11th Biennial Bay-Delta Science Conference

BUILDING RESILIENCE THROUGH DIVERSITY IN SCIENCE
April 6–9, 2021

Virtual#BDSC2021

ORAL
ABSTRACTS2021 Bay-Delta Science Conference: Oral Abstracts
Table of Contents

Information ................................................................................................................... 2
Navigating this booklet ............................................................................................. 2
Tuesday Scheduled Sessions ..................................................................................... 3
Smelt Science for Management ............................................................................... 3
Physical Processes: Shaping the Bay-Delta ............................................................ 6
Food Web Foundations .......................................................................................... 10
New Habitat, New Science: Advances in Wetland Restoration .............................. 13
IEP Special Session: The Value of Long-term Biological Monitoring in the San
Francisco Estuary .................................................................................................. 17
Special Featured Session: Raising Awareness and Shifting the Paradigm:
Fostering Diversity, Inclusion and Equity in the Bay-Delta System (Featured Special
Session) ................................................................................................................. 21
Wednesday Scheduled Sessions .............................................................................. 24
Salmon Science for Management .......................................................................... 24
Global Climate Change at the Estuary Scale ......................................................... 28
Getting into the Weeds: Aquatic Vegetation ........................................................... 32
Social Science and Human Dimensions ................................................................ 36
IEP Session: Success at Different Trophic Levels: Gaining Insight from Nutrients toOtoliths ................................................................................................................... 39
Thursday Scheduled Sessions .................................................................................. 43
Advances in Understanding Thermal Effects on Salmon and TemperatureManagement for Salmon in the Central Valley ....................................................... 43
Flood and Other Hazards ....................................................................................... 47
Multiple Perspectives on Sediment in the Bay and Delta: Supply, Transport, andSink in a Complex Environment ............................................................................. 51
Linkages Among Physics, Chemistry, and Biology in the Sacramento Deep Water
Ship Channel.......................................................................................................... 54
IEP Session: Fish Habitat Spatial Arrangements: Experience from Across theEstuary and Beyond ............................................................................................... 58
Friday Scheduled Sessions ....................................................................................... 62
Integrating Data and Population Models: Understanding Factors that AffectSensitive Fish Populations ..................................................................................... 62
Contaminants and Toxins ...................................................................................... 65

Information: Navigating this booklet
Birds and Their Habitats in the Bay-Delta .............................................................. 69
Greenhouse Gas Exchange and Wetland Accretion in the Bay-Delta System:
Implications for Science, Policy, and Management in the Sacramento-San Joaquin
Delta, Suisun Marsh, and San Francisco Bay ........................................................ 73
IEP Session: Using Aquatic Surveys for Estimation and Communication: Bias,
Quantification, and Display .................................................................................... 77
On-demand talks ....................................................................................................... 81
An Update on Salt Marsh Harvest Mouse Ecology and Future Perspectives(SMHM) .................................................................................................................. 81
Fish Biology (FB).................................................................................................... 85
Food Web Linkages (FWL) .................................................................................... 86
Franks Tract Reimagined: Integrating Recreation, Navigation, Ecology and Water
Quality for Landscape Redesign in the Heart of the Delta (FT) .............................. 88
Monitoring (M) ........................................................................................................ 91
Salmon Biology (SB) .............................................................................................. 94
Smelt Biology (OB)................................................................................................. 97
Water Quality (WQ) ................................................................................................ 99
Wetlands and Floodplains (WF) ........................................................................... 101

Information
Presenting authors are underlined. Talks included in the Interagency Ecological
Program (IEP) track are indicated by "(*IEP)."

Navigating this booklet
Scheduled Sessions are organized by day, room, and talk order (just as they appear in
the program). On-demand talks are included in the final section, listed by theme thenalphabetically by first author. The number-letter key (e.g., 001-SMHM) should help you
navigate to the correct on-demand talk on the conference website.

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Tuesday Scheduled Sessions: Smelt Science for Management

Tuesday Scheduled Sessions
Smelt Science for Management
Responses of Wild Delta Smelt to Climate Variation
Levi Lewis1, Malte Willmes2 | 3, Christian Denney1, Wilson Xieu1, Bruce Hammock4,
Swee Teh4, Andrew Schultz5, Nann Fangue1, James Hobbs1 | 6
1Wildlife, Fish, and Conservation Biology, University of California, Davis, 2Institute ofMarine Sciences, University of California, Santa Cruz, 3NOAA Southwest Fisheries
Science Center, Santa Cruz, 4School of Veterinary Medicine, University of California,
Davis, 5U.S. Bureau of Reclamation, Bay-Delta Office, 6California Department of Fish
and Wildlife
Presenting author email: lslewis@ucdavis.edu
Climate models, laboratory experiments, and distribution data all indicate that Delta
Smelt are likely to be negatively impacted by future changes in California’s climate. In
order to prevent the extinction of this critically endangered species, our society needs toquickly and significantly invest in novel and effective conservation approaches. The
severity of future impacts on the wild population, however, remains uncertain, possibly
limiting the political will for expediency in addressing this ecological crisis. Using otolithbased approaches, we examined how the growth, phenology, and life history of Wild
Delta Smelt respond to variation in environmental conditions. Our results examining wild
fish confirm previous findings and indicate that population dynamics of wild Delta Smelt
could be even more sensitive to climate change than previously thought. Results of thiswork can be used to forecast how different climate scenarios are likely to impact theremnant Delta Smelt population and, perhaps, to also help identify and justify effective
interventions.
Quantifying the Evolutionary Potential for Delta Smelt Persistence in a Warming
HabitatJoanna Griffiths1 | 2, Will Mulvaney3, Amanda Finger4, Brittany Davis5, Melinda
Baerwald5, Tien-Chieh Hung3, Nann Fangue2, Andrew Whitehead1
1Department of Environmental Toxicology, University of California, Davis, 2Departmentof Wildlife, Fish, and Conservation Biology, University of California, Davis, 3Fish
Conservation and Culture Laboratory, University of California, Davis, 4Department of
Animal Science, University of California, Davis, 5California Department of Water
Resources
Presenting author email: jsgriffiths@ucdavis.edu

Long-term persistence of the endangered Delta Smelt (Hypomesus transpacificus) will
depend, in part, on whether the species harbors the genetic variation necessary toadapt to changing environmental conditions such as warm temperatures. Temperatures3

Tuesday Scheduled Sessions: Smelt Science for Managementin the San Francisco Bay-Delta are increasing and extreme temperature spikes are
becoming more common. The availability of additive genetic variation for traits that
affect fitness directly determines the ability to evolve; however, nothing is currently
known about the presence of genetic variation for resistance to elevated temperature in
Delta Smelt. We performed a quantitative genetics experiment to test whether Delta
Smelt harbor the necessary genetic variation for adaptation to elevated temperatures.
We established crosses between wild and hatchery-reared (domesticated) fish andraised siblings from each family in both an optimal temperature (15 ) and an elevatedtemperature (18 ). We estimated thermal tolerance and genotyped 1,000 fish raised inthese two thermal environments. Genetic variation for thermal tolerance will indicate
whether the species has the capacity to evolve adaptations to warming temperatures inthe Delta. Our experiments will also reveal whether domesticated and wild fish differ intheir thermal tolerance abilities. Together, this information can be used to manage therefuge population and inform supplementation by maintaining genetic variation that may
be crucial for resilience in a changing Delta.
An Individual-Based Model of Delta Smelt Population Dynamics: A Versatile Tool
for Life-Cycle Analyses of Management Actions
Kenneth Rose1, Wim Kimmerer2, Derek Hilts3, Li-Ming He3, Matt Nobriga3
1University of Maryland Center for Environmental Science, 2Estuary & Ocean Science

Center, San Francisco State University, 3U.S. Fish and Wildlife Service

Presenting author email: krose@umces.edu
Tools to evaluate the effects of stressors and natural variation on Delta smelt at the
population level are needed for the design of effective conservation and recovery
actions. Individual-based life-cycle models are well suited to incorporating spatial
information and for simulating the complex interactions between the transport andmovement of individuals and dynamic environmental conditions. We describe a Delta
Smelt individual-based model (DSIBM) that follows the daily reproduction, growth,survival, and movement of individuals from eggs through adults within the same spatial
grid as that used by the DSM2 hydrodynamic model. An earlier version of the DSIBM
was developed by Rose, Kimmerer, and others more than eight years ago. We recently
updated the model by incorporating new Delta Smelt biology and adding new features
for exploratory analyses. These advanced features include: tightly coupling the IBM to
environmental conditions generated from DSM2, expanding the historical years
simulated to 1990-2012, adding capability to use CALSIM output to drive 82-year
simulations under synthetic hydrology, and adding an option to examine effects ofsupplementation. We have also demonstrated two analyses often not included incomplex IBMs and are of particular use to management: an optimization algorithm tohelp examine trade-offs between alternative restoration actions, and a computationallyefficient Monte Carlo uncertainty analysis leading to a statistical meta-model of the IBM
dynamics that is solved very fast. We briefly describe these advances with selected
example analyses. The updated version of the DSIBM is undergoing calibration and4Tuesday Scheduled Sessions: Smelt Science for Management
validation to establish model skill and the results will inform how to appropriatelyinterpret model results for alternative scenarios. The updated and expanded model
provides a quantitative tool for providing mechanistic explanations for Delta Smelt
population responses to variation in environmental conditions and multiple stressors,and for comparative analysis of the effectiveness of alternative management actions.
How Can Isotopes Inform Understanding of Life History Diversity in Wild Longfin
Smelt
Christian Denney1, Levi Lewis1, Malte Willmes2 | 3, James Hobbs1 | 4
1Wildlife, Fish, and Conservation Biology, University of California, Davis, 2Institute forMarine Sciences, University of California, Santa Cruz, 3NOAA Southwest Fisheries
Science Center, Santa Cruz, 4California Department of Fish and Wildlife
Presenting author email: ctdenney@ucdavis.edu

The Longfin Smelt (Spirinchus thaleichthys) is an estuarine species that is distributed up
and down the western coast of North America. The population in the San Francisco
Estuary, which represents the southernmost extent of the species, has seen precipitous
declines due to water diversions, climate change, and other human impacts. To better
protect and manage this population, it is important to have an improved understandingof its life history and ontogeny. However, Longfin Smelt are too small for traditional
tracking technologies such as acoustic tags. One potential solution is the use of otolithgeochemical analysis. Stable isotopes of elements in the water are incorporated into thehard parts of the fish as they grow, and potentially represent a history of theenvironment the fish experienced throughout its life. Here we demonstrate the use ofstrontium and oxygen isotopes to estimate the changes in salinity that individual fish
have experienced during their lives, as a proxy for movement throughout the estuary.
Additionally, we discuss the differences between the use of each isotope, and how they
can complement each other with greater specificity at high and low salinities. We findthat stable isotopes reveal a diversity of life history strategies and that different groups
of individuals are utilizing different areas of the estuary throughout their lives. Longfin
Smelt appeared to hatch and rear in fresh to brackish water, exhibiting the use of
several natal habitats. Timing of movement into more brackish water was relatively
consistent among groups. This life history diversity represents a potential source of
resiliency but also complicates management actions.
Estimation of Longfin Smelt Hatching Distribution, Abundance and Entrainment
using Three-Dimensional Hydrodynamic and Particle-Tracking Models
Edward Gross1, Wim Kimmerer2, Josh Korman3, Levi Lewis4, Scott Burdick1,
Lenny Grimaldo55Tuesday Scheduled Sessions: Physical Processes: Shaping the Bay-Delta
1Resource Management Associates, 2Estuary & Ocean Science Center, San FranciscoState University, 3Ecometric Research, 4Department of Wildlife, Fish and Conservation
Biology, University of California, Davis, 5California Department of Water Resources
Presenting author email: edward.s.gross@gmail.com

The distribution of larval fishes in estuaries is influenced by where they hatch and their
movements after hatching. In the San Francisco Estuary, the threatened longfin smelt(Spirinchus thaleichthys) spawn adhesive eggs in shallow, fresh to brackish water.
Attached eggs hatch and the larvae disperse seaward toward higher-salinity water.
Actual locations of spawning are unknown, and cannot be inferred from distributions oflarvae because intense tidal mixing erases the history of movement. Humaninterventions such as manipulations and diversions of freshwater flow may contribute tothe ongoing decline of this species, and these effects depend on where the fish hatch.
We combined connectivity estimates from hydrodynamic and particle-tracking modelingwith trawl data in a Bayesian model to estimate the location and timing of hatching, as
well as natural mortality of larvae and losses to freshwater diversions. Longfin smelt
were estimated to have hatched further seaward than previously believed; estimateddiversion losses were small compared to natural mortality, and therefore pose only aminor risk to the population. Similar methods could be applied in other estuarine andcoastal systems where strong mixing reduces the ability of simpler models to predictspawning location and larval movement.

Physical Processes: Shaping the Bay-Delta
A Systematic Evaluation of Empirical X2 Models Published Over the Past 25
Years
John Rath1, Paul Hutton1, Eli Ateljevich2, Sujoy Roy1
1Tetra Tech, Lafayette, 2California Department of Water Resources

Presenting author email: john.rath@tetratech.com
Problem Statement: This work surveys the performance of several empirical models
that were developed over the past 25 years to relate freshwater flow and salinity in the
San Francisco Estuary. The estuary’s salinity regime, broadly regulated to meet urban,
agricultural and ecosystem beneficial uses, is managed in spring and certain fall months
to meet ecosystem objectives by controlling the 2 parts per thousand bottom salinity
isohaline position (referred to as X2). Multiple empirical models have been published forX2 since 1995, using different data and assumptions. Our goal was to compare theirperformance in a systematic manner using the same data for calibration and testing.
Approach: Five previously developed models, all configured to relate freshwater flow to
X2 position in the estuary, were recalibrated to a common data set and tested for
accuracy, mean and transient behavior using standard statistical approaches.
Results: Model performance was observed to vary with hydrology, year and season,and in some cases exhibited unique limitations due to mathematical
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Tuesday Scheduled Sessions: Physical Processes: Shaping the Bay-Delta
formulation. However, no single model was found to be consistently superior across awide range of tests and applications. One test revealed that the models performed
similarly when recalibrated to a uniformly perturbed input time series. Thus, while themodels may be used to identify anomalies or seasonal biases, their use as inverse
models to infer freshwater outflow through the estuary from salinity observations is notexpected to improve upon the accuracy of existing outflow estimates.
Conclusions/Relevance: This is the first simultaneous evaluation of the different
empirical X2 models published for the San Francisco Estuary over the past 25 years.
No model was found to be uniformly superior, and this work suggests that, for analyses
spanning a long hydrologic record, an ensemble approach may be preferable for
exploiting individual model strengths.
Hydrodynamic Metrics to Evaluate Tidal Marsh Dynamics in the Sacramento-San
Joaquin Delta
Paul Stumpner1, Stephen Andrews2, Matthew Young1, Jon Burau1
1U.S. Geological Survey, 2Resource Management Associates

Presenting author email: pstump@usgs.gov
The most ubiquitous landscape feature in the historic Delta were dendritic marsh
systems that periodically, from daily to spring-neap timescales, inundated the marsh
plain. Projects to restore landscapes to tidal marsh systems will provide support for
multiple food web constituents, including detrital and pelagic productivity. We
hypothesize that, with the hydrodynamic metrics developed, phytoplankton production
can be maximized and exported out of tidal marsh systems. Using a combination of fielddata and numerical modeling we demonstrate the utility of length-scale and volume-ratio
metrics to describe where phytoplankton production occurs within tidal marsh systems
and how phytoplankton biomass is exported out of these systems.
On neap tides, phytoplankton production occurs in the regions upstream of the tidal
excursion, because these regions are isolated from exchange at the mouth of thesystem, which creates longer residence time. The regions where higher production is
likely can be predicted by a length-scale ratio, the ratio of the tidal excursion to thechannel length. However, during spring tides, the marsh plain becomes inundated athigh water, significantly increasing the volume of water that exchanges with the system.
Optimal resource exchange from the tidal marsh system to surrounding channels occurs
as phytoplankton from the upper channels is flushed out of the system, and nutrientsare imported to the regions of longer residence time to allow for continued production on
the subsequent neap tide. Accordingly, we show that phytoplankton flux out of thesystem can be reasonably predicted using two metrics: the ratio of tidal prism at tidal
timescales: flood to ebb, and fortnightly timescales: spring tide to neap.
Finally, through the use of numerical modeling, we demonstrate, using thesehydrodynamic metrics, how the flux of phytoplankton out of these systems can be
maximized through changes in marsh elevation and berm height at the channel-marsh
plain interface.
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Tuesday Scheduled Sessions: Physical Processes: Shaping the Bay-Delta

Accurate, High Resolution, Measurements of River Surface Velocity andTurbulence Metrics Over Large Areas in the Sacramento River and Its
Implications for Water Resource Management
Seth Schweitzer1, Edwin (Todd) Cowen1
1DeFrees Hydraulics Laboratory, School of Civil and Environmental Engineering,

Cornell University

Presenting author email: seth.schweitzer@cornell.edu
Measurements of instantaneous water flow velocity, from which turbulence metrics arecalculated, are important for advancing the understanding of river hydrodynamics
beyond fundamentals such as discharge and mean velocity.
However, most velocity measurement methods that can be used in the field are capableof measuring only at a point, or along a transect of the river, but not over a twodimensional area. In addition, commonly used tools such as ADCPs (acoustic Doppler
current profilers) generally require temporal and spatial averaging, and therefore can
not resolve the instantaneous velocity.
We present instantaneous velocity and turbulence metrics measured in the sideboundary layer at two sites on the Sacramento River. The measurements were madeusing IR-QIV (Infrared Quantitative Imaging Velocimetry), a method developed by theauthors in a partnership between Cornell University, DWR Bay-Delta office, and USGS,
that uses images of the river surface collected using a sensitive thermal infrared
camera, and tracks thermal patterns at the surface of the river to calculate the timeresolved instantaneous two-dimensional surface velocity field. IR-QIV is capable ofcalculating the instantaneous velocity at high accuracy and high resolution, in both
space and time (centimeter scale, at rates of several Hz), and over a large area—up to
hundreds of square meters of the river surface.
This type of velocity measurement is uniquely suited to a wide range of applications,
including verification of computational flow models (CFD), and studying fish behavior,e.g., interaction between migrating fish and guidance structures/barriers or flow
diversions.
Monitoring Elevations of Tidal Marshes in San Pablo Bay-Delta: Update on
Surface Elevation Table (SET) Monitoring
Anna Kennedy1, Chase Freeman1, Glenn Guntenspergen2, Karen Thorne1
1U.S. Geological Survey, Western Ecological Research Center, 2U.S. Geological

Survey, Patuxent

Presenting author email: akennedy@usgs.gov
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Tuesday Scheduled Sessions: Physical Processes: Shaping the Bay-Delta
Accelerating sea-level rise, changes in storm frequency and intensity, shifting patterns
in freshwater flow and precipitation will impact marsh habitats and local wildlife
communities. Marsh elevations are a balance among local suspended sediment delivery
to the surface, subsidence, organic matter production, and tidal flooding for verticalaccretion. Monitoring marsh elevation in the San Francisco Bay-Delta, many managers
have questions – Are marshes keeping pace with sea-level rise? And is there enoughsediment for marsh accretion? To better assess stability and elevation building of tidal
marsh elevations over the near and long-term, we have been monitoring a network ofdeep rod Surface Elevation Tables-Marker Horizon (SETs-MH) since 2013 in San Pablo
Bay-Delta, CA. At each marsh site we have water level loggers deployed to assess
trends in water level and inundation relative to elevation change, as well as salinity.
Sites are located across a tidal and salinity gradient from Miner Slough, Browns Island,
Rush Ranch, San Pablo NWR, and Petaluma Marsh. The rate of elevation change hasvaried between sites and between the high and low marsh elevations within each site.
The average elevation change since installation is 26.61 mm/yr at Miner Slough, 6.78mm/yr at Browns Island, 1.85 mm/yr at Browns Island, 4.90 mm/yr at San Pablo NWR,
and 2.61 mm/yr at Petaluma. The current rate of sea-level rise at the San Francisco Bay
Golden Gate tide gauge is ~2 mm/yr, with most of our SET locations keeping pace withsea-level rise. Updated results from water logger will be provided with further insight into
tidal inundation and accretion patterns.
Sediment Transport Modeling Using Artificial Neural Network
Han Sang Kim1, Prabhjot Sandhu1, Minxue He1
1California Department of Water Resources

Presenting author email: hansang.kim@water.ca.gov
The Sacramento-San Joaquin Delta is characterized by an interconnected system ofsloughs, waterways, and a tidal outlet. Such complexity often makes it challenging tomodel the suspended sediment transport within the Delta using process-based
approaches (e.g., numerical models), because the mechanisms governing sedimenttransport are not yet fully understood. As a complementary tool, a machine learningmodel was developed. Employing the Long Short-Term Memory (LSTM) Networks,
which are a type of Artificial Neural Networks (ANN), the model can predict thesuspended sediment concentration (SSC) by treating the unknown as a missing piece ina recognized pattern, rather than relying on the governing equations behind the physics.
To train the model, historical records of flow and SSC at various locations within the
Delta were used. The study period was water years 2011 through 2016, but the training
period (i.e., range of observed data used to train the model) was varied to assess themodel’s sensitivity to the inputs and to determine the optimum model setup.
Comparison between the model-predicted SSC and the observation at fourteen key
locations within the Delta showed that the performance of the LSTM model iscomparable or superior to that of DSM2-GTM, a process-based transport model. The
study findings suggest that machine learning models can be an effective tool for
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Tuesday Scheduled Sessions: Food Web Foundations
sediment transport applications, especially when necessary inputs to numerical models(e.g., observation data) are not available or difficult to attain. In fact, the LSTM model
has a potential to become a valuable management tool in the future, as the fastchanging climate and intensifying weather events will make calibration of process-based
approaches increasingly difficult.

Food Web Foundations
Nutrient Status of San Francisco Bay
Erica Nejad1, Taylor Eddy1, James Cloern1
1U.S. Geological Survey

Presenting author email: enejad@usgs.gov
Managers in San Francisco Bay (SFB) are faced with the great challenge of protecting
the estuary from nutrient enrichment. Meeting this challenge requires scientificallygrounded information to determine when and how to implement policies of nutrient
control. Our five decade USGS sampling program in SFB was designed to capture
seasonal and spatial variability of water quality parameters including dissolved inorganic
nitrogen and phosphorus concentrations. In recent years, sampling for organic andparticulate N and P forms was added. We synthesize these data to assess the nutrient
status of SFB from lower South Bay to Suisun Bay. Our assessment is based in fivecategories that characterize nutrient pollution in estuaries: (1) the estuarine setting andindicators of current water quality, (2) external nutrient sources and input rates, (3)concentrations and forms of SFB nutrients, (4) nutrient-based indicators of the potential
for algal biomass production and the degree to which that potential is realized, (5)budgets to estimate the fates of externally derived nitrogen and phosphorus. We foundthat despite the high nutrient inputs and concentrations, SFB is not impaired by hypoxia,
recurrent HABs, or excessive algal production. Causes for concern include nutrient
concentrations higher than other impaired estuaries, chronic presence of multiple algal
toxins, recent increases in primary production, and projected hydroclimatic conditions
that could increase the magnitude and frequency of algal blooms. In this presentation
we discuss our assessment of SFB’s nutrient status to inform nutrient management.
Loss, and Potential Recovery of Primary Production from the Sacramento-San
Joaquin Delta
James Cloern1, Sam Safran2, Lydia Smith Vaughn2, April Robinson2, Alison
Whipple2, Katharyn Boyer3, Judith Drexler1, Robert Naiman4, James Pinckney5,
Emily Howe6, Elizabeth Canuel7, Letitia Grenier2
1U. S. Geological Survey, 2San Francisco Estuary institute, 3San Francisco State

University, 4University of Washington, 5University of South Carolina, 6Nature
Conservancy, 7Virginia Institute of Marine Science
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Tuesday Scheduled Sessions: Food Web Foundations
Presenting author email: jecloern@usgs.gov
Humans are changing the Earth’s surface at an accelerating pace, with significant
consequences for impacted ecosystems and their biodiversity. Landscapetransformation has far-reaching implications including reduced net primary production(NPP) available to support ecosystems, reduced energy supplies to consumer
organisms, and disruption of ecosystem services. Anthropogenic activities have
reduced global NPP available to terrestrial ecosystems by nearly 25%, but the loss of
NPP from wetland ecosystems is unknown. We used a simple approach to estimate
aquatic NPP from measured habitat areas and habitat-specific areal productivity in the
Sacramento-San Joaquin Delta, comparing historical and modern landscapes and a
scenario of wetland restoration. Results show that a 77% loss of wetland habitats(primarily marshes) has reduced ecosystem NPP by 94%, carbon (energy) flow toherbivores by 89%, and detritus production by 94%. To our knowledge, this is the firstestimate of lost NPP across multiple producer groups in a large wetland ecosystem. Our
results also show that attainment of the Delta Plan’s habitat restoration goals could
recover 12% of lost NPP and measurably increase carbon flow to consumers, including
at-risk species and their food resources. This study illustrates how a simple approachfor estimating the loss of ecosystem functions from measured habitat losses can guideconservation plans by establishing historical baselines, projecting functional outcomesof different restoration scenarios, and establishing performance metrics to gauge
success.
Floodplain Trophic Subsidies Support Juvenile Salmon in a Highly Altered River
Network
Mollie Ogaz1, Anna Sturrock1 | 2, Nicholas Corline1 | 3, Ryan Peek1, Kelly Neal1,
Dana Myers1, Sierra Schluep1, Marissa Levinson1, Rachel Johnson1 | 4, Carson
Jeffres1
1Center for Watershed Sciences, University of California Davis, Davis, CA 95616,

2University of Essex, School of Life Sciences, Wivenhoe Park, UK, 3College of Natural

Resources and the Environment, Virginia Polytechnic Institute and State University,
Blacksburg, VA 24061, 4Southwest Fisheries Science Center, National Marine FisheriesService, National Oceanic and Atmospheric Administration, Santa Cruz, CA 95060
Presenting author email: mhogaz@ucdavis.edu
Trophic subsidies transport nutrients and energy from areas of surplus to areas of
deficit, driving food web structure and growth opportunities for fishes and other taxa. In
the Sacramento-San Joaquin River Delta, large reductions in productivity, fueled byhabitat loss and invasive species, have impacted its ability to support resident andmigratory fishes. Despite this habitat loss, remnant patches of floodplain and other offchannel habitats continue to produce high densities of high-energy prey items (e.g.
large-bodied cladoceran zooplankton), increasing growth rates of juvenile Chinook
salmon able to access these habitats. However, the extent to which advection of theseprey items into downstream habitats also supports the diet of native fishes in the Delta
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Tuesday Scheduled Sessions: Food Web Foundations
is less well understood. Here, juvenile Chinook salmon (Oncorhynchus tshawytscha)and zooplankton were sampled from locations above and below the outlets of the two
major floodplains draining into the Delta (Yolo Bypass and Cosumnes River floodplain).
We analyzed spatiotemporal patterns in juvenile salmon stomach fullness and dietcomposition annually from 2014 to 2018, incorporating a range of hydroclimaticconditions. The results suggest significant advection of invertebrates from the two
floodplains into the Delta, particularly in wetter years 2016 and 2017. Cladocera – inparticular, Daphnia pulex - dominated the diet of salmon caught immediately below thefloodplains and decreased with increasing distance downstream. Stomach fullness
index and cladocera abundances (both in stomach samples and the ambient watercolumn) were also higher in years characterized by higher flows and longer inundation
periods. Overall, these data suggest that flow-assisted ‘food delivery’ from floodplains
and other off-channel habitats could play a key role in supporting the growth of juvenile
salmonids in the Delta, and emphasize the importance of maintaining a diverse habitat
mosaic and foodscape to support resilient fish populations.
A Synthesis of Productivity Estimates for the Abundant Copepod
Pseudodiaptomus Forbesi
Wim Kimmerer1, Austin Gearty1, Anne Slaughter1, Toni Ignoffo1
1Estuary & Ocean Science Center, San Francisco State University

Presenting author email: kimmerer@sfsu.edu
Phytoplankton productivity in the San Francisco Estuary is available to fish only after it
has been consumed by one or two trophic levels of zooplankton. Althoughphytoplankton primary production is reasonably well known, we know less about theefficiency by which grazing and growth convert phytoplankton to zooplankton biomass.
To fill this gap in knowledge, we synthesized data from >100 measurements of growthrate and >200 measurements of reproductive rates of Pseudodiaptomus forbesi fromseveral field-based projects starting in 2006. Data were separated into four habitat
types: brackish and fresh open-water estuarine channels, the Cache Slough Complex(CSC), and the Yolo Bypass toe drain. Neither growth nor reproduction was related tosalinity, reinforcing previous work showing that the seaward limit of this euryhaline
population is not determined by salinity tolerance. Rates of growth and reproduction
were chronically food limited. Growth rate was related to chlorophyll concentration by asaturating function that explained about 24% of the variance. This function did not differ
among habitat types, so higher growth rates in the CSC and especially the Yolo Bypass
were mainly due to higher phytoplankton biomass. Chlorophyll was a weaker predictorof reproductive rate but the estimated maximum rate was about twice as high in the
CSC as in the other habitats. Estimated secondary production by copepods was ~5% of
estimated primary production, consistent with the important role of microzooplankton asa partial intermediate trophic level that reduces foodweb efficiency. These results
highlight how variability in foodweb processes is key to variability in energy available tohigher trophic levels. Results for shallow, off-channel habitats are encouraging, but our12

Tuesday Scheduled Sessions: New Habitat, New Science: Advances in Wetland
Restoration
ability to scale these habitats up may limit their quantitative contribution to the pelagic
food web.
Zooplankton Community Response to Extreme Environmental Events in the
Cache-Lindsey Slough Complex
Kim Luke1, John Durand1, Chris Jasper2
1University of California, Davis Center for Watershed Sciences, 2Vollmar Natural Lands

Consulting

Presenting author email: kaluke@ucdavis.edu
In the past decade, the north Delta has been subject to drought, high flows, and record
temperatures. Climate change will continue to exacerbate these events. To help
understand how the food source of native Delta fishes may be impacted, we are
analyzing monthly zooplankton samples collected since 2012 from the north Delta. The
areas of focus are within the Cache-Lindsey Slough Complex (CLC), specifically upper
slough sites. The CLC is influenced by agriculture, water export, artificial lakes,
restoration sites, wetlands, and natural upland inputs. Cache and Lindsey Slough varysignificantly in water input, flow, and nutrient load, and have very different plankton
dynamics.
Our initial results build on previous studies that show higher densities of zooplankton
near terminal ends of slough complexes, and abundance shifts in response to local
flows from precipitation, irrigation and flood control districts, and agriculture. Our study
compares the hydrodynamically different Cache and Lindsey Sloughs, as well as
upstream and downstream slough sites within each. We compare samples taken during
drought years with very wet years to understand how flow effects nutrient dynamics andfood web response. Our spatial, temporal, and hydrodynamic study will support
management of adjacent landscapes to help offset impacts of climate change, andcreate optimal nutrient and flow dynamics for food webs.

New Habitat, New Science: Advances in Wetland Restoration
After the Breach - First Year Monitoring of the Tule Red Tidal Restoration ProjectRamona Swenson1, Damien Kunz1, Rachel Brownsey1
1Environmental Science Associates

Presenting author email: rswenson@esassoc.com
The Tule Red Tidal Restoration Project (led by Westervelt and SFCWA, with DWR)
restored and enhanced 420 acres of tidal wetlands in Suisun Marsh, with the goal ofincreasing primary and secondary productivity to enhance food supplies for listed fishes(delta smelt, juvenile salmonids, and longfin smelt). In October 2019, the outer natural
13

Tuesday Scheduled Sessions: New Habitat, New Science: Advances in Wetland
Restoration
berm of a former duck club was breached to restore tidal flows to constructed channels,
ponds and pannes. During the first year after breaching (June-December 2021), ESA
measured physical, water quality, and biological conditions to test hypotheses of tidal
marsh function and restoration.
A bathymetric survey documented the outboard breach channel deepening and interior
channels re-sizing and widening. Water level gauges documented increasing tidal
conveyance at the outboard channel. The back marsh was fully connected, with flows
limited by channel conveyance at ebb and flood tides. Large ponds flooded on springtides and were disconnected during neap cycles, as designed. Small pannes on thehigh marsh stayed inundated. Chlorophyll-a concentrations were higher in the ponds
than the channel. Dissolved oxygen levels were variable August-September, sometimes
below 5 mg/L in a dead-end channel, which was likely due to algal blooms. Methyl
mercury (unfiltered water) averaged 0.05-0.21 ng/L, similar to other restored tidal
wetlands. Vegetation mapping documented pickleweed establishment on theconstructed habitat berm, poor plant establishment near the levee crown, and rapid
revegetation in the tidal marsh. Phragmites is colonizing new areas from pre-existing
stands. Invasive plant mapping in May guided weed management.
The ponds are functioning as designed: high hydrologic residence time to enhance
productivity, with periodic tidal exchange to export resources through channel to Grizzly
Bay. Monitoring by other partners of foodweb, fish (larval longfin smelt were
documented in the channel), birds and Phragmites complement these findings andbroaden lessons learned from this newly restoring site.
Dutch Slough Tidal Marsh Restoration Monitoring: Launching a Program to Track
Ecosystem Development
Scott Jones1, Molly Ferrell2, Katherine Bandy2, Karen Thorne1
1U.S. Geological Survey, Western Ecological Research Center, Davis, CA, 2California

Department of Water Resources, Sacramento, CA
Presenting author email: sfjones@usgs.gov

Tidal wetland restoration is increasingly used to meet habitat goals in the San Francisco
Bay-Delta. Thousands of acres of additional restoration is planned in the near-term,using the green infrastructure of tidal wetlands to protect against rising tides, provide
habitat for key plant and animal species, and ensure continued ecosystem processes
like nitrogen removal and carbon storage. However, the effectiveness of tidal wetland
restoration and the trajectory of restoration sites is still unclear, especially at the
freshwater-saltwater interface (~2 ppt salinity). The Dutch Slough Tidal MarshRestoration Project was designed to be a living laboratory for scientific studies and will
be breached within the next two years, creating an opportunity to study the benefits ofrestoration when compared to other land uses and to inform adaptive management of
tidal wetland restoration trajectories. We will quantify conditions pre- and post-breach at
Dutch Slough, in nearby reference Delta islets, and in former tidal wetlands under
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Tuesday Scheduled Sessions: New Habitat, New Science: Advances in Wetland
Restoration
agricultural production to compare land uses. We will track development of vegetation
composition and abundance, elevation capital, water quality in channel andgroundwater (nutrient concentrations, salinity, turbidity), soil carbon and nitrogen stocks,
and greenhouse gas emissions. This project will quantify key long-term tidal wetland
processes including elevation change, carbon sequestration, methane emission, andnutrient removal, providing baseline information that will inform response of tidal
freshwater wetlands to sea-level rise, drought, and other climate/anthropogenic
changes. The integrated monitoring program at Dutch Slough will include UC Davis
Bohart Entomology Museum, Cramer Fish Sciences, River Partners, and others.
Ultimately, initial responses and long-term evolution of this site will provide crucial
information to inform adaptive management of restoration projects, future restoration
design in the Bay-Delta and beyond, and tidal wetland baselines as climate change
alters conditions across the Estuary.
Montezuma Wetlands Project: Early Results and Lessons Learned from a Newly
Breached Marsh
Cassie Pinnell1 | 2, Douglas Lipton3, Roger Leventhal4, Jim Levine1
1Montezuma Wetlands, LLC, 2Vollmar Natural Lands Consulting, Inc, 3Lipton

Environmental Group, 4FarWest Restoration Engineering

Presenting author email: cpinnell@vollmarconsulting.com
The Montezuma Wetlands Project is a multi-phase restoration project that uses dredged
sediment to raise elevations in diked, subsided baylands to restore ~2,000 acres of atidal wetland ecosystem. This project is unique, as it receives most of its revenue fromthe acceptance of dredged sediments. These include sediments not suitable forunconfined aquatic disposal, then buried and isolated in an anoxic environment under at
least 3 feet of cleaner sediments. The project owns the highest rate sediment offloading
system west of the Mississippi, and has operated successfully since 2003 by placing
almost 9 million cubic yards. The project is on target to accomplish its restoration goals
in support of the Long-Term Management Strategy (LTMS), established by a joint effortof the Corps and other federal, state and regional agencies to maximize the safe
beneficial reuse of sediment dredged from SF Estuary.
Montezuma breached its first phase of over 500 acres in October 2020, and has beenmonitoring development of the new marsh system. Early post-breach monitoring data
includes fish use, vegetation development, water quality, and tidal channel formation.
Early monitoring indicates the breach was successful, with encouraging physical (tidal
flows matching with target site elevations), chemical (water quality), and biological (early
wildlife use) results. Ongoing monitoring over the coming years will provide importantdata on early marsh development. Pre-breach data includes detailed elevation andhabitat surveys and over 15 years of biological and chemistry sampling results, whichdocumented safe handling of the sediments. The extensive data collected has allowed
Montezuma to adaptively manage and improve its restoration methods to increase
resiliency for sea-level rise and changing needs and conditions. By working in
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Tuesday Scheduled Sessions: New Habitat, New Science: Advances in Wetland
Restoration
collaboration with regulatory agencies, project partners, and the Technical Review
Team, Montezuma has pioneered many new scientific and engineering approaches andmethods for large-scale tidal marsh restoration.
Reconnecting Delta Food Webs: Evaluating the Influence of Tidal MarshRestoration on Energy Flow and Prey Availability for Native Fishes
Susan De La Cruz1, Isa Woo1, Albert Ruhi2, Jake Sousa3, Megan Pagliaro2, Lenny
Grimaldo4, Stacy Moskal1, Linda Standlee5, Darcy Austin5
1U.S. Geological Survey, Western Ecological Research Center, San Francisco Bay

Estuary Field Station, 2University of California, Berkeley, 3ICF, 4California Department of
Water Resources, 5State Water Contractors
Presenting author email: sdelacruz@usgs.gov
In the upper San Francisco Estuary species introductions, tidal wetland loss, andwatershed modifications have led to long-term declines in primary productivity andnative fish populations. While expansive tidal wetland restoration is planned for theregion, our knowledge on how pelagic, benthic, and terrestrial components of Delta foodwebs interact is cursory. This data gap precludes systematic understanding ofrestoration benefits for native fishes such as delta smelt (Hypomesus transpacificus),
longfin smelt (Spirinchus thaleichthys), and salmonids. The goal of our research is toelucidate the effects of tidal marsh restoration on food web structure and prey quality for
native fishes. To accomplish this, we are comparing pelagic, benthic, and terrestrial
prey resources, fish catch, trophic structure, and multiple physical variables among six
relict and recently breached wetlands. Preliminary findings from our first year ofsampling indicate that early season (Feb) prey availability and food web complexity
were limited at all wetlands compared with late season (May), suggesting less
opportunity, capacity and realized function for early season fish. Additionally, we founddifferences in native fish catch and size among sites during spring sampling, including
the presence of 70 longfin smelt (mean fork length + SE = 31.0+0.35 mm) at the mouthof the Tule Red restoration that were statistically larger than 48 longfin smelt (28.9+0.41mm) captured within Chipps Island (F1,116 = 15.51; P < 0.001). We are currently
completing invertebrate prey identification and calorimetry, fish diet, stable isotope andecosystem metabolism analyses on our first year samples as well as preparing for asecond year of sampling. Results from this on-going project will address key Bay-Delta
management questions centered on how restoration of tidal wetland structure translates
into the recovery of food web processes and improved fish habitat.
How Do Food Webs Change Following Tidal Restoration? a Preliminary
Assessment of Restoration Success in Two Fish Restoration Project (FRP)
Wetlands
Christy Bowles1, Michelle Avila1, Emma Davidson1, Daniel Ellis1, Stacy Sherman1
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Tuesday Scheduled Sessions: IEP Special Session: The Value of Long-term
Biological Monitoring in the San Francisco Estuary
1California Department of Fish and Wildlife

Presenting author email: christy.bowles@wildlife.ca.gov
Much of the tidal wetland restoration in the Sacramento-San Joaquin Delta and Suisun
Marsh (the Upper SF Estuary) is being constructed under the premise that wetland
restoration will increase the resilience of Delta Smelt, Longfin Smelt, and rearing
Chinook salmon. We examined changes in water quality and food webs following
restoration of tidal wetlands at two sites: Decker Island and Yolo Flyway Farms.
The Fish Restoration Program (FRP) Monitoring Team is tasked with developing
monitoring plans for tidal wetland sites. We approach restoration for fish using a wholeecosystem approach, collecting data on the physical habitat and multiple levels of thefood web. We sample water quality, nutrients, primary producers (phytoplankton andvegetation), invertebrates (mesozooplankton, macrozooplankton, surface, epiphytic,
and benthic), and fish at and adjacent to each of our restoration sites. Data arecollected and analyzed using a BACI (Before-after-control-impact) design; each
restoration site is paired with a reference wetland site and is sampled before and after
restoration.
We analyzed patterns in phytoplankton, invertebrate, and fish abundance and diversity(richness and evenness) using GLMM with restoration status, season, year, and region
as factors. We examined differences in species composition of phytoplankton,
invertebrates, and fish using PerMANOVA. Overall, abundance of all food web levels
was highly variable, with differences between wetlands, years, and seasons. Species
composition differed between seasons and wetlands.
This study provides a much-needed look at how food webs change following restorationof tidal wetlands. Through monitoring we can empirically understand the potential of
tidal restoration to provide food and habitat for at-risk fish as the sites evolve. Findings
will be shared with scientists and managers across the SF Bay Delta community to
inform future tidal restoration projects.

IEP Special Session: The Value of Long-term Biological Monitoring in
the San Francisco Estuary(*IEP) The Value of Long-Term Monitoring of the San Francisco Estuary for Delta
Smelt and Longfin Smelt
Trishelle Tempel1, Timothy Malinich1, Jillian Burns1, Arthur Barros1, Christina
Burdi1, James Hobbs1
1California Department of Fish and Wildlife

Presenting author email: trishelle.tempel@wildlife.ca.gov
Long-term monitoring programs are an important tool for understanding ecosystemchange but are rare due to the challenges of supporting these types of studies over17

Tuesday Scheduled Sessions: IEP Special Session: The Value of Long-term
Biological Monitoring in the San Francisco Estuary
time. The California Department of Fish and Wildlife has been conducting long termmonitoring surveys in the upper San Francisco Estuary for over 60 years, and thislongevity has been made possible by adapting to suit management needs, expanding
our knowledge about the Estuary, and legal mandates requiring their continuation. The
surveys produce annual abundance indices for multiple life stages of Delta Smelt(Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys), and are usedin protective measures to minimize entrainment into the large water diversions in thesouth Delta and facilitate our understanding of the drivers of population declines. The
long-term decline of native smelt species occurred as a part of four major regime shifts
in the ecosystem; Pre-Clam, the time before the invasion of the overbite clam
(Potamocorbula amurensis; past-1986), Post-Clam, the time leading up to the Pelagic
Organism Decline (POD; 1987-2001), the POD (2002-2012), and a new regime we
identify as the Climate Shift (2013-present day). While some regimes are linked tosingle causes (i.e., the invasion of P. amurensis), others are correlated with multiple
environmental stressors including decreased freshwater flow (drought, freshwater
diversion), invasive species, changes in food availability and composition, andcontaminants. Our changing climate is exacerbating the impact of existing stressors andaccelerating population decline which while require new, innovative strategies toameliorate impacts to Delta and Longfin Smelt.
(*IEP) The Influence of Environmental Conditions in Long Term Fish Abundance
DataJames White1
1California Department of Fish and Wildlife

Presenting author email: James.White@Wildlife.ca.gov
The California Department of Fish and Wildlife has been conducting long-termmonitoring studies in the upper San Francisco Estuary to document the distribution andrelative abundance of fish and zooplankton to inform management of freshwater flows
since 1959. The value of this long-term monitoring relies on the consistency of thesurvey design and execution, sampling gear and catchability over time. However,catchability is known to be affected by environmental conditions such as water clarity,
which has greatly increased over time. Here we attempt to explain long term patterns infish catch for the Fall Midwater Trawl and Summer Townet surveys within the San
Francisco Estuary relative to environmental conditions such water clarity and water
outflow as influencing factors. For many fish species, we have found a long-term
decrease in catch which has been compounded during periods of low flow, high watertemperature, and high water clarity. These factors potentially increase the ability of fishto avoid or escape capture by trawl nets, reduce their presence in the water column via
lack of feeding or predator avoidance, or some combination thereof. Reduced use of
pelagic habitat means reduced carrying capacity for fishes. These results highlight theimportance of understanding the role of environmental conditions in the context ofcatchability and the value of long-term datasets to give insights into these relationships.
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Tuesday Scheduled Sessions: IEP Special Session: The Value of Long-term
Biological Monitoring in the San Francisco Estuary(*IEP) Invasion of the Water Body Snatchers: Invasive Goby Trends from the San
Francisco Bay Study and Summer Townet Survey.
Timothy David Malinich1, Emily Y. Campbell1, Kathy Hieb1, Steve Slater1
1California Department of Fish and Wildlife

Presenting author email: timothy.malinich@wildlife.ca.gov,
emily.campbell@wildlife.ca.gov
The California Department of Fish and Wildlife (CDFW), part of the Interagency
Ecological Program, has been informing resource managers, the scientific community,
and the public on the San Francisco Estuary (Estuary) fish and invertebrate community
abundance and diversity through long-term monitoring studies such as the Summer
Townet Survey (STN) and the San Francisco Bay Study (SFBS). These surveys haveproduced invaluable datasets that are used to identify subtle and significant changes
occurring within the Estuary, such as the Pelagic Organism Decline (POD). A more
recent change in the Estuary, observed by STN and SFBS, has been the rapid
population growth of invasive goby Tridentiger species (i.e. trigonocephalus, bifasciatus,and barbatus) even following the sharp decline of common pelagic species. Abundance
patterns measured by STN, which catches fish species in the water column during theirlarval and early-juvenile stages, show that yearly production of Tridentiger species isincreasing. Similar patterns in abundances of juvenile and adult Tridentigers have been
observed by the SFBS otter trawl, a demersal sampling survey, which provides a spatial
context to Tridentiger populations across the Estuary. Factors that contributed to the
POD may be impacting the presence of Tridentigers in the Estuary. However,environmental factors such as increasing water clarity, which negatively affected pelagic
fishes, may be benefiting benthic communities by increasing benthic production. We
compare our observations to other demersal species, such as native gobies andsculpins, to determine if there is a growing benthic trophic community or only the rising
success of invasive gobies. Monitoring by STN and SFBS on Tridentiger abundances
will help inform how rising goby populations impact the health and structure of aquaticcommunities, and the response of fish to management actions for species of concern(i.e. salmon, smelt, sturgeon) in the Estuary.
(*IEP) Fish Food, Outflow, and Management Implications: The Values of LongTerm Zooplankton Monitoring in the SFE
Arthur Barros1, April Hennessy1, Christina Burdi1, Laura Twardochleb2, Steven
Slater1
1California Department of Fish and Wildlife, 2California Department of Water Resources

Presenting author email: arthur.barros@wildlife.ca.gov

19

Tuesday Scheduled Sessions: IEP Special Session: The Value of Long-term
Biological Monitoring in the San Francisco EstuaryLong-term Interagency Ecological Program surveys conducted since the 1970s havedescribed the overall historical trends in zooplankton resource within the San Francisco
Estuary (SFE). Zooplankton communities in the estuary have changed dramaticallysince surveys began as a result of changes in outflow and phytoplankton communities,
as well as other habitat modifications[TL1] . Zooplankton are a vital trophic link between
aquatic primary producers and higher-level consumers of the SFE, as primaryconsumers of phytoplankton they facilitate the flow of carbon into a large and complex
food web. Zooplankton in the SFE are also a key food source for several endangered
and threatened species, notably the Delta Smelt (Hypomesus transpacificus) andLongfin Smelt (Spirinchus thaleichthys). IEP surveys have shown that substantialchanges in zooplankton communities have been linked to major declines in the pelagic
fishes of the upper estuary. One goal of the Flow Alteration Management and Synthesis
Team (FLOAT-MAST) is to determine how freshwater outflow through the estuary
impacts the distribution and abundance of key zooplankton species to better manage forsmelt food resources in the estuary. The FLOAT-MAST has synthesized research
overviewing the mechanisms in which outflow affects resource availability. Thesemechanisms include: increasing stratification in the water column, dictating thehorizontal positioning of the low-salinity zone, and through the spatial subsidy ofzooplankton to the low salinity zone from upstream populations. Preliminary analysis
utilizing an integrated dataset of long-term zooplankton sampling in the SFE shows
varying relationships between outflow and the abundance and distribution for key preyspecies. Determining if and how outflow may be used to improve the availability of preyspecies will allow for more informed management decisions to increase food access forimperiled fish populations.
(*IEP) The Value of Long-Term Zooplankton Monitoring for Detecting Impacts of
the Suisun Marsh Salinity Control Gate Managed Flow Action
Christina E. Burdi1
1California Department of Fish and Wildlife

Presenting author email: christina.burdi@wildlife.ca.gov
Zooplankton communities in the San Francisco Estuary (SFE) have been altered by
freshwater flow regulation, water diversions, and species introductions. Zooplankton are
an important component of the food web and prey for many SFE fish species, including
Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys).
The California Department of Fish and Wildlife’s (CDFW) Summer Townet (STN) andFall Midwater Trawl (FMWT) are two long-term monitoring projects that target pelagic
fishes in the upper SFE. Beginning in 2005, these surveys added zooplankton sampling
to detect trends in food availability for fish. The Suisun Marsh Salinity Control Gates(SMSCG) managed flow action is one of the Delta Smelt Resiliency Strategies toincrease accessible habitat for Delta Smelt by maintaining fresh water in Montezuma
Slough. In 2018 the gates were operated in August to facilitate movement of Delta
Smelt into Suisun Marsh. In support of monitoring for the SMSCG action, STN and
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Tuesday Scheduled Sessions: Special Featured Session: Raising Awareness andShifting the Paradigm: Fostering Diversity, Inclusion and Equity in the Bay-Delta System(Featured Special Session)
FMWT increased sampling frequency and added three additional stations to detect
impacts to the zooplankton community. There was no action in 2019 and 2020, however
additional sampling was still conducted to determine seasonal trends in non-action
years. Meso-zooplankton samples that target copepods and cladocerans were collectedbi-weekly from July to October. Zooplankton biomass in Suisun Marsh was compared tosurrounding areas such as the lower Sacramento River and Suisun Bay. The copepods
Acartiella sinensis and Pseudodiaptomus spp. were the dominant species during thistime and are important prey for fish. 2019 showed higher meso-zooplankton biomass
than 2018, and a decrease in biomass occurred in August in all years, which consistent
with historic trends. Long-term monitoring allows for the detection of historic trends todetermine the impact of adaptive management actions such as the SMSCG on thezooplankton community and therefore to zooplanktivorous fish in the SFE.

Special Featured Session: Raising Awareness and Shifting theParadigm: Fostering Diversity, Inclusion and Equity in the Bay-Delta
System (Featured Special Session)
Employee-Led Efforts to Foster Equity and Inclusion at the U.S. Geological
SurveyAlexandra Etheridge1, Tina Roberts-Ashby2, Kristen Bennett3
1U.S. Geological Survey, 2U.S. Geological Survey Geology, Energy, and Minerals

Science Center, Reston, VA, 3U.S. Geological Survey Astrogeology Science Center,
Flagstaff, AZ
Presenting author email: aetherid@usgs.gov
A lack of diversity in geosciences limits science reach and relevance, particularly in anage of climate non-stationarity with impacts amplified in marginalized sectors of society.
Recognizing structural and cultural barriers to diversity internal and external to the U.S.
Geological Survey (USGS), a growing population of USGS employees lead multiple
efforts aimed at cultivating an inclusive peer culture while engaging the workforce indiscussion about the impacts of harm and exclusion in the workplace. Three examples
will be discussed.
1. USGS StepUp! Employee Empowerment Strategies (USGS SEES) is a 4-hour peerled, open-source bystander intervention workshop created in late 2017. The authors
have since offered USGS SEES workshops to hundreds of co-workers and funding
partners while expanding the pool of facilitators to include employees representing
USGS, several academic institutions, and several federal science agencies.
2. The USGS Peer Support Worker (PSW) program provides peer-to-peer support for
USGS employees within science centers across the nation. PSWs facilitate awarenessof issues specific to the peer culture in their workplace, such as overcoming harmful
biases, challenging crude language during field campaigns, or finding work/life balance21

Tuesday Scheduled Sessions: Special Featured Session: Raising Awareness andShifting the Paradigm: Fostering Diversity, Inclusion and Equity in the Bay-Delta System(Featured Special Session)
during extended telework. PSWs are also trained internally to provide resources tomitigate misconduct while providing support to co-workers who have specific concerns.
3. In June 2020, USGS hosted a workshop titled Preventing Harassment in Science:
Building a Community of Practice for Meaningful Change. The workshop brought
leaders of anti-harassment efforts together to share best practices to reduce
harassment in the scientific workplace.
Results from each of these efforts show that a sense of belonging can be curated
culturally through open dialogue that promotes awareness and empowered preventionof harm. Sustaining these and other employee-led initiatives pushes scientificworkplaces toward enhanced science relevance when all members of society can safely
participate in offering solutions to society’s most pressing problems.
Making Waves: Piloting Community Engagement in Adapting to Rising Tides
Melissa Jones1
1Executive Director, Bay Area Regional Health Inequities Initiative

Presenting author email: mjones@barhii.org
In 2017, the Bay Area Regional Collaborative (BARC), the San Francisco Bay
Conservation and Development Commission (BCDC), and the Metropolitan
Transportation Commission (MTC) launched the Adapting to Rising Tides (ART) Bay
Area project.
The ART project was the first regional-scale effort to plan for sea-level rise and otherclimate impacts for the Bay Area's communities, natural systems, and criticalinfrastructure. In 2018-2019, the Bay Area Regional Health inequities Initiative (BARHII)
worked with BARC to create a unique strategy for public health and communities to pilot
deep community engagement processes in two under-resourced locations.
This work had three goals: understand how local vulnerability and resilience factors
impact our region, strengthen the ability of community organizations to positively shaperesilience planning, and increase the capacity of public agencies to meaningfully partnerwith community-based organizations to understand local conditions and improve climate
resilience and health equity.
Youth Advocates: Increasing the Voices of the Most Impacted
Elaine Labson1
1Little Manila Rising

Presenting author email: elaine@littlemanila.org
The history and preservation of South Stockton and marginalized communities is Little
Manila Rising’s foundation. Our focus on environmental justice is an opening to take22

Tuesday Scheduled Sessions: Special Featured Session: Raising Awareness andShifting the Paradigm: Fostering Diversity, Inclusion and Equity in the Bay-Delta System(Featured Special Session)that same lens of using history as a tool for building equity. Little Manila Rising has
been focusing on South Stockton for nearly twenty years. The people who built theorganization are South Stocktonians and their families are also South Stocktonians.
They have educated and guided youth from South Stockton who now have created theirown families and call South Stockton home. Moreover, South Stockton consists ofcensus tracts that rank in the 95-100 percentile of pollution, high PM 2.5 rates,
disproportionate asthma rates, and population burdened areas in the state. These arecommunities that have been negatively impacted by environmental, educational,
economic, and health issues due to systemic policies and systems.
Youth Advocates for Environmental Justice
Little Manila Rising is currently focusing on educating youth on environmental justiceand civic systems to the neighborhoods/residents in South Stockton. Through the workof AB 617, a legislation bill that allows for a community-led process with participationfrom California’s communities experiencing high environmental burdens from poor air
quality to engage in the AB 617 process, our youth advocates have been able toengage in citizen science and become community experts in environmental justice.
They have testified at the California Air Resource Board for systems change andfacilitated workshops on environmental justice issues affecting South Stockton. The
goal is to share the experiences and voices of the youth who are directly impacted by
the inequities and injustices that impact Stockton. We will also talk about community
involvement, community leadership, and regulatory reform through the work of AB 617.
White-Led Leadership in Complex Ecological Systems
Sarah Myhre1
1Rowan Institute

Presenting author email: sarahmyhre@rowaninstitute.org
What is an appropriate role for white ecologists, environmental scientists, and land-use
planners? How can whiteness be directly dissected and addressed in order to be used
as a tool for deconstructing systemic inequity and structural violence? In this talk, theframework and lane of white-led leadership, within institutions, research labs, andacademic settings, will be focused upon, with the goal of harnessing the deconstructionof whiteness to actively engage in institutional anti-racism, harm-reduction, and power
redistribution.

23

Wednesday Scheduled Sessions: Salmon Science for Management

Wednesday Scheduled Sessions
Salmon Science for Management
Mechanisms, Impacts, and Mitigation for Thiamine Deficiency and Early Life
Stage Mortality in Central Valley Salmon
Rachel Johnson1, Nate Mantua2, Jacques Rinchard3, Heather Bell4, Taylor
Lipscomb5, Anne Todgham4, John Field2, Nann Fangue4, Dennis Cocherell4,
Donald Tillitt6, Kevin Kwak7, Brett Kormos7, Bruce Finney8, Steven Litvin9, Illiana
Ruiz-Cooley10, Carson Jeffres4, Scott Foott5, Mark Adkinson7, Steve Lindley2, Dale
Honeyfield6, William Ardren5, Thomas William2
1NOAA Fisheries, Southwest Fisheries Science Center and UC Davis, 2NOAAFisheries, Southwest Fisheries Science Center, 3State University of New York,Brockport, 4University of California Davis, 5U.S. Fish and Wildlife Service, 6U.S.
Geological Survey, 7California Department of Fish and Game, 8Idaho State University,
9Monterey Bay Aquarium Institute, 10Moss Landing Marine Laboratory
Presenting author email: Rachel.Johnson@noaa.gov
Thiamine Deficiency Complex (TDC) is a nutritional deficiency of thiamine (vitamin B1)
recently linked with high mortalities of early life stages of Chinook salmon in Central
Valley (CV) hatcheries. Clinical signs of TDC are anorexia and sporadic spinning prior
to death. Offspring of female salmon with reduced levels of thiamine are prone to TDC.
The current hypothesis: a narrowing of the diversity of CV Chinook salmon marine dietand/or a more southerly ocean distribution where prey are either deficient in thiaminelevels or high in thiaminase (Northern anchovies). Thiaminase is an enzyme that
destroys or inactivates thiamine, and was identified as the primary explanation for low
levels of thiamine and subsequent onset of TDC in Great Lakes and Baltic Sea
salmonids. While the cause may be due to a reorganization of marine food webs, there
are significant consequences to salmon populations in freshwater. TDC was firstobserved in CV hatcheries in broodyear (BY) 2019 spring, fall and late-fall Chinook
salmon, and then in BY2020 winter run and spring run. TDC continues to afflict CV
salmon stocks and we will continue our surveillance of BY2020 eggs and progeny fromother populations. Our work to-date has revealed prophylactically treating female winterrun with thiamine resulted in significant improvements to egg thiamine concentration(35.0 ± 7.2 nmol/g) and survival of progeny of this endangered species. Baseline levelsof egg thiamine in un-treated winter run were low (5.2 ± 4.4 nmol/g), resulting in 50% of
their fry expressing TDC symptoms. Our work has generated significant insights andnecessary data needed to quantify impacts to naturally spawning populations, which
remains the greatest data gap relevant for conservation, water project operations, andharvest management. Our rapid scientific inquiry into this new stressor has resulted inactionable science to support salmon hatchery management and assess populationlevel impacts.

24

Wednesday Scheduled Sessions: Salmon Science for Management
Insights into the Life History and Habitat Use of Historical Salmon in the BayDelta Watershed
Malte Willmes1 | 2, Flora Cordoleani1 | 2, Anna Sturrock3, Jeff Rosenthal4, Jelmer
Eerkens5, Levi S. Lewis6, James A. Hobbs6, Rachel Johnson1 | 2 | 3
1Institute of Marine Sciences, UC Santa Cruz, Santa Cruz, CA, 95064, USA, 2National

Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, CA, 95064,
USA, 3Center for Watershed Sciences, University of California Davis, Davis, California
95616, USA, 4Far Western Anthropological Research Group, Davis, California 95618,
USA, 5Department of Anthropology, University of California Davis, Davis, California
95616, USA, 6Department of Wildlife, Fish, and Conservation Biology, University ofCalifornia Davis, Davis, California 95616, USA
Presenting author email: mwillmes@ucsc.edu
Climate change is resulting in increasingly frequent and extreme weather events in
California, transforming the Central Valley watershed and the San Francisco Estuary.
Chinook Salmon (Oncorhynchus tshawytscha) have long thrived in California’s variableclimate, including prolonged drought periods, by utilizing a vast habitat mosaic andhighly adaptable life history phenology. However, habitat loss and simplification,
modified flow regimes, and management practices that have promoted synchrony
among populations, are threatening the long-term survival of Central Valley Chinook
Salmon. Surveys and geochemical tools have provided crucial insights for salmon
populations in California. However, these data were collected after significant population
declines and extirpation from a large fraction of historic habitat had occurred and thus
may miss key aspects of potential salmon life history.
We applied a suite of morphological and geochemical tools to Chinook Salmon otoliths(ear stones) collected from an archaeological site (1835-1870 CE) from the lower
Feather River to reconstruct age, size, and migratory behavior. We then contrasted our
findings with modern Chinook Salmon from the same watershed and with populations
throughout the Central Valley. Our analyses showed that these historic salmon
exhibited a broader age distribution with age-3 and age-4 dominating, while theirmodern counterparts were shifted to younger ages and had a truncated age structure.
The natal origins and rearing behaviors of the historic population suggest that mostoriginated from the local watershed and used a diverse range of rearing habitats. In
contrast to their modern counterparts, these historic salmon did not migrate fully to theocean but appear to have stayed in the Estuary at low salinities. This represents a life
history strategy that has been lost for California Chinook Salmon and showcases thepotential for archaeological fish remains to provide unique insights into past salmon
populations to guide future conservation, management, and recovery.
Using Multiple Years of Data to Link Environmental Covariates to Juvenile
Steelhead Population Dynamics in the South Delta
Adam C. Pope1, Russell W. Perry1, Rebecca A. Buchanan225

Wednesday Scheduled Sessions: Salmon Science for Management
1Western Fisheries Research Center, U.S. Geological Survey, 2Columbia Basin

Research, University of Washington

Presenting author email: apope@usgs.gov
Estimation of demographic parameters for threatened and endangered fish populationsin the Sacramento-San Joaquin Delta is key to understanding their viability. To manage
for these populations’ success, demographic parameters such as travel times andsurvival must be linked to environmental covariates to provide insight into how
management actions affect population dynamics. For steelhead (Oncorhynchus mykiss)in the San Joaquin River, until recently efforts to quantify population dynamics havelargely focused on a single year at a time. More recent work aimed at using multiple
years of data to better understand linkages between steelhead population dynamics andenvironmental variables such as river flow or freshwater exports has focused on these
relationships at near Delta-wide spatial scales. Additionally, low steelhead survival
through the Delta has made parameter estimation difficult since fewer survivors lead tosparse data and greater parameter uncertainty, particularly in tidal regions farthest
downstream from release.
We used a Bayesian complete data likelihood structure to analyze acoustic telemetry
data for steelhead released into the San Joaquin River near Vernalis each spring from2011 through 2016. By modeling survival and travel time on multiple years of data, wewere able to quantify the relationship between these demographic parameters and key
environmental and operational variables including San Joaquin river flows at Vernalis,
inflow to export ratios, Old and Middle River flow index, and whether a temporary barrier
to fish passage at the head of Old River was installed. Our model framework allowed
simultaneous modeling of multiple, smaller-scale spatial regions within the Delta inorder to pinpoint where the effects of changing variables might be observed. We will
present these associations within the context of travel time and survival estimates fromprevious analyses. Our results should prove useful to managers seeking to mitigate
effects of operations on the native steelhead population.
The Drought and the Deluge: Daily and Reach-Specific Estimates of Survival,
Travel-Time and Routing Probabilities Through the Sacramento River Delta and
Yolo Bypass for Winter-Run Chinook Salmon from 2014-2018
Dalton Hance1, Russell Perry1, Adam Pope1, Arnold Ammann2, Jason Hassrick3,
Gabe Hansen1
1U.S. Geological Survey, Western Fisheries Research Center, 2NOAA Fisheries, 3ICF

Presenting author email: dhance@usgs.gov
Problem Statement: The endangered Sacramento River winter-run Chinook salmon(Oncorhynchus tshawytscha) is a major species of concern for management of water
resources in the Sacramento-San Joaquin River Delta. In particular, understanding daily
and reach-specific survival in relation to environmental conditions and the probability ofentering and surviving through Yolo Bypass or the interior Delta are critical26

Wednesday Scheduled Sessions: Salmon Science for Management
management needs. However, most existing estimates are based on late-fall run
Chinook salmon and the relationships may differ for winter-run Chinook.
Approach: We analyzed multiple years of acoustic telemetry data for juvenile winter-run
Chinook Salmon to generate reach-specific estimates of survival, travel time and routing
probabilities in relation to daily flows and temperatures in the Sacramento-San JoaquinRiver Delta and Yolo Bypass. Our study spans the years from 2014 through 2018 andtemporally contrasts the intense drought conditions during the winters of 2013-2014 and2014-2015 as well as the extremely wet winter of 2016-2017. We developed a novel
statistical mark-recapture model to efficiently estimate daily survival and travel times
while accounting for imperfect detection and tag battery failure.
Results: We found that daily discharge tended to have a positive effect and maximum
water temperature a negative effect on survival in most reaches. Winter-run Chinook
salmon were increasingly likely to enter the Yolo Bypass with increasing stage height
above the Fremont Weir. Additionally, survival through Yolo Bypass was equivalent tosurvival in the mainstem Sacramento despite much longer travel times. Survival throughthe interior Delta was consistently low.
Relevance: Our results establish relationships between flow, water temperature, andsurvival for winter-run Chinook salmon. These relationships can be used to informmanagement actions affecting this endangered population.
Counting the Needles in the Haystack: Estimating Juvenile Production ofEndangered Winter Run Chinook Salmon Leaving the Delta
Russell W. Perry1, Brian Pyper2, Rachel C. Johnson3, Arnold J. Ammann3, Joshua
A. Israel4, Bryan Matthias5
1U.S. Geological Survey, Western Fisheries Research Center, Columbia River

Research Laboratory, 2Fish Metrics Inc., 3NOAA Fisheries, 4U.S. Bureau of
Reclamation, 5U.S. Fish and Wildlife Service
Presenting author email: rperry@usgs.gov

Problem Statement: Juvenile production estimates of salmon populations exiting the
Delta have been identified as a key management parameter. Although trawl catch data
provide a relative index of abundance and outmigration timing of juvenile Chinook
salmon, estimating absolute abundance for federally endangered winter run Chinook
salmon has proven elusive due to 1) difficulty in estimating trawl sampling efficiency, 2)
inaccuracy of race assignment based on length-at-date criteria, and 3) inability to
distinguish unmarked hatchery-origin fish from wild fish.
Approach: Here, we analyze data from a novel study design that pairs acoustic tagged(AT) fish with releases of coded wire tagged (CWT) hatchery Chinook salmon. In thishybrid design, a multistate mark-recapture model applied to AT fish is used to estimate
survival to the Chipps Island trawl site. In turn, survival estimates allowed us toestimate the abundance of CWT fish available to be captured by trawls and trawl gear27

Wednesday Scheduled Sessions: Global Climate Change at the Estuary Scaleefficiency. Given estimates of trawl efficiency, we then estimated total abundance andrun timing of winter run Chinook salmon from genetic monitoring data that identified true
winter run in subsamples of the daily trawl catch.
Results: We found the hybrid study design allowed for daily and tow-level covariates tobe incorporated into the model to quantify factors affecting gear efficiency. Simulations
revealed that bias in abundance and run timing estimates was low even at small
population sizes and trawl efficiency as low as 0.5%. We will present preliminary
juvenile production estimates of true winter run Chinook salmon for 2018 – 2020 andcontrast these estimates against length-at-date classified winter run and hatchery origin
winter run.
Relevance: Devising methods to estimate abundance of juvenile salmon entering andexiting the Delta is critical for developing long-term monitoring data for assessing
population status, informing life cycle models, and guiding management actions
affecting endangered populations.

Global Climate Change at the Estuary Scale
Integrated Modeling of Climate and Land Change Impacts on Future Dynamic
Wetland Habitat in California’s Central Valley
Tamara Wilson1, Elliott Matchett2, Kristin Byrd1, Erin Conlisk3, Matthew Reiter3,
Cynthia Wallace1, Lorraine Flint4, Alan Flint4, Monica Moritsch1
1U.S. Geological Survey, Western Geographic Science Center, Moffett Field, CA, USA,

2U.S. Geological Survey, Western Ecological Research Center, Dixon, CA, USA, 3Point

Blue Conservation Science, Petaluma, CA USA, 4U.S. Geological Survey, California
Water Science Center, Sacramento, CA, USA
Presenting author email: tswilson@usgs.gov

California’s Central Valley is a highly productive agricultural region, but also a key
stopover along the Pacific migratory flyway, providing critical habitat for wintering
waterbirds in North America. Understanding and forecasting the distribution,
abundance, and connectivity of surface water and wetland habitats, as well as the
response of wildlife that depend on these habitats, is essential for maximizing the valueof management decisions for wildlife, ecosystems, and ecosystem services in thisregion. To identify potential future wetland habitat under a broad range of climate andland use scenarios, we integrated a climate-driven hydrologic water use model with aspatially explicit land change model. First, we adapted the non-spatial Water Evaluation
and Planning model for Central Valley’s waterbird habitat (WEAP-CVwh) to model five
future land use and climate scenarios from 2011 to 2101. Scenarios were developedwith multiple stakeholder engagement activities and represent a divergent range of
future climates, perennial expansion rates, water allocation priorities (i.e. for wetlands
and winter flooded agriculture), and habitat restoration goals. Next, we used the WEAP28

Wednesday Scheduled Sessions: Global Climate Change at the Estuary Scale
CVwh scenarios as input to the spatially-explicit Land Use and Carbon Scenario
Simulator (LUCAS) model to produce 270-m mapped scenario projections of land use
and flooded habitat out to 2101 based on varying climate futures, water availability,
management decisions, and competitive land-use related water demand. Our results
show significant declines (25 and 33%) in future flooded cropland habitat availability by
2101, even under favorable climate conditions, exposing habitat vulnerability to bothclimate, water prioritization and availability, and human land use. Even if the waterbird
and shorebird habitat restoration targets set forth in the Central Valley Joint Venture(CVJV) Implementation Plan are realized, such efforts may prove ineffective if notcoupled with both land use and water resource co-management.
Mapping Social Vulnerability to Climate Change in the Delta and Suisun Marsh
Avery Livengood1, Annie Merritt1, Harriet Ross1, Molly Williams1, Corianna
Flannery2, Jenna Seim3
1Delta Stewardship Council, 2California Department of Fish and Wildlife, 3California

Employment Development Department

Presenting author email: annie.merritt@deltacouncil.ca.gov
As part of the Delta Adapts climate change vulnerability assessment (VA), the Delta
Stewardship Council created a custom social vulnerability index (SVI) to identify themost socially vulnerable communities to climate change in the Delta and Suisun Marsh.
Delta Adapts defines vulnerability as the intersection of exposure to climate hazards,
sensitivity to those hazards, and adaptive capacity, or the ability to respond to andrecover from climate hazards. The SVI captures sensitivity and adaptive capacity toflooding, extreme heat, and wildfire smoke, by using 14 socioeconomic and healthindicators at the census block group and tract scale. Indicators were selected basedon a literature review that identified factors that increase vulnerability to the three
climate hazards of interest. Results indicate that the most socially vulnerable
communities are in West Sacramento, Antioch, Pittsburg, Stockton, and much of thesouthern Delta. In the Delta Adapts VA, climate hazard exposure data was overlaid on
the SVI results to identify communities most vulnerable to current and future climate
hazards.
The SVI has many potential uses relevant to Delta management. Understanding thesources of climate vulnerability in the Delta and how they interact to increase
vulnerability can help decisionmakers prioritize projects, research, andfunding to address those sources and increase the resilience of Delta communities. The
SVI is already being applied in this way: applicants for 2021 Delta Science Awards are
directed to use the SVI to evaluate whether their research project will benefit specificvulnerable communities in the Delta. Local governments could use the SVI as partof local climate vulnerability assessments to comply with SB 379. Ultimately, the SVI will
inform climate adaptation planning in the Delta region and help ensure that adaptation
actions are equitable.

29

Wednesday Scheduled Sessions: Global Climate Change at the Estuary Scale
Results of Integrated Modeling of the Physical Systems of the San Francisco BayDelta Estuary and Watershed for Future Scenarios
Noah Knowles1, Rosanne Martyr2, Fernanda Achete3, Mick van der Wegen4, Julia
Vroom4, Lisa Lucas1, Michelle Stern1, Dan Cayan5
1U.S. Geological Survey, Menlo Park, 2Climate Analytics gGmbH, Berlin, 3Federal

University of Rio de Janeiro, 4Deltares, Inc., 5Scripps Institution of Oceanography,
University of California, San Diego
Presenting author email: nknowles@usgs.gov

An improved understanding of how changes in climate may affect the San Francisco
Bay-Delta is needed to provide a context for long-term planning. The U.S. Geological
Survey has led a project (CASCaDE 2) designed to link models of the Bay-Delta estuary
and its watershed to help better understand the possible impacts of climate change on
the combined system. Meteorological quantities projected by an ensemble of global
climate models (GCMs) have been translated by models of watershed hydrology,
operations, and sediment into managed daily inflows, temperatures, and sediment loads
at the estuarine boundaries. The associated trends at the Delta boundaries include
increased wet-season Delta inflows, increased magnitude and frequency of extreme
high inflows, reduced dry-season inflows, increased water temperatures, and anincreased sediment supply. Linked hydrodynamical and water-quality modeling tools arebeing used to evaluate the impacts of these projected changes on the estuary. Results
describing changes over the 21st century for a scenario from a moderately warmer andwetter GCM include increased mean water levels and tidal ranges throughout the Delta
driven by sea level rise; increased water temperatures throughout the Delta that roughly
parallel the surface air temperature increase; increased salinity intrusion, particularly inthe dry season; additional reservoir releases required to comply with environmental
standards; and minor changes in salinity stratification, primarily in deeper channels.
Results for suspended sediment concentrations will also be discussed.
Re-Calibrating Sacramento and San Joaquin Water Year Types in a Changing
ClimateWyatt Arnold1, Romain Maendly1
1California Department of Water Resources

Presenting author email: wyatt.arnold@water.ca.gov
The Sacramento and San Joaquin water-year type indices are fundamental to theoperations of the State Water Project and Central Valley Project. Changes in theseasonal and total availability of water as a result of climate change may alter thefrequency distribution of the Sacramento and San Joaquin water year types. A
recalibration of water year types to shifting seasonal runoff patterns driven byatmospheric warming is tested for the California Water System. The analysis uses a
decision scaling approach previously developed and applied by both the California
30

Wednesday Scheduled Sessions: Global Climate Change at the Estuary Scale
Department of Water Resources and Delta Stewardship Council for climate change
vulnerability assessments. A paleo-informed 1,100-year climate trace of daily
precipitation and temperature is systematically perturbed to explore the climate
vulnerability domain of the California Water System to the full range of changes
projected by global climate models at a mid-century time horizon. Streamflows,developed using the Sacramento Soil Moisture Accounting distributed hydrologic model(SAC-SMA-DS), are input to the water system model, CalLite 3.0 to simulate thecoordinated operations of the California Water System. Because CalLite 3.0 simulates
the current regulatory framework built around water year types, the modeling platform iscapable of exploring how modifying water-year type calculations may affect Delta water
management objectives. With recalibration of water year types to maintain the historical,
paleo-informed estimated frequency of occurrence, the analysis suggests a tradeoff of
10,000 acre-feet between average annual Delta exports and Net Delta outflows per
degree Celcius of temperature rise, which is shown to mitigate some portion ofincreases in average annual salinity at key locations in the Delta. The results underline
the importance of anticipating more certain large-scale hydrologic changes driven byatmospheric warming and provide insight into potential policy levers for mitigating
impacts.
Spatial, Seasonal, and Climate Change Signals in Water Temperatures in theUpper San Francisco Estuary from 11 Discrete Monitoring Programs
Samuel Bashevkin1, Brian Mahardja2, Larry Brown3
1Delta Science Program, Delta Stewardship Council, 2U.S. Bureau of Reclamation,
3U.S. Geological Survey

Presenting author email: sam.bashevkin@deltacouncil.ca.gov
Temperature has profound impacts on ecosystem functions and biodiversity, fromsubcellular to community scales. Climate change is expected to increase watertemperatures in the upper San Francisco Estuary (SFE), which could impact native
species by inducing physiological stress, increasing predation pressure, interfering withreproduction, increasing food demands, and synergistically interacting with the effects ofother stressors. The continued persistence of many species may depend on localized
regions of temperature refuge, which could be co-located with restoration efforts toachieve maximum benefits. Before we can identify areas of refuge or adapt to expectedwater temperature increases, we must study the past to understand spatiotemporalwater temperature patterns and quantify the rate of temperature increase across theupper SFE. To accomplish these objectives, we compiled an integrated discretetemperature dataset of 11 boat-based surveys in the upper SFE, comprising over
100,000 temperature records from 1969-present. Using this dataset, we fit aspatiotemporally explicit generalized additive model to quantify the spatial landscape ofwater temperature for each year and month in the dataset. This model can generatetemperature estimates for each month and year in any location covered by the discretemonitoring dataset. Then, to estimate the rate and spatial variability of temperature31

Wednesday Scheduled Sessions: Getting into the Weeds: Aquatic Vegetation
increases, we fit a generalized additive mixed model to the subset of this dataset with
fixed sampling locations. This latter model estimated the linear rate of temperature
increase over all years in the dataset and allowed that rate to vary seasonally andspatially. Temperature increased significantly over time (average of 0.02 °C/year), andthis rate varied seasonally and spatially. These findings can be used to estimate
expected impacts of climate warming on native species and to prioritize restoration sites
based on past and expected future temperature trends.

Getting into the Weeds: Aquatic Vegetation
Using Sentinel-2 to Provide Open-Access Tools for Plant and Water Mapping in
the Sacramento Bay-Delta
Julia Burmistrova1, Christiana Ade1, Shruti Khanna2, Mui Lay3, Adam Weingram1,
Erin Hestir1
1University of California, Merced, 2California Department of Fish and Wildlife, 3Universityof California, Davis

Presenting author email: jburmistrova@ucmerced.edu
Building resilient Bay-Delta ecosystems is underpinned by monitoring, and satellite
remote sensing provides many robust and diverse monitoring methods. Satellite remotesensing offers systematic, repeat measurements that create time series of different
performance metrics, for example, aquatic vegetation community composition, plant
traits, and their change over time, wetland biomass turnover, or dynamics of floodplain
inundation. The Sentinel-2 mission, recently launched by the European Space Agency,
provides free, open access data and an excellent opportunity to develop ecosystem
performance metrics from satellite remote sensing. The mission provides a 5-day revisit
time, 10-meter spatial resolution on the ground for 4 bands in the visible and nearinfrared region, and 20-meter spatial resolution for another 9 bands ranging from thevisible to the shortwave-infrared region. The Sentinel-2 sensors, and theirreplacements, are fully funded for the next two decades, offering the opportunity for highresolution, high-frequency continuous mapping in the entire Delta regularly. Using
imagery downloaded from 2017 to 2020, we created open-source software workflowsfor 20-meter resolution aquatic vegetation functional type maps, phenology time series
and derived metrics, and inundation metrics of a variety of restoration sites and the Yolo
Bypass. Regular meetings with different stakeholders and working groups, such as theInteragency Ecological Program, provided feedback to strengthen these tools' utility fora broad range of managers, agencies, and other interested parties. The long term
objective of this work is to ensure that all methods developed for this project, including
algorithms with rigorous uncertainty quantification and well-documented open-source
software workflows for monitoring aquatic and marsh plant communities, can be usedbroadly to meet Delta science and management needs.

32Wednesday Scheduled Sessions: Getting into the Weeds: Aquatic Vegetation
Invasive Aquatic Vegetation Detection using Hyperspectral Remote Sensing from
UAV
Erik Bolch1, Erin Hestir1
1University of California, Merced

Presenting author email: ebolch@ucmerced.edu
Invasive plants are non-native species that can spread rapidly, leading to detrimental
economic, ecological, or environmental impact. In aquatic systems such as the
Sacramento-San Joaquin River Delta in California, USA, management agencies use
manned airborne hyperspectral remote sensing missions to map and track annualchanges in invasive aquatic plants. Advances in unmanned aircraft and sensor
miniaturization are enabling higher spatial resolution species mapping, which ispromising for early detection of invasions before they spread over larger areas. This
study compared maps made from unmanned aircraft-based hyperspectral remotesensing with the manned airborne hyperspectral remote sensing-derived maps thatcurrently produced for monitoring invasive aquatic plants in the Sacramento-San
Joaquin Delta. Concurrent imagery was collected using the HyMap sensor and the
Nano-Hyperspec at a wetland study site and classification maps generated using
random forest models were compared. Classification accuracies were comparable
between the Nano- and HyMap-derived maps, with the Nano-derived map having aslightly higher overall accuracy. Additionally, the higher resolution of the Nano imagery
allowed detection of patches of water hyacinth present in the study site that the HyMap
could not. This study establishes the techniques and workflows for vegetation
community assessments in support of the Proposition 1 CDFW-funded research project"Ecosystem Engineering Impacts of Water Primrose in the Delta." However, it would not
be feasible to operate the Nano as a replacement to HyMap at scale despite its
improved detection capabilities to due to the high costs associated with overcomingarea coverage limitations. Overall, unmanned aircraft-based hyperspectral remotesensing provides comparable or improved capability, and we suggest it could be used tosupplement existing monitoring programs by focusing on target areas of high ecologic
or economic priority, or to support scientific investigations, such as floating aquaticvegetation invasion dynamics.
The Potential of Satellite Remote Sensing Time Series to Uncover Wetland
Phenology under Unique Challenges of Tidal Setting
Gwen Miller1, Iryna Dronova1, Patty Oikawa2, Sara Knox3, Lisamarie WindhamMyers4
1University of California, Berkeley, 2California State University, East Bay, 3University of

British Columbia, 4U.S. Geological Survey

Presenting author email: gjmiller@berkeley.edu

33

Wednesday Scheduled Sessions: Getting into the Weeds: Aquatic Vegetation
The San Francisco Bay Delta (Bay Delta) is one of the largest continuous estuarine
systems in the United States. It is well known that wetland vegetation sequesters
carbon in their below and above ground biomass, however through plant and microbial
respiration greenhouse gases such as carbon dioxide and methane are released backinto the atmosphere. This makes understanding of seasonal plant growth within
wetlands a vital input into greenhouse gas modeling; however, across the large study
region with limited site access frequent field surveys of biomass become impractical.
Here our goal is to extrapolate the seasonal vegetation growth curve and assess its
regional variation within the Bay Delta using vegetation indicators from the time seriesof publicly available images of Landsat 8, a multispectral satellite. In this effort, we also
aim to address the major challenges for landscape-scale assessments of wetland plant
phenology due to spatial and temporal variability in tidal flooding and plant biomass,
impacting the satellite signal of vegetation.
Using Google Earth Engine (GEE), we acquired and processed Landsat, climate, andelevation data within the Bay Delta region focusing on the years 2013–2020. Using a
subset of the data from GEE we trained a series of models estimating Landsat-based
indicators of plant greenness over a given time period. We compared models using
Akaike Information Criterion analysis and determined the highest-support model
including temperature, elevation, Palmer drought severity index, day of the year, andthe historical mean greenness observed at the given pixel.
Results indicate that our modeling approach can estimate plant greenness within the
Bay Delta’s tidal marshes reasonably well. Higher model errors were observed largely inmanaged marshes, salt ponds, and disturbed marshlands. Our approach circumvents
mentioned challenges and provides a useful tool for estimating wetland phenology tosupport ecosystem modeling over large spatial scales.
Ecosystem Engineering Impacts of Invasive Submerged Aquatic Vegetation in the
Delta
Judith Drexler1, Shruti Khanna2, Jessica Lacy3
1U.S. Geological Survey, California Water Science Center, 2California Department ofFish and Wildlife, 3U.S. Geological Survey, Coastal and Marine Science Center
Presenting author email: jdrexler@usgs.gov

Invasive submerged aquatic vegetation (SAV) acts as an ecosystem engineer byaltering water chemistry, plant community composition, and phytoplankton productivity.
Less is known about how invasive SAV affects long-term ecosystem processes such ascarbon storage and sediment dynamics. In this study, we determined whether Egeria
densa (Brazilian waterweed), a globally invasive species of SAV, is storing “bluecarbon” and trapping sediment required by adjacent marshes to maintain their elevationin the tidal frame. We studied three sites in the Sacramento-San Joaquin Delta withdiffering energy dynamics. At each site, we collected (1) five surficial push cores in
sediments within and outside of E. densa patches, (2) two sediment cores on the marsh34

Wednesday Scheduled Sessions: Getting into the Weeds: Aquatic Vegetation
plain, and 3) two gravity cores under E. densa patches. Bulk density, % organic carbon,
and loss on ignition were determined for all cores and 210Pb, and 137Cs were measured
in marsh and gravity cores. Our results show that E. densa patches function as sinks
for carbon and inorganic sediment under all three energy regimes studied. Compared tomarshes, E. densa patches have greater inorganic sedimentation rates (E. densa: 1103
– 5989 g m-2 yr-1, marsh: 393 – 1001 g m-2 yr-1, p < 0.01) and vertical accretion rates (E.
densa: 0.4 – 1.3 cm yr-1, marsh: 0.3 – 0.5 cm yr-1, p < 0.05), but similar carbon
accumulation rates (E. densa: 59 – 242 g C m-2 yr-1, marsh: 109 – 169 g C m-2 yr-1, p >0.05). Due to its harmful traits, planting E. densa to achieve carbon storage benefits
would likely result in a disproportionate amount of negative impacts vs. positive gains.
Our results suggest that invasive estuarine SAV such as E. densa reduces theresilience of adjacent marshes to sea-level rise by trapping sediment that would
otherwise have been available for marsh accretion.
Floating Wetlands for Food-Web, Greenhouse Gas Benefit and Potential
Subsidence Reversal
Steven Deverel1 | 2, Carson Jeffres2 | 3, Sabina Dore1 | 2, Nicholas Corline2
1HydroFocus, Inc., 2Virginia Tech, 3University of California, Davis, Center for Watershed

Science

Presenting author email: sdeverel@hydrofocus.com
The Delta pelagic food web no longer adequately supports native
species. Development of management strategies for food-web support and habitat forfish species of concern is a key goal and substantial challenge. It is expected that
restoration of tidal-wetland food webs will produce resources that will benefit species ofconcern on-site, and through export, will support pelagic habitat in adjacent waters andregionally. However, Delta-island subsidence substantially inhibits timely and largescale tidal restoration in most of the central and western Delta. While the food-web andhabitat benefits of fresh-water tidal wetlands that dominated the pre-reclamation Delta
are not well documented, recent research provided a reasonable case for experimental
implementation. Considering the difficulty of creating tidal habitat on subsided Deltaislands, floating peat mats that could provide marsh habitat, which is hydraulicallyconnected to Delta waterways, are being investigated on Bouldin Island. Peat blocks
were excavated from the Twitchell Island wetland which was permanently flooded in
1997 and placed in eight mesocosms (18-foot diameter Doughboy pools) on Bouldin
Island in 2019. The peat blocks have continued to float and produce emergent
vegetation (primarily Schoenoplectus sp).
Floating peats supported zooplankton communities in the pelagic space between thebenthos and the peat mat. Zooplankton function as a trophic link between basal carbon
sources (detrital/primary production) and higher trophic levels. As such, zooplankton
abundance and species composition are good indicators of productive potential.
Zooplankton abundances remained relatively stable throughout the year after the peats
were placed in the mesocosms. There was an apparent lag in colonization by35

Wednesday Scheduled Sessions: Social Science and Human Dimensions
macroinvertebrates but as the sites became colonized over time, taxa observed weretypical of wetland habitats. Water quality data, gas flux measurements andquantification of wetland biomass provide evidence for the GHG benefit of floating peats
on subsiding peat soils and long-term continued flotation.

Social Science and Human Dimensions
Hunters as Stakeholders in the Bay-Delta Watershed
Virginia Matzek1, Frank Lupi2, Liam Healey1
1Santa Clara University, 2Michigan State University

Presenting author email: vmatzek@scu.edu
Hunters are major recreational users of the Bay-Delta watershed, hunting waterfowl in
its freshwater and tidal marsh areas as well as deer and upland gamebirds in theriparian forests and grasslands along its source rivers. As part of a larger project aimed
at assessing the economic value to hunters of riparian and tidal marsh restoration, wesurveyed more than 1100 hunters about their experiences during hunting season 201920. Preliminary data show that waterfowl hunters were more satisfied with the quality of
the habitat in Central Valley managed ponds and in Suisun Marsh than in sites recently
reclaimed from industrial uses in the North Bay and South Bay. Deer and gamebird
hunters generally preferred restored sites to unrestored sites, but responses on habitat
quality were more mixed. Loss of the spring turkey season to COVID-19 shutdowns
complicated this analysis and decreased sample sizes. We also report results from asmaller survey on the demographics of hunters, their preferences for water andvegetation management at hunt areas, and their opinions about the effects of drought,
fire, climate change, and invasive species on the sustainability of the sport. Our findings
can help inform managers of wildlife refuges and wildlife areas about the needs andpreferences of this important stakeholder group.
From California’s Water Wars to America’s Culture Wars: A Media Analysis of the
Delta Smelt Controversy
Caleb Scoville1
1Tufts University

Presenting author email: caleb.scoville@tufts.edu
In recent decades Americans’ attitudes about environmental issues have becomepolarized along partisan lines. While significant research demonstrates this broad trend,
we know less about the meso-level processes that produce and sustain such divisions.
Drawing on over 3,000 news articles, nearly 14,000 Tweets, and Google search data, I
analyze the public sphere controversy surrounding the delta smelt, an endangered
species of fish caught in the center of California water politics. Legal protections of the36

Wednesday Scheduled Sessions: Social Science and Human Dimensions
species have impacted water conveyance to farms and cities. Most observers view thecontroversy as a simple reflection of pre-existing interests. This explanation cannot
capture the cultural appeal of the delta smelt to right-wing observers disproportionate toits modest impact on water policy. Offering an alternative explanation, I show that how
the delta smelt became a means by which California’s “water wars” became enrolled
into America’s “culture wars.” I show that the delta smelt is more meaningful for
opponents to environmental protection than proponents, and for those outside California
than inside of it. Next, I trace the controversy over time to show how skillful partisan
elites articulated continuity between a narrow set of material interests and broader
partisan identities which stand in symbolic opposition to liberal environmentalism bydrawing on extant cultural, political, and geographic resentments. Finally, I show how
the delta smelt’s unique symbolic power owes in part to its physical characteristics asan “uncharismatic microfauna.” By showing how the delta smelt became a symbol ofpartisan animosity, this study offers a processual and case-analytic complement to theburgeoning body of quantitative work on environmental partisan polarization.
Wings Landing Tidal Habitat Restoration Project Environmental Education
ProgramForest Halford1, Ryan Lopez1, Skip Moss1, Tom Taylor1, Caitlin Roddy2, Trisha
Velasquez2
1Natural Resources Group, Inc., 2California Department of Water Resources

Presenting author email: rlopez@natural-resources-group.com, ttaylor@naturalresources-group.com
The 267-acre Wings Landing Tidal Habitat Restoration Project is located in the Upper
Suisun Marsh and was completed in fall of 2020. Permit conditions required publicaccess; however post-restoration site constraints left no publicly accessible land. Most
marsh or wetland restoration projects are located far from public access points withlimited, difficult, or distant access. The close proximity of Wings Landing to the public
Suisun City boat launch provided the unique opportunity for safe water access to therestoration site. The Wings Landing Project Team developed the Wings Landing Tidal
Habitat Restoration and Suisun Marsh Natural History and Cultural Kayak Tour Program(Program). The Program supports environmental education for low income and minority
students through a partnership with a local Title I middle school. The Program also
partners with a local Native American Tribe and will provide opportunities for Native
American youth to experience their cultural heritage within the Suisun Marsh. Researchshows that children who spend time outdoors in natural environments experience
improved health and cognitive functions, strong motor coordination, reduced stress,enhanced social skills, increased enthusiasm toward school, and have fewer
attendance problems. The Program provides direct community outreach to local youth,
many of whom have not had opportunities to learn about the cultural, recreational, andecological importance of the Suisun Marsh, despite it being located in their “back yard”.
Under the Program, groups of students will paddle kayaks to the Wings Landing Tidal
37

Wednesday Scheduled Sessions: Social Science and Human Dimensions
Habitat Restoration Site where instruction will be provided on natural history, birding,wetland ecology, tidal marsh restoration, and Native American history by trained
docents. This Program will expand the environmental benefits of the Wings Landing
Tidal Habitat Restoration Project beyond its biological attributes, to include the social
sciences and address environmental justice issues in underserved communities.
Surfacing Areas of Consensus and Disagreement Across Diverse Practitioner
Groups to Inform Science & Restoration Priorities for Salmonids in the Bay Delta
Natascia Tamburello1, Cedar Morton1, Clint Alexander1, Collaborative Adaptive
Management team (CAMT) Salmonid Sub-Committee2
1ESSA Technologies Ltd., 2Collaborative Adaptive Management team (CAMT) Salmonid

Subcommittee

Presenting author email: ntamburello@essa.com
The many organizations and programs working to support salmonid recovery in the Bay
Delta have given rise to numerous initiatives, each with their own specific objectives,approaches, and recommended priority activities. However, a lack of alignment andcoordination of mandates across these initiatives have made it challenging tounderstand science, management, and monitoring priorities of greatest benefit tosalmonids in a way that also considers stakeholder perspectives, a key aspect of the
Delta Stewardship Council’s Science Action Agenda.
To shed light on cross-cutting priorities, previously proposed salmonid science,
management, and monitoring activities were first collated from a wide range of existingplans, strategies, and studies. This set of over 300 prospective activities formed thebasis of a rigorous online Q-survey that solicited perspectives on the relative benefits ofactivities from 50 experienced salmonid science and management practitioners acrossa diverse range of organizations. Analysis of results revealed practitioner perspectives
on the relative benefits and implementability of activities as well as the level ofagreement in responses across organizations. Results were used to shortlist a set of 41
activities across three themes that emphasize key dimensions to consider in decisionmaking: (1) beneficial activities with high across-group consensus regarding benefits;(2) beneficial activities also considered easiest to implement; and (3) beneficial activities
with the least across-group consensus about benefits.
By comparing activities within each theme, practitioners can identify potential projects
representing low-hanging fruit, opportunities for collaboration, or areas where more
information and discussion is needed to increase alignment. This study will also assist
planners to more effectively consider the human dimensions of natural resource
management decisions in their deliberations on potential projects intended to benefit
salmonids in the Delta and, in doing so, also help to support the objectives of the
Science Action Agenda.

38

Wednesday Scheduled Sessions: IEP Session: Success at Different Trophic Levels:
Gaining Insight from Nutrients to Otoliths
Governing Multiple Forms of Connectivity in the Bay-Delta
Annika Keeley1, Eva Bush1
1Delta Stewardship Council, Delta Science Program

Presenting author email: annika.keeley@deltacouncil.ca.gov
Governance of cross-scale dependent systems such as estuaries requires integratingknowledge about biophysical and ecological connectivity in its multiple forms andscales. While scientists, managers, and policy-makers are increasingly recognizing theimportance of connectivity, ecosystems with strong cross-boundary dependencies
challenge current environmental governance structures. Managing connectivity, in eachof its forms, requires building social connectivity to increase the flow of information andsocial and financial capital among both formal and informal governance bodies. We
describe the diverse forms of connectivity in the San Francisco Estuary in their naturaland human-impacted states, and demonstrate the human dimensions of restoring
ecosystem processes. Connectivity occurs along four spatial dimensions: cross-scale toadjacent and distant ecoscapes, longitudinally, laterally, and vertically. It involves
marine, brackish and freshwater aquatic, and terrestrial systems. Work in the Bay-Delta
shows that for restoring connectivity to distant ecoscapes collaboration between
international jurisdictions, finding multi-benefit solutions, and devising funding
mechanisms for large-scale restoration are vital. Restoring longitudinal connectivity isdifficult to balance with flood control and water supply for human communities andagriculture, and intense management actions sometimes need to replace naturalprocesses. Reestablishing lateral and vertical connectivity in estuaries, for example
through reconnecting floodplains to the rivers and curbing groundwater overdraft, canbe a trade-off between water use for humans and ecosystems. Economic disparities
need to be considered in the planning process when leveraging ecosystem services offloodplains such as flood control. To increase ecosystem resilience in the Bay-Delta werecommend (1) identifying a set of metrics to represent estuarine connectivity andmonitor changes in connectivity over time, (2) assessing tradeoffs among the different
forms of connectivity, (3) creating or enhancing social networks for conservation,
management, and restoration of natural processes, and (4) governing, managing, andproviding funding at a system level to regain natural connectivity.

IEP Session: Success at Different Trophic Levels: Gaining Insightfrom Nutrients to Otoliths(*IEP) A View from the Landscape Scale: Using Spatial Variation of Nutrients andPhytoplankton Across the Delta to Identify Underlying Biogeochemical Processes
Brian Bergamaschi1, Tamara Kraus1, Katy O'Donnell1, Jeniffer Soto-Perez1, Emily
Richardson1, Ayelet Delascagigas1, Elizabeth Stumpner1, Chuck Hansen1, Angela
Hansen1, Alan Gelber1, Crystal Sturgeon1, Bryan Downing1
1U.S. Geological Survey, California Water Science Center

39

Wednesday Scheduled Sessions: IEP Session: Success at Different Trophic Levels:
Gaining Insight from Nutrients to Otoliths
Presenting author email: bbergama@usgs.gov
Identifying management actions that may help protect pelagic food webs in the
Sacramento-San Joaquin Delta (Delta) is difficult because of the complex interactions
between phytoplankton, nutrients, hydrodynamics, and landscape features. Gaining abetter understanding of these interactions is important to help evaluate effects of the
upgrade to the Sacramento Regional Wastewater Treatment Plant (SRWTP) as well as
the potential effects of future changes, such as additional nutrient-management actions,large-scale wetland restoration, drought, flood, levee failure or changes to water
management.
We investigated these interactions by characterizing the abundance and distribution ofnutrients and phytoplankton across much of the Delta during different hydrologic
conditions using high-speed moving-boat surveys. The concentration and spatial
distribution of all major nutrient forms were collected simultaneously with information
about the major classes of phytoplankton and associated water quality conditions.
These data comprised spatial surveys that used continuous underway high frequency
sampling and measurements onboard a high-speed boat, allowing for thecharacterization of spatial variation across the breadth and width of the Delta.
The results reveal astonishing variation across both space and time, with nutrient
concentrations varying from near zero to eutrophic, most often related to hydrologic
mixing and water residence time. Phytoplankton productivity appeared to be a strong
sink for nutrients in the Delta, suggesting that phytoplankton uptake is a larger control
on nutrient concentrations than previously appreciated. Phytoplankton abundance
ranged from near detection to bloom concentrations, with large variation in community
composition, but little direct relationship to nutrient concentration or form. Contrary to
expectations, we did not observe significant nutrient depletion near landscape-scalefeatures such as open water habitats, submerged aquatic vegetation beds, extensive
wetlands or exposed sediments, suggesting these habitat types do not act as major
sinks for nutrients in the Delta.
(*IEP) Nine Years of Flow Pulses: A Synthesis of Water Quality, Plankton
Subsidies and Fish Communities in the North Delta
Brittany Davis1, David Bosworth1, Ted Flynn2, Nicole Kwan1, Rosemary Hartman1,
Sarah Perry1, Jesse Adams1, Jenna Rinde3, Catarina Pien1, Mallory Bedwell1, Traci
Treleaven1, Amanda Maguire1, Jeff Jenkins1, Hailey Wright1, Jared Frantzich1,
Laura Twardochleb1
1California Department of Water Resources, 2Delta Stewardship Council, 3California

Department of Fish and Wildlife

Presenting author email: brittany.e.davis@water.ca.gov,
laura.twardochleb@water.ca.gov
Resource management in the San Francisco Estuary (SFE) is largely focused on
maintaining freshwater inflow to improve habitat conditions for endangered fishes such40

Wednesday Scheduled Sessions: IEP Session: Success at Different Trophic Levels:
Gaining Insight from Nutrients to Otoliths
as Delta Smelt (Hypomesus transpacificus). In addition to habitat, food-limitation in the
SFE is hypothesized to be a driver of fish declines. Studies in the North Delta region of
the SFE have shown that phytoplankton blooms and increases in zooplankton
abundance have followed hydrological changes (i.e. flow pulses or above-average
flows) in the Yolo Bypass during summer or fall. These observations led to an ongoing
adaptive management strategy known as the North Delta Flow Action, using a managed
flow action to alter summer-fall net outflow in the Yolo Bypass to increase the availabilityof plankton in important downstream fish habitat in the Cache Slough Complex.
Through coordinated water operations, three augmented flow pulses have now been
conducted with the overall goal to redistribute food through the North Delta andpotentially trigger a downstream plankton bloom. However, the effects of flow actions on
downstream food availability have varied across years. Here, we present a synthesis
study of all summer-fall flow events in the Yolo Bypass monitored since 2011 to 2019 toevaluate the efficacy of the management action to improve habitat and food conditions
downstream for Delta Smelt. We compiled, integrated and analyzed physical, chemical,
and biological monitoring data (e.g., phytoplankton, zooplankton, fish) from Interagency
Ecology Program surveys throughout the North Delta to quantify meaningful changes inwater quality and biota in response to non-managed and managed-flow pulses.
Additionally, we assessed how pulse water source (agriculture drainage or Sacramento
River), hydrologic year, and antecedent conditions may influence food web responses
to flow pulses. This synthesis provides critical information for adaptive management offlow actions and ecological resources in the North Delta.
(*IEP) I’m not that Shallow – Surprising Similarity in Zooplankton Communities
Collected at Different Depths Near Wetland Restoration Sites.
Rosemary Hartman1, Michelle Avila2, Arthur Barros2, Christy Bowles2, Daniel
Ellis2, April Hennessy2, Trishelle Tempel2, Stacy Sherman2
1California Department of Water Resources, 2California Department of Fish and Wildlife

Presenting author email: rosemary.hartman@water.ca.gov
Wetland restoration has been identified as a key management tool for increasing foodavailability for at-risk fishes in the San Francisco Bay-Delta Estuary. To characterize thebenefits of restoration sites, it is critical to quantify the abundance and composition offood resources in and near the wetlands. Characterization of zooplankton communities
is considered particularly important, but accurate analysis of zooplankton samples istime-consuming and expensive. The recently established Fish Restoration Program
Monitoring Team assessed whether data from existing IEP surveys could be used tocharacterize shallow-water zooplankton communities prior to restoration. During thespring of 2017-2019, FRP collected zooplankton samples near the mouth of tidal
wetland sites, or immediately outside future restoration sites, and compared themto samples collected roughly concurrently in adjacent channels by IEP long-termmonitoring surveys. We found many seasonal and landscape-scale differences in
species composition, but very few differences in community composition between
41

Wednesday Scheduled Sessions: IEP Session: Success at Different Trophic Levels:
Gaining Insight from Nutrients to Otoliths
shallow and deep samples collected concurrently. We found higher overall CPUE in the
deeper samples collected by IEP, but this may be due to inconsistencies in towing
speed and gear type, rather than habitat differences.
(*IEP) Every Cog and Wheel: Understanding the Importance of Genomic Diversity
in Central Valley Chinook Salmon
Mariah Meek1, Shannon O'Leary1 | 2, Tasha Thompson1, Melinda Baerwald3
1Michigan State University, 2St. Anselm College, 3California Department of Water

Resources

Presenting author email: mhmeek@msu.edu
The field of genomics is rapidly increasing our understanding of biodiversity and its
distribution across species and populations. This includes recent advances in theidentification and quantification of genomic diversity in Central Valley Chinook salmon.
These advances have strong implications for the conservation and management of thedifferent run types. In this talk, we will both provide a synthesis of the recent
developments in our understanding of genomic diversity in Central Valley Chinook
salmon, as well as present the results of our new analyses of genomic diversity.
Together with previous work, this new assessment demonstrates the uniquecontribution of each Chinook tributary population to the genetic portfolio of the entire
Central Valley population complex, and emphasizes the need to protect each run andtributary to ensure the health and sustainability of Central Valley Chinook salmon.
Additionally, we will highlight how we are using these new insights to develop better
tools to allow rapid genetic identification of the different Chinook runs. This tool
development will revolutionize the way we can identify the ESA listed runs in the field in
real time and drastically improve our ability to sustainably manage Central Valley
Chinook salmon.
(*IEP) Years in their Ears: What can Fish Earbones Tell Us About Spring-Run
Chinook Salmon Success in an Increasingly Volatile Climate?
Flora Cordoleani1 | 2, Corey Phillis3, Anna Sturrock4, George Whitman5, Rachel
Johnson2 | 5
1University of California, Santa Cruz, 2NOAA Fisheries, 3Metropolitan Water District,
4University of Essex, 5University of California, Davis

Presenting author email: flora.cordoleani@noaa.gov
To track changing climate regimes, many species have shifted their phenology,
distribution, and abundances. For salmon populations, life history diversity is one way tobuffer themselves against natural or anthropogenic perturbations. Plasticity in migration
timing may be particularly important, as their ability to respond spatially to adverse
42Thursday Scheduled Sessions: Advances in Understanding Thermal Effects on
Salmon and Temperature Management for Salmon in the Central Valley
ambient conditions is constrained by the configuration of the stream network. In theCentral Valley, land-use changes have fragmented river corridors and restricted accessto high-elevation habitats that would have otherwise provided thermal refugia for
Chinook salmon populations. Therefore, restoring local landscapes that support climateadapted behaviors is critical to increase salmon resilience to future climate changes.
To investigate how life history diversity may allow threatened Central Valley spring run
Chinook (CVSC) salmon populations to persist in a warming climate we used otolithstrontium isotopes to reconstruct the juvenile migratory strategies of adults sampled inMill, Deer and Butte Creeks (the last three self-sustaining CVSC populations) between
2003 and 2018. For Mill and Deer Creek populations we found that yearling migrants,
an increasingly rare phenotype, were critical to cohort success during drought years.
Cool summer temperatures, critical for supporting the yearling strategy, were only foundin a few accessible Central Valley tributaries. Providing access into high elevation
habitats might be vital to allow these populations to persist in a rapidly changing climate.
For Butte Creek returns, we found that most had emigrated as subyearlings, andstrongly benefited from access to the Sutter Bypass floodplain for increased growth
opportunities. Our findings are an important step towards identifying the management
strategies that will protect and promote expression of life-history diversity that
contributes to CVSC recovery and stability in California’s warming climate.

Thursday Scheduled Sessions
Advances in Understanding Thermal Effects on Salmon andTemperature Management for Salmon in the Central Valley
Physiological Variation in Thermal Traits among Eight Populations of Chinook
Salmon from the West Coast
Kenneth Zillig1, Robert Lusardi1 | 2, Dennis Cocherell1, Nann Fangue1
1Department of Wildlife, Fish and Conservation Biology, University of California, Davis,
2Center for Watershed Sciences, University of California, Davis

Presenting author email: kwzillig@ucdavis.edu
Fish populations, and salmonids specifically, are known to match their physiology to the
local thermal environment. This physiological plasticity can be a result of acclimatizationand local adaptation. Chinook salmon exist across a large latitudinal range, withindividual populations experiencing a variety of temperature regimes. Within California
Chinook salmon, those living at the southern range boundary appear to be quite
thermally tolerant; however, without direct comparisons with other populations anditerated across acclimation regimes, our understanding of the thermal capacity of
Chinook salmon remains limited. Our work compares the thermal biology among 8
populations of Chinook salmon: five California hatchery populations, including Central
Valley Spring and Winter-run, and three populations form Oregon and Washington
hatcheries. Each population was reared at three acclimation temperatures (11, 16 and43

Thursday Scheduled Sessions: Advances in Understanding Thermal Effects on
Salmon and Temperature Management for Salmon in the Central Valley
20°C) to explore interpopulation variation in acclimation capacity and thermal
physiology. Physiological thermal performance metrics included growth, critical thermal
maxima swimming capacity and energetics (i.e., aerobic scope). Results indicate that
populations do differ in their thermal capacity and acclimation response, with variation
occurring over a latitudinal range and among life-history strategies (run-timing). Our
work is relevant to the management of salmonid populations undergoing rapid
environmental change. Understanding the differences between populations, and theircapacity to acclimate or adapt to future climate conditions is essential to effectively
managing these vulnerable stocks.
Survival Thresholds for Chinook Salmon Smolts in the Sacramento River
Cyril Michel1, Jeremy Notch1, Flora Cordoleani1, Arnold Ammann2, Eric Danner2
1University of California, Santa Cruz & NMFS-SWFSC, 2NMFS-SWFSC

Presenting author email: cyril.michel@noaa.gov
In California’s Central Valley, studies have found that increased streamflow can improvesurvival of imperiled juvenile salmon populations during their oceanward migration.
These studies have not explored the potential nonlinearities between flow and survival,
giving resource managers the difficult task of designing flows intended to help salmon
without clear guidance on flow targets. We used an information theoretic approach toanalyze migration survival data from 2,436 acoustic-tagged juvenile Chinook salmon
from studies spanning differing water years (2013-2019) to extract actionable
information on the flow-survival relationship in the Sacramento River. This relationshipwas best described by a step function, with three flow thresholds that we defined asminimum (4,259 cfs), historic mean (10,712 cfs), and high (22,872 cfs). Survival varied
by flow threshold: 3.0% below minimum, 18.9% between minimum and historic mean,
50.8% between historic mean and high, and 35.3% above high. We also found evidence
that these flow-survival thresholds were likely driven by water temperatures, fish travel
times, and floodplain connectivity.
We used these thresholds to design alternative hydrographs over the same years that
implemented managed spring pulse flows so as to leverage these survival thresholds.
We compared predicted cohort migration survival between actual and alternativehydrographs. Managed hydrographs with pulse flows that targeted high survival
thresholds were predicted to increase annual cohort migration survival by 55% to 132%
without any additions to the water budget, and by 79% to 330% with a modest addition
to the water budget. These quantitative estimates of the biological consequences ofdifferent flow thresholds provide resource managers with critical information for
designing flow regimes that benefit salmon in California’s highly constrained water
management arena.

44

Thursday Scheduled Sessions: Advances in Understanding Thermal Effects on
Salmon and Temperature Management for Salmon in the Central Valley
Exploring the Drivers of River Temperature Below a Large Dam, an Example fromthe Sacramento River
Miles Daniels1, Eric Danner2
1University of California, Santa Cruz, Institute of Marine Sciences, Affiliated with:

Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine
Fisheries Service, National Oceanic and Atmospheric Administration, 2Fisheries
Ecology Division, Southwest Fisheries Science Center, National Marine FisheriesService, National Oceanic and Atmospheric Administration
Presenting author email: miles.daniels@noaa.gov
Water flow and temperature play a critical role in salmon health, especially during earlylife stages where exposure to high water temperature in spawning grounds can drive
high mortality rates. Large reservoirs can fundamentally alter downstream watertemperatures, and dams are often operated to protect thermal regimes of downstream
ecosystems. In this study we modeled water temperature dynamics in a large regulated
river (Sacramento River, CA) to better understand how thermal flux, and ultimately rivertemperature, responded to different physical drivers. Specifically, we used global
sensitivity analysis to identify the dominant physical drivers of temperature in the
Sacramento River and explored how these drivers varied over space and time. We alsosought to better understand the relationship between upstream boundary conditions(dam discharge temperature and volume) and under what conditions downstream watertemperature responded more to perturbations of either of these two inputs.
Understanding spatial and temporal extents of drivers of water temperature and therelative importance of these factors is critical when managing for river watertemperature. This presentation will focus on understanding the drivers of river watertemperature in the Sacramento and relate findings to the management of anadromous
fish species.
The Biophysical Basis of Thermal Tolerance in Salmon Eggs and the Implicationsfor Sacramento River Winter-Run Chinook Salmon
Eric Danner1, Ben Martin1 | 2 | 3, Miles Daniels1 | 2, Peter Dudley1 | 2, Neosha Kashef1 |2, David Stafford1 | 2, William Reeder4, Daniele Tonina4, Annelise Del Rio3, Scott
Foott5
1Southwest Fisheries Science Center, National Marine Fisheries Service, National

Oceanic Atmospheric Administration, 2University of California Santa Cruz, 3University of
Amsterdam, 4Center for Ecohydraulics Research, University of Idaho, 5U.S. Fish andWildlife Service
Presenting author email: eric.danner@noaa.gov
Construction of Shasta Dam created Lake Shasta, the largest reservoir in California andlargest provider of water, via the Sacramento River, to the Delta. The dam blocks the
upstream migration of anadromous fish, including endangered Sacramento River
45

Thursday Scheduled Sessions: Advances in Understanding Thermal Effects on
Salmon and Temperature Management for Salmon in the Central Valley
Winter-run Chinook salmon (SRWRCS), which are now forced to spawn in themainstem Sacramento River below the dam. Salmon eggs require cold water todevelop, and operations of Shasta Dam now control the thermal quality of the remaining
SRWRCS spawning habitat. There is not enough cold water in the thermally stratified
reservoir to meet temperature targets in all years, resulting in significantly lower
observed egg to juvenile survival when temperature targets are exceeded. However,this decrease in observed survival is significantly lower than what can be explainedusing temperature criteria derived from laboratory experiments.
We have attempted to address this discrepancy through a series of models and refinedlaboratory experiments. Our work has resulted in two main conclusions. First, egg
thermal tolerance is not fixed, but depends on the complex interactions between
developmental stage, ambient O2 concentration, interstitial flow velocity, and theproximity to neighboring eggs. Second, as a result of this complex interaction, thermal
tolerance is significantly lower under field conditions than had been predicted fromlaboratory experiments. There are important management implications of this work
because the amount and timing of water release from Shasta Dam has significant
impacts on egg survival, and also on the amount of water reaching the Delta. To placethese findings within a management context, we developed a biophysical model of O2
limitation that provides a mechanistic explanation for the elevated thermal sensitivity offish embryos. This model can be used to quantify the temperature dependent egg
mortality associated with any range of water operations scenarios, including near andlong-term climate impacts.
Quantification of Thermal Impacts Across Freshwater Life Stages to Improve
Temperature Management of Anadromous Salmonids
Alyssa FitzGerald1 | 2, Sara John1 | 2, Travis Apgar3, Benjamin Martin4
1Institute of Marine Sciences, University of California Santa Cruz, 2Fisheries Ecology

Division, Southwest Fisheries Science Center, National Marine Fisheries Service,
National Oceanic and Atmospheric Administration,, 3Ecology and Evolutionary Biology,
University of California Santa Cruz, 4Department of Theoretical and Computational
Ecology, University of Amsterdam
Presenting author email: alyssa.fitzgerald@noaa.gov
Temperature is the major controlling factor that influences ectotherms via their daily andlong-term survival. Here we examine temperature effects on the survival of Chinook
salmon (Oncorhynchus tshawytscha), a species of high economic and conservation
importance. We implement a framework that provides a quantitative approach forassessing incremental changes in temperature on survival across runs and life stages
using the best thermal performance models currently available for Chinook. Thesetemperature-dependent models were combined with local spatial distribution andphenology data to translate spatial-temporal stream temperature data into maps of life
stage-specific physiological performance in space and time. Specifically, we converted
temperature-dependent performance (i.e. energy used by adults during pre-spawn
46Thursday Scheduled Sessions: Flood and Other Hazards
holding, mortality of eggs during incubation, and juvenile growth rate) into a common
currency that measures survival in order to compare thermal effects across life stages.
Based on two years of temperature data for three managed rivers in the Central Valley,
California, temperature-dependent mortality during pre-spawning holding was more
limiting than embryonic mortality or juvenile mortality prior to smolting. We also foundthat threatened Central Valley spring-run Chinook were more thermally vulnerable thanfall-run, and high temperatures may inhibit successful reintroduction to two rivers where
spring-run have been extirpated. To increase Chinook population sizes, especially forthe threatened and declining spring-run, our results indicate that adults may need more
cold-water holding habitat than currently available in order to reduce pre-spawningmortality stemming from high temperatures. To conclude, our framework is an effective
way to calculate thermal impacts on multiple salmonid runs and life stages within a river
over time, providing local managers the information to minimize negative thermal
impacts on salmonid populations, particularly important during years when cold-water
resources are scarce.

Flood and Other Hazards
Delta Flood Risk under Climate Change: Key Findings from the Delta Adapts
Flood Risk Analysis
Andrew Schwarz1, Cory Copeland1, Kaylee Griffith1, Erin Mullin1, Justin
Vandever2, Ricky Torres-Cooban2, Phillip Mineart2, Jamie Anderson3, Prabhjot(Nicky) Sandhu3, Brad Tom3
1Delta Stewardship Council, 2AECOM, 3California Department of Water Resources

Presenting author email: Andrew.Schwarz@water.ca.gov
The Delta Stewardship Council, with the assistance of partner agencies and consultant
AECOM, developed a climate change vulnerability assessment for the Sacramento-San
Joaquin Delta (Delta) also known as Delta Adapts. One critical vulnerability is increased
flood risk due to higher riverine inflows and sea level rise. Unfortunately, it is difficult tomodel the influence of climate change on the Delta’s flood risk because of its uniquegeometry, and tidal and riverine influences. The combined influence of projected fluvial
inflows and sea level rise on planning scenarios in the Delta requires making choices
across multiple dimensions of uncertainty. In order to address this difficulty, we used anovel approach employing Bayesian methods with a decision-scaling framework. This
allowed the team to simulate millions of potential future conditions to stress test theexisting system of levees and channels. The resulting analysis was used to develop
flood maps that show existing and future projected flood risk throughout the Delta interms of likelihood of flooding. Flood maps will be used in a wide array of public
outreach and education settings as well as policy and investment decision making.
Ultimately, the results will be used to inform future climate change adaptation decisions,investments, and policies.

47

Thursday Scheduled Sessions: Flood and Other Hazards
The presentation will provide a high-level overview of the data and methods used todevelop the model, a demonstration of the flood mapping produced, and a discussion of
how the maps are being used for communication of flood risk and adaptation decision
making.
Delta Adapts: Assessing Ecosystem Vulnerability to Climate Change
Dylan Chapple1, Annika Keeley1, Kirstin Tremain Davis2, Tayler Tharaldson2,
Kerstin Kalchmayr2
1Delta Science Program, 2AECOM

Presenting author email: dylan.chapple@deltacouncil.ca.gov
The loss of the majority of ecosystems in the Bay-Delta has heavily compromised thefunctioning of the remnant ecosystems, which are anticipated to
be further impacted by climate change. It is critical to establish a solid understandingof current Bay-Delta ecosystem vulnerabilities to climatechange and identify opportunities for adaptation. To understand specific regional climate
vulnerabilities, the Delta Stewardship Council conducted a climate changevulnerability
assessment, estimating exposure, sensitivity, and adaptive capacity
ofdominantecosystemtypes to sea level rise, increasing air temperature, and changes inlocal precipitation within the Delta and Suisun Marsh. Results indicate that by 2085,
rising sea levels will put remaining tidal wetlands at risk of transitioning to low
marsh or drowning. Of the ecosystems currently protected by levees, 73% are at risk offlooding due to levee overtopping by 2085 resulting from a combination of sea level riseand storm events. This risk is especially high in the Central Delta and Suisun Marsh.
Projected reductions in spring and fall precipitation and increased inter-annual
precipitation variability will stress Delta species, favor less diverse species
assemblages, and lead to increased presence of non-native species. Increases in bothaverage air temperature and extreme heat days, especially when occurring sequentially,
will stress Delta plant and wildlife species and alter ecosystem dynamics. The
vulnerability assessment highlights the importance of resilience-focused ecosystem
restoration in the Bay Delta. Actions should include (1) substantially increasing natural
ecosystems acreage through restoration and management, (2) increasing shade by
expanding the extent of riparian vegetation throughout the Delta, (3) restoringtidal wetlandswith upland connection, and (4) implementing subsidence reversal
wetlands to reduce the likelihood of levee failure. The vulnerability
assessment provides the foundation for developing and communicating climate resilient
restoration strategies as a mechanism for adaptation throughout the Bay-Delta.

48

Thursday Scheduled Sessions: Flood and Other Hazards
Earthquake Event Selection for Regional Seismic Hazard Analysis of Levee
Systems
Scott Brandenberg1, Zehan Liu1, Pengfei Wang1, Paolo Zimmaro2, Jonathan
Stewart1
1University of California, Los Angeles, 2University of Calabria

Presenting author email: sjbrandenberg@ucla.edu
Probabilistic seismic hazard analysis is generally performed at a single site, where
ground motion hazard from all of the faults that might shake the site is integrated toexpress the annual probability of exceedance as a function of ground motion intensity.
This site-based calculation is then often repeated at many different sites to develop
uniform hazard maps, expressing the ground motion intensity measure values
associated with a specific annual probability of exceedance. While such maps areuseful for selecting a ground motion intensity measure for structures or otherinfrastructure systems with geographic footprints that may be approximated as a point,
they are not appropriate for application to spatially distributed infrastructure systems
such as levees. The problem is that many different earthquake events contribute to thehazard at each site, and none of those events on their own will produce uniform hazard
shaking levels over a spatially distributed infrastructure system. Rather, spatiallydistributed infrastructure systems must be analyzed using an adequate number ofscenario events to reasonably represent the hazard. We present a method for selecting
an event subset from a probabilistic seismic hazard disaggregation, and adjusting therates of occurrence of the events in the subset to recover the target hazard curve. We
select the event subset based on the percent contribution to the seismic hazard at a setof locations, and then utilize a weighted least squares regression approach to identify
the rates for the event subset. We illustrate the procedure for Bacon Island in the
Sacramento / San Joaquin Delta.
Integrating Climate Driven Hydrologic and Subsidence Models and GeophysicalData to Predict Delta Levee Failure Risks
Sandra Bachand1, Scott Brandenberg2, Paolo Zimmaro2
1Bachand & Associates, 2UCLA Samueli School of Engineering

Presenting author email: sandra@bachandassociates.com
The Delta is integral in managing California Water as a critical surface water conduit tomeet domestic, agricultural and wildlife water needs. Water supply and quality
management relies on a vast levee system, much on peat soils and all at risks fromsubsidence, climate change and earthquakes. Effective management of this levee
system will increasingly rely upon more efficient and accurate assessments leveraging
technological and data advances. This project is part of a Next Generation MultiHazard Levee Assessment for Delta levees to assess subsidence, climate change, andearthquake impacts on levee integrity using Bacon Island levees as an example. For
49

Thursday Scheduled Sessions: Flood and Other Hazards
this project, RMA’s 3D SF Estuary Model predicts future water levels in response to
climate change and Hydrofocus’ SUBCALC and SEDCALC models estimate futuresubsidence. Geophysical data collected by Lawrence Berkeley Lab will begroundtruthed against soil boring and cone penetrometer data records and used to map
heterogeneous underlying soil conditions impacting levee strength and permeability
estimates. Here, we provide an overview of our approach to integrate these data tobetter model levee failure mechanisms from seepage and overtopping risks. In greater
detail, we focus on overtopping to follow initial erosion from wave overtopping toward
likely overtopping failure. Future river stages are predicted higher from sea-level rise
and tidal amplitude increases. We analyze potential overtopping in 2050 and 2100 due
to 10, 20, 50, and 100-yr storms. We estimate erosion based upon Briaud (2017) who
accurately predicted overtopping-induced failure in the New Orleans 2008 flood
event. We calculate erosion caused by over-topping induced shear stresses bysumming erosion for each time step during a storm event with significant erosion
indicating potential failure. We will discuss the increasing likelihood of overtopping
failure (2050, 2100) and the implications for future levee height requirements.
Modeling High Water Events to Inform a Multi-Hazard Levee Risk Assessment
Stephen Andrews1, Richard Rachiele1, Scott Burdick1
1Resource Management Associates

Presenting author email: steve@rmanet.com
With approximately 1100 miles of levees within the Delta and future increases in sea
level rise and land subsidence, identifying levees with the highest risk of failure is criticalto preserving life and infrastructure within the Delta. This modeling effort is part of alarger group effort to evaluate levee risk due to long-term stressors (sea level rise,subsidence) and short-term events (flooding, earthquakes) in an integrated way, andusing the best available data and modeling approaches. To assess high water risk,
hydrodynamic model simulations were performed using the RMA 2D Bay-Delta Model.
The model grid and boundaries were recently calibrated for high water events in the
Delta as part of work for the Central Valley Flood Protection Plan 2016 Update. A seriesof high flow simulations were run to represent storm events with recurrence intervals of
10, 20, 50 and 100 years. These simulations were run using both a high and low
estimate of future sea level rise as specified by the State of California Sea Level Rise
Guidance document. For each sea level rise and flood event scenario, there were two
sets of simulations: one assuming a 'hard shoreline', where present-day Delta
shorelines are maintained (levee heights keep pace with sea level rise), and anotherwhere low-lying levees are allowed to overtop based on present-day elevations. Spatial
maps of calculated maximum water levels were developed for comparison against
existing levee elevations and to inform the seepage and overtopping levee risk
analyses. Additional simulations performed with long-term planned restoration projects
in place reduced peak Delta water levels.

50

Thursday Scheduled Sessions: Multiple Perspectives on Sediment in the Bay andDelta: Supply, Transport, and Sink in a Complex Environment

Multiple Perspectives on Sediment in the Bay and Delta: Supply,
Transport, and Sink in a Complex Environment
Is There Enough? the Future of Bayland Sediment Supply and Demand under aChanging Climate
Scott Dusterhoff1, Katie McKnight1, Letitia Grenier1
1San Francisco Estuary Institute

Presenting author email: scottd@sfei.org
Sediment is a critical resource that is essential for sustaining San Francisco Bay tidal
marshes and mudflats (i.e., baylands) under a changing climate. Currently, there areapproximately 80,000 acres of baylands that will need an increased sediment supply tokeep pace with sea-level rise (SLR). In addition, tens of thousands of acres of restored
tidal marsh planned throughout the Bay will need sediment to fill subsided areas andmaintain tidal marsh elevation into the future. With an increasing bayland sedimentdemand and recent studies showing a declining Bay sediment supply, there is a criticalneed to determine if there will be enough sediment delivered to the Bay to support
baylands over the long-term.
This talk presents the findings from an EPA-funded effort focused on comparing
bayland sediment demand and sediment supply to the end of the 21st century for
scenarios that consider bayland extent and climate change impacts. Sediment demand
was assessed for existing baylands and for existing baylands plus 24,000 acres ofplanned tidal marsh restoration assuming 1.5 ft of SLR by 2050 and an additional 5.0 ft
of SLR by 2100. Bay sediment supply from the Delta and local Bay tributaries wasassessed for a wetter future and drier future by using precipitation from downscaled
global circulation models to calculate runoff and sediment loading to the Bay. The
results show that there will likely not be enough sediment coming into the Bay under awetter or drier future to sustain all existing baylands, with the deficit being far greater inSouth Bay-Lower South Bay than Suisun Bay-San Pablo Bay. The findings are used todetermine future bayland resilience with respect to vertical accretion around the Bay.
Outside sediment sources that should be called upon to support long-term bayland
resilience are also discussed.
How Do Physical and Biological Properties of Bed Sediments Influence
Erodibility?
Jessca Lacy1, Maureen Downing-Kunz2, Francis Parchaso3, Samantha McGill1,
David Hart2, Jan Thompson3, Emily Zierdt Smith3, Rachel Allen1, Lukas
WinklerPrins4, Andrew Stevens1
1U.S. Geological Survey, PCMSC, 2U.S. Geological Survey, CAWSC, 3U.S. Geological

Survey, WMA, 4University of California, Berkeley
Presenting author email: jlacy@usgs.gov
51

Thursday Scheduled Sessions: Multiple Perspectives on Sediment in the Bay andDelta: Supply, Transport, and Sink in a Complex Environment
Sediment and sediment transport are important components of the physical habitat andecology of the San Francisco estuary. Numerical sediment transport models, used to
predict sediment movement, erosion, and deposition, require specification of properties
including critical shear stress, erodibility, and particle settling velocity. There are few
field measurements of these properties in muddy systems like San Francisco Bay. This
project investigates the role of hydrodynamic forcing, physical properties of sediment,
and benthic infauna on erosion parameters in the shallows of San Pablo and Grizzly
Bays, where wind waves frequently mobilize fine sediments. During summer 2019 andwinter 2020 study periods, we measured time series of waves, currents, depth, salinity,
suspended-sediment concentration (SSC), and particle size in suspension at the twosites. We collected bed sediment 5 or 6 times per study period to analyze for bulk
density and grain size distribution. Simultaneously, we measured erodibility in an
erosion microcosm designed for this purpose. We also measured the abundance ofbenthic infauna in replicate 0.052 m2 area samples collected every two weeks. Despite
the similarities in the settings of the two sites, results show clear differences between
them and between the study periods. Bed shear stress due to waves was greater in
San Pablo Bay than Grizzly Bay. Bulk density of surficial sediment was lower in winterthan summer in Grizzly Bay, whereas in San Pablo Bay there was no significant
seasonal difference. The abundance and community composition of benthic infaunavaried between the two embayments and the two periods. We are investigating how
these variations influence sediment erodibility as measured by two methods: in theerosion microcosm, and from time-series measurements of near-bed velocity and
SSC. In future work, we will evaluate the sensitivity of model predictions of SSC andsediment transport to the observed range of erodibility parameters.
Variations in Microcosm Measured Bed Erodibility in Grizzly Bay and San Pablo
Bay, Summer 2019 and Winter 2020
David Hart1, Maureen Downing-Kunz1, Darin Einhell1, Selina Davila Olivera1
1U.S. Geological Survey

Presenting author email: dhart@usgs.gov
Quantifying variability in the erodibility of bed sediments is critical for developing robust
sediment transport models. As part of a larger U.S. Geological Survey study seeking toquantify the roles of hydrodynamics and biology on erodibility and hydrodynamic
roughness, a series of sediment cores were eroded using a Gust microcosm and theresults analyzed to assess temporal variations in bed erodibility in two subembaymentsof San Francisco Estuary—Grizzly Bay and San Pablo Bay—during summer 2019 andwinter 2020. Eleven erosion experiments were completed at each site over the courseof the study, six in summer and five in winter, totaling 22 experiments. The Gust
microcosm takes a collected sediment core and uses a rotating disc and radiallypumped water at the sample water surface to generate a nearly uniform and known
shear stress across the sample sediment bed. For each experiment two sedimentcores were collected and simultaneously eroded in individual microcosms though a52

Thursday Scheduled Sessions: Multiple Perspectives on Sediment in the Bay andDelta: Supply, Transport, and Sink in a Complex Environment
fixed range of shear stresses (range: 0.01 - 0.60 Pa). The effluent turbidity from eachcore was monitored and sampled for suspended sediment concentration to determine
individual erosion rates. Early results show that the critical shear stress necessary toinitiate erosion is consistently low and invariable (range: 0.03 - 0.075 Pa) while totaleroded mass (kg/m2) at applied shear stress of 0.45 Pa varies by an order of magnitude(range: 0.023 – 0.29 kg/m2). Further analyses of the results are currently underway.
Evaluating the Effect of Realignment of Coyote Creek on Sediment Supply to
Bothin Marsh, Marin County, California
Michael MacWilliams1, Aaron Bever1, Roger Leventhal2
1Anchor QEA, LLC, 2Marin County DPW Flood Control

Presenting author email: mmacwilliams@anchorqea.com
Bothin Marsh is a narrow urban-fronting marsh in Marin County which provides habitat
for threatened and endangered species. Bothin Marsh and adjacent infrastructure,including the Mill Valley-Sausalito Multi-Use Path, are subject to significant flooding
during high tides. The marsh is experiencing erosion and loss of habitat, which are
expected to worsen with sea level rise. A 2-D hydraulic model, HEC-RAS, was used toscreen alternatives that minimize upstream flood impacts by realigning Lower Coyote
Creek, currently an adjacent straightened flood control channel, through Bothin Marsh.
A 3-D hydrodynamic, wave, and sediment transport model was then applied to evaluate
how the realignment would affect sediment supply to Bothin Marsh. The simulations
indicated that, even under existing conditions, sediment originating from Coyote Creek
provides a significant portion of the sediment supply to Bothin Marsh. Realignment
increases the predicted deposition of sediment from upstream tributaries in Bothin
Marsh. However, the model also predicted that the increased connectivity between
Bothin Marsh and Richardson Bay because of the realignment resulted in less net
sediment accumulation in Bothin Marsh during periods with lower creek flows and low tomoderate tidal ranges. The net sediment deposition in Bothin Marsh during the analysis
period was predicted to be 37% higher under the realignment alternative than under
existing conditions. These results highlight the complex interactions which can affectsediment supply from both upstream and downstream sources, and that must be
considered in effective restoration design. The results indicated that the benefit ofincreasing the connectivity between Coyote Creek and Bothin Marsh on sedimentsupply from the creek outweigh the potential reduction in net sediment supply because
of increased tidal exchange under the realignment alternative evaluated. This study
demonstrates the potential benefits of reconnecting flood control channels into
sediment-starved marshes for resiliency as sea levels rise.
Sediment Deposition and Marsh Accretion Properties in San Pablo Bay-Delta
Karen Thorne1, Chase Freeman1, Kevin Buffington1
53

Thursday Scheduled Sessions: Linkages Among Physics, Chemistry, and Biology in
the Sacramento Deep Water Ship Channel
1U.S. Geological Survey

Presenting author email: kthorne@usgs.gov
Sediment deposition is an important component of accretion processes that builds tidal
marsh elevations relative to local sea levels. Interactions among suspended sedimentconcentration, tidal hydrodynamics, wind and waves, and distance to sediment source
influence deposition rates within marshes and locations throughout the San Pablo BayDelta, CA. Spatial and seasonal variation of storm flooding and sediment transport
processes can also affect short-term deposition rates within a tidal marsh. Determining
spatio-temporal patterns of sediment deposition across tidal marsh landscapes is key tounderstanding accretion rates and helps inform sea-level rise vulnerability. Here, wesought to answer the questions - what determines the amount of sediment deposition
on a marsh surface? and does this vary across San Pablo Bay-Delta? We deployed
feldspar marker horizons and sediment traps in tidal marshes to determine sedimentdeposition amounts over months and years. We found variation in marsh surface
sediment deposition rates across geographic locations and within marshes. Also similar
to previous studies, we found sediment deposition was highest closer to channels andat lower elevations. Mineral deposition rates were greater at brackish marsh sites in
Suisun Bay-Delta (Rush Rach, Browns Island, and Miners Slough) when compared withmarsh sites in San Pablo Bay (Petaluma marsh, China Camp SP, and San Pablo Bay
NWR). Organic matter deposition was greater at brackish marsh sites, presumablyreflecting the different plant communities due to the salinity gradients. Our study
suggests sediment deposition varies across the San Pablo Bay-Delta estuary and isdriven by site specific characteristics such as marsh elevation and channel complexity.
An introduction to a new study starting in 2021 located in south SFB measuring marsh
deposition will also be presented. A greater understanding of the seasonality and spatial
heterogeneity in marsh mineral deposition and elevations is needed.

Linkages Among Physics, Chemistry, and Biology in the Sacramento
Deep Water Ship Channel
Sacramento Deepwater Ship Channel Science and Delta Ecosystem
Rehabilitation
Erwin Van Nieuwenhuyse1
1U.S. Bureau of Reclamation

Presenting author email: evannieuwenhuyse@usbr.gov
Since 2012, Reclamation has sponsored monitoring and research in the Sacramento
Deepwater Ship Channel (SDWSC) because, though manmade, it is one of the mostscientifically interesting features of the Sacramento-San Joaquin Delta and, more
importantly, because of the positive contribution it could make to a broader effort toenhance the Delta’s primary (plant) food supply. This broader effort includes theCalifornia Department of Water Resources North Delta Food Subsidy Action and54

Thursday Scheduled Sessions: Linkages Among Physics, Chemistry, and Biology in
the Sacramento Deep Water Ship Channel
creation of 8,000 acres of restored tidal wetlands over the next decade.
Boosting primary productivity is necessary to increase the abundance of plant-eating
crustaceans and insects that constitute the bulk of Delta Smelt, Longfin Smelt, juvenile
Chinook salmon and most other fish diets. The underlying assumption is that, in mostcircumstances, a well-fed fish is likely to fair better (survive and reproduce) than apoorly-fed one. This assumption is supported by the generally positive correlation
observed between annual fish production and primary production among lakes andestuaries worldwide. The upper section of the SDWSC supports moderate levels of
primary production regulated by thermal stratification, light intensity and nitrogenconcentration. Because the SDWSC has no net flow, however, little of this production
reaches the middle section, where Delta Smelt tend to congregate, and even less istransported to the relatively nitrogen-rich lower Sacramento River, where it could
potentially provide a seed source for blooms. Reclamation’s 2019 Biological
Assessment for the long-term operation of the Central Valley Project includes aprovision (programmatic-scale proposed action) to determine the feasibility of boosting
SDWSC primary production and export by adaptively managing inflow and nutrient
supply at its upstream end. Continued research will be needed to develop and calibratemodels and other quantitative tools required to assess the feasibility of this proposed
action and to predict and document outcomes of subsequent management decisions.
Phytoplankton and Zooplankton Dynamics in the Sacramento Deep Water
Shipping Channel
Adrianne Smits1, Luke Loken2, Erwin Van Nieuwenhuyse3, Randy Dahlgren1,
Steven Sadro1
1University of California, Davis, 2U.S. Geological Survey, 3U.S. Bureau of Reclamation

Presenting author email: asmits@ucdavis.edu
The Sacramento-San Joaquin Delta supports relatively low phytoplankton biomass
compared to other aquatic ecosystems despite generally high nutrient concentrations.
Variation in rates of primary production has important implications for zooplankton
community dynamics, energy flow between trophic levels, food web structure, and many
species of native fishes. Here, we describe spatial and temporal patterns in
phytoplankton and zooplankton biomass and community structure throughout the
Sacramento Deep Water Ship Channel (DWSC) in relation to potential physical,
chemical, and biological drivers. Sampling was conducted over an eight year period(2012 – 2020) at 12 stations spanning a 40 km reach from Rio Vista to West
Sacramento. Spatially, algal biomass was highest in the upper portion of the DWSC,
where primary production transitioned from being light limited due to high turbidity tonutrient limited due to longer water retention times and increased water clarity. Althoughcharacterized by higher variability, zooplankton biomass generally mirrored spatial
patterns in phytoplankton biomass, becoming elevated in the uppermost part of the
DWSC. Communities of phytoplankton and zooplankton co-varied along the DWSC’s
longitudinal axis; while diatoms, copepods, and smaller bodied species typical in lotic
55

Thursday Scheduled Sessions: Linkages Among Physics, Chemistry, and Biology in
the Sacramento Deep Water Ship Channel
environments were abundant throughout the DWSC, the community of the upperchannel regularly included chlorophytes, cryptophytes, cladocerans, and other larger
bodied species typical in lentic environments. We illustrate the extent to which spatial
and temporal patterns in community structure at the base of the DWSC food web are
responding to phenological patterns in water temperature, light, turbidity, nutrient
availability, and hydrodynamic characteristics. Our analysis suggests that management
strategies to boost the pelagic food web and promote secondary production of
zooplankton and/or fisheries should consider the spatial and temporal heterogeneity ofmultiple physical and chemical properties that regulate ecosystem functions in thenorthern Sacramento-San Joaquin Delta.
Hydrodynamics Drive Pelagic Communities and Food Web Structure in a Tidal
Environment
Matthew Young1, Frederick Feyrer1, Paul Stumpner1, Veronica Larwood1, Oliver
Patton1, Larry Brown1
1U.S. Geological Survey

Presenting author email: mjyoung@usgs.gov
Hydrodynamic processes can lead to accumulation and/or dispersal of water column
constituents, including sediment, phytoplankton, and particulate detritus. Using a
combination of field observations and stable isotope tracing tools, we identified howhydrodynamic processes influenced physical habitat, pelagic communities, and foodweb structure in a freshwater tidal system. The pelagic habitat of a terminal channel
differed spatially, likely aligning with differences in hydrodynamics. Three zones that weclassified by exchange with downstream habitat had distinct water quality
characteristics, supported different densities of zooplankton and nekton, and exhibited
disparate support from benthic and pelagic trophic pathways to pelagic consumers.
Hydrodynamically driven zones and their emergent characteristics appeared sensitive tohydrology, as elevated runoff was correlated with a shift in hydrodynamic habitat andorganismal distributions. The results of our study highlight the relationship betweenhydrodynamic processes, biological responses, and climate, and suggest that
understanding the physical processes can improve understanding of pelagic habitats
and communities.
Dispersion and Stratification Dynamics in the Upper Sacramento Deep Water Ship
ChannelLeah Lenoch1, Paul Stumpner1, Jon Burau1, Luke Loken1, Steve Sadro2, Erwin Van
Nieuwenhuyse3
1U.S. Geological Survey, 2University of California, Davis, 3U.S. Bureau of Reclamation

Presenting author email: llenoch@usgs.gov

56

Thursday Scheduled Sessions: Linkages Among Physics, Chemistry, and Biology in
the Sacramento Deep Water Ship Channel
Hydrodynamics control the movement of water and material within and among habitats,where timescales of mixing can exert bottom up regulatory effects on aquatic
ecosystems through their influence on primary production. Habitat restoration efforts in
the San Francisco estuary are focused on increasing productivity to support fisheries
and ecosystem services. The Sacramento Deep Water Ship Channel (DWSC) is aterminal channel that, although entirely human-made and engineered, exhibits physicaland biological characteristics like the dead-end sloughs that were common in thehistoric Delta and supports endemic, endangered Delta smelt. We investigated thephysical mechanisms that control mixing and thermal stratification in the upper DWSC.
Our study was conducted in conjunction with a whole-ecosystem experiment
investigating whether phytoplankton production and biomass would respond to nitrate
additions, which could potentially be exported to food-limited regions in the Delta.
Analysis of the mixing mechanisms and timescales revealed that tidal currents and wind
controlled mixing and stratification that developed due to heat fluxes at the surface. On
average, longitudinal mixing over the average tidal excursion length (2.6 km) occurred
every 14 hours, while vertical mixing over the total depth (8 m) occurred on average
every 1.5 hours. Longitudinal and vertical dispersion increased during periods of highwind, and wind speed had a greater influence on dispersion rates than tidal currents.
Thermal stratification developed on most days, temporarily inhibiting vertical mixing but
was rapidly broken down by wind-induced mixing. Days with stronger stratification had
greater concentrations of chlorophyll. However, stratification rarely (5 out of 78 days)
persisted overnight, which may be an important limitation on algal bloom formation. The
observations of the physical mechanisms in the DWSC that affect stratification andinterconnectivity among habitats that enhance primary production may be useful in
informing habitat restoration elsewhere in the Delta.
Whole Ecosystems Experiments Unravel Effects of Nutrients, Light, andHydrodynamics on Productivity in the Upper Sacramento-San Joaquin Delta
Luke Loken1, Steve Sadro2, Leah Lenoch1, Paul Stumpner1, Randy Dahlgren2, Jon
Burau1, Brian Bergamaschi1, Erwin Van Nieuwenhuyse3
1U.S. Geological Survey, 2University of California, Davis, 3U.S. Bureau of Reclamation

Presenting author email: lloken@usgs.gov
The Sacramento-San Joaquin Delta has experienced long-term declines in multiple
measures of aquatic ecosystem health, including decreases in pelagic phytoplankton
and native fishes. Nutrient subsidies may be a bottom-up strategy to increase
productivity in the delta to the ultimate betterment of the pelagic food web. Although
primary production through much of the delta does not appear nutrient limited,waterways where flushing rates are low, such as the upper portion of Sacramento Deep
Water Ship Channel (DWSC), can become nitrogen limited under certain
circumstances. We conducted a whole ecosystem field experiment in the upper portionof the DWSC to test whether adding nitrogen, when and where it appeared limiting,would stimulate primary productivity. Following periods of nitrogen addition (as nitrate),
57

Thursday Scheduled Sessions: IEP Session: Fish Habitat Spatial Arrangements:
Experience from Across the Estuary and Beyond
gross primary production and chlorophyll biomass increased. However, the ecosystem
responses were brief (<2 days) as primary production also responded to variation inhydrodynamics and light availability. The influence of wind, tides, and stratification wereequally important as nutrients and light in regulating productivity. Our experimentcaptured dynamics at a transition point along a spatial continuum within the DWSC. In
landward ecosystems, hydrologic isolation and higher water clarity indicate that primary
productivity is regulated by nutrient availability. Moving seaward, production appears to
be regulated by light limitation and the continual resuspension of sediment, reflecting
faster water velocities and connections with the greater Delta waterway. Thus,
productivity along the DWSC reflects gradients in hydrodynamics, and generalizing
controls of other biogeochemical processes and community dynamics require a spatial
framework that accounts for connectivity among ecosystems. All told, our experimentillustrates the high degree of heterogeneity among factors controlling primary production
in a relatively simple channel, emphasizing the importance of hydrodynamics and theneed for high frequency sampling in space and time to evaluate ecosystem energetics
and food web dynamics in estuaries.

IEP Session: Fish Habitat Spatial Arrangements: Experience fromAcross the Estuary and Beyond
Four Decades of Juvenile Fish Responses to Hydroclimate: Advancing a StateSpace Modeling Approach in the San Francisco Estuary
Denise Colombano1, Stephanie Carlson1, James Hobbs2, Albert Ruhi1
1Department of Environmental Science, Policy, and Management, University ofCalifornia, Berkeley, 2California Department of Fish and Wildlife

Presenting author email: denise.colombano@berkeley.edu
In the San Francisco Estuary, the relative magnitude of marine vs. freshwater influences
varies with hydroclimate patterns. Over the last decade, abundant research has shown
how such fluctuations drive primary and secondary production; however, variation intarget species and sampling methodology across monitoring programs often hindered
synthesis, limiting generalizability. Here we used Multivariate Autoregressive StateSpace (MARSS) models on CDFW Bay Study otter and midwater trawl long-term data
to examine juvenile fish dynamics and the influence of environmental fluctuations andtrends. Specifically, we built a set of species- and spatially-structured MARSS models toanswer the following questions: How does juvenile fish abundance vary along theestuarine gradient over time? How do watershed hydrology and ocean conditions
explain inter-annual variation in abundance across the different species, and along theestuarine gradient? We focused on 15 common young-of-the-year fishes sampled at 35
core stations from 1980 to 2018. Overall, mean annual Delta outflow best explained
community-wide abundance fluctuations. Notably, anadromous species such as longfin
smelt (Spirinchus thaleichthys), striped bass (Morone saxatilis), and American shad
(Alosa sapidissima) responded similarly, with significant positive responses to flow58

Thursday Scheduled Sessions: IEP Session: Fish Habitat Spatial Arrangements:
Experience from Across the Estuary and Beyond(‘freshening’) in the lower estuary (e.g., San Pablo Bay, Central Bay). In contrast,
marine-dependent species such as Pacific herring (Clupea pallasii), Northern anchovy(Engraulis mordax), and English sole (Parophrys vetulus) displayed the opposite
pattern, with significant negative responses to flow (‘salinity intrusion’) in the upper
estuary (e.g., Suisun Bay). Building on these findings, we plan to further quantify thepotential effects of historical and future hydroclimatic anomalies (flood vs. drought) and
explore the life-history mechanisms that may confer response diversity--and thus
temporal stability--at the community level. This work may advance the notion that
directional trends, fluctuations, and extremes in the environment (due to water
management and climate) will continue to reshape estuarine fish communities in the
future.
(*IEP) Space Jam: A Spatially Explicit History of Estuary Fish Species
Dylan Stompe1, Peter Moyle1, John Durand1
1University of California, Davis, Center for Watershed Science

Presenting author email: dkstompe@ucdavis.edu
The San Francisco Estuary (estuary) is a dynamic and highly altered system withmyriad abiotic and biotic changes since its widespread colonization by EuropeanAmericans in the 1800s. As a result of these changes and others, including overfishingand pollution, many native and some introduced species have experienced drastic
declines in the past 100 years. To track these species declines several state and federal
agencies, as well as research groups at the University of California, Davis, haveoperated regular estuary fish surveys dating back to the late 1950s. While most of thesefish surveys are designed to track estuary-wide fish abundance, they are logistically
restricted in their total number of stations, frequency of sampling events, and differing
gear types. These constraints mean that a single survey likely does not capture all of
the intricacies in long-term species trends, as changes in species distribution, behavior,
and/or changes to the condition of sampling sites may artificially alter capture efficiency.
To combat this, we have combined eight surveys that have operated continuously
between 1980 and present into a spatially explicit integrated dataset, capturing 30 yearsof trends in estuary fish abundance at a much higher seasonal and spatial density than
could be provided by any single survey. By leveraging this data in a yearly aggregate
format, we examine trends in the distribution of several important estuary species overtime.
(*IEP) Suisun Marsh on the Edge of Resilience in an Era of Rapid Change
John Durand1, Teejay O'Rear1, Peter Moyle1
1University of California, Davis

Presenting author email: jrdurand@ucdavis.edu
59Thursday Scheduled Sessions: IEP Session: Fish Habitat Spatial Arrangements:
Experience from Across the Estuary and Beyond
UC Davis has been researching water quality, invertebrates, fishes and wetlands aspart of the Suisun Marsh Fish Study since 1980. During that period, the Bay-Delta has
been subject to droughts, floods, record temperatures, species invasions, and food web
degradation. Suisun Marsh remained largely resilient to these stressors. Since a decline
in the early 1980s, native fish catch in Suisun mostly remained stable, even while
introduced fish have increased. Much of the marsh avoided aquatic weed and claminvasions, and pelagic food remained abundant in terminal sloughs and managed
wetlands. Remnant tidal wetlands created habitat for juvenile and adult fishes and new
wetlands were being restored. Even stakeholder conflicts over water management andlow dissolved oxygen levels were resolved through coordinated action. Some of thisresilience was likely due to its location in the low-salinity zone, its complex
geomorphology, and its long, shallow, low gradient slope to uplands.
However, there are early signs that Suisun Marsh may be entering a new phase ofvulnerability. In the years following the 2012-16 drought, the marsh has had elevatedwater temperatures and clarity. The typical post-drought recovery pattern has not been
seen for many fishes, including Delta smelt, which have not been detected since 2015,
and longfin smelt, which are increasingly rare. An emerging threat to wetland restorationis the invasive alligator weed, which is tolerant of brackish water. Sea level rise will soon
submerge the outer marsh, while upland marsh will be compressed against the growing
urban interface. Solutions will emerge by incorporating science into management
practices, seeking novel collaborations among stakeholders and agencies, and using
traditional practices to better integrate the working landscape with naturalistic
restorations.
(*IEP) Differences Between Surface and Bottom Temperatures in the Upper San
Francisco Estuary: Implications for Temperature Refugia
Brian Mahardja1, Samuel Bashevkin2, Larry Brown3, Catarina Pien4, Michelle
Nelson4, Rosemary Hartman4, Brittany Davis4, Michael Beakes1
1U.S. Bureau of Reclamation, 2Delta Stewardship Council, Delta Science Program,
3U.S. Geological Survey, 4California Department of Water Resources

Presenting author email: bmahardja@usbr.gov
Water temperature is an important water quality parameter to monitor in estuaries as it
is one of the main factors underlying distribution, growth rate, and survival of key fish
species. Climate change is expected to have especially profound effects on the upper
San Francisco Estuary (SFE), because water temperatures are highly influenced byrising air temperatures. As the upper SFE warms, an important question is whether
depth can provide temperature refugia for thermally sensitive listed fish species. Overthe years, monitoring programs in the upper SFE have collected tens of thousands of
discrete water temperature measurements at both the surface and near-bottom of thewater column. To evaluate when and where thermal stratification occurs in the upper
SFE, we compiled an integrated discrete temperature dataset from 11 different boatbased surveys and used a spatiotemporally explicit generalized additive model to60

Thursday Scheduled Sessions: IEP Session: Fish Habitat Spatial Arrangements:
Experience from Across the Estuary and Beyond
identify patterns of stratification. Because most discrete data are collected during
daytime, we also used data from four continuous water quality stations to better
understand how thermal stratification changes through the course of a day and tovalidate our findings. Our results demonstrate that the upper SFE is a well-mixed
system overall with little thermal stratification under most circumstances. We didobserve cooler bottom water temperature relative to surface in certain regions of the
Delta relatively often in the summer when surface water temperature is high (>~21 C).
We also observed situations where bottom water temperature was warmer relative tothe surface, which appeared to occur more often in the Suisun Bay region in the winterand spring when air temperature is low. Although these occasional thermal
stratifications may offer some respite during extremely warm summer days, they arelikely too unpredictable in time and space to play a major role in the health and survivalof thermally sensitive fishes.
(*IEP) Investigating Longfin Smelt Utilization of Coastal Estuaries North of the
San Francisco Estuary
Colin Brennan1, Shawn Acuna2, Daniel Cox1, Lenny Grimaldo3
1ICF, 2Metropolitan Water District of Southern California, 3Department of Water

Resources

Presenting author email: Colin.Brennan@icf.com
The San Francisco Estuary is home to the southernmost reproducing population ofLongfin Smelt. At the edge of the species’ range, it is considered a distinct population
due to a low likelihood of southward gene flow contributing to genetic diversity. Despite
rigorous studies within the estuary, a critical gap exists in our knowledge of the potential
influence that marine immigration has on this anadromous population. Our study
consisted of targeted surveys during 2019 and 2020 to identify coastal estuaries northof San Francisco Estuary where spawning might occur. We determined the importanceof estuary size on the occurrence of larval Longfin Smelt and the environmental factorsthat might predict the presence of larvae. In the wet winter of 2019, we observed low
occurrence and densities of larval Longfin Smelt in Humboldt Bay and the Eel River.
Higher densities and occurrences of larvae were detected in the dry winter of 2020 at
Humboldt Bay and the Eel River with additional detections at the Klamath and Mad
rivers. No larvae were detected in the coastal estuaries sampled in Mendocino,
Sonoma, and Marin counties closer to the San Francisco Estuary. In 2019, increased
freshwater outflow appeared to reduce larval Longfin Smelt recruitment due to greater
advective transport to sea. While a population of Longfin Smelt appears to exist north ofCape Mendocino, our results indicate that coastal estuaries in proximity to the San
Francisco Estuary either do not support recruitment in years with high variation inhydrology or that immigration is extremely rare. Our study highlights the need formonitoring over the range of hydrologic conditions with detection probabilities that can
improve future assessments of gene flow between populations.

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Friday Scheduled Sessions: Integrating Data and Population Models: Understanding
Factors that Affect Sensitive Fish Populations

Friday Scheduled Sessions
Integrating Data and Population Models: Understanding Factors that
Affect Sensitive Fish Populations
Life Cycle Modeling Using State-Space Models for Data Integration to Identify
Factors Affecting Delta Smelt Recruitment, Survival and Population Growth Rates
Leo Polansky1, Lara Mitchell2, William E. Smith1, Matthew L. Nobriga1, Ken B.
Newman3
1U.S. Fish and Wildlife Service, Bay-Delta Fish and Wildlife Office, 2U.S. Fish andWildlife Service, Lodi Field Office, 3Biomathematics & Statistics Scotland and School ofMathematics, The University of Edinburgh, Edinburgh, UK
Presenting author email: leo_polansky@fws.gov
Population models are most often described at an annual time step and fit using datafrom the same survey each year. But scientific understanding and management
strategies are both improved when finer temporal resolution models are constructed thatfactor the population growth rate into a product of recruitment and life stage-specificsurvival rates. We use a hierarchical state-space model framework to describe the delta
smelt life cycle fit to a sequence of abundance estimates from multiple surveys, eachwith unique abundance estimation biases and uncertainties. These models quantify theeffects of biotic and abiotic factors on recruitment and seasonal survival of 25 years ofdelta smelt population dynamics, including management relevant ones such as various
measures of net freshwater flow in the species’ estuarine environment. Life cycle model
results allow retrospective assessments of the good and bad years as measured by therealized growth rates and the relative contributions of manageable and unmanageable
sources of mortality to survival processes, as well as predictions given observed
environmental conditions. The linkage of abundances through time described by the life
cycle models provides a path to quantitatively connect covariates controlling vital rates
to the population growth rate to predict the outcomes of alternative management
strategies. We describe which vital rates were the relatively limiting factors resulting in
low population growth over the 25 years and what the corresponding observed
covariates were, and how the probability of positive growth changes over a wide rangeof management relevant environmental scenarios.
Decision Analysis to Identify Optimal State-Dependent Restoration Policies for
Chinook Salmon
Adam Duarte1, James Peterson2
1U.S. Department of Agriculture Forest Service, Pacific Northwest Research Station,
2U.S. Geological Survey, Oregon Cooperative Fish and Wildlife Research Unit,

Department of Fisheries and Wildlife, Oregon State University
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Friday Scheduled Sessions: Integrating Data and Population Models: Understanding
Factors that Affect Sensitive Fish Populations
Presenting author email: jt.peterson@oregonstate.edu
Anadromous fish are a valued resource for their economic, cultural, and ecologicalimportance. Yet, their reliance on both freshwater and ocean environments makes themsusceptible to myriad human-induced stressors throughout their life cycle, which havecontributed to their decline in California’s Central Valley. We will describe the Chinook
salmon (Oncorhynchus tshawytscha) decision-support models developed by the Central
Valley Project Improvement Act Science Integration Team as part of a larger structured
decision-making effort aimed at maximizing natural adult production of Chinook salmon
in California's Central Valley. We will then describe the decision-analytic tools thestakeholder group used to solve the models, explore model results, and develop a
restoration strategy. Overall, we found that actions targeted at one run were detrimental
to others, which was unexpected. Furthermore, information uncovered during thisprocess was used to direct efforts towards targeted research/monitoring to reduce
critical model uncertainties and make better restoration decisions moving forward.
Collectively, the results of our study revealed a restoration strategy that can be applied
at a broad scale and may be applied to systems with similar constraints.
Applying the Winter-Run Life Cycle Model to Pressing Hydromanagement
Questions in the Central Valley
Noble Hendrix1, Ann-Marie Osterback2, Evan Sawyer3, Brett Harvey4, Corey
Phillis5, Eric Danner6, Steve Lindley6
1QEDA Consulting, LLC, 2University of California, Santa Cruz & NMFS Southwest

Fisheries Science Center, 3NOAA Fisheries West Coast Region, 4California Departmentof Water Resources, 5Metropolitan Water District, 6NOAA Fisheries Southwest Fisheries
Science Center
Presenting author email: noble@qedaconsulting.com
Successful management of California's fresh water resources requires balancing
consumptive and non-consumptive water use with fish species that depend critically on
the same resources. Numerous water management decisions are being evaluatedcurrently; many with the goal of providing protection for endangered species such as
winter-run Chinook salmon. Scientists at UC Santa Cruz, NOAA Fisheries, USGS, and
QEDA Consulting have developed a winter-run life cycle model (WRLCM) to support
such decision-making in the Central Valley. The WRLCM is capable of incorporatingother models that run at finer spatial and temporal scales (e.g., SALMOD and anenhanced particle tracking model to track smolt survival, ePTM) and has beenstatistically fitted to winter-run abundance data from multiple life stages. The WRLCM
has been applied in several important decisions: 1) to evaluate long term operational
scenarios that reflect modified water diversions, reservoir management, and export
levels; 2) to determine whether Shasta temperature management and reintroduction of
winter-run to tributaries above Shasta dam can improve juvenile survival during
droughts; and 3) to define how restoration and associated survival experiments canultimately lead to increased productivity of the winter-run population. Results of the63

Friday Scheduled Sessions: Integrating Data and Population Models: Understanding
Factors that Affect Sensitive Fish Populations
Shasta evaluation indicated that temperature management in critical water years andreintroduction to natal tributaries above Shasta dam can act synergistically to help
buffer negative impacts of drought conditions. WRLCM results indicated that the optimal
location for restoration (Delta versus Lower Sacramento River) depends on the survival
benefits due to restoration. As a result, experiments to estimate the survival benefits ofrestoration are critical for maximizing the efficacy of restoration projects. Models suchas the WRLCM provide an important component to decision-making because of theirability to evaluate alternative actions, even under parametric and structural uncertainty,
and to evaluate the utility of data collection to reduce that uncertainty.
The Enhanced Particle Tracking Model: Bridging Science and Management
Vamsi Krishna Sridharan1 | 2, Doug Jackson3, Andrew Hein2, Russel Perry4, Adam
Pope4, Eric Danner2, Steven Lindley2
1University of California, Santa Cruz, 2Southwest Fisheries Science Center, National

Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa
Cruz, 3QEDA Consulting, 4U.S. Geological Survey
Presenting author email: vamsi.sridharan@noaa.gov

Science-based management of multipurpose water systems is challenged by two scaledisconnects: (1) top-down: the macroscopic (on the order of tens of kilometers over
several days) drivers and stressors that govern animal migration through complex
environments and the levers that can be controlled by managers are often disconnectedfrom local environmental cues that the animals respond to, and (2) bottom-up: themicroscopic (on the order of a few meters over a few seconds) behavior patterns
observed in laboratory studies are often not easily generalizable. The top-down
disconnect results in empirical correlations between observed migration patterns andmacroscopic environmental conditions that are not typically flexible enough to deal with
out-of-sample situations such as alternative management scenarios. The bottom-up
disconnect results in mechanistic models with ad-hoc rules that are not driven by dataor constrained by biological plausibility so that, yet again, the applicability of thesemodels to out-of-sample situations becomes problematic. Ecological models that serve
as decision support tools therefore need to serve as a bridge to the macroscopic
system-control levers in a manner that does not introduce gross inconsistencies in
representing the environmental cues with minimal indefensible assumptions about the
microscopic behaviors. The enhanced Particle Tracking Model (ePTM) is a juvenile
salmon migration model that has been constructed with these two principles to translate
what is known about microscopic salmon behavior dynamics to macroscopic migration
patterns within the Delta that can be altered by hydrological and water operation levers.
In this talk, we will describe the model and discuss how to extend mechanistic model
development of this complex ecohydrodynamic system by utilizing higher quality
datasets that are becoming available.

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Friday Scheduled Sessions: Contaminants and Toxins
Merging Computational Fluid Dynamics and Machine Learning to Reveal Fish
Migration Strategies
Simone Olivetti1, Mike Gil2, Vamsi Sridharan3, Andrew Hein3
1University of California Santa Cruz, 2University of Colorado, Department of Ecology

and Evolutionary Biology, 3National Oceanic and Atmospheric Administration,
Southwest Fisheries Science Center
Presenting author email: simoneolivetti.eng@gmail.com

Understanding how migratory animals interact with dynamic physical environments
remains a major challenge in migration biology. Interactions between migrants and wind
and water currents are often poorly resolved in migration models due to both the lack ofa high-resolution environmental data, and a lack of understanding of how migrants
respond to fine scale structure in the physical environment. Here we develop ageneralizable, data-driven methodology to study the migration of animals throughcomplex physical environments. Our approach combines validated Computational Fluid
Dynamic (CFD) modeling with animal tracking data to decompose migratory movements
into two components: movement caused by physical forcing, and movement due toactive locomotion. We then use a flexible recurrent neural network model to relate local
environmental conditions to locomotion behavior of the migrating animal, allowing us topredict a migrant's force production, velocity and trajectory over time. We apply thisframework to a large dataset containing measured trajectories of migrating Chinook
salmon through a section of river in California's Sacramento-San Joaquin Delta. We
show that the model is capable of describing fish migratory movements as a function of
local flow variables, and that it is possible to accurately forecast migratory movement
behavior of individual migrants on which the model was not trained. After validating ourmodel, we show how our framework can be used to understand how migrants respondto local flow conditions, how migratory behavior changes as overall conditions in thesystem change, and how the energetic cost of migratory movements depend on
environmental conditions in space and time.

Contaminants and Toxins
What’s HAB-Ening to Our Water and How can We Best Manage It?
Meghan Klasic1, Rachel Lamb2, Kelsey Leonard3, Vanessa Vargas4
1Center for Environmental Policy and Behavior, University of California, Davis,

2Geographical Sciences, University of Maryland, College Park, 3McMaster University,

Hamilton, ON, Canada, 4University of Maryland Center for Environmental Science
Presenting author email: mrklasic@ucdavis.edu

Harmful algal blooms (HABs) are one of the greatest contemporary social-ecologicalchallenges. HABs alter marine and freshwater food webs, cause mass aquatic life
mortalities, and lead to human illness and death. HABs have an immense impact on theeconomy, costing an average of $49 million annually between 1987–92 in the United
65Friday Scheduled Sessions: Contaminants and Toxins
States, with 45% of costs coming from public health impacts. These impacts, coupledwith complications from climate change, underscore the urgent need to understand how
to best manage our watersheds and social-ecological systems. In California, despite
HABs in the Bay-Delta, current state efforts are underfunded and underdeveloped.
Comparatively, Lake Erie watershed managers have addressed HABs for more than 40
years. This work involves a complex governance system from binational agreements
down to watershed-level planning efforts. Lake Erie provides a unique opportunity for
Bay-Delta managers to learn best management practices to proactively address BayDelta HABs and reduce impacts. We conducted social-ecological network analyses tobetter understand the Lake Erie governance system and decision-making processes
over the last 10 years through document analysis and interviews. Preliminary findings
show that: 1) the HABs governance system in Lake Erie is complex and polycentric(1500+ unique actors); 2) high-level plans claim multi-level collaboration yet most work
is completed as local “random acts of restoration”; 3) plans show sweeping
collaboration, while interviews reveal that work is largely conducted in clusters; and 4)
tribes, métis, and first nations continue to be excluded from substantive collaboration.
Given that climate change will increase the intensity and frequency of HABs, California
water experts can glean strategies and cautionary tales from the Lake Erie case study
to develop a more robust and anticipatory management approach for the Bay-Delta.
This research can help managers better target strategies to address HABs while
fostering collaborative efforts to ensure long-term Delta ecosystem sustainability.
Bioaccumulation Potential of Chlorpyrifos in Hyalella Azteca: Implications for the
Bay-Delta Region
Nadhirah Johanif1, Kaley Major2, Michael Lydy3, Donald Weston4, Kara E Huff
Hartz3, Richard Connon5, Helen Poynton2
1School for the Environment, UMass Boston, 2University of Massachusetts Boston,

3Southern Illinois University, 4University of California, Berkeley, 5University of California,

DavisPresenting author email: nabilahnadhira.ah001@umb.edu
Mutations in the target site acetylcholinesterase (AChE) gene within the freshwater
amphipod Hyalella azteca has allowed these invertebrates to tolerate organophosphate(OP) insecticides up to 1000-fold higher than their wildtype counterparts. OPs, likechlorpyrifos, are commonly detected in the Bay-Delta region due to their application inagriculture practices and often exceed the 0.04 ug/L chronic US EPA benchmark foraquatic organisms. Since resistant animals can survive in highly contaminated waters,
there is potential for them to accumulate higher insecticides, increasing the risk fortrophic chemical transfer within the food web. Since H. azteca can provide a major
portion of fish diets in some habitats, including species found in the Bay-Delta region,
the question we ask is, “can resistant H. azteca bioaccumulate OPs at higher rates than
non-resistant animals, and if so, what does it mean for the Bay-Delta food web?”66

Friday Scheduled Sessions: Contaminants and Toxins
In this project, we conducted toxicokinetic experiments to estimate the uptake andelimination rate constants of chlorpyrifos in resistant and non-resistant H. azteca. We
also compared chlorpyrifos bioaccumulation between resistant and non-resistant H.
azteca by exposing them to 14C-chlorpyrifos for 28 hours and measuring the bodyburden. Our results indicate that both populations accumulate similar body burdens
when exposed to the same concentration of chlorpyrifos. We then investigated theaccumulation of 14C-chlorpyrifos in only resistant animals at six different concentrations,with four concentrations above the lethal threshold for non-resistant animals. We foundthat resistant animals exposed to higher concentrations can accumulate up to 50 times
more. These results infer that bioaccumulation potential can be more significant inchlorpyrifos resistant H. azteca and may be an essential factor in assessing the full
impacts of toxicants on critical Bay-Delta food webs in order to restore the health of thewatershed
A New Model to Address Legacy Gold Rush Mercury in the Delta
Jamie Anderson1, Reed Harris2, Dave Hutchinson2, Carol DiGiorgio1, Han Sang
"Hans" Kim1
1California Department of Water Resources, 2Reed Harris Environmental, Ltd.

Presenting author email: jamie.anderson@water.ca.gov
A mercury cycling model for the Sacramento-San Joaquin Delta was created to support
the Delta Mercury Control Program. Mercury mined in California’s Coastal Range andused in the Sierra Nevada Gold Rush in the 1800’s continues to contaminate water thatflows into the Sacramento-San Joaquin Delta today. The mercury bioaccumulates andbiomagnifies in fish, which poses a threat to human health if contaminated fish areeaten. To support the goal of reducing methylmercury concentrations in the Delta, thehydrodynamic and water quality Delta Simulation Model 2 was expanded to add
suspended sediments, a sediment bed, and three forms of mercury(methylmercury, inorganic divalent mercury (Hg(II)) and elemental mercury (Hg0)). The
Delta Mercury Model (DSM2-Hg) results for October 1999 to July 2006 show that theDelta is a net sink for sediment solids, inorganic mercury and methylmercury. The
magnitudes and relative importance of different mercury sources vary widely during
wetter and drier years. Typically, the Sacramento River is the main source of mercury in
the Delta, however in wet years when the Yolo Bypass floods, the Bypass cancontribute up to half of the annual methylmercury. Internal production of methylmercury
was inconsequential relative to methylmercury supplied from tributary inflows. The
findings from this study and future application of the Delta Mercury Model (DSM2-Hg)
can help identify management actions to reduce methylmercury concentrations in the
Delta.

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Friday Scheduled Sessions: Contaminants and Toxins
3D Modeling of Methylmercury as a Conservative Tracer in the Sacramento-San
Joaquin Delta
Lisa Lucas1, A. Robin Stewart1, Fernanda Achete2, Jacob Fleck1, Noah Knowles1,
Rosanne Martyr3, Mark Marvin-DiPasquale1, Mick van der Wegen4, Lisamarie
Windham-Myers1
1U.S. Geological Survey, 2Universidade Federal do Rio de Janeiro, 3Climate Analytics

gGMBH, 4IHE Delft Institute for Water Education, Deltares

Presenting author email: llucas@usgs.gov
Understanding how water availability and management impact water quality is achallenge in coastal ecosystems like the San Francisco Bay-Delta (SFBD), wheremultiple contaminant sources, hydrologic forcing, and anthropogenic flow manipulations
vary across space and time. Mercury (Hg), a legacy contaminant that reduces water
quality, is found throughout the SFBD and accumulates through the food web as
methylmercury (MeHg) to levels considered dangerous for humans and wildlife. General
patterns of MeHg concentrations in the SFBD are known, but it is not well understood
how upstream and downstream MeHg sources are transported and mixed throughout
the Delta by time-varying freshwater flows, tides, baroclinic processes, and water
management actions. Consequently, we do not understand which aqueous MeHg
sources are most influential in areas with high fish Hg concentrations, creating achallenge for management entities attempting meaningful, science-based regulation of
MeHg sources.
Numerical 3D hydrodynamic and water quality models (Delft3D-FM and DELWAQ) areapplied in the SFBD to study the influence of hydrodynamics on the spatial andtemporal patterns of aqueous MeHg. This modeling is focused on physical transport of
MeHg as influenced by river flow, tides, and infrastructure operations. As such, MeHg ismodeled with multiple conservative tracers representing individual sources. Althoughbiogeochemical processes are known to influence MeHg patterns, their neglect in thisfirst modeling phase helps us address the question: To what extent do physicaltransport processes explain observed MeHg patterns in the SFBD?
Preliminary simulation results for Water Years 2011 and 2012 indicate that MeHg
source distributions are seasonally dynamic and strongly influenced by water
management and tributary sources but regain a consistent distribution by October
during both wet and dry years. These results match the relatively stable long-term Hg
pattern in sport fish tissues and highlight the important influence of physical transport onwater quality in the region.
Current-Use Pesticides in Zooplankton, Water, and Suspended Sediment
Collected from the Sacramento-San Joaquin Delta
James Orlando1, Michelle Hladik1, Corey Sanders1, Matt DeParsia1, Jared
Frantzich2, Brittany Davis2
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Friday Scheduled Sessions: Birds and Their Habitats in the Bay-Delta
1U.S. Geological Survey, 2California Department of Water Resources

Presenting author email: jorlando@usgs.gov
Zooplankton are a key food source for juvenile fishes in the Sacramento-San Joaquin
Delta (Delta), including Chinook Salmon and the endangered Delta Smelt. Studies haveshown long-term declines in total zooplankton biomass in the Delta as well as changes
in zooplankton species composition and linked these declines to reductions in nativefish populations. To better understand the potential causes of these changes as well as
to understand the quality of zooplankton now available as food for native Delta fish,
zooplankton, water and suspended sediment samples were collected from two sites inthe Delta and analyzed for a large suite of current-use pesticides and degradates.
Samples were collected biweekly in the summer/fall 2017 and 2018, and from May
2019-March 2020 at a site in the Yolo Bypass and at a comparison site on the
Sacramento River below Sacramento.
During the three sampling periods a total of 29 pesticides were detected in zooplankton,
and 70 of the 73 samples contained multiple pesticides (up to 17 per sample). The mostfrequently detected compounds in zooplankton were 3,4-dichloroanline, azoxystrobin,bifenthrin, p,p’-DDD, p,p’-DDE, pendimethalin, and thiobencarb. Water samples
collected concurrently with zooplankton samples contained a total of 52 distinct
pesticides and all samples contained from 3 to 34 pesticides. Only 12% of suspendedsediment samples contained pesticides. On average, Sacramento River zooplankton
samples contained more pesticides than zooplankton from the Yolo Bypass, whereas
the opposite was true for pesticides detected in water.
The pesticides detected and their timing of detection often differed between
zooplankton, water and suspended sediment, indicating that pesticides in zooplankton
are an important piece of the contaminant puzzle. Finally, several pesticides, including
the pyrethroid insecticides cyfluthrin, cyhalothrin, cypermethrin, esfenvalerate, andpermethrin were only detected in zooplankton, indicating that zooplankton may be an
important pathway for these highly toxic pesticides within the Delta ecosystem.

Birds and Their Habitats in the Bay-Delta
Breeding Waterbird Population Declines in South San Francisco Over the Past
Two Decades
Alex Hartman1, Josh Ackerman1, Carley Shacter1, Mark Herzog1, Max Tarjan2,
Yiwei Wang2, Cheryl Strong3, Rachel Tertes3, Nils Warnock4
1U.S. Geological Survey, 2San Francisco Bay Bird Observatory, 3U.S. Fish and Wildlife

Service, 4Audubon Canyon Ranch

Presenting author email: chartman@usgs.gov
Former salt evaporation ponds in South San Francisco Bay support large populations ofbreeding waterbirds. In 2006, the South Bay Salt Pond (SBSP) Restoration Project69

Friday Scheduled Sessions: Birds and Their Habitats in the Bay-Deltabegan the process of converting 50-90% of these ponds, now managed as wildlife
habitat, into tidal marsh. We compared American avocet and black-necked stilt
abundance in south San Francisco Bay before (2001) and after (2019) approximately
1300 ha of ponds were breached to tidal action to begin tidal marsh restoration. Overthe 18-year period, American avocet numbers declined 13.5% (2765 in 2001 vs. 2391 in2019) and black-necked stilt numbers declined 30.0% (1184 in 2001 vs. 828 in 2019).
Forster’s terns were not surveyed in 2001 but numbered 2675 birds in 2019. In 2019,
managed ponds accounted for only 25.8% of suitable habitats, yet contained 53.9%,
38.6%, and 65.6% American avocet, black-necked stilt, and Forster’s tern observations,
respectively. Conversely, tidal marsh and tidal mudflats accounted for 42.9% of suitable
habitats, yet contained only 18.4%, 10.3%, and 19.8% American avocet, black-necked
stilt, and Forster’s tern observations, respectively. Using a separate nest monitoringdataset, we found that nest abundance in south San Francisco Bay declined for all three
species during 2005-2019. Average annual nest abundance during 2017-2019 declined
53%, 71%, and 36%, for American avocets, black-necked stilts, and Forster’s terns,
respectively, compared to 2005-2007. Loss of island nesting habitat due to tidal marsh
conversion and an increasing population of predatory California gulls are two potential
causes of these declines. All three species established nesting colonies on newly
constructed islands within remaining managed ponds, however, these new colonies
have not made up for the steep declines observed at other historical nesting sites.
Retaining more managed ponds with nesting islands during future phases of the SBSP
Restoration Project may help to limit further breeding waterbird population declines.
Seasonal Resource Partitioning among Demographic Groups of Western
Sandpipers: Implications for Shorebird Ecology and Conservation in the San
Francisco Bay Estuary
Laurie Hall1, Susan De La Cruz1, Isa Woo1, Tomohiro Kuwae2, John Takekawa1 | 3
1San Francisco Bay Estuary Field Station, Western Ecological Research Center, U.S.

Geological Survey, 2Coastal and Estuarine Environment Research Group, Port andAirport Research Institute, 3Suisun Resource Conservation District
Presenting author email: lahall@usgs.gov

The San Francisco Bay estuary is visited by over half a million wintering and migratory
shorebirds each year, accounting for nearly two-thirds of migratory shorebirds along the
Pacific Flyway. These shorebirds rely on adequate prey in the estuary to maintain theirbody condition and prepare for breeding. Increased competition for prey during
migration, a period of high energy expenditure and increased shorebird densities, could
result in age- and sex-related dietary specialization that would facilitate resource
partitioning among demographic groups. We quantified the contribution of biofilm,
microphytobenthos, and benthic invertebrates to the diets of western sandpipers(Calidris mauri) from different demographic groups during mid-winter(January/February) and at the onset of the breeding migration (April) using stable
isotope mixing models. Western sandpipers are sexually dimorphic with females having
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Friday Scheduled Sessions: Birds and Their Habitats in the Bay-Delta
significantly greater body mass and bill length than males. Diet composition differed
between seasons and among demographic groups. In winter, prey consumption was
similar among demographic groups, but, in spring, diet composition differed with billlength and body mass explaining 31% of the total variation in diet composition.
Epifaunal invertebrates made up a greater proportion of the diet in males which had
lesser mass and shorter bills than females. Consumption of Polychaeta increased withincreasing bill length and was greatest in adult females. In contrast, consumption of
microphytobenthos, thought to be an important food source for migrating sandpipers,
increased with decreasing bill length and was greatest in juvenile males. Our results
provide the first evidence that age- and sex-related dietary specialization in western
sandpipers facilitate seasonal resource partitioning that could reduce competition during
spring at the onset of the breeding migration. Our study underscores the importance of
examining resource partitioning throughout the annual cycle to inform fitness anddemographic models and facilitate conservation efforts.
Coordinated Mapping to Assess Local, Regional and Coast-Wide Change in
Wetlands and Related Habitat Types
Cristina Grosso1
1San Francisco Estuary Institute

Presenting author email: cristina@sfei.org
The San Francisco Estuary Institute (SFEI) is coordinating several new inventories of
wetlands and other habitat types in the Sacramento-San Joaquin Delta, Bay Area, andalong California’s coast. Together these inventories will meet the need for standardized
maps to assess net change in the distribution, abundance, diversity, and condition of
surface water habitats due to management actions and climate change.
These projects will apply the California Aquatic Resource Inventory (CARI; sfei.org/cari)methods. The final maps will be publicly available online through EcoAtlas(ecoatlas.org). The projects are funded by the Environmental Protection Agency and the
Ocean Protection Council, and are scheduled to be completed by 2023.
In collaboration with the Sacramento-San Joaquin Delta Conservancy and a multiagency Bay-Habitat Mapping Workgroup, SFEI will produce the Delta Aquatic Resource
Inventory (DARI; sfei.org/dari) for Suisun and the Delta.
The Ocean Protection Council (OPC; opc.ca.gov) and SFEI will develop an inventory ofwetlands and other surface waters of all California’s coastal HUC-8 watersheds, to help
implement the OPC’s 2020-2025 Strategic Plan. Development of this coastal inventory
will be advised by a new statewide wetland mapping committee of the California
Wetland Monitoring Workgroup.
A regional, multi-partner team will update the inventory of Bay Area baylands. The
Baylands Change Basemap will be a fundamental component of the San Francisco
Estuary Wetlands Regional Monitoring Program (sfestuary.org/wrmp), to help
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Friday Scheduled Sessions: Birds and Their Habitats in the Bay-Delta
coordinate baylands protection and restoration, detect regional landscape change, andpromote a shared view of the regional landscape.
These projects will yield crosswalks among regional aquatic resource classification
systems, allowing inventories to be compiled across regions. The results will enable allinterests to assess regional and coast-wide net change in the distribution, abundance,
diversity, and condition of the resources, in the context of population growth and climatechange.
(*IEP) Identifying High Priority Areas for Bird Conservation in the Delta
Kristen Dybala1, Kristin Sesser1, Matt Reiter1
1Point Blue Conservation Science

Presenting author email: kdybala@pointblue.org
The Sacramento–San Joaquin Delta provides habitat to an abundant and diverse
community of birds, despite extensive human modifications to the ecosystem over the
past 150 years, but is likely only a small fraction of what the Delta’s bird community
once was. Restoring a healthy Delta ecosystem requires providing habitat for birds
year-round, which in turn requires integrating the full diversity of the Delta’s bird
community in scientific analyses, conservation strategies, and restoration goals. To
address this science need and identify areas that are a high priority for birdconservation, we analyzed the spatial distributions of waterbird and riparian landbird
populations throughout the Delta. Drawing on extensive bird surveys conducted in the
Delta and surrounding areas in recent years, we focused on 5 groups of waterbird
species and 9 riparian landbird species that collectively represent the diversity of habitat
needs of each group. For each of these taxa, we used boosted regression tree models
to identify predictive relationships between the probability of species presence orabundance and covariate metrics representing the surrounding landscape at multiple
spatial scales. From these models, we developed maps representing the predicteddistribution of waterbird and riparian landbird species on the landscape. We then used
the Zonation spatial prioritization algorithm to identify the areas of the Delta’s landscapethat are the most important to maintaining these bird populations. The results represent
the current state of the science on the spatial distribution and abundances of different
bird taxa across the Delta and the areas with a high confidence of importance to birdconservation. Our results also provide a baseline from which the effects of observed or
projected changes to the Delta’s landscape can be compared, facilitating the integrationof a broader number of bird species in conservation planning and policy decisions.
Resilient Staten Island: Pilot Application for Landscape Scenario Analysis
Alison Whipple1, Samuel Safran1, Dawit Zeleke2, Emily Wells3, Steve Deverel4,
Josue Medellín-Azuara5, Spencer Cole5, Alexander Guzman5, Jose RodríguezFlores5, Letitia Grenier1
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Friday Scheduled Sessions: Greenhouse Gas Exchange and Wetland Accretion in the
Bay-Delta System: Implications for Science, Policy, and Management in the
Sacramento-San Joaquin Delta, Suisun Marsh, and San Francisco Bay
1San Francisco Estuary Institute - Aquatic Science Center, 2The Nature Conservancy,
3Conservation Farms and Ranches, 4HydroFocus, 5University of California, Merced
Presenting author email: alison@sfei.org
Most land uses within the Delta continue to erode landscape resilience and associatedecosystem functions and services by perpetuating peat loss and land subsidence andlimiting natural processes and habitat for wildlife. Determining what to do where to
support landscapes that serve diverse objectives is a central need for planning in the
Delta. Doing so requires that land use changes and restoration actions be evaluated
together for multiple costs and benefits. To explore this, we conducted a pilot scenario
analysis for Staten Island, a 9,200 acre Delta island owned by The Nature
Conservancy. Based on physical conditions as well as agricultural and wetland
restoration objectives, we developed six potential future land use scenarios. These werethen evaluated using existing tools and methods across a suite of metrics relating to
expected hydrologic connectivity, subsidence reversal, change in GHG (greenhousegas) flux, ecosystem functions, and economic impact. This analysis illustrated theimportance of rice for maintaining economic viability while also slowing or reversing land
subsidence on peat soils. Further, evaluating these factors at the landscape scale
showed how introducing managed and tidal wetlands could provide habitat and carbon
sequestration benefits, with the loss of agricultural revenue made up in part by carbon
market revenue but also crops grown elsewhere on the island. The pilot application also
helped identify additional metrics and uncertainties (e.g., levee failure risk reduction,
capital costs, additional habitat and recreation benefits) that should be addressed infuture evaluations. By envisioning and evaluating new practical approaches to the
management of subsided lands in the Delta, this effort supports the continued
development and integration of tools and approaches for establishing sustainable Delta
futures that recover needed ecosystem functions while maintaining the Delta’s
economy, culture, and sense of place.

Greenhouse Gas Exchange and Wetland Accretion in the Bay-Delta
System: Implications for Science, Policy, and Management in the
Sacramento-San Joaquin Delta, Suisun Marsh, and San Francisco Bay
Carbon Greenhouse Gas Fluxes and Water Biogeochemistry in a Restored
Wetland with Managed Hydrology in the Sacramento-San Joaquin Delta
Ariane Arias-Ortiz1 | 2, Erin Lynch2, Daphne Szutu1, Joseph G. Verfaillie1, Isabel
Reche3, Adina Paytan2, Dennis D. Baldocchi1
1Ecosystem Science Division, Department of Environmental Science, Policy andManagement, University of California, Berkeley, CA 94720, USA, 2Institute of Marine
Sciences, University of California, Santa Cruz, CA 95064, USA, 3Departamento de
Ecología and Instituto del Agua, Universidad de Granada, 18071 Granada, Spain
Presenting author email: aariasortiz@berkeley.edu
73Friday Scheduled Sessions: Greenhouse Gas Exchange and Wetland Accretion in the
Bay-Delta System: Implications for Science, Policy, and Management in the
Sacramento-San Joaquin Delta, Suisun Marsh, and San Francisco Bay
To mitigate the effects of climate change and risks associated with sea level rise, yearround flooding of peat soils to develop freshwater wetlands has been used as aneffective management plan to reverse land subsidence and sequester carbon. The
capacity of restored wetlands to offset greenhouse gas emissions, although proved
significant, is still an active area of research. Specifically, our understanding of howorganic matter is mineralized and partitioned into carbon dioxide (CO2), methane (CH4),
and dissolved organic carbon (DOC) in these systems remains limited. It is particularly
uncertain how variable water quality influences carbon greenhouse gas emissions onannual timescales. Changes in salinity are known to reduce productivity and affect CH4biogeochemistry, while an increase in DOC concentrations can produce more
greenhouse gases through enhanced microbial activity and photochemicaltransformations. This study explores seasonal changes in water biogeochemistry in a
restored freshwater wetland with managed hydrology and assesses the relations
between water chemistry and greenhouse gas emissions. We combine the use of highfrequency eddy covariance atmospheric flux measurements with water depth,
temperature, dissolved oxygen, dissolved pCO2, conductivity, turbidity and fluorescentdissolved organic matter, pH, DOC and inorganic carbon data, collected using aquaticsensor and discrete sampling. Using a 4-year long dataset we explore the relationships
between DOC and greenhouse gas emissions and the existence of potential hot periodsof dissolved organic carbon mineralization that result from the interplay between internal
ecosystem carbon cycling and environmental conditions. Preliminary results show that
DOC concentrations in surface wetland waters are high and temporally variable (5-79
mg L-1) with a seasonal trend that is compounded by water table depth. Our results willserve to assess the contribution of DOC mineralization to greenhouse gas emissions
and the magnitude of the ecosystem carbon budget that remains in the aquaticcompartment.
The Delta Blue Carbon and Wetland Resilience Project: Data Synthesis andScenario Evaluation for the Past, Present, and Future Delta
Lydia Smith Vaughn1, April Robinson1, Donna Ball1, Judith Drexler2, Steven
Deverel3, James Morris4, Letitia Grenier1
1San Francisco Estuary Institute, 2U.S. Geological Survey, 3HydroFocus, Inc.,
4University of South Carolina

Presenting author email: lydiav@sfei.org, april@sfei.org
Wetland restoration in the Delta has the potential to mitigate the effects of land-surface
subsidence by rebuilding marsh elevation via vertical accretion. Restored wetlands may
benefit the climate through carbon sequestration while conferring flood protection andresilience to sea level rise and creating habitat for wetland-dependent species. The
ability of restored wetlands to provide these benefits, however, depends on the siting
and timing of restoration. Benefits to the climate depend on carbon accretion rates,
methane emissions, and the magnitude of avoided baseline emissions. The long-term
resilience of tidal wetlands in the Delta depends on the rate of sea level rise, accretion74

Friday Scheduled Sessions: Greenhouse Gas Exchange and Wetland Accretion in the
Bay-Delta System: Implications for Science, Policy, and Management in the
Sacramento-San Joaquin Delta, Suisun Marsh, and San Francisco Bay
rates, and available migration space. Our understanding of these effects continues toimprove as more data become available from field and modeling studies. However, thecomplex set of biophysical and land use factors governing restoration outcomes andopportunities has made it challenging to optimize wetland restoration planning. To
inform such restoration planning, the San Francisco Estuary Institute, USGS, Universityof South Carolina, and HydroFocus, Inc., are using models and data synthesis togenerate Delta-wide datasets of wetland elevation, carbon storage, greenhouse gas
emissions, and tidal marsh resilience for historical (pre-European settlement), modern,
and future (restoration and sea level rise) scenarios. Datasets, models, and associateduncertainties will be added to the Delta Landscapes Scenario Planning Tool, a GISbased tool for evaluating outcomes of user-defined land use scenarios. With spatially
explicit metrics of carbon storage, methane emissions, subsidence, and marsh
accretion and migration, this tool offers land use planners a synthetic means to compare
the expected climate benefit and resilience of wetlands to sea level rise under different
restoration scenarios.
Advancing the Wetland Accretion Rate Model of Ecosystem Resilience(WARMER-2): Improved Parameterization for San Francisco Bay-Delta
Kevin Buffington1, Karen Thorne1, Chris Janousek2
1U.S. Geological Survey, 2Oregon State University

Presenting author email: kbuffington@usgs.gov
Understanding the rates and spatial patterns of tidal wetland elevation change relative
to sea-level is essential for projecting future vulnerability of ecosystems and built
landscapes in estuaries. Building from previous approaches and using an enhanced
and more flexible modeling framework (WARMER-2), we explored plant community
transitions, belowground carbon storage, and sea-level rise impacts to San Francisco
Bay-Delta (SFBE) wetlands through 2100. We improved model parameterization for
SFBE marshes by incorporating recent experimental results of plant species sensitivity
to flooding and salinity gradients as well as site-level estimates of organic matterdecomposition. To account for a dynamic tide range under sea-level rise, we leveraged
results from a Delta hydrodynamic model. The revised framework includes an improved
calibration scheme that accurately reconstructs soil profiles, quantifies parameter
uncertainty through Monte Carlo simulations, and provides an estimate of carbon burial
rates.
Using WARMER-2 we evaluated the future vulnerability of Petaluma River, Rush
Ranch, and Browns Island marshes located along a salinity gradient to varying
scenarios of sea-level rise, salinization, and changes in sediment availability. All threemarshes were sensitive to changes in sediment availability, but sites with higher starting
elevations or space for upland transgression persisted longer under higher sea-level
rise scenarios than sites lower in elevation. Using the multi-plant species transition
model for organic matter inputs, WARMER-2 predicted increased resilience and higher
75

Friday Scheduled Sessions: Greenhouse Gas Exchange and Wetland Accretion in the
Bay-Delta System: Implications for Science, Policy, and Management in the
Sacramento-San Joaquin Delta, Suisun Marsh, and San Francisco Bay
rates of carbon accumulation compared with projections assuming no temporal change
in the plant community. The WARMER-2 modeling framework is a flexible tool forassessing alternative tidal marsh futures under sea-level rise, sediment, and salinity
scenarios and providing information to resource managers.
Integration of Science and Implementation of Land-Use Change for Increased
Sustainability
Steven Deverel1, Campbell Ingram1 | 2 | 3, Rodd Kelsey3, Sabina Dore3
1HydroFocus, Inc., 2Delta Conservancy, 3The Nature Conservancy

Presenting author email: sdeverel@hydrofocus.com
There has been substantial progress in the scientific understanding and quantification of
the nature and effects of subsidence, with increasing evidence of unsustainability
including decreased arability, increased pressure on levees and water supply
vulnerability, large greenhouse gas emissions and declines in native species. There isalso increasing evidence of the co-benefits that can come with subsidence mitigationthat would increase ecosystem sustainability and resilience. While there is more thelearn, there is an urgent need to implement solutions more rapidly that can stop andreverse the Delta’s unsustainable trajectory. Alternate land uses such as permanently
flooded, managed wetlands and rice provide a substantial net GHG emissions reduction
benefit relative to the status quo and mitigate and reverse subsidence. Participation incarbon-offset trading is part of the solution. With the approval of the American Carbon
Registry protocol for California deltaic wetlands, there has been an increase in thenumber of landowners interested in conversion to rice cultivation and managed
wetlands to engage the carbon market. The CARB Offset Protocol Development
Taskforce has recommended that the ACR protocol be adopted into the AB-32
Compliance Program. This will likely have a significant effect on the value of Delta
carbon and result in increased interest in land conversion in the most deeply subsided
areas of the Delta. Applied interdisciplinary data collection, analysis and modelingintegrated with implementation of land use changes and carbon offset trading is key tosuccessful transition to a more sustainable trajectory and viable ecosystem. This
pioneering integrated approach is ongoing on several islands including Staten Island
where large scale conversion is heading toward a mosaic of rice, wetlands and othercrops that will reduce GHG emissions, provide ecosystem benefits and increased longterm economic viability. We will provide an overview of current projects and progress.
Quantifying Carbon Benefits of Tidal Wetland Restoration in the Delta: Decision
Support using a Robust, Integrated and Data-Driven Model
Patty Oikawa1, Ellen Stuart-Haentjens2, Brian Bergamaschi2, Julie Shahan1, Iryna
Dronova3, Gwen Miller3, Sara Knox4, Sarah Russell4, Lisamarie Windham-Myers276

Friday Scheduled Sessions: IEP Session: Using Aquatic Surveys for Estimation andCommunication: Bias, Quantification, and Display
1California State University East Bay, 2USGS, 3University of California, Berkeley,
4University of British Columbia

Presenting author email: patty.oikawa@csueastbay.edu
Planned tidal wetland restoration in the Bay Delta will help restore important ecosystemservices including support of pelagic food webs and protection of coastal regions fromsea level rise. However, the ability of tidal marshes to deliver these ecosystem services
is strongly related to their long-term stability and climate resilience. Because the longterm stability of these habitats is strongly linked to their net carbon balance, we havemeasured the net carbon balance of two tidal marshes and have used the data todevelop a modeling tool to predict carbon sequestration, subsidence reversal, andclimate resilience of tidal wetlands. Our first site is a historic tidal marsh in the Suisun
complex and the second is an actively restoring polyhaline marsh in the San Francisco
Bay. Each site is outfitted with an eddy covariance tower and lateral carbon flux
monitoring station allowing us to continuously quantify atmospheric (CO2 and CH4) andhydrologic (DIC, DOC, POC) exchange of carbon. Due to the high frequency datacollection, we are able look at a wide range of temporal scales to determine how thedifferent carbon fluxes respond to environmental drivers. For example, soil temperatureand tidal inundation are strong predictors of DIC export at the daily to monthly scale. We
have used these data to parameterize and test a new biogeochemical model MEMPEPRMT which accurately predicts atmospheric exchange of CO2 and CH4 as well as
sediment accretion. This tool has been under development with feedback from the Delta
stakeholder community. We plan to conduct regional modeling of greenhouse gas
exchange from existing and proposed wetlands in the Delta region and project tidal
marsh resilience up to 2100. This will improve understanding of how landscape-scale
restoration projects in the Delta will affect carbon cycling and sediment dynamics andimprove stakeholders’ ability to participate in carbon markets.

IEP Session: Using Aquatic Surveys for Estimation andCommunication: Bias, Quantification, and Display(*IEP) Relative Catchability Bias Among Sampling Gears for Fish Species Within
the San Francisco Estuary
Brock Huntsman1, Brian Mahardja2
1U.S. Geological Survey, 2U.S. Bureau of Reclamation

Presenting author email: bhuntsman@usgs.gov
Gears used to monitor fish species can only sample a fraction of available fish habitat,
an inherent bias in all fisheries monitoring programs referred to as “catchability.” Gear
retention efficiency is a component of catchability and is defined as the retention offishes once in contact with the gear, a source of bias that can be affected by numerous
aspects of gear deployment (e.g., net size, deployment speed, mesh size). We
assessed relative retention efficiency differences among four long-term fish monitoring77

Friday Scheduled Sessions: IEP Session: Using Aquatic Surveys for Estimation andCommunication: Bias, Quantification, and Display
surveys from the San Francisco Estuary (SFE): the Bay Study Otter Trawl (BSOT), the
Bay Study Midwater Trawl (BSMT), the Fall Midwater Trawl (FMWT), and the Suisun
Marsh Otter Trawl (SMOT). We used generalized additive models with a spatiotemporal smoother to predict gear-specific estimates of abundance for 45 different fish
species within large and small size classes. We included the survey as a fixed effectwith the FMWT as the reference condition (intercept). The slope coefficients thenrepresent a retention efficiency among gear types relative to the FMWT, referred to as acatch ratio. Significant differences in relative retention efficiency were determined bywhether 95% confidence intervals of the catch ratio did not include 1.0. We found fromcatch ratios that 45%, 82%, and 70% of fish species in large size-classes were captured
in higher abundance in the FMWT than in the BSMT, BSOT and SMOT, respectively.
Fish species in small size classes were similarly captured in higher numbers in the
FMWT, where 46%, 73%, and 59% of fish species were captured in higher abundancein the FMWT than in the BSMT, BSOT and the SMOT, respectively. Our results
demonstrate that catchability is a significant source of bias among SFE monitoring
efforts that must be addressed when developing biological metrics using catch frommultiple surveys.
(*IEP) Let’s Stop Guessing: Using Quantitative Tools Developed During LongTerm Monitoring Review to Evaluate Survey Regime Alterations
Jereme Gaeta1 | 2, Stephanie Fong1 | 2
1California Department of Fish and Wildlife, 2Interagency Ecological Program

Presenting author email: jereme.gaeta@wildlife.ca.gov
Evaluating and, when appropriate, modifying sampling regimes is a challenge inherent
to all long-term monitoring programs, particularly in the face of reduced resources
associated with altered funding, personnel constraints, equipment failures, or evenglobal pandemics. While sensitivity analyses are readily available to evaluate theconsequence of altering sampling regimes of single species or univariate monitoring
programs, approaches to effectively evaluate spatiotemporally complex community
monitoring programs are not. Here we present an analytical framework and associatedmetrics to assess the consequence of reduced sampling regimes on our ability tounderstand fish communities. Specifically, we combine spatiotemporally explicit
principal tensor analyses and hierarchical cluster analyses to test whether reduced
Interagency Ecological Program trawl survey effort influences our understanding of the
San Francisco Estuary fish community as detected via otter and midwater trawl gears.
We found that, depending on how the monitoring program is altered, the loss of a single
station could drastically degrade our understanding of the fish community or theelimination of a suite a stations could have little to no effect. Intuitively, the effect of
reduced sampling is highly dependent on how a long-term monitoring program isaltered. Methods to assess reduced sampling regimes are greatly needed today in the
San Francisco Estuary as agencies face reduced resources and limited capacity tomaintain sampling programs during the COVID-19 pandemic. While the need to adjust78

Friday Scheduled Sessions: IEP Session: Using Aquatic Surveys for Estimation andCommunication: Bias, Quantification, and Display
long-term monitoring programs was the impetus for this body of work, our work
highlights the risk associated with uninformed change. Our work provides a promisingframework to quantitatively optimize resource allocation while minimizing information
loss.
(*IEP) Quantifying Changes in Gear Efficiency to Reduce Bias in Estimating LongTerm Abundance Trends
Bryan Matthias1, Russ Perry2, Joseph Kirsch3, Noble Hendrix4, Adam Pope2
1U.S. Fish and Wildlife Service, 850 S. Guild Avenue, Lodi, CA 95240, 2U.S. Geological

Survey, Columbia River Research Laboratory, 5501A Cook-Underwood Road, Cook,
WA 98605, 3U.S. Fish and Wildlife Service, Georgia Ecological Services Field Office,Rome, GA 30161, 4QEDA Consulting, LLC, Seattle, WA 98103
Presenting author email: bryan_matthias@fws.gov

Long-term monitoring programs were often designed to track temporal trends inabundance. However, the ability of a program to accurately track population trends isdependent on the assumption that catch (or catch per unit effort) is proportional to true
abundance. This assumption is often violated because gear efficiency (the proportion ofavailable individuals caught at a given site) is not static over time and may be influenced
by site-specific factors, such as water velocity, turbidity, substrate composition, etc.
Here we used an N-mixture model, which relied on multi-pass depletion surveys(referred to as efficiency surveys; n = 188 surveys) from 2014-2018, to estimate theeffects of site-specific factors on the capture efficiency of juvenile Chinook salmon
Oncorhynchus tshawytscha sampled in the U.S. Fish and Wildlife Delta Juvenile FishMonitoring Program beach seine surveys. We identified a negative relationship between
seine efficiency and water velocity, indicating that juvenile Chinook sampled at sites
with (or during periods of) lower water velocity had a higher chance of being captured
than those sampled at sites with higher water velocity. This model was then applied todata collected outside of these efficiency surveys, which used a single seine haul ateach site, to estimate weekly juvenile Chinook salmon abundance trends from 20002019. Results from this work provide more accurate spatio-temporal trends in juvenile
Chinook abundance and use of the Sacramento-San Joaquin River Delta system byreducing systematic bias associated with changes in gear efficiency from site-specificfactors, such as water velocity. Further, by incorporating efficiency surveys within longterm monitoring programs we can monitor for changes in gear efficiency and identify
other sources of bias.
(*IEP) Real Time Tidal Excursion Mapping and Constituent Tracking, Fishery
Surveys and Tools to Support Tidally Influenced Pelagic Habitat Identification
Jon Burau1, Nathan Hemenway1, Jon Donovan1, David Osti1
1U.S. Geological Survey

79

Friday Scheduled Sessions: IEP Session: Using Aquatic Surveys for Estimation andCommunication: Bias, Quantification, and Display
Presenting author email: david@34north.com
Problem Statement: Ready access to real time and curated data presented together
with tools to place the data appropriately in the tidal transport framework of the Delta will
help enhance research, decrease response-time to evaluations of change, acceleratescientific consensus, and improve support for managers.
Approach: One impediment to scientific consensus about the impacts of water
operations on endangered species protections in the San Francisco Delta and Estuary
is access to real time operations and data simulations that demonstrate and visualize
accurate conditions in relation to tidal excursions. For example, accurately depicting
conditions from field measurements of salt and sediment concentrations (or turbidity)
made from boat surveys (e.g. along-channel transects) often involve campaigns that arelong in duration compared to a tidal cycle. As a result, they can provide a spurious
picture of the spatial distribution of concentrations and how they vary over time. This
project makes use of existing concentration and flow data collected at fixed stations toprovide maps of the spatial patterns in the concentration data. In addition we include
operations and fish surveys snapshots and make it available through a publiclyavailable web platform together with tools to visualize, explore and perform basic
analyses. In the near term, our findings demonstrate feasible methods and results
using the existing monitoring network to better understand constituent fields related totidal excursions. We will demonstrate methods to replace boat surveys to report andunderstand turbidity conditions for regulatory analysis. In the long term this project
aims to add additional near real time data sources and methods to the decision-making
tool box to ensure that fish are protected and exports can be made available to water
users.
(*IEP) Web Based Approaches to Fisheries Data Communication
Tom Pham1 | 2, Cyril Michel1 | 2, Jeremy Notch1 | 2, Alex McHuron1 | 2, Rebecca
Robinson1 | 2, Renae Logston1 | 2
1NOAA, 2University of California, Santa Cruz

Presenting author email: tom.pham@noaa.gov
Juvenile Salmon Acoustic Telemetry System (JSATS) technology is used throughout
California’s Central Valley to tag and track outmigrating juvenile salmonids to monitor
movement and survival rates. Traditional approaches to convey these data can bedifficult to access and engage a larger audience. Here, we provide alternative methods
to increase accessibility through interactive data visualization in two different ways 1). A
real-time tracking website 2). A retrospective Shiny web application. Both are generatedusing openly accessible R programming code, making the data visualization andanalyses reproducible and transparent to users.
A website was developed using R Markdown to provide real-time data of tagged fish in
the Central Valley. The website provides summaries and visualizations of detected fish
numbers, reach-specific survival, routing probability, survival to the different real-time80On-demand talks: An Update on Salt Marsh Harvest Mouse Ecology and Future
Perspectives (SMHM)
receivers deployed throughout the Sacramento River, Delta, and Bay, and receiverdiagnostics.
A web application was developed using the Shiny package in R. The application gives
users the ability to explore retrospective project data for past groups of tagged fish
based on user defined parameters. Primary features include: summaries andvisualizations of receiver redeployments, outmigration animations, tagged fish metrics,
frequency of detections by time of day, survival estimates, and travel times.
Together, these tools provide stakeholders and the general public with immediate dataon real-time analytics for current undergoing projects as well as a retrospective look oncompleted projects in an engaging and accessible online format. The real-time website
can be accessed at https://calfishtrack.github.io/real-time and the Shiny app can beaccessed at https://oceanview.pfeg.noaa.gov/shiny/FED/telemetry/.

On-demand talks
An Update on Salt Marsh Harvest Mouse Ecology and Future
Perspectives (SMHM)
001-SMHM: A New Non-Invasive Genetic Survey Technique for the Endangered
Salt Marsh Harvest Mouse
Cody Aylward1, Robert Grahn1, Laureen Barthman-Thompson2, Douglas Kelt1,
Benjamin Sacks1, Mark Statham1
1University of California, Davis, 2California Department of Fish and Wildlife

Presenting author email: cmaylward@ucdavis.edu
Salt marsh harvest mice (SMHM; Reithrodontomys raviventris) are an endangered
species endemic to the San Francisco Estuary (SFE). SMHM habitat has declined byapproximately 90% during the past two centuries. The contemporary range of SMHM –one of the most basic pieces of information needed for effective conservation – is poorly
understood. Endangered species surveys can be logistically challenging, leaving many
parts of their historical range unsurveyed for decades. One additional challenge to
SMHM surveys is that genetic verification is required to reliably distinguish SMHM fromtheir congener, the western harvest mouse (WHM; R. megalotis). A simple and reliable
technique for assessing the occupancy status of marshes is critical to filling longstanding knowledge gaps in the modern range of SMHM. To this end, we developed anon-invasive genetic survey for SMHM and sympatric rodents. We placed bait andbedding into bait stations with permanent openings – allowing mice to enter and exit
freely – and placed bait stations along transects at Joice Island in Suisun Marsh. After 7
days, scat samples were collected from the bait stations. Fecal samples were present in
9 of 10 stations deployed at Joice Island. We developed a genetic species identification
assay for simultaneous detection of 5 common SFE rodents (SMHM, WHM, house
mouse (Mus musculus), deer mouse (Peromyscus sp.), and vole (Microtus californicus).
81On-demand talks: An Update on Salt Marsh Harvest Mouse Ecology and Future
Perspectives (SMHM)
Using control DNA, we verified sensitivity of each target species with as little as 0.01
ng/uL of DNA, and no false-positives. When Joice Island scat samples were subject tothe genetic test, SMHM were detected at 8 stations and WHM were detected at 3
stations, including two stations where both species were detected. This non-invasive
survey technique can provide much needed occupancy information for SMHM where
live-trapping efforts may be resource-prohibitive.
002-SMHM: A Bigger Picture of a Tiny Critter: A Range-Wide Assessment of theSalt Marsh Harvest Mouse
Katie Smith1 | 2, Laureen Barthman-Thompson3, John Takekawa4
1University of California, Davis, 2WRA Inc.,3California Department of Fish and Wildlife -Suisun Marsh Unit, 4Suisun Resource Conservation District
Presenting author email: ratsmith@ucdavis.edu

The endangered salt marsh harvest mouse (SMHM; Reithrodontomys raviventris)
presumably once occurred in virtually all of the marshes of the San Francisco Estuary.
Today, the species exists largely as isolated populations with little to no connectivity inmany parts of its range. Some of these populations occur in relatively large contiguous
marsh areas (e.g., Suisun Marsh), while others persist in smaller marshes (e.g., Santa
Venitia Marsh). Research efforts and long-term monitoring has focused largely on
contiguous marsh complexes under public ownership (e.g., Suisun Marsh, Don
Edwards Wildlife Refuge, Eden Landing Ecological Reserve), and many smaller
marshes are rarely even surveyed. This bias in research and monitoring not only leaves
holes in our understanding of SMHM occupancy throughout the Estuary, but also
potentially fuels misunderstanding about habitat value, as large marshes are more likely
to see persistent SMHM occupancy than smaller marshes with identical vegetation,hydrology, etc., simply though stochastic processes. In an effort to better understandthe state of SMHM as a species and their habitat requirements, to ultimately make more
effective management and recovery decisions, we are conducting a NFWF-funded
range-wide survey of SMHM this year. We will also be using historical and recent data
to model habitat suitability and occupancy. This presentation will present the results of
the initial range-wide habitat model that will guide this survey effort, as well as an
overview of the survey plan. Those who are interesting in providing feedback on thesurvey plan, or who wish to participate in the survey effort are encouraged to attend thistalk or contact Katie Smith at ksmith@wra-ca.com.
003-SMHM: Salt Marsh Harvest Mouse Home Range and Habitat Selection in
Managed and Tidal Wetlands of Suisun Marsh: Implications for Endangered
Species Conservation and Management
Melissa Riley1 | 2, Katie Smith1 | 3, Sadie Trombley1, Carla Angulo4, Monica Zhang182

On-demand talks: An Update on Salt Marsh Harvest Mouse Ecology and Future
Perspectives (SMHM)
1University of California, Davis, 2California Department of Fish and Wildlife, 3WRA Inc.,
4University of San Francisco

Presenting author email: melriley@ucdavis.edu
The salt marsh harvest mouse (Reithrodontomys raviventris, SMHM) is endemic to themarshes of the San Francisco Bay Estuary. In the 1970s SMHM were State andFederally listed as endangered, primarily due to habitat loss and fragmentation. Suisun
Marsh contains over half of the remaining SMHM habitat, and is critical for futureconservation of the species. Management in Suisun Marsh is primarily focused onproviding waterfowl habitat through manipulation of managed wetlands, but this was
initially thought to be incompatible with SMHM recovery which stressed the need for thepreservation and restoration of tidal wetlands with monocultures of pickleweed(Salcornia pacifica). Emerging research has shown that managed and tidal wetlands in
Suisun can be just as valuable to SMHM, supporting similar population sizes withsimilar survival and growth rates. In addition, studies have shown that SMHM may be
more of habitat generalists within marshes versus specialists keying in on pickleweed.
So, what defines "good" SMHM habitat? Are SMHM true specialists? Or are they more
adaptable due to their apparent plasticity in places like Suisun? While ourunderstanding of SMHM habitat requirements is evolving, defining "good" SMHM
habitat is critical to future conservation and management throughout the species range,
especially as tidal restoration is implemented and new threats like sea level rise
emerge. To better understand SMHM habitat requirements in Suisun, we conducted aradio-telemetry study in paired tidal and managed wetlands. SMHM were collared andtracked seasonally over the course of three years. Using information from the telemetry
study, we evaluated SMHM home ranges and habitat selection. SMHM home ranges
were similar in tidal and managed wetlands, indicating the importance of both wetland
types in future conservation and management efforts.
004-SMHM: Development of a Morphological Key for the Southern Salt MarshHarvest Mouse using Genetically Verified IndividualsMark Statham1, Laureen Barthmann-Thompson2, Susan Fresquez1, Ben Sacks1
1University of California, Davis, 2California Department of Fish and Wildlife

Presenting author email: statham@ucdavis.edu
The salt marsh harvest mouse (SMHM; Reithrodontomys raviventris) is a State andFederally listed endangered species endemic to the coastal marshes of the San
Francisco Estuary of California. Of two subspecies, the southern (R. r. raviventris) ismost endangered and lacks reliable morphological field tools to distinguish from thesympatric western harvest mouse (WHM; R. megalotis). We trapped and collected
genetic samples and morphological data from 204 harvest mice from 14 locations fromacross the range of the southern SMHM. Genetic species identification indicated these
to be composed of 48 SMHM and 156 WHM, which we compared at ten morphologicalcharacters. Most continuous characters overlapped between species. Color characters83On-demand talks: An Update on Salt Marsh Harvest Mouse Ecology and Future
Perspectives (SMHM)
were significantly differentiated and we identified a number of species-specificdiagnostic pelage categories in both species. A random forest analysis indicated that
ventral coloration of the abdomen and the ventral tail hair color were the most useful fordifferentiating between species. We used these two morphological characters todevelop a decision tree which correctly classified 94% of harvest mice to species with
99% accuracy. These findings suggest that our decision tree can be used to reliably
identify the species of most harvest mice in the range of the southern SMHM, with asmall proportion (6% in our study) needing genetic confirmation. The decision tree
should be tested on additional harvest mice that were not used in its development,
particularly from novel locations across the range.
005-SMHM: Pathogens and Ectoparasites of Salt Marsh Harvest Mice
(Reithrodontomys Raviventris Halicoetes) in Suisun Marsh
Sadie Trombley1 | 2, Douglas Kelt1, Janet Foley1, Deana Clifford3, Laureen
Barthman-Thompson3
1University of California, Davis, 2California Department of Water Resources, 3California

Department of Fish and Wildlife

Presenting author email: sadie.trombley@water.ca.gov
We surveyed pathogens and ectoparasites in the federally endangered salt marsh
harvest mouse (Reithrodontomys raviventris halicoetes; SMHM) and sympatric rodents
in Suisun Marsh. Although SMHM have been well studied, some cryptic threats, such as
disease, have largely been ignored in recovery planning. We determined baseline
health data on SMHM and investigated the relationships among pathogen andectoparasite prevalence and environmental variables, including season and habitat
management (e.g., naturally tidal grids versus non-tidal diked grids), as well as
individual risk factors such as age, sex, reproductive status, and body condition. Due todifferences in the biotic communities and abiotic conditions in diked and tidal ponds, wehypothesized that the risks of disease transmission in diked and tidal habitats may
differ, with potentially important implications for resource/landscape managers. We
tested all rodent species for infection with Bartonella spp., Borrelia spp., Rickettsia spp.,
Francisella tularensis, Leptospira spp., Cryptosporidium spp., Giardia spp., andToxoplasma gondii via PCR. We captured 625 individual rodents, including 439 SMHM.
Over one-third of SMHM tested positive for at least one pathogen or ectoparasite. Four
percent of SMHM were infected with F. tularensis holarctica, a highly virulent bacteriumthat causes mortality in rodents shortly after infection. Additionally, we detected
pathogenic strains of Bartonella, Leptospira, Cryptosporidium, Giardia, and an
unidentified Borrelia sp. among the captured rodents. The prevalence of multiple
pathogens varied by season and by host species. The only pathogen that was
associated with habitat management was Bartonella spp. in SMHM; this was moreprevalent in diked than in tidal grids. The detection of certain pathogens andectoparasites in this study suggest spillover from non-wetland specialist rodents to
SMHM. Understanding the relationships between disease risk and environmental84On-demand talks: Fish Biology (FB)
variables, including the potential risk posed by other rodent species to SMHM, is criticalto the conservation and management of this endangered species.

Fish Biology (FB)
006-FB: Lamprey Populations in California’s Central Valley: Genetic Analysis of aMultispecies Complex
Grace Auringer1, Pascale Goertler2, Amanda J. Finger1
1Department of Animal Science, University of California, Davis, 2Delta StewardshipCouncil, Delta Science Program

Presenting author email: gmauringer@ucdavis.edu
Lampreys, a group of jawless, eel-like fishes, are extant representatives of the first
known vertebrates. Survival to modern times depended on lampreys’ parasitic strategy;
however, multiple non-parasitic species have evolved. A current complication tolamprey population genetic research is the difficulty in determining an accurate species
identification based on morphological features at the larval life stage. At least six
species of lamprey (Entosphenus spp. and Lampetra spp.) occur in California
watersheds, and many species’ ranges overlap. All are listed as California Species ofSpecial Concern; yet, little is known about interspecific and intraspecific genetic
structure of lamprey populations throughout the state. In this pilot study, we applied
restriction-site associated DNA sequencing (RADseq) to lamprey samples (N=480)
collected opportunistically through several ongoing salmon surveys. Our dataset
captures individuals from various species, life stages, and geographic locations
throughout northern California. Analysis of 480 individuals genotyped at variable SNPs
(single nucleotide polymorphisms) throughout the genome showed high levels ofdivergence between species and varying patterns of genetic structure within andbetween populations. Future work includes the development of SNP markers to
distinguish between all lamprey species in California. The reported results facilitate themanagement of genetic diversity in lamprey and may inform management unit
delineations in the Bay-Delta region.
007-FB: Clear Water but Murky Understanding: Investigating the Decline of Tule
Perch in the Northern SFE
Caroline Newell1, Chris Jasper2, Brian Williamshen1 | 3, Teejay O'Rear1 | 3, John
Durand1 | 3
1Center for Watershed Sciences, University of California, Davis, USA, 2Vollmar NaturalLands Consulting, Sacramento, CA, 3Wildlife, Fish and Conservation Biology, Universityof California, Davis
Presenting author email: clsnewell@ucdavis.edu
85On-demand talks: Food Web Linkages (FWL)The UC Davis North Delta Arc project has been studying fish communities in thenorthern region of the upper San Francisco Estuary using otter trawls, beach seines,
and boat electro-fishing since 2012. Trends in the region reflect wider trends observedin the Delta - increases in aquatic weeds and non-native fish species abundance withsimultaneous decreases in native fish species. To better understand drivers of thesetrends we use native tule perch (Hysterocarpus traskii) as a case study. Tule perch
have become rarer in otter trawl catches since the summer of 2015. Low flows, clear
water and high temperatures during the 2012-2016 drought fostered aquatic weed
growth. Concurrently, the non-native species largemouth bass, redear sunfish, andbluegill catches increased substantially. Drought, SAV recruitment, and competitionand predation by non-native species have all contributed to the decline of tule perch inthis region. Tule perch and most native fishes face multiple stressors, and Bay-Delta
restoration projects which aim to provide safe refuge for native species must prioritize
addressing root issues in order to be successful. These include restoring flows to
restored sites, managing invasive species, and reducing water clarity.

Food Web Linkages (FWL)
008-FWL: The Review of Science of Non-Native Species in a Dynamic Delta
Stephen Brandt1, James Cloern1, Virginia Dale1, Harindra Joseph Shermal
Fernando1, Tanya Heikkila1, Thomas Holzer1, Jay Lund1, Diane McKnight1, Robert
Naiman1, Lisa Wainger1
1Delta Independent Science Board

Presenting author email: brandt.disb@gmail.com
The San Francisco Bay-Delta is one of the most invaded estuaries in the world. Indeed,
non-native species are a large part of what is now the Sacramento-San Joaquin Delta(Delta) ecosystem. The invasion of new non-native species threatens the achievementof the coequal goal of “protecting, restoring, and enhancing the Delta ecosystem.”
Reducing the impact of non-native species is a one of core strategies highlighted in the
Delta Plan.
As part of its legislative mandate to provide scientific oversight of programs that support
adaptive management, the Delta Independent Science Board (Delta ISB) undertook areview to better understand the scientific needs related to this complex issue. The
review process included an extensive literature review, two panel discussions eachcomposed of five experts who explored the state of science, and public comments.
Additionally, Delta ISB members participated in several workshops and scientificsessions, presentations, and discussions with managers.
In the presentation, the Delta ISB will present key findings and recommendations fromthe review, such as the need to develop a comprehensive, spatially explicit, food-web
model for the Delta. One of the primary impacts of non-native species is to disrupt orchange food webs and nutrient cycling. Understanding the role of non-native species in86On-demand talks: Food Web Linkages (FWL)
the food web is fundamental for predicting and evaluating impacts. The review alsostresses that the ongoing threat assessments for invasive species should be evaluatedconsidering a changing environment and multiple drivers, especially climate.
Management needs to move beyond individual species management to address how to
set ecosystem goals in recognition of an ever-changing species pool and highuncertainty. The Delta ISB encourages a broader, more forward-looking, integrated
approach to non-native species science in the Delta to inform management goals.
009-FWL: Managed Floodplain Fish Food: Bringing Dry-Side Food Webs to WetSide Fish
Jacob Montgomery1, Jacob Katz1
1California Trout

Presenting author email: jacob@caltrout.org
One primary benefit a fish gets from a floodplain is abundant food resources. Floodplain
habitat restoration for salmon in California’s Sacramento Valley fall into two strategies:
wet-side floodplain access and dry-side floodplain management. “Wet-side” indicatesfloodplains within the levee footprint of the Sacramento Valley. During flood conditions,fish in rivers can pass volitionally on and off wet-side floodplains to access foraging andrearing habitat. “Dry-side” indicates floodplains beyond the levee footprint of the
Sacramento Valley. Fish in the rivers are completely cut-off from these habitats,regardless of environmental conditions. While restoration to increase the frequency andduration of wet-side floodplains is critical for the Sacramento Valley’s salmonid
populations, including dry-side managed floodplains in the conservation strategy may
also contribute to achieving population goals. In the winter and spring of 2018-2019 andagain in 2020-2021, managed floodplain export pilot management actions wereconducted on 5,000 acres of flooded agricultural land in Yolo County, California. Our
hypothesis was that in-river zooplankton abundance and fish growth rates would be
elevated at the managed floodplain outfall, relative to upstream. We measured water
quality, zooplankton species and abundance, and juvenile Chinook salmon growth rates
with PIT-tagged, hatchery-origin fish in enclosures. Fish growth rate analysis showedfish experienced growth rate benefits at least up to a mile downstream from the
managed floodplain outfall location. Multiple water management companies and utility
districts across the Sacramento Valley maintain similar infrastructure to what was usedin these pilot actions and service up to 300,000 acres of potential managed agricultural
floodplain. Incorporated into winter environmental water management practices, thisunused resource may provide substantial food resources to rearing and out-migrating
juvenile salmon in the Sacramento Valley system.

87On-demand talks: Franks Tract Reimagined: Integrating Recreation, Navigation,
Ecology and Water Quality for Landscape Redesign in the Heart of the Delta (FT)
010-FWL: High Primary Production in Seasonally Managed Wetlands of Suisun
Marsh
Alice Tung1, Kyle Phillips1, Peggy Lehman2, Steven Sadro3, John Durand1
1University of California, Davis, Center for Watershed Sciences, 2California Departmentof Water Resources, 3Univeristy of California, Davis, Environmental Science and Policy
Presenting author email: amatung@ucdavis.edu

Suisun Marsh encapsulates a mosaic of novel, working landscapes, in which thehydrology of formerly open tidal wetlands is replaced with managed wetlands. The
managed wetlands are characterized by seasonal flooding for waterfowl, which typicallyoccurs between fall through spring, followed by drying periods through summer for land
maintenance. Major restoration projects are currently underway to restore tidal flow tothese managed to create shallow habitat for threatened and endangered fishes.
Nonetheless, managed wetlands will continue to comprise most of the Suisun Marshlandscape while their ecological contributions to the San Francisco Estuary remain
largely unknown.
The goal of the UC Davis Suisun Ponds Project is to develop a baseline understandingof pelagic food production in managed wetlands. To characterize phytoplankton
production and its drivers, we monitored phytoplankton community composition,
chlorophyll a concentration, nutrient concentration, and physical conditions throughout
two hydroperiods in the eastern marsh at the Potrero Duck Club and Meins Landing,and one hydroperiod in the western marsh at Wings Landing. We sampled 8-11 stations
in each wetland and 1 station outside of the wetland in the parent sloughs near thecontrol structure between 2018 and 2020.
Our data suggests that the Suisun managed wetlands can be major hotspots for
phytoplankton productivity shortly following fall inundation. In all three managed
wetlands, bursts of exceptionally high productivity persisted into the winter months until
seasonal decreases in water temperature or freshwater flushes from precipitation
decreased concentrations. The capacity for high production in these wetlands provides
an opportunity for active management of lower food web production to support nativefish in adjacent sloughs during critical feeding periods.

Franks Tract Reimagined: Integrating Recreation, Navigation, Ecology
and Water Quality for Landscape Redesign in the Heart of the Delta(FT)
011-FT: Franks Tract Futures Reimagined, Habitat Restoration in a Novel
Ecosystem
Carl Wilcox1
1California Department of Fish and Wildlife

88On-demand talks: Franks Tract Reimagined: Integrating Recreation, Navigation,
Ecology and Water Quality for Landscape Redesign in the Heart of the Delta (FT)
Presenting author email: Carl.Wilcox@wildlife.ca.gov
Franks Tract Futures Reimagined is a collaborative planning process initiated by the
California Department of Fish and Wildlife as a follow up to the Delta Smelt Resiliency
Strategy 2018 Franks Tract feasibility study. The process prioritized working with thelocal community, local agencies, and interested stakeholders to develop a habitat
enhancement plan for Franks Tract using a transparent and collaborative process tonavigate tradeoffs between interests. The process and proposed changes embody
conservation guidance for the region described in the 2018 A Delta Renewed and 2019
Delta Conservation Framework.
Franks Tract, a shallow flooded island, is a popular recreational and fishing destinationin the Delta, with associated benefits to the local economy. Currently dominated byaquatic weeds and non-native fishes, it also significantly affects hydrodynamics andwater quality in the central Delta. As one of the least subsided islands in the central
Delta, it is a strong candidate for improvements to navigation, shoreline recreation,water quality and ecosystem function. The planning effort focused on how best to
modify Franks Tract to increase habitat heterogeneity and ecological function while
meeting multiple objectives. Planning recognized Franks Tract and the greater Delta asa novel ecosystem. Given the novelty of the system, both biologically and sociologicallymanagement actions to recreate historical habitat attributes must be considered in thatlight. The planning effort along with ongoing evaluation of trends in change within the
Delta make it apparent that future ecosystem restoration be approached from both
ecological and social perspectives. Aquatic weeds are a primary driver in determining
the value of Delta habitat for native fish species and projects must design to minimize
them, while social perspectives of what is good habitat in the Delta must be reconciled
to gain broader support.
012-FT: Co-Design and Franks Tract Futures
Brett Milligan1
1University of California, Davis

Presenting author email: bmilligan@ucdavis.edu
In the Delta, large-scale ecological restoration and water quality improvement projects
can impact local communities and stakeholders in a variety of ways. When thesecommunities are not integrated into the planning and design of such projects, the results
are often unsupported and limited in function. Co-design refers to design approaches
that attempt to involve all stakeholders in a project’s planning and design process toensure that the results meet the interests and needs of all involved. Franks Tract
Futures (FTF) is an example of a large-scale restoration project in the central Delta(over 3,000 acres) that utilized an integrative co-design process to try address diverseand competing stakeholder interests.
This presentation will illustrate the FTF co-design process. Sequenced over a year, thisprocess included public meetings, stakeholder interviews, on-line geo-spatial public89On-demand talks: Franks Tract Reimagined: Integrating Recreation, Navigation,
Ecology and Water Quality for Landscape Redesign in the Heart of the Delta (FT)surveys (SoftGIS), structured decision making (STM), and a series of in-person design
workshops. Extensive stakeholder input at the beginning of the project ensured that
local and public interests – including the provision of recreational features andsustainment of boating navigability - were integrated into technical and ecologicalproject objectives. STM served to transparently establish and measure diverse project
performance criteria. Through an iterative process of testing, evaluation andrefinement, multiple design concepts were whittled down to a preferred concept withwide support across public and state interests.
The results of the FTF design process demonstrate that Delta conservation and climate
adaptation projects can garner support from the publics they effect, if thosecommunities and their needs are integrated into the design process. Likewise, codesign should be approached as a co-learning effort for all involved, which in thisexample, showed how recreational, ecological and water quality improvements could be
welded together and advance what ‘multi-benefit’ landscape projects can be.
013-FT: Modeling Franks Tract Futures: Quantifying Diverse Stakeholder Interests
Eli Ateljevich1, Kijin Nam1
1California Department of Water Resources

Presenting author email: Eli.Ateljevich@water.ca.gov
The Franks Tract Futures project nested well-resolved 3D hydrodynamics modelingwithin a structured decision-making framework in order to find a suitable and moresustainable landscape design for Franks Tract. Modeling provided both a means of
iterative refinement of designs as well as an aid in crafting metrics to represent diverse
stakeholder interests such water quality improvement, fish entrainment reduction,navigability, drought protection and resilience to flood and sea level rise. A key findingof the modeling was that many of the designs achieve water quality and entrainment
reduction goals sought by agency participants and perform well under sea level rise.
The degree of improvement depends not only on large scale decisions such asplacement of large landforms but also on finer configuration decisions such as the sizingof channels through the region. Modeling was used to explore the trade-offs between
navigability and water quality, and the extent to which both objectives could be met
simultaneously.
014-FT: Project Evaluation with Structured Decision Making and Map-Based
Surveys
Kathleen Berridge1, Alejo Kraus-Polk2, Dan Ohlson3
1ESA, 2University of California, Davis, 3Compass

Presenting author email: akrauspolk@ucdavis.edu
90On-demand talks: Monitoring (M)Large scale multi-benefit projects that affect many and varied stakeholders arechallenging to evaluate. The 2020 Franks Tract Futures Reimagined project relied on
two primary methods for evaluation of the design concepts, structured decision making(SDM) and map-based survey. In this presentation, we will introduce the SDM and mapbased concept design survey, describe the overall performance criteria, identify key
tradeoffs, and discuss results. We will also discuss adaptations made to solicit local andpublic input due to the COVID-19 related shelter in place. We will compare and contrast
the results between SDM, which relied heavily on input from the stakeholder andadvisory committees, and the map-based survey which gathered public feedback on
positive and negative perspectives on the features, location, and access components ofthe design concepts. Lastly, we will discuss how the combination of methods enabled
local stakeholders to collaborate with technical experts throughout the co-design
process, how perceptions shifted during the process, and how a broadly supported
alternative emerged to move forward to the next stage of detailed planning.

Monitoring (M)015-M: Automating the Drudgery: Using Artificial Intelligence to Detect Trash andTobacco Product Waste
Lorenzo Flores1, Tony Hale1, Shelly Moore1
1San Francisco Estuary Institute

Presenting author email: lorenzof@sfei.org
With the advent of the State Water Board’s Trash Amendments in 2015, cities, counties,
and state agencies have set their sites on a target of zero waste escaping into ourreceiving waters. Most recognize, however, that this progress will take work. And thatwork will require evidence. For many municipalities interested in monitoring their
management actions designed to reduce the release of trash, automation is an
attractive proposition. After all, monitoring trash over broader areas with greater
frequency is challenging and often costly.
With funding from the Ocean Protection Council and the California Department of Public
Health, the San Francisco Estuary Institute and Southern California Coastal Water
Research Project developed two new publicly available machine learning algorithms
that can advance the detection of trash in general and cigarette butts in particular. The
team leveraged both aerial imagery and coordinated fieldwork to measure theeffectiveness of the algorithms in identifying the target items. The results are very
promising and have been featured in a Trash Monitoring Playbook, issued by the Ocean
Protection Council, which provides guidance for the adoption of trash monitoring
methods to complement programmatic objectives.
During development, the team shared information and approaches with colleagues
conducting similar work in West Sacramento, the Central California Coast, and acrossthe state. This sharing of approaches from the State Water Board, 2ndNature, and91

On-demand talks: Monitoring (M)Caltrans has opened the field of artificial intelligence to new audiences as publicagencies seek to implement solutions that can benefit from these technologicaladvances.
The team will also share the results of the specific trash studies while also discussing
the implications for the refinement and operationalizing of this work on trash monitoringin the Bay-Delta region and beyond.
016-M: A Path Forward for Environmental DNA Methods in the Bay-Delta
Ravi Nagarajan1, Mallory Bedwell2, Ann Holmes1, Thiago Sanches1, Shawn
Acuña3, Melinda Baerwald2, Scott Blankenship4, Richard Connon5, Daphne Gille2,
Andrea Schreier1
1University of California, Davis, Genomic Variation Laboratory, 2California Departmentof Water Resources, 3Metropolitan Water District of Southern California, 4Cramer Fish
Sciences - Genidaqs, 5University of California, Davis, Department of Anatomy,
Physiology and Cell Biology
Presenting author email: rpnagarajan@ucdavis.edu, mallory.bedwell@water.ca.gov

Environmental DNA (eDNA) methods have the potential to complement existing
monitoring and support management decision-making in the Bay-Delta. However, there
remains a need to communicate the strengths and limitations of these methods,
especially in the context of complex environments like estuaries. The eDNA symposium
held at UC Davis on January 29, 2020, brought together regional scientists, managers,
and worldwide leaders in the field to explore the potential for eDNA methods inestuaries. Following up on the success of this well-attended event, the organizing
committee and presenters are drafting a manuscript to summarize insights from thesymposium and explore how eDNA methods can be applied to estuaries in general andspecifically to the management challenges found in the Bay-Delta. Here we present key
findings from this work. First, we will briefly review critical considerations for eDNA
studies in general and attempt to distill the “state of the science”. In addition, the uniquechallenges of applying eDNA methods in complex estuarine environments will be
examined and the current status of eDNA resources and published studies in the BayDelta will be reviewed. We will also present the results of a poll asking regional agency
scientists to list species of management concern and illustrate how eDNA methods canbe applied for these species and suggest where more research is needed. Finally, we
will provide recommendations for enhancing communication and collaboration between
eDNA scientists and managers, and outline some best practices that will build
confidence in eDNA methods as complementary tools for estuarine ecosystemmanagement.

92

On-demand talks: Monitoring (M)017-M: Taking Stock of the “monitoring Enterprise” to Support Adaptive
Management of the Delta
Marc Nelitz1, Cedar Morton1, Natascia Tamburello1, Greg Shellenbarger2, Jay
Singh2, Caitlin Semmens1, E.J. Koford3, Tom Lagerquist3, Vince Resh4, Steve
Brandt5, Tracey Collier6, Harindra Fernando7, John Wiens5
1ESSA Technologies Ltd, 2CBEC Eco Engineering, 3Pax Environmental, 4University ofCalifornia, 5Oregon State University, 6NOAA Fisheries (retired), 7University of Notre
DamePresenting author email: mnelitz@essa.com

Climate change, aging water and levee infrastructure, growing human population,
threatened native species, exotic species invasions, and balancing human andecosystem needs for water create major challenges for achieving the Delta’s co-equalgoals. A comprehensive and integrated network of monitoring, with open access todata, and strong linkages to decision-making are important for reliably measuring anddetecting changes in the Delta, and understanding how to respond to these rapidtransitions.
To understand the relevance, efficiency, and level of coordination, the Delta
Independent Science Board completed the first phase of a comprehensive review of the“monitoring enterprise” to document activities and develop recommendations aroundhow data collection can better meet the needs of agencies and support adaptive
management. This review was guided by the following questions:
Are there potential gaps / redundancies in serving the relevant needs of decision
makers?
What is the level of coordination of data collection across different organizations?
Are there other opportunities to increase efficiencies in monitoring?
What is the data quality of monitoring to address purposes and needs for data?
Are data accessible to the public, decision makers, and other scientists?
What resources are being dedicated to monitoring?
To answer these questions, metadata were collected for over 150 monitoring activities
that serve the needs of decision makers as reflected by 7 management themes inherent
in the Delta Plan and 23 science themes that represent the complex socio-economic,
environmental, habitat, and species components of the Delta.
This presentation will highlight initial insights around these questions, alongside theimportance of and pathways for making progress around three “big moves”. These “bigmoves” represent more transformative changes that may be difficult to implement, but
are fundamentally necessary since the complexity, urgency, and long-standing nature ofmany challenges facing the Delta dictate an urgent need for doing things differently.

93On-demand talks: Salmon Biology (SB)

Salmon Biology (SB)018-SB: (*IEP) Investigation of a Potential Mortality Hotspot for Juvenile Chinook
SalmonAmanda Agosta1, Colby Hause2, Gabriel Singer2, Nann A. Fangue1, Andrew Rypel1
1University of California, Davis, 2California Department of Fish and Wildlife

Presenting author email: aagosta@ucdavis.edu
Previous acoustic telemetry studies suggest a high mortality risk for juvenile Chinook
salmon within flooded island habitats of the interior San Francisco Bay-Delta. We
performed predation experiments using a field tethering approach combined with anexperimental release of 100 acoustically tagged salmon to quantify mortality risk ofjuvenile salmon in the mainstem San Joaquin River compared to an interior putative hot
spot for mortality (i.e. Franks Tract). Following deployment of tethered fish, predation
events occurred at an average depth of 2.5m and after 66 minutes of deployment.
Overall, predation rates were low at all sites, and there was no difference in relative
predation risk between vegetated and unvegetated sites. Overall, outmigration survivalof acoustically tagged fish to the ocean was low (2%), presumably because of reduced
flows. However, the fact that some fish successfully egressed Franks Tract andemigrated to the ocean indicates Franks Tract is not always a complete mortality sink.
Additional research is needed in multiple water years to investigate temporal variability
in mortality risk associated with flooded island habitats of the interior Delta.
019-SB: American River Chinook Salmon Survival in Relation to Redd Water
Quality: The Role of Spatial and Temporal Variability
Annelise Del Rio1, Erin de Leon Sanchez1, Benjamin Martin2 | 3, Rachel Johnson1 |2, Nann Fangue1, Joshua Israel4, Anne Todgham1
1University of California, Davis, 2National Oceanic and Atmospheric Administration,
3University of Amsterdam, 4U.S. Bureau of Reclamation

Presenting author email: amdelrio@ucdavis.edu
River management to support Central Valley salmonids often focuses on releases ofcold water from dams to maintain temperatures within a tolerable range. Several
modeling and laboratory studies, however, suggested that recent high embryo mortalityof winter run salmon may be due to interactions between warm water temperatures, lowdissolved oxygen, and low flows. Understanding the impact these stressors have on
salmon embryos in natural incubation habitats is difficult because there is a lack of dataon the abiotic conditions salmon embryos experience in Central Valley rivers. To study
the relationship between environmental conditions and salmon embryo survival in theAmerican River we measured several abiotic variables across spatial, temporal, andseasonal scales relevant to fall-run Chinook salmon. We created 24 artificial redds in
the American River in November (12 redds) and December (12 redds), spanning the94On-demand talks: Salmon Biology (SB)
spawning season. Each redd had three tubes of 200 fall-run Chinook salmon embryos
and a logger continuously recording dissolved oxygen and temperature within thegravel. We measured temperature, dissolved oxygen, pH, turbidity, salinity, andconductivity above and within the gravel at each redd as well as water flow and depth
weekly. When lab-reared controls reached the swim up stage the egg tubes wereretrieved from the river. We measured hatching success and evaluated thedevelopmental stage of dead eggs. Overall, embryo survival in the field was low andhighly variable, potentially due to periods of hypoxia and variable egg quality. Variables
including mean dissolved oxygen, maximum temperature, water velocity and depth,
substrate size, site, and spawning month significantly influenced hatching success. By
determining which water quality variables, in addition to temperature, have the greatest
effects on survival these results can inform water management strategies to promotesalmon survival for sensitive early life stages.
020-SB: Targeted Application of 3D Routing in a Full-Delta PTM
Doug Jackson1, Xiaochun Wang2, Russell Perry3, Adam Pope3
1QEDA Consulting, LLC, 2California Department of Water Resources, 3U.S. Geological

SurveyPresenting author email: doug@QEDAconsulting.com
Particle tracking models (PTMs) have proven to be invaluable tools for predicting thesurvival of outmigrating Chinook salmon smolts through the Sacramento-San Joaquin
Delta. By coupling hydrodynamic, salmon behavior, and predation models, PTMs
enable prediction of smolt travel time and routing, and consequently survival, under awide a range of environmental conditions and water management scenarios.
However, full-Delta PTMs have been largely limited to 1D hydrodynamic models due tothe prohibitive computational requirements of 3D models. While 1D models are suitable
for some applications, certain dynamics cannot be captured by their simplifiedhydrodynamic and spatial structures, such as the effects of local flow on fish
entrainment at key junctions where fish are routed from the mainstem Sacramento River
into the low-survival interior Delta. There is a pressing need for models that improveprediction of such critical aspects while remaining computationally tractable.
Towards this end, we are developing the next version of DWR’s ECO-PTM toaccommodate either a 1D hydrodynamics model (DSM2), a fully 3D unstructured gridmodel (SCHISM), or a hybrid combination of 1D and 3D grids. The hybrid structure
leverages SCHISM to improve prediction of routing in a few key junctions, obtaining
much of the benefit of the 3D model with only a modest increase in computational
expense.
We will describe the design of the hybrid DSM2/SCHISM-based model, present initialmodel results using the SCHISM junction model in lieu of the original ECO-PTM’s
statistical entrainment models, and compare the qualitative behavior of particles to 2D
acoustic telemetry fish track data we used to inform particle behavior.
95

On-demand talks: Salmon Biology (SB)This work represents an important advance towards a modeling platform that will
improve estimates of smolt survival under different environmental and water
management scenarios, enhancing our ability to promote the survival of endangeredsalmonids in the face of climate change and other stressors.
021-SB: Validating Feature Level Habitat Use with Acoustic Telemetry: 2Dimensional Positioning Capabilities of Vemco V3 Tags and HR3 Receivers
Eric McDermott1, Gregg Horton1, Brian Mulvey2, Dale Webber3, David Smith2
1Sonoma Water, 2U.S. Army Corps of Engineers (ERDC), 3Innovasea

Presenting author email: Eric.mcdermott@scwa.ca.gov
In 2008 the National Marine Fisheries Service issued a Russian River Biological
Opinion (RRBiOp) compelling Sonoma Water and the USACE to implement habitat
enhancements along 6 of the 14 miles of mainstem Dry Creek downstream of Warm
Springs Dam (Lake Sonoma). Storage and releases from Lake Sonoma provide flood
protection and a source of water which is conveyed through Dry Creek to Sonoma
Water’s collection system along the mainstem Russian River. Off-channel habitats(backwaters, alcoves, and side channels) have been constructed with the aim ofproviding low-velocity, high-cover rearing habitat while allowing continued use ofmainstem Dry Creek for water conveyance. Validating the use of constructedenhancement sites has primarily been accomplished through traditional monitoring
methods such as snorkel surveys and PIT (Passive Integrative Transponder) systems,
both of which provide a snapshot in time of habitat use at the site scale. With the use of
Vemco V3 acoustic tags paired with an array of multiple HR3 receivers, we sought toobtain additional data on habitat use at the feature scale in one of the constructed sidechannels. We tagged 150 (100 natural and 50 hatchery origin) juvenile steelhead (85193 mm) and released them after a 2 to 11 day acclimation period in live boxes in thechannel. Prior to fish release, we deployed stationary receivers to facilitate creation of 2dimensional tracks of tagged salmonids within the array. Preliminary results showednatural origin fish remaining in the site longer than hatchery fish, diel movement
patterns, and use of constructed features such as log jams, root wads, pools, and riffles
on a continuous basis. To assess the utility of this approach for similar evaluations
elsewhere, we plan to utilize the data to calibrate various models and inform future
habitat designs.
022-SB: Understanding the Impacts of Floodplain Availability on Chinook Salmon(Oncorhynchus Tshawytscha)
Sara Hugentobler1, Mariah Meek1
1Michigan State University

Presenting author email: hugentob@msu.edu
96On-demand talks: Smelt Biology (OB)Climate change is having widespread effects on environments, including an increasing
frequency and severity of droughts. This can be problematic for species with dependent
on specific environmental conditions and can lead to an overall loss in biodiversity.
California’s Central Valley is predicted to be one of the most water scarce areas in theworld in the face of climate change, which could lead to negative consequences for thenative and endemic species that live there. Drought conditions present uniquechallenges for the federally listed Central Valley Chinook Salmon (Oncorhynchus
tshawytscha), which use the already limited floodplain in the Central Valley as rearing
habitat. Flood plains, such as the Yolo Bypass, can be disproportionately affected bydrought and stream flow changes, affecting the fitness of Chinook salmon. We areinterested in understanding how different water conditions (drought versus flood) andspecific environmental conditions (water flow, temperature, pH, DO) influence the runcomposition and abundance of juvenile Chinook salmon in the floodplain (Yolo Bypass)versus the mainstem of the Sacramento River. Chinook from the Yolo Bypass andareas along the Sacramento River were sampled and genotyped with an innovative
genetic panel and identified at the run level (Fall, Late Fall, Winter, and Spring) from2012-2019. These data were then combined with specific environmental conditions
obtained from cdec.water.gov and input into a linear regression with the environmental
data used as predictors. Initial data analysis suggests that the abundance of all runs are
impacted negatively by poor water conditions in the Bypass. Losing this diversity in the
Bypass may have overall negative effects on the sustainability of the species as well as
the stability of the ecosystem. Chinook are of enormous economic, cultural, andecological value in California and understanding how they are impacted by drought iscrucial to their survival and persistence.

Smelt Biology (OB)023-OB: Experimental Contrasts among Otolith, Histological, and Genetic
Indicators of Growth and Condition for Critically Endangered Delta Smelt(Hypomesus Transpacificus)
Rachel Fichman1, Wilson Xieu1, Feng Zhao1, Malte Willmes2 | 3, James Hobbs1 | 4,
Tien-Chieh Hung5, Andrew Schultz6, Bruce Hammock7, Swee Teh7, Robert
Lusardi1, Levi Lewis1
1Wildlife, Fish, and Conservation Biology, University of California, Davis, 2Institute ofMarine Sciences, University of California, Santa Cruz, 3National Oceanic andAtmospheric Administration, Southwest Fisheries Science Center, Santa Cruz,
4California Department of Fish and Wildlife, 5Fish Conservation and Culture Laboratory,
University of California, Davis, 6U.S. Bureau of Reclamation, 7School of Veterinary
Medicine, University of California, Davis
Presenting author email: rafichman@ucdavis.edu
Accurate inferences of fish growth and condition are imperative for the conservation andmanagement of endangered species, like Delta Smelt (Hypomesus transpacificus).
Otoliths are commonly used to estimate fish growth and condition; however, the97On-demand talks: Smelt Biology (OB)sensitivity of otolith-based growth reconstructions in relation to other biomarkers ofgrowth and condition remains unknown. Here, we contrast the sensitivity (in timing andmagnitude) of otolith, histological, and genetic biomarkers of growth for adult Delta
Smelt. Growth was manipulated over 60 days using variation in food rations. We thencontrasted the timing and magnitude of responses of fish in different treatments withrespect to their otolith accretion rate, liver glycogen, DNA:RNA, and somatic growth
metrics. Condition factor, hepatosomatic index, and otolith accretion rates, eachdiverged significantly among treatments within a few days of the initiation of theexperiment, indicating the highest temporal sensitivity to food limitation, with otolith
accretion rates 40% faster in fed versus unfed treatments. Differences in otolith
accretion rates were significantly correlated with changes in biomass, but not with fish
length, indicating that otolith accretion may serve as a proxy for overall growth, but notlength, per se, in older Delta Smelt. These results indicate that otolith accretion rates
can provide high-resolution and biologically relevant proxies for reconstructing the
growth history of wild adult Delta Smelt.
024-OB: Presentation withdrawn
025-OB: The Effect of Substrate on the Spawning Behavior and Egg Fertilization
Success of Cultured Delta Smelt (Hypomesus Transpacificus)
Yi-Jiun Tsai1, Samantha Chase1, Evan W. Carson2, Leanna Zweig2, Tien-Chieh
Hung1
1University of California, Davis Fish Conservation and Culture Laboratory, 2U.S. Fish

and Wildlife Service, San Francisco Bay-Delta Fish and Wildlife Office
Presenting author email: Yjtsai@ucdavis.edu

We examined the effect of substrate on spawning behavior and egg fertilization successin cultured H. transpacificus under laboratory conditions. Specifically, we asked whether
substrate affects the behaviors exhibited during spawning, the frequency of spawning
behaviors, or the resulting egg fertilization rate. We addressed these questions byconducting no-choice substrate behavioral trials, in which five ripe females and fivemature males were placed into a flow-through tank containing either control (acrylic),
sand, or pebble substrates. Fish were allowed to spawn naturally for four days and all
behavioral interactions were video recorded. After behavioral trials ended, eggs wereincubated for three additional days and then assessed for fertilization success. Videos
were analyzed for spawning behavior, in which we quantified the number of spawns(spawning behavior ending in egg release) and attempts (spawning behavior without
egg release) that occurred. We found that substrate did not affect the sequence or
expression of spawning behaviors, nor did it affect the number of spawns and attempts
that occurred. We also found that substrate did not affect either the percentage of total
eggs fertilized or the number of fertilized eggs when controlling for the total number of
eggs laid. In addition, we documented the first known observation of rare diurnal98

On-demand talks: Water Quality (WQ)
spawning in the predominantly nocturnal-spawning population. Our results suggest that
cultured H. transpacificus can spawn on natural and artificial substrates, regardless of
their preferences. In conjunction with the findings of other studies, our results alsosuggest that, in the absence of choice and under laboratory conditions, substrate may
not affect reproductive success. Instead, other environmental (e.g. water velocity) or
social (e.g. sex ratio) conditions may be more important. Such findings are important to
informing ongoing habitat restoration efforts within the Delta.
026-OB: (*IEP) Improving the Longfin Smelt Larviculture Protocol: Responses of
the Early Life Stages of Longfin Smelt to Temperature, Salinity, and Turbidity
Yuzo Yanagitsuru1, Madison Main1, Itza Daza1, Dennis Cocherell1, James Hobbs1 |2, Levi Lewis1, Tien-Chieh Hung1, Richard Connon1, Nann Fangue1
1Univeristy of California, Davis, 2California Department of Fish and Wildlife

Presenting author email: yyanagit@ucdavis.edu
Over the last decade the UCD Fish Conservation Culture Laboratory has beendeveloping a captive culture for the threatened longfin smelt to provide researchers witha sustainable source of individuals to conduct the studies necessary to determine theirenvironmental requirements and to serve as a captive population for supplementation
efforts. Prior to 2019, these efforts have been hindered by <1% survival to 80 days posthatch. However, recent changes to larviculture protocols informed by physiologicalstudies on the early life stages of longfin smelt have led to a marked improvement inculturing efforts, yielding approximately 50% larval survival in 2019-2020. We present
two studies, one examining temperature effects and another on salinity effects on theearly life stages of longfin smelt, that informed this change to the larviculture protocol.
We additionally present a third study examining turbidity effects on larvae that may
inform further changes to the culture protocol. In the first experiment, we exposed
embryos and larvae to three different temperatures: 9, 12 or 15, and found that hatch
success and the final length that yolk-sac larvae achieved are greater at cooler
temperatures of 9 and 12. In our second experiment, we exposed yolk-sac larvae to arange of salinities between freshwater (0.4 ppt) and seawater (32 ppt) and found thatsurvival and yolk absorption was highest at intermediate salinities of 5-10 ppt. Finally, in
our third experiment we reared larvae at 10, 20 or 40 NTU turbidities and found thatsurvival was highest at the highest turbidity of 40 NTU. Overall, we are encouraged tofind that small changes in environmental conditions can improve the survival of longfin
smelt and are hopeful that a successful culture for the species will be developed soon.

Water Quality (WQ)027-WQ: Copy Number Variation of Mutated Ace-1 Gene Involved in Pesticide
Resistance in Hyalella Azteca Within the Cache Slough Complex
Victoria Deery1, Kaley Major1, Donald Weston2, Helen Poynton1, Nadhirah Johanif199

On-demand talks: Water Quality (WQ)
1University of Massachusetts, Boston, 2University of California, Berkeley

Presenting author email: victoria.deery001@umb.edu
The epibenthic crustacean, Hyalellaazteca are found throughout the Cache Sloughcomplex of the Sacramento-San Joaquin Delta. They are an important prey item for fish
species of concern within the Bay-Delta and are frequently used for sediment toxicity
testing to determine environmental health. Due to high pesticide loading, especiallyduring storm events, many H. azteca populations throughout the Cache Slough
Complex have evolved resistance toorganophosphate pesticides (OPs) throughselection of a point mutation in acetylcholinesterase (ace-1). However, evidence
suggests that additional mechanisms may be involved including copy number variation(CNV) in the ace-1 gene. To better understand this potential mechanism, the number oface-1 gene copies of individual H. azteca was quantified and correlated to organism
resistance and acetylcholinesterase activity.
Using quantitative PCR, we quantified the number of ace-1 gene copies by comparing
its amplification to the quantities of two single copy reference genes. These conserved
reference genes, Ran Binding Domain and UracilPhosphoribosyltransferase, wereidentified as single copy according to a Benchmarking Universal Single-Copy Ortholog(BUSCO) list. We then compared ace-1 copy number in single individuals to whether
they had a resistance mutation as well as the activity of acetylcholinesterase, both in theabsence and presence of OP insecticides. By quantifying the number of ace-1 genes inrelation to the degree of resistance, we expect to better understand how H. azteca arebecoming resistant and provide insight into the relative importance CNV in OP
insecticide resistance. Because resistant H. azteca can serve as vector for trophic
transfer of OP insecticides to fish species of concern, understanding the mechanisms ofresistance in their prey species is important for the overall health of the Bay-Delta.
028-WQ: Identifying Cyanobacterial Harmful Algal Bloom Toxins in Delta
Invertebrates: Implications for Native Species and Human Health
Ellen Preece1, Timothy Otten2, Janis Cooke3, David Senn4
1Robertson-Bryan Inc., 2Bend Genetics, 3Central Valley Regional Water Quality Control

Board, 4San Francisco Estuary Institute

Presenting author email: ellen@robertson-bryan.com
Cyanobacteria harmful algal blooms (CHABs) are a growing water quality problem inthe Delta. Filter-feeding invertebrates compound risks associated with CHABs bybiomagnifying cyanotoxins; as such, shellfish can serve as both time-integrated
samplers of toxin levels in the water column and bio-sentinels of health risks through thefood web. Little work has been done to characterize MC concentrations in Delta
shellfish. It is critical to determine the extent of MC accumulation in Delta shellfish sincethese organisms are consumed by native species, including sturgeon, and humans. Our
primary goal is to analyze Delta shellfish and water samples to determine when MCs
enter the Delta food web, their geographic distribution, and the magnitude and duration100On-demand talks: Wetlands and Floodplains (WF)
of impairment. Sampling began in August 2020 and is continuing to occur monthly. We
have collected Asian clams (Corbicula fluminea) from 10 sampling sites throughout theDelta and crayfish (Pacifastacus leniusculus) from a subset of these sites. Althoughsampling will continue through August 2022, we have gathered enough data to begin
characterizing MC shellfish contamination. MC in water samples have remained
relatively low (i.e., max <5 µg/L); however, MC in shellfish have been high andwidespread. In August, MC was detected in Asian clams at all 10 sampling sites. In thefollowing months little to no MC was detected in water or shellfish samples at theuppermost Sacramento River sites (i.e., Cache Slough) but the toxin continued topersist in shellfish samples from the other sampling sites. To date, maximum MC
measured as high as 1,105 ng/g in Asian clams from Franks Tract and 1,751 ng/g incrayfish from the San Joaquin River near Turner Cut. Ultimately, this work will fill an
important data gap concerning MC contamination in brackish and freshwater shellfish
and the implications for managed species, their communities, and human health risks.

Wetlands and Floodplains (WF)
029-WF: Elevated Mercury Exposure in Raccoons and Striped Skunks from
Suisun MarshSarah Peterson1, Josh Ackerman1, Alex Hartman1, Mike Casazza1, Cliff Feldheim2,
Mark Herzog1
1U.S. Geological Survey, Western Ecological Research Center, 2California Departmentof Water Resources

Presenting author email: sepeterson@usgs.gov
Bioaccumulation of environmental contaminants, such as mercury, in mammalianpredators can serve as an indicator of ecosystem health. Methylmercury is the most
toxic form of mercury for animals and it biomagnifies through food webs andbioaccumulates in mid and upper trophic level predators. Within the San Francisco Bay
Estuary, we quantified hair mercury concentrations of raccoons (Procyon lotor) andstriped skunks (Mephitis mephitis) from Grizzly Island in Suisun Marsh. The mean
(standard error; range) mercury concentration in adult hair grown from 2015 to 2018
was 28.50 µg/g dw (3.05 µg/g dw; range: 4.46 – 81.01 µg/g dw) in raccoons and 4.85
µg/g dw (0.54 µg/g dw; range: 1.53 – 27.02 µg/g dw) in striped skunks. From acomprehensive review of terrestrial and aquatic mammalian hair mercury
concentrations (excluding bats and humans), raccoons from Suisun Marsh were among
the highest concentrations observed for wild mammals. Hair mercury concentrations inskunks and raccoons were not related to animal size, but mercury concentrations werehigher in skunks in poorer body condition. Large inter-annual differences in hair mercury
concentrations suggest that methylmercury exposure to mammalian predators variedamong years. Yearly mean raccoon and skunk hair mercury concentrations increased
with the amount of wetted habitat (wetlands and channels). Furthermore, during 2017,individual raccoon hair mercury concentrations increased with the proportion of eachanimal’s home range that was wetted habitat, as quantified using global positioning101On-demand talks: Wetlands and Floodplains (WF)
system (GPS) collars. Estimates of liver mercury concentrations derived from hairconcentrations indicated that 19% of adult raccoons in the study may have been close
to or above the proposed liver toxicity benchmark of 30 mg/kg (ww) for impaired
reproduction in mammals. The elevated mercury concentrations in raccoons and skunks
suggest that other wildlife at similar or higher trophic positions may also be exposed toelevated methylmercury bioaccumulation in brackish marshes.
030-WF: Tidal Habitat Restoration at Lower Yolo Ranch
Chris Campbell1, Carl Jensen2
1cbec eco engineering, 2ICF International

Presenting author email: c.campbell@cbecoeng.com
In conjunction with the California Department of Water Resources (DWR), Westlands
Water District, Hallmark Group, ICF, and cbec eco engineering designed, permitted,
and constructed a 2,149-acre tidal marsh restoration project in the Lower Yolo Bypass
near the Cache Slough Complex. The goal of the project was to benefit native fish,
including delta smelt (Hypomesus transpacificus) and winter- and spring-run salmonids.
The Lower Yolo Ranch Restoration Project, which adjoins the Yolo Flyway Farms tidal
marsh restoration project completed in 2018, represents a significant milestone with thecompletion of a ‘turn key’ tidal marsh restoration project to partially fulfill mitigation
obligations associated with the ongoing operation of the State and Federal Water
Projects, which both deliver irrigation and municipal water to Central and Southern
California. The design development and entitlement of the project was overseen by themulti-agency Fish Agency Strategy Team, or FAST, which is tasked with approving
mitigation for the ongoing need. The Lower Yolo Restoration Project was designed totake advantage of the large areas of the site that were at ideal elevations for tidal marsh
restoration, and that would contribute to the food web of the Cache Slough Complex
quickly and without large amounts of earthwork. Construction of the project, under acompressed schedule, began in August 2020 and was completed in October 2020.
DWR, in conjunction with the California Department of Fish and Wildlife, will begin
collecting monitoring data at the site in 2021.
031-WF: Mercury Trends in Seasonal Wetlands of the Los Banos Wildlife Area
Danielle Jones1, Andrew Gordus2, Nigel Quinn3, Marc Beutel1, Peggy O'Day1
1University of California, Merced, 2California Department of Fish and Wildlife, 3Lawrence

Berkeley National Laboratory

Presenting author email: djones47@ucmerced.edu
Export of mercury and methylmercury from managed seasonal wetlands in the San
Joaquin River Basin (SJRB) is a significant but understudied source of water quality102On-demand talks: Wetlands and Floodplains (WF)
impairment to the Delta, and contributions from wetlands in the SJRB, such as those of
the Los Banos Wildlife Area (LBWA), are unknown. Water samples were collectedduring flood-up from August 2019 through November 2019 at multiple locations in the
LBWA, including the San Luis Canal (SLC), which supplies water to two seasonal ponds(70A and 71A). Total mercury concentrations in unfiltered samples from the SLC ranged
from 0 - 17 ng/L (mean: 8.3 ± 4.9 ng/L), whereas concentrations in filtered samples
were lower and less variable (mean: 2.1 ± 1.6 ng/L). In samples collected at the outlets
of both ponds, mercury concentrations increased during filling in both filtered andunfiltered samples (1-6 ng/L and 1-10 ng/L, respectively), and filtered mercury
concentrations were higher in the ponds than in SLC water. Methylmercury
concentrations from pond 70A were higher than SLC concentrations in both unfiltered(0.25 to 5.1 ng/L) and filtered (0.19 to 2.2 ng/L) samples. During flood-up, sulfate
concentrations were lower in the ponds compared to SLC water (36 vs. 58
mg/L respectively). During the flood-up period, the ponds behave as a source formethylmercury, likely due to methylation of dissolved mercury from SLC water and flushout from soils under sulfate-reducing conditions. In pond 70A, mercury andmethylmercury were mostly present in the water column, rather than sorbed toparticulate matter, and therefore more bioavailable and mobile. Understanding theseasonal trends of mercury export from wetlands in the SJRB could allow wetland
managers to develop cost effective habitat management practices that improve
compliance with San Joaquin River water quality objectives while sustaining wetland
habitat productivity.
032-WF: (*IEP) Sources and Sinks! What’s Going on with Mercury in Sacramento
Valley Tidal Wetlands?
Petra Lee1, Julianna Manning1
1California Department of Water Resources

Presenting author email: Petra.Lee@water.ca.gov
Legacy mercury contamination is problematic in California waterways because ofhistoric gold and mercury mining. The inorganic mercury from mines is methylated inwater bodies throughout California, and tidal wetlands have been suspected to produce
and be net exporters of mono-methylmercury (MeHg) into California’s Sacramento-San
Joaquin Delta and Suisun Marsh. The California Department of Water Resources(CDWR) characterized MeHg and total mercury imports and exports from four
Sacramento Valley tidal wetlands to determine net MeHg discharge; three of the tidal
wetlands were fresh water, and one was brackish. We collected concentration data from
one tidal cycle approximately monthly and collected continuous flow data, which wereused to calculate loads; loads were calculated per 25-hour tide and estimated permonth using the continuous flow data. CDWR also compared mercury ebb and flood
concentrations to determine if there was a significant difference. Based on the collected
data and analyses, none of the four wetlands appear to be a significant net exporter ofparticulate or filtered MeHg to receiving waters. Concentrations of MeHg were not103On-demand talks: Wetlands and Floodplains (WF)
significantly higher leaving than enter the wetlands and there was not a measurable
annual increase in MeHg loads in receiving waters due to the tidal wetlands. Twowetlands were net exporters of total mercury in the particulate or in all forms. The othertwo wetlands were net importers of total mercury in the filtered and particulate form,
depending on the wetland. The current assumption is that tidal wetlands are net
exporters of MeHg, resulting in expensive and time-consuming mitigation as well as
concern that tidal wetlands export MeHg to the Delta as more acreage is restored. This
study shows that tidal wetlands are unlikely to be significant net exporters of MeHg toreceiving waters though MeHg concentrations of biota within wetlands still need to beconsidered.
033-WF: Tracking the Course of a New Restoration: Initial Observations from theMontezuma Wetlands Complex
Elsie Platzer1, Kyle Phillips1, Teejay O'Rear1, Caroline Newell1, John Durand1
1University of California, Davis, Center for Watershed Sciences

Presenting author email: eplatzer@ucdavis.edu
Newly restored sites offer unique opportunities to monitor wetland dynamics as they
develop over time. As of November 2020, we have begun conducting monthly beachseines, otter trawls, and vegetation surveys in Montezuma Wetlands, a tidal restoration
complex near Collinsville, CA which was breached in late October of the same year.
Preliminary data show invasive Mississippi silverside (Menidia audens) andalligatorweed (Alternanthera philoxeroides) are already abundant. While alligatorweed
may impede desirable native fish species, including salmon and delta smelt, theabundance of silverside and invertebrates appear to support a diverse array of
shorebirds, waders, and other waterfowl, as well as mammals. However, as the sitematures, emergent vegetation growth, changing sediment characteristics, and newly
colonizing organisms will continue to alter community composition. Evidence fromnearby reference sites suggests that native and pelagic fishes may benefit fromrestored habitats with long or mixed residence times, including managed wetlands,
which control the rate of water exchange, concentrate zooplankton, selectively offer
passage for fish species, and restrict invasive species access. Observations on the
rapidly changing Montezuma Wetlands complex will inform future restoration projects inthe Delta, allowing managers to maximize habitat provisioning for target species.
034-WF: Implementation of Multi-Benefit Juvenile Salmonid Habitat Restorationon the Lower Yuba River: The Hallwood Side Channel and Floodplain Restoration
Project
April Sawyer1, Chris Hammersmark1, Sam Diaz1, Katie Wrightson1, Paul Cadrett2,
Jeff Mathews3, Joe Merz4, Kirsten Sellheim4, Philip Colombano4, Aaron ZettlerMann5, Tyler Goodearly5104On-demand talks: Wetlands and Floodplains (WF)
1cbec inc., eco engineering, 2U.S. Fish and Wildlife Service, Anadromous Fish

Restoration Program, 3Yuba Water Agency, 4Cramer Fish Sciences, 5South Yuba River
Citizens League
Presenting author email: a.sawyer@cbecoeng.com
Anthropogenic actions on the Lower Yuba River dating back to the Gold Rush alteredgeomorphic and hydraulic conditions, and subsequently available habitat for rearing
juvenile salmonids. The Hallwood Side Channel and Floodplain Restoration Project wasdeveloped to address the United States Fish & Wildlife Service Anadromous Fish
Restoration Program’s goal to double natural production of anadromous fish in Central
Valley rivers. The Project was designed to enhance ecosystem processes to support
juvenile rearing fall-run and spring-run Chinook salmon and California Central Valley
steelhead. The Project is supported by numerous agencies and stakeholders and takes
a novel approach by leveraging relationships with aggregate mining landowners tofacilitate economically efficient habitat enhancement. After several years of planning,
design, permitting, and pre-project monitoring, 89 acres of habitat was enhanced as
Phase 1 implementation was completed in 2020. A network of perennial and seasonal
side channels was created and an unnatural constraint separating the main channel
from its floodplain was removed. The remaining Phases will proceed over 3 - 5 years
and create or enhance up to a total of 157 acres of seasonally inundated floodplain
habitat, 1.7 miles of perennial channels, and 6.1 miles of seasonal side channels andalcoves. Beyond habitat enhancement, the project also provides significant local flood
benefits by reducing water surface elevations by several feet and also reducing
pressure on training walls that bound the floodway. A design based on restoring lateralconnectivity and removing unnatural constraints coupled with a robust monitoring
program will provide valuable information at a large-scale regarding restoration successand lessons-learned and be applicable in both upslope and Bay-Delta settings.
035: Hindcasting Alviso Slough Pond System Morphodynamics
Mick van der Wegen1 | 2, Johan Reyns1 | 2, Bjorn Robke2, Bruce Jaffe3, Judy Nam4,
Jessica Lowering4
1Deltares, 2UN-IHE, 3U.S. Geological Survey, 4Valley Water

Presenting author email: m.vanderwegen@un-ihe.org
Alviso Slough area, South San Francisco Bay, is the site of an ongoing effort to restore
former salt production ponds to intertidal habitat. As restoration proceeds and thelevees surrounding the former salt production ponds are breached, the increase in tidal
prism and associated sediment scour in the sloughs will remobilize legacy mercury
deposits. A numerical model that is able to assess patterns of sediment transport,
erosion, and the fate of remobilized sediments can improve mercury remobilization
estimates and inform management actions.
The goal of the current research is to validate a 2D geomorphic model for Alviso Sloughand surrounding ponds using bathymetric surveys, hydrodynamic measurements and105On-demand talks: Wetlands and Floodplains (WF)
observations of suspended sediment concentrations during the 2010-2016 period. The
2D geomorphic numerical model applies the Delft3D Flexible Mesh (software by
Deltares) coupled with the SWAN wave model that describes detailed interaction
between hydrodynamics, wave action, sediment transport, and geomorphic change on ahigh-resolution mesh.
The morphodynamic model results shows that observed water levels and erosion andsedimentation patterns can be reproduced with skill. This includes for example theamount of sediment that entered pond A6 after enforced breaches. The associatedsuspended sediment concentrations are more difficult to reproduce, but are of sameorder of magnitude as observations. The model reveals tide residual flow and sedimenttransport patterns throughout the A6-A7-A8 pond system that are usually difficult tomeasure. These residual flow and transport patterns are the result of subtle, tide
residual transports.
Our model shows that we can skillfully reproduce observed morphodynamic
developments in the Alviso Slough pond system. This is of particular use to assess
future pond restoration scenarios and intervention measures. Future research work may
focus on breaching and sea level rise scenarios as well as on including vegetation
dynamics to forecast marsh development.

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