The Dynamics of Fine-Grain Sediment 

Dredged from Santa Cruz Harbor 

By Curt D. Storlazzi, Christopher H. Conaway, M. Katherine Presto, Joshua B. Logan, 

Katherine Cronin, Maarten van Ormondt, Jamie Lescinski, E. Lynne Harden, Jessica R. 

Lacy, and Pieter K. Tonnon 

Photo of Santa Cruz Harbor on 10/03/2009 by the California Coastal Record Project 

http://www.californiacoastline.org/

Open-File Report 2011-1045 

U.S. Department of the Interior

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

KEN SALAZAR, Secretary 

U.S. Geological Survey 

Marcia K. McNutt, Director 

U.S. Geological Survey, Reston, Virginia: 2011 

For product and ordering information: 

World Wide Web: http://www.usgs.gov/pubprod 

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its natural and living resources, natural hazards, and the environment: 

World Wide Web: http://www.usgs.gov 

Telephone: 1-888-ASK-USGS 

Suggested citation: 

Storlazzi, C.D., Conaway, C.H., Presto, M.K., Logan, J.B., Cronin, K., van Ormondt, 

M., Lescinski, J., Harden, E.L., Lacy, J.R., and Tonnon, P.K., 2011. The dynamics of 

fine-grain sediment dredged from Santa Cruz Harbor: USGS Open-File Report 2011-

1045, 110 p. [http://pubs.usgs.gov/of/2011/1045/] 

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 .....................................................................................................................1

Background Information and Project Objectives ...........................................................2 

Study Area.....................................................................................................................2 

Operations.......................................................................................................................4 

Time-Series Physical Process and Turbidity Measurements ........................................4 

Grain-Size and Turbidity Mapping ................................................................................6 

Suspended-Sediment Sampling for Laboratory Analyses ............................................7 

Numerical Wave, Circulation, and Sediment-Transport Modeling ................................7 

Equipment and Data Review ........................................................................................7 

Research Platform and Field Operations.....................................................................12 

Data Acquisition and Quality.......................................................................................12 

Results...........................................................................................................................12 

Inner Harbor Dredge Sediment Discharge ..................................................................12 

Regional Oceanographic and Atmospheric Forcing ....................................................13 

River Water Discharge.................................................................................................13 

Tides............................................................................................................................13 

Waves..........................................................................................................................13 

Currents.......................................................................................................................16 

Turbidity.......................................................................................................................16 

Temperature ................................................................................................................16 

Salinity .........................................................................................................................22 

Spatial Variations in Water-Column Properties ..........................................................22 

Spatial Variations in Beach and Seabed Surficial Grain Size .....................................22 

Trapped Sediment Accumulation and Grain Size .......................................................26 

Sediment Geochemistry .............................................................................................26 

Numerical Wave, Circulation, and Sediment-Transport Modeling ..............................30 

Discussion.....................................................................................................................41 

Distribution of Forcing Conditions................................................................................41 

Spatial and Temporal Variability in Circulation Patterns and Water-Column 

Properties ....................................................................................................................42 

Sediment Geochemistry .............................................................................................49 

Sediment Dynamics ....................................................................................................50 

Summary of Findings...................................................................................................55 

Acknowledgments........................................................................................................58 

References Cited ..........................................................................................................58 

Additional Digital Information .....................................................................................62 

Direct Contact Information ..........................................................................................62 
iv

Figures 

Figure 1. Map of the study area in northern Monterey Bay, California ............................3 

Figure 2. Location of the survey sites, moorings, and instrument packages ...................5 

Figure 3. Harbor dredging and Terrestrial Imaging System (TIS) data..........................14 

Figure 4. Regional meteorologic, oceanographic, and fluvial data during the 

study period ....................................................................................................................15 

Figure 5. Tides, waves, currents, and turbidity at Tripod A (Sea Floor Observatory 

at 9 m depth)...................................................................................................................17 

Figure 6. Tides, waves, currents, and turbidity at Tripod B (12 m depth) ......................18

Figure 7. Tides, waves, currents, and turbidity at Tripod C (20 m depth)......................19

Figure 8. Tides, waves, currents, and turbidity at Tripod D (30 m depth)......................20

Figure 9. Principal axis ellipses and mean current speeds and directions at the 

study sites.......................................................................................................................21

Figure 10. Temperature and salinity data during the study period.................................23

Figure 11. Spatial variability in optical backscatter during the surveys..........................24 

Figure 12. Spatial variability in light transmission during the surveys............................25 

Figure 13. Spatial variability in beach and seabed surficial grain size...........................27

Figure 14. Grain size distribution of sediment on the seabed and collected in 

sediment traps ................................................................................................................28

Figure 15. FLOW model computational grids ................................................................31 

Figure 16. Initial conditions in the CCA FLOW model....................................................32

Figure 17. Observation points in the MBY FLOW model...............................................33

Figure 18. WAVE model computational grids ................................................................34

Figure 19. Details of FLOW and WAVE models’ computational grid SC01...................35

Figure 20. Map of modeled wave heights......................................................................36

Figure 21. Map of modeled currents over a tidal cycle during small wave conditions ...37

Figure 22. Map of modeled currents over a tidal cycle during large wave conditions....38

Figure 23. Map of modeled suspended-sediment concentrations over a tidal cycle .....40 

Figure 24. Map of modeled sediment accumulation during the 2009 dredge 

disposal project...............................................................................................................41 

Figure 25. Map of modeled sediment accumulation at two times the daily rate of 

fine-grain sediment discharge (650 m3

/day) of the 2009 dredge disposal project..........42 

Figure 26. Map of modeled sediment accumulation at four times the daily rate of 

fine-grain sediment discharge (975 m3

/day) of the 2009 dredge disposal project..........43 

Figure 27. Map of modeled combined maximum bed shear stress ...............................44

Figure 28. Wave, current, and combined shear stresses at the main study sites..........46

Figure 29. Suspended-sediment concentrations as a function of combined shear 

stress at the main study sites .........................................................................................47

Figure 30. Daily mean suspended-sediment flux before the start of dredging...............51

Figure 31. Daily mean suspended-sediment flux during the dredging...........................52

Figure 32. Daily mean suspended-sediment flux after the dredging..............................53

Figure 33. Daily mean suspended-sediment flux during the storm and flood after 

the dredging....................................................................................................................54

Figure 34. Regional meteorologic, oceanographic, fluvial, and resulting 

turbidity data during the study period..............................................................................56
v

Tables 

Table 1. Experiment personnel ......................................................................................63 

Table 2. Instrument package sensors ............................................................................64 

Table 3. Instrument package location information..........................................................65 

Table 4. Flying Eyeball sample location information ......................................................66 

Table 5. Beach Ball sample location information ...........................................................67 

Table 6. Water Column Profiler cast location information ..............................................68 

Table 7. Sediment sample location and depth information ............................................68 

Table 8. Sediment settling velocities..............................................................................69 

Table 9. Harbor daily dredge volumes ...........................................................................69

Table 10. Meteorologic, oceanographic, and river discharge statistics..........................70 

Table 11. Wave statistics ...............................................................................................70 

Table 12. Current statistics.............................................................................................71 

Table 13. Turbidity statistics...........................................................................................72 

Table 14. Temperature statistics....................................................................................72 

Table 15. Salinity statistics.............................................................................................73 

Table 16. Sediment sample grain-size information ........................................................73 

Table 17. Carbon and nitrogen signatures of sediment samples...................................74 

Table 18. Short-lived radionuclide activity in sediment samples....................................75

Table 19. Elemental composition of harbor sediment samples......................................76

Table 20. Elemental composition of trap sediment: First deployment............................77

Table 21. Elemental composition of trap sediment: Second deployment.......................78

Table 22. Elemental composition of trap sediment: Third deployment...........................79

Table 23. Elemental composition of seabed and tripod sediment samples ...................80 

Table 24. Sediment-flux statistics...................................................................................81 

Appendixes 

Appendix 1. Optical Backscatter Sensor (OBS) Suspended Sediment 

Concentration (SSC) Calibration Information .................................................................83 

Appendix 2. Acoustic Doppler Current Meters (ADCM) Suspended Sediment 

Concentration (SSC) Calibration Information .................................................................85 

Appendix 3. Water Column Profiler (WCP) Optical Backscatter Profiles ......................86 

Appendix 4. Water Column Profiler (WCP) Light Transmission Profiles.......................89 

Appendix 5. Water Column Profiler (WCP) Chlorophyll Profiles ...................................92 

Appendix 6. Beach Ball (BB) and Flying Eyeball (FE) Surficial Grain-Size 

Measurements................................................................................................................95 

Appendix 7. Numerical Model Calibration and Validation Information ..........................99 

Appendix 8. 2009 Year Day to Calendar Day Conversion Table ................................110 
The Dynamics of Fine-Grain Sediment 

Dredged from Santa Cruz Harbor 

By Curt D. Storlazzi1

, Christopher H. Conaway1, M. Katherine Presto1, Joshua B. 

Logan1

, Katherine Cronin2, Maarten van Ormondt2, Jamie Lescinski2, E. Lynne Harden3, 

Jessica R. Lacy1, and Pieter K. Tonnon2 

1

U.S. Geological Survey, Pacific Coastal and Marine Science Center, 400 Natural Bridges Drive, Santa 

Cruz, CA 95060 

2

Deltares, P.O. Box 177, 2600MH Delft, the Netherlands 

3

University of California at Santa Cruz, Earth and Planetary Sciences Department, 1156 High Street, 

Santa Cruz, CA 95064 

Abstract 

 In the fall and early winter of 2009, a demonstration project was done at Santa Cruz 

Harbor, California, to determine if 450 m3

/day of predominantly (71 percent) mud-sized 

sediment could be dredged from the inner portion of the harbor and discharged to the coastal 

ocean without significant impacts to the beach and inner shelf. During the project, more than 

7600 m3 of sediment (~5400 m3 of fine-grain material) was dredged during 17 days and 

discharged approximately 60 m offshore of the harbor at a depth of 2 m on the inner shelf. The 

U.S. Geological Survey’s Pacific Coastal and Marine Science Center was funded by the U.S. 

Army Corps of Engineers and the Santa Cruz Port District to do an integrated mapping and 

process study to investigate the fate of the mud-sized sediment dredged from the inner portion of 

Santa Cruz Harbor and to determine if any of the fine-grain material settled out on the shoreline 

and/or inner shelf during the fall and early winter of 2009. This was done by collecting highresolution oceanographic and sediment geochemical measurements along the shoreline and on 

the continental shelf of northern Monterey Bay to monitor the fine-grain sediment dredged from 

Santa Cruz Harbor and discharged onto the inner shelf. These in place measurements, in 

conjunction with beach, water column, and seabed surveys, were used as boundary and 

calibration information for a three-dimensional numerical circulation and sediment dynamics 

model to better understand the fate of the fine-grain sediment dredged from Santa Cruz Harbor 

and the potential consequences of disposing this type of material on the beach and on the 

northern Monterey Bay continental shelf. 

Introduction

 Harbor depths and channels commonly are maintained through active dredging programs. 

The dredged material can be deposited in a variety of locations, including offshore and nearshore 

disposal sites. Because transporting material offshore for disposal can be costly, nearshore 

disposal can be a more cost effective alternative. However, due to the high percentage of finegrain material often found in harbors (from terrestrial run-off and settlement processes), 

nearshore disposal is not necessarily an environmentally ideal solution. Nearshore dredgematerial disposal is not currently a common practice in central California because of the potential 

negative impacts, caused by turbidity or fine-grain sedimentation, on the sensitive species and 

habitats managed by the National Marine Sanctuary Program. Currently, regulations prohibit the 
2

discharge of sediment that is more than 20 percent mud (<0.063 mm) by mass into the coastal 

ocean. The 20 percent mud threshold currently is under consideration by a variety of 

management and research agencies to determine whether it is an appropriate guideline for all 

environments. 

Background Information and Project Objectives 

The area offshore of the City of Santa Cruz in northern Monterey Bay, California, is a 

complicated coastal setting of sea cliffs, pocket beaches, and low-relief bedrock reefs (Storlazzi 

and others, 2008) that is impacted by a variable wave climate due to its south-facing orientation 

(Storlazzi and others, 2007). Spatially- and temporally-variable wave conditions and the 

complex, shallow, rocky seabed in this area have restricted comprehensive field surveys in the 

past. Recent innovations in field techniques and equipment now make it possible to perform a 

detailed analysis of the sedimentological nature and physical processes operating on this type of 

complex coastline. Understanding the sedimentology and physical processes off Santa Cruz is 

important not only because it is part of the Monterey Bay National Marine Sanctuary (MBNMS) 

and encompasses rich coastal and marine ecosystems in the area, but also because these same 

environments are important areas for local economic and recreational activities. It is increasingly 

important to provide scientific data that allow government agencies involved with dredgedisposal operations to make the best informed management decisions. 

The goal of the project described here was to determine the behavior of 5,400 m3 of finegrain sediment dredged from the inner portion of Santa Cruz Harbor and discharged at a depth of 

2 m approximately 60 m offshore. This work follows a number of previous studies investigating 

the discharge of smaller volumes of fine-grain sediment from Santa Cruz Harbor on the inner 

shelf (Griggs, 1991; McLaren, 2000; Watt and Greene, 2002; Watt, 2003; Sea Engineering Inc., 

2006), all of which suggested that fine-grain sediment dredged from the harbor would not 

deposit in observable quantities on the inner shelf. Similar to the previous projects, part of this 

project was designed to determine if the fine-grain material dredged from the inner part of Santa 

Cruz Harbor and disposed approximately 60 m offshore at a depth of 2 m would deposit in 

observable quantities along the shoreline and on the inner shelf. However, the bulk of this effort 

was intended to provide insight on the physical processes controlling the persistence (or lack 

thereof) of fine-grain dredge material on, and its advection off, the inner shelf to the mid-shelf 

(30-70 m depth) mud belt identified by Edwards (2002). 

These measurements support the ongoing process studies being done as part of the U.S. 

Geological Survey’s Pacific Coastal and Marine Science Center (USGS-PCMSC) Program’s 

Benthic Habitats (Pacific) and Applied Sediment Transport Projects; the ultimate goal is to better 

understand the impact of sediment dynamics on benthic habitats along the U.S. west coast. The 

following report details the study location, the experimental set-up, in place observations, and a 

numerical modeling investigation to determine the transport pathways of the fine-grain dredged 

material.

Study Area 

Spatial and temporal measurements of oceanographic and sedimentologic conditions 

were made during the fall and early winter of 2009 in northern Monterey Bay, California (fig. 1). 

The coast of central California lies along an active tectonic margin whose uplift has resulted in a 

rugged coastline with high sea cliffs cut into coastal mountains, narrow river valleys, and a 

relatively narrow continental shelf. The Monterey Bay area lies within a dextral strike-slip 

tectonic setting that comprises the transform boundary between the Pacific and North American 

tectonic plates. The shoreline is characterized by steep (up to 100 m high), actively eroding 

coastal bluffs that often are incised into uplifted marine terraces and are commonly 
3

FIGURE 1. Map of the physiography of the study area in northern Monterey Bay, California; data from the U.S. 

Geological Survey’s California Seafloor Mapping Program (http://walrus.wr.usgs.gov/mapping/csmp/). Darker, smooth 

areas represent sediment-covered seabed characterized by fine sand and mud; the lighter but smooth areas are 

sediment-covered seabed characterized by coarser sand; the lighter, rough areas are regions where bedrock is 

exposed on the seabed. The red and yellow shades denote shallower areas, and the blues and purples denote deep 

areas. The heavy dashed line defines the project study area. 

fronted by low, wave-cut shore platforms, or pocket beaches. These seacliffs are dissected at 

irregular intervals by larger pocket beaches that form at the mouths of coastal streams and by 

infrequent continuous beaches in sheltered bays. The small, steep perennial streams and a few 

larger rivers in northern Monterey Bay are the primary sources of coarse-grained sediment to the 

littoral environment (Best and Griggs, 1991). During the last glacial maximum at 22 ka, streams 

flowed across the exposed continental shelf and cut channels through the bedrock (Anima and 

others, 2002); the mouths of many of these streams were inundated during the Holocene 

transgression, forming low-gradient floodplains, coastal lagoons, and marshes (Griggs and 

Savoy, 1985). The Santa Cruz Harbor was constructed by dredging Woods Lagoon in the 1960s, 

and it receives perennial fluvial input from Arana Creek. The inner shelf is characterized by 

intermittent rock outcrops that support dense kelp forests and it is covered predominantly by 

medium- to fine-grain sand to the 30 m isobath, where the sediment transitions predominantly to 

silts and clays, an area termed the “mud belt” by Edwards (2002). Seacliff erosion, with longterm rates ranging from zero to >30 cm/year, is episodic and locally variable (Griggs and Savoy, 
4

1985), typically occurring during the infrequent combination of high tides and extreme storm 

waves. 

The offshore wave climate along central California can be characterized by three 

dominant modes: the Northern Hemisphere swell, the Southern Hemisphere swell, and local 

wind-driven seas (Storlazzi and Wingfield, 2005). The Northern Hemisphere swell typically is 

generated by cyclones in the North Pacific Ocean off the Aleutian Islands during the winter 

months (November-March) and can attain deep-water wave heights exceeding 8 m. The 

Southern Hemisphere swell is generated by storms off New Zealand, Indonesia, or Central and 

South America during summer months and, although generally itproduces smaller waves than 

the Northern Hemisphere swell, this swell often has very long periods (15+ s). The local seas 

typically develop rapidly when low-pressure systems track near central California in the winter 

months or when strong sea breezes are generated during the spring and summer. Storms with 

deep-water wave heights in excess of 5 m occur five times a year on average. 

Operations 

This section provides an overview of the different aspects of the project and information 

about the personnel, equipment, and field operations used during the study. See table 1 for a list 

of personnel involved in the experiment and tables 2 through 6 for complete listings of 

instrument and deployment information. 

An integrated study to characterize both the sedimentological nature of the coastline and 

inner shelf and the spatial and temporal variation in physical processes in northern Monterey Bay 

was done during the fall and early winter of 2009 (fig. 2). The data were collected by means of 

beach and inner shelf mapping, water-column surveys, geochemical analyses of suspended 

sediment, oceanographic instrumentation, and numerical modeling. All of the data will be 

collected according to USGS standards and, thus, be the foundation for any future comparisons. 

These surveys, initiated in October 2009 and running through December 2009, determined the 

impacts of the dredge-disposal demonstration project on the study area and provide insight into 

pathway(s) of the fine-grain sediment off the inner shelf.

Time-Series Physical Process and Turbidity Measurements

The USGS Sea Floor Observatory off the end of the Santa Cruz Wharf overlapped with 

the demonstration project. This system, the only one of its kind in the world, provided 

continuous measurements of the forcing physical mechanisms [tides, waves, currents, and/or 

internal waves (Storlazzi and Jaffe, 2002; Storlazzi and others, 2003)] that drive sediment 

dynamics and the resulting suspended-sediment concentrations and surficial seabed grain sizes. 

This real-time, cabled, observational platform system was supplemented by three additional selfcontained seabed tripods from October 2009 through December 2009 to make similar physical 

measurements (tide, wave, current, and suspended-sediment concentration [turbidity]) close to 

the discharge site off the harbor and further offshore near the 30 m isobath, where the mid-shelf 

mud belt begins (fig. 2). The time series data from these four instrument packages were used to: 

(1) determine if the ambient oceanographic conditions that typify the northern part of the bay are 

quiescent enough for fine-grain dredge sediment discharged during the project to fall out of 

suspension and accumulate in observable quantities on the inner shelf, or if the conditions are 

energetic enough to keep the fine-grain sediment in suspension; (2) provide continuous time 

series measurements of suspended-sediment concentrations starting before and running through 

the course of the demonstration project to determine the magnitude and direction of sediment 

flux; and (3) provide the necessary boundary and calibration information for a numerical model 

of the dredge discharge plume (see below). 
5

FIGURE 2. Map showing the location of the survey sites, moorings, and instrument packages. The instrument sites 

and survey area cover both the San Lorenzo River and the Santa Cruz Harbor, the two potential significant inputs of 

sediment to the study area, and extend offshore to the 30 m isobath where the mid-shelf “mud belt” begins. 
6

Grain-Size and Turbidity Mapping 

Seabed Grain-Size Mapping 

The monthly USGS Flying Eyeball (Chezar and Rubin, 2004; Rubin and others, 2007) 

surveys were extended through the end of the demonstration project in the 2009-2010 winter. 

These surveys of surficial seabed-sediment grain size, taken at 42 locations off Santa Cruz in 

water depths between 5 m and 25 m (fig. 2), were carried out during the 2008-2009 winter to 

investigate the impact of river floods and winter storms on the sediment distribution in northern 

Monterey Bay. The Flying Eyeball (FE) system uses a magnified digital image of the seabed to 

measure grain size. Because the measurements are based only on the surface layer, these data are 

more accurate than grab samples that integrate both surface and subsurface grains. This makes 

the FE system uniquely suited to measure the active surface layer that would result from any 

dredge material settling on the seabed. FE surveys were focused on the dredge-disposal area of 

operations. The surveys were completed before, during, and following the demonstration project 

to determine if the dredge-disposal operations resulted in observable deposition of fine-grain 

material on the seabed in the study area. FE surveys during winter 2008-2009 provided a first-ofits-kind view of the heterogeneous nature, both in space and time, of seabed surficial grain-size 

variability on the inner shelf and provided invaluable background information that aided in the 

analysis of the data acquired during the demonstration project. 

Beach Grain Size 

The USGS Beach Ball (BB) uses similar technology to the FE but in a portable, handheld package. BB surveys were done in the swash zone and at the wet/dry line between Cowell 

Beach and Black Point (fig. 2) to determine if fine-grain dredge material was being deposited 

onshore. These surveys were completed before, during, and after the demonstration project in 

concert with the offshore FE surveys to determine if the dredge-disposal operations resulted in 

significant deposition of fine-grain material along the shoreline in the study area. 

Together, the BB and FE provided quantitative data on surficial sediment grain size from 

the wet/dry line on the subaerial beach, through the nearshore, and to the mud belt on the mid 

continental shelf.

Beach Monitoring 

The quantitative data provided by the BB and FE systems were supplemented by visual 

observations made by Santa Cruz Port District personnel on the beaches adjacent to the disposal 

zone at all times during dredging operations. Personnel made observational sweeps and collected 

digital photography of the beaches peripheral to the disposal area between the San Lorenzo River 

mouth (to the west) and 20th Avenue (to the east). These sweeps were done to determine if finegrain sediment (mud) from the dredge-disposal operations were impacting the beach and to halt 

dredge operations if impact occurred. The data from these surveys are not included in this report. 

Nearshore Turbidity Mapping 

Vertical profiles of water temperature, salinity, and turbidity were made using a 

conductivity-temperature-depth (CTD) profiler with an additional optical backscatter (OBS), 

transmissometer (Xmiss), PAR (photosynthetically-active radiation), and chlorophyll (chl) 

sensors. These surveys were done in concert with the Beach Ball and Flying Eyeball surveys 

before, during, and after the end of the demonstration project at 14 of the Flying Eyeball 

sampling stations on the inner shelf (fig. 2). These profiles were acquired to determine if the 

dredge-disposal operations resulted in significant changes in water-column properties (for 
7

example, turbidity and light availability for photosynthetic organisms) in the study area. In 

addition to this, time-series imagery of the dredge-disposal outfall area was collected using the 

USGS Terrestrial Imaging System (TIS), which was deployed to provide visual records on the 

impact of storms, waves, and the dredge-disposal operations on sea surface-water properties in 

the study area. 

Suspended Sediment Sampling and Geochemical Source Determinations 

The USGS deployed four sediment traps on moorings across the inner shelf to collect 

material for geologic and geochemical analyses. Geochemical analyses were done on the 

collected material to try to determine if the sediment transiting the area was dredge material, 

relict shelf sediment, or material delivered by the San Lorenzo River during the course of the 

study. The geochemical data, in conjunction with the data from the tripods and Flying Eyeball, 

provided insight into the presence and quantity of dredge material on the inner shelf. 

Numerical Wave, Circulation, and Sediment Transport Modeling 

In place sensor data was combined with larger-scale wave models, NCEP-NAM wind 

model products (Gemmill and Peters, 1997), HF radar sea-surface currents (Paduan and Cook, 

1997), TOPEX/POSIDEN tides (Egbert and Erofeeva, 2002), and HYCOM circulation model 

data (Halliwell, 1998) to provide boundary information and calibration data for a coupled wavecurrent-sediment transport numerical model for the project area. The Delft3D package was used 

to develop a model of the study area in order to extrapolate the limited Eulerian point 

measurements spatially. Due to the errors inherent to such modeling, the goal was not to model 

the dredge-disposal plume with extreme precision (which would be difficult), but rather to 

examine the effects of waves, winds, and tides on circulation and sediment transport through the 

study area to gain insight into the fate of the fine-grain dredge material. 

Equipment and Data Review 

Tripods 

Four upward-looking acoustic Doppler current meters (ADCM) and three downwardlooking ADCMs were mounted on four tripods between the 9 m and 30 m isobaths in northern 

Monterey Bay (Tripods A-D, fig. 2). The upward-looking ADCMs sampled from just above the 

tripods (2 m above the seabed) up to the sea surface to collect data for calculating tides (m) and 

profiles of mean current speeds (m/s) and mean current directions (°True). Directional wave data 

also were recorded by the ADCMs; these data included significant wave height (m), dominant 

wave period (s), mean wave direction (°True), and directional spread (°). The downward-looking 

ADCMs sampled 0.5-m above the seabed to allow calculation of near-bed mean current speeds 

(m/s) and mean current directions (°True). Acoustic backscatter data (dB) collected from the 

ADCMs for the current measurements also provided information on the amount of particulates in 

the water column and are used as a qualitative measurement of turbidity. 

 Four conductivity and temperature (CT) sensors measured water temperature (°C) and 

doivity (S/m), from which salinity (PSU) was calculated. Sensor types and locations are listed in 

tables 2 and 3. Six 880-μm optical backscatter sensors (OBS) recorded the amount of infrared 

light reflected off particles in the water column, which is a function of the particle size and 

density of particles. These OBSs provided turbidity data in either raw voltages or Nephelometric 

Turbidity Units (NTU). The OBSs were calibrated to suspended-sediment concentrations (SSC) 

in mg/l in the laboratory using suspended sediment collected from the tripods (appendix 1). The 

OBS on Tripod A was calibrated to NTUs via field cross-calibration with the water-column 
8

profiler’s (WCP) OBS. The OBSs on the tripods were mounted at or near the level of the ADCM 

sampling volumes in order for the OBS data to be correlated with the along- and cross-shore 

velocity data from the ADCMs to calculate suspended-sediment flux (appendix 2). All the sensor 

types and locations are listed in tables 2 and 3. 

Flying Eyeball 

Surveys of seabed grain size were made using FE digital imaging system (Chezar and 

Rubin, 2004; Rubin and others, 2007) to collect information on seabed surficial sediment grain 

size. At each survey location, a minimum of three images were acquired to account for withinsite variability; the resulting three (at a minimum) grain sizes were then averaged to produce one 

statistically significant mean grain-size value for each location using the algorithms derived by 

Buscombe and Messelink (2009) and Buscombe and others (2010). The FE position information 

is listed in table 4. The FE surveys were completed before [09/23/2009 (2009 YD 266), 

10/23/2009 (2009 YD 296)], during [10/29/2009 (2009 YD 302), 11/10/2009 (2009 YD 314)], 

and after [11/24/2009 (2009 YD 328)] the dredge disposal. 

Beach Ball 

Surveys of beach grain size were made using the BB digital imaging system to collect 

information on subaerial beach surficial sediment grain size. At each survey location, a minimum 

of three images were acquired in the swash zone and a minimum of three samples were taken at 

the wet/dry line to account for variability over the course of a tidal cycle and within the swash 

zone (for example, beach cusp horns and troughs); the resulting six (at a minimum) grain sizes 

were then averaged to produce one statistically significant mean grain size-value for each 

location using the algorithms derived by Buscombe and Messelink (2009) and Buscombe and 

others (2010). The BB position information is listed in table 5. The BB surveys were completed 

before [10/23/2009 (2009 YD 296)], during [10/29/2009 (2009 YD 302), 11/10/2009 (2009 YD 

314)], and after [11/24/2009 (2009 YD 328)] the dredge disposal. 

Water Column Profiler 

Surveys of water-column properties were made using a CTD profiler with OBS, Xmiss, 

PAR, and chl sensors to collect vertical profiles of water temperature (°C), salinity (PSU), 

density (kg/m3

), turbidity (NTU), transmission (percent), PAR (mE), and chl (mg/m3). The 

surveys were done to address both along- and cross-shore variability in water-column properties 

in northern Monterey Bay and to put the high temporal resolution but spatially limited 

measurements made by the CTs and SLOBSs on the tripods in the context of larger spatial 

patterns throughout the study area. The greater density of points near the coastline were 

established to identify areas where sediment might be entering the bay (San Lorenzo River or 

Santa Cruz Harbor dredging). The profiling extended offshore to the 30 m isobath to examine the 

extent of mixing with oceanic waters. 

The OBS on the WCP was calibrated to suspended-sediment concentrations (SSC) in 

mg/l using suspended-sediment samples collected by using a Niskin sampler at multiple 

locations throughout the survey area during the profiling operations. The total mass of suspended 

sediment in the water column during a given survey was calculated by summing the SSCs (in 

mass per volume) throughout the water column for each profile to determine a mass per area, 

then interpolating between all of the profiles to produce a total mass for the study area. The 

profiler data position information is listed in table 6. The WCP surveys were completed before 

[10/16/2009 (2009 YD 289), 10/28/2009 (2009 YD 301)], during [11/12/2009 (2009 YD 316)], 

and after [11/25/2009 (2009 YD 329), 12/14/2009 (2009 YD 348)] the dredge disposal. 
9

Terrestrial Imaging System (TIS) 

Imagery of the dredge-disposal outfall was collected using the TIS, which consists of a 

Harbortronics time-series digital-imaging system. This system is comprised of a Pentax K200D 

10-megapixel digital SLR camera, a control unit, and battery in a waterproof housing with an 

external solar panel. The TIS was mounted on the Santa Cruz Harbor lighthouse on the harbor 

entrance western jetty at an elevation of approximately 15 m. The TIS was oriented to provide an 

unobstructed view of the dredge-disposal outfall. This system collected a time series of hourly 

images to provide information on the natural frequency and duration of processes impacting the 

study area (sediment plumes, storms and waves). The TIS took images every hour throughout the 

deployment. The system’s deployment and location information is listed in tables 2 and 3. 

Sediment Collection and Grain-Size Analyses 

Sediment traps were deployed during the experiment (October 2009 - December 2009) to 

collect suspended sediment from the water column. The sediment traps, which consisted of a 78-

cm-long funnel, with an internal diameter of 26 cm at the top that tapered down to 4 cm, were 

deployed on moorings with their openings approximately 5 m above the seabed in a cross-shore 

array extending from the 10 m isobath to the 30 m isobath. A baffle was placed in the top of each 

tube trap to reduce turbulence and minimize disturbance by aquatic organisms (Bothner and 

others, 2006). Because of the energetics of the inner shelf environment, the traps did not measure 

net vertical sediment flux to the seabed. This is because material falling into the trap has a much 

lower potential for resuspension than the same material that settles on the adjacent seabed 

(Bothner and others, 2006). In addition, the traps may preferentially collect coarser particle sizes 

because of their higher settling velocity than finer particles. Particles with slow settling 

velocities relative to the circulation and exchange of water contained in the trap can be 

underrepresented in the collected samples (for example, Gardner and others, 1983; Baker and 

others, 1988). Sediment trap collection tubes were in place during 2009 Year Days 292–313, 

313–336, and 336–349, representing two periods during dredging times (early and late) and after 

dredging times (including post-dredging storm and flood). It should be noted that these collection 

times somewhat overlap the various pre- and post-dredging categories described elsewhere in 

this document. The sediment traps’ position and depth information is listed in table 7. 

In addition, seabed sediment-grab samples were collected by divers at the main study 

sites. The bulk grain sizes of the sediment samples were analyzed using Beckman Coulter 

Counter (silt and clay fractions) and 2 m settling tubes (sand fraction), and within each grain size 

fraction the percent carbonate was determined with a UIC Coulometer. The critical shear stresses 

for the initiation of transport were calculated using the modified Shield parameter methodology 

of Madsen (1999); the values for coarse sand, fine sand, and coarse silt (mud) transport are 0.372 

N/m2

, 0.185 N/m2, and 0.131 N/m2, respectively (table 8). 

Sediment Geochemistry 

Subsamples of suspended sediment collected in sediment traps and seabed sediment were 

processed for chemical analysis, including carbon and nitrogen isotopic and elemental 

composition, short-lived radioisotope activity, and trace-element composition in order to 

determine the sediment source (river, relect-shelf sediment, or dredge material). Efforts were 

taken to minimize contamination of samples for geochemical analysis by rinsing all parts of 

sampling equipment coming in contact with sediment with dilute HCl and with deionized water. 

The sediment traps were constructed avoiding contaminating materials wherever possible. 

During transport, sediment traps and collection tubes were protected in clean polyethylene bags, 

and handling of traps and sampling tools was done using clean polyethylene gloves whenever 
10

possible. Immediately before deployment, traps and collection tubes were conditioned with local 

seawater. 

In addition to suspended-sediment and seabed-sediment samples, samples of Santa Cruz 

Harbor material from the areas to be dredged (North Harbor areas A1, A2, A2A, A3, A4) were 

taken from sediment cores collected by Red Hills Environmental, Inc., in July 2009 using a 

Vibracore sampling system. Sampling was done using methods designed to minimize potential 

contamination, and subsamples were taken along the entire length of the sediment core. A 

technical report describing the Santa Cruz Harbor cores’ locations and physical and chemical 

characteristics was completed by Red Hills Environmental, Inc. After collection, sediment 

samples were immediately frozen to prevent microbial degradation. Samples for geochemical 

analysis were then freeze dried, disaggregated, dry sieved with a nylon mesh to less than 100-

μm, and then homogenized using a mortar and pestle. 

Analyses for carbon and nitrogen isotopic and elemental composition were done at the 

USGS Menlo Park Stable Isotope Laboratory in California. Approximately 6 mg of sediment 

was weighed into a silver capsule and treated to remove carbonate material in a sealed chamber 

(desiccator) with HCl vapor. Samples were then dried in an oven for 3 hours at 50°C, sealed into 

a tin capsule, and stored in a desiccator until analysis. Instrumental analysis was performed with 

a Carlo Erba 1500 elemental analyzer attached to a Micromass Optima mass spectrometer. 

Analyses for radionuclides were done at the USGS Santa Cruz Marine Geochemistry and 

Radiochemistry Laboratory. Samples were placed in 10 mL standard geometry plastic tubes and 

sealed. The samples were analyzed more than 14 days after sealing to allow time for secular 

equilibrium of 222Rn and 226Ra. Gamma counting was done for about 24 hours using a high-purity 

germanium well detector for 210Pb (46 keV), 228Ra (338 keV, 912 keV), 226Ra (352 keV), 7Be (476 

keV), 226Ra (609 keV), 137Cs (662 keV), and 234Th (63 keV). Excess 210Pb (210Pbxs) was calculated 

as the difference between total 210Pb activity and 226Ra activity. 

Analyses for trace metals were done at the USGS Denver Analytical Chemistry 

Laboratory. Trace-element composition of sediment samples was determined by using a multiacid (low temperature mixture of hydrochloric, nitric, perchloric, and hydrofluoric) digestion and 

instrumental analysis by inductively coupled plasma-mass spectrometry (ICP-MS).

Numerical Circulation and Sediment-Transport Modeling 

A Delft3D coupled wave-current-sediment transport numerical circulation model of 

northern Monterey Bay was constructed in order to extrapolate the limited Eulerian point 

measurements spatially and to examine the effects of waves, winds, and tides on circulation and 

sediment transport in the study area. The Delft3D Online Morphology system (Lesser, 2009; 

Delft user manual, 2006) was used to obtain estimates of sediment transport in the study area. 

The main components are the coupled Delft3D-WAVE and the Delft3D-FLOW modules. FLOW 

forms the core of the model system, simulating water motion due to tidal and meteorological 

forcing, by solving the unsteady shallow-water equations that consist of the continuity equation, 

the horizontal momentum equations, and the transport equation under the shallow water and 

Boussinesq assumptions. Vertical accelerations are assumed minor compared to gravitational 

acceleration (shallow-water assumption) reducing the vertical momentum equation to the 

hydrostatic-pressure relation. By specifying boundary conditions for bed (quadratic-friction law), 

free surface (wind stress), lateral boundaries (water level, currents, discharges), and closed 

boundaries with free-slip conditions at the coasts, the equations can be solved on a staggered grid 

using an Alternating Direction Implicit method (Stelling 1984; Leendertse, 1987; Delft, 2006). 

Wave effects, such as enhanced bed shear stresses and wave current forcing due to 

breaking, are integrated in the flow simulation by running the third generation WAVE model. 

WAVE is based on discrete spectral action balance equations, computing the evolution of 
11

random, short-crested waves through the SWAN wave processor (Holthuijsen and others, 1993; 

Booij and others, 1999; Ris and others, 1999). Physical processes include: generation of waves 

by wind, dissipation due to whitecapping, bottom friction and depth-induced breaking, and 

nonlinear quadruplet and triad wave-wave interactions. Wave propagation, growth, and decay are 

solved periodically on subsets of the flow grid. The results of the wave simulation, such as wave 

height, peak spectral period, and mass fluxes are stored on the computational flow grid and are 

included in the flow calculations through additional driving terms near surface and bed, 

enhanced bed shear stress, mass flux, and increased turbulence (Walstra and others, 2000). 

In this study the Delft3D Online Morphology model (online approach) was used to 

resolve the sediment-transport patterns dynamically. Suspended sediment transport was 

computed by the advection-diffusion solver. To describe sediment characteristics, additional 

formulations are included to account for density effects of sediment in suspension, sediment 

settling velocity, vertical diffusion coefficient for sediment, suspended-sediment correction 

vector and sediment exchange with the bed (Van Rijn, 1993). The Partheniades-Krone transport 

formulation for cohesive sediment was used for the finer-grained dredge material. The elevation 

of the bed is updated dynamically at each computational time-step by calculating the change in 

mass of the bottom sediment resulting from the sediment gradients. One sediment fraction was 

applied to describe the dredge-disposal material. Real-time modeling was employed in this study. 

Complete overviews of the basics, testing, and validation of the Delft3D Online Morphology 

have been reported in Lesser (2009). See Walstra and others (2000), and Van Rijn (1993; 

2007a,b,c) and Van Rijn and others (2007) for the transport formulations. 

Surface currents in Monterey Bay have strong modes of variability (Paduan and Cook, 

1997). At longer time scales, currents show patterns that evolve with major wind reversals and 

the proximity of mesoscale eddies. At the shorter time scales, current fluctuations are dominated 

by semidiurnal tidal forcing and diurnal wind (sea-breeze) forcing. Hydrodynamics along the 

Santa Cruz coastline are governed mostly by these large-scale current patterns. In order to model 

the fate of the dredge plume from Santa Cruz Harbor, it was important to predict these 

fluctuations, both on the short and longer timescales. For reasons of computational efficiency, 

the large-scale circulation in Monterey Bay (and further offshore) was computed with a cascade 

of hydrodynamic models with varying spatial resolution. The model used to investigate the 

dredge-disposal plume (Santa Cruz model) was nested within the smallest of these models 

through a one-way nesting procedure. 

Miscellaneous Data Sources 

Regional oceanographic and meteorological data were provided by the National Data 

Buoy Center’s buoy #46042-Monterey Bay (NDBC, 2010) deployed approximately 40 km to the 

southwest of Santa Cruz in the central portion of the bay. The buoy provided averages of 

barometric pressure (mb), air temperature (°C), wind speed (m/s), wind direction (°True), wave 

height (m), wave period (s), and wave direction (°True) every hour. The buoy’s location is listed 

in table 3. Discharge data (m3/s) for the San Lorenzo River at Santa Cruz were provided by the 

USGS National Water Information System gage station #11161000-San Lorenzo River at Santa 

Cruz (NWIS, 2010); the gage station location is listed in table 3. The Santa Cruz Port District 

provided data on the volumes (m3

) of mud- and sand-sized fractions of material dredged each 

day. Navigation equipment for deployment, recovery, and survey operations included hand-held 

WAAS-equipped GPS units and a computer with positioning and mapping software. The 

positioning and mapping software enabled real-time GPS position data to be overlain on images 

of previously collected high-resolution swath bathymetry, shaded-relief bathymetry, 5 m 

isobaths, and aerial photographs of terrestrial portions of the maps. 
12

Research Platform and Field Operations

The instrumentation tripod and sediment-trap mooring deployments and recoveries were 

done using the University of California at Santa Cruz’s (UCSC) R/V Paragon, the USGS R/V 

Parke Snavely, and the R/V Shana Rae. The instruments were deployed by lowering them to the 

seabed and detaching them from the lowering line using a Pelican quick-release hook. The 

tripods along the 20 m and 30 m isobaths were recovered using an acoustic release, which, when 

triggered, released a float and recovery line that was used to winch the tripods back onboard the 

vessel. The tripod along the 14 m isobath and the sediment-trap mooring were recovered by 

scuba divers attaching a lifting line to the tripod or mooring weight, which was then winched 

onboard the recovery vessel. All of the tripods and sediment-trap mooring were situated on the 

sandy seabed in water depths ≤30 m. The FE and WCP surveys were done from the USGS R/V 

Frontier. The BB surveys were done on foot. Surficial seabed sediment samples at the sedimenttrap mooring sites were collected by scuba divers. 

Data Acquisition and Quality 

Data were acquired for 55 days during the period between October 22, 2009, and 

December 15, 2009 (2009 Year Day [YD] 295-349). During the experiment, four periods were 

observed and quantified: late summer conditions before the dredge-disposal experiment (2009 

YD 295-301), during the dredging (2009 YD 302-324), fall conditions following the dredgedisposal experiment (2009 YD 325-339), and the first large winter storm and flood after the end 

of the experiment (2009 YD 340-349). More than 400,000 data points were recorded by the 

ADCPs, CTs, and OBSs; more than 126 profiles were recorded by the WCP during 4 surveys. 

The TIS collected 1013 images, and the FE and BB collected 1747 and 392 images, respectively, 

during 5 surveys. The raw data were archived and copies of the data were post-processed for 

analysis. 

The ADCM, CT, OBS, TIS, WCP, FE, and BB data generally were of high quality. 

Instrument controller issues on Tripod A (Sea Floor Observatory) caused intermittent power 

problems and, thus, resulted in long gaps in data. In order to obtain turbidity values higher in the 

water column, we computed suspended-sediment concentrations (in mg/L) for the OBS as 

addressed above. Calculated suspended-sediment concentrations were then correlated to 

colocated ADCM current velocity data to compute suspended-sediment fluxes. 

The water-column profiler data were very high in quality; as typical, the data near the 

seabed often displayed spikes due to the sensors’ interaction with the seabed. Electronic issues 

with the WCP’s PAR sensor made the data unreliable, and therefore, these data are not presented 

in this report. The mooring along the 15 m isobath (Mooring-15 m) was struck and destroyed 

sometime after 2009 Year Day 313, and therefore, no suspended-sediment samples were 

collected from this mooring for grain size and geochemical analyses during the last two sampling 

periods (2009 YD 313-336 and 336-349). All errors are given as ± one standard deviation unless 

otherwise specified.

Results 

This section reviews the data collected by the instruments during the deployments and 

addresses the significance of the findings to better understand the oceanographic conditions in 

the study area. 

Inner Harbor Dredge Sediment Discharge 

The dredging was done only during weekdays between October 29, 2009 (2009 YD 302) 

and November 20, 2009 (2009 YD 324). The total daily dredge discharge ranged from 76 to 
13

1153 m3/day, with a mean discharge of 450±237 m3/day; overall, 7649 m3 of sediment was 

dredged, 70.9 percent of which was mud-sized (<63 μm) material (fig. 3a, table 10). The total 

daily dredge discharge of mud-sized material ranged from 20 to 417 m3

/day, with a mean daily 

discharge of 319±133 m3/day; the total daily discharge of sand-sized (>63 μm) material ranged 

from 31 to 772 m3/day, with a mean daily discharge of 131±172 m3/ day. Imagery from the TIS 

showed no apparent surface plume resulting from the dredge operations (fig. 3b-d), with the only 

turbidity visible in the imagery occurring on 2009 YD 311 (fig. 3e), which corresponded to a 

period of larger-than-normal wave heights and periods (see following section). Evidence of large 

waves can be observed by the presence of white bubbles in the water generated by waves 

breaking along the shoreline (wide surf zone along Twin Lakes Beach) and along the harbor 

breakwater (along the breakwater and tailing off to the east) can been seen in figure 3d. 

Regional Oceanographic and Atmospheric Forcing 

The study period from October 2009 through December 2009 covered the end of dry, 

low-energy summer conditions through the beginning of the wet, energetic winter season (fig. 4; 

table 10). The barometric pressure ranged from 1004.1 mb to 1024.4 mb, with a mean pressure 

of 1017±3.5 mb (fig. 4a). The water temperature ranged from 11.62oC to 15.26oC with a mean 

temperature of 12.77±0.79oC (fig. 4b). The mean winds speeds offshore of Monterey Bay ranged 

from 0.34 m/s to 15.39 m/s, with a mean speed of 6.32±3.18 m/s; the mean wind direction was 

264.1±109.9° (fig. 4c). The waves that impacted Monterey Bay during the course of the 

experiment had significant wave heights ranging from 0.95 m to 6.88 m, with a mean significant 

height of 2.72±1.03 m (fig. 4d). Dominant wave periods varied from 4.55 s to 23.53 s, with a 

mean dominant period of 13.22±3.08 s (fig. 4e). The mean wave direction was 299.5±18°.

Northwesterly winds and relatively small waves dominated the period of study and were 

associated with dry, stable weather; this forcing characterized approximately 70 percent of the 

study period. Strong, south winds were associated with drops in barometric pressure from storms 

that usually coincided with the arrival of larger waves (for example, 2009 YD 308-312 and 343-

348).

River Water Discharge 

Daily discharge data provide a measure of the stream response to precipitation in the 

study area. Discharge ranged from 0.25 m3

/s to 5.47 m3/s, with a mean discharge of 0.63±0.89 

m3/s (table 10). The greatest discharge during the period of study coincided with the heavy 

precipitation during 2009 YD 345-349 (fig. 4f). None of the small coastal lagoons (Schwann 

Lagoon at Twin Lakes State Beach, Blacks Beach, or Moran Lagoon) breached during the period 

of study. 

Tides 

The study period encompassed more than 4 complete spring-neap tidal cycles (fig. 5-8a). 

The tides in northern Monterey Bay are typical for California; mesotidal, mixed, semi-diurnal 

with two uneven high tides and two uneven low tides per day, thus the tidal period is slightly 

longer than 6 hours. The maximum spring tide range during the deployment was approximately 

2.5 m, and the diurnal and mean tidal ranges were approximately 1.5 and 1.0 m, respectively. 

Waves 

The waves measured at the Tripod A site near the end of the Santa Cruz Municipal Wharf 

were consistently from the southwest due to refraction around Point Santa Cruz, with mean 

significant wave heights and dominant periods on the order of 0.35 m and 15 s; this site 
14

FIGURE 3. Plot of harbor dredging volumes and Terrestrial Imaging System (TIS) photographs. A, Volume of 

sediment dredged, in cubic meters, of both mud- (red) and sand-sized (blue) sediment. B, Image of dredge-disposal 

area on October 27, 2009, before dredging commenced. C, Image of dredge-disposal area during dredging on 

November 2, 2009. D, Image of dredge-disposal area during dredging on November 7, 2009, during large wave 

conditions. E, Image of dredge-disposal area during dredging on November 15, 2009. 
15

FIGURE 4. Time-series plots of regional meteorologic, oceanographic, and fluvial data during the study period. A,

Barometric pressure, in millibars. B, Water temperature, in degrees Celsius. C, Red: wind speed, in meters per 

second; Blue: wind speed and direction, in meters per second from degrees true north. D, Red: wave height, in 

meters; Blue: wave height and direction, in meters from degrees true north. E, Wave period, in seconds. F, River 

discharge, in cubic meters per second. The period of dredge-disposal operations and the post-dredging storm and 

flood are denoted by the light grey (2009 Year Days 302-324) and dark grey boxes (2009 Year Days 340-349), 

respectively. 
16

experienced the smallest waves in the study area due to refraction (table 11). The waves 

propagating over the sites farther to the east (Tripod B) and offshore (Tripods C and D) 

underwent less refraction and, thus, measured larger wave heights (0.85 m, 1.00 m, and 1.18 m 

for Tripods B, C, and D, respectively) and more westerly wave directions (218.5°, 230.7°, and 

251.5° for Tripods B, C, and D, respectively) than Tripod A. 

Currents 

Similar to the wave heights, current speeds were greater to the east and offshore (fig. 5-8, 

table 12); the tidal currents flood to the north and ebb to the south. The mean current speed at 

Tripod A (depth ~9 m) was 0.02±0.02 m/s close to the seabed (fig. 5). The mean current speeds 

at Tripod B (depth ~12 m) were approximately twice the speeds measured at Tripod A, with a 

mean current speed of 0.05±0.03 m/s close to the surface and 0.05±0.02 m/s close to the seabed 

(fig. 6). The mean current speed at Tripod C (depth ~20 m) was greater (0.08±0.05 m/s) close to 

the surface than at Tripod B, but slower (0.03±0.02 m/s) close to the seabed (fig. 7), possibly due 

to greater influence of wind-driven surface currents and thermal stratification. The currents at 

Tripod D (depth ~30 m) were the fastest, with the mean current speeds of 0.09±0.05 m/s close to 

the surface and 0.05±0.03 m/s close to the seabed (fig. 8). 

Overall, the mean currents offshore along the 20 m and 30 m isobaths were much 

stronger and more uniform than those closer to shore, where the mean currents were weaker and 

more variable (fig. 9). Close to the seabed, the currents primarily were oriented cross-shore 

(north-south) closer to shore, but alongshore (east-west) to the west at Tripod D along the 30 m 

isobath. Currents near the surface primarily were oriented alongshore. Surface currents close to 

shore (sites A and B) typically were to the east, while surface currents at the offshore sites (C 

and D) typically were to the west. 

Turbidity 

 The turbidity in the northern part of the bay ranged between 0 NTU and 693 NTU (fig. 

5-8), with a mean turbidity of 19±23 NTU (table 13). The near-bed turbidity at Tripod A, off the 

wharf (depth ~9 m), was between 0 NTU and 311 NTU, with a mean turbidity of 29±35 NTU. 

The near-bed turbidity at Tripod B (depth ~12 m) was between 0 NTU and 311 NTU, with a 

mean turbidity of 29±35 NTU. The turbidity at Tripod C (depth ~20 m), in the lower water 

column at a height of 2 m above the seabed, was between 1 NTU and 61 NTU, with a mean 

turbidity of 6±6 NTU, while the near-bed turbidity was between 0 NTU and 490 NTU, with a 

mean turbidity of 22±36 NTU. The near-bed turbidity at Tripod D was between 2 NTU and 693 

NTU, with a mean turbidity of 23±32 NTU. Near-bed turbidity was, in general, higher during 

and after the dredging than before the dredging, and was greatest during the storm and flood 

following the dredge-disposal experiment. 

Temperature 

The near-bed water temperature at Tripod B ranged between 10.89°C and 14.31°C, with 

a mean temperature of 12.12±0.79°C (fig. 10a; table 15). The near-bed water temperature at 

Tripod C was between 10.82°C and 13.79°C, with a mean temperature of 11.85±0.66°C. The 

near-bed water temperature at Tripod D was between 10.56°C and 13.59°C, with a mean 

temperature of 11.58±0.56°C. The inshore and offshore sites showed similar seasonal patterns in 

decreasing temperature during the deployment. The daily near-bed temperature variations did not 

appear to be coherent between instrument sites. At times the offshore sites showed greater daily 

variation than the inshore sites, while at other times the inshore sites showed greater daily 
17

FIGURE 5. Time-series plots of tides, waves, currents, and turbidity at Tripod A (Sea Floor Observatory at 9 m 

depth). A, Tide, in meters. B, Wave height, in meters. C, Wave period, in seconds. D, Current speed and direction, in 

meters per second from degrees true north close to the seabed (depth is 8.5 m). E, Turbidity, in National Turbidity 

Units (NTU). 
18

FIGURE 6. Time-series plots of tides, waves, currents, and turbidity at Tripod B (12 m depth). A, Tide, in meters. B,

Wave height, in meters. C, Wave period, in seconds. D, Current speed and direction, in meters per second from 

degrees true north close to the surface (depth is 2 m, in green) and lower in the water column (depth is 6 m, in blue). 

E, Turbidity, in National Turbidity Units (NTU). 
19

FIGURE 7. Time-series plots of tides, waves, currents, and turbidity at Tripod C (20 m depth). A, Tide, in meters. B,

Wave height, in meters. C, Wave period, in seconds. D, Current speed and direction, in meters per second from 

degrees true north close to the surface (depth is 2 m, in green and lower in the water column (depth is 18 m, in blue). 

E, Turbidity, in National Turbidity Units (NTU). 
20

FIGURE 8. Time-series plots of tides, waves, currents, and turbidity at Tripod D (30 m depth). A, Tide, in meters. B,

Wave height, in meters. C, Wave period, in seconds. D, Current speed and direction, in meters per second from 

degrees true north close to the surface (depth is 2 m, in green) and lower in the water column (depth is 28 m, in blue). 

E, Turbidity, in National Turbidity Units (NTU). 
21

FIGURE 9. Map showing principal axis ellipses and mean current speeds and directions, in meters per second from 

degrees true north, at the main study sites for the entire period of study. Data from close to the seabed, the lower 

water column, and close to the surface are shown in blue, green, and red, respectively. 
22

variability and the offshore sites showed less variation. This variability may be caused by 

variations in the propagation of deeper, cooler oceanic water replacing warmer nearshore waters 

driven by the tidal cycle. 

Salinity 

Near-bed salinity in the study area was between 19.64 PSU and 35.21 PSU, with a mean 

salinity of 34.83±0.31 PSU (fig. 10b; table 16). The near-bed salinity at Tripod B was between 

23.41 PSU and 33.23 PSU, with a mean salinity of 31.06±1.87 PSU. The near-bed salinity at 

Tripod C was between 33.14 PSU and 33.59 PSU, with a mean salinity of 33.43±0.06 PSU. The 

near-bed salinity at Tripod D was between 33.10 PSU and 33.61 PSU, with a mean salinity of 

33.35±0.11 PSU. The brief, low salinity levels that quickly returned to pre-event levels likely are 

spurious data that were caused by wave-driven sediment blocking the conductivity sensor. 

Spatial Variations in Water-Column Properties 

The OBS on the WCP provided turbidity values in NTUs, which are useful for comparing 

to U.S. Environmental Protection Agency guidelines for water clarity. The turbidity before 

dredge-disposal operations generally was low except for the nearshore region off the Santa Cruz 

Harbor’s west jetty and extending east (down-coast in terms of wave direction) from that point 

(fig. 11; appendix 3). It appeared that wave-breaking on the west jetty resulted in increased 

sediment resuspension, and this plume was advected eastward past the harbor mouth, Twin 

Lakes Beach, and Black Point. The total mass of sediment suspended in the water column across 

the study area calculated from the OBS during the pre-dredge survey was 58.1±9.9 metric tons. 

During dredge operations, turbidity increased approximately 40 NTUs offshore and to the east of 

the harbor mouth; while elevated, these turbidity values were less than those observed during a 

red tide that occurred before the beginning of dredge-disposal operations as identified in the chl 

data (appendix 5). The total mass of sediment suspended in the water column across the study 

area calculated from the OBS during dredging was 43.8±11.1 metric tons. Following the dredgedisposal operations, most of the offshore turbidity values returned to their pre-dredging levels, 

except at survey sites #16 and #33, which were approximately 1000 m and 300 m offshore 

Seabright Beach and Twin Lakes Beach, respectively. The total mass of sediment suspended in 

the water column across the study area calculated from the OBS following the dredging was 

52.1±11.9 metric tons. 

Similar to the turbidity, the light transmission from the Xmiss on the WCP before dredge 

disposal operation generally was low except for the nearshore region off Seabright Beach and 

Black Point (fig. 12; appendix 4). It appeared that wave-breaking on the harbor’s western 

breakwater resulted in increased sediment suspension. During dredge operations, transmission 

decreased approximately 15 percent offshore and to the east of the harbor mouth; although 

lower, these transmission values were less than what was observed during a red tide that 

occurred before the beginning of the dredge-disposal operations as identified in the chl data 

(appendix 5). Following dredge-disposal operations, most of the offshore transmission values 

returned to their pre-dredging levels, except at survey sites #32 and #33, which were 

approximately 150 m and 300 m offshore Twin Lakes Beach.

Spatial Variations in Beach and Seabed Surficial Grain Size 

 There were no statistically significant differences in surficial sediment size observed by 

the BB system along the shoreline during the period of investigation (fig. 13). While there was 

variability at each location (determined from the multiple samples taken at each location 

(appendix 6), there was no observed change in grain-size class over time along the shoreline. 

Offshore, there were no statistically significant differences in surficial sediment size observed by 
23

FIGURE 10. Time-series plots of temperature and salinity data during the study period. A, Water temperature, in 

degrees Celsius. B, Salinity, in practical salinity units (PSU). Data from Tripod B (12 m depth), Tripod C (20 m depth), 

and Tripod D (30 m depth) are shown in red, green, and blue, respectively. No salinity data are presented for Tripod 

B because sediment clogged the doivity cell and resulted in spurious salinity values. 

the FE system on the seabed during the demonstration project (fig. 13). The same number of sites 

experienced a fining of grain size by one grain-size class as experienced a coarsening of grainsize class (two each) during the dredge operations. Following the cessation of dredging, three 

sites fined by one grain-size class, and four sites coarsened by one grain-size class. The 

variability in surficial grain size at each seabed site was, in general, greater farther offshore than 

close to shore (appendix 6). 
24

FIGURE 11. Map showing spatial variability in optical backscatter, in National Turbidity Units (NTU), during the 

surveys. Data from before, during, and after the dredge-disposal operations are shown in the upper right, lower, and 

upper left sectors of the circles, respectively. 
25

FIGURE 12. Map showing spatial variability in light transmission, in precent, during the surveys. Data from before, 

during, and after the dredge-disposal operations are shown in the upper right, lower, and upper left sectors of the 

circles, respectively. 
26

 Burial or exhumation of bedrock occurred at 7 sites; two sites became buried and two 

sites were exhumed during the dredge operations, and two sites were buried and one site was 

exhumed after the end of the dredging. These burials and exhumations did not occur at sites 

immediately adjacent to the dredge-disposal sites, and there is no evidence to suggest that they 

were caused by the dredge-disposal operations. All rocky sites that were buried were covered by 

medium- to fine-grain sand; none of the sampling sites were characterized by very fine sand or 

mud before, during, or after the dredge operations.

Trapped Sediment Accumulation and Grain Size 

The grain size of the sediment collected in the traps shows a very different distribution 

than the seabed samples. The seabed at sediment trap mooring sites was predominantly (mean 

was 82.9 percent) a poorly sorted fine sand (mean size of 0.1758±0.1312 mm) with lesser 

percentages of silt, clay, and gravel (mean was 12.5 percent, 3.5 percent, and 1.1 percent, 

respectively; fig.14). The material collected in sediment traps was primarily (mean was 65.1 

percent) very poorly sorted medium silt (mean size of 0.0251±0.0018 mm) with lesser 

percentages of clay and sand (mean was 20.9 percent and 14.0 percent, respectively) with no 

gravel. This difference in grain size between the seabed and what accumulates in sediment traps 

is not uncommon; finer-grained, lighter particles can be more easily resuspended and carried 

higher up into the water column and thus to the height of the trap’s opening than coarser 

particles. Once these fine-grain particles settle into the trap, they cannot be resuspended and 

advected away as could the same-sized material on the adjacent seabed. Furthermore, as 

discussed above, the sediment traps collect coarser particle sizes preferentially because of their 

higher settling velocity. Overall, the trap sediment accumulation rates varied between 0.676 and 

0.827 mg/cm2/day, with a mean accumulation rate of 0.770±0.071 mg/cm2/day and showed no 

general cross-shore trend (table 16). 

Sediment Geochemistry 

Sediment Carbon and Nitrogen Contents and Isotopic Compositions 

Carbon and nitrogen isotopic and elemental compositions of sediment (table 17) show 

statistically significant differences in sediment chemistry between Santa Cruz Harbor material 

and suspended sediment collected in sediment traps. There were significant differences in 

percent C (p=0.03, Student’s t-test), 15N (p=0.02, Student’s t-test), 13C (p=10-8, Student’s t-test), 

and the molar ratio of carbon to nitrogen (p=10-5, Student’s t-test). In addition, there were 

statistically significant differences in the chemistry of suspended sediment collected during 

dredging and post-dredging periods. The elemental carbon data (percent C) showed a significant 

difference in the means between the early-, late-, and post-dredging collection periods (p=0.008, 

ANOVA), with the percent C in the post-dredging collection period being lower than the two 

dredging collection periods. Similarly, there was a significant difference in the elemental 

nitrogen (percent N) in suspended sediment during the different collection times (p=0.042, 

ANOVA), with the percent N being lowest in the post-dredging period. There was, however, no 

significant difference in the mean molar ratio of carbon to nitrogen (C/N) among the three 

periods (p=0.39, ANOVA), and no significant difference in suspended-sediment accumulation 

rate in the traps (p=0.08, ANOVA). 
27

FIGURE 13. Map showing spatial variability in beach and seabed surficial grain size, by grain-size class, during the 

surveys. Data from before, during, and after the dredge-disposal operations are shown in the upper right, lower, and 

upper left sectors of the circles, respectively. 
28

FIGURE 14. Plot showing grain-size distribution of sediment on the seabed and collected in sediment traps. A,

Distribution, in quarter-phi intervals. B, Distribution, by grain-size class. Data from the 10 m, 15 m, 20 m, and 30 m 

mooring sites are shown in red, orange, green, and blue, respectively. The data from the seabed samples are shown 

by solid lines, the sediment-trap samples (height above bottom, 5 m) are shown by dashed lines, and the black solid 

line denotes the data from 2 m above the bottom at the Tripod D (30 m depth) site. 

Short-lived Radionuclides 

Results for short-lived radioisotope analyses are shown in table 18. In trap-collected 

suspended sediment, 7Be activity was less than 1.2 dpm/g during dredging activity. In suspended 

sediment, 7Be activity was relatively higher (0.92–1.88 dpm/g) in post-dredging compared with 
29

activity levels during dredging (0.0–1.14 dpm/g). It is difficult to compare most of the shortlived radioisotopes in sediment-trap material directly with the sediment collected from Santa 

Cruz Harbor because the harbor sediment was analyzed a substantial length of time (about 250 

days) after their collection date [07/15/2009-07/17/2009 (2009 Year Days 196-198)], and there 

was a substantial amount of time between harbor sediment sampling and dredging. Nevertheless, 

210Pbxs (half life=22.3 years) was significantly lower in harbor sediment compared to suspended 

sediment collected in traps (p=0.0001, 0.0002; Student’s t-test). 

Elemental Concentrations 

 The sedimentary contents of 35 elements (Ag, Al, As, Ba, Be, Ca, Ce, Co, Cr, Cs, Cu, Fe, 

Ga, K, La, Li, Mg, Mn, Mo, Na, Nb, Ni, P, Pb, Rb, Sb, Sc, Sr, Th, Ti, Tl, U, V, Y, Zn) for dry 

weight elemental concentrations in sediment determined by ICP-MS are shown in tables 19-23. 

With the exception of silver (Ag), which was always below the limit of detection (1 ppm), all 

elements were above the limits of detection reported by the USGS CR Mineral Resources Team 

Analytical Chemistry Laboratory. A subset of 16 of these elements (Al, As, Ba, Co, Cr, Cu, Fe, 

K, Mg, Mn, Mo, Ni, P, Pb, Ti, Zn) was selected for closer examination. 

 Among the trap-collected sediment, there was a significant positive correlation (p<0.05, 

linear regression) between the fraction of fine-grain material present (either as a percentage of 

silt or as a pecerntage of silt+clay) and the concentration of Co, Cr, Fe, and Ni. A single value (1 

out of 10) for grain size (Trap-20 m, 2009 Year Day 336–349 collection), which was farthest 

from the rest, prevented the inclusion of Mg, Mn, and Ti with elements showing a significant 

correlation. However that single grain-size value was not a significant outlier in the grain-size 

data for either percent silt or percent mud (p>0.01, Grubb’s test). Other elements show a 

significant positive [As, Cu, Mo, Pb, Zn (and percent C)] or negative (Ba, K) correlation with 

percentage clay (p<0.05, linear regression). Of the subset of 16 elements reviewed in detail, none 

show a significant correlation with both percentage clay and percentage silt or percentage mud 

(silt+clay). When considering all 35 elements analyzed, however, Cs, Li, and V are exceptions to 

this lack of significant correlation. Looking at the correlation coefficient for these elements, Cs 

correlates slightly better with percentage clay than percentage silt (R=0.88 vs. 0.77), Li shows 

little difference (R=0.81 versus 0.83), and V correlates slightly poorer with percentage clay than 

percentage silt (R=0.64 versus 0.70). Percentage C was significantly and positively correlated 

(p<0.05, linear regression) to a number of elements in both Santa Cruz Harbor (As, Cu, Fe, Mg, 

P, Pb, Zn) and trap-collected sediment samples (As, Cu, Mo, P, Pb, Zn). Similarly, percentage C 

showed a significant negative correlation (p<0.05, linear regression) to Ba in harbor sediment, 

and to Al and K in trap-collected sediment. 

 Significant changes in the mean values of percentage C and percentage clay are 

associated with the different collection periods for the sediment traps. The percentage clay was 

significantly higher in the late dredging period (Year Days 313–336) compared to early or postdredging time periods (p<0.05, Students’ t-test), with enrichments in mean values of 1.2 and 1.6 

times, respectively. In addition there was a significant decrease in percentage C between the lateand post-dredging periods (p<0.05, Students’ t-test). The mean percentage C in the trap-collected 

sediment from the late-dredging period is 1.3 to 1.9 times higher than the percentage C in 

sediment collected in early- and post-dredging periods, respectively. Similar changes are seen in 

elements significantly correlated with percentage clay or percentage C (As, Cu, Mo, Pb, Zn). 

There was no significant change in percentage silt over the collection periods (p>0.05, ANOVA), 

and elements showing significant correlations with percentage silt (Co, Cr, Fe, Ni) also showed 

no significant change over the collection periods (p>0.05, ANOVA). 

 The concentration of Co, Cr, Mg, Mn, Ni, and Ti in trap-collected sediment showed a 

significant positive correlation (p<0.05, linear regression) with distance from shore as measured 
30

south from the mouth of Santa Cruz Harbor (mooring distances were about 0.4, 1.2, 2.5, and 4 

km from shore for the 10, 15, 20, and 30 m traps, respectively). One element, Pb, showed a 

significant negative correlation with distance. Percentage silt, clay, and C showed no significant 

correlation with distance offshore (p>0.05, linear regression). To account for changes in 

elemental concentration unrelated to changes in grain size, elements showing a significant 

correlation to a grain-size fraction (percentage silt or percent clay) were normalized to that 

fraction. After normalization to percentage silt, Co, Cr, and Ni still showed a significant positive 

correlation to distance offshore. After normalization to percent clay, Cu and Mo but not Pb 

showed a significant negative correlation to distance offshore. 

 The concentrations of 10 elements (Al, Co, Cr, Cu, Fe, Mn, Mo, Pb, Ti, Zn) were 

significantly higher in Santa Cruz Harbor sediment than in trap-collected sediment (p<0.05, 

Student’s t-test), and the concentrations of one element (K) was significantly lower. Elements 

showing the greatest average concentration enrichment in harbor sediment compared to trapcollected sediment were Cu and Zn, at 4.3 and 2.3 times, respectively. When using percentage C 

corrected data for elements that show a significant linear correlation with percentage C (harbor 

and mooring considered separately), two elements (Cu, Zn) were significantly higher in Santa 

Cruz Harbor sediment than in trap-collected sediment samples (p<0.05, Student’s t-test). Cu was 

2.5 times and Zn was 1.3 times in Santa Cruz Harbor sediment than in trap-collected sediment 

samples, and two elements significantly lower (As, P), with As was 1.3 times and P was 2.1 

times higher in the sediment traps. Normalizing to percentage clay would be ideal for this 

enrichment calculation, but percentage clay data were not generated by the USGS for harbor 

sediment. Nevertheless, percentage C is a reasonable proxy for percentage clay in systems where 

percentage C represents fine, organic material, which is likely the case in Santa Cruz Harbor. 

Numerical Wave, Circulation, and Sediment Transport Modeling 

Circulation Model Boundary Forcing 

 Open boundary conditions for the Santa Cruz model (SC01) were obtained from a larger 

FLOW model of Monterey Bay (MBY). This model, in turn, was nested in a FLOW model of 

Central California (CCA). Figure 15 shows the three FLOW model grids applied in this study. 

The models included the effects of:(1) spatially and time-varying wind and atmospheric pressure, 

(2) salinity and temperature stratification, (3) heat exchange with the atmosphere through solar 

radiation and evaporation, and (4) Coriolis forcing. 

 The CCA and MBY models both contained 44 vertical (z) layers, ranging in thickness 

from 1 m at the surface to several hundreds of meters near the ocean floor. The horizontal grid 

spacing of the CCA model ranged from ~5000 m along the offshore boundary to ~1500 m inside 

Monterey Bay. The grid-cell sizes in the MBY model ranged from ~2000 m offshore to 500 m 

along the boundaries of the SC01 model. Bathymetry data for the MBY and CCA models were 

obtained from the National Geophysical Data Center’s Coastal Relief Model (2010).

 The CCA and MBY models were forced along their open boundaries by weakly 

reflective Riemann conditions (Verboom and Slob, 1984). The Riemann invariant time series f(t)

for each z-layer is given by: 

, 

where U is the normal velocity per layer, ζ is the water level, g is the gravitational constant, and 

d is the local water depth. 
31

FIGURE 15. Map showing the FLOW model computational grids CCA (black), MBY (red), and SC01 (green). 

 Open boundary forcing data for the CCA model was obtained from a combination of the 

TOPEX/POSEIDON global tide data (Egbert and Erofeeva, 2002) and the global HYCOM flow 

model output (Halliwell, 1998) that does not include tides. The normal velocity (U) was taken as 

the sum of the baroclinic currents from the HYCOM model and the tidal currents obtained from 

the TOPEX/POSEIDON model. The water level, ζ, was computed as the sum of the sea surface 

height from the HYCOM model and tide levels from the TOPEX/POSEIDON model. Salinity 

and temperature boundary conditions for the CCA model also were taken from the HYCOM 

model. Furthermore, both the CCA and MBY models were initialized with currents, salinity and 

temperatures from the HYCOM model (fig. 16). Spatially and time-varying wind and 
32

FIGURE 16. Map and cross-sections showing the Initial conditions in the CCA FLOW model. A, Surface temperature, 

in degrees Celsius, and surfacecurrent speeds and directions, in meters per second from degrees true north. B,

Cross-section of temperature, in degrees Celsius. C, Cross-section of salinity, in practical salinity units (PSU). The 

location of the cross-section is shown as a black line in A. 

atmospheric pressure fields applied in the CCA, MBY, and SC01 models were obtained from the 

NCEP-NAM model (Gemmill and Peters, 1997).

The results of the MBY model were assessed by comparing them against in place 

observations at five sites (fig. 17). The focus of this comparison was for surface currents and 

surface temperatures during the 2-month period of the dredge experiment. Observed current 

speeds at these locations were obtained from HF radar data (Paduan and Cook, 1997). It must be 

noted that the accuracy of the HF radar data, especially for the distant locations 46042 and 

46239, is poor. The MBY model was able to reproduce the diurnal wind-driven fluctuations 

reasonably well at all five sites (appendix 7). The residual currents in both the MBY model and 

the observations compared well for the nearshore sites (in particular MBM1, and to a lesser 

extent MBM0 and Tripod D at 30 m), but generally were poorer at the more distant NDBC buoys 

46042 and 46239. It is interesting to note that, whereas the modeled meridional (north-south) 

residual currents at Tripod D along the 30 m isobath closely resembled the observations, the 

zonal (east-west) currents in the model did not match the observations at all. 

 The MBY model was capable of hindcasting the temperature fluctuations during the 2 

month period (appendix 7). In particular, the sudden decrease in temperatures around October 

30, 2009 (2009 Year Day 303), was reproduced well. This strong upwelling event appeared to be 
33

FIGURE 17. Map showing the observation points in the MBY FLOW model used for validation and calibration. 

related to the peak in winds out of the north that drove strong southward-directed surface 

currents. 

 A number of experiments (not presented here) with the CCA and MBY models revealed 

the sensitivity of the model output to wind forcing, indicating the need for accurate wind input in 

the model. A comparison between the model wind input obtained from the NCEP-NAM model 

and local observation was therefore carried out to assess the quality of the wind product that was 

used (appendix 7). At the most offshore site (NDBC buoy 46042), the wind predictions closely 

matched the observations. However, closer to the shore, the model predictions appeared to 

deteriorate (see stations MBM0 and MBM1). It appears that the NCEP-NAM model significantly 

under-predicted the diurnal sea-breeze, as well as the wind speeds during some of the highvelocity wind events. 
34

Wave Model Boundary Forcing 

Wave effects, such as enhanced bed shear stresses and wave current forcing due to 

breaking, are integrated in the flow simulation by running the WAVE model on a grid (WAV1) 

surrounding Monterey Bay (fig. 18). The bathymetry for the wave grid was provided by the 

USGS based on the NGDC Coastal Relief Model (2010). Time-varying boundary conditions for 

the wave model for the period of study were derived from the NDBC buoy 46042 (2010) situated 

at the western edge of the WAV1 grid. The significant wave height (m), peak period of the 

energy spectrum (s), mean wave direction (degrees), directional standard deviation (-), wind 

speed (m/s), and wind direction (degrees) were prescribed. 

FIGURE 18. Map showing the WAVE model computational grids WAV1 (black) and SC01 (blue). 

Fine-Scale Hydrodynamics and Sediment Transport 

The results of the WAV1 simulations, such as wave height, peak spectral period, and 

mass fluxes, were stored on the computational SC01 grid and included in the flow calculations 

through additional driving terms near surface and bed, enhanced bed shear stress, mass flux, and 
35

increased turbulence (Walstra and others, 2000). In this study, wave effects, flow, and the 

resulting sediment-transport patterns were computed on the detailed SC01 grid off Santa Cruz 

Harbor. The curvilinear (land-boundary fitting) SC01 model grid consisted of 10 layers in the 

vertical. The maximum horizontal grid spacing at the outer edge of the domain was 

approximately 300 m, becoming progressively finer towards the area of interest to a minimum 

grid spacing of 16 m (fig. 19). The San Lorenzo River water discharge for the simulated period 

also was included in this model. 

FIGURE 19. Map showing the details of FLOW and WAVE models’ computational grid SC01. 

 Simulated water levels in the SC01 model compared well with predicted water levels 

(appendix 7). The WAVE model performed well in the SC01 domain, with root-mean squared 

errors between the model and the observations averaging 0.31 m in this bathymetrically-complex 

and, thus, refractive environment (appendix 7); the locations where large waves break along the 

bedrock reefs off Point Santa Cruz and Soquel Point were well-reproduced, as were the quiescent 

locations of Cowell’s Beach and the Santa Cruz Municipal Wharf (fig. 20). Modeled surfaceand bottom-current speeds were compared with observation data from the ADCMs at three 

locations within the SC01 domain. Results at Tripod D along the 30 m isobath showed that the 

near-bed current velocities, the important forcing for sediment transport, were reproduced well, 

with root-mean squared errors between the model and the observations averaging 0.062 m/s; the 

errors between the near-surface measured and modeled current velocities was slightly greater, 

averaging 0.083 m/s (appendix 7). Note the significant shear in the water column (fig. 21-22), 

with the near-surface currents often heading at different speeds and in different directions than 

the near-bed currents, similar to that observed at the tripod locations (fig. 9). During large wave 

conditions (fig. 22), wave shoaling and breaking generated strong eastward-directed currents 
36

FIGURE 20. Map of modeled wave heights, in meters, in the study area. A, During large (deep-water height is 4.3 m 

at 15.2 s from 302°) wave conditions. B, During small (deep-water height is 1.2 m at 12.7 s from 270°) wave 

conditions. Note how the locations where large waves break along the bedrock reefs off Point Santa Cruz and Soquel 

Point were well-reproduced, as were the quiescent locations of Cowell’s Beach and the Wharf (fig. 1). 
37

FIGURE 21. Map of modeled current speeds and directions, in meters per second from degrees true north, over a 24-

hour tidal cycle during small wave conditions (fig. 20A). A, Near-surface currents. B, Near-bed currents. 
38

FIGURE 22. Map of modeled current speeds and directions, in meters per second from degrees true north, over a 24-

hour tidal cycle during large wave conditions (fig. 20B). A, Near-surface currents. B, Near-bed currents. 
39

close to shore that are virtually nonexistent during lower wave-energy conditions (fig. 21); the 

strong eastward-directed alongshore current dissipated near Capitola due to wave energy 

divergence (fig. 20a). 

A single cohesive sediment fraction was included to represent the dredge-disposal outfall. 

The disposal of the dredge material was simulated as a discharge of fine sediment at the location 

of the end of the dredge discharge pipe in the model domain. The dredge start and stop times 

were adjusted to represent the 60.9 hours of pumping that took place. The dispersal of sediment 

in the water column from the dredge plume was compared with measurements of suspended 

sediment from the WCP casts. Several time-series plots of bottom and surface concentrations 

were made, but the temporally-limited measurements made it difficult to come to any concrete 

conclusions about the behavior of the model. 

The movement of the simulated plume also was compared with a higher resolution timeseries of OBS measurements at three tripod locations. Those measurements also contained 

background concentrations of the coarser seabed-sediment fractions, not included in the model, 

and the large peaks coincided with large wave events that resuspended large volumes of seabed 

sediment not related to the dredge plume, even after 2009 Year Day 324 when the dredging had 

been completed. A settling velocity of 0.0005 m/s was required to simulate the distribution of 

fine sediment in the water column correctly. A number of sensitivity tests (not shown) indicated 

that with a smaller setting velocity, the dredge plume peaks in suspended-sediment concentration 

were overestimated. 

 The importance of the outer boundary forcing conditions, such as waves, for the 

simulation of the sediment plume can be seen in figure 23. During low wave-energy conditions 

(deep-water height=1.2 m at 12.7 s from 270°), the plume was advected offshore to the 

southwest by subtidal flows. During larger wave-energy conditions (deep-water height=4.3 m at 

15.2 s from 302°), however, the plume bifurcated, with some of the plume heading offshore to 

the southwest as during lower wave-energy conditions and some entrained in the strong 

eastward-directed alongshore flow and transported to the east, similar to the modeling done by 

Sea Engineering, Inc. (2006). As wave energy decreased off Capitola (fig. 20a), the strong 

eastward-directed alongshore currents weakened (fig. 22), and the suspended sediment became 

entrained in the southwestward-directed subtidal flow, and was driven to the southwest, where it 

dissipated. Initially, these waves and flow patterns resulted an initial deposit on the order of 3.5 

cm thick just offshore of the end of the discharge pipe that was eroded within 3 days. The 

sediment was advected eastward and resulted in a thin (thickness~0.1 cm) modeled deposit of 

fine-grain sediment on the seabed offshore of Capitola for approximately 20 days (fig. 24); this 

thin deposit subsequently was eroded again and advected offshore to the southwest out of the 

study area in the direction of the mid-shelf mud belt by the beginning of December. Due to the 

small errors in modeled wave and current patterns, and relatively low suspended-sediment 

concentrations, the thin, temporary accumulation patterns produced by the model off Capitola are 

well within the error of the model and may not be real. The modeled sediment-accumulation 

patterns are a mix of the transport patterns for low wave-energy conditions (fig. 21) at the 

beginning of the study and transition into higher wave-energy conditions (fig. 22) towards the 

end of the dredge-disposal experiment. 

The model also was run in two simulations to evaluate the potential sedimentation that 

could occur if fine-grain sediment was discharged at two times (650 m3

/day; fig. 25) and four 

times (925 m3/day; fig. 26) the rate of the 2009 dredge disposal project (450 m3/day of 71 percent 

fine-grain sediment~325 m3/day of fine sediment). Both simulations show similar patterns to the 

predicted transport and deposition during the 2009 dredge-disposal experiment (fig. 24), with 

initial thick deposition just offshore of the end of the dredge discharge pipe (~35 cm and ~80 cm 

for the 650 m3/day and 925 m3/day daily dredge volumes, respectively). These initial deposits off 
40

FIGURE 23. Map of modeled suspended-sediment concentrations, in grams per liter, over a 24-hour tidal cycle. A, 

During small large wave conditions (fig. 20A). B, During large wave conditions (fig. 20B). 

the end of the dredge discharge pipe persisted for longer (~20-25 days) than were modeled for 

the 2009 experiment when 325 m3/day of fine sediment were dredged. Similar to the 2009 

experiment, these initial deposits off the dredge discharge pipe were eroded, advected eastward, 

and formed a thin (thickness~1-2 cm) temporary deposition deposit off Capitola for 

approximately 30 days, then were subsequently eroded and advected offshore to the southwest 
41

FIGURE 24. Map of modeled sediment accumulation, in millimeters, in the study area during the dredge-disposal 

project. The resulting sediment accumulation is thin (thickness is approximately 0.1 cm) and temporary in nature 

(residence time on the seabed is on the order of 20 days). 

out of the study area in the direction of the mid-shelf mud belt by the beginning of December. 

While the sediment accumulation patterns produced by the model for these higher discharge 

rates are greater than the patterns for the 2009 dredge-disposal experiment, due to the small 

errors in modeled wave and current patterns, and relatively low suspended-sediment 

concentrations, the projected sediment accumulations off Capitola may not be real. 

Lastly, the model suggests that during both low and high wave-energy conditions as were 

observed during the study, combined wave and current shear stresses were sufficient to inhibit 

the substantial deposition of mud throughout the model domain (fig. 27). Note how under large 

wave conditions, the regions where shear stress are low enough to allow for the deposition of 

mud (critical shear stress for mud ~0.14 N/m2

) are so far offshore that they are not in the SC01 

model domain shown. 

Discussion 

Distribution of Forcing Conditions 

The surveys and instrument deployments in northern Monterey Bay described here took 

place during the months of October-December, at the transition from summer conditions through 

the beginning of winter (fig. 4). During the experiment four periods were observed and 

quantified: late summer conditions before the dredge-disposal experiment (2009 YD 295-301), 

during the dredging (2009 YD 302-324), fall conditions following the dredge-disposal 
42

FIGURE 25. Map of modeled sediment accumulation, in millimeters, in the study area at two times the daily rate of 

fine-grain sediment discharge (650 m3

/day) of the 2009 dredge-disposal project. The resulting sediment accumulation 

is thin (thickness is approximately 1.0 cm) and temporary in nature (residence time on the seabed is on the order of 

30 days). 

experiment (2009 YD 325-339), and the first large winter storm and flood after the end of the 

experiment (2009 YD 340-349). 

Spatial and Temporal Variability in Circulation Patterns and Water-Column 

Properties

The circulation patterns are described below for each of the sets of oceanographic 

conditions and their implications for the transport of sediment in northern Monterey Bay. 

Before Dredging 

The period preceeding the harbor dredge-disposal experiment (2009 YD 295-301) was 

characterized by consistent strong daily winds out of the northwest (fig. 4c) and deep-water 

waves out of the northwest (fig. 4d). These strong northwest winds and northwest waves, which 

are reduced significantly in the northern part of Monterey Bay due to refraction, resulted in little 

mixing and strong stratification in the water column. This stratification is evident in the large 
43

daily swings in temperature (fig. 10a) that are indicative of internal tidal bores and high crossshore and vertical temperature variability, declining water temperatures, and increasing salinity 

values that generally result from strong upwelling (Storlazzi and others, 2003). The strong winds 

and stratification resulted in relatively high current speeds, and thus, relatively high current shear 

stresses (fig. 28a). These stresses were sufficient to keep coarse silt and even fine sand in motion, 

preventing mud deposition in the study area except at the protected Tripod A location. 

The period before dredging followed the San Lorenzo River’s first significant flood 

(discharge=48.7 m3/s) of the season on 2009 YD 286; river discharge was approaching base flow 

levels (order~0.5 m3/s) by the start of the study on 2009 YD 290 (fig. 4f). Elevated turbidity 

levels at all of the tripods generally coincided with the larger-than-normal wave heights during 

2009 YD 296-299 (figs. 5-8). The comparisons between combined (wave+current) shear stresses 

and the resulting suspended-sediment fluxes near the bed (fig. 29), however, suggest that some 

of the elevated suspended-sediment fluxes near the seabed were due to the advection of material 

(high suspended-sediment concentrations at low shear stresses), and not only the resuspension of 

FIGURE 26. Map of modeled sediment accumulation, in millimeters, in the study area at four times the daily rate of 

fine-grain sediment discharge (925 m3

/day) of the 2009 dredge-disposal project. The resulting sediment accumulation 

is thin (thickness is approximately 2.0 cm) and temporary in nature (residence time on the seabed is on the order of 

30 days). 
44

FIGURE 27. Map of modeled combined maximum bed shear stress, in Newtons per square meter, in the study area. 

A, During large (deep-water height is 4.3 m at 15.2 s from 302°) wave conditions. B, During small (deep-water height 

is 1.2 m at 12.7 s from 270°) wave conditions. 
45

material on the seabed (higher suspended-sediment concentrations at higher shear stresses). 

These higher suspended-sediment concentrations at low shear stresses possibly are due to the 

advection of sediment from the 2009 YD 286 flood over the seabed near the tripods. Although 

the beach and seabed sampling were not done during the larger-than normal wave event during 

2009 YD 296-299, the beach and seabed surveys surrounding this event display a primarily 

medium- to fine-grain beach and seabed (fig. 13), suggesting that if any fine-grain flood 

sediment settled out, it was resuspended rapidly by the combined shear stresses and advected out 

of the study area. The data from the water-column surveys show a clear water column, except off 

Twin Lakes Beach and Black Point (figs. 11-12). 

During Dredging 

The period during the harbor dredge-disposal experiment (2009 YD 302-324) generally was 

characterized by weaker daily winds out of the northwest than those observed before the start of 

dredging (fig. 4c) and deep-water waves out of the northwest (fig. 4d). This general trend was 

punctuated by a period of waves out of the southwest and southerly winds (2009 YD 307-310) 

followed by larger-than-normal waves with long periods out of the northwest (2009 YD 310-

314). Due to the breakdown in northwest wind forcing between 2009 YD 307-310, the water 

column became mixed and warmed as upwelling shut down (fig. 10a). The weaker, less 

consistent winds and stratification resulted in lower current speeds, and thus current shear 

stresses were weaker than observed before the start of dredge-disposal operations (fig. 28a). The 

current shear stresses were high enough to keep coarse silt in motion intermittently except at 

Tripod A off the wharf, where the current shear stresses were not sufficient to keep coarse silt in 

motion. The combined (wave+current) shear stresses were sufficient to inhibit the deposition of 

coarse silt and even to keep fine sand often in motion, except at the location of Tripod A. 

Elevated turbidity levels at all of the tripods generally coincided with larger-than-normal waves 

during the period of dredging (figs. 5-8). The long-period waves out of the southwest caused 

slightly higher turbidity on 2009 YD 307; the larger waves out of the northwest on 2009 YD 

310-314 resulted in turbidity levels exceeding 100 NTUs at all of the tripod sites. The strong 

correlation between combined (wave+current) shear stresses and the resulting suspendedsediment fluxes (fig. 29) suggests that resuspension of material from the seabed (higher 

suspended-sediment concentrations at higher shear stresses) was the driving factor behind the 

high turbidity levels and suspended-sediment concentrations near the seabed during the dredgedisposal operations. 

While not sampled concurrently with the larger-than normal wave event on 2009 YD 

310-314, the beach and seabed surveys during this time period display no consistent change from 

a primarily medium- to fine-grain beach and seabed (fig. 13), suggesting that if deposition of 

fine-grain dredge sediment occurred in the study area, it was not great enough to cause a largescale shift in either the beach or seabed sediment to finer grain sizes. Similar to the data collected 

before the dredge-disposal operations, the data from the water-column surveys during the dredge 

operations show a clear water column, except off the dredge disposal site and Black Point where 

turbidity levels were higher than before the start of dredging (figs. 11-12), suggesting that the 

plume of fine-grain sediment discharged by the dredge-disposal operations was advected 

offshore to the southwest. The turbidity levels apparently caused by the dredge operations, 

however, were not significantly greater than those observed in the study area before the 

commencement of dredging.

After Dredging 

The period just after the harbor dredge-disposal experiment (2009 YD 325-339) generally 

was characterized by weaker daily winds and larger deep-water waves out of the northwest than 
46

those observed before the start of dredging (fig. 4c-d); this general trend was punctuated by a 

minor storm with some rain and small southwesterly waves, followed by large northwesterly 

waves (2009 YD 330-332). The weak northwest wind forcing and larger waves resulted in little 

to no water column stratification due to a lack of wind-driven upwelling (fig. 10a). The weaker 

and less consistent winds and stratification resulted in lower current speeds, and thus, lower 

current shear stresses than observed before the start of the dredge-disposal operations (fig. 28a). 

FIGURE 28. Time-series plot of wave, current, and combined shear stresses, in Newtons per square meter, at the 

main study sites. Data for Tripod A (Sea Floor Observatory), Tripod B (12 m), Tripod C (20 m), and Tripod D (30 m) 

are shown in red, orange, green, and blue, respectively. The horizontal dotted, dashed, and dot-dashed black lines 

denote the critical shear stresses for coarse silt (mud), fine sand, and coarse sand transport, respectively. 
47

The current shear stresses were high enough to keep coarse silt in motion only intermittently at 

Tripod D’s location along the 30 m isobath. The combined (wave+current) shear stresses were 

great enough to inhibit the deposition of coarse silt and to keep fine sand often in motion in the 

study area, except at the location of Tripod A off the wharf.

FIGURE 29. Scatter plots of near-bed suspended-sediment concentrations (SSC), in milligrams per liter, as a function 

of combined shear stress, in Newtons per square meter, at the main study sites. Data from before the start of 

dredging, during the dredging, after the dredging, and during the post-dredging storm and flood are shown in blue, 

red, green, and orange, respectively. 
48

Elevated turbidity levels at all of the tripods generally coincided with larger-than-normal 

waves following the period of dredging (figs. 5-8). The large waves out of the northwest caused 

turbidity levels exceeding 100 NTUs at all of the tripod sites. The strong correlation between 

combined (wave+current) shear stresses and the resulting suspended-sediment fluxes (fig. 29) 

suggests that resuspension of material from the seabed (higher suspended-sediment 

concentrations at higher shear stresses) was the driving factor behind the high turbidity levels 

and suspended-sediment concentrations near the seabed during most of the period following the 

end of dredge-disposal operations. However, during the few days following the end of dredge 

operations (2009 YD 324-327), turbidity levels were elevated, while the shear stresses were low 

(fig. 28), suggesting that the advection of material, possibly from the dredge-disposal operations, 

past the study sites. 

While not sampled concurrently with the larger-than normal wave event on 2009 YD 

330-332, the beach and seabed surveys during this time period display no consistent change from 

a primarily medium- to fine-grain beach and seabed (fig. 13), suggesting that if deposition of 

fine-grain dredge sediment occurred in the study area, it was not great enough to cause a largescale shift in either the beach or seabed sediment to finer grain sizes. Similar to the data collected 

before dredge-disposal operations, the data from the water-column surveys after dredge 

operations show a clear water column, except directly off the dredge disposal site and Black 

Point where turbidity levels continued to be higher than they were before the start of dredging 

(figs. 11-12). This suggests that some of the fine-grain sediment discharged by the dredgedisposal operations may have been resuspeded inshore of the tripods and advected offshore to the 

south. Farther offshore, however, the turbidity levels decreased to their pre-dredging levels. 

 

Post-Dredging Storm and Flood 

The final portion of the study period (2009 YD 340-349) was characterized by the San 

Lorenzo River’s second significant flood (daily mean discharge=4.6 m3

/s) of the season on 2009 

YD 345 (fig. 4f); this flood was an order of magnitude smaller than the first flood of the season 

that preceded the dredge-disposal operations. The storm started on 2009 YD 340 with rainfall 

(not shown) and the winds slowly changing from the northwest to southwest (fig. 4c) as the 

region of low pressure passed over central California. By 2009 YD 345, the winds were blowing 

strongly from out of the south, the river was discharging water at a rate of more than 4 m3

/s (fig. 

4f), and the wave period decreased (fig. 4e) as locally generated wind waves became more 

pronounced. These strong south (downwelling-favorable) winds and waves resulted in intense 

mixing, a break-down in stratification, and the advection of warmer offshore water into the bay, 

as evident in the increase in temperature (fig. 10a). Such temperature increases are indicative of 

downwelling (Storlazzi and others, 2003). While the inner shelf water temperatures increased 

due to downwelling, the influx of freshwater from the San Lorenzo River resulted in decreases in 

salinity along the 20 m and 30 m isobaths (fig. 10b). The southerly winds did not generate high 

current speeds or current shear stresses high enough to keep coarse silt in motion at the shallower 

tripod locations (fig. 28a). However, when combined with the short-period storm waves, the 

combined (wave+current) shear stresses were great enough to inhibit the deposition of coarse silt 

and fine sand throughout all of the study area; coarse sand was kept in motion at all but the 

location of Tripod A off the wharf. The current-induced shear stresses typically were not 

sufficient to resuspend the material on the seabed inshore of the 30 m isobath. The wave-induced 

stresses, however, generally were sufficient to inhibit the deposition of mud at all of the four 

instrument sites. Under the combination of waves and currents, even fine-grain sand was 

generally in motion; during large wave events, even coarse sand is mobilized at all of the four 

instrument sites. 
49

Elevated turbidity levels at all of the tripods generally coincided with discharge from the 

San Lorenzo River and storm waves, which resulted in levels exceeding 100 NTUs at all of the 

tripod sites (figs. 5-8). Although there was some correlation between combined (wave+current) 

shear stresses and the resulting suspended-sediment fluxes (fig. 29) that suggested near-bed 

turbidity was due to the resuspension of seabed material, often the turbidity levels were elevated 

while the shear stresses were low (fig. 28), suggesting that the sediment causing the elevated 

turbidity levels resulted from the advection of material, possibly from the dredge-disposal 

operations but likely due to discharge from the San Lorenzo River, past the study sites. Due to 

the rough atmospheric and oceanographic conditions, no beach, seabed, or water-column surveys 

were done during this time period. 

Sediment Geochemistry

 The observed differences in percent C, 15N, 13C, and C/N between Santa Cruz Harbor 

sediment and trap-collected suspended sediment suggest that the material collected in the 

sediment traps did not originate from the material dredged from the harbor (specifically the north 

harbor areas). Although percent C and percent N contents of trap-collected sediment changed 

between the early-, late-, and post-dredging collection periods, the lack of change in C/N with 

time suggests a change in the fraction of organic material accumulating, but not a change in the 

predominant source of organic material. Carbon isotopic compositions of both harbor sediment 

and suspended sediment collected in traps are distinct from that of San Lorenzo River suspended 

sediment (13C~ -28‰, Conaway, unpublished data). Because of the differences in 13C between 

the harbor, trap-collected suspended sediment, and San Lorenzo River suspended sediment, it is 

unlikely that recent or contemporaneous material from the San Lorenzo River or dredge disposal 

from the north harbor are a substantial part of the organic fraction of material collected in 

sediment traps. Carbon and nitrogen isotopic and elemental composition data provide insight into 

the nature and origin of material accumulating in the harbor and the suspended sediment 

collected offshore. Compared to typical average compositional values of major particulate 

organic matter sources (Kendall and others, 2001), the 15N, 13C, and C/N values of harbor 

sediment samples are consistent with aquatic macrophytes, C3 terrestrial plants, or a mixture of 

the two. Similarly, carbon and nitrogen isotopic composition and C/N molar ratios of suspended 

sediment collected in traps are consistent with a mixture of plankton and particles derived from 

aquatic macrophytes. 

 The short-lived radionuclide data show the lack of a substantial contribution of recent 

sediment from the San Lorenzo River to suspended sediment collected in the sediment traps 

during the dredging period. Suspended sediment collected from the San Lorenzo River during a 

high-flow event on 10/17/2009 (2009 Year Day 290) had 7

Be activity of 6.9–23 dpm/g and a 

7

Be/210Pbxs ratio of 1.4–2.4 (Conaway, unpublished data). Although 7Be has a short half life of 53 

days, the values for San Lorenzo River sediment would not be expected to change much over the 

23 day period of the first trap deployment (2009 Year Day 313) and the last suspended sediment 

collection date (2009 Year Day 349) occurred only slightly more than one half-life of 7Be after 

the flood event. These values are substantially higher than the 7

Be values observed in trap 

collected suspended sediment (<1.2 dpm/g) during dredging activity, indicating that suspended 

sediment collected was not predominantly (re)suspended material from the recent San Lorenzo 

River storm event. The relatively high activity of 7Be in trap-collected suspended sediment postdredging compared to trap-collected suspended sediment during dredging may reflect the 

resuspension or input of some recent San Lorenzo River material in the post-dredging storm and 

flood period (2009 Year Days 340–349), or alternatively direct wet deposition (through 

rainwater) of 7

Be to the ocean, and sorption to suspended sediment. Because 210Pb is scavenged 

rapidly from the water column to suspended sediment, it is difficult to make any comparison 
50

between 210Pbxs activities in harbor sediment and trap-collected sediment. This suggests that the 

fine-grain sediment dredged from the harbor was either not transported to these locations or was 

diluted to such a degree compared to resuspended seabed sediment that it was difficult to identify 

in the trap samples. 

 Elements associated with fine-grain material or organic matter, such as particle-reactive 

contaminants, are expected to show a positive correlation with percent clay or percent C. 

Conversely, elements associated with discrete mineral grains may show a positive correlation 

with the abundance of coarser grain-size fractions or percent silt. Note that all samples were 

sieved to 100 micron (very fine sand) before geochemical analysis, and therefore we consider 

percent silt to be representative of the silt and very fine sand fractions. The observed correlation 

of Cu, Pb, and Zn with percent clay and organic C suggests that these elements behave as 

particle-reactive, organic-associated elements. The correlation of Co, Cr, Fe, and Ni with percent 

silt suggests that these elements are associated with (natural) mineral grains, presumably 

ferromagnesian minerals. 

 Spatial and temporal trends of the contents of elements in the sediment trap-collected 

material are related predominantly to grain size and organic matter. The observed early-, late-, 

and post-dredging trend in percent C, and associated changes in elements As, Cu, Mo, Pb, Zn, 

are interpreted to mean that an increase in fine-grain, organic-rich (high percent C) material 

collected in the sediment traps at mooring sites close to the end of the dredging period resulted in 

an increase in particle-reactive, organic-associated, and redox-sensitive elements compared to 

other collection periods. The positive correlation of Co, Cr, and Ni in the sediment traps with 

increasing distance from shore reflects a changing lithology as marine sediment predominates. 

The observed offshore decrease in Cu and Mo is interpreted to mean that Cu and Mo are derived 

from land, whereas Pb, which showed no change after grain-size normalization, may be more 

pervasive in the shore-shelf system. The up to 2-fold enrichment of Cu and Zn in north harbor 

sediment relative to sediment collected at the moorings shows that sediment collected at the 

mooring locations was not predominantly from the harbor, although geochemical changes in 

sediment during dredging or transport are a possibility. 

Sediment Dynamics 

 The calculated suspended-sediment fluxes from the four tripods (figs. 30-33) for the four 

periods (before, during and after dredge operations and during the following storm and flood) 

show two consistent trends. First, the near-bed suspended-sediment fluxes were always an order 

of magnitude greater (~100 tons/m2/day) than those observed higher (>2 m above the seabed) in 

the water column (~10 tons/m2/day). Since coarser grain sizes have faster settling velocities 

(table 8) and are not resuspended to great heights above the seabed, it can be assumed that these 

higher near-bed suspended-sediment fluxes generally represent coarser-grained material. 

Conversely, the suspended-sediment fluxes higher in the water column likely are slower-settling 

fine-grain material, presumably including the mud-sized material dredged during the 

demonstration project. Second, there was vertical shear in suspended-sediment flux at each 

tripod site, meaning that the direction of suspended-sediment flux always varied vertically 

through the water column at a given location. These two observations, combined, suggest that 

large quantities of primarily coarse-grained sediment moved through the study area near the bed 

and smaller quantities of finer-grained sediment generally headed in a different direction higher 

in the water column. The lack of sufficient quantities of material in the sediment traps that could 

be geochemically linked to the harbor dredge disposal or deposition of fine-grain material on the 

seabed, in conjunction with the low suspended-sediment concentrations measured by the tripods, 

suggests that the fine-grain dredge-disposal outfall was diluted significantly and advected 
51

FIGURE 30. Map showing the daily mean suspended-sediment fluxes, in metric tons per square meter per day, 

before the start of dredging (2009 YD 295-301). Data from close to the seabed, the lower water column, and close to 

the surface are shown in blue, green, and red, respectively. Note the difference in scale of the vectors. 
52

through the study area such that net deposition on the seabed did not occur and the flux of 

material at the height and location of the traps was minimal. 

FIGURE 31. Map showing the daily mean suspended-sediment fluxes, in metric tons per square meter per day, 

during the dredging (2009 YD 302-324). Data from close to the seabed, the lower water column, and close to the 

surface are shown in blue, green, and red, respectively. Note the difference in scale of the vectors. 
53

 Before the start of dredging (2009 YD 295-301; fig. 30), sediment flux near the seabed 

and in the lower water column was obliquely onshore to the northeast; the sediment flux near the 

FIGURE 32. Map showing the daily mean suspended-sediment fluxes, in metric tons per square meter per day, after 

the dredging (2009 YD 325-339). Data from close to the seabed, the lower water column, and close to the surface are 

shown in blue, green, and red, respectively. Note the difference in scale of the vectors. 
54

surface was low in magnitude and oriented primarily offshore. During the dredge operations 

(2009 YD 302-324; fig. 31), there was both vertical and horizontal shear in sediment flux, with 

FIGURE 33. Map showing the daily mean suspended-sediment fluxes, in metric tons per square meter per day, 

during the storm and flood after the dredging (2009 YD 340-345). Data from close to the seabed, the lower water 

column, and close to the surface are shown in blue, green, and red, respectively. Note the difference in scale of the 

vectors. 
55

the sediment flux near the seabed at all sites oriented obliquely onshore to the northeast and 

higher in magnitude offshore. The sediment flux in the entire water column off Black Point was 

oriented obliquely offshore to the southeast, while offshore along the 20 m and 30 m isobaths the 

sediment flux in water column was offshore to the southwest. 

After the cessation of dredging (2009 YD 325-339; fig. 32), the sediment flux in the 

lower water column and near the surface off Black Point was oriented alongshore to the east, 

while offshore along the 30 m isobath the sediment flux in the lower water column and near the 

surface was weakly offshore to the southwest. Similar to the period of dredge operations (fig. 

31), there was both vertical and horizontal shear in sediment flux during the storm and flood 

after the dredging (2009 YD 340-345; fig. 33). The sediment flux off Black Point was oriented 

obliquely alongshore to the southeast. Offshore, the sediment flux close to the seabed was 

onshore to the north along the 20 m isobath and to the east along the 30 m isobath, but it was to 

the west in the mid water column and near the surface. Overall, the net flux of what is assumed 

to be coarse-grained material near the seabed was primarily to the east into the bay. Fine-grain 

material higher up in the water column, presumably including the mud-sized sediment dredged 

from the Santa Cruz Harbor, was offshore to the southeast close to shore along the 12 m isobath 

and offshore to the southwest farther from shore along the 20 m and 30 m isobaths.The 

atmospheric (winds) and oceanographic (waves) forcing observed during the harbor dredgedisposal experiment was typical of the fall and winter months in the study area (Storlazzi and 

Wingfield, 2005), as was the fluvial discharge from the San Lorenzo River (NWIS, 2010), as 

shown in figure 34. This suggests that the resulting levels of near-bed shear stress (high enough 

to inhibit deposition of mud), turbidity levels, and sediment-flux patterns (onshore sand and 

offshore mud transport) observed during the dredge-disposal experiment likely are characteristic 

of the time period (October-November). 

Summary of Findings 

More than 400,000 measurements of oceanographic forcing and the resulting watercolumn and seabed properties were made in northern Monterey Bay, California, to understand 

the sediment dynamics and fate of fine-grain sediment dredged from the inner portion of Santa 

Cruz Harbor. These measurements were made in the 17-day period during which more than 7600 

m3

 of sediment was dredged from Santa Cruz Harbor and discharged approximately 60 m 

offshore of the harbor at a depth of 2 m on the inner shelf. Key findings from these 

measurements and analyses include: 

1) Waves and circulation generally were more vigorous to the east of the wharf and farther 

offshore. Flow was primarily to the east near the seabed close to shore and to the west and 

offshore higher up in the water column. 

2) There did not appear to be significant net deposition of mud from either the San Lorenzo 

River or the Santa Cruz Harbor dredge-disposal operations because there was no shift to a finer 

grain-size class along the beach or on the inner shelf. 

3) The difference between the grain size on the seabed and that captured in the sediment traps 

demonstrates that there was fine-grain, muddy sediment transported through the study area. 

4) Chemical analysis of sediment, including C and N isotopic and elemental composition and 

short-lived radioisotope analyses, demonstrated that suspended sediment collected in sediment 

traps was not recent fluvial sediment from the San Lorenzo River or material discharged from 
56

FIGURE 34. Time-series plot of regional meteorologic, oceanographic, fluvial, and resulting turbidity data during the 

study period. A, Red: wind speed, in meters per second; Blue: wind speed and direction, in meters per second from 

degrees true north. B, Red: wave height, in meters; Blue: wave height and direction, in meters from degrees true 

north. C, Wave period, in seconds. D, River discharge, in meters cubed per second. E, Near-bed turbidity, in National 

Turbidity Units (NTU), at the four tripods in the study area. The period of dredge-disposal operations and the postdredging storm and flood are denoted by the light grey (2009 Year Days 302-324) and dark grey boxes (2009 Year 

Days 340-349), respectively. The heavy black horizontal lines in parts A-C show the 15-year averages (Storlazzi and 

Wingfield, 2005) and the 29-year average in part D (NWIS, 2010).
57

the dredging of northern Santa Cruz Harbor. Based on the observed sediment fluxes and 

numerical modeling results, this suggests that Santa Cruz Harbor dredge material and San 

Lorenzo River sediment made up a small fraction of total suspended material in the study area. 

5) Except off the end of the wharf, the current shear stresses were high enough to keep coarse silt 

from settling out of suspension and depositing on the seabed only intermittently under the 

conditions observed during the experiment. However, in conjunction with the wave-induced 

shear stresses, the combined (wave+current) shear stresses generally were sufficient to inhibit the 

deposition of coarse silt and often kept fine sand in motion in the study area during the 

experiment. This was true for all instrument locations except off the wharf, where the combined 

shear stresses were sufficient to inhibit the deposition of coarse silt only intermittently during the 

course of the experiment. 

6) The net flux of what is assumed to be coarse-grained material near the seabed primarily was to 

the east into the bay under the oceanographic conditions observed during the course of the 

experiment. Transport of finer-grained material higher in the water column, including 

presumably the mud-sized sediment dredged from Santa Cruz Harbor, was offshore to the 

southeast along the 12 m isobath and offshore to the southwest farther along the 20 m and 30 m 

isobaths. 

7) The numerical model results suggest that the dredge-disposal plume would be advected 

alongshore to the southwest during low wave-energy conditions. During larger wave-energy 

conditions, the dredge-disposal plume would be advected first to the east towards Capitola. 

These modeled patterns resulted in temporary (maximum residence time = 20 days), thin 

(maximum thickness = 0.0011 m) deposition of fine-grain sediment on the seabed offshore 

Capitola. In the model, the dredge material subsequently was eroded from this temporary 

depocenter offshore Capitola and advected offshore to the southwest in the direction of the midshelf mud belt before the end of the dredging period. Due to the small errors in modeled wave 

and current patterns, and low modeled suspended-sediment concentrations, the thin, temporary 

accumulation patterns predicted by the model are well within the error of the model and are not 

assumed to be real. 

8) Together, oceanographic observations, model results, and laboratory analyses suggest that the 

predominantly mud-sized sediment dredged from Santa Cruz Harbor and discharged to the 

coastal ocean: (a) did not result in observable deposition of fine-grain sediment on the beach and 

inner continental shelf, (b) likely was advected alongshore to the east, then offshore to the 

southwest in the direction of the mid-shelf mud belt, and (c) resulted in turbidity values lower 

than those values observed during a large wave event or a small flood of the San Lorenzo River. 

9) The atmospheric (winds) and oceanographic (waves) forcing observed during the Santa Cruz 

Harbor dredge-disposal experiment was typical of the fall and winter months in the study area, 

suggesting that the resulting levels of near-bed shear stress (high enough to inhibit deposition of 

mud) and sediment flux patterns (onshore sand transport, offshore mud transport) likely are 

characteristic of the time period (October-November). 

 These data provide information on the nature and controls on flow and water-column and 

seabed properties in northern Monterey Bay, California, during late summer through winter 

conditions. A number of interesting phenomena were observed that indicate the complexity of 

coastal circulation and sediment dynamics in the northern part of the bay and may help 
58

researchers and regulators to better understand the implications of the processes on sediment 

dynamics.

Acknowledgements 

This work was funded primarily by the U.S. Army Corps of Engineers’ (USACE) San 

Francisco District, the USGS’s Pacific Coastal and Marine Science Center (USGS-PCMSC), and 

the Santa Cruz Port District. The research was carried out as part of the USGS’s Benthic Habitats 

(Pacific) and Applied Sediment Transport Projects; the ultimate goal is to better understand the 

importance of sediment dynamics on benthic habitats along the U.S. west coast. This scientific 

research was done under Monterey Bay National Marine Sanctuary (MBNMS) research permit 

MBNMS-2009-025. Peter Mull (USACE) coordinated the funding and contributed advice on 

project planning. Brian Foss and the Santa Cruz Port District staff helped with project planning 

and provided significant logistical help and facilities to support our field operations. Mike 

Torresan (USGS) and Angela Lam (USGS) processed the sediment-trap samples for grain-size 

distributions. Peter Swarzenski (USGS) provided the geochemical radionuclide data. Carbon and 

nitrogen elemental and isotopic composition were processed by Steve Silva (USGS) and Doug 

Choy (USGS); samples for trace element composition were processed by Monique Adams 

(USGS). The Santa Cruz Harbor samples were provided by Steve Krcik of Red Hill 

Environmental. Erica Burton (MBNMS) helped with the permitting for this project. Rachel 

“Charlie” McGillis provided logistical support for the small boat survey operations. We would 

also like to thank Renee Takesue (USGS) and Steve Watt (USGS) who contributed numerous 

excellent suggestions and a timely review of our work. 

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62

Additional Digital Information

For additional information on the instrument deployments, please see: 

Tripod and Sediment Trap Deployments 

http://walrus.wr.usgs.gov/infobank/i/id209mb/html/i-d2-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/i/id309mb/html/i-d3-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/i/ir209mb/html/i-r2-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/i/ir309mb/html/i-r3-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/i/ir409mb/html/i-r4-09-mb.meta.html 

Seabed (Flying Eyeball) Surveys 

http://walrus.wr.usgs.gov/infobank/f/fe109mb/html/f-e1-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/f/fe209mb/html/f-e2-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/f/fe309mb/html/f-e3-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/f/fe409mb/html/f-e4-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/f/fe509mb/html/f-e5-09-mb.meta.html 

Water Column (CTD Profiler) Surveys: 

http://walrus.wr.usgs.gov/infobank/w/wc109mb/html/w-c1-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/w/wc209mb/html/w-c2-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/w/wc309mb/html/w-c3-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/w/wc409mb/html/w-c4-09-mb.meta.html 

http://walrus.wr.usgs.gov/infobank/w/wc509mb/html/w-c5-09-mb.meta.html 

For an online PDF version of this report, please see: 

http://pubs.usgs.gov/of/2011/1045/. 

For more information on the U.S. Geological Survey Western Region’s Coastal and Marine 

Geology Team, please see: 

http://walrus.wr.usgs.gov/. 

Direct Contact Information 

Project Information 

Curt D. Storlazzi (Project Chief): cstorlazzi@usgs.gov
63

Table 1. Experiment personnel. 

Person Affiliation Responsibilities

Curt Storlazzi USGS Chief Scientist, oceanographer, diver

Christopher Conaway USGS Co-chief Scientist, geochemist

Joshua Logan USGS Information specialist, diver, vessel captain

Kathy Presto USGS Oceanographer, instrument specialist

Katherine Cronin Deltares Numerical modeler

Maarten van Ormondt Deltares Numerical modeler

Lynne Harden UCSC Geologist

Jamie Lescinski Deltares Numerical modeler

Jessica Lacy USGS Oceanographer

Pieter Tonnon Deltares Numerical modeler

Pete dal Ferro USGS Mechanical technician, diver, vessel captain

Tim Elfers USGS Mechanical technician, vessel captain

George Tate USGS Supervisory marine technician

Thomas Reiss USGS Diver

Peter Harkins USGS Mechanical technician

Cordel Johnson USGS Mechanical technician

Kurt Rosenberger USGS Oceanographer

Andy Ritchie USGS Geographer

Jamie Grover USGS R/V Parke Snavely vessel captain

Jim Christman - R/V Shana Rae vessel captain

Andrew Reynaga UCSC R/V Paragon vessel captain
64

Table 2. Instrument package sensors. 

Site Name Height Above 

Bed

[m]

Depth

[m]

Sensors

Tripod A (9 m) 2.0 to surface 9 RD Instruments 1200 kHz Workhorse ADCM profiler

0.5 9 Sontek 5000 kHz ADCM velocimeter

0.5 9 D&A Instruments OBS-3

0.3 9 D&A Instruments OBS-3

1.0 9 Seabird SBE-37SI Microcat doivity-temperature sensor

Tripod B (12 m) 1.0 to surface 12 Nortek 600 kHz AWAC ADCM profiler

0.5 12 Aquatec/Seapoint 210-TY optical backscatter sensor

0.5 12 Seabird SBE-37SI Microcat doivity-temperature sensor

Tripod C (20 m) 2.0 to surface 20 RD Instruments 600 kHz Workhorse ADCM profiler

1.0 20 Nortek 2000 kHz Aquadopp ADCM profiler

2.0 20 Aquatec/Seapoint 210-TY optical backscatter sensor

0.5 20 Aquatec/Seapoint 210-TY optical backscatter sensor

1.3 20 Seabird SBE-37SI Microcat doivity-temperature sensor

Tripod D (30 m) 2.0 to surface 30 RD Instruments 600 kHz Workhorse ADCM profiler

0.5 30 Nortek 2000 kHz Aquadopp ADCM profiler

0.5 30 Aquatec/Seapoint 210-TY optical backscatter sensor

1.3 30 Seabird SBE-37SI Microcat doivity-temperature sensor

Trap-10 m 5 10 Sediment trap

Trap-15 m 5 15 Sediment trap

Trap-20 m 5 20 Sediment trap

Trap-30 m 5 30 Sediment trap

Terrestial Imaging System 

(TIS) - [15]* Harbortronics time-lapse digital camera package

NDBC buoy - [5]* ARES payload

*Height, in meters 
65

Table 3. Instrument package location information. 

Site Name Latitude

[decimal degrees]

Longitude

[decimal degrees]

Tripod A (9 m) 36.9569030 -122.0170036

Tripod B (12 m) 36.9533102 -121.9954277

Tripod C (20 m) 36.9384208 -122.0042870

Tripod D (30 m) 36.9237328 -122.0030674

Trap-10 m 36.9576419 -122.0028116

Trap-15 m 36.9506359 -122.0035570

Trap-20 m 36.9385923 -122.0046942

Trap-30 m 36.9243497 -122.0034216

Terrestial Imaging System (TIS) 36.960672 -122.002175

NDBC buoy 36.789 -122.404

NWIS stream gauge 36.990833 -122.030833

Harbor dredge outfall 36.9612436 -121.9997965
66

Table 4. Flying Eyeball sample location information. 

[A minimum of three samples were taken as close to each location as possible.] 

Site ID/number Latitude

[decimal degrees]

Longitude

[decimal degrees]

FE 1 36.9596971 -122.02250

FE 2 36.9579024 -122.02108

FE 3 36.9542971 -122.02112

FE 4 36.9506918 -122.02117

FE 5 36.9470866 -122.02121

FE 6 36.9434813 -122.02126

FE 7 36.9615077 -122.02103

FE 8 36.9614705 -122.01654

FE 9 36.9578653 -122.01658

FE 10 36.954260 -122.01663

FE 11 36.9506547 -122.01668

FE 12 36.9470495 -122.01672

FE 13 36.9434442 -122.01677

FE 14 36.9614332 -122.01204

FE 15 36.9578280 -122.01209

FE 16 36.9542227 -122.01214

FE 17 36.9506174 -122.01218

FE 18 36.9470122 -122.01223

FE 19 36.9434069 -122.01228

FE 20 36.9613958 -122.00755

FE 21 36.9577905 -122.0076

FE 22 36.9541852 -122.00765

FE 23 36.9505800 -122.00769

FE 24 36.9469747 -122.00774

FE 25 36.9433695 -122.00779

FE 26 36.9606140 -122.00310

FE 27 36.9577529 -122.00311

FE 28 36.9541476 -122.00315

FE 29 36.9505424 -122.00320

FE 30 36.9469371 -122.00325

FE 31 36.9433319 -122.00329

FE 32 36.9598570 -121.99855

FE 33 36.9577151 -121.99861

FE 34 36.9541098 -121.99866

FE 35 36.9505046 -121.99871

FE 36 36.9468993 -121.99876

FE 37 36.9432941 -121.99880

FE 38 36.9571037 -121.99311
67

FE 39 36.9540719 -121.99417

FE 40 36.9504666 -121.99422

FE 41 36.9468614 -121.99426

FE 42 36.9432561 -121.99431

FE 43 36.9386683 -122.00379

FE 44 36.9339908 -122.00379

FE 45 36.9294030 -122.00357

FE 46 36.9239602 -122.00362

Table 5. Beach Ball sample location information. 

[A minimum of three samples were taken in the middle of the swash zone, and three 

samples were taken at the wet/dry line as close to the location as possible.]

Site ID/Number Latitude

[decimal degrees]

Longitude

[decimal degrees]

BB 1 36.9611924 -122.0237600

BB 2 36.9626055 -122.0206446

BB 3 36.9632251 -122.0164798

BB 4 36.9629243 -122.0117562

BB 5 36.9622105 -122.0072010

BB 6 36.9612606 -122.0031108

BB 7 36.9613768 -121.9987895

BB 8 36.9597686 -121.9942191
68

Table 6. Water Column Profiler cast location information.

Site ID/Number Latitude

[decimal degrees]

Longitude

[decimal degrees]

WC 8 36.9614705 -122.01654

WC 9 36.9578653 -122.01658

WC 10 36.9542600 -122.01663

WC 14 36.9614332 -122.01204

WC 15 36.9578280 -122.01209

WC 16 36.9542227 -122.01214

WC 20 36.9613958 -122.00755

WC 21 36.9577905 -122.00760

WC 22 36.9541852 -122.00765

WC 26 36.9606140 -122.00310

WC 27 36.9577529 -122.00311

WC 28 36.9541476 -122.00315

WC 29 36.9505424 -122.00320

WC 30 36.9469371 -122.00325

WC 32 36.9598570 -121.99855

WC 33 36.9577151 -121.99861

WC 34 36.9541098 -121.99866

WC 38 36.9571037 -121.99311

WC 39 36.9540719 -121.99417

WC 43 36.9386683 -122.00379

WC 46 36.9239602 -122.00362

Table 7. Sediment sample location and depth information. 

USGS Sample 

Identifier

Sample Type Latitude

[decimal degrees]

Longitude

[decimal degrees]

Water Depth

[m]

Sample Depth

[m]

Trap-10 m Sediment trap 36.9576419 -122.0028116 10 5

Trap-15 m Sediment trap 36.9506359 -122.0035570 15 10

Trap-20 m Sediment trap 36.9385923 -122.0046942 20 15

Trap-30 m Sediment trap 36.9243497 -122.0034216 30 25

Seabed-10 m Sea floor 36.9576419 -122.0028116 10 10

Seabed-15 m Sea floor 36.9506359 -122.0035570 15 15

Seabed-20 m Sea floor 36.9385923 -122.0046942 20 20

Seabed-30 m Sea floor 36.9243497 -122.0034216 30 30

Tripod D (30 m) Tripod 36.9237328 -122.0030674 30 28
69

Table 8. Sediment settling velocities. 

[Assumes a sediment bulk density of 2650 kg/m3 in 12oC water.]

Grain Class Grain Diameter

[mm]

Settling Velocity

[m/s]

Coarse sand 1.000 0.1125524

Fine sand 0.200 0.0173889

Coarse silt 0.040 0.0096930

Fine silt 0.010 0.0006241

Clay 0.003 0.0000564

Table 9. Harbor Daily Dredge Volumes.

[N.D., No dredging occurred.]

2009 Year 

Day

Mud-sized (<63 μm) material

[m3]

Sand-sized (>63 μm) material

[m3]

Total

[m3]

302 372 71 443

303 372 164 536

304 N.D. N.D. N.D.

305 N.D. N.D. N.D.

306 392 44 436

307 20 57 76

308 412 47 459

309 341 202 543

310 346 82 428

311 N.D. N.D. N.D.

312 N.D. N.D. N.D.

313 413 31 443

314 205 101 306

315 359 177 535

316 134 57 191

317 38 38 76

318 N.D. N.D. N.D.

319 N.D. N.D. N.D.

320 403 95 498

321 398 99 497

322 417 83 501

323 417 111 528

324 381 772 1153
70

Table 10. Meteorologic, oceanographic, and river discharge statistics.

[All statistics were calculated for 2009 Year Days 295-349; wind and wave direction is “From”.]

Site Name Mean ± 1 std deviation Minimum Maximum

Sea level barometric pressure [mb] 1017.1±3.5 1004.1 1024.4

Water temperature [oC] 12.77±0.79 11.62 15.26

Wind speed [m/s] 6.32±3.18 0.34 15.39

Wind direction [oTrue] 264.1±109.9 0.0 359.9

Wave height [m] 2.72±1.03 0.95 6.88

Wave period [s] 13.22±3.08 4.55 23.53

Wave direction [oTrue] 299.5±18.0 182.3 333.4

River discharge [m3/s] 0.63±0.89 0.25 5.47

Table 11. Wave statistics. 

[All statistics were calculated for 2009 Year Days 295-349; wave direction is “From”.] 

Site Name Parameter Mean ± 1 Std Deviation Minimum Maximum

Tripod A (9 m) Height [m] 0.50±0.26 0.18 1.61

Period [s] 14.9±2.9 4.2 22.3

Direction [oTrue] 212.0±63.7 180.8 359.1

Tripod B (12 m) Height [m] 0.85 ±0.36 0.30 2.55

Period [s] 10.9±2.1 3.2 15.3

Direction [oTrue] 218.5±7.3 192.9 238.1

Tripod C (20 m) Height [m] 1.00±0.35 0.40 2.46

Period [s] 12.2±5.5 2.0 25.6

Direction [oTrue] 230.7±11.4 176.9 267.4

Tripod D (30 m) Height [m] 1.18±0.38 0.52 2.72

Period [s] 11.7±5.4 2.1 25.6

Direction [oTrue] 251.5±14.6 190.3 291.4
71

Table 12. Current statistics.

[All statistics were calculated for 2009 Year Days 295-349; current direction is “Going to”.] 

[N.S., Near-surface observation.] 

[N.B., Near-seabed observation.] 

Site Name Parameter Depth

[m]

Mean ± 1 Std Deviation Minimum Maximum

Tripod A (9 m) Speed [m/s] 8.5 (N.B.) 0.02±0.02 0.00 0.28

Direction [oTrue] 8.5 (N.B.) 198.65±101.10 0.15 356.79

Tripod B (12 m) Speed [m/s] 1.0 (N.S.) 0.052±0.03 0.00 0.21

Direction [oTrue] 1.0 (N.S.) 155.8±93.7 0.0 359.9

Speed [m/s] 11.0 (N.B.) 0.045±0.02 0.00 0.15

Direction [oTrue] 11.0 (N.B.) 159.9±100.2 0.0 359.9

Tripod C (20 m) Speed [m/s] 1.0 (N.S.) 0.08±0.05 0.00 0.30

Direction [oTrue] 1.0 (N.S.) 187.9±84.1 14.3 359.5

Speed [m/s] 17.5 (N.B.) 0.03±0.02 0.00 0.13

Direction [oTrue] 17.5 (N.B.) 184.9±81.4 14.2 358.7

Tripod D (30 m) Speed [m/s] 1.0 (N.S.) 0.09±0.05 0.00 0.31

Direction [oTrue] 1.0 (N.S.) 164.6±80.6 0.8 358.6

Speed [m/s] 26.5 (N.B.) 0.05±0.03 0.00 0.17

Direction [oTrue] 26.5 (N.B.) 159.9±100.2 0.0 359.9
72

Table 13. Turbidity statistics. 

[All statistics were calculated for 2009 Year Days 295-349.]

Site Name Time Period

[2009 Year Days]

Depth

[m]

Mean ± 1 Std 

Deviation

[NTU]

Minimum

[NTU]

Maximum

[NTU]

Tripod A (9 m) Experiment [295-349] 8.5 39±41 1 118

Pre-Dredging [295-301] 8.5 45±47 1 118

Dredging [302-324] 8.5 36±39 1 79

Post-Dredging [325-339] 8.5 36±33 3 36

Storm and Flood [340-349] 8.5 41±38 1 74

Tripod B (12 m) Experiment [295-349] 11 29±35 0 311

Pre-Dredging [295-301] 11 11±7 1 53

Dredging [302-324] 11 20±33 0 245

Post-Dredging [325-339] 11 43±39 2 311

Storm and Flood [340-349] 11 37±31 2 261

Tripod C (20 m) Experiment [295-349] 18 6±6 1 61

Pre-Dredging [295-301] 18 5±0 1 23

Dredging [302-324] 18 5±36 1 32

Post-Dredging [325-339] 18 8±7 2 42

Storm and Flood [340-349] 18 11±16 1 61

Experiment [295-349] 19.5 22±36 0 490

Pre-Dredging [295-301] 19.5 8±7 1 48

Dredging [302-324] 19.5 11±16 0 159

Post-Dredging [325-339] 19.5 31±26 1 184

Storm and Flood [340-349] 19.5 47±70 1 490

Tripod D (30 m) Experiment [295-349] 29.5 17±20 2 693

Pre-Dredging [295-301] 29.5 11±6 4 52

Dredging [302-324] 29.5 14±16 3 132

Post-Dredging [325-339] 29.5 22±19 4 169

Storm and Flood [340-349] 29.5 23±32 2 693

Table 14. Temperature statistics.

[All statistics were calculated for 2009 Year Days 295-349.] 

Site Name Depth

[m]

Mean ± 1 Std Deviation

[

o

C]

Minimum

[

o

C]

Maximum

[

o

C]

Tripod B (12 m) 11 12.12±0.79 10.89 14.31

Tripod C (20 m) 20 11.85±0.66 10.82 13.79

Tripod D (30 m) 30 11.58±0.56 10.56 13.59
73

Table 15. Salinity statistics.

[All statistics were calculated for 2009 Year Days 295-349.]

Site Name Depth

[m]

Mean ± 1 Std Deviation

[PSU]

Minimum

[PSU]

Maximum

[PSU]

Tripod B (12 m)* 12 31.06±0.1.87 23.41 33.23

Tripod C (20 m) 19 33.43±0.06 33.14 33.59

Tripod D (30 m) 29 33.35±0.11 33.10 33.61

*Statistics are low due to biofouling of the sensor’s doivity cell.

Table 16. Sediment sample grain-size information.

[N.D., No data.]

USGS Sample 

Identifier

Average Trap 

Collection Rate

[mg/cm2/day]

Gravel

[percent]

Sand

[percent]

Silt

[percent]

Clay

[percent]

Mud

[percent]

Mean Size

[mm]

Trap-10 m 0.676 0.00 16.34 62.51 21.15 86.91 0.0260

Trap-15 m 0.827 0.00 13.42 65.03 21.55 86.58 0.0249

Trap-20 m 0.824 0.00 16.63 63.22 20.15 87.80 0.0267

Trap-30 m 0.754 0.00 9.79 69.60 20.60 86.81 0.0227

Seabed-10 m N.D. 0.04 69.15 23.92 6.89 88.36 0.0822

Seabed-15 m N.D. 0.00 97.04 2.04 0.93 95.08 0.3702

Seabed-20 m N.D. 0.17 83.55 13.04 3.23 97.76 0.1279

Seabed-30 m N.D. 4.33 81.84 10.89 2.93 75.72 0.1232

Tripod D (30 m) N.D. 0.00 47.06 41.78 11.16 67.24 0.0552
74

Table 17. Carbon and Nitrogen Signatures of Sediment Samples.

USGS sample 

identifier

Time frame

[2009 Year Days]

C

[percent]

N

[percent]

δ15N δ13C C/N

[molar ratio]

Trap-10 m 292-313 1.95 0.275 7.77 -21.65 8.3

Trap-15 m* 292-313 2.06 0.277 6.01 -21.26 8.7

Trap-20 m 292-313 1.83 0.236 7.19 -21.98 9.1

Trap-30 m 292-313 1.20 0.153 6.03 -22.56 9.2

Trap-10 m 313-336 2.60 0.343 6.74 -22.17 8.8

Trap-20 m 313-336 2.27 0.295 5.54 -21.98 9.0

Trap-30 m 313-336 2.00 0.219 6.43 -23.32 10.7

Trap-10 m 336-349 1.19 0.159 6.28 -21.86 8.7

Trap-20 m 336-349 1.18 0.147 5.89 -21.77 9.3

Trap-30 m 336-349 1.19 0.154 2.61 -22.09 9.0

Tripod D (30 m) After 350 1.05 0.129 5.11 -20.91 9.5

Seabed-10 m After 350 0.28 0.043 3.33 -24.02 7.6

Seabed-15 m After 350 0.34 0.041 1.85 -22.73 9.7

Seabed-20 m After 350 0.26 0.033 2.38 -22.17 9.2

Seabed-30 m After 350 0.33 0.041 0.74 -23.79 9.3

A1 - harbor Before 302 2.48 0.21 5.18 -25.58 14.1

A2 - harbor Before 302 3.33 0.25 4.75 -25.70 15.4

A2A - harbor Before 302 2.05 0.15 3.74 -25.05 15.6

A3 - harbor Before 302 3.99 0.32 5.80 -25.50 14.5

A4 - harbor Before 302 1.93 0.17 4.00 -24.87 13.6

*Data is available only for the Mooring-15 m’s first sampling period because it was destroyed sometime after 2009 

Year Day 313.
75

Table 18. Short-lived Radionuclide Activity in Sediment Samples. 

[Radionuclide activity in disintegrations per minute per gram [dpm/g] in sediment. Excess 

210Pb (210Pbxs) is calculated as the difference between total 210Pb activity and 226Ra activity.] 

USGS 

sample 

identifier

Time 

frame

[2009 

Year 

Days]

7

Be

[dpm/g]

210Pb

[dpm/g]

Mean 

226Ra

[dpm/g]

210Pbxs

[dpm/g]

137Cs

[dpm/g]

234Th

[dpm/g]

234Th/226Ra 7

Be:210Pbxs

Trap-10 

m

292-

313 0.66±0.40 4.2±0.4 1.0±0.1 3.3±0.4 0.04±0.01 7.4±0.39 7.65 0.20

Trap-15 

m*

292-

313 1.14±0.40 8.7±0.4 2.3±0.1 6.4±0.4 0.14±0.08 15.5±0.45 6.87 0.18

Trap-20 

m

292-

313 0.87±0.97 10.5±0.8 2.7±0.1 7.8±0.8 0.11±0.05 4.5±0.60 1.65 0.11

Trap-30 

m

292-

313 0.00±0.00 10.6±1.3 2.7±0.1 8.0±1.3 0.18±0.07 5.2±0.70 1.97 0.00

Trap-10 

m

313-

336 0.00±0.00 10.0±0.9 2.5±0.2 7.5±0.9 0.22±0.06 10.3±0.70 4.18 0.00

Trap-20 

m

313-

336 0.00±0.00 15.1±1.0 1.8±0.2 13.4±1.0 0.41±0.18 17.1±0.87 9.77 0.00

Trap-30 

m

313-

336 0.31±0.25 10.1±0.9 2.4±0.2 7.7±0.9 0.26±0.09 13.5±0.89 5.52 0.04

Trap-10 

m

336-

349 1.82±0.78 4.6±0.5 2.3±0.1 2.2±0.6 0.08±0.02 4.2±0.41 1.79 0.82

Trap-20 

m

336-

349 1.88±0.73 6.0±0.5 2.3±0.1 3.7±0.5 0.10±0.03 37.1±2.89 15.87 0.52

Trap-30 

m

336-

349 0.92±0.58 7.0±0.7 1.9±0.1 5.1±0.7 0.11±0.03 7.2±0.52 3.82 0.18

Tripod 

D (30 

m)

After 

350 0.19±0.75 5.7±0.6 1.9±0.1 3.7±0.6 0.08±0.02 3.1±0.39 1.59 0.05

Seabed10 mAfter 

350 0.08±0.51 4.1±0.4 2.7±0.1 1.4±0.4 0.00±0.00 3.3±0.44 1.20 0.06

Seabed15 mAfter 

350 0.37±0.53 4.8±0.5 4.0±0.1 0.8±0.5 0.03±0.01 3.8±0.59 0.95 0.48

Seabed20 mAfter 

350 0.28±0.49 5.7±0.6 5.6±0.1 0.1±0.6 0.03±0.02 6.1±0.47 1.08 2.01

Seabed30 mAfter 

350 0.00±0.00 4.1±0.5 2.5±0.1 1.6±0.5 0.06±0.02 2.6±0.35 1.06 0.00

A1 -

harbor

Before 

302 3.05±2.69 3.0±0.5 1.8±0.1 1.2±0.5 0.15±0.04 1.6±0.46 0.90 2.57

A2 -

harbor

Before 

302 0.00±0.00 2.7±0.4 1.8±0.1 0.9±0.4 0.10±0.02 1.0±0.40 0.53 0.00

A2A -

harbor

Before 

302 3.54±2.70 1.8±0.3 2.5±0.1 -0.7±0.4 0.00±0.00 1.7±0.32 0.70 -5.29

A3 -

harbor

Before 

302 0.00±0.00 4.4±0.4 1.7±0.1 2.7±0.4 0.27±0.08 2.0±0.31 1.16 0.00

A4 -

harbor

Before 

302 0.00±0.00 2.2±0.4 2.8±0.1 -0.6±0.4 0.00±0.00 2.2±0.44 0.81 0.00

*Data is available only for the Mooring-15 m’s first sampling period because it was destroyed sometime after 2009 

Year Day 313.
76

Table 19. Elemental composition of harbor sediment samples. 

[Elemental composition of sediment in parts per million (ppm) as determined by mass spectrometry. 

Sediment collected before 2009 Year Day 302. “<1” is below the analytical detection limit.] 

Element A1-harbor A2-harbor A2A-harbor A3-harbor A4-harbor

Ag <1 <1 <1 <1 <1

Al 71200 78300 74900 78000 73300

As 7.4 9.9 5.8 12.6 5.7

Ba 674 638 725 583 758

Be 1.5 1.4 1.3 1.5 1.3

Ca 18100 14400 19900 13000 16700

Ce 36.6 40.6 34.9 43.8 31.6

Co 10.3 12.3 10.5 10.8 10.7

Cr 66.1 78.2 64.1 85.6 87.9

Cs 3.4 4.2 2.9 4.7 3.2

Cu 86.8 98.2 60.8 158 23.3

Fe 33300 39200 29800 41400 28900

Ga 16.7 17.9 16.2 18.1 15.6

K 14500 14200 15000 15400 16200

La 18.7 20.2 17.3 21.9 15.8

Li 30.5 33.7 25.8 41.5 30.1

Mg 9560 9820 9270 10600 8940

Mn 360 419 344 281 561

Mo 1.5 1.8 1.4 2.4 2.8

Na 23000 23100 25100 23100 19700

Nb 7.8 7.5 7.2 7.9 6.7

Ni 28.6 38.6 26.8 40.6 49.5

P 741 872 454 910 364

Pb 23 27.9 23 31.3 17.4

Rb 62.8 67.4 61.2 75.7 66.4

Sb 1.1 0.9 0.68 1 0.75

Sc 12.3 13.8 11.5 13.6 11.3

Sr 312 269 352 234 286

Th 5.81 6.66 4.93 7.65 4.95

Ti 3850 3770 3780 3720 3150

Tl 0.5 0.48 0.38 0.54 0.44

U 1.98 2.36 2.03 2.62 2.32

V 106 119 97 123 89.7

Y 14.2 16.4 13.7 17 13.1

Zn 140 174 111 230 67.7
77

Table 20. Elemental composition of trap sediment: First deployment.

[Elemental composition of sediment in parts per million (ppm) as determined by mass spectrometry. 

Sediment collected 2009 Year Days 292-313.]

Element Trap-10 m Trap-15 m Trap-20 m Trap-30 m

Ag <1 <1 <1 <1

Al 56600 58000 56200 57000

As 6.8 5.9 6 5.2

Ba 788 812 753 786

Be 1.6 1.6 1.3 1.3

Ca 16000 12700 12100 10800

Ce 42.1 42.5 42.2 39.9

Co 5 5.4 6.4 6.3

Cr 54 55.4 63.7 61

Cs 3.6 3.6 3.8 3.7

Cu 21.1 18.7 18 15.8

Fe 19600 19800 21600 20300

Ga 13.2 13.8 13.1 13

K 16900 17700 16200 16800

La 21.8 21.3 21.4 20.3

Li 26.8 26.7 30.8 30

Mg 7460 7880 8970 8380

Mn 183 187 207 196

Mo 1.5 1.4 1.2 0.93

Na 21100 22400 22200 19400

Nb 9.3 9.2 9.2 8.6

Ni 26.4 29.3 38.4 38.1

P 933 926 838 616

Pb 16.7 15.7 14.8 13.1

Rb 82.9 85.7 81.9 83.9

Sb 0.88 0.51 0.53 0.42

Sc 7 6.8 7.5 7.2

Sr 298 278 262 263

Th 7.53 7.1 8.03 7.5

Ti 2510 2540 2690 2530

Tl 0.54 0.49 0.46 0.49

U 2.56 2.53 2.47 2.29

V 68 67.3 72 69.2

Y 13.2 12.6 13.1 12.2

Zn 64 62.2 61.9 54.7
78

Table 21. Elemental composition of trap sediment: Second deployment*. 

[Elemental composition of sediment in parts per million (ppm) as determined by mass spectrometry. 

Sediment collected 2009 Year Days 313-336.]

Element Trap-10 m Trap-20 m Trap-30 m

Ag <1 <1 <1

Al 49800 54800 70600

As 7.5 8.2 6.8

Ba 673 656 634

Be 1.2 1.5 1.3

Ca 15100 12900 16600

Ce 39.3 45 35.4

Co 5.3 7.3 8.3

Cr 55.5 76.6 88.4

Cs 3.9 4.7 4.4

Cu 32 23.2 22.2

Fe 20900 25500 30900

Ga 12.3 13.7 15.5

K 14700 15200 20100

La 19.6 22.8 17.7

Li 29 36.5 37.7

Mg 8810 12400 15300

Mn 171 211 245

Mo 1.5 1.5 1.4

Na 29800 35500 33100

Nb 7.8 9 8.3

Ni 29.1 49.7 54.8

P 905 972 861

Pb 17.1 15.9 13.5

Rb 76.3 83.8 87.4

Sb 0.45 0.63 0.62

Sc 7.2 8.6 10.3

Sr 272 266 240

Th 6.84 9.03 6.78

Ti 2340 2720 3120

Tl 0.42 0.46 0.49

U 2.44 2.64 2.16

V 70.7 85.8 94.1

Y 12.4 13.4 12.7

Zn 72.3 74 79.3

*Trap-15 m was destroyed sometime during this deployment; no sample was recovered.
79

Table 22. Elemental composition of trap sediment: Third deployment*. 

[Elemental composition of sediment in parts per million (ppm) as determined by mass spectrometry. 

Sediment collected 2009 Year Days 336-349.]

Element Trap-10 m Trap-20 m Trap-30 m

Ag <1 <1 <1

Al 66400 68900 68200

As 6 5.6 5.9

Ba 789 806 741

Be 1.2 1.2 1.4

Ca 22200 18600 16700

Ce 32.1 35 31.1

Co 4.3 5.4 6.5

Cr 43 52 67.3

Cs 2.7 2.9 3.3

Cu 16.6 13.2 15.7

Fe 17600 20000 23200

Ga 13.4 14.1 14.3

K 22300 22400 21200

La 16.3 17.7 15.6

Li 19.4 21.4 26

Mg 7920 9370 12400

Mn 194 232 219

Mo 1.1 0.9 0.9

Na 34100 33200 43100

Nb 7.8 8.5 7.7

Ni 18.6 27.2 39.4

P 814 769 774

Pb 13.4 13.1 12.2

Rb 79.7 81.5 80.5

Sb 0.5 0.64 0.51

Sc 6.4 7.3 8.2

Sr 308 290 269

Th 5.36 6.02 5.93

Ti 2530 2840 2720

Tl 0.43 0.42 0.44

U 1.89 1.87 1.78

V 59.9 67.7 73.3

Y 11.5 12.5 11.2

Zn 56 53.7 58.8

*Trap-15 m was destroyed during the previous deployment; no sample was recovered.
80

Table 23. Elemental composition of seabed and tripod sediment samples. 

[Elemental composition of sediment in parts per million (ppm) as determined by mass spectrometry. 

Sediment collected after 2009 Year Day 350.]

Element Seabed-10 m Seabed-15 m Seabed-20 m Seabed-30 m Tripod D (30 m)

Ag <1 <1 <1 <1 <1

Al 64500 63900 74100 67300 66900

As 3.2 4.2 4.2 4.1 6

Ba 939 881 986 908 777

Be 1.2 1.2 1.4 1.3 1.2

Ca 19500 18800 24100 16200 18400

Ce 37.2 53.2 65.4 35.4 34.7

Co 3.1 3.7 5.6 4.1 5.8

Cr 28 36.5 47.6 34.2 59.1

Cs 1.7 1.8 1.8 2 3.1

Cu 6.2 7.9 9.3 6.9 14.6

Fe 12000 14800 20700 14200 22300

Ga 12.8 13.5 15.8 13.4 14.1

K 24100 23400 26200 24300 22200

La 17.9 25.9 30.5 17.2 17.4

Li 10.6 12.1 12.9 16.6 22.3

Mg 4550 5200 7150 5380 9270

Mn 245 338 530 216 224

Mo 0.65 0.78 0.78 0.53 0.99

Na 24700 24600 27300 24800 29700

Nb 10 14 19 8.6 7.7

Ni 7.9 10.2 12.3 15.4 28.5

P 564 794 882 524 705

Pb 12.3 12.7 13.7 11.8 14

Rb 80.8 78.9 83.9 81.8 82.2

Sb 0.38 0.81 0.62 0.39 0.47

Sc 5.4 6.4 8.7 5.9 7.7

Sr 301 285 330 292 284

Th 4.89 18 8.38 6.1 6.04

Ti 2940 4220 6140 2570 2700

Tl 0.4 0.51 0.45 0.48 0.47

U 1.86 3.29 2.79 1.74 2.13

V 43.2 52.5 74.3 46.5 67.9

Y 13.6 17.8 23.3 11.9 11.7

Zn 32.9 40.2 47.7 36.2 57.4
81

Table 24. Sediment-flux statistics.

[All statistics were calculated for 2009 Year Days 295-349. Direction is “Going to”.]

Site name Time period

[2009 Year Days]

Depth

[m]

Total sediment flux

[metric tons/m2]

Average daily sediment flux

[metric tons/m2]

Direction

[

o

True]

Tripod A (9 m) Experiment [295-349] 8.5 163.981 5.471 140.51

Pre-Dredging [295-301] 8.5 53.102 10.622 257.52

Dredging [302-324] 8.5 179.543 11.973 122.13

Post-Dredging [325-339] 8.5 0.424 0.424 94.84

Storm and Flood [340-349] 8.5 42.855 4.765 167.65

Tripod B (12 m) Experiment [295-349] 3 2.16 0.04 139.4

Pre-Dredging [295-301] 3 0.48 0.07 194.5

Dredging [302-324] 3 0.85 0.04 128.8

Post-Dredging [325-339] 3 0.79 0.05 113.2

Storm and Flood [340-349] 3 0.24 0.02 120.1

Experiment [295-349] 9 6.77 0.12 81.8

Pre-Dredging [295-301] 9 6.67 0.95 31.2

Dredging [302-324] 9 0.64 0.03 128.5

Post-Dredging [325-339] 9 4.58 0.31 113.2

Storm and Flood [340-349] 9 8.83 0.88 120.1

Experiment [295-349] 10.5 7585.42 137.92 89.2

Pre-Dredging [295-301] 10.5 105.46 15.07 26.1

Dredging [302-324] 10.5 1505.45 65.45 80.8

Post-Dredging [325-339] 10.5 990.65 66.04 63.5

Storm and Flood [340-349] 10.5 442.63 44.26 166.1

Tripod C (20 m) Experiment [295-349] 3 4.47 0.08 259.5

Pre-Dredging [295-301] 3 0.73 0.10 82.7

Dredging [302-324] 3 1.77 0.08 261.5

Post-Dredging [325-339] 3 0.28 0.02 123.1

Storm and Flood [340-349] 3 3.57 0.36 263.4

Experiment [295-349] 16.5 21.75 0.40 237.1

Pre-Dredging [295-301] 16.5 2.89 0.41 78.8

Dredging [302-324] 16.5 8.65 0.38 232.9

Post-Dredging [325-339] 16.5 1.18 0.08 317.9

Storm and Flood [340-349] 16.5 15.97 1.60 238.9

Experiment [295-349] 19.5 36172.52 657.68 17.1

Pre-Dredging [295-301] 19.5 220.08 31.44 21.6

Dredging [302-324] 19.5 3706.55 161.15 29.2

Post-Dredging [325-339] 19.5 4650.62 310.04 21.7

Storm and Flood [340-349] 19.5 1769.84 176.98 358.9

Tripod D (30 m) Experiment [295-349] 3 3.15 0.06 273.4

Pre-Dredging [295-301] 3 0.19 0.03 212.4

Dredging [302-324] 3 0.58 0.03 268.4

Post-Dredging [325-339] 3 0.36 0.02 239.9

Storm and Flood [340-349] 3 2.24 0.22 286.6
82

Experiment [295-349] 26.5 28.85 0.52 258.7

Pre-Dredging [295-301] 26.5 1.84 0.26 132.5

Dredging [302-324] 26.5 10.68 0.46 257.4

Post-Dredging [325-339] 26.5 2.43 0.16 287.7

Storm and Flood [340-349] 26.5 16.83 1.68 261.1

Experiment [295-349] 29.5 55388.58 1007.07 60.1

Pre-Dredging [295-301] 29.5 494.65 70.66 84.8

Dredging [302-324] 29.5 10,843.21 471.44 47.0

Post-Dredging [325-339] 29.5 6248.29 416.55 68.5

Storm and Flood [340-349] 29.5 910.25 91.03 74.4 1

Missing data from 2009 Year Days 298-299, 305, 309-311, 321-338, and 341. 2

Missing data from 2009 Year Days 298-299. 3

Missing data from 2009 Year Days 305, 309-311, and 321-324. 4

Missing data from 2009 Year Days 325-338. 5

Missing data from 2009 Year Day 341.
83

Appendix 1 

Optical Backscatter Sensor (OBS) Suspended Sediment Concentration (SSC) 

Calibration Information 

Sample Sample volume

[l]

Sediment mass

[g]

Concentration

[mg/l]

OBS

[NTU]

SCH-1 10 0.004 7.86 2

SCH-2 10 0.049 92.28 14

SCH-3 10 0.640 1189.59 169
84

Sample Sample volume

[l]

Sediment mass

[g]

Concentration

[mg/l]

OBS

[NTU]

SFO-1 50 2.632 52.64 0.0845

SFO-2 50 5.109 102.18 0.1103

SFO-3 50 10.106 202.12 0.1677

SFO-6 50 37.548 750.96 0.4953

SFO-10 50 125.230 2504.60 1.0833
85

Appendix 2 

Acoustic Doppler Current Meters (ADCM) Suspended Sediment Concentration (SSC) 

Calibration Information 
86

Appendix 3 

Water Column Profiler (WCP) Optical Backscatter (OBS) Profiles 

Appendix 3.1: Profiles of variation in turbidity, in National Turbidity Units, with depth for the 5 watercolumn surveys. 
87

Appendix 3.2: Profiles of variation in turbidity, in National Turbidity Units, with depth for the 5 watercolumn surveys. Colors same as Appendix 3.1.
88

Appendix 3.3: Profiles of variation in turbidity, in National Turbidity Units, with depth for the 5 watercolumn surveys. Colors same as Appendix 3.1. 
89

Appendix 4 

Water Column Profiler (WCP) Light Transmission (Xmiss) Profiles 

Appendix 4.1: Profiles of variation in light transmission, in precent, with depth for the 5 water-column 

surveys. 
90

Appendix 4.2: Profiles of variation in light transmission, in precent, with depth for the 5 water-column 

surveys. Colors same as Appendix 4.1. 
91

Appendix 4.3: Profiles of variation in light transmission, in precent, with depth for the 5 water-column 

surveys. Colors same as Appendix 4.1.
92

Appendix 5 

Water Column Profiler (WCP) Chlorophyll (chl) Profiles 

Appendix 5.1: Profiles of variation in chlorophyll, in milligrams per cubic meter, with depth for the 5 watercolumn surveys. 
93

Appendix 5.2: Profiles of variation in chlorophyll, in milligrams per cubic meter, with depth for the 5 watercolumn surveys. Colors same as Appendix 5.1. 
94

Appendix 5.3: Profiles of variation in chlorophyll, in milligrams per cubic meter, with depth for the 5 watercolumn surveys. Colors same as Appendix 5.1. 
95

Appendix 6 

Beach Ball (BB) and Flying Eyeball (FE) Surficial Grain-Size Measurements 

Appendix 6.1: Spatial variation in mean grain size and variability in grain size, in microns, for the grainsize surveys on 10/23/2009 (2009 Year Day 296). 
96

Appendix 6.2: Spatial variation in mean grain size and variability in grain size, in microns, for the grainsize surveys on 10/29/2009 (2009 Year Day 302). 
97

Appendix 6.3: Spatial variation in mean grain size and variability in grain size, in microns, for the grainsize surveys on 11/10/2009 (2009 Year Day 314). 
98

Appendix 6.4: Spatial variation in mean grain size and variability in grain size, in microns, for the grainsize surveys on 11/24/2009 (2009 Year Day 328). 
99

Appendix 7 

Numerical Model Calibration and Validation Information 

Appendix 7.1: Comparison of computed (MBY model) and observed (HF Radar) surface current velocities 

at Station 46042 – MONTEREY 27 NM West of Monterey Bay. 
100

Appendix 7.2: Comparison of computed (MBY model) and observed (HF Radar) surface current velocities 

at Station 46091 – MBM0. 
101

Appendix 7.3: Comparison of computed (MBY model) and observed (HF Radar) surface current velocities 

at Station 46092 – MBM1. 
102

Appendix 7.4: Comparison of computed (MBY model) and observed (HF Radar) surface current velocities 

at Tripod D (30 m). 
103

Appendix 7.5: Comparison of computed (MBY model) and observed surface water temperatures. 
104

Appendix 7.6: Comparison of computed (NCEP-NAM model) and observed wind speeds. 
105

Appendix 7.7: Simulated versus NOAA predicted water levels at Santa Cruz Harbor. 
106

Appendix 7.8: Observed (blue) versus simulated (red) surface and bottom current velocities at Tripod D 

(30 m). 
107

Appendix 7.9: Observed versus simulated wave heights at Tripod B (12 m). 
108

Appendix 7.10: Observed versus simulated wave heights at Tripod C (20 m).
109

Appendix 7.11: Sediment concentration near the bed at Tripod B (12 m) with (upper panel) and without 

(lower panel) waves. 
110

Appendix 8 

2009 Year Day to Calendar Day Conversion Table 

2009 Year Day Calendar Day 2009 Year Day Calendar Day

244 1-Sep 305 1-Nov

245 2-Sep 306 2-Nov

246 3-Sep 307 3-Nov

247 4-Sep 308 4-Nov

248 5-Sep 309 5-Nov

249 6-Sep 310 6-Nov

250 7-Sep 311 7-Nov

251 8-Sep 312 8-Nov

252 9-Sep 313 9-Nov

253 10-Sep 314 10-Nov

254 11-Sep 315 11-Nov

255 12-Sep 316 12-Nov

256 13-Sep 317 13-Nov

257 14-Sep 318 14-Nov

258 15-Sep 319 15-Nov

259 16-Sep 320 16-Nov

260 17-Sep 321 17-Nov

261 18-Sep 322 18-Nov

262 19-Sep 323 19-Nov

263 20-Sep 324 20-Nov

264 21-Sep 325 21-Nov

265 22-Sep 326 22-Nov

266 23-Sep 327 23-Nov

267 24-Sep 328 24-Nov

268 25-Sep 329 25-Nov

269 26-Sep 330 26-Nov

270 27-Sep 331 27-Nov

271 28-Sep 332 28-Nov

272 29-Sep 333 29-Nov

273 30-Sep 334 30-Nov

274 1-Oct 335 1-Dec

275 2-Oct 336 2-Dec

276 3-Oct 337 3-Dec

277 4-Oct 338 4-Dec

278 5-Oct 339 5-Dec

279 6-Oct 340 6-Dec

280 7-Oct 341 7-Dec

281 8-Oct 342 8-Dec

282 9-Oct 343 9-Dec

283 10-Oct 344 10-Dec

284 11-Oct 345 11-Dec

285 12-Oct 346 12-Dec

286 13-Oct 347 13-Dec

287 14-Oct 348 14-Dec

288 15-Oct 349 15-Dec

289 16-Oct 350 16-Dec

290 17-Oct 351 17-Dec

291 18-Oct 352 18-Dec

292 19-Oct 353 19-Dec

293 20-Oct 354 20-Dec

294 21-Oct 355 21-Dec

295 22-Oct 356 22-Dec

296 23-Oct 357 23-Dec

297 24-Oct 358 24-Dec

298 25-Oct 359 25-Dec

299 26-Oct 360 26-Dec

300 27-Oct 361 27-Dec

301 28-Oct 362 28-Dec

302 29-Oct 363 29-Dec

303 30-Oct 364 30-Dec

304 31-Oct 365 31-Dec