Sediment Geochemistry of Corte Madera Marsh, San 

Francisco Bay, California: Have Local Inputs 

Changed, 1830–2010?

Open-File Report 2013–1042

U.S. Department of the Interior 

U.S. Geological Survey 
This page left intentionally blank 
Sediment Geochemistry of Corte Madera Marsh, San 

Francisco Bay, California: Have Local Inputs 

Changed, 1830–2010?

By Renee K. Takesue and Bruce E. Jaffe 

Open-File Report 2013–1042

U.S. Department of the Interior 

U.S. Geological Survey 
U.S. Department of the Interior 

SALLY JEWELL, Secretary 

U.S. Geological Survey 

Suzanne M. Kimball, Acting Director 

U.S. Geological Survey, Reston, Virginia: 2013 

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Suggested citation: 

Takesue, R.K., and Jaffe, B.E., 2013, Sediment geochemistry of Corte Madera Marsh, San Francisco 

Bay, California: Have local inputs changed, 1830–2010?: U.S. Geological Survey Open-File Report 

2013-1042, 23 p., http://pubs.usgs.gov/of/2013/1042/. 

Any use of trade, product, or firm names is for descriptive purposes only and does not imply 

endorsement by the U.S. Government. 

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.
iii

Contents 

Abstract............................................................................................................................................................................1

Introduction ......................................................................................................................................................................2

Site Description................................................................................................................................................................3

Approach..........................................................................................................................................................................3

Methods ...........................................................................................................................................................................5

Marsh Sediment Collection ..........................................................................................................................................5

Watershed and Bay Sediment Collection.....................................................................................................................5

Analyses of Trace and Rare Earth Elements ...............................................................................................................5

Sediment Core Age-Depth Models ..............................................................................................................................6

Results.............................................................................................................................................................................6

Geochemical Signatures of River, Creek, and Bay Sediment......................................................................................6

Sacramento and San Joaquin Rivers.......................................................................................................................6

San Francisco Bay (Corte Madera and San Rafael Bays) .......................................................................................6

Corte Madera Creek .................................................................................................................................................6

Sedimentary Records...................................................................................................................................................7

Historical Variations of Geochemical Tracers in Corte Madera Marsh ........................................................................9

Pre–1850 ..............................................................................................................................................................9

1850–1910............................................................................................................................................................9

1910–1950............................................................................................................................................................9

1950–1990............................................................................................................................................................9

1990–Present .......................................................................................................................................................9

Contaminant Heavy Metals in Corte Madera Marsh ..................................................................................................14

Lead and Antimony.................................................................................................................................................14

Iron, Cobalt, Copper, and Nickel ............................................................................................................................14

Discussion......................................................................................................................................................................16

Heterogeneity of Marsh Sediment Geochemistry ......................................................................................................16

Regional Heterogeneity..........................................................................................................................................16

Low Marsh Heterogeneity.......................................................................................................................................17

Diagenetic Heterogeneity .......................................................................................................................................17

Ecological Implications of Diagenetic Metal Enrichments...................................................................................18

Historical Inputs to Corte Madera Marsh....................................................................................................................18

Fluvial Sediment Inputs ..........................................................................................................................................18

Contaminant Inputs ................................................................................................................................................19

Current Sediment Budgets: Are Local Watersheds Making up the Difference? ........................................................19

Conclusions ...................................................................................................................................................................20

Acknowledgments..........................................................................................................................................................21

References.....................................................................................................................................................................21
iv

Figures 

1. Map of the San Francisco Bay area and the Sacramento-San Joaquin Rivers and Delta. Circles show 

locations where river and creek sediment were collected; crosses show locations where bay mud was 

collected; diamond shows the location of the Selby lead smelter........................................................................ 2

2. Aerial image of Corte Madera Marsh showing transects and core locations........................................................... 4

3. Graphs showing aluminum (Al)-normalized mean trace-element contents of fine sediment from Sacramento 

(SAC; n=2) and San Joaquin (SJ; n=2) Rivers, San Francisco Bay (Bay; n=8), and Corte Madera Creek 

(Creek; n=3). A) chromium (Cr), B) zirconium (Zr), C) scandium (Sc), D) thorium (Th), E) heavy rare earth 

elements (HREE), and F) total rare earth elements (TOT REE). Error bars show ±1 σ; n, number of 

samples................................................................................................................................................................ 7

4. Graphs showing NASC-normalized mean rare earth element patterns in fine sediment from A) Rivers, B) 

Bay and Creek, C) Corte Madera Marsh Transect N cores, and D) Corte Madera Marsh Transect S cores. 

The vertical scale of panel A) is two times larger than the others. Error bars show ±1 σ. .................................. 8

5. Graphs showing historical sediment-geochemical variations in Corte Madera Marsh cores from Transects N 

and S: aluminum (Al) content, Al-normalized thorium (Th) content, and Al-normalized total rare earth 

element (TOT REE) content. ............................................................................................................................. 10

6. Graphs showing historical sediment-geochemical variations in Corte Madera Marsh cores from Transects N 

and S: Al-normalized chromium (Cr) content, Al-normalized zirconium (Zr) content, and Al-normalized 

scandium (Sc) content. ...................................................................................................................................... 11

7. Graphs showing NASC-normalized REE patterns in fine sediment from high, middle, and low marsh cores 

along Transect N for the five sediment-input periods. ....................................................................................... 12

8. Graphs showing NASC-normalized REE patterns in fine sediment from high, middle, and low marsh cores 

along Transect S for the five sediment-input periods......................................................................................... 13

9. Graphs showing historical variations of Al-normalized Pb and Sb contents of fine sediment from Corte 

Madera Marsh Transects N (top row of graphs) and S (bottom row of graphs)................................................. 15

10. Graphs showing historical variations of Al-normalized Fe and Co contents of fine sediment from Corte 

Madera Marsh Transects N (top row of graphs) and S (bottom row of graphs)................................................. 16

11. Graph showing historical variations of Al-normalized Rb content of fine sediment in the three Corte Madera 

Marsh cores that spanned the period from pre-disturbance to present. ............................................................ 19

Table 

1. Description of Corte Madera Marsh sedimentary records using a 210Pb–based CRS age model. .......................... 8
v

Conversion Factors 

Inch/Pound to SI 

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

inch (in.) 2.54 x 104 micrometer (μm)

foot (ft) 0.3048 meter (m)

yard (yd) 0.9144 meter (m)

mile (mi) 1.609 kilometer (km)

Volume

gallon (gal) 3.785 liter (L) 

Area

acre 4,047 square meter (m2)

acre 0.4047 hectare (ha)

acre 0.004047 square kilometer (km2)

square inch (in2) 6.452 square centimeter (cm2)

square foot (ft2) 929.0 square centimeter (cm2)

square foot (ft2) 0.09290 square meter (m2)

square mile (mi2) 259.0 hectare (ha)

square mile (mi2) 2.590 square kilometer (km2) 

Mass

ounce, avoirdupois (oz) 28.35 gram (g) 

ounce, avoirdupois (oz) 0.02835 milligram (mg)

Liquid Concentration

pounds per gallon 1.19826 x 105 milligrams per liter (mg/L)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows: 

°F=(1.8×°C)+32 

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as follows: 

°C=(°F-32)/1.8

Vertical coordinate information is referenced to the insert datum name (and abbreviation) here for instance, “North American 

Vertical Datum of 1988 (NAVD 88).” 

Horizontal coordinate information is referenced to the insert datum name (and abbreviation) here for instance, “North American 

Datum of 1983 (NAD 83).” 

Altitude, as used in this report, refers to distance above the vertical datum. 
This page left intentionally blank 
Sediment Geochemistry of Corte Madera Marsh, San 

Francisco Bay, California: Have Local Inputs Changed, 

1830–2010?

By Renee K. Takesue and Bruce E. Jaffe 

Abstract 

Large perturbations since the mid-1800s to 

the supply and source of sediment entering San 

Francisco Bay have disturbed natural processes 

for more than 150 years. Only recently have 

sediment inputs through the Sacramento-San 

Joaquin Delta (the Delta) decreased to what 

might be considered pre-disturbance levels. 

Declining sediment inputs to San Francisco Bay 

raise concern about continued tidal marsh 

accretion, particularly if sea level rise accelerates 

in the future. The aim of this study is to explore 

whether the relative amount of local-watershed 

sediment accumulating in a tidal marsh has 

changed as sediment supply from the 

Sacramento-San Joaquin Rivers has decreased. 

To address this question, sediment geochemical 

indicators, or signatures, in the fine fraction (silt 

and clay) of Sacramento River, San Joaquin 

River, San Francisco Bay, and Corte Madera 

Creek sediment were identified and applied in 

sediment recovered from Corte Madera Marsh, 

one of the few remaining natural marshes in San 

Francisco Bay. Total major, minor, trace, and 

rare earth element (REE) contents of fine 

sediment were determined by inductively 

coupled plasma mass and atomic emission 

spectroscopy. Fine sediment from potential 

source areas had the following geochemical 

signatures: Sacramento River sediment 

downstream of the confluence of the American 

River was characterized by enrichments in 

chromium, zirconium, and heavy REE; San 

Joaquin River sediment at Vernalis and Lathrop 

was characterized by enrichments in thorium and 

total REE content; Corte Madera Creek sediment 

had elevated nickel contents; and the composition 

of San Francisco Bay mud proximal to Corte 

Madera Marsh was intermediate between these 

sources. Most sediment geochemical signatures 

were relatively invariant for more than 150 years, 

suggesting that the composition of fine sediment 

in Corte Madera Marsh is not very sensitive to 

changes in the magnitude, timing, or source of 

sediment entering San Francisco Bay through the 

Delta. Nor does there appear to be a ubiquitous 

increase in the proportion of fine sediment from 

Corte Madera watershed accumulating in the 

marsh during the last 20 years when sediment 

inflows through the Delta have decreased to predisturbance levels. We conclude that a large, 

well-mixed reservoir, such as the transportable 

fine sediment pool in San Francisco Bay, is the 

primary source of sediment to Corte Madera 

Marsh, and this source buffers the marsh against 

changes in sediment supply from the Delta and 

local watersheds. This study also found that 

Corte Madera Marsh sediment between about 

10–30 centimeters depth is highly contaminated 

with lead, likely a legacy of lead smelter 

operations near Carquinez Strait and leaded 

gasoline use.

 
2

Introduction 

River-borne sediment delivery to San 

Francisco Bay, California, has changed 

substantially since urbanization began in the 

1850s. Historically, the majority of sediment was 

derived from the Sacramento and San Joaquin 

Rivers (Krone, 1979) (fig. 1). Between 1853 and 

1884, hydraulic gold mining in the northwestern 

Sierra Nevada introduced nine times more 

sediment than typical into rivers and streams 

flowing into San Francisco Bay (Gilbert, 1917). 

Although intense unregulated hydraulic mining 

was relatively short-lived, its legacy persisted for 

decades (Krone, 1979, 1996; James, 1999, 2004), 

and regulated hydraulic mining resumed on a 

smaller scale in the 20th century (James, 2005). 

In the early to mid-1900s, a second pulse of 

sediment, about one-half as large as that from 

hydraulic mining, appeared to be associated with

Figure 1. Map of the San Francisco Bay area and the Sacramento-San Joaquin Rivers and Delta. Circles show locations 

where river and creek sediment were collected; crosses show locations where bay mud was collected; diamond shows the 

location of the Selby lead smelter. 
3

the urbanization of local watersheds and 

agricultural development of the Sacramento-San 

Joaquin Delta (the Delta) (Schoellhamer, 2011); 

however, there are insufficient measurements to 

corroborate this mechanism. After 1970, 

sediment input to San Francisco Bay decreased 

further because of the implementation of erosion 

controls in local watersheds (Wright and 

Schoellhamer, 2004) and the end of agricultural 

expansion (Schoellhamer, 2011). The magnitude 

of sediment input to San Francisco Bay through 

the Delta is estimated to be roughly similar today 

as that prior to human intervention (pre-1850) 

(Schoellhamer, 2011). Schoellhamer (2011) and 

references therein identify five periods (rounded 

to the nearest decade) of varying sediment input 

to San Francisco Bay: pre-1850, 1850–1910, 

1910–1950, 1950–1990, 1990–present. 

Tidal marshes in San Francisco Bay are 

nourished by siliciclastic sediment, typically silt 

and clay, that is carried by the tide and falls out 

of suspension when water flow slows over marsh 

vegetation (Reed, 2000). Tidal marshes began 

forming around San Francisco Bay about 6,000 

years ago when the estuary took up its current 

position landward of the Golden Gate and sea 

level rise slowed to about 1–2 mm/yr (Atwater 

and others, 1979; Reed, 1995). Human 

perturbations have, until recently, resulted in 

excess sediment supply to San Francisco Bay that 

is thought to have created an erodible sediment 

pool on the bed (Schoellhamer, 2011), favoring 

tidal marsh creation or expansion (Atwater and 

others, 1979; Watson, 2008). Since the depletion 

of this erodible sediment pool in the late 1990s, 

the transport of suspended sediment by the tides 

in San Francisco Bay has become supply-limited 

(Schoellhamer, 2011). The present-day source of 

sediment could be an important factor if tidal 

marsh accretion is to keep pace with sea level 

rise (Reed, 1995; Kennish, 2001; Watson, 2004; 

McKee and others, 2006; Watson and Byrne, 

2012). Because of decreasing sediment inputs 

through the Delta since the mid-1900s, local 

watersheds are believed to account for 50 percent 

or more of the sediment flux to San Francisco 

Bay (Schoellhamer and others, 2005; McKee and 

others, 2006), whereas, historically, the 

proportion was about 15 percent (Porterfield, 

1980). This study aims to explore historical and 

present-day sources of sediment to Corte Madera 

Marsh, one of the few undisturbed historical 

marshes in San Francisco Bay (Atwater and 

others, 1979). 

Site Description 

Corte Madera Marsh has undergone few 

human perturbations, making it a site where it 

may be possible to recover historical sedimentary 

records. The 4 km2 tidal marsh lies to the south 

of Corte Madera Creek (fig. 2). Development in 

the marsh is limited to two power transmission 

towers in the low marsh, a houseboat community 

along the creek, and 0.05 km2

 of fill at the 

landward edge. Marshland north of Corte Madera 

Creek has been developed into the Larkspur 

Ferry Terminal. 

The watershed of Corte Madera Creek is 

small, 73 km2

, and 90 percent of its area is 

developed for urban and residential use. In the 

1960s, the lower reach of Corte Madera Creek 

was channelized and hardened for flood and 

erosion control. Ninety-one percent of sediment 

carried by the creek comes from the uplands 

(Smeltzer and others, 2000). Suspended-sediment 

concentrations during the five wet seasons 

(November–May) for which data are available 

(1978–80, 2010–11) averaged 38 ± 17 mg/L 

(U.S. Geological Survey, 2012), about equal to 

the mean suspended-sediment concentration in 

the bay water column at nearby Point San Pablo 

during 1999–2006 (Schoellhamer, 2011). 

Approach 

The underlying geologies of watersheds 

that can contribute sediment to San Francisco 

Bay are quite distinct (Alt and Hyndman, 2000). 

Corte Madera Creek drains Franciscan rocks of 

the Coast Range, which consists of 

metamorphosed oceanic chert, shale, basalt, and 
4

Figure 2. Aerial image of Corte Madera Marsh showing transects and core locations. 

ultramafic rocks and serpentine (Murray and 

others, 1991). The Sacramento and San Joaquin 

Rivers and their tributaries drain the granitic 

Sierra Nevada Range (Alt and Hyndman, 2000) 

and its alluvium filling the Central Valley 

(Goldhaber and others, 2009). In addition, 

watersheds tributary to the Sacramento River, 

where most gold mining took place (the 

American, Bear, Yuba, and Feather watersheds), 

contain metamorphosed mafic and ultramafic 

oceanic crust interleaved with continental crust 

(Girty and others, 1996; Alt and Hyndman, 

2000). These rocks have distinct mineralogical 

and geochemical compositions that can be 

preserved during weathering, erosion, and 

transport of sediment and used as source 

attributes once sediment has been deposited in 

distal locations (McLennan and others, 1993). 

A geochemical approach was used to 

distinguish fine sediment (<63 μm, silt and clay) 

from Sacramento and San Joaquin Rivers, San 

Francisco Bay, and Corte Madera Creek—all 

potential sources of sediment to Corte Madera 

Marsh—and to describe how inputs from these 
5

sources varied historically in Corte Madera 

Marsh. Bay sediment is expected to be a mixture 

of river and local tributary sediment, and could 

include legacy sediment from the hydraulic 

mining period (Krone, 1996; Jaffe and others, 

2007). Immobile trace elements, such as 

chromium (Cr), scandium (Sc), thorium (Th), and 

zirconium (Zr) and rare earth elements (REE), 

are the most reliable indicators of source-rock 

composition because of their refractory nature in 

minerals (Rollinson, 1993). Mafic and ultramafic 

rocks contain more Cr, Sc, and heavy REE 

(HREE; erbium [Er], thulium [Tm], ytterbium 

[Yb], and lutetium [Lu]) than granitic rocks or 

marine sediment, whereas granitic rocks contain 

more Th, Zr, light REE (LREE; lanthanum [La], 

cerium [Ce], praseodymium [Pr], neodymium 

[Nd], and promethium [Pm]) and total REE (TOT 

REE) contents. Serpentine, which co-occurs with 

Franciscan and Sierran metamorphic rocks, is 

enriched in Cr and nickel (Ni) (Oze and others, 

2004). The common rock-forming mineral 

hornblende and the accessory mineral sphene, 

which are associated with Sierran granite 

(Yancey and Lee, 1972), are enriched in the 

middle REE (MREE; samarium [Sm], europium 

[Eu], gadolinium [Gd], terbium [Tb], dysprosium 

[Dy], and holmium [Ho]). 

Methods 

Marsh Sediment Collection 

Six 50 cm-long sediment cores were 

collected in the low, middle, and high marsh in 

November 2010, January 2011, and May 2011 

along Transects N and S (fig. 2) by colleagues 

from the University of San Francisco (USF). 

Cores were sectioned into 2 cm-thick layers, 

dried at 60 C, and disaggregated. Subsamples of 

dried sediment were provided to the U.S. 

Geological Survey (USGS) for geochemical 

analyses. 

Watershed and Bay Sediment Collection 

Streambed sediment was collected from 

Corte Madera Creek at the town of Ross 

(Lagunitas Road bridge, 5.5 km upstream of the 

mouth) on June 30, 2011 (fig. 1). As part of a 

larger bay-wide sampling initiative, bay sediment 

was collected in Corte Madera and San Rafael 

Bays (fig. 1) using a Smith-McIntyre grab 

sampler aboard the USGS R/V Parke Snavely on 

January 27, 2012. Because of the ship’s draft, 

bay sediment was collected between 1.5 and 2 m 

water depth. The upper 0–2 cm of sediment was 

subsampled on board ship and stored frozen until 

processing. River bank sediment was collected 

from the Sacramento River at Sacramento (70 km 

upstream of the Delta) on October 18, 2010, and 

the San Joaquin River at Vernalis (83 km 

upstream of the Delta) and Lathrup (66 km 

upstream of the Delta) on October 2, 2010 (fig. 

1). 

Analyses of Trace and Rare Earth Elements 

Marsh, creek, river, and bay sediment was 

dried at 60 C, disaggregated, and dry-sieved in a 

stainless steel sieve to obtain 0.2 g of the fine 

fraction (<63 μm diameter). This aliquot was sent 

to the USGS Central Mineral and Environmental 

Resources Science Center, which sub-contracted 

SGS Laboratories, a nationally recognized testing 

laboratory, to measure total sedimentary contents 

of major, minor, trace, and REE elements. A 

sodium peroxide sinter and acid digestion were 

used to accomplish total sediment decomposition 

(Meier and Slowik, 2002), followed by 

inductively coupled plasma atomic emission and 

mass spectrometry quantification of total element 

concentrations. Major elements are reported on a 

weight percent basis (wt %); trace elements are 

reported in parts per million (ppm), which is 

equivalent to micrograms per gram. Missing data 

represent samples without sufficient material to 

perform geochemical analyses. 

Total sedimentary elemental contents were 

normalized by aluminum (Al) to account for 

differences in the amounts of silt, clay, and 
6

organic material in the fine fraction. Sedimentary 

REE contents were normalized by a North 

American shale composite (NASC) as given by 

Rollinson (1993) to show differences from 

average sedimentary rock. A sample with a shalelike REE composition would have REENASC

values = 1.0.

Sediment Core Age-Depth Models 

Sediment core age-depth models, or 

chronologies, based on activities of short-lived 

cosmogenic radionuclides 137Cs and 210Pb were 

provided by J. Callaway (USF, unpub. data, 

2012). Age-depth models based on the 

assumption of a constant rate of 210Pb supply 

(CRS) were adopted for the geochemical study 

because this approach accounts for variable 

sediment accumulation rates (Appleby and 

Oldfield, 1992). 210Pb radionuclide activities 

unsupported by the geologic background were 

undetectable or absent in sediment more than 

100–150 years old. In the absence of other 

estimates of age-depth relationships, those 

determined by CRS in datable sediment horizons 

were linearly extrapolated to sediment horizons 

that could not be dated directly, a reasonable 

assumption for stable depositional environments 

(Appleby and Oldfield, 1992). 

Results 

Geochemical Signatures of River, Creek, and 

Bay Sediment 

Sacramento and San Joaquin Rivers 

Two samples of Sacramento River (SAC) 

sediment collected downstream of the confluence 

with the American River near downtown 

Sacramento had characteristics of both granitic 

and ultramafic source rocks: mean Al-normalized 

Cr, Zr, and HREE contents were highly enriched 

and Al-normalized Sc contents moderately 

enriched compared to sediment from other 

sources (fig. 3A–C, E). The HREE enrichment 

gave the mean REENASC profile of SAC sediment 

a steep positive slope (fig. 4A) and a (Lu/La)NASC

ratio >1 (fig. 3E). Average SAC sediment had a 

double-peaked MREE enrichment at Eu and Tb 

(fig. 4A). 

San Joaquin River (SJ) sediment at Vernalis 

and Lathrop had a marked granitic character: 

high mean Al-normalized Th and TOT REE 

contents (fig. 3D, F) and a LREE enrichment 

(fig. 4A). The LREE enrichment gave the mean 

REENASC profile of SJ sediment a negative slope 

(fig. 4A) and a (Lu/La)NASC ratio <1 (fig. 3E). SJ 

sediment had a single-point MREE peak at Eu 

(fig. 4A). 

San Francisco Bay (Corte Madera and San Rafael 

Bays)

Mean values of mafic rock indicators—Alnormalized Cr, Sc, and a HREE enrichment— 

were intermediate in San Francisco Bay sediment 

at 1–2 m depth in Corte Madera and San Rafael 

Bays compared to SAC and SJ sediment. San 

Francisco Bay sediment also had the lowest mean 

Al-normalized Zr content (fig. 3B). The mean 

REENASC profile of bay sediment had 

characteristics of both mafic and granitic sources, 

having a slightly positive slope (Lu/La)NASC=1.1 

(fig. 3E) and a single-point MREE enrichment at 

Eu (fig. 4B). 

Corte Madera Creek 

Streambed sediment from Corte Madera 

Creek at Ross had the second-highest mean Alnormalized Cr content and lowest mean Alnormalized Sc content among the potential 

sources of sediment to Corte Madera Marsh (fig. 

3A, C). The mean Al-normalized Zr content was 

lower than in river sediment but higher than in 

bay sediment (fig. 3B). The element Ni is 

enriched in mafic and ultramafic rocks and 

serpentine, such as are found in the Corte Madera 

watershed. The mean Al-normalized Ni value in 

Corte Madera Creek sediment was three times 

higher than in granitic SJ sediment and two times 

higher than in SAC and San Francisco Bay 
7 

Figure 3. Graphs showing aluminum (Al)-normalized mean trace-element contents of fine sediment from Sacramento (SAC; 

n=2) and San Joaquin (SJ; n=2) Rivers, San Francisco Bay (Bay; n=8), and Corte Madera Creek (Creek; n=3). A) chromium 

(Cr), B) zirconium (Zr), C) scandium (Sc), D) thorium (Th), E) heavy rare earth elements (HREE), and F) total rare earth 

elements (TOT REE). Error bars show ±1 σ; n, number of samples. 

sediment. The REENASC profile of Creek 

sediment was relatively flat through the LREE 

(except La) and MREE (except Eu) and enriched 

in HREE (fig. 4B). 

Sedimentary Records

210Pb- and 137Cs-based dating criteria were 

satisfactory in all but the low-marsh core from 

Transect S (J. Callaway, unpub. data, 2012). CRS 

chronologies suggest that three of the Corte 

Madera Marsh cores contain sediment records 

extending to the period before major 

perturbations to San Francisco Bay’s sediment 

budget in the early 1850s (table 1).

108

16 25

43

0

20

40

60

80

100

120

140

160

2.8

2.0

2.3

1.9

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

110

45

23

35

0

20

40

60

80

100

120

140

160

180

0.8

1.6

0.9 0.8

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

17

20

14 14

0

5

10

15

20

25

1.7

0.8

1.1 1.0

0.0

0.5

1.0

1.5

2.0

Figure 3

A) Cr B) Zr C) Sc

D) Th E) HREE F) TOT REE

SAC SJ Bay Creek

Sites

Al-normalized Cr (x 104)

(Lu / La)NASC

SAC SJ Bay Creek

Sites

SAC SJ Bay Creek

Sites

SAC SJ Bay Creek

Sites

SAC SJ Bay Creek

Sites

SAC SJ Bay Creek

Sites

Al-normalized Zr (x 104)

Al-normalized Sc (x 104)

Al-normalized Th (x 104)

Al-normalized TOT REE (x 104)
8

Figure 4. Graphs showing NASC-normalized mean rare earth element patterns in fine sediment from A) Rivers, B) Bay and 

Creek, C) Corte Madera Marsh Transect N cores, and D) Corte Madera Marsh Transect S cores. The vertical scale of panel 

A) is two times larger than the others. Error bars show ±1 σ. 

Table 1. Description of Corte Madera Marsh sedimentary records using a 210Pb–based CRS age model. 

[Values in parentheses indicate a lower level of confidence in the age-depth relationship because there was not good 

agreement between the 210Pb-based and 137Cs-based age models] 

Metric Low marsh Middle marsh High marsh

Transect N

Record length (years) 94 102 181

Start of record (date) 1916 1908 1829

Transect S

Record length (years) (124) 176 163

Start of record (date) (1887) 1835 1848
9

Historical Variations of Geochemical Tracers in 

Corte Madera Marsh 

Sediment geochemical variations are 

described for the five sedimentation periods 

defined by Schoellhamer (2011). 

Pre–1850

Corte Madera Marsh cores from the high 

marsh of Transect N, the middle marsh of 

Transect S, and the high marsh of Transect S 

contained sediment deposited before 1850. All 

sediment deposited before 1850 had lower Al 

contents, 5–6 wt % (fig. 5) than modern river, 

bay, and creek sediment, 7–8 wt %. In the high 

marsh of Transect N, sediment deposited predisturbance had the lowest Al-normalized Cr 

content, being one third lower than in 

subsequently deposited sediment (fig. 6) and 

among the lowest TOT REE contents (fig. 5). 

REENASC patterns of pre-disturbance sediment 

were relatively flat with the exception of small 

positive Eu anomalies, and had magnitudes 

ranging 40–60 percent lower than the NASC 

(figs. 7, 8). 

1850–1910

In the mid-1850s, the Al-normalized Cr 

content abruptly doubled in high marsh sediment 

of Transect N and remained high until present 

day (fig. 6). Other source-rock indicators—Th, 

TOT REE, Zr, and Sc—varied little during this 

period (figs. 5, 6). Marsh sediment had higher Al 

contents near the end of the period than at the 

beginning, when hydraulic mining impacts were 

greatest, but the increase was not monotonic and 

the timing differed along Transects N and S (fig. 

5). Additionally, at the end of this period, a 4–6 

cm-thick sediment layer, with double-peaked 

MREE enrichments and elevated magnitudes, 

was deposited across the entire marsh in the late 

1880s or early 1900s (figs. 7, 8). 

1910–1950

Sedimentary TOT REE contents increased 

slightly over this period (fig. 5), as did Alnormalized Cr (fig. 6). The 1900s was the first 

period when it was possible to compare sediment 

geochemistry among low, middle, and high 

marsh elevations. Sediment accumulating in the 

low marsh had higher and more variable Alnormalized Zr contents than sediment at higher 

elevations (fig. 6); however, marsh Zr contents 

were well below those of river, bay, and creek 

sediment (fig. 3). Along Transect N, low marsh 

sediment had lower and more variable Alnormalized Sc contents (fig. 6). These low marsh 

Sc contents were similar in magnitude to that of 

granitic SJ sediment and Corte Madera Creek 

sediment (fig. 3). Another distinctive 

characteristic of low marsh sediment was that it 

had higher, more shale-like REENASC

magnitudes, generally 0.6–0.8, compared to 

middle or high marsh sediment, which had 

magnitudes generally ranging 0.4–0.7 (figs. 7, 8). 

There also were differences in REENASC patterns 

between Transects N and S. Middle and high 

marsh sediment along Transect N generally had 

double-peaked MREE enrichments, whereas 

sediment along Transect S generally had a single 

MREE peak at Eu (figs. 7, 8). 

1950–1990

Al-normalized Cr, Sc, and TOT REE 

contents increased slightly during this period 

(figs. 5, 6). For several years around 1980, 

sediment across all elevations of Transect N and 

possibly at the low marsh of Transect S had 

higher TOT REE contents (fig. 5) and doublepeaked MREE enrichments (figs. 7, 8) which, in 

combination, were characteristic of Sacramento 

River sediment. 

1990–Present

The uppermost 6 or 8 cm of Corte Madera Marsh 

sediment were deposited during the last 20 years, 

when sediment inputs through the Delta were 

historically low. Al-normalized TOT REE 

contents decreased during this period in the low 
10

marsh of Transect S, the middle marsh of 

Transect N, and the high marsh of Transect S. 

Sediment deposited 4–6 cm below the surface 

(approximately 1994) in the middle marsh of 

Transect S had extremely high Cr and Zr contents 

and low Sc contents (fig. 6) accompanied by a 

HREE enrichment (fig. 8). Less extreme Cr and 

Zr enrichments also occurred in the surface layer 

(0–2 cm) at this site. 

Figure 5. Graphs showing historical sediment-geochemical variations in Corte Madera Marsh cores from Transects N and S: 

aluminum (Al) content, Al-normalized thorium (Th) content, and Al-normalized total rare earth element (TOT REE) content. 
11

 

Figure 6. Graphs showing historical sediment-geochemical variations in Corte Madera Marsh cores from Transects N and S: 

Al-normalized chromium (Cr) content, Al-normalized zirconium (Zr) content, and Al-normalized scandium (Sc) content. 
12

Figure 7. Graphs showing NASC-normalized REE patterns in fine sediment from high, middle, and low marsh cores along 

Transect N for the five sediment-input periods. 
13

Figure 8. Graphs showing NASC-normalized REE patterns in fine sediment from high, middle, and low marsh cores along 

Transect S for the five sediment-input periods. 
14

Contaminant Heavy Metals in Corte Madera 

Marsh

Several heavy metals associated with 

human industrial and urban activities were 

enriched in the sediment of Corte Madera Marsh. 

Downcore lead (Pb) variations and potential 

sources were described in “Corte Madera Marsh 

Sediment Geochemistry, Part 1” (R. Takesue, 

written commun., 2011) without a temporal 

context. Here, 210Pb-based CRS age models are 

used to give Pb and other trace metal variations a 

historical context. 

Lead and Antimony 

Natural background levels (pre–1850) of Pb 

and antimony (Sb) in Corte Madera Marsh 

sediment were 15 ± 2 (1σ) ppm and 0.7±0.1 (1σ) 

ppm, respectively. Concomitant Pb and Sb 

enrichments 2 times higher than background first 

appeared in the 1880s and became prevalent after 

1900 (fig. 9). Highest Pb and Sb enrichments, 

around 30 and 15 times higher than background, 

respectively, occurred around 1950 in the middle 

and high marsh of Transect N. Sediment Pb and 

Sb contents were only about one-half as large 

along Transect S, and were higher in the middle 

marsh than the high marsh. After 1980, Pb and 

Sb levels in Corte Madera Marsh sediment 

returned to moderately low levels, 2 and 3 times 

above pre-industrial background, respectively. 

Iron, Cobalt, Copper, and Nickel 

The transition metals iron (Fe), cobalt (Co), 

copper (Cu), and nickel (Ni) experienced 

concomitant subsurface enrichments to varying 

degrees depending on marsh elevation. 

Downcore profiles of Fe and Cu are shown in 

figure 10. In cores from Transect N, highest 

enrichments occurred 36–42 cm below the marsh 

surface, and in cores from Transect S 

enrichments occurred from 36 to at least 52 cm. 

Al-normalized Fe contents had the highest 

enrichments, 2 to 7 times above background 

levels, whereas Co, Ni, and Cu were between 1 

and 4, 2, and 3 times above background, 

respectively. 
15

Figure 9. Graphs showing historical variations of Al-normalized Pb and Sb contents of fine sediment from Corte Madera 

Marsh Transects N (top row of graphs) and S (bottom row of graphs). 
16

Figure 10. Graphs showing historical variations of Al-normalized Fe and Co contents of fine sediment from Corte Madera 

Marsh Transects N (top row of graphs) and S (bottom row of graphs).

Discussion 

Variations of geochemical source-rock 

indicators in the sediment record of Corte 

Madera Marsh are consistent with our 

understanding of historical changes in sediment 

source and supply to San Francisco Bay. 

However, variations are ubiquitous across the 

whole marsh in only a few instances, raising a 

question about the significance of patterns. 

Before interpreting historical sediment 

geochemical variations in Corte Madera Marsh, it 

is important to understand the sources of 

variability in the sediment record.

Heterogeneity of Marsh Sediment 

Geochemistry 

Regional Heterogeneity 

Regional heterogeneity was evident from 

comparisons of sediment geochemistry along the 

north and south transects. Transect N is in an area 

of the marsh 150 m from Corte Madera Creek 
17

that contains tidal channels branching off from 

the creek. In contrast, Transect S is in an area of 

the marsh 450 m from the creek that does not 

contain creek-fed tidal channels. Thus the region 

of the marsh along Transect N is expected to 

receive a greater fraction of sediment from the 

local watershed than the region of the marsh 

along Transect S. The REENASC patterns of 

sediment accumulating along Transects N and S 

were indeed different, particularly in the middle 

and high marsh. Sediment along Transect N was 

characterized by a double peak in the MREE (fig. 

4C). Sediment along Transect S, although 

containing a diminished double peak, was 

characterized by a single MREE peak at Eu that 

resembled the pattern in San Francisco Bay 

sediment (fig. 4D). Therefore some of the 

sediment geochemical heterogeneity between 

Transects N and S comes from greater inputs of 

San Francisco Bay sediment to the southern 

region of the marsh (Transect S). This suggests 

that sedimentary records along Transect N are 

more suitable for studies about sediment input 

from Corte Madera watershed. 

The lack of similarity of the REENASC

patterns, specifically the MREE double peak, in 

sediment from Corte Madera Creek at the town 

of Ross and sediment accumulating in the 

northern region of Corte Madera Marsh, suggests 

that the local watershed end member was not 

well defined in this study. Smeltzer and others 

(2000) determined that more than 90 percent of 

suspended sediment carried by Corte Madera 

Creek is eroded from the uplands. The 

assumption for the creek sampling scheme was 

that streambed fine sediment at the town of Ross 

was representative of fine sediment from upland 

basins and the material discharged by Corte 

Madera Creek. Because fine sediment at the 

landward edge of Corte Madera Marsh did not 

resemble fine sediment in the streambed at Ross, 

we concluded that fine sediment in the streambed 

at Ross was not a suitable corollary for fine 

sediment runoff from the local watershed. 

Low Marsh Heterogeneity 

Geochemical variations occurring only in 

low marsh cores point to a nearshore influence on 

the composition of sediment accumulating in the 

low marsh. The middle and high marsh are 

primarily affected by tidal flows (Reed, 2000; 

Lacy and Hoover, 2011), whereas the low marsh 

can be an energetic environment impacted by 

wind waves and ferry wakes (Lacy and Hoover, 

2011). Waves and wakes resuspend sediment on 

intertidal mudflats (Brand and others, 2010; Lacy 

and Hoover, 2011) and this sediment can be 

deposited in the low marsh (Ganju and others, 

2005). The influence of strong hydrodynamic 

forces acting on the low marsh is illustrated by 

elevated Zr contents and sporadic Cr, Zr, and 

HREE enrichments in low marsh cores. These 

elements are enriched in dense “heavy 

minerals”—chromite (Morrison and others, 

2009), zircon (Hoskin and Ireland, 2000), and 

garnet (Grauch, 1989)—that require higher 

energies for mobilization and transport. Another 

line of evidence for a nearshore influence on low 

marsh sediment geochemistry is the higher 

magnitude of REENASC patterns in the low marsh 

compared to the middle and high marsh. Low 

marsh REENASC magnitudes approach those of 

San Francisco Bay sediment, suggesting the 

presence of nearshore sediment in low marsh 

cores. Therefore, some of the sediment 

geochemical heterogeneity across marsh 

elevations is attributable to inputs of nearshore 

sediment by waves and wakes in the low marsh, 

making low marsh sedimentary records less 

suitable than middle and high marsh records for 

studies about sediment derived from Corte 

Madera watershed. 

Diagenetic Heterogeneity

The covariance of Fe with Co, Ni, and Cu, 

and to a lesser extent manganese (Mn), in deep 

sediment horizons of Corte Madera Marsh 

suggests that a diagenetic process was 

responsible for the heterogeneity of these metals 

in the sediment column. Sedimentary Fe is very 

sensitive to microbial (diagenetic) reduction-
18

oxidation (redox) processes. Microbes reduce Fe 

and sulfate, making the ingredients for pyrite 

available. When pyrite precipitates in nearshore 

sediment, transition metals Co, Cu, and Ni 

commonly co-precipitate resulting in positive 

correlations with Fe in certain sediment horizons 

(Lord and Church, 1983; Huerta-Diaz and Morse, 

1992), similar to the measurements in Corte 

Madera Marsh. Because subsurface redox 

processes can be site-specific, they can result in 

heterogeneous distributions of diagenetically 

sensitive elements in reducing marsh sediment. 

Ecological Implications of Diagenetic Metal Enrichments 

Diagenetic enrichments of sedimentary Cu 

and Ni are of concern because they can have 

adverse effects on biota (MacDonald, 1994). Cu 

contents of Corte Madera Marsh sediments 

[mean=47 ± 10 (1σ) ppm, range=31–98 ppm] 

were less than the level at which adverse 

biological effects usually occur (108 ppm) 

(Florida Department of Environmental 

Protection, 1994). The Ni content of Corte 

Madera Marsh sediment, on the other hand 

[mean=93±11 (1σ) ppm, range=64–129 ppm], 

always exceeded this level (43 ppm) (Florida 

Department of Environmental Protection, 1994) 

because of a high natural geologic background 

(Hornberger and others, 1999; Yee and others, 

2007; Morrison and others, 2009). 

Historical Inputs to Corte Madera Marsh 

Fluvial Sediment Inputs 

The primary fluvial sources of sediment to 

Corte Madera Marsh—the Sacramento and San 

Joaquin Rivers and Corte Madera Creek—had 

distinct geochemical signatures imparted by the 

rocks of their respective watersheds. However, 

sediment geochemical signatures in Corte 

Madera Marsh have varied little over historical 

time scales despite large human-induced 

perturbations to the source and supply of 

sediment to San Francisco Bay. One exception 

was a marsh-wide shift in REENASC patterns and 

magnitudes around the turn of the 20th century 

that correspond with two large California floods 

in 1906 and 1909. The lack of increases of SAC 

and SJ geochemical indicators commensurate 

with the timing and magnitude of decadal-scale 

perturbations suggests that the geochemical 

composition of Corte Madera Marsh sediment 

was not very sensitive to sediment-input changes 

originating at the Delta. One explanation for this 

decoupling could be that the decades-long 

residence time of sediment in the northern reach 

of San Francisco Bay (Krone, 1979) combined 

with the distance (60 km) between the Delta and 

Corte Madera Marsh contributed to an 

attenuation or dilution of river-borne sedimentary 

signals. Another possible explanation for the 

discrepancy between expected and measured 

geochemical variations in Corte Madera Marsh is 

that historical sedimentological changes affected 

a coarser size fraction (sand-sized and larger 

particles) than typically accumulates in tidal 

marshes. 

The element rubidium (Rb) was not 

investigated here as a source-rock indicator 

because it is removed from parent rocks by 

weathering processes, yet its pattern of variation 

in Corte Madera Marsh sediment appears 

compelling. Rb is hosted in micas (biotite, 

muscovite) and potassium-rich feldspars (Mason 

and Moore, 1982), minerals characteristic of 

Sierra granite. During weathering, Rb is removed 

from primary minerals, adsorbs to secondary 

clays, and can be transported with the clay 

fraction (Nesbitt and others, 1980). In Corte 

Madera Marsh sediment, Al-normalized Rb ratios 

have a dog-leg pattern of variation: ratios are 

highest pre-disturbance; decrease quasi-linearly 

over a 20 year-long period beginning around 

1860 or 1890; then stabilize at values that are 11–

17 percent lower through the present day (fig. 

11). The discrepancy in the date of the apparent 

shift in the high marsh of Transect S could be 

related to an error in the age-depth model in older 

sediment horizons. The dog-leg pattern suggests 
19

Figure 11. Graph showing historical variations of Al-normalized Rb content of fine sediment in the three Corte Madera Marsh 

cores that spanned the period from pre-disturbance to present. 

there was a period of mixing of the pre-1860 

inventory of transportable sediment in San 

Francisco Bay and a new, lower-Rb end member, 

and this period of mixing roughly coincided with 

the period when hydraulic mining inputs were 

greatest. The end result of the inferred input of 

lower-Rb sediment was a compositional shift of 

the transportable sediment inventory in San 

Francisco Bay that has persisted until present 

day. 

Contaminant Inputs 

Previous investigations of Pb and Pb 

isotopes in San Francisco Bay sediment cores 

identified an anthropogenic Pb increase 

(Hornberger and others, 1999; Ritson and others, 

1999) but were unable to distinguish between 

smelter emissions and leaded gasoline aerosols as 

potential sources because of the similarity of 

their isotopic compositions (Rabinowitz and 

Wetherill, 1972; Ritson and others, 1999). The 

CRS age model forecasts initial modest increases 

in marsh Pb contents (to about 40 ppm) several 

decades prior to the introduction of leaded 

gasoline in 1923, which uniquely ascribes this 

initial Pb increase to smelter emissions. Highest 

Pb enrichments in marsh sediment, over 400 

ppm, occurred during a period when both the 

smelter and leaded gasoline were in use. Two 

lines of evidence point to a smelter source for the 

highest degree of Pb contamination in the 

sediment record of Corte Madera Marsh. First, 

Pb enrichments were accompanied by Sb 

enrichments; Sb is a component of Pb ore and cooccurs with Pb in emissions and fallout from 

smelters (Ragaini and others, 1977). Second, the 

magnitude of the Pb enrichment in Corte Madera 

Marsh, more than 600 m from the highway, was 

higher than would be expected from a vehicular 

source. Around major highways, soil Pb levels 

decrease exponentially within a few hundred 

meters of the road, reaching levels of 10s ppm 

(Ratcliffe, 1982; Trombulak and Frissell, 2000). 

Leaded gasoline consumption peaked in the early 

1970s (Dunlap and others, 2000) and this source 

likely accounted for moderate Pb enrichments in 

marsh sediment between 1960 and 1980 that 

were unaccompanied by Sb enrichments. 

Current Sediment Budgets: Are Local 

Watersheds Making up the Difference? 

According to calculations by Schoellhamer 

and others (2005), normal water years are 

currently characterized by about equal amounts 

of sediment entering San Francisco Bay from 

local watersheds as through the Delta, whereas 
20

during 1955–90 sediment entering through the 

Delta was over a third higher. These patterns 

raise the question of whether sediment from local 

watersheds is playing a greater role in marsh 

accretion than in the past. In Corte Madera 

Marsh, the upper 6 or 8 cm of the sediment 

column correspond to the period used by 

Schoellhamer and others (2005) to describe the 

current sediment input period for San Francisco 

Bay. There was little indication based on 

sediment geochemistry that the proportion of 

sediment from the local watershed of Corte 

Madera Creek has increased over the last 20 

years. Geochemical source-rock indicators were 

generally no different in the upper 6 or 8 cm of 

marsh sediment than in underlying horizons. One 

exception was the element Ni, which is enriched 

in mafic and ultramafic rocks, serpentine, and 

wastewater. In one of the six cores (middle marsh 

of Transect S), Al-normalized Ni contents 

increased almost 30 percent between about 1987 

and 2010. While this pattern is consistent with 

the expectation of greater local sediment input, it 

does not co-occur along Transect N, the region of 

the marsh likely to contain a local watershed 

geochemical signal, and is thus too localized to 

be conclusive at this time. 

Conclusions 

Decreasing sediment inflows through the 

Sacramento-San Joaquin River Delta to San 

Francisco Bay raise concerns about the supply of 

sediment for future tidal marsh accretion. A 

sediment geochemical approach was used in 

Corte Madera Marsh, a relatively undisturbed 

natural marsh, to explore the question– are local 

watersheds making up the difference? 

Sedimentary records recovered from Corte 

Madera Marsh spanned the period from around 

1830 to 2010, according to sediment 

chronologies based on the assumption of a 

constant rate of radionuclide supply and the 

linear extrapolation of age-depth relationships to 

sediment horizons that could not be dated 

directly. Over the last 150 years there have been 

large perturbations to the amount and source of 

sediment entering San Francisco Bay through the 

Sacramento-San Joaquin River Delta, and the 

fine fraction (silt- and clay-sized particles) of this 

sediment is geochemically distinct from fine 

sediment from Corte Madera watershed and San 

Francisco Bay, being enriched in Cr, Zr, Sc, and 

HREE (SAC); and Th and TOT REE (SJ). 

Historical variations of these geochemical 

indicators were surprisingly small in the fine 

fraction of Corte Madera Marsh sediment, 

suggesting that there was not a quantitative 

relationship between fine sediment entering San 

Francisco Bay through the Delta and fine 

sediment accumulating in Corte Madera Marsh. 

There was a degree of marsh sediment 

geochemical heterogeneity that appeared to be 

related to the location of sediment cores relative 

to the nearshore edge of the marsh and Corte 

Madera Creek. Because of marsh 

geomorphology, sediment records at middle and 

high elevations of the northern region of Corte 

Madera Marsh were most likely to receive 

sediment inputs from the local watershed. 

However, there was little indication based on 

sediment geochemical indicators that local 

watershed inputs to the marsh have changed. 

Rather, the fine sediment sources to Corte 

Madera Marsh during 1990–2010 appear to be 

the same as the historical sources. This finding 

points to a large volume of relatively 

homogeneous fine sediment that has persisted for 

decades as the primary source of sediment to 

Corte Madera Marsh, and is supported by 

historical sedimentary Rb contents. Transportable 

fine sediment in San Francisco Bay could be this 

source. If this is the case, then Corte Madera and 

other marshes around San Francisco Bay could 

be buffered against changes in sediment supply 

through the Sacramento-San Joaquin Delta and 

local watersheds as long as there is a reservoir of 

transportable fine sediment in San Francisco Bay 

(Reed, 1995). Legacy inputs of the contaminant 

Pb to Corte Madera Marsh are present 10–30 cm 

below the marsh surface and can be attributed to 

smelter emissions in sediment horizons in which 

Sb enrichments co-vary with Pb enrichments, and 
21

to leaded gasoline aerosols when Sb contents are 

close to the natural geologic background. 

Acknowledgments 

The authors thank the San Francisco 

District of the U.S. Army Corps of Engineers for 

funding that made this work possible; the 

California Department of Fish and Wildlife for 

permission to access Corte Madera Ecological 

Reserve; the San Francisco Bay Conservation 

and Development Commission for program 

coordination; John Callaway at the University of 

San Francisco for access to sediment core 

material and chronologies; Amy Foxgrover of the 

U.S. Geological Survey for assistance with maps; 

Leticia Diaz of the U.S. Geological Survey for 

assistance with sample processing; and 

Christopher Conaway and Maureen DowningKunz for suggestions that improved this 

manuscript. 

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