e.g., Snohomish River Basin Salmon
Conservation Plan 2005, Puget Sound Partnership Action Agenda 2012, Snohomish Basin 3-year Work
Plan 2012) but such efforts are rare. In addition, bird surveys will achieve monitoring goals outlined in
the Washington Wildlife Conservation Strategy (WDFW and the North American Marsh Bird
Monitoring Program (Conway 2011). Many stakeholders and individual projects would benefit from
comprehensive monitoring efforts, yet little coordination and collaboration occurs. The comprehensive
monitoring plan for the Qwuloolt project (Rice et al. 2011) provides a template for project level
restoration monitoring in the Snohomish that addresses a wide array of abiotic (e.g., land forms,
hydrology) and biotic (vegetation, invertebrates, birds, fishes, and mammals) attributes, and is now
informed and refined by three full years of implementation. We propose to facilitate effective project
level monitoring continue and expand system-wide monitoring efforts in support of the restoration and
recovery of the Snohomish River estuary by: 1) ensuring the continuation of basic, ongoing fish
monitoring; 2) continuing avian monitoring at reference and project sites; 3) installation of additional
hydrologic and elevation/sedimentation monitoring equipment; and 4) expanded system-wide and
project level monitoring through outreach and planning activities to increase participation by more
stakeholders, and acquire additional funding. As noted above, the proposed efforts are relevant to at least
eight Puget Sound Action Agenda items.
PROJECT TASK DESCRIPTION This research project will examine several components of the ecosystem across the estuarine landscape
to help evaluate restoration effectiveness and response to climate change. We will quantify seasonal
abundance and composition of both fish and bird communities, as well as assess the individual condition
juvenile salmon. The proposed project is particularly relevant to a number of objectives under the Puget
Sound Action Agenda Strategic Initiative: Protection and Restoration of Habitat.
General Project Timeline
The project is broken in to four specific tasks which will largely be conducted simultaneously
throughout the funding period with the exception of the development of the Quality Assurance Project
Plan which will be finalized and approved prior to data collection.
TASK/MILESTONE OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP
1. Project Management
2. QAPP Development
3. Planning and Outreach
4. Data Collection
5. Analysis and Writing
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Project Tasks
Planning and Outreach. The proposed project is intended to inform WRIA 7 stakeholders and
Snohomish Estuary project proponents of the existing and future ecological conditions of the Snohomish
River system. A goal of this project is to ensure that the proper information is collected to allow
stakeholders and project proponents to implement adaptive management strategies to ensure the
successful recovery of the Snohomish River watershed. This project seeks to develop a cooperative and
coordinated effort, pooling resources from all Snohomish estuary stakeholders and project proponents.
The aim of the coordination is to conduct effective and relevant monitoring efforts, fill data gaps,
implement adaptive management in light of changing climatic conditions, and seek further support to
continue the necessary monitoring needs of the Snohomish estuary. Information and collaboration
among stakeholders and project proponents will be organized by the Snohomish Basin Capital Programs
Coordinator (Morgan Ruff, Tulalip tribes) and disseminated through the Snohomish Estuary Working
Group. These efforts will help to promote a consistent, effective, efficient, and long-term monitoring
from project level to system-wide efforts. The Estuary Working Group will provide an ideal forum for
sharing this information, aligning current monitoring efforts, and collaborating for future strategies. A
workshop on monitoring results and strategies will be conducted early in the project and a report will be
produced at the end.
Data Collection. Data collection will begin upon EPA approval of the QAPP and will be conducted by
Tulalip Staff, PI, Wildlife Biologist, Field Technician, Field Biologist, NOAA NWFSC staff, and
volunteers. NOAA NWFSC will be sub-contracted to assist with the data collection effort and additional
funding resources will be used to fund Tulalip staff for data collection efforts. Data will be collected to
assess the current conditions across the Snohomish Estuary system, long-term monitoring sites will be
establish for assessing and tracking long-term changes in the estuary, and efforts will be made to assist
in the development of predictive models (e.g. Battelle’s Finite Volume Coastal Ocean Model, USGS
rapid assessment protocol (RAP) for Potential Sediment Accretion) which assess future climate change
implications in the Snohomish watershed. Across the estuary, biological data will be collected for birds
and fish, hydrological conditions will be assessed utilizing water column profiling instruments, and
longterm sediment conditions will be monitored utilizing sediment surface elevation tables (SET) sites
located across the estuary. Data collection sub-tasks are as follows:
Data Collection Sub-Tasks
OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP
Fish Sampling
Bird Surveys
Hydrologic Data Loggers
Water Profiling
SET Installation/ Sampling
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1) Fish. NOAA’s Northwest Fisheries Science Center (NWFSC) has been monitoring fish in the
Snohomish estuary for over a decade in collaboration with Tulalip Tribes. This work has never received
substantial dedicated funding and was suspended in 2011. Through a restoration monitoring
collaboration between NOAA and the Tulalip Tribes, year-round estuary-wide monitoring was resumed
in 2012 with significant improvements in the sampling scheme, including full coverage of the estuary
from tidal freshwater to nearshore, and stratified random site selection. Application and development of
a system-wide monitoring template has been closely related to intensive, pre-breach monitoring
strategies conducted at the Qwuloolt restoration site (Rice et al. 2011) by NOAA/NWFSC and Tulalip
Tribes since 2009. Additionally, the overall monitoring approach is consistent with recommendations
being developed to evaluate regional salmon recovery efforts (Puget Sound RITT, 2012) and is based on
the extensive work done in the Skagit River estuary (e.g., Beamer et al. 2005) that the NWFSC has been
a contributor to since 2001. Through the implementation of a system-wide monitoring strategy in the
Snohomish, this project aims to expand long-term monitoring efforts and further develop a rigorous
monitoring program of habitat (e.g., hydrology and sediment) and biota (e.g. fish and bird). A key
component of this proposal is to expand and formalize collaborations with other lead entities in the area
(e.g. Snohomish County), coordinating project level monitoring, and integrating it into estuary-wide
efforts.
2) Birds. Bird surveys were initiated in 2012 for the purpose of assessing marsh bird and overall avian
abundances before and after tidal inundation in the Qwuloolt restoration project area. Marsh bird
abundance and distribution over space and time indicate habitat quality and can be used as measures of
restoration success (Neckles et al. 2002, U. S. EPA 2002). Combined with a similar USGS study in the
Nisqually estuary, this bird monitoring effort will contribute to a region-wide effort comparing effects of
restoration on birds in the Puget Sound. In addition to measuring the effects of restoration on avian
assemblages, this study will also contribute to a national and regional database of marsh bird population
assessments. Tidal salt marsh bird populations are currently undersampled and in need of a focused
monitoring effort (Conway and Droege 2006). Standardized monitoring protocol for marsh birds has
been developed (Conway and Droege 2006, Conway et al. 2011) to facilitate a large-scale monitoring
effort and database for assessing regional or range-wide population trends and identifying declining
species before they become endangered. Efforts for this project aim to provide a baseline dataset from
restoration projects (e.g. Qwuloolt & Smith Island) and reference sites for monitoring effects of climate
change and predicted sea-level rise on avian assemblages and marsh dependent birds in the Snohomish
estuary.
3) Hydrology. Limited monitoring of basic hydrology has been conducted by NOAA/NWFSC and
Tulalip Tribes; including discrete water column profiling and continuous water level, salinity, and
temperature monitoring within the Snohomish estuary. While these efforts have been limited in spatial
and temporal extent, the data collected thus far have provided useful insights into the dynamic salinity
gradients within the estuary and the relationships between tides, river flow, salinity, and temperature,
and established pre-restoration “baseline” conditions across the estuary. Hydrology is a key driver of
estuarine ecosystems and expanding both the spatial and temporal coverage of hydrological monitoring
within the Snohomish estuary would provide several major benefits: (1) improve our understanding of
existing physical and biological patterns within the estuary, (2) provide baseline and response data to
evaluate restoration effectiveness and responses within the estuary, and (3) provide calibration data to
refine previously developed hydrodynamic models (e.g. Battelle’s Finite Volume Coastal Ocean Model,
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USGS rapid assessment protocol (RAP) for Potential Sediment Accretion)to evaluate potential climate
change impacts within the estuary.
With these benefits in mind, we propose water column sampling using CTD profilers during key
flow and tide stages (e.g., spring and neap tide series; high and low tide stages; and high, average, and
low flow conditions) at previously sampled stations in the mainstem and Ebey Slough, as well as
expansion into previously omitted sections of Steamboat, Union, and Ebey Sloughs. Additionally, we
propose installation of continuous water level, salinity, and temperature sensors at previously monitored
stations in Ebey Slough as well as additional sensors at key hydrological bifurcations and gradients (as
delineated from previous water column profile data) within the system. In addition to improving our
understanding of existing physical and biological patterns, and providing baseline and response data for
restoration actions, these hydrological data can be used to refine and expand the temporal and spatial
calibrations for the Finite Volume Coastal Ocean Model (FVCOM) that was developed for the
Snohomish estuary in 2006 (Yang and Khangaonkar 2008). In combination with a larger scale
circulation model of Puget Sound that is capable of nesting the Snohomish River estuary FVCOM
model (Khangaonkar et al. 2011), temporal and spatial expansions of hydrological calibration data can
be used to evaluate longer term estuary responses to forcing from Puget Sound and potential climate
change scenarios. Future hydrologic loading scenarios using IPCC A1b and B2 emissions scenarios
downscaled to the Pacific Northwest can be used in combination with the nested Snohomish River
estuary FVCOM model to assess the sensitivity of hydrodynamic and water quality parameters to
climate change stressors. For example, these scenarios could be used to evaluate the impacts of potential
reductions in summer flows coupled with sea level rise due to climate change, which could result in
upstream propagation of salinity and loss of brackish tidal marsh habitat.
4) Sediment Dynamics. A key determinant of coastal wetland vulnerability to sea level rise (SLR) is
whether the surface elevation in the intertidal zone can keep pace with sea level rise. It is crucial to
quantify the vertical movement of coastal wetland surfaces, which will help identify sites under threat
from SLR, thus informing conservation, mitigation and adaptation. The USGS is establishing a network
of coastal marsh monitoring sites in the Pacific Northwest and California during 2012 and 2013 to assess
the vulnerability of these coastal wetlands to changes in sea -level rise (Guntenspergen personal
communication). Rod Surface Elevation Table - Marker Horizon method (RSET and SET-MH) is the
method used. Because of funding limitations only one site has so far been established in Puget Sound -
Nisqually National Wildlife Refuge in the southern portion of the Sound. In addition to the USGS effort,
researchers at Western Washington University have SET sites in northern Puget Sound (Kairis and
Rybczyk 2010). Establishment of the SET/MH sites at Qwuloot and across the Snohomish River Estuary
would provide valuable additional information not only for the Snohomish, but for these larger efforts
and increase the generality of the results. Previous studies have revealed high across-site variability in
the processes that contribute to surface elevation change, making assumptions of uniformity in processes
across wetlands inappropriate. This highlights the need for site-specific data across a network of sites
that accurately represent local processes in order to evaluate the outcome of different sea level rise
scenarios.
DATA QUALITY OBJECTIVES AND MEASUREMENTS CRITERIA Data Quality Objectives (DQOs) are the quantitative and qualitative terms field personnel and project
managers use to describe how good the data needs to be in order to meet the project’s objectives. DQOs
for measurement data (referred to here as data quality indicators) are precision, accuracy,
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representativeness, completeness, comparability, and measurement range. The overall QA objective for
analytical data is to ensure that data of known and acceptable quality are provided. To achieve this goal,
data must be reviewed for 1) representativeness, 2) comparability, 3) precision, 4) accuracy (or bias),
and 5) completeness. Precision, accuracy, completeness, sample representativeness and data
comparability are necessary attributes to ensure that analytical data are reliable, scientifically sound, and
legally defensible.
Representativeness is the degree to which data from the project accurately represent a particular
characteristic of the environmental matrix which is being tested. Our study design helps insure
representativeness by stratifying both random and index sites across the estuarine landscape as a
function of channel length and connectivity. Index sites are distributed across the major estuarine
zones/habitat types (Cowardin et al. 1979) and are supplemented by randomly selecting additional sites
within each zone. Our year-round sampling design ensures we have sufficient temporal coverage. Sites
selected to monitor hydrology throughout the system were selected to represent the major transition
areas (e.g. channel bifurcations) as informed by previous data collection and model development
(Khangaonkar et al. 2011). Bird count and sediment dynamics survey designs will incorporate sites
within, and adjacent to, the project and reference sites and represent different habitat types along an
elevation gradient.
Comparability is the measurement of the confidence in comparing the results of one sampling event
with the results of another achieved by using the same matrix, sample location, sampling techniques and
analytical methodologies. Our survey design employs index sites to be repeatedly sampled, and our
twice monthly sampling program ensures we sample on a similar tides series to reduce sources of
temporal variation.
Accuracy and Precision: Accuracy is the degree to which samples reflect the true value of the system,
and bias can be measured as a difference from the true estimate. Precision is the degree to which
separate measurements agree. While it is difficult to evaluate accuracy and precision for some measures
because of tradeoffs with representative and completeness, we will use methods that have been cross-
validated with similar projects throughout Puget Sound and will operate and maintain technical
equipment according to manufacturer’s standards as outlined in the Quality Control section below.
Completeness: Our stratified random survey design which incorporates index sites strives for
completeness by sampling throughout the year across several environmental gradients representative of
the system.
SPECIAL TRAINING AND CERTIFICATION
The project team has extensive experience working in the project area using collection methods as
outlined in the proposed study. All primary field personnel have current cpr and first aid certifications,
small boat handling training, and have completed all health and safety requirements as identified by their
respective employers.
Todd Zackey is the Marine and Nearshore Program Manager for the Tulalip Tribes Natural Resources
Department and has been working for the Tribes for over a decade. He manages the GIS (Geographic
Information Systems) and Nearshore Programs for the department and is responsible for mapping,
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monitoring, assessing, and protecting the Tribes’ nearshore and marine resources on and off the
reservation. Todd has conducted and been involved in a variety of monitoring and research projects in
the nearshore areas of the Whidbey Basin including water quality monitoring, mapping of intertidal
habitat, and studying juvenile salmon utilization of the Snohomish River estuary, pocket estuaries, and
small coastal streams. Todd is a member of the San Juan Salmon Technical Advisory Group, and Co-
Chair of the Island County Salmon Technical Advisory Group.
Joshua Kubo is the Salmon Recovery Scientist for the Tulalip Tribes Natural and Cultural Resources
Department.
Dr. Casimir Rice has been studying anthropogenic impacts in Puget Sound at NWFSC since 1990 and
has extensive experience monitoring and evaluating nearshore marine and estuarine ecosystems. He
currently is managing monitoring efforts in the Snohomish estuary and has led the effort to develop an
adaptive monitoring plan for the Qwuloolt restoration project.
Joshua Chamberlin is a fisheries biologist at NWFSC with 9 years of experience studying the ecology
of nearshore marine and estuarine ecosystems in Puget Sound. He has been involved in monitoring
efforts in the Snohomish River estuary since 2005 and currently coordinates field collection activities for
the Qwuloolt restoration project and Snohomish system-wide monitoring effort.
Jason Hall is fisheries biologist at NWFSC with 11 years experience in fisheries research in the Puget
Sound. He began working in the Snohomish River estuary in 2009 and has been involved in fish and
hydrology monitoring, RTK GPS surveys, and GIS analyses associated with the Snohomish system-
wide monitoring effort.
Jason Schilling is a wildlife biologist with the Tulalip Tribes.
DOCUMENTS AND RECORDS Complete documentation for field sampling teams may include but is not limited to the following forms:
Site sampling data records
Sample container labels
Field sampling log books
Data collected for fish sampling and hydrology will be electronically entered into a Filemaker Pro
database. All samples will be referenced using a numbering system allowing cross-reference to site and
date sampled. Data will be stored electronically at the NWFSC and with the Tulalip Tribe. In the event
of computer malfunction, paper datasheets will be available for data entry. Field Teams will maintain
field notes and all documents and data collected will be assessed after each sampling to maintain proper
QA/QC measures. Individual samples taken for further processing at the NWFSC lab will be given
unique sample numbers and individual labels that identify both individual and site/sampling parameters
will be attached to all samples.
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Bird count and sediment dynamics data will be recorded in field logs and entered into a digital format
upon completion of each sampling event. Digital copies will be distributed among the PI, project
manager, and contracted staff.
The PI will be responsible for sharing copies of the final QAPP with all members of the research team.
4. DATA GENERATION AND ACQUISITION
SAMPLING PROCESS DESIGN (Experimental Design)
Study Site Selection
Sites selection and sample design were created using several different criteria and existing datasets
depending on the type of sample collection or task. Below are the procedures as they pertain to each
component of data collection:
1) Fish: A combination of index and random monitoring stations were used to monitor fish within
the Snohomish River estuary. Index site locations were based on previously sampled index sites
which were known to be fishable with a beach seine. Random monitoring stations were
randomly selected from a GIS derived polyline of fishable shorelines. This polyline layer was
derived from aerial RGB orthophotos taken during a 2009 LiDAR survey of the Snohomish
River estuary during a low tide. The polyline layer was further classified by functional habitat
zones and allocation of random sites drawn per sampling event was based on the relative
proportions of calculated shoreline within each habitat zone. A minimum distance of separation
between points of 150 m was enforced for all random draws within each sampling event.
2) Bird Counts: See sampling methodology below...
3) Hydrology: Vertical water profile sample stations were established from the estuary mouth at
Jetty Island to the town of Snohomish within the main river and distributary network; including
the mainstem river, Ebey Slough, Steamboat Slough, and Union Slough (where accessible by
boat at high and low tide). The sample stations were distributed throughout the sample area with
approximately 1 km spacing between stations. Continuous water level logger stations were
established at the main bifurcations of the system and at key transitional hydrology zones as
identified by previous monitoring and modeling efforts.
4) Sediment Dynamics: Sites selected for monitoring sediment dynamics will be chosen to
represent various habitat types along an elevation gradient both within, and adjacent to, the
project site. Consultation with USGS scientists will occur in early 2013 to finalize the sampling
plan which will be submitted for review and approval.
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SAMPLING METHODOLOGY
Fish
Beach seines will be used to sample "mainstem" habitats throughout the Snohomish River estuary.
Sampling will occur twice per month between February and September and then once a month between
October and January. We will use standard Puget Sound beach seine measuring 36m in length and 1.8m
(wings) to 3.0m (bag) in height made of 3mm (wings) to 1.5mm (bag) knot-less nylon mesh. The seine
is set in a semi-circle from upstream to downstream with one end held on shore and the other set from
the boat. Once the net is set, both sides are pulled in together with 3 or 4 individuals until the entire
catch is consolidated in the bag (i.e. center of the net). Fish are immediately removed from the bag and
placed into 5-gallon buckets with fresh water from the site where they are held for processing. Up to 25
individuals of each species will be measured to fork length where applicable and to total length when no
fork is present. Any additional individuals of each species will be counted. Up to 10 each, marked and
unmarked, juvenile Chinook salmon will be taken from each zone, as described, above for further
processing. Any individuals that appear unduly stressed or dead upon retrieval of the net will be selected
before healthy individuals are sacrificed. In addition, surface water temperature and salinity will be
measured and recorded at each site using a YSI Professional Plus Mulitparameter meter.
Bird Counts
Breeding-season point count surveys will be conducted to account for focal marsh bird species (Table 1)
and all other birds. Surveys for these species will be conducted following Standardized North American
Marsh Bird Monitoring Protocol (Conway 2011) and A Unified Strategy for Monitoring Changes in
Abundance of Terrestrial Birds Associated with North American Tidal Marshes (Conway and Droege
2006). The project area and the reference site will be divided into 16-hectare or 400 meter grids. Point-
count surveys will be placed within the center of each grid. Surveys will begin 30 minutes prior to
sunrise and up to three hours after sunrise. Surveys will consist of three parts: 1) a 5-minute passive
listening period during which all species seen or heard are detected 2) a 5-minute passive listening
period during which focal marsh bird detections and estimated distances are recorded 3) playback
recordings of secretive marsh birds, including Sora, Virginia rail, American bittern, American coot, and
pied-billed grebe. Digital vocalizations of each secretive species will be broadcast for 30 seconds,
followed by 30 seconds of silence. We will survey each marsh (references and Qwuloolt) every other
month during the non-breeding season (July 1st – May 14
th) and three times over the course of the
breeding season (May 15st - June 30
th). Surveys will occur during the first week following high tide
because of increased detectability of salt marsh passerines that occurs at this time. Time permitting, we
will also sample at low tides. In addition to using the standardized methods for recording marsh bird use,
we will collect the following information at each point: Tidal stage, moon phase, water depth, salinity,
and current or ongoing management actions at the site.
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Table 1. Focal marsh bird species for bird count surveys, Snohomish River estuary, Marysville, WA, USA.
Focal species
green heron (Butorides virescens)
great blue heron (Ardea herodias)
northern harrier (Circus cyaneus)
osprey (Pandion haliaetus)
Sora (Porzana carolina)
Virginia rail (Rallus limicola)
American bittern (Botaurus lentiginosus)
Wilson’s Snipe (Gallinago delicata)
American coot (Fulica americana)
pied-billed grebe (Podilymbus podiceps)
Hydrology
Water column sampling using Seabird
19plusV2 CTD profilers during key
flow and tide stages (e.g., spring and
neap tide series; high and low tide
stages; and high, average, and low flow
conditions) at previously sampled
stations in the mainstem and Ebey
Slough, as well as expansion into
previously omitted sections of
Steamboat, Union, and Ebey Sloughs
(Figure 1). Once on site, CTD units
will be deployed alongside the boat and
lowered at approximately 1m/sec until
the unit contacts the bottom and
retrieved at the same speed. Data will
be downloaded after each sampling
event and stored in digital format in
multiple locations.
Temperature, salinity, and water level
will be continuously monitored at 12
sites throughout the estuary using
Solinst Model 3001 LTC Levelogger
Junior dataloggers. Loggers will be
placed in 3” PVC well pipe and
secured to existing pilings at each site.
The top of each well will be surveyed
using real-time kinematic (RTK) GPS
to provide for corrections/comparisons
Figure 1. Locations for CTD casts (red dots) and continuous
temperature, salinity, and water level loggers (green dots) in the
Snohomish River estuary.
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among sites. Data will be recorded at 10 minute intervals and individual loggers will be downloaded and
recalibrated every 60 days.
Sediment Dynamics
The RSET and SET-MH developed by the USGS fills the critical need for precise and easily replicable
local surface elevation change measurements. The RSET-MH was developed to quantify the surface and
shallow subsurface processes contributing to wetland surface elevation change. An RSET involves very
simple technology; it consists of a benchmark rod driven through the soil profile to resistance (typically
10-25 m depth), and a portable horizontal arm that is attached at a fixed point to measure the distance to
the substrate surface, using vertical pins. Installation, maintenance and data collection require minor
training.
Total surface height measurements have confidence intervals of ±1.3 mm, a figure well within the
annual rate of eustatic SLR. RSETs are the only tool that can capture surface elevation change with this
precision. RSET data are usually complemented with shallow accretionary monitoring using artificial
soil marker horizons (MH) typically made of feldspar, which simultaneously quantify rates of vertical
surface accretion (i.e., sediment deposition). The complete RSET MH setup provides net surface
elevation change above the benchmark depth; moreover, as it has been repeatedly shown that vertical
accretion is not a valid substitute for surface elevation change, the complete setup is necessary to
identify the contribution of surface and shallow subsurface processes to surface elevation change at a
specific site. Repeated measurements allow chronicling of net surface elevation change, which can be
integrated with region-specific relative SLR (tide gauge data) to determine whether the surface elevation
has kept pace with SLR over that time period.
RSET data can inform assessments of wetland vulnerability to SLR and bolster SLR wetland models to
support science-based policy. RSET networks will contribute to increased confidence in identifying
coastal wetland vulnerability, to more informed science based policy, and to improved accuracy and
efficiency of coastal conservation, mitigation, and adaptation responses.
The USGS has established protocols for the installation of the RSET/MH technology and will provide
training sessions for this effort. USGS personnel will be in the field during installation to ensure quality
control. USGS also has established protocols and templates for data collection and analysis and will
provide these templates and training for this effort (Boumans 1993). USGS and WWU will provide this
technical assistance as an in-kind effort for this project.
SAMPLE HANDLING AND CUSTODY All fish samples collected during beach seining will be immediately placed on ice and taken back to the
NOAA NWFSC Mukilteo Research station for processing and archival by contracted NOAA staff.
Individuals collected at a given site will be labeled accordingly with site information, date of collection,
and the total number and species of individuals included in each sample. Once returned to the lab each
individual will be given a unique sample number before being measured and weighed. After initial
measurements otoliths and stomachs will be extracted and archived for later analysis. Otoliths will be
removed and placed dry into 20mL scintillation vials labeled with sample number, site name, date of
collection and individual lengths and weights. Individual stomachs will be removed and placed into
20mL scintillation vials and fixed with a neutral buffered formalin solution for preservation of gut
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contents until analysis. Stomach vials will be labeled with sample number, site name, date of collection
and individual lengths and weights. Once otoliths and stomachs are removed from each sample,
carcasses will be placed in individual Ziploc bags labeled with sample number, site name, date of
collection and individual lengths and weights and immediately frozen and archived for stable isotope or
genetic analysis. All sample handling, transporting, and processing will be performed by field collection
staff responsible for collecting the respective samples.
ANALYTICAL METHODS Fish abundance and bird count data will be assembled as a site x species matrix and analyzed using
multivariate statistical techniques with the PRIMER statistical package (Clarke 1993). Abundance and
count data will likely be transformed to reduce potential bias caused by extremely large values. All
analyses will be conducted on resemblance matrices constructed using the Bray-Curtis similarity
coefficient. Species richness for bird count data will be computed using SPECRICH, a program that
computes total number of species from empirical species abundance distribution data, based on methods
described by Burnham and Overton (1979). Detection probability will be calculated for all focal marsh bird
species using the program DISTANCE.
QUALITY CONTROL All methods for data collection will be cross-validated with referenced sources. In addition all field
instruments will be calibrated throughout the sampling period according to the methods outlined by
specific manufacturers. Comments will also be added to database describing specific deviations in
quality control. During data analysis, outliers will be defined as data points surpassing 95% confidence
intervals. Outliers will not be discarded, but will be flagged for further consideration.
INSTRUMENT/EQUIPMENT TESTING, INSPECTION AND MAINTENANCE
Field Instruments
Field instruments that will be used to monitor system-wide hydrology (temperature, salinity, water level)
will be maintained in accordance with the manufacturer’s manual. Field instrument operation and
maintenance logbooks will be maintained for the project. Field instruments will be tested annually by
manufacturer.
INSTRUMENT/EQUIPMENT CALIBRATION AND FREQUENCY
Field Instruments
Field instruments will be calibrated before deployment and on site after every download event (every 2
months) in accordance with methods recommended by the manufacturer using the proprietary software.
Records of calibration will be stored digitally on field computers after every calibration event.
INSPECTION/ACCEPTANCE OF CONSUMABLE SUPPLIES Consumable supplies in the field and laboratory will consist of sample bags/containers, sampling
supplies, reagents and SRM’s. The quality of SRM’s and other consumable supplies such as sample
bottles used for this project should be documented by the supplier and certificates should be available to
EPA on request.
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NON-DIRECT MEASUREMENTS (SECONDARY DATA) All secondary data pertains to GIS-related work related to survey design. Site selection for fish sampling
and hydrology was based on secondary data as outlined in Table 3.
Table 3. Secondary data used in survey design.
Data Source Layer URL
LiDAR DEM and
RGB Orthophotos
Watershed
Sciences
Multiple http://pugetsoundlidar.org/
Hyrdography
1:100,000
NHD NHDplus http://www.horizon-systems.com/nhdplus/
DATA MANAGEMENT Sample collections for each sample type at each site will be recorded in Filemaker Pro electronic
databases, and samples will be cross-referenced within this database by site and date. Data will be
handled by different people according to Table 4. All data will be backed up immediately after
downloading from instruments or after acquisition.
Table 4. Data management strategy for each type of measurement
Metric Procedure Person responsible
Hydrology Sample acquisition, data download,
archiving, analysis
Jason Hall
Fish
Sample acquisition
Data acquisition, archiving, analysis
Casey Rice, Joshua
Chamberlin
Birds Sample acquisition
Data acquisition, archiving, analysis
Jason Schilling
Sediment Dynamics
Sample acquisition
Data acquisition, archiving, analysis
Todd Zackey
5. ASSESSMENTS AND RESPONSE ACTIONS
Quality assurance (QA) assessments will be conducted during the course of this project. Given the short
time frame, only one assessment is planned before completion of the project. The quality assurance
assessment performed during this project may include the following:
1) Oversight of field sampling activities.
2) Oversight of sample handling and chain-of-custody procedures.
Quality assurance assessments (Technical System Audit or Quality System Review) will be conducted
by the EPA Region 10 Puget Sound Team including the QA Manager or designee. If, for any reason, the
schedules or procedures above cannot be followed, the project manager shall complete Attachment 1 –
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Sample Alteration Form (SAF). The SAF should be reviewed and approved by the QAO. The
laboratory should be given a copy of the QAO approved SAF for reference and project file.
Corrective action procedures that might be implemented from the assessments or detection of
problems/obstacles encountered during project implementations will be resolved and documented in
Attachment 2 – Corrective Action Form.
6. DATA VALIDATION AND USABILITY VERIFICATION AND VALIDATION METHODS Data Verification
Data verification is a consistent and systematic process that determines whether the data have been
collected in accordance with the QAPP. Data verification will include a review of the findings of all QA
assessment activities including:
1) Field Collection Procedures
2) Sample Labeling Methods
3) Chain-of-Custody Procedures
If any deviations are identified, the potential impact of those deviations on the reliability of the data will
be assessed, and the information will be provided to the project manager.
Data Validation
Data validation is an evaluation of the technical usability of the verified data with respect to the planned
objectives of the project. Data validation consists of evaluation of all individual samples collected and
analyzed to determine if the results are within acceptable limits. Quantitative or qualitative limits of
acceptability are defined for precision, accuracy, representativeness, comparability, and completeness.
RECONCILIATION WITH USER REQUIREMENTS
Anticipated Outputs and Outcomes
Outputs. The proposed work will assess the existing condition of several biotic and abiotic components
of the estuarine ecosystem as a response to ongoing restoration efforts and climate change. Our goal is to
monitor the present condition of the estuary as it relates to species composition and abundance (fish &
birds), hydrology, and sediment dynamics and to synthesize the data and compare the results to pre-
restoration conditions. System-wide monitoring of fish use and hydrology will enable us to determine
patterns of spatial and temporal variation throughout the estuary and help provide context and inform
future management decisions. Bird counts and sediment dynamics within the project site and at adjacent
reference sites will provide critical information on pre-restoration conditions and help to create a
hypothesized trajectory for conditions as they respond to restoration.
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Outcomes. These outputs relate to several important short-term and long-term outcomes. Our results will
feed directly into the comprehensive adaptive management plan developed for the Qwuloolt restoration
project (Rice et al. 2011). Continued fish sampling and hydrology data collection, expanded bird counts,
and additional sediment dynamics data will supplement the existing pre-breach dataset and ensure
Results from the system-wide monitoring component of the proposed work will not only provide context
for past and present restoration projects (Qwuloolt, Union Slough) but may also be used to inform future
management decisions regarding restoration projects by providing critical data for prioritizing future
sites throughout the estuary.
7. REFERENCES
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monitoring.
Rowse, M., and K. L. Fresh. 2003. Juvenile salmonid utilization of the Snohomish River estuary, Puget
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Wentworth-Davis, T. 2011. Current and Future Bird Use of the Project Area. Appendix D in Smith
Island Restoration Project. Snohomish County Department of Public Works, Everett, WA.
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Collection (ERDC TN-WRAP-00-02), U.S. Army Engineer Research and Development Center,
Vicksburg, MS. www.wes.army.mil/el/wrap
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circulation in a braided estuary. Journal of Coastal Research. 171-180.