Sam SafranStephen AndrewsRobin Grossinger

Letitia Grenier

A new dimension to historical ecologyInsights from a 3D hydrodynamic model of the pre-development estuary

CWEMF 2015 ∙ 3/10/15

34 North

Bay-Delta Science ConferenceSacramento, CANovember 15, 2016

Use an understanding of changes in patterns and processes…to inform landscape scale restoration…

that supports desired ecological functions.

Delta Landscapes Project

?past present

First Mallard SloughSheldrake Slough

Enright et al. 2012

“The severed land–water interactions profoundly change current and water temperature dynamics. The northern reach of the San Francisco estuary contains hundreds of modified or disconnected terminal tidal sloughs where the current and temperature regime is probably considerably changed. A proper characterization of the change would require sophisticated modeling.”

Enright et al. 2012

Project Goals

Characterize hydrodynamics of Delta prior to large-scale changes to its geometry and hydrology:

• Marsh reclamation• Levee construction• Channel cutting,

straightening, dredging, armoring

• Permanently flooded islands

• Upstream dams• Delta water exports• Seal-level rise

Covella & Fairchild, ca. 1910; courtesy Bank of Stockton Historical Photograph Collection Russell Lee, Shasta Dam construction, 1942; courtesy Library of Congress

Note: No large marshes or blind channels left in Delta to study (and very few analogues globally).

Project Goals

Consider implications of changes w/r/t ecosystem health and future management actions

Compare historical and contemporary hydrodynamics

• Understand what has and has not changed using a variety of hydrodynamic metrics Note:

Similar approach to 2D landscape changes

Characterize hydrodynamics of Delta prior to large-scale changes to its geometry and hydrology:

• Marsh reclamation• Levee construction• Channel cutting,

straightening, dredging, armoring

• Permanently flooded islands

• Upstream dams• Delta water exports• Seal-level rise

Process overview

DWR: Tariq Kadir, Guabiao Huang

RMA: Steve Andrews, Ed Gross, John DeGeorge, Stacie Grinbergs

SFEI: Sam Safran, Robin Grossinger, Letitia Grenier

UC Davis, CWS: Andy Bell, Bill Fleenor, Alison Whipple, Ed Gross, Steve Micko, Fabian Bombardelli, Muy Lai, Amber Manfree

Process overview

DWR: Tariq Kadir, Guabiao Huang

RMA: Steve Andrews, Ed Gross, John DeGeorge, Stacie Grinbergs

SFEI: Sam Safran, Robin Grossinger, Letitia Grenier

Metropolitan Water District (funding, SFEI & RMA): Paul Hutton

UC Davis, CWS: Andy Bell, Bill Fleenor, Alison Whipple, Ed Gross, Steve Micko, Fabian Bombardelli, Muy Lai, Amber Manfree

Process overview

Historical Bath

Hydrology and Other Inputs

Hydrodynamic Model

Results, Analysts, Implications

Bay-Delta Science Conference 2014.. . .

Development and Calibration of the Historical Delta Model

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tidal extent of the historicalSan Francisco Bay-Delta Estuary

tidal marshtidal open water

upstream limit of19th century Coast Survey data

Method 1Method 2Method 3Determining historical bathymetry

Method 1: Topo to Raster

• areas with dense historical soundings• interpolated directly between

points/contours

USCS 1867

Method 1Method 2Method 3Determining historical bathymetry

Method 2: Thalweg spline

• areas with only thalweg depths• interpolated between points using a

cubic spline• assumed parabolic channel shape

Ringgold 1850

Method 1Method 2Method 3Determining historical bathymetry

Method 3: Width-depth regression

• areas with no data• use channel width to estimate depth

based on historical data• assumed parabolic channel shape

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Method 1Method 2Method 3Determining historical bathymetry

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• Carquinez and upstream• Topography and bathymetry circa 1850• Generated at 2 m resolution• Modern fixed datum (NAVD88)• Alignment with historical ecology layers

Historical Delta DEM

Historic Grid Construction • Flow-aligned quadrilateral elements

follow levee crests in main channels

• Triangular elements fill tidal plains

• Low-order channels captured implicitly using subgrid

• - 125,000 elements

Full model 1

grid extent

RMA Resowce Management Associates

Hydrodynamic Model Information • UnTRIM Computational Engine

• 30 hydrodynamic and scalar transport model • Utilizes unstructured orthogonal grid • Computationally efficient and stable • Developed and maintained by V. Casu IIi (Univ. of Trento, Italy) • Casulli and Cheng (1992), Casu IIi and Walters (2000), Casu IIi and Stelling (201 0)

• zO bed friction parameterization

• Generalized length scale vertical turbulence closure scheme (Warner, 2oos)

• Implemented by Bundesanstalt fur Wasserbau (BAW)

• Constant wind stress, evaporation, and precipitation by region

• Target moderate grid resolution with subgrid

• Produces improved estimates of cell volume and channel conveyance

R MA RESOURCE MAHAGENEHT ASSOCIATES

WATER RESOURCES ENG I NEERING

Model geometry with contoured subgrid bathymetry

Hydrology

• from modified C2Vsim model (Kadirand Huang 2016, DWR): “Estimates of Natural and Unimpaired Flows for the Central Valley of California”

• Natural flows: takes rim flows and subtracts water lost on valley floor to evapotranspiration (plus other changes)

• Covers range of water year types (wet, dry, critical)

In general, the pre-development system has:• higher peak flows in the winter and spring • higher sustained flows in the late spring and early summer• lower outflows in the late summer and fall

from RMA Pre-development

Contemporary

• Analyses run to date• Channel velocity• Tidal prism • Tracer runs / source water fingerprinting• Isohaline position• Low salinity zone habitat characteristics• Net- heterotrophic vs. net-autotrophic habitats

Model results

• Analyses run to date• Channel velocity• Tidal prism • Tracer runs / source water fingerprinting• Isohaline position• Low salinity zone habitat characteristics• Net- heterotrophic vs. net-autotrophic habitats

Model results

0 1,000 2,000 3,000

Fluvial or detached

Flow-through

Other blindchannels

Blind adjacent tomarsh

modern

hist.mod.

hist.mod.

hist.mod.

hist.mod.

channel length (km)historical modernChannel type by length

Dendritic channels (adjacent to marsh)

Dendritic channels (not adjacent to marsh)

Looped channels

Detached or fluvial

- higher residence times- lower organic matter exchange

- higher residence times- higher organic matter exchange

- lower residence times

- lower residence times

Channel velocity

Water velocity influences many things:• distribution of FAV/SAV (Hestir 2010)

• structure of algae assemblages in rivers (Leland et al. 2011)

• local population abundance of plankton, nekton, and benthic organisms (Ketchum 1954 , Rzoska 1978, Nicols and Pamatmat 1988)

How has loss of dendritic channels influenced availability of low-velocity habitat?

• Effects on juvenile salmon migration and rearing:

• rate of travel increases with average downstream water velocity (Horn and Blake 2004)

• seek out low-velocity refuge to hold at night, which is thought to be limited in contemporary system (Burau et al. 2007)

Eiko Jones

Channel velocity

San Joaquin RiverElk Slough #1 (mouth)Elk Slough #2Elk Slough #3 (head)

00:00 12:00 00:00 12:00 00:00 12:0002Jul2008 03Jul2008 04Jul2008

Cro

ss-s

ectio

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ave

rage

d ve

loci

ty (

m/s

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-0.8

-0.6

-0.4

-0.2

0.0

0.2

0.4

0.6

0.8

1.0

Velo

city

(m/s

)

• Compared average velocities in a mainstem and a blind channel

• Maximum cross-sectionally averaged velocity over one week:

San Joaquin = 0.79 m/sElk Slough mouth = 0.43 m/s

-46%

Channel velocity

San Joaquin RiverElk Slough #1 (mouth)Elk Slough #2Elk Slough #3 (head)

00:00 12:00 00:00 12:00 00:00 12:0002Jul2008 03Jul2008 04Jul2008

Cro

ss-s

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ave

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d ve

loci

ty (

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-0.8

-0.6

-0.4

-0.2

0.0

0.2

0.4

0.6

0.8

1.0

Velo

city

(m/s

)

• Compared average velocities in a mainstem and a blind channel

• Maximum cross-sectionally averaged velocity over one week:

San Joaquin = 0.79 m/sElk Slough mouth = 0.43 m/sElk slough head = 0.15 m/s

-81%

Channel velocity

• Compared average velocities in a mainstem and a blind channel

• Maximum cross-sectionally averaged velocity over one week:

San Joaquin = 0.79 m/sElk Slough mouth = 0.43 m/sElk slough head = 0.15 m/s

Blind network every ~2 km

• If low velocity refuge available in blind tidal sloughs, landscape would have functioned very differently for smolt

Note: Blind sloughs also likely conducive to prolonged periods of residency and rearing (Hering et al. 2010)

0 1,000 2,000 3,000

Fluvial or detached

Flow-through

Other blindchannels

Blind adjacent tomarsh

modern

hist.mod.

hist.mod.

hist.mod.

hist.mod.

channel length (km)historical modernChannel type by length

Dendritic channels (adjacent to marsh)

Dendritic channels (not adjacent to marsh)

Looped channels

Detached or fluvial

- higher residence times- lower organic matter exchange

- higher residence times- higher organic matter exchange

- lower residence times

- lower residence times

Tracer runs

A conceptual model of changes in the slough physical gradients (Chris Enright, BDSC 2010)

“Modern Delta characteristic engineered-morphology”“Historical Delta morphology”

low “distance to different” high “distance to different”

Low flow tracer runs, which let us view the movement and dispersal of water, are a first step towards illustrating this concept.

Tracer runs- conclusions

Qualitative observations from visual inspection:

Total areal dispersion after three days is similar in historical and modern systems…

…but historical systems are less mixed from a gross areal perspective:• Gradients are more pronounced

in historical system• Greater range of constituent

concentrations within a given distance.

• Lower “distance to different”• Greater potential opportunity

for fish to fine-tune position vis-a-vie tracer concentration.

historical contemporary

Source water fingerprinting

Methods

• Tagged each major Delta inflow with fixed amount of tracer

• Run model and see where tracer ends up

Ecological implications

• Expected to influence organisms that use stream-specific chemical signals to navigate their environment

• Natal homing in salmon: adult fish migrate from the open ocean to the specific stream of their birth to reproduce

• Olfactory cues are particularly important during freshwater migration phase• Juvenile salmon “imprint” on chemical signals of their home stream• Use olfactory memory of home stream waters to navigate upstream

• Tracer runs help us see the historical and modern landscape from the perspective of an adult salmon

Source water fingerprinting

Relative concentration of San Joaquin River water in critically dry year

Historical Modern

60 km

100%

5%

80%

60%

40%

20%

San Joaquin signal is “truncated”

Source water fingerprinting

Relative concentration of Sacramento River water in critically dry year

Sacramento signal is “diffused”

Historical Modern100%

5%

80%

60%

40%

20%~50 km from confluence ~90 km from confluence

University of Washington

I Find River Mouth I _ _ _ O~eaQ-----------------j------------------------R•ver I I . Enter River .

l Home Odor

Present? No Leave

Yes River

Lateral Movements Yes

Leave Home Odor? Find Bank:

~ 1 No ~s

Odors Present?

~ No Zig-Zag

I Swim I ~0 I I Home? Upriver Backtrack Upriver I Yes?

I Spawn I Find Qu1 Peter Johnsen

• nn, based on Yes

Odors? No

Source water fingerprinting

Historical Modern

60 km

100%

5%

80%

60%

40%

20%

Any challenges to natal homing related to source water distribution compounded by other stressors

• Higher cost to “mistakes” or inefficiencies• Diminished ability for “collective navigation” (Berdahl et al. 2014)

Concluding thoughts

• Temperature• Residence time• Primary productivity• Habitat connectivity

• Habitat variables for life cycle models

• Understanding changes in mechanisms for species-flow relationships

• Studying how the estuary’s hydrodynamics have changed can:• (1) help improve our understanding of the desirable

ecosystem functions provided by the historical system • (2) improve our ability to recover these functions now and

into the future

• Only the beginning. There are many possible applications.

Concluding thoughts

• Temperature• Residence time• Primary productivity• Habitat connectivity

• Habitat variables for life cycle models

• Understanding changes in mechanisms for species-flow relationships

• Studying how the estuary’s hydrodynamics have changed can:• (1) help improve our understanding of the desirable

ecosystem functions provided by the historical system • (2) improve our ability to recover these functions now and

into the future

• Only the beginning. There are many possible applications.

• Historical hydrology and geometry drove greater variability at the landscape-scale. Reestablishing aspects of historical geometry (e.g. blind channels) might be a practical tool for improving ecological function.

For more…

“Ecological implications of modeled hydrodynamic changes in the upper San Francisco Estuary”

Technical memos“Hydrodynamic and Salt Transport of the Pre-Development Upper San Francisco Estuary”

For more…

Manuscript (Andrews, Gross and Hutton, in review):“Modeling salt intrusion in the San Francisco Estuary prior to anthropogenic influence.”

Historical DEM slider (UC Davis)www.watershed.ucdavis.edu/experiments/delta_hdem/deltademslider.html

sams@sfei.orgsteve@rmanet.com

Thank you…

• Paul Hutton• Bill Fleenor• Andy Bell• Alison Whipple• Mui Lay• Amber Manfree• John DeGeorge• Ed Gross• Tariq Kadir• Guabiao Huang• Chris Enright

Delta Landscapes Project funded by the funded by the California Department of Fish and Wildlife and the Ecosystem Restoration Program

Independent collaboration with the UC Davis Center for Watershed Scienceand the California Department of Water Resources.

Historical Delta hydrodynamics project funded by the Metropolitan Water District

Contemporary Delta hydrodynamic model developed by Resource Management Associates (RMA)