Final Report
December, 2008
Review/Synthesis of Historical Environmental Monitoring
Data Collected at the San Francisco Deep Ocean Disposal
Site (SF-DODS) in Support of EPA Regulatory Decision to
Revise the Site's Management and Monitoring Plan
Prepare
US EPA Region 9
75 Hawthorne Street
San Francisco, CA 94105
EPA ORDER No. EP069000274
Prepared by:
Germane & Associates, Inc.
12100 SE 46th Place
Bel levue,WA 98006
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Final Report
Review/Synthesis of Historical
Environmental Monitoring Data Collected at
the San Francisco Deep Ocean Disposal Site
(SF-DODS) in Support of EPA Regulatory
Decision to Revise the Site's Management
and Monitoring Plan
Prepared for
US EPA Region 9
75 Hawthorne Street
San Francisco, CA 94105
EPA ORDER No. EP069000274
Prepared by
Joseph Germane
Peggy Myre
Lorraine Read
Drew Carey
Submitted by
Germane & Associates, Inc.
12100 SE 46th Place
Bellevue, WA 98006
December, 2008
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TABLE OF CONTENTS
LIST OF FIGURES IV
1.0 INTRODUCTION 1
1.1 BACKGROUND 2
1.2 STATEMENT OF NEED 3
2.0 REVIEW OF PAST MONITORING DATA 6
2.1 DREDGED MATERIAL DISPOSAL OPERATIONS 6
2.2 MONITORING SUMMARY 8
2.3 REVIEW OF PHYSICAL OCEANOGRAPHY MONITORING AND MODELING 11
2.3.1 Oceanographic Monitoring 11
2.3.2 Physical Oceanography Results 12
2.3.3 Modeling Results 13
2.3.4 Discussion of Physical Oceanography and Modeling Results 14
2.3.5 Conclusions from Past Physical Oceanographic and Modeling Studies 15
2.4 REVIEW OF PHYSICAL DATA 15
2.4.1 Mapping the Dredged Material Footprint 16
2.4.2 Review of Historical SPI Survey Results 18
2.4.2.1 Evaluation of Benthic Impairment 20
2.4.3 Conclusions 23
2.5 REVIEW OF CHEMICAL DATA 23
2.5.1 Sediment Characteristics of the SF-DODS and the Reference Area 24
2.5.2 Current SMMP Chemical Monitoring Protocols 26
2.5.2.1 SF-DODS Surveys and Sample Design 27
2.5.3 Summary of Chemical Monitoring of the SF-DODS 29
2.5.3.1 Physical Parameters 29
2.5.3.2 Chemical Parameters 30
2.5.3.2.1 Metals 30
2.5.3.2.2 Organics 31
2.5.4 Chemical Monitoring Conclusions 32
2.6 REVIEW OF BIOLOGICAL DATA 32
2.6.1 Pelagic Seabird and Marine Mammal Monitoring 32
2.6.1.1 Bird and Mammal Data 33
2.6.1.2 Bird and Mammal Results 34
2.6.1.3 Bird and Mammal Discussion 35
2.6.1.4 Bird and Mammal Conclusions 36
2.6.2 Pelagic Fish Monitoring 36
2.6.2.1 Pelagic Fish Data 36
2.6.2.2 Pelagic Fish Results 38
2.6.2.3 Pelagic Fish Discussion 39
2.6.2.4 Pelagic Fish Conclusions 40
2.6.3 Benthic Community Monitoring 40
2.6.3.1 Benthic Community Data 40
2.6.3.2 Benthic Community Results 41
2.6.3.3 Benthic Community Discussion 43
2.6.3.4 Power Analysis of Benthic Results 44
2.6.3.5 Benthic Community Conclusions 45
ii
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2.7 C
2.7.1
2.7.2
2.7.3
2.7.4
1 SUI
^ONFIRMA TION STUDIES
Bioassay and Bioaccumulation Results
Bioassay and Bioaccumulation Conclusions
Caged Mussel Bioaccumulation Results
Confirmation Studies Conclusion
VIMARY OF CONCLUSIONS
45
46
47
47
48
51
3.0
4.0 REFERENCES CITED 53
FIGURES 61
APPENDIX 83
111
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LIST OF FIGURES
Figure 1 Location of the San Francisco Deep Ocean Disposal Site (SF-DODS).
Figure 2 Monthly disposal volumes compared with date of monitoring surveys and
number of SPI stations sampled.
Figure 3 Deployment and operation of the sediment profile imaging (SPI) system;
acoustic pinger signal doubles for 10 seconds after strobe is fired to signal
successful image acquisition in deep-water operations.
Figure 4 Potential sampling locations for the SF-DODS monitoring surveys.
Figure 5 Equipment used to collect sediment samples during past monitoring
surveys at the SF-DODS.
Figure 6 Core locations most commonly sampled for sediment chemistry during the
entire period of monitoring at the SF-DODS from 1996-present (circles),
and more recently (squares).
Figure 7 Location of the current meter and sediment trap moorings deployed by
USGS from November 1997 to November 1998. Borders in green
indicate boundaries of the Cordell Bank (north), Gulf of the Farallones
(center) and Monterey Bay (south) National Marine Sanctuaries.
Figure 8 Summary compilation of dredged material thickness maps from all
surveys between 1996-2007. Cumulative line represents all areas where
dredged material has been detected > 5 cm thick. Large numbers at
stations indicate depth of dredged material (cm) from 2007 survey.
Figure 9 Left Panel: Deposition (cm) from model year 1996 using USGS current
data. Contours are 1, 2, 5, 10, 20, 30, and 34 cm. Right Panel: Distribution
of recently placed dredged material from the October-November 1997
sediment survey of the SF-DODS.
Figure 10 Sediment profile image from the SF-DODS taken during the 1997 survey
(Station 9) within the boundary shows evidence of a distinct layer of
dredged material and an epibenthic animal grazing on the surface
(elasapoid holothurian, Scotoplanes globosa). Scale: width of profile
image = 14.5 cm.
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Figure 11 Sediment profile image from north of the SF-DODS taken during the 1996
survey (Station 31) shows ambient sediment without dredged material.
Scale: width of profile image - 14.5 cm.
Figure 12 This sediment profile image from the center of the SF-DODS taken during
the 2006 survey (Station 13) shows evidence (burrows, voids, and portions
of worms against the faceplate) of Stage 3 taxa at depth even though
dredged material thickness exceeds the height of the camera's prism.
Figure 13 Empirical Cumulative Distribution Function (CDF) and Conditional
Cumulative Distribution Functions (CCDF) curves for the RPD endpoint.
Curves that are further to the right have a higher median RPD value for the
distribution (i.e.generally better conditions), and steeper curves indicate
distributions with less variability.
Figure 14 Relationship between Average Dredged Material depth and Average RPD,
as measured in SPI surveys at the SF-DODS.
Figure 15 Diversity data from the SF-DODS (after Table 4-2 ENSR 2005). Diversity
values for each station are shown on y-axis, plotted against the estimated
volume disposed since last sampling (thousands of cubic yards).
Figure 16 Benthic community metrics from the SF-DODS (Table 4-2, ENSR 2005)
plotted against actual dredged material depth (cm) measured in sediment
profile images.
Figure 17 Range (minimum to maximum) concentration of total fine-grained
sediment (silt and clay) in samples collected from the SF-DODS and the
SF-DODS reference area (columns) relative to volume of dredged material
disposed at the site during that year (line), in cubic yards (xlO"5). Baseline
samples collected in 1990-91. Surveys conducted in 2003-04 distinguished
samples collected in dredged material (DM} from those with no dredged
material present (ambient, or AME). The number of samples is shown in
the center of the column.
Figure 18 Range (minimum to maximum) of total organic carbon (TOC) in samples
collected from SF-DODS, the reference area, and from dredged material
source areas (columns). Baseline samples collected 1990-91. Ambient
stations are those with no measurable dredged material. Outlier points
shown separately for Footprint category. Source data summarized as
reported over 1994-2006 (Appendix Table 2). The number of samples is
shown in the center of the columns; U=unknown number of samples.
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Figure 19 Range (minimum to maximum) concentration of silver in samples
collected from the SF-DODS and the reference area (columns). Baseline
samples collected 1990-91. Green line showing maximum silver value
reported from dredged material source areas through 2000 (0.6 ppm), for
2001-2003 (0.84 ppm), and from 2004 to present (1.4 ppm). The number
of samples is shown in the center of the columns.
Figure 20 Location of the 21 stations used for pelagic fish monitoring surveys in the
vicinity of the SF-DODS. D stations are disposal site stations; B stations
are "buffer area" stations; and P stations are "peripheral area" stations.
Figure 21 Power Analysis Results from the SF-DODS benthic community data:
relationship between the number of replicates per site vs. the Minimum
Detectable Difference (MDD) as a percentage of the mean, given a type I
error rate (alpha) = 0.05 and 80% power.
VI
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1.0 INTRODUCTION
The disposal of dredged material in ocean waters, including the territorial sea, is
regulated under the Marine Protection, Research, and Sanctuaries Act of 1972 (MPRSA),
33 U.S.C. § 1401, ff. The MPRSA prohibits disposal activities that would unreasonably
degrade or endanger human health or the marine environment. Under the Act, the U.S.
Environmental Protection Agency (EPA) and the U.S. Army Corps of Engineers
(USAGE) have joint authority for regulating ocean disposal of dredged material and for
managing ocean disposal sites. Permits for the transportation and disposal of dredged
material into ocean waters are issued by the USAGE (or, in the case of federal projects,
authorized for disposal under MPRSA §103(e)) only after EPA concurs that
environmental criteria and conditions established by EPA are applied. EPA designates
Ocean Dredged Material Disposal Sites (ODMDS). Management of an ocean disposal
site consists of (1) regulating the quantities, types of material, times, rates, and methods
of disposing dredged material at an ocean disposal site; (2) developing and maintaining
an effective monitoring program for the site; (3) recommending changes for site use,
disposal amounts, or timing based on periodic evaluation of site monitoring results; and
(4) enforcing permit conditions for approved dredging projects.
The San Francisco Deep Ocean Disposal Site (SF-DODS) was designated as the nation's
deepest ODMDS in 1994 after a comprehensive 2-year ocean studies program and site
designation environmental impact statement (EPA 1993). The SF-DODS is located
approximately 80 kilometers (50 miles) off the coast in the Gulf of the Farallones region,
in water depths ranging from 2,500 to 3,000 meters (8,200 to 9,840 feet) (Figure 1).
Designation of the SF-DODS was effective on 8/11/1994. There is a Site Management
and Monitoring Plan (SMMP) that details site use requirements (EPA 1998). Dredged
material was first placed at the site in 1995.
The SF-DODS has two distinguishing characteristics that set it apart from other open-
water dredged material disposal sites in the United States: 1). It is located off the
continental shelf in water depths exceeding 3,000 meters; and, 2). The SMMP (EPA,
1994, revised in 1996 and 1998) is incorporated in the site's Final Rule [40 CFR 228.15
(1)(3)] (EPA 1999a).
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1.1 Background
The EPA Final Rule initially designating the SF-DODS for dredged material disposal was
published on August 11, 1994 (59 FR 41243). This initial rule established an "interim"
allowable disposal volume of 6 million cubic yards per year. The maximum allowable
disposal volume was reduced to 4.8 million cubic yards per year starting in January, 1997
(EPA Final Rule of December 30, 1996, 61 FR 68964). The reduction in allowable
disposal volume was based on a revised prediction of long-term dredging needs
conducted by the interagency Long Term Management Strategy (LTMS) for San
Francisco Bay (LTMS 1996, 1998). The limit of 4.8 million cubic yards per year was
subsequently made permanent in the EPA Final Rule published on July 23, 1999 (64 FR
39927). Through the 2007 disposal year, almost 16 million cubic yards of dredged
material have been diverted to the SF-DODS from traditional in-Bay sites, reducing risks
of disposal-related impacts within those sensitive waters, and, as described in this report,
that reduction of risk has been accomplished without causing any significant impacts to
the ocean.
Because of the unique setting of the SF-DODS (distance from shore and depth of water),
there was a great deal of uncertainty (and because of that, initial controversy) during the
site designation process about the behavior of dredged material during descent and its
impacts after deposition on the seafloor. There is a wealth of information available about
the environmental impacts of dredged material disposal in shallower coastal marine
environments (Newell et al. 1998; Fredette and French 2004; also see
http://el.erdc.usace.army.mil/dots/). However, before the designation of the SF-DODS,
there was little available information on best management practices or long-term impacts
of dredged material disposal in deep water (> 500 meters). In order to address all the
concerns brought up during the site designation process and in response to comments on
the final Environmental Impact Statement (EIS), both the USAGE and EPA sponsored a
series of multidisciplinary monitoring studies as part of the initial designation process and
continued this diverse array of studies as part of the SMMP in the ensuing years after
disposal operations started in 1995.
Even though the location of the SF-DODS was specifically selected to avoid important
fishery areas and geographically unique or otherwise sensitive habitats, this disposal site
has been the subject of the most intensive monitoring of any disposal site in Region 9,
and it is one of the most actively and intensively monitored sites in the nation. To date,
15 years of monitoring data have been collected for the SF-DODS, and, on average, the
field monitoring activities have cost approximately $1 million each year.
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1.2 Statement of Need
While initially there were no data from sites in similar settings to support many of the
predictions made in the site designation EIS (US EPA 1993), after 15 years of post-
disposal operation monitoring, EPA is now in an excellent position to review all the
results to date and consider the appropriate changes to the SMMP in the spirit of adaptive
management. Several management actions affecting how the SF-DODS was used and
monitored have been taken since the disposal site was initially designated by EPA in
1994. The practical lessons that were learned from the first project to use the site (the
Port of Oakland 42-Foot Deepening Project) resulted in EPA clarifying many of the
mandatory conditions contained in the 1994 rule. These clarifications were initially
included in both instructions to the USAGE in 1997 and then in the SMMP
Implementation Manual (EPA 1998). In 1999, EPA published a final rule (Appendix A,
64 FR 39927) codifying these changes. These actions included:
• establishing a permanent annual disposal volume limit of 4.8 million yds3 (reduced
from 6.0 million yds3);
reducing the size of the surface disposal zone from a 1,000-m radius circle to 600-m
radius, to better ensure that deposition of dredged material outside of the SF-DODS
boundary would be minimized;
• reducing the maximum acceptable sea state for transportation of material to the SF-
DODS from 18 feet to 16 feet;
• clarifying that disposal vessels may not be loaded to more than 80 percent of bin
volume to minimize risk of spillage during transit through adjacent National Marine
Sanctuaries;
clarifying that each disposal vessel must be inspected prior to departure for the SF-
DODS, and that a certification checklist must be completed and signed by the tug
captain and the independent inspector for each trip;
• clarifying that disposal vessels may transit within the three mile exclusion zone
around the Farallones Islands only when they are within the westbound vessel traffic
lane established by the US Coast Guard;
clarifying that the disposal vessel (scow) must have an acceptable navigation
tracking system, and that the system must indicate the position of the opening and
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closing of the disposal vessel doors associated with disposal (tug's navigation system
serves as secondary or backup);
• including a provision that, in addition to reporting to EPA and the USAGE, the
permittee must report any potential or actual violations of the SMMP (such as
dredged material discharges) within the boundaries of a National Marine Sanctuary
to the appropriate Sanctuary manager within 24 hours;
• clarifying the frequency of trips that include on-board independent observers
(regarding potential seabird and marine mammal impacts) to a minimum of once per
month and once every 25 disposal trips; and
clarifying that complete dredging and disposal records must be submitted to EPA and
the USAGE at a minimum at the end of each project, annually for long-term projects,
and at whatever other interval may be requested by EPA or the USAGE.
In addition to these overall site management changes, EPA has modified some technical
aspects of the annual monitoring program based on results obtained from previous years'
monitoring. For example, additional benthic monitoring stations have been added over
time to continue to successfully map the most distant margins of dredged material
deposition around the disposal site. Also, the chemical analysis of off-site sediment
samples as called for under Tier 2 in the SMMP has routinely been conducted, even
though Tier 2 Chemical Monitoring was not triggered by the results of the Tier 1 studies.
The site designation Final Rule (40 CFR 228.15 paragraph (k)(vi)(3)(ix)) calls for the
three tier site monitoring as well as periodic confirmatory monitoring concerning
potential site contamination. The guidance for this site monitoring is described in the
SMMP (EPA 1998). The periodic confirmatory monitoring is to be conducted at least
once every three years to confirm that pre-disposal sampling and testing requirements are
in fact adequately characterizing the potential toxicity of the sediments (EPA, 1994,
1998). To date, this confirmatory monitoring has been conducted once in 1997-1998.
The Final Rule states that once disposal operations begin at the site, the monitoring
program should be implemented through December 31, 1998 (40 CFR 228.15 paragraph
(k)(vi)(3)(x). After this time, the Regional Administrator may establish a minimum
annual disposal volume (not to exceed 10% of the designated site capacity at any time)
below which the monitoring program need not be fully implemented. EPA has invoked
this provision to focus the monitoring on potential benthic impacts and suspend
confirmatory monitoring.
Based on the wealth of information collected at this site over the past 15 years during the
ocean studies program leading to the site EIS and continuing through the post-designation
monitoring surveys, EPA is now in a position to fully address the concerns brought up
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during the EIS process as well as the uncertainties that existed initially about the behavior
and impacts of dredged material disposal in offshore waters at these great depths. In the
sections that follow, we will review and summarize the results to date of the physical,
chemical, and biological studies performed in the water column and on the seafloor as
well as the bird and mammal observations conducted since disposal operations began. At
the end of the report we provide conclusions based on the review of the monitoring data
collected through 2007.
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2.0 REVIEW OF PAST MONITORING DATA
There exists a wealth of detailed information in the individual monitoring reports from
each year's study, and interested readers are encouraged to examine any of the individual
reports listed in the bibliography for details (SAIC 1991, 1992a, 1999a, 1999b; SAIC et
al., 2003, 2004, 2005;.Tetra Tech 1999, 2000, 2001, 2002; ENSR 2005, 2006, 2007,
2008). The SF-DODS is located in an area of historical ocean disposal (SAIC 1991) and
was established within Study Area 5, the environmentally preferred alternative for an
ocean disposal site as identified in the site designation EIS (EPA 1993). This particular
region of the ocean has been used historically as a chemical and conventional munitions
disposal area; between 1951-1954, the general region also was used for disposal of low-
level radioactive waste containers from defense-related, commercial, and laboratory
activities (EPA 1993).
The site is located in a naturally dynamic, highly variable hydrodynamic region. This
area of the ocean is seasonally influenced by three distinct water masses: warm (12-16°C)
oceanic water, cooler newly-upwelled coastal water (8-10°C), and to a lesser extent lower
salinity San Francisco Bay water. The convergence of these water masses results in
frontal areas which vary with location and season in the vicinity of the disposal site.
Typically, the warmer oceanic water dominates the area in the winter, while cooler
upwelled water dominates in the late spring and early summer. However, changes in the
dominant water mass at the disposal site itself are at times observed to occur even within
a single day. Changes also occur on a longer time scale: for example, a major El Nino
episode was in progress in 1998, followed by a La Nina episode in 1999. The area's
oceanographic conditions are thus naturally quite variable on both short and long time
frames.
The current site monitoring program for the SF-DODS as defined in the SMMP (EPA
1998) includes annual monitoring in three interdependent modules: Physical Monitoring,
Chemical Monitoring, and Biological Monitoring. Each type of monitoring is "tiered" to
ensure that adequate information for decision-making is collected in a cost-effective
manner. For example, if adequate information is available in Tier I for a particular type
of monitoring (i.e., physical, chemical, or biological), additional data collection in
subsequent tiers is not required. In addition, the program calls for "periodic confirmatory
monitoring" to address certain issues of public concern raised during the site designation
process.
2.1 Dredged Material Disposal Operations
The site first received dredged material in 1993 as a result of a Section 103 ocean
disposal permit granted to the US Navy for their dredging activities at the Alameda Naval
Air Station and the Oakland Naval Supply Center Base. Approximately 1.2 million cubic
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yards (mcy) of dredged material was sent to what later became the SF-DODS site
between May and December of 1993; in September, 1993, the Navy conducted a
sediment profile imaging (SPI) survey at the disposal site at the midpoint of disposal
operations to verify that the material was behaving as predicted by the modeling
conducted in support of their Section 103 permit application (PRC 1995). This first post-
disposal monitoring survey showed two important results:
1. Mapped location and thickness of the dredged material footprint matched
reasonably well with the modeled dredged material dispersion predictions.
2. Impacts to the benthic community were less than anticipated; sediment profile
images showed evidence that mixing and recolonization of the dredged material
that was deposited on the seafloor had already begun..
After the Navy's one-time use of the area for their Section 103 permit, the site was
officially designated two years later as an ocean disposal site by EPA. Since that time, the
SF-DODS has received material from a variety of projects such as channel deepening in
inner and outer Oakland Harbor, Richmond Harbor, and construction for the San
Francisco Bay Bridge. Since the start of disposal activities in 1993, the site has received
over 16 mcy of dredged material through 2007 (Table 1 and Figure 2). The volumes
presented here are bin volumes, meaning volumes calculated by summing the estimated
volume for each bargeload of material. Sums of individual projects from 1995-2007 are
available in Appendix Table 3.
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Table 1. Annual volumes of dredged material disposed at the SF-DODS
Estimated Bin Volume (cubic yards)
Disposal Year
1993
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
Total:
Estimated
Volume (cy bin)
1,200,000
243,980
1,022,254
4,642,864
2,561,584
350,200
380,650
696,872
848,084
1,052,285
446,000
149,600
1,078,302
1,425,900
16,098,575
Source
US Navy
EPA 2002
EPA 2002
EPA 2002
EPA 2002
EPA 2002
SI-ADISS1
SI-ADISS1
SI-ADISS1
SI-ADISS1
SI-eTrac2
SI-eTrac2
SI-eTrac2
SI-eTrac2
Silent Inspector (Automated Disposal Surveillance System) in
combination with USAGE Volume Tracking Database
2Silent Inspector (eTrac Engineering)
Includes Bodega Bay
2.2 Monitoring Summary
The results of the monitoring activities conducted since 1991 will be presented and
discussed in detail below (Sections 2.3-2.7). For orientation, we provide a brief review of
the techniques and monitoring activities conducted at the SF-DODS (Table 2).
Physical Oceanography
Physical Oceanographic studies are conducted as part of site designation activities to
validate and improve models used to predict dispersion of dredged material in the water
column and deposition of dredged material on the seafloor at the SF-DODS. The initial
studies were conducted prior to site designation as part of the US Navy project. These
initial studies were vital in defining the expectation of dispersion and deposition at the
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site. Subsequent studies would be considered Tier 2 studies under Physical Monitoring
(Table 2).
Physical Monitoring
The Physical Monitoring outlined in the site SMMP (EPA 1998) is conducted to
determine the distribution of dredged material on the seafloor at the SF-DODS. Tier 1
monitoring is used to map the footprint of dredged material. If significant dredged
material accumulation (>5 cm) is found outside the site boundary and Tier 1 chemical
monitoring cannot establish that the material meets suitability guidelines for open water
disposal of dredged material, Tier 2 physical monitoring might be conducted to improve
the models used to predict dispersion in the water column and deposition on the sea floor.
In Tier 1, a sediment profile camera system (Rhoads and Germano 1982, 1986, 1990) is
used to document the extent and thickness of the dredged material deposit both within the
site boundaries and in the surrounding vicinity (Figure 3). Annual SPI surveys are
conducted at selected locations within a standardized 1 nautical mile [nm] station grid
(Figure 4). The objective for the SPI surveys is to define the spatial extent of the dredged
material deposits.
Chemical Monitoring
Tier 1 Chemical Monitoring consists of collection, processing, and preservation of
sediment samples from boxcores (Figure 5). These preserved sediments are used for
chemical analysis in Tiers 1 and 2. In Tier 1, samples collected within the dredged
material footprint are analyzed for common metals and organic contaminants. In Tier 2,
samples collected outside the footprint and outside the disposal site boundaries are
analyzed. In practical terms, this strict sampling and analysis protocol has been modified
to provide comparative analysis of apparent, recent, or historical dredged material
compared to ambient, so stations from outside the site have always been both sampled
and analyzed (Figure 6; Section 2.5).
Biological Monitoring
Tier 1 Biological Monitoring has included monitoring of pelagic communities and
benthic communities. Pelagic monitoring included regional surveys of seabirds, marine
mammals and mid-water column fish populations. After the initial three year period
following site designation, biological monitoring was focused on benthic assessments.
Benthic monitoring consists of collecting and preserving box core samples in Tier 1
(Figure 5) and analysis of samples in Tier 2 (which is triggered if >5 cm of material is
found outside the designated site boundaries). Tier 2 analysis includes a comparison of
the benthic community within the dredged material footprint to benthic communities
outside the footprint.
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Confirmatory Monitoring
Confirmatory Monitoring consisted of sampling sediments from the dredged material
footprint for 10 day bioassay and 28 day bioaccumulation testing and comparing the
results to samples from outside the footprint and to pre-dredge testing results. Caged
mussels were deployed in near-surface arrays around the disposal site for a year and the
tissues analyzed for contaminants. An additional year of current meter data collectin was
also conducted, and computer modeling run using these new data, for comparison with
the original oceanography data and dispersion modeling conducted for the site
designation EIS. Confirmatory Monitoring has only been conducted once, based on the
results and the relatively low volume of dredged material disposed at the site since 1998
(Section 2.7).
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Table 2. Monitoring activities at the SF-DODS
Types and Tiers
Physical
Tier 1
Tier 2
Tier3
Chemical
Tier 1
Tier 2
Tier3
Biological
Tier 1 Pelagic
Tier 2 Benthic
Tier 2 Pelagic
Tier 2 Benthic
Tier 3 Pelagic
Tier 3 Benthic
Confirmatory
Monitoring activity
Sediment Profile Imaging
Current measurements and
modeling
Advanced ocean studies
Sediment sampling and
footprint analysis
Chemistry analysis outside
footprint and boundary
Tissue bioaccumulation
Birds, Fish, Mammals
Box core collection
Additional surveys
Benthic community analysis
Advanced studies
Advanced studies
Bioassay and
bioaccumulation
Caged mussel
bioaccumulation
Years
1996-2007
1991-2*, 1997-8
None
1990-1991*
1996-2007
1 997-2004 }
Reference area studies (1990-
1995)
1996-2001
1996-2008
None
1996-2003
None
None
1998
1997-8
* Baseline studies were conducted prior the site designation.
J Chemistry analysis has been conducted on Tier 2 samples although Tier 2 has not been
triggered.
2.3 Review of Physical Oceanography Monitoring and
Modeling
2.3.1 Oceanographic Monitoring
As part of the site feasibility studies prior to the initiation of disposal activities, current
meters were deployed by SAIC and the Naval Postgraduate School (NPS) at six moorings
between March 1991 and February 1992, and the data were used for model inputs
(Abdelrhman 1992, SAIC 1992b, Tetra-Tech 1992, Hamilton and Ota 1993). The
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mooring locations were selected to provide broad regional data for disposal site selection.
The initial modeling approach took current values from this set of data and projected the
fall trajectories of surrogate particles from seven size classes. The model runs were used
to generate predicted footprints of disposed material on the seafloor and to predict
transport of particles relative to the boundaries of National Marine Sanctuaries. These
model results were later compared with the dredged material map prepared from
sediment profile images collected at the disposal site (Hamilton 2001 based on the data
collected in SAIC 1996, 1999a, 1999b).
As part of the Third Year Confirmatory Monitoring, current meters and sediment traps
were deployed at three moorings from November 1997 to November 1998 by the EPA
and USGS after the disposal site had been designated and was in active use. These data
as well as pre-designation data were used in a comparative modeling study (Hamilton,
2001, and formally written up in Noble et al. 2006). The 1997-8 mooring locations were
selected to monitor the water column properties and the amount of suspended material
found near the SF-DODS during actual disposal operations as well as to evaluate whether
dredged material was transported into the Gulf of Farallones National Marine Sanctuary
(Figure 7).
2.3.2 Physical Oceanography Results
Mean currents over the slope off the Farallon Islands tended to flow toward the northwest
parallel to depth contours, but the mean flows were very weak. Within the water column
the mean flows above 400 m depth near the disposal site were 2-8 cm/s. Near the
seafloor, mean currents flowed down the submarine canyon toward the disposal site (the
mooring was located up-slope, east, from the disposal site). Near bed currents were also
weak with mean flows less than 4 cm/s.
Mean current speed and direction did not adequately describe the complexity of currents
in the region around the disposal site. Tidal currents near the bottom flow in and out of
the submarine canyon and were the dominant component of current fluctuations.
Subtidal currents (fluctuations in current strength with periods longer than 33 hours) were
dominant in the water column shallower than 1000 m. The subtidal current fluctuations
could reverse the mean current flow over much of the upper water column. Subtidal
currents tended to be highly correlated within the water column and across the region,
averaging 15-20 cm/s. Although these subtidal currents were highly coupled within the
water column, they were independent of the near-bottom subtidal currents.
Resuspension potential near the disposal site was estimated from both near bed current
measurements and assumptions of boundary layer conditions (Noble et al. 2006). Bed
shear stress calculations suggested that fine sand would not be resuspended during the
measurement period but suggested that silt and clay might be resuspended into the 10m
thick boundary layer above the seabed. However, turbidity measurements in this
boundary layer from transmissometers at two of the moorings (D2 and Rl) did not
correlate with measured current speed (and resultant bed shear stress). Current speed at
the bottom was very low and consistent. It is difficult to validate the light attenuation
December, 2008 12
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measurements because the near bottom sediment traps at D2 and Rl were lost and the
transmissometer failed at Dl (Figure 7) where near bottom sediment was collected. The
observed near-bottom light attenuation had small peaks and increasing noise at mooring
D2 from July to October 1998 during a period of low significant wave height. Noble et
al. (2006) speculate that these peaks may have represented turbidity from higher disposal
activity during the summer months. However, the disposal activity during these months
was actually much lower than the preceding months (Figure 2) when there was very little
measured light attenuation. The observed turbidity in the bottom boundary layer did not
appear to be generated by either bed resuspension or dredged material disposal and must
have come from events further away.
The most striking finding from the 1997-1998 data collection was the sediment trap
results. Trap contents from the top traps at the two moorings along the barge transit route
to the disposal site had unusually high concentrations of fine sand (the reference site trap
ca. 20 miles away was empty). The bottom trap at the mooring near the disposal site
collected large amounts of material with similar composition to the ambient bottom
sediment. Trace metal analysis results suggested that sediments collected near the
disposal site had enriched levels of Co, Cr, Mn, Pb, and V over another mooring and the
EPA reference site (see Figure 7) values. The top traps near the disposal site had the
highest concentrations of Co, Cd, and Pb; bottom trap sediments were collected in
discrete time layers that showed considerable variation but generally lower values than
the top trap. Trace metals and PAHs measured in mussels showed no evidence of uptake
above reference except for Al, Mn, Se and Sn. Noble et al. (2006) concluded that the
sand-sized material collected in sediment traps near the surface came from dredged
material spilling from disposal barges transiting to the disposal site. They also concluded
that the potential for resuspension of material at the disposal site was low, and any
material resuspended from the bottom by currents would likely be transported primarily
along the slope to the northwest, not upslope toward the sediment traps (Figure 7).
As a result of these sediment trap findings, EPA evaluated archived barge sensor data and
discovered that many scows were indeed leaking sediments en route. Subsequent EPA
scrutiny of the scows and compliance actions significantly reduced the amount of
material lost during transit.
2.3.3 Modeling Results
The size and thickness of the dredged material footprint has been monitored on an annual
basis since 1995. The majority of the dredged material volume has remained within the
site's boundaries every year. Also, as predicted, a thin apron of material has spread out
beyond the site's margin over a 12 year period (Figure 8).
The models developed for predicting disposal at SF DODS were particle-tracking
algorithms (Hamilton 2001). These model results give a statistical representation of the
deposition of particles on the bottom. This is achieved by dividing the dredged material
into size classes with distinct sinking rates, and each size class is tracked by a small
number of surrogate particles released at hourly intervals at the disposal site. The
modeled results for SF DODS were calculated from the predicted movement of particles.
Particle movement was calculated from a combination of sinking rates and horizontal
December, 2008 1 3
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transport based on the current meter results from the 1991-1992 study, using the volume
disposed in 1996 (calculated as 2.952 mcy for the 'disposal year' 1996-1997 at the time
of the study; see Table 1 for calendar year data); this was then compared to similar
modeling results using the 1997-1998 current meter data. The particle results were
converted to a deposition depth on a modeled seafloor based on bathymetry. The
comparison with actual disposal footprints measured from the 1997-1998 season was
reasonable and provided confidence in the modeled predictions (Figure 9).
2.3.4 Discussion of Physical Oceanography and Modeling Results
The model used for predicting the fate of disposed material at the SF-DODS was a
conservative approach developed because of limitations in existing disposal models for
deep water. Models of disposal assume that the material leaving the barge behaves as a
cloud of particles and water (effectively a dense liquid) that sinks under the influence of
gravity during a convective descent phase. This continues until the cloud either impacts
the bottom or entrains sufficient water to reach neutral buoyancy (collapse phase;
Johnson 1990). These models do not deal explicitly with the material's fate after it
reaches the collapse phase. In deep water, disposed sediments reach neutral buoyancy
well before they reach the bottom (at roughly 1000 m depending on water content) and
begin to spread horizontally and fall as individual particles.
The SAIC model begins with a mean monthly particle load at the surface and tracks
individual particles. This will likely overestimate the dispersion of particles because it
does not account for the convective descent phase of disposal. The actual disposal
activity at the SF-DODS is not composed of mean monthly particle loads, but consists of
discrete disposal events interacting with the particular water column characteristics for
each event. The particle tracking algorithms assume individual particles are released
over a period of time (in this scenario, coarse silt particles take 25 days to reach the
seafloor in 3000 m of water). This most closely approximates the "cloud" of loose
material released in the water column during disposal but does not account for the
coherent mass of material that falls rapidly through the water column before entrainment
of water slows descent and disperses the mass. The movement of water masses near the
surface is most likely to affect the "cloud", and the movement of water masses deeper in
the water column will affect the transport of the dispersed mass of individual particles.
This conservative approach has been able to establish that even in the worst case
scenarios; disposal activities will contribute very few particles to the seafloor within the
nearby marine sanctuary. However, this model approach will not provide sufficient
precision to model footprints accurately enough to guide subsequent monitoring
activities, and therefore should not be used for this purpose. Deposition footprints within
the disposal site could be modeled more effectively with a two phase model. However,
current meter records are limited in the vicinity of the disposal site; accurate prediction of
particle fate and transport would need to be conducted with accurate data on current
conditions existing close to the site during the disposal activities. This level of data
collection and subsequent modeling is not warranted, because disposal footprints can be
verified and monitored much more cost-effectively with actual seafloor observations (as
required by the SMMP).
December, 2008 14
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Current meter records from the 1997-1998 deployments were expected to provide more
clarity about El Nino conditions. Both 1991-1992 and 1997-1998 are considered be
strong El Nino years (http://ggweather.com/enso/years.htm). The results from that set of
current data (with different spatial and vertical coverage) seemed to indicate that in these
years; relatively strong poleward flow on the Farallones slope may differ from the
classical description of Hickey (1979). It remains unclear if La Nina or "average" years
produce distinctly different current patterns over time. However, actual seafloor
observations of deposition patterns indicate that the existing data do reasonably predict
deposition.
2.3.5 Conclusions from Past Physical Oceanographic and Modeling
Studies
Current meter records and particle tracking models have predicted that dredged material
released at the SF-DODS will contribute very little material to the water column or the
seafloor within the Gulf of the Farallones National Marine Sanctuary. Results suggested
that less than 2 mg/L of fine silt class material will reach the Sanctuary boundaries less
than 1% of the time during active disposal.
The current records and modeling support the conclusions in the EIS that material
deposited at the disposal site is not likely to be resuspended or transported by the
relatively weak near-bottom currents. If recently deposited sediments or bioturbated
surface layers were transported, they are likely to be transported along the slope to the
northwest (Noble et al. 2006).
Modeling of footprints on the seafloor corresponded reasonably well with the actual
deposition footprints detected with sediment profile imaging (SPI) for the years with
current meter data available. The model does not account for slumping or consolidation
of deposits, and SPI results may not always distinguish deposits from more than one year
of disposal. However, the results are sufficiently close to provide confidence that the
seafloor monitoring results and model estimates are comparable; therefore, the overall
conclusions reached in the EIS (EPA 1993) about the appropriateness of the physical
setting of the site based on the modeling runs were appropriate and applicable (Figure 9).
2.4 Review of Physical Data
Physical monitoring is designed to confirm (map) the dredged material footprint on the
bottom (Tier 1), and to help determine whether additional oceanographic studies are
needed to improve the models used to predict dispersion in the water column and
deposition on the sea floor (Tiers 2 and 3). In Tier 1, a sediment profile camera system
(Rhoads and Germano 1982, 1986, 1990) is used to document the extent and thickness of
the dredged material deposit both within the site boundaries and in the surrounding
vicinity. The SPI images allow analysts to distinguish locations with dredged material
layers (Figure 10) from the ambient seafloor (Figure 11) as well as reworking of dredged
material by recolonizing benthic animals (Figure 12). This mapping focuses on whether
dredged material is remaining within the site boundaries as predicted, i.e., whether there
December, 2008 1 5
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is a significant accumulation of dredged material outside the site boundary. The SMMP
defines a "significant dredged material accumulation" as five centimeters (5 cm) per year.
If less than 5 cm of dredged material accumulates outside the site boundaries in any one
year, then higher-tier physical monitoring will generally not be required. If greater than 5
cm accumulates outside the disposal site in any one year, then either higher-tier physical
monitoring will be initiated, or appropriate management actions will be taken.
2.4.1 Mapping the Dredged Material Footprint
The physical monitoring aspect of the current SMMP involves annual SPI surveys at
selected locations within the 1 nautical mile [nm] spaced station grid (Figure 4). SPI
observations were always taken at the 11 stations within the perimeter until 1997, after
which not every interior station was sampled every year. The objective for the SPI
surveys was to define the spatial extent and provide a footprint map of the dredged
material deposits. Consequently, some of the stations within the SF-DODS boundary
were dropped over time in exchange for more stations outside the previously-sampled
grid. In subsequent years, additional stations were added, particularly to the north and
west, in order to track the thin deposits of dredged material accumulating outside the site
boundary.
Generally, the majority of the dredged material has remained within site boundaries.
However, the apron of the deposit (thin layers that spread laterally from the main
deposition) has been expanding annually to encompass the footprint area (cumulative
deposits > 5cm all years, Figure 8). A number of known mis-dumps were identified
between 1995 and 2000 (EPA 2002) that resulted in some dredged material being placed
outside the site boundary. These mis-dumps and equipment failure on the scows
prompted modifications to the ocean disposal requirements discussed in Section 1.2,
including the scow certification checklist (incorporated on all subsequent disposal
operations after completion of the Port of Oakland -42 ft. deepening project in 1997).
Fewer mis-dumps occurred after 2000 (EPA, pers. comm.).
Although the cumulative area outside the site where dredged material has at any given
time exceeded 5 cm (Figure 8) is almost equal in area to the designated site (26.5 km2),
there have been no adverse impacts detected in the benthic community outside or inside
the site boundary even when thin layers accumulate outside the boundary (see below).
During the October 2000 monitoring survey, a substantial layer (> 14 cm) of distinctive
material was detected at Station 16 outside the site boundary (TetraTech, 2001). This
material was composed of fine sand overlying gray clay, and the monitoring report noted
that the gray clay may have been the previous years' material (Station 16 had an average
of 4.8 cm of material in the 1999 survey). However, the sand layer alone was 6 cm
December, 2008 16
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thick, exceeding the 5 cm definition of "significant" dredged material accumulation
outside the site perimeter year in a single year.
It was uncertain at the time whether the deposit seen at Station 16 was in fact dredged
material. The resolution of the basic sampling grid was not fine enough to conclusively
determine that this deposit was part of a "tongue" or "outgrowth" of material extending
from the disposal site as opposed to being an isolated area of mounding. In addition, the
sediment chemistry results for Station 16 appeared to be most similar to off-site stations
where little or no dredged material was present (EPA 2002). The apparently rapid
accumulation of material at station 16 since the previous survey was particularly
surprising given that only 660,980 yds3 of material had been discharged at the SF-DODS
since the 1999 survey. In contrast, a maximum average of only 4.8 cm had been
identified there in past years following as much as 3.6 million yds3 of disposal. Station
16 is approximately 100 meters shallower than (up slope from) the SF-DODS boundary,
and over 200 meters shallower than the center of the disposal site (Figure 8). Substantial
quantities of dredged material from properly disposed loads would not be expected to
disperse and settle in this location unless highly unusual oceanographic conditions were
present. Disposal records (based on automatically-collected scow tracking data)
indicated that there had been no known mis-dumps in the immediate vicinity of Station
16, either during 2000 or in previous years (EPA 2002).
Station 16, however, is at the foot of one of the steeper slopes in the vicinity of the SF-
DODS. Active slumping has been identified in the general area in the past (EPA 1993).
It was therefore possible that the relatively thick deposit detected at Station 16 after the
2000 monitoring event was related to slumping of native material from up-slope, rather
than a result of dredged material disposal. Higher-intensity sampling around Station 16
was therefore included in the 2001 survey to help identify whether the material was
indeed dredged material from the site or slumped native material from up-slope. A series
of 4 stations separated by 0.5 nautical mile was collected in a line radiating SE from the
disposal site (Stations 16NW, 16, 16 SE and 39; TetraTech 2002). Analysis of these
photographs showed that while a distinctive layer of dredged material from recent
disposal activity was not present, there was historical dredged material at all four stations,
ranging in thickness from 4.1 cm in the southeast end to 4.7 cm at the northwest end of
the transect closest to the disposal site. While the thick layer of dredged material
detected at Station 16 in the 2000 survey was not present in the 2001 survey, it did appear
that the sediment in the vicinity of this location was dredged material and not turbidites
from slumping of up-slope native sediment (TetraTech 2002).
Mapping the physical extent of the dredged material footprint has continued each year;
while the material continues to spread along a NW-SE axis as predicted from modeling
runs (see previous section), the results to date show that the apparent accumulated
thickness of dredged material outside the site boundary is still less than 10 cm (Figure 8).
Because the sediment is reaching the bottom as a rain of individual particles at these
December, 2008 1 7
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substantial water depths, the freshly deposited particles are constantly being reworked
into the underlying sediments by infaunal burrowing and feeding activity. It has become
increasingly difficult over time to distinguish between historical dredged material
deposits and deposits resulting from the past year's disposal activities within the site
boundary. However, the distinct optical and textural characteristics of dredged material
still allow scientists to discriminate between native sediment and the deposited material
so that the overall spatial extent of the material can be accurately tracked over time.
2.4.2 Review of Historical SPI Survey Results
Data from SPI surveys conducted between 1996 and 2006 were used to evaluate the
relationships between benthic community response and the presence, thickness, and
volume of dredged material disposed. For this purpose, historical SPI survey data were
compiled and reviewed for consistency; an initial inspection of the data identified several
stations from the October 1997 survey with curious results (thick layers of dredged
material reported along with large values for mean apparent RPD depth). The apparent
RPD depth (Redox Potential Discontinuity) is a visual (color change) measure of the
relative activity levels of burrowing deposit feeders. A deeper RPD is associated with
higher levels of activity and less disturbed conditions. A shallower RPD is associated
with lower levels of activity and recently disturbed conditions (such as dredged material
disposal).
An inspection of the corresponding sediment profile images for these reported results
indicated substantial errors in image interpretation and the need for a broader quality
assurance (QA) check of the historically-reported results. Every image from the January
1996, December 1996, and October 1997 surveys was reviewed by a qualified senior
scientist (J. Germano), and the reported SPI results for apparent RPD, successional stage,
and dredged material thickness were verified and corrected where necessary. The results
of this 100% QA check of these early SPI surveys showed the following:
• January 1996: 34 images reviewed from 28 stations.
o Mean apparent RPD was underestimated in only two replicate images by
approximately 50%. The corrected and remaining originally-reported RPD
values for site ranged from 0 to 3.6 cm.
o Dredged material thickness was generally underestimated by as much as
500%; the presence of dredged material was incorrectly indicated in six
replicates (five replicates missed the presence of dredged material, and one
image had dredged material reported that was not present).
December, 2008 1 8
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o Successional stage was underestimated in five replicates (originally reported
as Stages 1 or 2 when Stage 3 taxa were present).
• December 1996: 40 images reviewed from 28 stations.
o Mean apparent RPD was underestimated in six replicate images by as much as
70%. Both corrected and remaining originally-reported RPD values ranged
from 1.3 to 5.9 cm.
o Dredged material thickness measurements showed observation error with no
directional bias; overestimation error (up to 220%) was much greater than
underestimation error (70%). Presence/absence of dredged material was
accurate in all but one replicate image.
o Successional stage was correctly interpreted.
• October 1997: 48 images reviewed from 30 stations.
o Mean apparent RPD depth was overestimated in 11 replicate images by as
much as an order of magnitude. Corrected RPD values ranged from 0.5 - 4.7
cm (originally-reported RPD values ranged from 1.5 - 15cm).
o Dredged material thickness was underestimated in 25 replicate images by as
much as 600%. Presence/absence of dredged material was accurate in all
replicates analyzed.
o Successional stage interpretation was underestimated in 18 replicate images
(all were originally designated Stage 1, but should have been reported as
Stage 1 on 3, Stage 2-3, or Stage 3).
Based on this review, it appeared that the utility of the historical SPI surveys would be
limited due to inaccurate interpretation of some of the earlier images. Consequently,
further QA checks were performed on images with reported characteristics that either had
been shown to have a tendency to be misinterpreted or were just simply questionable.
We identified 119 additional images with high RPD values (>4.5 cm) and Stage 1, or
high RPD values and with reported dredged material thicknesses greater than 2 cm. Of
these, a random selection of approximately half these images was made. This resulted in
an additional 65 images selected (10% of the 621 images) from the December 2000 to
September 2004 surveys for a QA check with the following results:
o Mean apparent RPD was overestimated in every replicate chosen by as much
as 75%. Corrected RPD values ranged from 1.1 - 5.1 cm (originally reported
RPDs ranged from 1.9-7.5 cm).
o Dredged material thickness was accurately reported in 81% of the images. In
the remaining 12 images (19%), even the accurate interpretation of the
presence or absence of dredged material was a problem. In all but one image,
December, 2008 1 9
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dredged material presence was missed in the original results, but the results
subjected to QA review indicated thicknesses varied from 1.8 - 9.4 cm. In
one replicate, dredged material thickness was reported as 3.4 cm but should
have been recorded as being absent.
o Successional stage interpretation was underestimated in every replicate image.
Typically, the success!onal stage was reported as only Stage 1, but a QA
review indicated that these should have been reported as Stage 1 on 3, Stage
2-3, or Stage3.
In all, the QA review included 100% of the images from the three earliest surveys, and
10% of the images from the 2000 to 2004 surveys. Based on this QA review the
following conclusions were reached regarding the utility of the historical SPI survey
results for quantitative analysis:
• Mean apparent RPD. With the exception of the October 1997 survey, the RPD
results appear to have been originally reported without consistent bias and with
limited errors. The original data, replaced with results for the QA'd images, should
be acceptable for quantitative analysis.
• Dredged material thickness. The measurement of dredged material thickness
appears to have been inaccurately estimated in some of the historical surveys.
However, the most suspicious dredged material values were selected for QA, so the
corrected data set could be cautiously used for quantitative analysis. The
presence/absence of dredged material showed better accuracy (90% accuracy overall)
and should be suitable for inclusion in further correlation analyses.
• Successional Stage. The successional stage results appear to have been frequently
and consistently underestimated. We believe the reported data cannot reliably be
used in a quantitative analysis. The images that were reviewed, however, indicated
that Stage 3 animals had been present at nearly every station, including stations
within the site that had an accumulation of recent dredged material; in recent surveys,
evidence of Stage 3 taxa continue to be found within the site (Figure 12). At least
qualitatively, the results of the QA check can be used as evidence of benthic
recolonization throughout the site, even in the presence of dredged material.
Utilizing the available results from past monitoring surveys, including the corrected
historical SPI data (mean apparent RPD and presence/absence of dredged material),
historical annual disposal volumes (Table 1), and the benthic summary data (Table 4-2,
ENSR 2005), we investigated several relationships between dredged material volume,
presence, and benthic effects.
2.4.2.1 Evaluation of Benthic Impairment
December, 2008 20
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The mean apparent RPD data from the corrected historical SPI survey dataset were
evaluated to allow for comparisons among subsets of the data, including stations with or
without dredged material, and in years with large or small disposal volumes. The mean
apparent RPD is a proxy for benthic impairment, a shallow RPD would indicate some
recent disturbance or impairment of the benthic community.
The distribution of the RPD data were summarized using the overall cumulative
distribution function (CDF) and conditional CDFs (CCDF). The CCDFs are just CDFs
for subsets of the data ("conditional" on particular features of the dataset, such as dredged
material present; Figure 13). Information about the distribution is obtained from a CDF
or CCDF curve by reading the y-value (probability) associated with the x-value (RPD).
At each point on a curve, the y-value indicates what percent of the samples in that dataset
have RPD values less than or equal to the associated x-value. Curves that are further to
the right have a higher median RPD value for the distribution (i.e., generally better
conditions), and steeper curves indicate distributions with less variability. The data
shown in Figure 13 are summarized in Table 3.
Table 3. Number of Stations by Presence/Absence of Dredged Material and
Annual Disposal Volume
Annual
Disposal
Volume (yds3)
<100,0001
>250,0002
Totals
Dredged
Material Absent
8
124
132
Dredged
Material
Present
60
159
219
Totals
68
283
351
Includes October 1999 and December 2000 surveys, only.
Includes surveys from 1996-1997,1999,2001-2004, and 2006.
Using an RPD value of 1 cm or less to indicate the presence of a benthic impairment, the
data sets have the following features:
• 5% of all stations (18/351) have mean apparent RPD values < 1 cm.
• 8% (18/219) of the stations with dredged material present have mean apparent
RPD values <1 cm.
• None of the 132 stations with dredged material absent have mean apparent
RPD values < 1 cm.
• 24% (16/68) of the stations from small volume disposal years (<100K yds3)
have mean apparent RPD values < 1 cm.
• <1% (2/283) of the stations from large volume disposal years (>250K yds3)
have mean apparent RPD values < 1 cm.
December, 2008
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• Mean apparent RPD values tend to be higher when dredged material is absent
(Figure 13: CCDFs where dredged material is absent are found to the right of
the respective CCDFS where dredged material is present); and RPD values are
lower among the small volume disposal years.
There is a higher incidence of biological effects (i.e., RPDs < 1 cm) at stations where
dredged material is present (8% vs. 0% where dredged material is absent), but there is an
insufficient number of stations (only 18 out of 351) to suggest a widespread problem.
Surprisingly, relatively low annual disposal volumes do not suggest that the benthic
conditions are better (i.e., higher RPDs); in fact, the data suggest the opposite (Figure 13:
CCDFs for small volume stations have the lowest medians). If there are any effects of
disposal volumes on the incidence of lower RPDs, they cannot be separated from
temporal effects. While annual changes in recruitment could increase or decrease the size
of the potential community available to colonize newly deposited sediment, the most
likely explanation for the variation found in mean apparent RPD values is related to the
time interval between the monitoring cruise and the last disposal event. Given the thin
layers of material that are settling to the bottom, the majority of the recolonization on the
dredged material is from existing fauna either burrowing up through the newly-deposited
layer to re-establish themselves at the new sediment-water interface or lateral migration
from the ambient seafloor into the newly available habitat space.
The relationship between mean apparent RPD values and dredged material thickness is
illustrated in Figure 14. The range of mean apparent RPD values consistently decreases
as the depth of the dredged material increases. However, even at stations with dredged
material thickness as great as 13.5 cm, the mean apparent RPD values still exceed 1 cm,
an indication of biological reworking activity. Station 13, at the center of the disposal
site, has consistently had dredged material thicknesses of 12 cm or greater while mean
apparent RPD values improved from 0 cm in January 1996 to 1.9 cm in December 1996,
and then fluctuated between 0.8 cm and 2.1 cm.
The community metrics derived from the benthic grab results (discussed below in Section
2.6.3) were plotted against annual disposal volumes and station specific dredged material
depth from the corrected historical SPI surveys (Figures 15-16). Clearly, these
community metrics (i.e., Total Abundance per O.lm2, Valid Species count, Pielou's J, and
Fisher's log-a) do not show a relationship between disposal volumes nor dredged
material thickness. The ranges for abundance and valid species richness are quite
variable across the range of dredged material disposal and accumulation. These results
suggest that either a) spatial variability of the benthic activity is inherently greater than
the effect of disposal volumes or depth of accumulated dredged material, i.e., the
disposed dredged material has had no impact on the benthos; or b) these metrics do not
adequately represent biological impacts, or c) both.
December, 2008 22
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2.4.3 Conclusions
In summary, the both the SPI and benthic community results indicate that while there are
areas within and outside the disposal site boundaries where the benthic communities have
been affected by dredged material disposal, these conditions do not consistently persist
over time, nor are they strongly associated with dredged material thickness, dredged
material presence, or disposal activity:
• Very few RPD values are within the range of depressed biological activity
RPD values show a reduced range with increasing dredged material thickness,
but there are images indicating active biological reworking activity (RPD
values > 1 cm) on dredged material thicknesses as great as 13.5 cm.
Successional stage (in the corrected dataset) was predominantly 3 (or 1 on 3).
There are images showing Stage 3 animals even at the center of the disposal
site (Station 13) on dredged material thicknesses that exceeded the camera
penetration (Figure 12).
There are no apparent relationships among benthic community metrics and
annual disposal volumes or dredged material thickness.
Overall there is no evidence of major physical changes that suggest
widespread or long-term impairment of the benthic community as a result of
disposal operations.
2.5 Review of Chemical Data
The current SMMP Implementation Manual (EPA 1998) includes chemical monitoring of
disposed dredged material. Sediment samples have been collected from the area within
and surrounding the SF-DODS and analyzed for sediment chemistry each year since
monitoring began. A summary of the ranges of measured chemical values for each
monitoring year is provided in Appendix Table 1. Ranges were calculated for the
stations reported with no dredged material present ("Ambient") and for those with
measurable dredged material ("Footprint"), using 1A of the detection limit for values
reported below detection. Note that if a station had measurable dredged material during
one survey, it was classified as part of the footprint for all follow-on years, assuming
historical dredged material was still present at the station. Chemical values measured in
both Ambient and Footprint stations then were rolled up for all years, as presented in
Table 4.
Chemical measurements results generally have been compared to values measured in pre-
dredge test sediments (Appendix Table 2); no specific numeric criteria or statistical tests
have been used, just a simple comparison of maximum values between the two data sets.
This approach has been sufficient to date because, with minor exceptions, all of the
December, 2008 23
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chemical concentrations measured have been lower than maximum values reported from
the pre-dredge testing data. In many cases, the values are within the ranges measured
both during the baseline surveys, conducted in 1990-91 (SAIC 1991), and at the SF-
DODS reference area (EPA 1999; Table 4). This section presents a summary of the
sampling design and sediment chemistry results at the SF-DODS from 1996-2007, with
implications for modification of the chemical monitoring tier in the revised SMMP.
2.5.1 Sediment Characteristics of the SF-DODS and the Reference
Area
Both the SF-DODS and the SF-DODS reference area are located on the continental slope
outside of the mouth of San Francisco Bay (Figure 1). The SF-DODS was sited close to
the foot of the slope in an area characterized by slow deposition and by very little mass
movement of sediment. Mass movement of sediment has been largely restricted to the
steeper slopes that border submarine canyons and gullies (Chin and Ota 2001). The
reference area identified by EPA for the SF-DODS is located in approximately 1,285
meters of water, and is located approximately 35 kilometers from the SF-DODS (Figure
1). The reference area is located in shallower water on a plateau on the continental slope,
and is characterized by slow deposition and little documented sediment movement (Karl
2001). Long-term sedimentation rates in the vicinity of the reference site have been
reported at an average of 0.11 cm/decade over the last 10,000 years (Gardner et al. 1997).
The SF-DODS reference area is not sampled during the annual monitoring surveys of the
SF-DODS. During the process of dredged material projects, physical, chemical, and
biological testing data are collected and evaluated relative to reference as described in the
Ocean Testing Manual (EPA/USACE 1991). Sediment physical and chemical data have
been collected at the reference site both by the EPA (EPA 1999) and by the USGS
(Bothner et al. 1998; Chin and Ota 2001). The EPA has developed a reference area
database for comparison to dredged material projects, due to the expensive and
logistically difficult task of sampling at the reference area. The database includes several
sets of sediment test data including sediment chemistry, bioassay, and tissue
bioaccumulation data (EPA 1999).
December, 2008 24
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Table 4. Summary of range of sediment chemistry measured at SF-DODS and the reference area.
Chemical
Conventional
Total Solids (%)
Percent Fines
TOC (%)
Metals (mg/kg dw)
Arsenic
Cadmium
Chromium
Copper
Lead
Mercury
Nickel
Selenium
Silver
Zinc
Organics (ug/kg dw)
TPH
LPAHs
HPAHs
PAHs
Aldrin
Dieldrin
Total BHCs
Total DDTs
Total PCBs
Tri-n-butyltin
SF-DODS
Baseline
(1990-91)
Range
-
78-99
2.7-3.9
nd-5.2
nd-0.38
91 - 167
20-62
nd-12
0.13-0.24
77- 115
nd - 6.6
nd - 0.64
91 - 147
-
nd
nd - 220
-
-
nd
-
nd
nd
-
SF-DODS Ambient1 (1996-2007)
N
28
16
28
27
27
27
27
27
27
27
27
27
27
9
24
24
24
27
27
27
27
27
19
Range3
28-37
70-98
2.1 -3.2
2.9-5.4
0.1-0.53
40-90
28-64
5.2 - 25
0.02-0.16
54-86
1.8-4.6
0.2-1.2
67-113
10-35
8.9-144
20 - 192
30 - 336
0.39-2.8
0.13-2
0.74 - 22
1.4-24
9.5- 121
0.26- 1.8
AvgilSD
32 ±2
91 ±8.6
2.8 ±0.3
3.7 ±0.7
0.3 ±0.1
71 ± 13
44 ± 9.4
10.1 ±5.7
0.1 ±0.04
68 ±7.8
3.4 ±0.8
0.54 ±0.19
88 ±13
22 ±8
57 ±52
91 ±65
148± 115
0.87 ±0.67
0.77 ± 0.42
3.98 ±4.4
4.7 ±4.2
56 ±38
1.2 ±0.6
SF-DODS Footprint2 (1996-2007)
N
138
94
138
138
138
138
138
138
138
138
136
138
138
65
126
126
126
138
138
138
138
138
94
Range
17-65
29-98
0.51 -5.6
0.7 - 8.3
0.09-0.53
31 - 120
7.3 - 62
3.5-35
0.02 - 0.25
4.8-97
0.14-5
0.015-2.4
36-135
9-65
5.5 - 1298
14 - 2749
20 - 4047
0.24 - 3.6
0.08-2.4
0.38-17
1 - 15
5.6- 144
0.16-38
AvgilSD
40 ±7.6
71 ±15
2 ±0.7
3.6 ±1.3
0.24 ± 0.09
59 ± 16
33 ± 10
10 ±6.8
0.093 ± 0.049
59 ± 12
2.3 ±1.2
0.48 ±0.34
74 ±18
24 ± 11
64 ± 120
151 ±270
215 ±382
0.88 ± 0.64
0.88 ±0.55
3.4 ±2.7
4.2 ±2.3
58 ±37
1.6 ±3.9
SF-DODS
Reference
Range
33 - 594
40-84
0.63- 1.5
2.2-5.3
0.3 - 0.6
69 - 283
18-86
5.1-26
0.1-0.2
51 -238
0.6-2.6
0.2-1
61-288
nd- 17
nd-77
nd-115
nd - 192
nd
nd
nd
nd-2.1
1.9-3.94
nd- 1.3
nd: not detected All calculations made using 1/2 of the reported detection limit for values below detection.
Calculated over stations with no measurable dredged material in any survey (see text for further information).
Calculated over stations with measurable dredged material (see text for further information).
'Minimum - maximum reported range; data below detection are reported as 1/2 of the detection limit.
4Values from Bothner et al. 1998 as only values available.
December, 2008
25
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2.5.2 Current SMMP Chemical Monitoring Protocols
Chemical monitoring addresses the effects of dredged material deposition on the
chemical and physical characteristics of bottom sediments within and adjacent to the SF-
DODS. The overarching goal of routine chemical measurements is evaluation of the
long-term potential for contaminant accumulation in sediment and potential exposure of
benthic and demersal organisms to toxic and/or biologically-available contaminants. A
secondary benefit of the chemical monitoring module of the SMMP is to confirm that
only approved material is being disposed at the SF-DODS.
Pre-disposal testing is conducted to ensure that sediments approved for disposal at the
SF-DODS are not toxic and also do not pose a significant risk of adverse effects due to
bioaccumulation of contaminants. Therefore, the current SMMP assumes that, if the
sediment was approved for disposal at the SF-DODS, the ranges of chemistry values
associated with the approved suitable dredged sediments are applicable metrics to
compare against samples collected at the disposal site itself. No specific statistical tests
or method of summarizing the testing data have been recommended; in the bulk of
monitoring reports, this analysis consists of a simple comparison of maximum values
between the SF-DODS samples and from the pre-dredge test data.
Currently, chemical monitoring in Tier 1 consists of collecting and analyzing sediment
samples from within the perimeter of the SF-DODS. The SMMP also requires collection
of samples from outside the site boundaries for archival and potential chemical or
biological analyses in subsequent tiers; in almost all cases these samples have been
analyzed and results reported even when higher tier monitoring has not been triggered.
The sampling design has changed over the years; the footprint of dredged material near or
outside the perimeter of the site has been the most recent focus for sediment chemistry
sampling (see next section). The SMMP notes that if on-site sediment chemistry is
"significantly" elevated relative to that which was pre-approved for disposal, further
chemical monitoring at higher tiers will be required.
In the current SMMP, if significant elevations of chemicals within the site boundary are
detected, then Tier 2 monitoring is triggered, and the sediments collected from outside
the disposal site boundary are analyzed and compared in the same way as Tier 1. The
implication of this tier is that on-site chemical contamination is of less concern if it has
not spread outside of the boundaries; if the results of the off-site samples do not show
elevated values, then higher-tier chemical monitoring is not required. To date, samples
from both inside and outside of the SF-DODS have been sampled and analyzed
simultaneously. Tier 3 monitoring, if needed, includes chemical analysis of tissues from
fish and/or infaunal organisms collected from the site and its surroundings; based on
these results, the need for management actions is then evaluated.
December, 2008 26
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2.5.2.1 SF-DODS Surveys and Sample Design
Chemistry samples from this area in 1990-91 prior to the implementation of the
monitoring program were collected as part of the baseline monitoring for the US Navy
Section 103 disposal permit (SAIC 1991). These baseline samples represented
background conditions at the SF-DODS; baseline conditions were different from the
background conditions at the SF-DODS reference area, because material had been
historically disposed at the SF-DODS location (Chin and Ota 2001). Post-disposal
monitoring samples have been collected every year from 1996 to the present (Table 1).
In most of the reviewed reports, the data have been compared to samples collected from
dredging projects conducted since the prior monitoring survey, primarily from Richmond
and Oakland Harbors. In more recent monitoring years, the data have been compared to
cumulative data ranges (minimum-maximum) for pre-dredge testing data, because as
more sediment has been disposed at the SF-DODS, the ability to link sediment samples to
specific dredging projects has become increasingly problematic (Appendix Table 2).
In the most recent years of the reviewed monitoring data, stations were classified as
located within the apparent, recent, or historical dredged material footprint, or in ambient
sediments with no apparent dredged material present. Sediment samples have been
obtained during the annual monitoring surveys using a partitioned boxcore sampler
(Figure 5) at stations usually sampled in conjunction with the sediment profile imaging
(SPI) system. The ability to identify dredged material as "recent" or "historical" was
based on the analysis of sediment profile images. Ambient sediments, taken from
locations showing no dredged material (based on SPI results), are expected to have
similar physical and chemical attributes as the baseline data collected prior to the start of
dredged material disposal operations. Sediment samples from each survey are analyzed
for grain size, TOC, trace metals, chlorinated pesticides, polychlorinated biphenyls
(PCBs), polynuclear aromatic hydrocarbons (PAHs), and organotins. Laboratory
methods and quality control requirements are consistent with pre-disposal sediment
testing requirements (EPA/USACE 1991).
The stations selected for sediment sampling have varied from year to year, although there
has been some consistency for a few long-term stations. Stations have been classified as
being outside or inside the site (Figure 4); beginning in 2000, samples were collected
along the perimeter and outside of the site, rather than from the bulk of the dredged
material deposit, acknowledging that exposure to sediment inside the site is short-term
(until the next dredging episode). More recent surveys classified stations as being within
the apparent, recent, or historical dredged material footprint, or in ambient sediments
with no apparent dredged material present.
December, 2008 27
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Many stations have been sampled repeatedly through the years of monitoring (Figure 6).
The most consistently measured stations include Stations 10, 17, and 19; additional
station locations have been added as the dredged material footprint has expanded. The
location of the sampled stations is critical in that the SMMP has specific tiers tied to
whether the station is located within the perimeter of the disposal site boundary or outside
of the site (EPA 1998). The variability of the sample design over the last decade of
monitoring is an indication of the changing emphasis of chemical monitoring objectives.
In 1997, 11 out of 17 stations were located on or inside the disposal site boundary (65%),
and 9 out of 12 stations were located inside the site or along the perimeter in 1998 (75%).
In following years, the ratio of the number of stations located on or inside the site
boundary decreased (Table 5), with 46% in 1999 (6 out of 13 stations), 17% in 2000 (2
out of 12 stations), and 22% in 2001 (2 out of 9 stations). In the last three years of the
reviewed monitoring period (2002-04), the same 4 stations (approximately 25%) have
consistently been sampled inside the site: Station 13 (at the center), and Stations 17, 19,
and 23 (on the perimeter; see Figure 6).
Table 5. Ratios of inside versus outside sampling stations to the SF-DODS site boundary
Stations
Inside +
perimeter
Outside
Ratio
Inside/Total
1997
11
6
65%
1998
9
3
75%
1999
6
7
46%
2000
2
10
17%
2001
2
7
22%
2002
4
11
27%
2003
4
12
25%
2004
4
12
25%
The modification of the sampling design appears to reflect a change of focus from the
SMMP's Tier 1 (inside) to Tier 2 (outside) of the SF-DODS boundary. In recent years,
the sample locations have been placed farther from the site center to target the widening
spread of the dredged material apron. Also, detection of contaminants of concern in
surface sediments within the boundary has not only been rare, but is of less concern,
because the sediment within the boundary, by definition, is ephemeral; new surfaces are
constantly being created as new dredged material is deposited in subsequent years.
In summary, the change of selection of sediment sample locations from preferentially
inside to dominantly outside of the SF-DODS perimeter has changed the focus of the
monitoring from confirmation ("Is unacceptable sediment winding up at the site because
of poor criteria for pre-dredge testing?") to assurance that no degraded sediment located
outside of the site is causing unacceptable biological effects. Boxcore samples have
consisted of a composite of the top 10 cm of sediment, regardless of the actual thickness
December, 2008
28
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of the dredged material present; this is representative of the average mixing depth for
infauna (Boudreau 1998) and an appropriate sample of the biological exposure zone.
Confirmatory monitoring, if necessary, should use samples that consist exclusively of
dredged material for the most accurate comparison, but the body of data collected within
the SF-DODS site demonstrates no evidence that pre-dredge testing protocols are
insufficiently protective. Rarely have any contaminants been measured that were higher
than the maximum measured in the pre-dredging samples; a few exceptions are discussed
in the next section.
2.5.3 Summary of Chemical Monitoring of the SF-DODS
Monitoring results are summarized below for samples collected from stations with
measurable dredged material (as determined by SPI data) within the footprint of dredged
material, and for samples collected from stations with no dredged material (ambient).
The data are compared to baseline data (1990-91; SAIC 1991), as well as the SF-DODS
reference area (Table 4). In addition, the data are also compared to reported ranges of
chemical concentrations measured from the range of reported pre-dredge testing data
(Appendix Table 2). The reported ranges and material sources are summarized from
reported concentrations in the monitoring reports. All chemical results are reported in
dry weight units.
2.5.3.1 Physical Parameters
Both the SF-DODS and the reference area are on the continental slope in areas that are
atypically sandy relative to other continental slopes (Karl 2001). The sand source is
probably relict sediment from the San Joaquin-Sacramento River system that has been
transported and winnowed from the mouth of the San Francisco Bay estuary (Dean and
Gardner 2001). The mean grain size decreases with increasing depth on the slope, from
dominance by silty and clayey sands in Pioneer Canyon (near the SF-DODS reference
area), to primarily silt and clay closer to the disposal site itself (Karl 2001). Cores
collected from the reference and surrounding area by the USGS (Bothner et al. 1998)
resulted in grain size content similar to those recorded in the SF-DODS Reference Area
Database (EPA 1999), ranging from 40-84% fine-grained sediment (silt and clay; Table
4).
Sediment at the SF-DODS collected prior to the monitoring program during baseline
surveys was dominated by silt and clay, with a total fines content ranging from 78-99%
(SAIC 1991). This range was similar as measured in the first two monitoring surveys in
January and December of 1996, but the sand portion of samples collected at the SF-
DODS has increased following the period of large volume disposal in 1997-98 (Figure
December, 2008 29
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17). This results in a lower fine-grained fraction within the dredged material footprint
(70.7 ± 15%) as compared to ambient samples (90.6 ± 8.6; Table 4).
The highest total organic carbon (TOC) concentration reported during the SF-DODS
monitoring was 5.6% at station 116 in 2003 (SAIC et al. 2004), categorized as within the
dredged material footprint with small, but measurable dredged material (0.55 cm). Other
than that outlier value, the range of measured TOC within the footprint ranges from 0.5 to
3.5%, which is less than the range between the source material and baseline
measurements (Figure 18). The reported range of TOC measured in Richmond and
Oakland Harbors over the entire monitoring period (1994-2004; SAIC et al. 2005) is
quite narrow (0.08-1.7%, Appendix Table 2), which is typical of TOC in San Francisco
Bay sediments (SFEI 2007). Reported TOC in cores collected from just the upper 1 cm
of sediment at the reference site was similarly low (1.2-1.9%; Bothner et al. 1998).
However, ambient stations around SF-DODS were higher, ranging from 2.1-3.2% TOC;
and TOC in the baseline studies around SF-DODS was also high at 2.7-3.9%. The higher
concentrations of TOC at the SF-DODS compared to reference and to Bay dredged
material, has implications towards potentially reducing the availability of contaminants,
although the active diagenetic processes at these water depths and temperatures are quite
different than those found in the source harbor locations (Bothner et al. 1998).
2.5.3.2 Chemical Parameters
Sediment chemistry values measured at the SF-DODS from 1996-2007 have, in almost
all cases, been well below those measured in the source pre-dredge test sediments, and
therefore have not triggered Tier 2 sampling and analyses (Appendix Table 2). There
have been reported detections of silver (Ag) and selenium (Se) higher than concentrations
reported in pre-dredge test data; these cases are discussed in more detail below. These
elevated concentrations have been in samples collected within or near the disposal site
boundary and were therefore detected more often in the earlier monitoring studies when
sampling was focused within the disposal site.
2.5.3.2.1 Metals
The incidence of measured metal concentrations reported at levels higher than in the
associated source material has been rare in SF-DODS monitoring. Silver was noted as
being higher than concentrations reported in pre-dredge test samples in some of the
surveys (Figure 19), with highest reported concentrations in 1996-97 (average for
footprint 1.0 mg/kg, Appendix Table 1). The highest detection of Ag (2.4 mg/kg) was at
the center station in December 1996 (EPA 2002), and therefore most likely associated
with the large volume of material disposed in that year (Table 1).
The apparently elevated concentrations of Ag reported from the disposal site monitoring
are due primarily to the relatively low concentrations measured in the source material.
Compared to ambient and to the reference areas, the concentrations are not particularly
elevated except for the high value in December 1996 (Table 4; Figure 19 combines
reference and footprint, see Appendix Table A-l for details). The maximum Ag
December, 2008 30
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concentration reported from the sediment characterization data for the in-Bay dredging
years 1997-2000 (EPA 2002) was 0.6 mg/kg (dry weight), lower than the maximum
measured at the reference site (1.0 mg/kg), the baseline samples (0.64 mg/kg), and in the
SF-DODS ambient sediment collected during the 2003-04 surveys (0.62 mg/kg,
Appendix Table 1). The highest reported Ag value from dredged material
characterization data following this period was 0.84 mg/kg from Oakland Harbor, and in
the 2004 monitoring year, a value of 1.4 mg/kg was reported for Oakland Harbor (SAIC
et al. 2005). Since 2002, the maximum Ag value has remained below this 1.4 mg/kg
threshold (Figure 19). It appears from these data that the high value in December 1996
has not reoccurred in any areas sampled within or outside the footprint of dredged
material.
Selenium (Se) was the only other metal measured at concentrations greater than that of
reported source ranges (Table 4). The highest Se concentration reported in pre-dredge
test samples was 2.0 mg/kg (SAIC et al. 2005). The maximum Se concentration
measured at the SF-DODS was higher than 2.0 mg/kg in almost all surveys conducted at
the SF-DODS; but this includes baseline and ambient monitoring samples as well as
sediments from the SF-DODS reference area (2.6 mg/kg). The highest reported Se value
was 6.6 mg/kg, measured during the baseline survey (SAIC 1991). This suggests a
potential persistent background source of Se, rather than uncharacterized dredged
material being the source of any elevated Se concentrations measured at the site. For
comparison, the maximum reported Se value measured in San Francisco Bay was 1.7
mg/kg (SFEI 2007).
2.5.3.2.2 Organics
The maximum concentration of polynuclear aromatic hydrocarbons (PAHs) measured in
SF-DODS sediments was 224 ug/kg for total low molecular weight (LMW) PAH, and
1,436 ug/kg for high molecular weight (HMW) PAH. These values are slightly higher
than LMW and HMW PAHs measured in baseline and ambient samples (maximum of 27
and 220 ug/kg, respectively) as well as in reference sediment (maximum of 77 ug/kg and
115 ug/kg, respectively), but far lower than the maximum measured in the source areas
for dredged material. The reported maximum LMW and HMW PAH concentrations for
samples deemed suitable for SF-DODS disposal are 13,993 ug/kg and 36,985 ug/kg for
samples from the Port of San Francisco (Appendix Table 2). Since the measured
concentrations of PAHs in post-disposal monitoring have remained well below the
maximum concentrations approved for disposal at SF-DODS, further sampling or
analysis for an upper level tier have not been triggered.
In more recent, surveys, low levels of detected pesticides were below those reported in
the tested sediments, so that no further analyses were triggered. The maximum
concentration of alpha-BHC measured in SF-DODS samples (12 ug/kg) was in 2002
(SAIC et al. 2003). By comparison, the highest reported value of alpha BHC over the
December, 2008 31
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dredging years 1994-2004 was 25 ug/kg (SAIC et al. 2005).
Total DDT (sum of detected concentrations for DDT and its degradation products DDD
and DDE) occasionally has been measured at above detectable levels in SF-DODS
samples over the years (maximum of 22.4 ug/kg in an ambient station in 2004); however,
these concentrations are an order of magnitude less than the maximum measured in the
source sediments (280 ug/kg ; SAIC et al. 2005). Continued confirmatory monitoring for
bioaccumulative chemicals of concern (BCOC) will further the confidence that the
testing program is effective at continuing to ensure that no bioaccumulative chemicals are
present at unacceptable levels at SF-DODS.
2.5.4 Chemical Monitoring Conclusions
Measured chemical concentrations in the sediment have generally not exceeded those
background values found either at the site prior to disposal or at the SF-DODS reference
area; the few chemical compounds whose concentrations have exceeded background
values have still been well below any value to cause any potential concern for biological
effects.
2.6 Review of Biological Data
The biological monitoring module of the current SMMP addresses the potential effects of
dredged material disposal on two marine ecosystem components: pelagic (seabirds,
marine mammals, and fish) and benthic/demersal (bottom-dwelling invertebrate
communities). Potential impacts to marine birds, mammals, and fish were expected to be
localized (limited to the immediate vicinity of the disposal site) and to occur within a
limited time frame during and immediately after actual disposal operations. Physical
impacts to the benthic community were expected to last somewhat longer and to be
readily detectable within the footprint area of dredged material accumulation (EPA
1993).
2.6.1 Pelagic Seabird and Marine Mammal Monitoring
Many species of marine birds and mammals are far-ranging in seasonal migration
patterns in and out of the Gulf of the Farallones region and/or over large areas within this
region. Consequently, there are inherent difficulties in directly linking any potential
effects from localized dredged material disposal in the relatively small area of the SF-
DODS to changes in regional populations without regard to other important factors.
These other factors can include regional climate variations, natural variations in regional
ocean circulation patterns, stochastic variations of biological populations, and human-
induced effects such as adverse impacts of fishing gear, point and non-point sources of
pollution, and marine debris. The SMMP therefore calls for any effects of dredged
material plumes on marine bird and mammal populations to be evaluated with a regional
December, 2008 32
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time series approach, using available long-term regional databases, such as those
containing Point Reyes Bird Observatory's (PRBO) 10+ years of annual breeding season
census data; other long-term regional databases may be utilized as well.
2.6.1.1 Bird and Mammal Data
Regional population censuses, with concurrent collection of oceanographic data, have
been conducted along transects through the disposal site as well as through adjacent areas
for comparison. Census data collected during these monitoring efforts have been
statistically compared to the disposal site and off-site areas, as well as to the historic
(PRBO) database. Additional observations on a smaller spatial scale have been
conducted regularly l by trained observers riding on disposal tugs traveling to and from
the SF-DODS. The focus of these observations was to assess any detectable real-time
disposal event impacts to marine birds and mammals using monitoring protocols already
established (PRBO) to assess these populations. Observers kept detailed logs of all
observations pertaining to marine birds and mammals prior to, during, and following an
observed disposal event.
Regional surveys and periodic observations of seabirds and marine mammals were
conducted by H.T. Harvey & Associates annually from 1996 through 2001. The annual
reports submitted to the Corps San Francisco District (H.T. Harvey and Assoc, 1997,
1998, 1999, 2000, 2001, 2002) covered monitoring during the periods from November 1
through October 31 of each study year (1995/1996 - 2000/2001). The regional surveys
were conducted during daylight hours concurrent with the three NMFS cruises (for
fisheries and limited oceanographic monitoring) that were timed each year to correspond
with the major oceanographic regimes or "seasons" in this region: the "Winter" or
Davidson Current season (Nov.-Feb.), the "Upwelling" season (March-June); and the
"Oceanic" season (July-Oct). The seabird and marine mammal surveys were conducted
while the NMFS vessel was in transit between ocean sampling stations. Periodic
observations were also conducted from tugs that towed disposal scows from San
Francisco Bay to and from the SF-DODS. These observations were conducted more
frequently in years of higher disposal (32 and 28 observational trips in 1997 and 1998,
and 3-7 trips in 1999-2001), and nearly year-round. Dredged material was discharged
during both daytime and nighttime trips.
Observations from disposal tugs initially were required at a minimum frequency of one trip
per month during any period when dredged material disposal is occurring. In the July, 1999
revised Final Rule and SMMP, EPA increased the frequency so that observers must also be
present at least once every 25 disposal trips. This ensures that an increased frequency of
observation takes place during periods of high disposal activity, as was experienced during
the Port of Richmond deepening project.
December, 2008 33
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2.6.1.2 Bird and Mammal Results
Beginning with the 1997 monitoring report, H.T. Harvey began presenting analyses of
both "large-scale" (waters within a 40 nautical mile [72 km] radius of the SF-DODS) and
"small-scale" (waters within 8 nautical mile [15 km] of the SF-DODS) data from seabird
and marine mammal observations. Evaluations included statistical comparisons among
years of the post-designation period data (1996 onward), as well as between the post-
designation and pre-designation periods (1985-1994) for the same area. As more data
became available over time, evaluations included comparisons among the three
oceanographic seasons and between periods of greater or lesser disposal activity.
Following the last survey in 2001, analyses were also conducted to evaluate whether
distribution and abundance patterns changed with distance from the SF-DODS within the
small-scale (<8 nm radius) area.
The results from all these surveys can be summarized by the following:
• During the observational trips, it was generally found that seabirds did not feed on
the scows. Exceptions were noted in the years when the scows carried material
from maintenance dredging projects (maintenance dredging projects remove a
relatively thin layer of material from the bottom, including the biologically active
surface sediments where infaunal invertebrates are found). In contrast, the other
projects considered to be "new work" construction tend to be dominated by
deeper sediments which are likely to contain a much lower density of infaunal
organisms. No marine mammals were seen associated with scows in transit or
during materials release during any of the cruises.
• Survey results from all years prior to 2001 showed little indication that disposal of
dredged material at the SF-DODS was affecting the distribution or feeding
behavior of seabirds, either regionally or at the "small scale" in the vicinity of the
disposal site. Regional abundance data showed that variations in observations of
seabirds were related to large-scale, warm-water events, unrelated to disposal of
dredged materials at the SF-DODS.
• Analyses following survey year 2001 indicated that seabird abundance increased
with increasing distance from the SF-DODS up to 3 nm (5.5 km) of the disposal
site center. It was also found that seabird abundance was statistically higher
during periods of no disposal activity, with the strongest effect confined to the
immediate vicinity (within 1 nm, or 1.8 km) of the disposal site. Note, however,
that the SF-DODS dimensions are approximately 7.5 km north to south and 4 km
east to west. Therefore the apparent effects on seabird abundance and distribution
identified in the 2001 report are largely confined to the area within the disposal
site boundaries.
• Region-wide, marine mammal abundances were reported to have shown annual
declines from 1996 to 2000, but increased somewhat in 2001. This pattern was
December, 2008 34
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consistent at both the small and large scales, and among all predominant marine
mammal species, and is thought to reflect a long-term decline in oceanic
productivity in the overall California Current system. There was no relationship
between marine mammal density and distance from the SF-DODS, nor between
mammal density and disposal activities, indicating that variation in marine
mammal densities were not related to disposal site activities at the SF-DODS.
2.6.1.3 Bird and Mammal Discussion
Scows carrying dredged material with higher densities of infaunal organisms provided
feeding opportunities for seabirds; however, the frequency of this happening was rare
throughout the monitoring period (1996-2001). When the dredged material did attract
seabirds, the risk of exposure to contaminants through the infaunal organisms was low
because of the chemical and biological testing required for the sediments destined for
open ocean disposal. Even if occasional feeding did occur on the scows carrying disposal
material, it would not have introduced any risk to seabird populations.
Seabird densities were lower at the disposal site during periods of high disposal activity.
The mean density of birds within 8 nm of the SF-DODS only varied by 2 birds per km2
between the periods of active and non-active disposal. It is possible that birds may be
avoiding the site because of noise, or because of decreased water clarity which would
limit feeding opportunities for piscivores and planktivores. Within one nautical mile of
the disposal site center, the species having the highest densities during non-disposal
periods were generalists, including large gulls, Northern Fulmars, and albatrosses,
followed by piscivores and planktivores. Lower abundances of piscivores and
planktivores during periods of disposal activity could be explained by disturbance from
disposal vessel traffic, or lower water clarity which limits visibility when diving or for
seeing food items near the surface when on the wing. The abundance of piscivores was
three times higher at 1-3 nm than they were at 0-1 nm during periods of disposal activity.
This could be explained by a re-distribution of the birds which had been feeding at the
disposal site center but moved to the closest waters that were not affected by disposal
activity.
Linear regression analyses of the log-transformed seabird and marine mammal densities
were used to evaluate the importance of environmental variables, distance from the
disposal site, and disposal site activities. Statistically significant regression coefficients
(p<0.05) were used to infer importance of independent variables. The data used in the
regression analyses were density observations from continuous 15-minute intervals. The
sample sizes were very high (typically ranging from ca. 300 to 3000) which led to
statistically significant results even with very low R2 values. The seabird results for the
2001 survey reported statistically significant models with R2 values ranging from 13% to
27% of the variance explained. While the statistical significance of these results may be
valid, their ecological significance may not be particularly strong because of the small
December, 2008 35
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differences detected as a result of the large sample sizes.
2.6.1.4 Bird and Mammal Conclusions
The extensive monitoring data collected between 1996 and 2001 generally indicated that
the densities of seabirds and marine mammals were not adversely affected by activities at
the SF-DODS. Density observations within the small scale vicinity of the SF-DODS
(within 8 nm) generally followed the same patterns as those observed on the large scale
(within 40 nm). The apparent effects of disposal activities within the "inner" area of the
SF-DODS (from 1 to 3 nm) were viewed as a short-term impact of limited magnitude.
2.6.2 Pelagic Fish Monitoring
Similar to marine birds and mammals, many species of pelagic fish are far-ranging in
seasonal migration patterns and/or occur over large areas within the Gulf of the
Farallones region. Consequently, there are similar difficulties in directly linking any
potential effects of dredged material disposal at the SF-DODS to changes in regional
populations, without regard to other factors such as those listed previously for marine
birds and mammals. Any effects of dredged material disposal on selected pelagic fish
species were evaluated in part based on data from annual Juvenile Rockfish surveys
conducted by the National Marine Fisheries Service (NMFS). The rationale for targeting
larval and juvenile fish is their greater sensitivity relative to adult fish. The trawl surveys
occupy transects within the disposal site as well as in adjacent areas for comparison.
Catch statistics between transects were compared and evaluated in the context of the
historical NMFS database.
2.6.2.1
Pelagic Fish Data
Regional cruises were timed each year to correspond with the major oceanographic
regimes or "seasons" (Winter, Upwelling, and Oceanic) in this region (Table 6). The
National Marine Fisheries Service, Tiburon Laboratory (NMFS) conducted four seasonal
surveys from September 1996 to September 1997 (Roberts et al. 1998); subsequent
surveys from 1998 - 2001 were conducted by San Francisco State University (McGowan
et al. 2001, 2003). During each cruise, trawl samples were made at an array of 21
stations: four stations in the disposal site, ten "buffer area" stations, and seven "peripheral
area" stations (Figure 20). During some cruises, not all stations were sampled, and in
some cases, two additional shoreward stations were sampled when time permitted.
Table 6. Timing of trawl samples with monthly disposal volumes at the SF-DODS.
Survey
Monthly
Disposal
Volume
Survey
Monthly
Disposal
Volume
December, 2008
36
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Date
Sept. 1996
Feb/March
1997
June 1997
Sept. 1997
March
1998
May 1998
Sept. 1998
Feb. 1999
(yds3)
121,056
647,125
359,514
523,863
606,416
355,485
0
0
Season
Oceanic
Winter
Upwelling
Oceanic
Upwelling
Upwelling
Oceanic
Winter
Date
May
1999
Sept.
1999
Feb.
2000
May
2000
Sept.
2000
Feb
2001
May
2001
Sept.
2001
(yds3)
0
0
2,959
94,055
0
0
0
103,326
Season
Upwelling
Oceanic
Winter
Upwelling
Oceanic
Winter
Oceanic
Winter
Biological collections were made from the upper 200 meters of the water column by
bongo nets (for small planktonic organisms, focusing on small larval fish and
invertebrates), Tucker trawl (also for planktonic organisms, but especially for larger
fishes and euphausiids), and, midwater trawl gear (for larger taxa in the June 1997 cruise,
primarily pelagic juvenile rockfish).
A suite of ancillary oceanographic information was collected on each cruise, including
near-surface temperature and salinity (continuous measurement with a hull-mounted
thermosalinometer); current speed and direction (continuous measurement with an
Acoustic Doppler Current Profiler [ADCP]); and temperature, conductivity, ambient
light, and chlorophyll concentration to a depth of 500 meters (measurement at each
sampling station with a Conductivity-Temperature-Depth [CTD] instrument equipped
with a fluorometer). Chlorophyll was also measured directly from water samples taken at
the surface, the chlorophyll maximum depth (which varied by location, as identified by
the fluorometer data), and the 1% light level depth. In addition, water samples were
collected from eight depths (surface to 500 meters) at each station for nutrient chemistry
(nitrate and silicate).
Statistical analysis of catch data was done using analysis of variance (ANOVA) on
individual fish and planktonic species (only those present in at least 75% of the stations)
to test for differences in abundance among the three areas (disposal, buffer, and
peripheral). McGowan et al. (2001) also conducted a Discriminant Function Analysis
(DFA) on the community abundance data for fish and plankton to compare community
patterns among the three areas.
December, 2008
37
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2.6.2.2 Pelagic Fish Results
The oceanographic data collected during the cruises once again suggested that regional
oceanographic conditions exerted a predominant influence on the distribution,
abundance, and condition of zooplankton and juvenile fish in the Gulf of the Farallones
region. This was expected, because the SF-DODS is located in a dynamic hydrographic
region that experiences both distinct "seasons" and longer-term influences such as El
Nino and La Nina conditions.
The vertical profile of light-transmissivity layers in the study area may have indicated
detection of dredged material in the water column. In February of 2000 (140,800 yds3
disposal in January; 3000 yds3 disposal in February) there were two low transmissivity
depth strata observed through the study area, although none were observed in February
2001 (no disposal in January or February 2001). Similar patterns were observed during
the May and September sampling: the year with disposal volumes detected depth strata
with low light transmissivity, while the year with no disposal had none. Low light
transmissivity levels were not associated with reduced chlorophyll concentrations
(indicating a decrease in water column productivity). The duration or effect of this
reduced light transmissivity on fish distribution and abundance could not be detected with
the study design.
Analysis and comparison of the catch statistics revealed few statistically significant
differences between the disposal site and locations outside the site. Often, species
abundances appeared to be higher inside the disposal site than outside it. When disposal
activity at the SF-DODS was high during August 1998, rockfish, total fish, euphausiids,
and cephalopods all were more abundant inside the disposal site in the September 1998
survey (although these differences were not statistically significant).
Overall, there was no coherent pattern in the data to indicate any adverse effect of
disposal at the SF-DODS on abundance of juvenile fish or plankton. Abundances varied
by area, season and gear; with no consistent results suggesting lower abundance within
the disposal area. McGowan (2001) used DFA to compare the community data among
the three areas. The DFA resulted in correct classification of disposal stations by the
community characteristics, indicating that disposal stations tend to be similar amongst
themselves. The results did not indicate, however, how many buffer or peripheral
stations were classified into the same group as the disposal stations, so it is not clear if the
disposal area stations were distinctly different. The result showing the similarity of
disposal area stations may have been an artifact of the study design, which had the four
disposal stations clustered close together while the other stations were spread over a
much wider spatial scale (Figure 20). This community analysis was not repeated in the
2003 report.
December, 2008 38
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The availability of monitoring data from 1999 allowed some time-series evaluation to be
performed for Euphausiids. The winter cruise data on spatial distribution and relative
abundance of this important krill species was compared among the sampling areas
(disposal site, buffer, and peripheral) and among the four years (1996 through 1999).
The species was less abundant at the disposal site stations compared to buffer or
peripheral stations in 1996 and 1997. However, it was more abundant at the disposal site
compared to the buffer and peripheral areas in 1998 and 1999. Also, there seemed to be
no correlation between krill abundance and amount of dredged material disposed at the
SF-DODS in January and February (before the winter sampling cruises). From 1996
through 1998, the amount of January-February disposal increased each year at the SF-
DODS, and krill abundance also increased. But in 1999, when there was no disposal at
all at the SF-DODS in January or February, the pattern was reversed and krill was at its
highest abundance of any of the four years.
Sublethal effects, as indicated by physiological condition of juvenile rockfish, indicated
no adverse impacts attributable to the SF-DODS. The fish appeared to be growing faster
(1997) and were heavier (weight to length ratio, 1998) within the disposal site than
outside it. In 1999, the condition analysis for myctophid fish showed mean dry weight to
be slightly lower in the disposal site than outside it, but the difference was not statistically
significant. For the 2000 - 2001 surveys, on only one cruise (May 2001) did the relative
weight of myctophids differ among station groups, and the weight was heavier at the
Disposal site than the Buffer or Peripheral stations.
2.6.2.3 Pelagic Fish Discussion
Results of the physical/chemical profile indicated that the area was dynamic and highly
variable, both vertically and horizontally, although these conditions were well-described
with the water column profile data obtained. The survey design, which composited
taxonomic results over 200 meters of the water column, was not sensitive to the influence
of changing oceanographic conditions over the vertical profile sampled. McGowan
(2003) concluded that the survey design used was an oversimplification of the problem,
because it did not account for the scale and pattern of oceanographic influences on the
distribution and abundance of organisms. A better design would have been one that
focused on the three general areas (disposal, buffer, and peripheral) and also within
specific depth strata. However, the highly dynamic nature of the waters within the
vicinity of the SF-DODS suggests that any water column effect of dredged material
disposal on pelagic fish abundance would be obscured or overridden by the ocean
currents in this area.
Even with these caveats, the average abundance of pelagic fishes within the top 200m of
the water column did not show a consistent pattern across the disposal, buffer, and
peripheral areas. Some species were higher at the disposal site in one cruise and then
lower in another; similarly, there were no apparent differences in mean abundance among
December, 2008 39
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any of the areas. The statistical power of the ANOVAs used to detect differences among
areas for individual species abundances may have been rather low for some of the
individual species (low statistical power means that statistically significant differences
will not be found unless the differences are very large). However, the patterns in the data
presented (McGowan 2001, 2003) did not suggest a problem with reduced populations at
the disposal site.
2.6.2.4 Pelagic Fish Conclusions
The mean oceanographic conditions as well as the seasonal and inter-annual variability
were well described by the vertical and horizontal water column profiles taken during the
1996 - 2001 surveys. In addition to the oceanographic and biotic information obtained
during these surveys being useful for coastal resources management, the distribution,
abundance, and physiological condition of krill, fish larvae, and juvenile fishes does not
appear to be negatively affected by any of the dredged material disposal activities at the
SF-DODS.
2.6.3 Benthic Community Monitoring
The assumptions behind the benthic monitoring component of the SMMP's biological
module are somewhat different than for the pelagic environment. Adverse impacts to the
benthic infauna within the boundary of the disposal site are expected as a result of
disposal operations (EPA 1993). The major effect within the disposal site is expected to
be physical (mortality due to burial by deposited sediments, habitat modification due to
changes in sediment grain-size and texture, etc.). In addition, natural variation in benthic
population structure is expected over time both within and outside the disposal site.
Therefore, the need for detailed benthic community evaluation is only indicated if
significant accumulation (defined in the original SMMP as more than 5 cm) of dredged
material occurs outside the disposal site. Benthic infauna are still collected from
boxcores each time chemistry samples are taken inside and outside the disposal footprint
during the annual sediment sampling and preserved for archival storage in the event that
future analyses are required. However, unless the yearly physical accumulation of
dredged material outside the disposal site boundary exceeds the 5 cm trigger level,
benthic community samples are not analyzed but archived instead.
2.6.3.1 Benthic Community Data
ENSR (2005) analyzed 120 archived benthic infaunal samples collected between January
1996 - September 2003 and reviewed results. Samples were collected from a pre-
determined grid (Figure 4). Starting in 1999, the emphasis of the benthic infaunal
sampling shifted from an assessment of the immediate impacts of disposal within the site
boundary to an understanding of the impacts of dredged material deposition outside of
December, 2008 40
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the site boundary. A summary of the benthic locations sampled over the years of
monitoring is shown in Table 7. A single box core sample was collected at each
sediment sampling location, and the top 10 cm from 10 sub-cores (collectively equivalent
to a surface area of 0.1 m2) was processed for infaunal analysis. Organisms were sieved
using a 300 jim-mesh sieve, with specimens identified to the lowest possible taxonomic
category (usually species).
The calculation of benthic summary statistics included the number of valid species2 and
total density (individuals per 0.1 m2, includes indeterminate organisms of valid species).
Several diversity indices were also calculated, including Shannon's H' (base 2), Pielou's
evenness value J', Fisher's alpha (Clarke and Gorley 2001), and rarefaction (ESn) curves
(Sanders 1968 as modified by Hurlbert 1971). Multivariate analyses (cluster analysis and
PCA-H) were performed on the community data to evaluate and describe patterns in the
community structure among stations and over time.
2.6.3.2 Benthic Community Results
The benthic data resulting from the SF-DODS SMMP surveys are actually the first long-
term assessment of large-scale, deep sea disposal events. Previous review articles on
deep-sea recolonization (Pequegnat 1983; Thiel 2003) had no case studies except for
shallow-water analogs and are largely speculative about the impacts of dredged material
disposal. Pequegnat (1983) suspected that benthic impacts would be minimal from deep-
sea disposal, and the results found at the SF-DODS confirmed this prediction. However,
the SF-DODS results differed from small-scale deep sea recolonization tray experiments
in the western Atlantic using azoic sediment where recolonization was generally slow
(Grassle 1977; Grassle and Morse-Porteous 1987). Recolonization at the SF-DODS was
relatively rapid (less than 1 year), and the taxonomic composition of the communities
found at the SF-DODS boundary and in the ambient sediments was not affected by small
or moderate amounts of dredged material. In the center of the site, where the sediments
would require recolonization after complete burial of the native fauna, ENSR (2005)
found that the initial colonizers of disturbed sediments in the eastern Pacific were species
from the ambient fauna found at control locations and not any unusual opportunistic
species. Prionospio delta was the common and dominant spionid polychaete in the lower
slope assemblages documented at the SF-DODS and appeared as one of the early
colonizers along with foraminifera of the genus Bathysiphon (ENSR 2005).
2 valid species excludes juveniles and indeterminate specimens that could not be
identified to species level, epifauna, shell-borers, and parasites (ENSR 2005, p. 12)
December, 2008 41
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Table 7. Benthic box core samples collected as part of the SF-DODS monitoring surveys
(Table 3-1 from ENSR 2005).
Station
1
2
3
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
22
23
24
26
27
31
33
50
52
53
57
64
92
108
114
116
Total
Jan 1996
1
1
1
1
1
1
1
1
1
1
1
11
Dec 1996
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
17
Oct/Nov
1997
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
16
Oct 1998
1
1
1
1
1
1
1
1
1
1
1
1
12
Oct 1999
1
1
1
1
1
1
1
1
1
1
1
1
1
13
Oct 2000
1
1
1
1
1
1
1
1
1
1
1
1
12
Oct 2001
1
1
1
1
1
1
1
1
1
9
Sep 2002
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
15
Sep 2003
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
15
Total
" 2
" 3
" 3
r 5
" 5
r 4
" 3
" 7
" 4
" 5
" 4
r 4
" 2
r 6
' 9
r 4
" 7
r 5
1
r 7
" 3
r 1
' 5
r 1
" 1
r 1
" 1
" 2
" 5
r 2
" 2
r 1
' 2
" 3
120
The results from the seven years of benthic sampling at the SF-DODS following the start
of disposal operations at the site showed that the benthic fauna at the SF-DODS and
vicinity were highly resilient, and if dredged material were to stop for any prolonged
interval of time, the benthic community should return to a pre-disposal assemblage with a
relatively short period of time (2-3 years). The benthic results showed that disposal has
not caused regional degradation outside the site or even on the boundaries of the site
(ENSR 2005), and that the resident infauna are capable of reworking small amounts of
dredged material and coping with larger deposits of material such as those found at the
site center (Figure 12).
December, 2008
42
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2.6.3.3 Benthic Community Discussion
While there have been numerous studies documenting the rate and pattern of benthic
recolonization following seafloor disturbance (Rhoads et al. 1978; Santos and Simon
1980; Hall 1994) or dredged material disposal (Mauer et al. 1981a, 1981b, 1982, 1986;
Scott et al. 1987; Harvey et al. 1998) in shallower coastal waters, there are few
comparable studies of infaunal recolonization of deep-sea sediments in the eastern Pacific
(ENSR 2005). The majority of the few deep sea recolonization studies that have been
done have been carried out with trays of azoic sediment recovered over a series of time
intervals after placement; while these tray recolonization experiments are the only
practical way of studying recolonization on a small scale, they do introduce artifacts
(hydrodynamic flow disturbance, separation of experimental sediments from natural
substrata preventing recolonization by lateral or vertical burrowing) that render the
results somewhat unrealistic for predicting recolonization response to dredged material
disposal at depths such as those found at the SF-DODS. It was precisely this lack of
information about benthic community response to a large scale disturbance in the deep
sea that caused such a heightened concern during the site designation process and led to
the comprehensive benthic monitoring program in the SMMP.
The results presented in ENSR (2005) provide an interpretation of the community
structure present in the surface sediment samples. These data indicate that stations within
the SF-DODS boundary that are affected by large volumes of dredged material appear to
recolonize rapidly and by the same taxa that are normally found in the adjacent ambient
sediments. The handful of recolonization studies that have been done in the western
Atlantic generally have found that the colonizing species were not ones typically found in
the ambient fauna. In contrast, the few recolonization studies done in the eastern Pacific
deep sea (Levin and Smith 1984; Kukert and Smith 1992; Levin and DiBacco 1995) have
found that the initial colonizers in disturbed or azoic sediments appear to be species that
are relatively common in the surrounding sediment. The results from the SF-DODS
support these other eastern Pacific studies and seem to indicate that deep sea
recolonization patterns in the Pacific are quite different than those documented in the
western Atlantic. One suggested reason for this apparent resiliency of the native fauna in
the vicinity of the SF-DODS is because of the natural periodic slumping and turbidity
flows that occur in this region of the slope (ENSR 2005); the resident infaunal taxa in this
region may be pre-adapted to rapidly colonize areas of disturbed sediment.
This dataset is also valuable for allowing the evaluation of the background variability of
community parameters at the site, in the hopes of understanding what level of sampling
would be required to make solid inference regarding impacts from dredged material
disposal. This was accomplished with a power analysis to determine the number of
benthic samples per station that would be required to sufficiently characterize any
changes in community parameters among stations.
December, 2008 43
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2.6.3.4 Power Analysis of Benthic Results
The Tier 2 biological monitoring specified in the SMMP includes, ".. .a comparison of
the benthic community within the dredged material footprint to benthic communities in
adjacent areas outside of the dredged material footprint. An appropriate time-series
(ordinal) and community analysis shall be performed using data collected during the
current year and previous years to determine whether there are adverse changes in the
benthic populations outside of the disposal site which may endanger the marine
environment. " Similarly, Tier 3 biological monitoring includes, ".. .advancedstudies of
benthic communities to evaluate how these populations might be affected by disposal site
use. Such studies may include additional sampling stations, greater frequency of
sampling, more advanced sampling methodologies or equipment, or other additional
increased study measures compared to similar studies conducted in Tiers 1 or 2..."
Implicit in the monitoring required in Tier 2 and Tier 3 is the ability to detect a change in
benthic community structure between stations on dredged material and stations on
ambient sediment. In order to accomplish this, the sampling design for monitoring the
benthic infauna at the SF-DODS needs to be adequate for the intended data analyses. A
power analysis for a pair wise comparison approach will be used to illustrate the level of
sampling required to detect a reasonable change in benthic community metrics given the
level of variability documented at the site from the nine years of benthic data summarized
in the ENSR (2005) report. "Statistical power" is the probability of detecting a difference
when a difference really exists. The power of a test can be calculated as a function of the
sample size, the variance, the type I error level (a) and the "effect size" (Lipsey 1990).
The effect size is the minimum difference between sample means that is expected to be
statistically significant. If we fix a (at 5%) and the power (at 80%), and estimate
variance, we can calculate the relationship between the sample size and the effect size.
For a given number of samples per station, a very large effect size indicates that
variability is so high that only very large changes would be detected.
We first needed an estimate of the within-station variability. The historic sampling
design did not include multiple samples from single stations; therefore, the best estimate
of intrinsic variability was based on a group of stations that were most similar to one
another and did not have dredged material for two or more years. These stations may be
considered as close to "ambient" conditions as possible for this deep water site. ENSR
(2005) found that stations at or below the 2800m isobath were the most similar. We
identified the stations within this depth range which had no or trace amounts of dredged
material for two consecutive years in the SPI surveys. This automatically excluded the
January 1996 samples, because we didn't know exactly where the previous year's
dredged material was located. There were only four benthic stations that fit these criteria;
these were:
• Station 23 in December 1996;
December, 2008 44
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• Station 64 in September 2003;
• Station 92 in September 2002 and September 2003.
The standard deviation of these four stations was used as the background variance and to
calculate the effect size of a two-sample, two-sided t-test comparing the means between
two stations or between two time periods at a single station. The type I error rate (a) was
set at 5%, and power was set at 80%. The relationship between sample size (number of
replicates per station) and effect size (represented as a percent of the "ambient" mean
value) was calculated for the following summary metrics:
• total individuals (all species, per 0.1m2),
• number of valid species,
• Pielou'sJ,
• Fisher's log-series a,
• Shannon's H' (log 2).
Pielou's and Shannon's diversity indices had the lowest variability, and a typical design
of five replicates per station would allow the detection of a difference between means
equivalent to 10% or less of the ambient mean (Figure 21). The other metrics were more
variable, and an effect size of 20% of the ambient mean required eight replicates per
station (for Valid Species Count), and fifteen or sixteen replicate samples for Fisher's
alpha and Total Individuals, respectively. Five replicates at each station should achieve
an effect size equivalent to 50% of the ambient means for the most variable endpoints.
2.6.3.5 Benthic Community Conclusions
The benthic monitoring performed between 1995 - 2007 at the SF-DODS has eliminated
the concerns raised during the site designation process about the uncertainties with
benthic community response to deep sea dredged material disposal: the dredged material
is readily and rapidly recolonized by fauna from the species pool in the ambient
sediment, and there has been no indication of any degradation of benthic community
structure outside the site or in the surrounding area. We now know (similar to the results
that have been documented in dredged material disposal sites in shallower water) that
placing sediment that has passed the required testing for open-ocean disposal
(EPA/USACE 1991) causes a temporary but reversible perturbation in benthic
community structure; the new sediments are rapidly colonized by native taxa from the
surrounding area and the benthic community will recover to a pre-disposal assemblage
through successional processes in a few years.
2.7 Confirmation Studies
The existing SMMP for the SF-DODS requires periodic confirmatory monitoring at least
once every three years (EPA 1994). Samples collected from the dredged material
December, 2008 45
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footprint are collected and analyzed for bioassay and bioaccumulation testing following
Green Book methods (EPA/USACE 1991). In addition, current meters, sediment traps
and near-surface arrays of filter-feeding organisms (mussels) are required to be deployed
for at least a month during active site use (see Section 2.2). The purpose of this
monitoring was to confirm that: a), material disposed at the SF-DODS was in fact
adequately represented by pre-disposal sampling and testing, and b). that no substantial
bioaccumulation of sediment-associated contaminants may be occurring, especially
within the boundaries of the Gulf of the Farallones National Marine Sanctuary, as a result
of exposure to any suspended sediment plumes from multiple disposal events over time.
2.7.1 Bioassay and Bioaccumulation Results
In 1998, sediment was collected for bioassays from inside and outside the dredged
material footprint (EPA 2002). Samples were collected from the top 10 cm of the
boxcore (Figure 5); stations detected with dredged material present comprised the "Inside
Footprint" composite, while stations without any apparent dredged material comprised
the "Outside Footprint" composite. The samples were submitted for 10-day solid phase
acute toxicity tests, and 28-day bioaccumulation tests.
The solid phase 10-day acute toxicity tests were conducted using the amphipod
Ampelisca abdita and the polychaete Nephthys caecoides. The results showed that there
was no significant acute toxicity to either the amphipods or polychaetes associated with
the "Inside Footprint" samples. Toxicity was defined in the same way as in dredged
material testing protocols: a sample was considered toxic if survival was statistically
different from, and more than 10% (for the polychaete) or 20% (for the amphipod) less
the negative control. The SF-DODS reference area was not sampled, so all comparisons
were made to the more environmentally conservative negative control.
Bioaccumulation was evaluated from 28-day exposures with the clam Macoma nasuta
and the same polychaete as in bioassay testing (N. caecoides). Tissue concentrations of a
series of contaminants were measured, and comparisons were made between the sample
and control tissues (unexposed organisms of each species), as well as between the
"Inside" and "Outside" footprint samples. Results showed that most chemicals were not
elevated in the dredged material samples relative to control or the off-site samples. In the
M. nasuta samples, concentrations of chromium (Cr), PAHs, and DDT were statistically
higher in tissues exposed to on-site samples relative to samples collected outside of the
footprint. Similarly, lead and DDT were elevated in N. caecoides samples. Of these
compounds, however, only Cr in Macoma tissue was outside the range found in the SF-
DODS reference area database (USEPA 1999). For the few other values measured in
tissue that were higher than in reference (HPAH in N. caecoides, and dieldrin in both
species), there was no significant difference between the inside and outside footprint
samples.
December, 2008 46
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Although Cr was not elevated in the sediment or in tissues of the polychaete N.
caecoides, it was elevated in tissues of the clamM nasuta exposed to "Inside" sediments
relative to both "Outside" and control tissues. The measured value (1.2 mg/kg wet
weight) was higher than the range measured inM nasuta tissues exposed to SF-DODS
reference area sediment (0.2-0.5 mg/kg wet weight), and outside the range found in pre-
disposal testing (0.22-0.5 mg/kg). The measured chromium value was compared against
what little guidance there is for bioaccumulation in tissue, including the USAGE
Environmental Residue Effects Database (ERED) and was found to be within the range
of "lowest observed effects." The ERED, however, contains no Cr data specifically for
Macoma or for other organisms that might be a more direct surrogate indicator for
potential effects to benthic marine organisms. Confirmatory monitoring results, however,
showed that the detection of a small number of very low concentrations of contaminants
was restricted to the dredged material footprint itself.
2.7.2 Bioassay and Bioaccumulation Conclusions
There was no significant acute toxicity to either the amphipods or polychaetes associated
with the "Inside Footprint" samples. There were a small number of very low, but
elevated, concentrations of contaminants (relative to the negative control) present in the
dredged material footprint.
2.7.3 Caged Mussel Bioaccumulation Results
Data from deployment of mussel arrays were intended to test whether substantial
bioaccumulation of contaminants may be associated with exposure to suspended
sediment plumes from multiple disposal events. Although the minimum time for
deployment of the mussel arrays was one month, the mussels were deployed in
November 1997 and retrieved a year later in November 1998, during one of the most
intensive disposal periods (Table 1; both the Oakland and Richmond deepening projects
were using the site simultaneously). Six bags of 50 mussels each were deployed on each
of three moorings outside the disposal site at two depths (150m and 200m). After the
year of exposure, mussels were collected and tissues analyzed for 11 metals, PCB
congeners, pesticides, and PAHs.
Few compounds have established standards to which the tissue concentrations found in
the deployed mussels could be compared. The US Food and Drug Administration (FDA)
has published health based "Action Levels" in shellfish tissue for only seven compounds:
methyl mercury, total PCB, and the pesticides Aldrin, Dieldrin, Endrin, Heptachlor, and
Heptachlor epoxide. Four of these compounds were detected in mussel tissue from the
SF-DODS Confirmatory Monitoring program (CDFG 2000). However, in each case,
December, 2008 47
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detected mussel tissue concentrations from the SF-DODS Confirmatory Monitoring
program was one or more orders of magnitude lower than FDA Action Levels.
The SWRCB has developed "Maximum Tissue Residue Levels" (MTRLs) guidelines for
comparison to data obtained from their Mussel Watch program; the MTRLs are derived
by multiplying the human health based Water Quality Objective from the California
Ocean Plan (SWRCB 1997) by a theoretical bioconcentration factor for each compound
(for Aldrin, the MTRL was derived somewhat differently). As such, the MTRLs are
considered by the SWRCB to represent concentrations at and below which human health
would be protected from consumption offish and shellfish.
Four of these compounds were detected in mussel tissues from the SF-DODS
Confirmatory Monitoring program: Chlordane, DDT, Dieldrin, and total PCBs. Tissue
concentrations of DDT from around the SF-DODS were lower than the calculated
MTRLs. In contrast, tissue concentrations of Chlordane, Dieldrin, and total PCB were up
to an order of magnitude higher than their MTRLs. However, for all three of these
compounds, the actual concentrations in the mussels were only slightly above detection
limits. More importantly, at all stations including the reference station mooring (Rl), the
bioaccumulated concentrations of these compounds were very similar to one another.
These data may reflect either the organism background tissue concentration or a
background level of exposure across the region. The main conclusion is that the caged
mussel results indicate that proximity to the disposal site does not result in substantially
greater exposure to contaminants than could be expected throughout the open ocean
environment offshore of San Francisco Bay.
Another interesting finding was that the tissue levels measured in the mussels were
generally similar to those in the clam Macoma exposed in the 28-day bioaccumulation
test in reference site sediments. The primary exception was Cd, which was reported at 1-
2 orders of magnitude higher in the mussels. Cadmium values, however, were essentially
the same at all water column monitoring stations, including the reference site, and
therefore most likely reflected background tissue levels.
2.7.4 Confirmation Studies Conclusion
Confirmatory monitoring was incorporated in the original SMMP as a safeguard against
inadequate sampling or analysis of sediments permitted for disposal at the SF-DODS.
The review of data from the last decade of monitoring has demonstrated that there have
been very few elevated concentrations of contaminants measured in collected sediment
from the SF-DODS, and the few questionable values have been primarily in samples
from inside the site boundary. Suspended sediment plumes have not resulted in
substantial or increased uptake of contaminants by water column organisms outside the
SF-DODS boundary or within the Gulf of Farallones National Marine Sanctuary. This
December, 2008 48
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conclusion is based on results from monitoring during the 1997-1998 disposal season
when extensive disposal occurred. Therefore the need for confirmatory monitoring is not
warranted for routine SF-DODS monitoring. As stated above, a special study for
confirmatory monitoring using appropriate and valid sampling designs and statistical
methods could be conducted at any of the region's open-water disposal sites.
December, 2008 49
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3.0 SUMMARY OF CONCLUSIONS
Monitoring results from the SF-DODS (Section 2.0) produced the following conclusions:
• The thickest layers of dredged material have been confined within the designated
site boundary.
• During each year of disposal, a thin apron of material has spread out to varying
distances beyond the site boundary as predicted by the modeling. This apron has
rarely exceeded 5 cm per year.
• Neither the thin yearly deposits, nor the thicker cumulative deposit outside the site
boundaries have had any significant adverse impacts on the benthos.
• Based on SPI monitoring results, recolonization of the dredged material is very
rapid both within and outside the site (much more rapid than expected at the time
of the Site Designation EIS and development of the SMMP). The EIS predicted
that offsite deposition would have no significant adverse physical impacts, and
this has been demonstrated; furthermore, the rapid recovery of onsite stations has
shown that deposits > 10 cm in a year have no long term adverse effects.
• The 5 cm thickness of deposits outside the site boundary defined in the EIS as a
trigger for Tier 2 investigations or management actions has proven to be
unnecessarily conservative, because no observable adverse impacts have occurred
in areas outside the site having layers this thick; and recovery of even thicker
deposits both inside and outside the site has been very rapid.
• No plumes of dredged material from the disposal site are reaching or adversely
affecting the Gulf of Farallones Marine Sanctuary. Material found in sediment
traps was determined to come from leaking disposal barges, not SF-DODS, and
this source has been substantially reduced by separate EPA monitoring
requirements and compliance actions.
• While the modeling results were accurate enough to predict the general pattern of
sediment dispersion (verified by sediment trap and caged mussel studies) and
dredged material footprint (verified by SPI results), the regional currents are
variable enough so that more accurate model predictions of the dredged material
footprint would only be obtained with real-time information on water currents.
This eliminates the utility of using additional modeled output in the future to
predict subsequent changes to the dredged material footprint (it is more cost-
effective to just map the footprint than collect the water current data needed for
predictive modeling which would still need verification)
• There is no difference in benthic recovery rates with variation in dredged material
volume (Figure 21), indicating that the current annual disposal volume limit (4.8
December, 2008 51
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mcy) is within the range of normal adaptive response to disturbance by the
existing benthic community.
• Measured chemical concentrations in the sediment have generally not exceeded
those background values found either at the site prior to disposal or at the SF-
DODS reference area; the few chemical compounds whose concentrations have
exceeded background values have still been well below any value to cause any
potential concern for biological effects.
• There have been no adverse impacts to marine birds from disposal activities; the
only effect observed was small and limited to the immediate vicinity of the
disposal zone in the heaviest years.
• There have been no adverse impacts to marine mammals from disposal activities,
most observed changes were attributed to regional water mass changes.
• There have been no adverse impacts to pelagic fish from disposal activities, most
observed changes were attributed to regional water mass changes.
• Detailed analysis of 120 benthic samples revealed that stations within the SF-
DODS boundary that are affected by large volumes of dredged material have
recolonized rapidly and by the same taxa that are normally found in the adjacent
ambient sediments; stations outside the disposal site with thin layers of material
are similar to stations with no dredged material.
• Confirmation studies have shown no adverse biological effects from sediments
collected from both inside and outside the site and subjected to both bioassay and
bioaccumulation testing results.
• Caged mussel confirmation studies conducted at three different locations during
high volume disposal events revealed that tissue concentrations of detected
chemical compounds were similar to each other regardless of mooring location,
and that proximity to the disposal site does not result in substantially greater
exposure to contaminants than could be expected throughout the open ocean
environment offshore of San Francisco Bay.
• The monitoring program produced a unique and extremely valuable dataset. The
scientific and policy making communities have substantial data on deep benthic
environments including recovery rates, adequacy of modeling, feasibility of site
and confirmatory monitoring, and many new species have been described from
the sampling effort.
December, 2008 52
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Sanders, H.L. 1968. Marine benthic diversity: A comparative study. American Naturalist
102: 243-282.
San Francisco Estuary Institute (SFEI) 2007. The 2006 RMP Annual Monitoring
Results. San Francisco Estuary and the Regional Monitoring Program for Water
Quality in the San Francisco Estuary. SFEI Contribution 542. San Francsico
Estuary Institute, Oakland, CA.
Santos, S. L. and J. L. Simon. 1980. Response of soft-bottom benthos to annual
catastrophic disturbance in a south Florida estuary. Mar. Ecol. Prog. Ser. 3:
347-355.
Scott, J., D. Rhoads, J. Rosen, S. Pratt, and J. Gentile. 1987. Impact of Open-Water
Disposal of Black Rock Harbor Dredged Material on Benthic Recolonization at
the FVP Site. Technical Report D-87-4, NTIS No. AD-A184 166. Prepared for
U.S. Army Engineer Waterways, Experiment Station by Science Applications
International Corporation, Computer Sciences Corporation, University of Rhode
Island, and U.S. Environmental Protection Agency.
SWRCB (State Water Resources Control Board). 1997. California Ocean Plan -Water
Quality Control Plan, Ocean Waters of California. July 23, 1997. State Water
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Sacramento, California.
SWRCB. 2000. State Mussel Watch Program, 1995-1997 Data Report. Prepared by Del
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SWRCB. 2007. Draft Staff Report. Water Quality Control Plan for Enclosed Bays and
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TetraTech, 1992. Preliminary modeling for the purpose of estimating dredged material
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U.S. Environmental Protection Agency, San Francisco. Draft Final Report, 122
pp.
December, 2008 60
-------
TetraTech. 1999. San Francisco Deep Ocean Dredged Material Disposal Site (SF-
DODS) Monitoring Program. Physical, Chemical, and Benthic Community
Monitoring, October 1998. Submitted to USAGE, San Francisco District, San
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TetraTech. 2000. San Francisco Deep Ocean Dredged Material Disposal Site (SF-
DODS) Monitoring Program. Physical, Chemical, and Benthic Community
Monitoring, October 1999. Draft Report. Submitted to USAGE, San Francisco
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TetraTech. 2001. San Francisco Deep Ocean Disposal Site (SF-DODS) Monitoring
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TetraTech. 2002. San Francisco Deep Ocean Disposal Site (SF-DODS) Monitoring
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(ed.), Ecosystems of the Deep Oceans. Ecosystems of the World 28. Elsevier.
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(Eds). Use of Sediment Quality Guidelines and Related Tools for the Assessment
of Contaminated Sediment. Proceedings from the Pellston Workshop, 18-22
August 2002, Fairmont, Montana. Setae Press.
December, 2008 61
-------
FIGURES
61
-------
123°45'W
I
123°30'W
123°15'
123°
122°45'
122°30'
122° 15'
I
38°N
37°45'N
37°30'N
Pacific
Ocean
SF-DODS
perimeter
Prepared/mm SAIC and ENSR/AECOM reports
Cordell
\ Bank
•—~^> Point
Reyes
Farallon
Islands
Reference
Area
San
~7 Francisco
) Bay
San \ ^~x
Francisco \
~—i kilometers 0
Viautical miles 0
37°20'N
Figure 1: Location of the San Francisco Deep Ocean Disposal Site (SF-DODS).
-------
0)
Is
D)
I
800,000 -
700,000 -
600,000 -
500,000
400,000 -
300,000 -
200,000 -
100,000 --
• Volume (cy)
ASPI Samples (n)
30
A 38
A 28
28
A
i+hH
A 41
A 42
A 43
A44
A 36
A 39
A 32
31
A
A 26
urn-
1990
1992
1993 1994 1995 1996 1997 1998 1999 2000 2001
2002 2003 2004 2005 2006
2007
Figure 2: Monthly disposal volumes in cubic yards (bars) compared with date of monitoring surveys and number of SPI stations
sampled (triangles). Total volumes are provided in Table 1. The totals are all bin volumes (estimated from the barge volume), in units
of cubic yards. Bin volumes are likely greater than in situ volumes due to bulking and water entrainment caused by the dredging
process. The estimates were obtained as follows. The Navy project estimated volume was obtained from that project. The volumes
from 1995-1999 were obtained by summing the reported bin volumes from monthly project monitoring reports and as reported by the
EPA (EPA 2002). Volume estimates from 2000-2003 were based on the silent inspector system used during those years (ADISS, or
Automated Disposal Surveillance System), except for dredging in Oakland 2002, which was derived from the dredging contractor's
records. Volume estimates from 2004-2007 were based on the silent inspector system used during those years (eTrac). Individual
project sums are available in Appendix Table 3.
-------
Deployed
On the
seafloor
SPI image'
"Down" position
transecting the sediment-
water interface
Figure 3: Deployment and operation of the sediment profile imaging (SPI) system; acoustic
pinger signal doubles for 10 seconds after strobe is fired to signal successful image acquisition
in deep-water operations.
-------
123°35'W 123°34'W 123°33'W 123°32'W 123°31'W 123°30'W 123°29'W 123°28'W 123°27'W 123°26'W 123°25'W 123°24'W
37°45'N -
• 156
37°43'N -
37°41'N -
37°39'N
37°35'N
• 72 » 57
• 86 • 68 • 61 *49
«l2 • 13 • 14 *15
85 • 67 • 62 »48 • 20
• 84 • 66 • 63 »47 «21
• • 42 «^M — "»/0 «111
• 83 • 65 • 64 «46 • 4
120 »119 «118
»116 •11S 0114 • 113
• SF-DODS Station
Depth contour (m)
SF DODS perimeter
• 82 • 121
kilometers 0
nautical miles 0 1
Prepared from SA1C and ENSR/AECOM reports
Figure 4: Potential sampling locations for the SF-DODS monitoring surveys.
-------
The 0.25 m2 Sandia MK-III box corer
Detail of the partitioned box core showing the
25 subcores (10 x 10 cm).
Some of the subcores have been removed for chemistry
and biology samples.
Sediment being extruded for processing from
one of the subcores.
Figure 5: Equipment used to collect sediment samples during past monitoring surveys at the SF-DODS.
-------
123°35'W 123°34'W 123°33'W 123°32'W 123°31'W 123°30'W 123°29'W 123°28'W 123°27'W 123°26'W 123°25'W 123°24'W
37°45'N -
37°43'N -
37°4TN -
37°39'N
37°35'N
kilometers 0
A
N
2 4
• SF-DODS Station
"V/ Depth contour (m)
SF DODS perimeter
^^— Historical limits of dredged
material apron
••••' Historical limits of dredged
material apron uncertainty
nautical miles 0 1 2
Prepared from SAIC and ENSR/AECOM reports
O Sediment sampling
location (1996-present)
Sediment sampling
location (recent)
Dredged material >5 cm
Figure 6: Core locations most commonly sampled for sediment chemistry during the entire
period of monitoring at the SF-DODS from 1996-present (circles), and more recently (squares).
-------
123°45'W
I
123°30'W
123°15'
123°
122°45'
122°30'
122° 15'
I
38°N
37°45'N
37°30'N
Pacific
Ocean
37°20'N
San P
Francisco )
) Bay 4
San \ ^~x
Francisco \
Prepared/mm SAIC and ENSR/AECOM reports
Figure 7. Location of the current meter and sediment trap moorings deployed by USGS from November 1997 to November 1998.
Borders in green indicate boundaries of the Cordell Bank (north), Gulf of the Farallones (center) and Monterey Bay (south)
National Marine Sanctuaries.
-------
123°35'W 123°34'W 123°33'W 123°32'W 123°31'W 123°30'W 123°29'W 123°28'W 123°27'W 123°26'W 123°25'W 123°24'W
37°45'N -
37°43'N -
37°41'N -
37°40'N -
37°39'N -
37°35'N -
• 96 ) • 97 *98 «99 •100\ •101
92 93/* 94
• 78 «79 »80
1 I
71 • 58 (• 2I8
• 32 »33\ «34 /•105
• 87 • 69 • 60
^^__- — 370o~~
• 86 • 68 • 61
• 121 • 120 »119 «118 »117 • 116 *1
• 82
kilometers 0
•••
•••
nautical miles 0
A
2
^^•ZZZI
^^•ZZZZ
1
• SF-DODS Monitoring Station
~\^ Depth contour (m)
C~3 SF DODS perimeter
4
^^^^ ^-^ Historical limits of thin
dredged material "apron"
2
••••• Historical limits of dredged
material apron uncertainty
^^~ Cumulative dredged
material >5 cm
7 Numbers indicate depth of
' dredged material (cm) from
2007 survey
Prepared from S4/C and ENSR/AECOM reports
Figure 8: Summary compilation of dredged material thickness maps from all surveys
between 1996-2007. Cumulative line represents all areas where dredged material has been
detected > 5 cm thick. Large numbers at stations indicate depth of dredged material (cm)
from 2007 survey.
-------
1996 Model Results
Using USGS Currents
October-November 1997
Survey of SFDODS
123°33'W
37°42'N
123°29'W
123°25'W 123°33'W
123°29'W
37°39'N -
37°36'N
123°25'W
37°42'N
- 37°39'N
From Hamilton, 2001
Bathymetry immeters
37°36'N
<1 cm
1-5 cm
5-1 Ocm
>10cm
• SVPS Photography Station
® Box Core and SVPS Photography Station
SF DOGS perimeter
Figure 9: Left Panel: Deposition (cm) from model year 1996 using USGS current data. Contours are 1, 2, 5, 10, 20, 30,
and 34 cm. Right Panel: Distribution of recently placed dredged material from the October-November 1997 sediment
survey of the SFDODS. Station thicknesses are in cm. Survey data is from SAIC (1999b).
-------
Figure 10: Sediment profile image from the SFDODS taken within the boundary
during the 1997 survey (Station 9) within the boundary shows evidence of a
distinct layer of dredged material and an epibenthic animal grazing on the
surface (elasapoid holothurian, Scotoplanes globosa). Scale: width of profile
image =14.5 cm.
-------
Figure 11: Sediment profile image from north of the SFDODS taken during the
1996 survey (Station 31) shows ambient sediment without dredged material.
Scale: width of profile image - 14.5 cm.
-------
Figure 12: This sediment profile image from the center of the SF-DODS taken
during the 2006 survey (Station 13) shows evidence (burrows, voids, and
portions of worms against the faceplate) of Stage 3 taxa at depth (arrows)
even though dredged material thickness exceeds the height of the camera's
prism. Scale: width of profile image = 14.5 cm.
-------
1.0 -
0.8 -
0-6 ~\
.a
2
a.
0)
^ 0.4 -
D
O
0.2 -
0.0 -
CCDF - small volume (<100K);
dredged material present
(n=79)
CCDF - dredged material present
(n=219)
CCDF - large volume (>250K);
dredged material absent
(n=60)
CCDF - small volume (<100K);
dredged material absent
(n=72)
median
CCDF - large volume (>250K);
dredged material present
(n=140)
CCDF-small
volume (<100K);
(n=151)
CCDF - large volume (>250K);
(n=200)
CCDF - dredged material absent
(n=132)
CDF(n=351)
\
2
\
4
Average RPD (cm)
Figure 13: Empirical Cumulative Distribution Function (CDF) and Conditional Cumulative Distribution
Functions (CCDF) curves for the RPD endpoint. Curves that are further to the right have a higher median RPD
value for the distribution (i.e. generally better conditions), and steeper curves indicate distributions with less variability.
-------
o
6 -
o
o
E 4
•2,
a
DL
Of
U)
>
@ o
0
O _O
o°o @
_/-\ _, CJ __
ox
°
o
o
0°°
°°
o
GD
0
°
o
0
0
o -
O
I
0
\
10
15
Average (cm; from SPI)
Figure 14: Relationship between Average Dredged Material depth and Average
RPD, as measured in SPI surveys at the SF-DODS.
-------
200 -
Total Abundance
g 1 000 -
E
TO
T3
E
D
J3
< 600 -
S
O
I—
o
o
cP
8 8 eft
g cE
H a a i
o Ox
o
fit
B
° 1
0 §
1
r
1000
o
o
2000 3000
Volume disposed (1000 yd3)
Valid
1
"o
w
1
1 <-HJ
120
100
80
60
40
20
o
•I 8
o
o
1 °
o
.4
o
-]
H
Lr
0
§
0
-------
Total Abundance
Valid
IN
T™
o
CD 1 000 -
0)
o
co
"g 600-
13
0 200-
O
o
o o
to
tu
o : o
o 6% ° n ! S.
& 00 0°°° * ° o I £
d* o'fe^bio' ° i >
O Q O ° °
°a° ° ° o
0 0 j
r T i s r T i I
0 2 4 6 8 10 12 14
DM depth (cm) from SPI
Pielou's J
0.9 •
0.8 -
to 0.7 -
3
O
o ° ro
** ao o ° Oj IB
§ O O o O r?
O "™
jfl
fe
iH
o 01
o
8
140- _ .,
O (y
120- ° o°0°d& °° °
Ho o P o o
100- fc) fi «n S3 °
^-^ %8%°t°? Q OQ
6°-X° o%°% o
00j O
40- 0
o
20 -\ 0
i ! r T i ! r T
0 2 4 6 8 10 12 1
DM depth (cm) from SPI
Fisher's log
o
50 ~ j^p Q\
o o
a*-, ,r\rj ® cu^^^
eg55 o oooo o
S O^-C^^ *-^"^ r\
30 - o o o OQ© o
flo3 eapP °o° °
o
20-g°°0ooo o o
o
10 -
o
2 4 6 8 10
DM depth (cm) from SPI
12 14
2 4 6 8 10
DM depth (cm) from SPI
12
14
Figure 16: Benthic community metrics from the SF-DODS (after Table 4-2, ENSR 2005) plotted against actual dredged material depth (cm)
measured in sediment profile images.
-------
I
/
o
^<
-------
Reference
Baseline
Ambient 96-07 Footprint 96-07
Source
Figure 18: Range (minimum to maximum) of total organic carbon (TOC) in samples collected from the SF-DODS,
the reference area, and from dredged material source areas (columns). Baseline samples collected in 1990-91.
Ambient stations are those with no measurable dredged material. Outlier point shown separately for Footprint
category. Source data summarized as reported over 1994-2006 (Appendix Table B2). The number of samples is
shown in the center of the column; U=unknown number of source samples.
-------
Figure 19: Range (minimum to maximum) concentration of silver in samples collected from the SF-DODS and the
reference area (columns). Baseline samples collected in 1990-91. Green line showing maximum silver value
reported from dredged material source areas through 2000 (0.6 ppm), for 2001-2003 (0.84 ppm), and from 2004
to present (1.4 ppm). The number of samples is shown in the center of the columns.
-------
123°45'W
123°30'W
123°151
123°
I
122°45'
122°30'
122-15'
38°N
Cordell
Bank
Pacific
Ocean
37°45'N
-
B2 B3
SF-DODS
perimeter \ D3 D4
B4 B5
D1 D2
B6 B7 B8
S1
S2
37°30'N
-
5 Point
Reyes
^ Farallon
V Islands
P6
37°20'N
Reference
Area
Prepared from SA1C and ENSR/AECOM reports
kilometers 0
Viautical miles 0
San -C
Francisco i
Bay 4
San \
Francisco
20 \
10
Figure 20: Location of the 21 stations used for pelagic fish monitoring surveys in the vicinity of the SF-DODS. D stations are disposal site
stations; B stations are "buffer area" stations; and P stations are "peripheral area" stations.
-------
re
0)
re
Q
Q
0%
10
15
20
•Total Individuals
•Valid Species Count
Pielou's J
• Fisher's Log-series a
•Shannon's H'
25
30
35
Number of Replicates per Site
Figure 21: Power Analysis Results from the SF-DODS benthic community data:
relationship between the number of replicates
per site vs. the Minimum Detectable Difference (MOD) as a percentage of the mean,
given a type I error rate (alpha) = 0.05 and 80% power.
-------
APPENDIX
83
-------
Appendix Table 1
Chemical
Group
Conventionals
Metals
Chemical
TOC
Total Solids
Fines
Arsenic
Survey
Date
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
SF-DODS Ambient (1996-2007)
N
4
3
1
1
3
4
4
2
3
3
4
3
1
1
3
4
4
2
3
3
4
3
1
1
3
4
4
2
3
2
4
3
1
1
Range
2.4-3.2
2.1-2.3
-
2.06
-
2.37
-
2.91-3.09
2.79-2.97
2.8-3.03
2.76-3.05
2.85-3.17
2.76-3.23
30.7-32.1
29.1-34.1
-
35.1
-
37.1
-
28-32.9
28.8-32.3
29.4-31.8
30.3-31.4
31.05-32.8
30.8-32.4
94-97.2
84.7-90.4
-
69.9
-
83.5
-
94.7-96.5
89.3-98.2
91.6-98.3
91.3-94
88.1-97.8
71.9-90.9
3.1-5.4
2.9-5.3
-
3.1
-
3.3
-
Avg ± 1SD
2.7 ±0.3
2.2 ±0.1
-
2.1
-
2.4
-
3.03 ±0.1
2.9 ±0.1
2.9 ±0.1
2.9 ±0.2
3.03 ±0.2
3 ±0.2
31.5±0.6
32.4 ±2.8
-
35.1
-
37.1
-
30.5 ±2. 5
30.3 ±1.5
30.6±1.1
30.8 ±0.8
31.6±1
31.8±0.9
95.2 ±1.5
87 ±3
-
69.8
-
83.5
-
95.9 ±1
93.7 ±4
94. 8 ±3.4
92.7 ±1.9
93.9±5.1
81.4 ±13. 5
4.4 ±1
4.1 ±1.2
-
3.1
-
3.3
-
SF-DODS Footprint (1996-2007)
N
9
14
9
11
11
11
9
12
12
12
10
9
9
9
14
9
11
11
11
9
12
12
12
10
9
9
9
14
9
11
11
11
9
12
12
12
10
9
9
9
14
9
11
11
11
9
Range
1.6-2.8
0.9-2.3
1.4-2.6
0.5-2.9
0.7-2.7
1-3
1.5-3.1
0.9-3
0.7-5.6
1.2-3.4
1.2-2.6
1-2.8
1-2.8
17.3-52.3
32.1-46.8
33.5-51.5
32.8-65.2
20-55.2
29.9-53.4
28.2-49.8
32.7-55.4
31.3-52.3
31.6-52.4
31.8-53.3
33.1-55
35.1-49.6
75.2-96.2
64.3-88.6
40.3-71.8
29.3-86.8
40.7-87.1
47.6-90.4
57.7-84.1
39.5-96.6
44.9-91.6
48.8-88.7
43.3-98.4
41.9-88.6
54.9-84.6
0.7-7.5
2-7.5
1.7-3.3
2.1-4.1
2.6-4.1
2.4-4.8
3.2-4.6
Avg ± ISO
2.4 ±0.5
1.8 ±0.4
2.1 ±0.5
1.6 ±0.7
1.9 ±0.7
2.1 ±0.6
2.2 ±0.5
2.1 ±0.7
2.3 ±1.3
2.2 ±0.6
1.9±0.5
2 ±0.6
1.8 ±0.6
34.8±11.8
37.5 ±4
42. 8 ±6.8
47.9 ±9.2
39.5 ±9.8
39.8 ±7.2
38.7 ±6. 5
40.7 ±7.4
38 ±6.4
39.5 ±6
41.6 ±5.8
41.1 ±7.3
42 ±5. 5
90.2 ± 7
79 ±6.9
62.6 ±11. 6
54.4 ±19.3
67.9 ±15.3
77 ±13. 9
71.9±9.3
75.1 ±15.4
74.3 ±13.3
73. 3 ±12.1
74.6 ±15
70.8 ±13.5
71. 3 ±8. 3
3. 8 ±2.6
5.2 ±1.3
2.8 ±0.5
3 ±0.6
3.4 ±0.5
3. 3 ±0.7
3.8 ±0.5
84
-------
APPENDIX TABLE 1
Chemical
Group
Metals, cont.
Chemical
Cadmium
Cadmium
Chromium
Copper
Lead
Survey
Date
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
SF-DODS Ambient (1996-2007)
N
3
4
3
2
3
3
4
3
1
1
3
4
3
2
3
3
4
3
1
1
3
4
3
2
3
3
4
3
1
1
3
4
3
2
3
3
4
3
Range
3.2-3.9
2.9-3.4
3.4-4.3
3-3.3
3.5-4.4
3.1-4.1
0.3-0.37
0.1-0.18
-
0.19
-
0.41
-
0.29-0.43
0.23-0.48
0.3-0.37
0.16-0.2
0.29-0.53
0.28-0.38
85-90
66-75
-
52.4
-
59.6
-
55.3-58.1
64.2-71.1
79.2-85.2
40.2-54
83.4-86.1
72.1-77.2
50-57
42-47
-
34.4
-
28.3
-
30.2-52.1
33.8-50.2
41-54
36.6-39.1
42.4-64.2
28.3-44.9
20-25
8-16
-
AvgilSD
3. 5 ±0.4
3.1 ±0.2
3.8 ±0.4
3.1 ±0.2
4 ±0.5
3.6 ±0.5
0.32 ±0.03
0.14 ±0.04
-
0.19
-
0.41
-
0.34 ±0.08
0.33±0.11
0.33 ±0.03
0.18 ±0.03
0.37 ±0.14
0.32 ±0.06
87 ±2.2
71.7 ±4.9
-
52.4
-
59.6
-
56.3 ±1.6
67.1 ±3.1
81.2±3.5
47.1 ±9. 8
84. 9 ±1.4
73. 9 ±2.8
54. 5 ±3.1
44. 3 ±2.5
-
34.4
-
28.3
-
42.2 ±11.1
40.5 ±7.1
46. 5 ±6.7
37.8 ±1.8
53.9±11
37.1 ±8.3
22. 8 ±2.1
11.1±4.3
-
SF-DODS Footprint
N Range
12 2.4-5.7
12 2.5-7.6
12 2.5-7.2
10 2.3-6.1
9 2.9-8.3
9 2.6-6.8
9 0.14-0.52
14 0.11-0.19
9 0.12-0.28
11 0.09-0.27
11 0.16-0.52
11 0.16-0.41
9 0.26-0.42
12 0.12-0.53
12 0.12-0.42
12 0.18-0.33
10 0.12-0.21
9 0.14-0.29
9 0.15-0.42
9 40-92
14 61-120
9 60-81
11 31.1-56.2
11 37.1-59.5
11 48.9-70.6
9 38.2-51.9
12 31.6-55.6
12 42.7-73.6
12 51.2-89.2
10 33.2-73.4
9 51.7-80.5
9 49.5-73
9 36-53
14 29-62
9 7.3-21
11 16-36.7
11 20.7-44.8
11 20.2-46.5
9 27-55.2
12 17.8-44.3
12 19.6-46.7
12 21.6-44.7
10 20.2-40.8
9 24-52.4
9 20.6-37.1
9 16-29
14 6.6-35
9 3.5-8
(1996-2007)
AvgilSD
3. 3 ±0.8
3. 5 ±1.5
3.4 ±1.2
3.5 ±1
4 ±1.7
3. 8 ±1.4
0.31 ±0.1
0.14 ±0.02
0.19 ±0.05
0.15 ±0.06
0.3 ±0.1
0.27 ±0.07
0.33 ±0.05
0.27 ±0.1
0.27 ±0.09
0.27 ±0.05
0.17±0.03
0.24 ±0.05
0.22 ±0.08
67.9 ±20.2
78.7 ±15.1
69 ±7.9
42.2 ±7.5
47.5 ±7
56.9 ±6. 9
42.8 ±4.6
44.8 ±6.4
61 ±8.6
73.7 ±10. 3
47.6 ±15. 9
69.5 ±8.6
62.8 ±7.8
46. 3 ±6.2
42.1 ±9.3
14. 9 ±4.4
23 ±7.5
34.3 ±8
32.3 ±8.1
37 ±8.4
33.1 ±7.6
34.3 ±7.3
33. 9 ±6.6
29.1 ±5.4
40.4 ±8.8
29 ±4.6
22. 8 ±3. 8
21 ±8.7
5.8±1.5
85
-------
APPENDIX TABLE 1
Chemical
Group
Metals, cont
Chemical
Mercury
Mercury
Nickel
Selenium
Survey
Date
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
SF-DODS Ambient (1996-2007)
N
1
1
3
4
3
2
3
3
4
3
1
1
3
4
3
2
3
3
4
3
1
1
3
4
3
2
3
3
4
3
1
1
Range
6.64
-
5.16
-
7.7-8.4
6.9-7.4
7.5-8.9
6.5-7.3
7.4-8.4
6.6-7.4
0.03-0.035
0.03-0.082
-
0.11
-
0.02
-
0.1-0.12
0.09-0.13
0.118-0.124
0.132-0.158
0.129-0.156
0.1-0.13
69-72
67-74
-
54.1
-
59.1
-
64.1-70.4
62.8-67.4
68.9-72
55-60
83.2-85.6
60.2-63.8
3.7-4.4
1.8-2.3
-
3.2
-
3.4
AvgilSD
6.6
-
5.2
-
8 ±0.3
7.1 ±0.2
8.1 ±0.7
6. 9 ±0.5
7.9 ±0.5
7.1 ±0.4
0.031 ±
0.002
0.049 ±
0.029
-
0.11
-
0.02
-
0.113±
0.012
0.112±
0.017
0.121 ±
0.003
0.145±
0.018
0.147±
0.016
0.113±
0.015
69. 8 ±1.5
71 ±3.6
-
54.1
-
59.1
-
67.6 ±3.2
65. 5 ±2.3
70.1 ±1.7
57.5 ±3. 5
84.4 ±1.2
61.7±1.9
4 ±0.3
2 ±0.3
-
3.2
-
3.4
SF-DODS Footprint (1996-2007)
N Range
11 4.4-10.1
11 5.3-7.7
11 5.5-7.7
9 6.4-10
12 5.4-21.3
12 5.1-20.8
12 5.9-22.7
10 5.4-18.9
9 6.2-19.8
9 4.8-19.6
9 0.022-0.076
14 0.024-0.247
9 0.02-0.061
11 0.06-0.24
11 0.1-0.1
11 0.02-0.06
9 0.09-0.12
12 0.07-0.16
12 0.08-0.21
12 0.078-0.199
10 0.096-0.229
9 0.087-0.222
9 0.08-0.21
9 56-80
14 62-97
9 51-78
11 4.8-57.9
11 41.6-72.2
11 45.4-83.9
9 54.5-77.4
12 37.8-67.3
12 42.3-70.2
12 43.3-67.2
10 40.3-62.6
9 50-76
9 41.6-58.1
9 1.4-4
14 0.1-2.4
9 0.2-0.3
9 0.6-3.2
11 1-5
11 1.6-4.4
AvgilSD
6.9±1.8
6.5 ±0.7
6.4 ±0.6
7.4 ±1.2
9.1 ±5
7.7 ±4.2
8.4 ±4.6
7.6 ±4
8.3 ±4.3
9.2 ±5.3
0.035 ±
0.017
0.09 ±0.069
0.032 ±
0.013
0.11 ±0.061
0.1±0
0.033 ±0.01
0.103 ±0.01
0.103 ±
0.024
0.106±
0.035
0.11 ±0.031
0.131 ±
0.041
0.133±
0.039
0.121 ±
0.049
66. 8 ±6.5
72 ± 8.4
67 ±9.1
39.1 ±14. 3
57.3 ±8.5
61.7±11.3
61 ±7.3
56.1 ±8
59.2 ±8
58.3 ±7
51.6±6.7
69 ±8.7
51.8±5.2
2.8 ±0.9
1.1±0.8
0.2 ±0
2 ±0.9
3. 5 ±1.4
3±1
86
-------
APPENDIX
Chemical
Group
Metals, cont
Organics
Chemical
Silver
Zinc
Zinc
Diesel
Range
Organics
Survey
Date
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2001
2002
2003
2004
2005
SF-DO
N
3
4
3
2
3
3
4
3
1
1
3
4
3
2
3
3
4
3
1
1
3
4
3
2
3
3
3
4
3
2
TABLE 1
DS Ambient (
Range
-
3-3.8
2.7-3.2
4.4-4.6
2.3-2.6
3.5-3.9
3.4-3.7
0.2-0.4
0.68-1.2
-
0.35
-
0.53
-
0.504-0.609
0.45-0.62
0.472-0.641
0.431-0.485
0.489-0.618
0.46-0.54
94-100
92-100
-
71.2
-
71.6
-
85.3-104
74.5-85.4
84.6-94.7
67.5-70.3
102-113
67.3-75.5
12-14
21-24.5
11.5-12.5
19-24
1996-2007)
AvgilSD
-
3. 5 ±0.4
3 ±0.2
4.5 ±0.1
2.4 ±0.2
3.6 ±0.2
3. 5 ±0.2
0.328 ±
0.095
0.927±
0.261
-
0.35
-
0.53
-
0.562 ±
0.053
0.537 ±0.07
0.579 ±
0.093
0.458 ±
0.038
0.569 ±0.07
0.51 ±0.044
97 ±2.6
97 ±4.4
-
71.2
-
71.6
-
96 ±9.6
79.3 ±4. 5
88.8 ±5. 3
68.9 ±2
107.2 ±5.5
71.4±4.1
13±1
22.4 ±1.5
11.8±0.6
21. 5 ±3. 5
SF-DODS Footprint
N Range
9 2.7-2.7
12 0.3-4
12 0.5-3.1
12 0.8-4.3
10 0.2-2.4
9 0.4-3.2
9 1.1-3.1
9 0.08-0.8
14 0.06-2.4
9 0.015-0.37
11 0.14-0.38
11 0.25-0.73
11 0.3-0.83
9 0.42-1.27
12 0.222-0.783
12 0.22-0.71
12 0.278-0.62
10 0.24-0.544
9 0.24-0.634
9 0.21-0.73
9 68-100
14 76-120
9 69-110
11 36.3-75.1
11 45.5-95.7
11 48.6-84.6
9 63-97.9
12 42.1-135
12 43.2-85.8
12 46.8-82.7
10 41.2-71
9 54.5-96.1
9 43-67.2
9 33.5-33.5
12 7.5-24
12 13-22.5
12 7-11.5
10 7.9-35
(1996-2007)
AvgilSD
2.7 ±0
2.6 ±1.1
2.2 ±0.8
2.9 ±1
1.7±0.7
2.2 ±1
2.2 ±0.7
0.309 ±
0.228
1.055±
0.705
0.159±
0.139
0.244 ±
0.097
0.461 ±
0.138
0.458 ±
0.142
0.666 ±
0.288
0.468 ±0.15
0.443 ±0.14
0.469 ±
0.106
0.403 ±
0.101
0.436 ±
0.131
0.399±
0.157
91.6±9.8
94.3 ±10.9
91.7±13.8
52.2 ±13.6
72.8 ±14.9
69.2 ±11.8
73. 8 ±12.4
79.7 ±22.2
69.2 ±12
70.4 ±10. 8
58.9 ±8.2
83.9 ±13.6
58. 8 ±7.3
33.5 ±0
14 ±5.7
18.4 ±2.8
9.4 ±1.3
15. 9 ±7.6
87
-------
APPENDIX
Chemical
Group
Organics cont.
PAHs
Chemical
TPH
Total HPAH
Total LPAH
Total PAH
Total PAH
Survey
Date
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2005
2006
SF-DO
N
3
3
4
3
1
1
4
3
1
1
3
4
2
3
3
4
3
1
1
3
4
2
3
3
4
3
1
1
3
4
2
3
TABLE 1
DS Ambient (
Range
11-19
13-18
12-35
17-27
-
25
-
10
164-188
168-192
-
109-109
-
39.2
-
67.7-118.3
20.3-40.6
33.2-34.3
45.1-78.6
27.5-38.4
123-141
126-144
-
40
-
22.9
-
26.5-57.5
8.9-12.2
28.8-29.1
22.9-25.8
24.7-27.4
287-329
294-336
-
149
-
62
-
94.2-175.8
30-52.7
62.3-63
70.9-101.4
1996-2007)
AvgilSD
15.3±4
15.7±2.5
24.8 ±9.6
22 ±5
-
25
-
10
177±11
182. 7 ±12.9
-
109
-
39.1
-
101.2±29
31.4±9.9
33. 7 ±0.7
60.1 ±17
31.4±6
132.8 ±8.3
137 ±9.6
-
40
-
22.9
-
39.4 ±16.1
10.7±1.7
28.9 ±0.2
24 ±1.6
25.7±1.5
309.8 ±19.3
319.7 ±22.5
-
149
-
62
-
140.6±41.9
42.1 ±11.4
62.6 ±0.5
84.1 ±15.7
SF-DODS Footprint
N Range
9 7.1-28
9 8.8-22
9 9-25.1
14 13-50
9 24-42
1 1 25-25
11 12.5-12.5
11 10-65
9 124-176
14 136-1119
9 104-172
11 78-645
11 33.8-223.5
11 21.5-138.5
9 75-415
12 38.8-313.6
12 13.6-230.8
10 27.3-493
9 29-2749
9 19.2-507.7
9 78-217.5
14 102-239
9 78-129
1 1 35-77
11 18.8-49.5
11 19.7-27.9
9 49.4-104
12 17.1-39.6
12 5.5-37
10 20-86.2
9 14.8-1298
9 17.4-86.7
9 217-389.5
14 238-1358
9 182-301
11 118-722
11 52.5-258.5
11 41.1-164.4
9 129-519
12 62.6-353.2
12 20-267.8
10 47.2-579.2
9 43.8-4047
(1996-2007)
AvgilSD
14.1 ±5. 9
13.1 ±4.8
15.3 ±5.6
27.1 ±10.1
30.8 ±5.5
25 ±0
12.5 ±0
31.4±16.1
155.1 ±19.4
265. 8 ±263
131.6±21.6
196 ±169.2
112.9±51.7
71 ±29.4
136.6 ±
107.9
98.9 ±73.2
49.1 ±60.8
90. 5 ±142.9
362.5 ±
895.9
149 ±160.4
132.2 ±39.5
125 ± 34
98.7 ±16.2
44. 9 ±11. 5
31.9±8
24 ± 2.4
60 ±17.1
25. 3 ±5. 8
11.7±8.7
29.5 ±20.1
168.2 ±
423.9
34.7 ±21. 9
287.3 ±51. 5
390.8 ±
293.9
230.2 ±37.8
240.9 ±
178.5
144.8 ±57.1
95 ±30. 9
196.6 ±
124.3
124. 3 ±77.9
60.8 ±69.3
120 ±162.7
530.7 ±
1319.4
-------
APPENDIX TABLE 1
Chemical
Group
PAHs, cont
PCBs
Pesticides
Chemical
Total PCB
Aldrin
Dieldrin
Total BHC
Survey
Date
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
SF-DODS Ambient (1996-2007)
N
3
4
3
1
1
3
4
3
2
3
3
4
3
1
1
3
4
3
2
3
3
4
3
1
1
3
4
3
2
3
3
4
3
1
1
Range
52.2-65.8
101-115.5
105.5-120.5
-
70
-
60
-
9.5-15.5
19.6-22.1
20-24
52-55.5
51.5-52
51.5-52
0.6-0.7
0.65-0.75
-
2
-
1
-
1.9-2.8
0.39-0.44
0.41-0.6
0.65-0.7
0.65-0.65
0.65-0.65
0.8-0.95
0.85-0.95
-
2
-
1
-
0.47-0.55
0.13-0.15
1.3-1.45
0.65-0.7
0.65-0.65
0.65-0.65
2.2-2.55
2.35-2.7
-
6
-
3
-
AvgilSD
57.1 ±7.5
110.1 ±6. 8
115.2 ±8.4
-
70
-
60
-
11.8±3.2
21 ±1.1
21.4 ±2.2
53.8±2.5
51.8±0.3
51.7±0.3
0.66 ±0.05
0.7 ±0.05
-
2
-
1
-
2. 5 ±0.52
0.41 ± 0.02
0.48 ±0.11
0.67 ±0.04
0.65 ±0
0.65 ±0
0.88 ±0.06
0.92 ±0.06
-
2
-
1
-
0.52 ±0.05
0.14 ±0.01
1.37 ±0.08
0.67 ±0.04
0.65 ±0
0.65 ±0
2.43 ±0.17
2. 55 ±0.18
-
6
-
3
-
SF-DODS Footprint (1996-2007)
N Range
9 40.5-594.4
9 65-109.5
14 75.5-139
9 66-109.5
1 1 70-70
11 50-50
11 60-60
9 143.5-143.5
12 5.6-32.2
12 12.3-20.3
12 12.5-33.6
10 40-52
9 30.1-51.5
9 40-47.8
9 0.4-0.65
14 0.46-0.7
9 0.4-0.65
11 2-2
11 1-1
11 1-1
9 1.45-1.45
12 0.72-3.6
12 0.24-0.4
12 0.24-0.85
10 0.5-0.65
9 0.37-0.65
9 0.5-0.6
9 0.5-0.85
14 0.7-2.4
9 0.55-0.85
11 2-2
11 1-1
11 1-1
9 1.8-1.8
12 0.28-2
12 0.08-0.91
12 0.15-1.2
10 0.5-0.65
9 0.37-0.65
9 0.5-0.6
9 1.2-2.4
14 1.66-2.55
9 1.45-2.4
11 6-6
11 3-3
11 3-3
9 5.4-16.6
AvgilSD
183.7±
181.4
93.1 ±15.6
99±15.1
83 ±14.1
70 ±0
50 ±0
60 ±0
143.5 ±0
11.1±6.9
17.2 ±2.6
18. 9 ±5.4
42.4 ±4.2
41.2 ±7.3
42.6 ±3. 7
0.56 ±0.09
0.58 ±0.07
0.5 ±0.08
2±0
1±0
1±0
1.45 ±0
1.99 ±0.94
0.34 ±0.05
0.38 ±0.16
0.53 ±0.05
0.52 ±0.1
0.53 ±0.04
0.74 ±0.13
0.99 ±0.54
0.67 ±0.11
2±0
1±0
1±0
1.8±0
0.63 ±0.58
0.33 ±0.26
0.67 ±0.36
0.53 ±0.05
0.52 ±0.1
0.53 ±0.04
2 ±0.43
2. 13 ±0.25
1.9 ±0.29
6±0
3±0
3±0
7.22 ±3.7
89
-------
APPENDIX TABLE 1
Chemical
Group
Pesticides,
cont.
Organotins
Chemical
Total BHC
Total DDTs
Tri-n-
butyltin
Survey
Date
2002
2003
2004
2005
2006
2007
1996-Jan
1996-Dec
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
1999
2000
2001
2002
2003
2004
2005
2006
2007
SF-DO
N
3
4
3
2
3
3
4
3
1
1
3
4
3
2
3
3
1
3
4
3
2
3
3
DS Ambient (
Range
6.4-22.25
1.74-4.22
0.74-10.69
2.1-3.25
1.95-2.6
1.61-1.95
3.85-4.6
6.45-7.55
-
6
-
3
-
4.33-7.01
1.45-1.91
3.63-23.75
3.35-3.8
2.5-4.59
1.77-2.09
-
1.5
-
1.55-1.8
0.6-0.65
0.26-0.28
1.6-1.65
1.55-1.65
1.55-1.6
1996-2007)
AvgilSD
12. 95 ±8.28
2. 81 ±1.14
4. 56 ±5. 36
2.67 ±0.81
2.17 ±0.38
1.84 ±0.2
4.24 ±0.33
7.08 ±0.57
-
6
-
3
-
5. 99 ±1.45
1.65 ±0.2
10.92 ±
11.14
3.58 ±0.32
3. 39 ±1.07
1.94 ±0.16
-
1.5
-
1.67 ±0.13
0.64 ± 0.02
0.26 ±0.01
1.63 ±0.04
1.61 ±0.05
1.57 ±0.03
SF-DODS Footprint
N Range
12
12
12
10
9
9
9
14
9
11
11
11
9
12
12
12
10
9
9
11
11
9
11
12
12
10
9
9
2.71-14.1
0.46-8.12
0.38-5.08
1.5-3.4
1.1-4.4
1.28-4.06
2.45-5.2
5.05-8.7
2.55-5.21
6-9
3-3
3-5.4
5.4-5.4
2.33-11.5
1.04-3.33
2.73-15.31
1.5-4.2
1.78-4.6
1.37-2.9
0.5-38
1.5-1.5
1.6-1.8
1.1-4.2
0.36-1.9
0.16-3.2
0.95-1.6
0.81-1.8
0.95-3.9
(1996-2007)
AvgilSD
7.73 ±4.78
2. 13 ±1.98
2.38 ±1.4
1.92 ±0.64
2.16±1.11
1.74 ±0.88
3. 67 ±0.8
6. 35 ±0.92
3. 39 ±0.76
6.55 ±1.21
3±0
3. 57 ±0.74
5.4 ±0
5.05 ±2.43
1.82 ±0.8
7.03 ±4. 12
2.84 ±0.87
3.06 ±1
1.74 ±0.47
4 ±11.28
1.5±0
1.78 ±0.07
1.6 ±0.87
0.69 ±0.41
0.57 ±0.87
1.25 ±0.17
1.34 ±0.28
1.6 ±0.9
90
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Appendix Table 2. Summary of range of sediment chemistry measured at SF-DODS and source areas.
Chemical
Conventionals
Total Solids (%)
Percent Fines
TOC (%)
SF-DODS
Baseline (1990-91)
Range
-
78-99
2.7-3.9
Metals (mg/kg dw)
Arsenic
Cadmium
Chromium
Copper
Lead
Mercury
Nickel
Selenium
Silver
Zinc
nd-5.2
nd-0.38
91-167
20-62
nd-12
0.13-0.236
77-115
nd-6.6
nd-0.64
91-147
Organics (ug/kg dw)
Diesel Range Organics
TPH
LPAHs
HPAHs
PAHs
Aldrin
Dieldrin
Total BHCs
Total DDTs
Total PCBs
Tri-n-butyltin
nd: not detected
-
-
nd
nd-220
-
-
nd
-
nd
nd
-
SF-DODS Monitoring Data (1996-2007)
N
168
167
168
167
167
167
167
167
167
167
165
167
167
91
76
152
152
152
167
167
167
167
167
115
Min
17.25
29.3
0.51
0.7
0.09
31.1
7.3
3.5
0.0195
4.8
0.14
0.015
36.3
7
9
5.5
13.6
20.0
0.24
0.08
0.38
1.035
5.6
0.1625
Max
65.2
98.44
5.59
8.3
0.53
120
64.2
35
0.247
97
5
2.4
135
35
65
1,298
2,749
4,047
3.6
2.4
22.25
23.75
143.5
38
All calculations made using 1/2 of the
reported detection limit for values below
detection.
Dredged Material Characterization Data
(1994-2006)
Min
32
1.28
0.08
3.18
0.05
38
4.91
6.74
0.004
0.89
0.1
0.038
31.5
-
-
50
320
-
-
15
25
0.2
61
-
Max
82.9
99.3
1.71
14.7
1.1
303
214
132
6.05
140
2
14
566
-
-
13,993
36,985
-
-
43
25
280
149
-
Max Source
POA
RIH
RIH
RIH
OIH
POO
OIH
OIH
OIH
OOH
RIH
OIH
OIH
-
-
POSF
POSF
-
-
RIH
RIH
RIH
OOH
-
SF-DODS Reference
Range
33-59
40-84
0.63-1.45
2.2-5.33
0.3-0.6
69.2-283
18.3-86.3
5.1-26
0.1-0.2
50.9-238
0.6-2.6
0.2-1
60.8-288
-
nd-17.1
nd-77
nd-115
nd-192
nd
nd
nd
nd-2.1
1.9-3.9
nd-1.3
All calculations made using 1/2 of the reported detection limit for values below detection.
'OIH = Oakland Inner Harbor; OOH = Oakland Outer Harbor; POA = Port of Oakland; PJH = Richmond Inner Harbor; POSF = Port of San Francisco
91
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Appendix Table 3
Year Project Bin Volume (cy)
1995 Port of Oakland 42 Ft Deepening 243,980
1996 Port of Oakland 42 Ft Deepening 1,022,254
1997 Port of Oakland 42 Ft Deepening 3,689,426
Port of Richmond 38 Ft Deepening 953,438
1998 Port of Oakland 42 Ft Deepening 682,185
Port of Richmond 38 Ft Deepening 1,879,399
1999 Oakland Inner and Outer Federal Channel 350,200
2000 Oakland Inner and Outer Federal Channel 380,650
2001 Oakland Inner and Outer Federal Channel 242,195
Richmond Inner Federal Channel 454,677
2002 Bay Bridge 272,911
Oakland Inner and Outer Federal Channel 312,460
Richmond Inner Federal Channel 262,713
2003 Oakland Inner and Outer Federal Channel 451,500
Richmond Inner Federal Channel 600,785
2004 Bodega Bay 105,000
Port of Oakland Inner and Outer Federal
Channel 165,000
Port of San Francisco Pier 35 68,000
Richmond Inner Federal Channel 108,000
2005 Port of San Francisco Pier 35 40,000
Port of Oakland Berth 30 109,600
2006 Port of Oakland 50 Ft Deepening (3D) 253,802
Port of Oakland 50 Ft Deepening (3E) 98,000
Port of San Franci sco Pier 27 71,340
Port of San Francisco Pier 35 54,000
Richmond Inner Federal Channel 601,160
2007 Port of Oakland Berths 21,600
Port of Oakland 50 Ft Deepening (3D) 98,400
Port of Oakland 50 Ft Deepening (3E) 714,000
Port of San Franci sco Pier 3 5 87,900
Richmond Terminal 3 24,600
Richmond Inner Federal Channel 479,400
December, 2008 92
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