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Theresa A. Fregoso

Publications and source records attributed to Theresa A. Fregoso.

15 recordsLinked to original sources
USGS2025

Contributions of erosion, deposition, and human activities to a change in sand storage in the bed of San Francisco Bay, California, 1980s to 2010s

This study by the U.S. Geological Survey (USGS) provides estimates of the change in sand storage in bed sediments from the 1980s to 2010s in the San Francisco Bay area, California. The study is part of a larger project called “Research to Understand Impacts of Bay Sand Mining on Sand Transport in San Francisco Bay and the Outer Coast” that has the goal of providing information for the California Coastal Conservancy to inform decision making regarding sand mining activities. Information from this study will contribute to the sand budget for the San Francisco Bay system by accounting for sand made available by erosion of bay sediment and sequestered by deposition in the bay. Sediment budgets for estuaries typically account for change in sediment storage in the bed without discriminating for sediment size. However, the physics of mud and sand erosion, deposition, and transport differ. Sediment budgets that treat mud and sand separately give a more complete understanding of the system, including how human activities related to sediment size, such as sand mining, affect the system. We used bathymetric change analysis in combination with a three-dimensional model to generate estimates of net change in sand storage within the San Francisco Bay floor. We document sediment volume change from a 1980s bathymetric surface to a 2010s bathymetric surface, in combination with information on the sand content of the bed sediment derived from sediment cores and surface samples from six different sediment studies, to estimate the net change in sand volume in the bed of San Francisco Bay. This analysis includes areas heavily affected by human activities (such as sand mining, dredging, and sediment disposal) as well as regions more representative of natural transport processes. Overall, the sediment bed of San Francisco Bay is losing sand. Across the total area surveyed in San Francisco Bay, including areas affected by natural processes, oyster shell beds, and human activities, a net loss of about 17 million cubic meters (Mm 3 ) of sand from the sediment bed occurred from the 1980s to 2010s, at a rate of about 0.8 Mm 3 per year. For the period of this study, sand loss from bed level changes in permitted sand-lease mining areas (about 11 Mm 3 ) accounts for about two-thirds of the total sand loss throughout the study area. It is important to consider potential uncertainty bounds when interpreting these findings. A key part of the report is an assessment of the uncertainties in our estimates of sand volumes. We estimate that variability in modeled sand content values of Bay floor sediments could result in an uncertainty of approximately 25 percent of the net sand volume change. Even larger uncertainty amounts may be associated with uncertainty in the systematic errors in the bathymetric surveys. Further refining estimates of uncertainty in bathymetric change is important in guiding the use of this study. The results presented here can fill a critical gap that may enable the creation of the first comprehensive sand budget of San Francisco Bay.

California↗
USGS2023

Sediment deposition, erosion, and bathymetric change in San Francisco Bay, California, 1971–1990 and 1999–2020

Bathymetric change analyses document historical patterns of sediment deposition and erosion, providing valuable insight into the sediment dynamics of coastal systems, including pathways of sediment and sediment-bound contaminants. In 2014 and 2015, the Office for Coastal Management, in partnership with the National Oceanic and Atmospheric Administration (NOAA) Office of Coastal Management, provided funding for new bathymetric surveys of large portions of San Francisco Bay. A total of 93 bathymetric surveys were conducted during this 2-year period, using a combination of interferometric sidescan and multibeam sonar systems. These data, along with recent NOAA, U.S. Geological Survey (USGS), U.S. Army Corps of Engineers, and private contractor surveys collected from 1999 to 2020 (hereinafter referred to as 2010s), were used to create the most comprehensive bathymetric digital elevation models (DEMs) of San Francisco Bay since the 1980s. Comparing DEMs created from these 2010s surveys with USGS DEMs created from NOAA’s 1971–1990 (hereinafter referred to as 1980s) surveys provides information on the quantities and patterns of erosion and deposition in San Francisco Bay during the 9 to 47 years between surveys. This analysis reveals that in the areas surveyed in both the 1980s and 2010s, the bay floor lost about 34 million cubic meters of sediment since the 1980s. Results from this study can be used to assess how San Francisco Bay has responded to changes in the system, such as sea-level rise and variation in sediment supply from the Sacramento-San Joaquin Delta and local tributaries, and supports the creation of a new, system-wide sediment budget. This report provides data on the quantities and patterns of sediment volume change in San Francisco Bay for ecosystem managers that are pertinent to various sediment-related issues, including restoration of tidal marshes, exposure of legacy contaminated sediment, and strategies for the beneficial use of dredged sediment.

California↗
USGS2023

Observations and morphodynamic modeling of decadal-scale morphologic change in estuaries under sea level rise

Sea level rise is expected to affect coastal areas all around the world, including the estuarine environment. New bathymetry collected in 2014 provided a unique opportunity to test the modeling of Elmilady et al. (2019), who presented a morphodynamic DELFT3D model of San Pablo Bay, California, that included detailed tidal water movement, wind-wave action, sediment transport, and resulting bed level updates. Their hindcasts (1856–1983) showed significant skill in reproducing observed patterns and volumes of deposition and erosion in San Pablo Bay. Their forecasts (1983–2100) showed that sea level rise results in increased deposition, loss of intertidal flats because of drowning, and a greater channel volume. The model, in general, forecasted observed trends in change from 1983 to 2014. Morphodynamic modeling is a promising approach for identifying the effect of sea level rise on estuarine environments.

California↗
USGS2023

Successful hindcast of 7 years of mud morphodynamics influenced by salt pond restoration in south San Francisco Bay

Alviso Slough in South San Francisco Bay has been experiencing restoration of adjacent former salt-production ponds into muted tidal ponds, tidal ponds, and salt marsh. As a result, tidal prism through Alviso Slough has increased and mercury-contaminated sediment has been remobilized. We developed a 2D, high-resolution, process-based model (Delft3D FM-wave) to hindcast observed morpho-dynamic developments and to investigate associated sediment flux in the slough and pond system. Our results contrastingly demonstrate that a successful hindcast of the observed morphodynamic trend is made while reproducing observed intratidal suspended sediment concentrations in Alviso Slough remains a challenge. Our explanation is that the model is able to capture spatial gradients in the tide-residual sediment transports as the result of the large-scale management actions in the system, i.e., the opening of the salt ponds. These tide-residual processes are generally difficult to measure over an entire domain, but are very relevant to model the morphodynamic development. Our model provides a promising tool to trace eroding contaminated sediments to the benefit of restoration project managers and to support planning and design phases of adaptive management measures.

California↗
USGS2019

Slough evolution and legacy mercury remobilization induced by wetland restoration in South San Francisco Bay

Coastal wetlands have a long history of degradation and destruction due to human development. Now recognized as one of the most productive ecosystems in the world, substantial efforts are being made to restore this critical habitat. While wetland restoration efforts are generally viewed as beneficial in terms of providing wildlife habitat and flood control, they are often accompanied by dramatic physical and chemical changes that may result in unintended consequences, which are rarely studied. Alviso Slough, a tidal slough in South San Francisco Bay, California, is the site of an ongoing effort to restore former salt-production ponds to intertidal marsh habitat. Restoration is complicated by the fact that (1) the ponds undergoing restoration are severely subsided and (2) subsurface sediments within the slough and surrounding ponds are contaminated with legacy mercury deposits. Due to concerns regarding mercury remobilization, restoration has proceeded in a cautious, methodical manner. To assess the amount of legacy mercury remobilized since restoration began, we developed a technique of combining high-resolution, biannual measurements of bathymetric scour with mercury concentration measurements from sediment cores. We estimate that 52 kg (±3) of mercury was remobilized in the 6 years since restoration began. Net bathymetric change analyses revealed seasonal trends of peak erosion during the winter months and little to no net change during summer months. Our analyses provide crucial insight on the spatial and temporal scales of geomorphic evolution within a tidal slough resulting from both natural (seasonal) variability and restoration actions. The technique presented here could be applied to other study sites and various sediment-associated contaminants of concern to aid in the design and management of restoration projects aiming to minimize negative impacts from legacy contaminants.

California↗
USGS2019

A revised continuous surface elevation model for modeling

A digital elevation model (DEM) is an essential component of any hydrodynamic model. The Delta Modeling Section (Section) has maintained a database of bathymetry soundings and levee surveys for decades and published a 10-meter (10m) DEM for the San Francisco Bay and Sacramento-San Joaquin Delta (Delta) (California Department of Water Resources 2012). In collaboration with the U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center, the California Department of Water Resources (DWR) has continued to upgrade these DEMs based on newer survey data and improved interpolation methodologies. An updated San Francisco Bay-Delta bathymetric/topographic digital elevation model was published by the USGS (Fregoso, Wang, Ateljevich, and Jaffe 2017). Both DWR and USGS continue to work on the elevation models for several reasons. First, high-resolution multibeam bathymetry data continues to become available. A good portion of the newer collections are performed at locations where bathymetry data is lacking, or of poor quality, or where model sensitivity to bathymetry is known to be high, so the effort has a high return on investment. Recent high-resolution multibeam datasets easily support the development of accurate 2-meter (2m) DEMs, although shallow water, turbidity, vegetation, and the gap between the multibeam data and terrestrial data from light detection and ranging (LiDAR) remain vexing issues that fuel development of enhanced techniques. In some locations, migration toward 2m resolution models is motivated by geographical structure even where there has been little improvement in the underlying data. DEMs at 10m resolution are insufficient to adequately describe small-scale terrain features, such as levee crests or the main conveyance channel through a narrow reach, such as Middle River. As a result, elevation modelers have traditionally needed to perform feature enforcement for 10m DEMs, but not for the Section’s 2m DEMs which do resolve these features (California Department of Resources 2012). There are several other problems associated with a coarse target resolution, including reduced conveyance and rough contours where channels run oblique to the elevation model. In places where the topography demands a finer elevation model, the Section and others have adopted improved interpolation techniques for single-beam data to produce reasonable 2m DEMs that preserve features on appropriate scales.

California↗
USGS2017

Description of gravity cores from San Pablo Bay and Carquinez Strait, San Francisco Bay, California

Seventy-two gravity cores were collected by the U.S. Geological Survey in 1990, 1991, and 2000 from San Pablo Bay and Carquinez Strait, California. The gravity cores collected within San Pablo Bay contain bioturbated laminated silts and sandy clays, whole and broken bivalve shells (mostly mussels), fossil tube structures, and fine-grained plant or wood fragments. Gravity cores from the channel wall of Carquinez Strait east of San Pablo Bay consist of sand and clay layers, whole and broken bivalve shells (less than in San Pablo Bay), trace fossil tubes, and minute fragments of plant material.

California↗
USGS2017

A new seamless, high-resolution digital elevation model of the San Francisco Bay-Delta Estuary, California

Climate change, sea-level rise, and human development have contributed to the changing geomorphology of the San Francisco Bay - Delta (Bay-Delta) Estuary system. The need to predict scenarios of change led to the development of a new seamless, high-resolution digital elevation model (DEM) of the Bay – Delta that can be used by modelers attempting to understand potential future changes to the estuary system. This report details the three phases of the creation of this DEM. The first phase took a bathymetric-only DEM created in 2005 by the U.S. Geological Survey (USGS), refined it with additional data, and identified areas that would benefit from new surveys. The second phase began a USGS collaboration with the California Department of Water Resources (DWR) that updated a 2012 DWR seamless bathymetric/topographic DEM of the Bay-Delta with input from the USGS and modifications to fit the specific needs of USGS modelers. The third phase took the work from phase 2 and expanded the coverage area in the north to include the Yolo Bypass up to the Fremont Weir, the Sacramento River up to Knights Landing, and the American River up to the Nimbus Dam, and added back in the elevations for interior islands. The constant evolution of the Bay-Delta will require continuous updates to the DEM of the Delta, and there still are areas with older data that would benefit from modern surveys. As a result, DWR plans to continue updating the DEM.

California↗
USGS2014

Late Holocene sedimentary environments of south San Francisco Bay, California, illustrated in gravity cores

Data are reported here from 51 gravity cores collected from the southern part of San Francisco Bay by the U.S. Geological Survey in 1990. The sedimentary record in the cores demonstrates a stable geographic distribution of facies and spans a few thousand years. Carbon-14 dating of the sediments suggests that sedimentation rates average about 1 mm/yr. The geometry of the bay floor and the character of the sediment deposited have remained about the same in the time spanned by the cores. However, the sedimentary record over periods of centuries or decades is likely to be much more variable. Sediments containing a few bivalve shells and bivalve or oyster coquinas are most often found west of the main channel and near the San Mateo Bridge. Elsewhere in the south bay, shells are rare except in the southernmost reaches where scattered gastropod shells are found.

California↗
USGS2013

Burial and exhumation of temperate bedrock reefs as elucidated by repetitive high-resolution sea floor sonar surveys: Spatial patterns and impacts to species' richness and diversity

To understand how chronic sediment burial and scour contribute to variation in the structure of algal and invertebrate communities on temperate bedrock reefs, the dynamics of the substrate and communities were monitored at locations that experience sand inundation and adjacent areas that do not. Co-located benthic scuba-transect surveys and high-resolution swath-sonar surveys were completed on bedrock reefs on the inner shelf of northern Monterey Bay, CA, in early winter 2009, spring 2010, and summer 2010. Analysis of the sonar surveys demonstrates that during the 8 months over which the surveys were conducted, 19.6% of the study area was buried by sand while erosion resulted in the exposure of bedrock over 13.8% of the study area; the remainder underwent no change between the surveys. Substrate classifications from the benthic transect surveys correlated with classifications generated from the sonar surveys, demonstrating the capacity of high-resolution sonar surveys to detect burial of bedrock reefs by sediment. On bedrock habitat that underwent burial and exhumation, species' diversity and richness of rock-associated sessile and mobile organisms were 50–66% lower as compared to adjacent stable bedrock habitat. While intermediate levels of disturbance can increase the diversity and richness of communities, these findings demonstrate that burial and exhumation of bedrock habitat are sources of severe disturbance. We suggest that substrate dynamics must be considered when developing predictions of benthic community distributions based on sea floor imagery. These results highlight the need for predictive models of substrate dynamics and for a better understanding of how burial and exhumation shape benthic communities.

California↗
USGS2012

Bathymetry and digital elevation models of Coyote Creek and Alviso Slough, South San Francisco Bay, California

In 2010, the U.S. Geological Survey (USGS), Pacific Coastal and Marine Science Center completed three cruises to map the bathymetry of the main channel and shallow intertidal mudflats in the southernmost part of south San Francisco Bay. The three surveys were merged to generate comprehensive maps of Coyote Creek (from Calaveras Point east to the railroad bridge) and Alviso Slough (from the bay to the town of Alviso) to establish baseline bathymetry prior to the breaching of levees adjacent to Alviso and Guadalupe Sloughs as part of the South Bay Salt Pond Restoration Project ( http://www.southbayrestoration.org ). Since 2010, the USGS has conducted fourteen additional surveys to monitor bathymetric change in this region as restoration progresses. The bathymetric surveys were conducted using the state-of-the-art research vessel R/V Parke Snavely outfitted with an interferometric sidescan sonar for swath mapping in extremely shallow water. This publication provides high-resolution bathymetric data collected by the USGS. For the 2010 baseline survey we have merged the bathymetry with aerial lidar data that were collected for the USGS during the same time period to create a seamless, high-resolution digital elevation model (DEM) of the study area. The series of bathymetric datasets are provided at 1 m resolution and the 2010 bathymetric/topographic DEM at 2 m resolution. The data are formatted as both X, Y, Z text files and ESRI Arc ASCII files that are accompanied by Federal Geographic Data Committee (FGDC) compliant metadata.

California↗
USGS2010

Estuarine sedimentation, sediment character, and foraminiferal distribution in central San Francisco Bay, California

Central San Francisco Bay is the deepest subembayment in the San Francisco Bay estuary and hence has the largest water volume of any of the subembayments. It also has the strongest tidal currents and the coarsest sediment within the estuary. Tidal currents are strongest over the west-central part of central bay and, correspondingly, this area is dominated by sand-size sediment. Much of the area east of a line from Angel Island to Alcatraz Island is characterized by muddy sand to sandy mud, and the area to the west of this line is sandy. The sand-size sediment over west-central bay furthermore is molded by the energetic tidal currents into bedforms of varying sizes and wavelengths. Bedforms typically occur in water depths of 15-25 m. High resolution bathymetry (multibeam) from 1997 and 2008 allow for subdivision of the west-central bayfloor into four basic types based on morphologic expression: featureless, sand waves, disrupted/man-altered, and bedrock knobs. Featureless and sand-wave morphologies dominate the bayfloor of west-central bay. Disrupted bayfloor has a direct association with areas that are undergoing alteration due to human activities, such as sand-mining lease areas, dredging, and disposal of dredge spoils. Change detection analysis, comparing the 1997 and 2008 multibeam data sets, shows that significant change has occurred in west-central bay during the roughly 10 years between surveys. The surveyed area lost about 5.45 million m3 of sediment during the decade. Sand-mining lease areas within west-central bay lost 6.77 million m3 as the bayfloor deepened. Nonlease areas gained 1.32 million m3 of sediment as the bayfloor shallowed slightly outside of sand-mining lease areas. Furthermore, bedform asymmetry did not change significantly, but some bedforms did migrate some tens of meters. Gravity cores show that the area east of Angel and Alcatraz Islands is floored by clayey silts or silty sand whereas the area to the west of the islands is floored dominantly by sand- to coarse sand-sized sediment. Sandy areas also include Raccoon Strait, off Point Tiburon, and on the subtidal Alcatraz, Point Knox, and Presidio Shoals. Drab-colored silty clays are the dominant sediment observed in gravity cores from central bay. Their dominance along the length of the core suggests that silty clays have been deposited consistently over much of this subembayment for the time period covered by the recovered sediments (Woodrow and others, this report). Stratification types include weakly-defined laminae, 1-3 mm thick. Few examples of horizontal lamination in very fine sand or silt were observed. Cross lamination, including ripples, was observed in seven cores. Erosional surfaces were evident in almost every core where x-radiographs were available (they are very difficult to observe visually). Minor cut-and-fill structures also were noted in three cores and inclined strata were observed in three cores. Textural patterns in central bay indicate that silts and clays dominate the shallow water areas and margins of the bay. Sand dominates the tidal channel just east of Angel and Alcatraz Islands and to the west of the islands to the Golden Gate. The pattern of sand-sized sediment, as determined by particle-size analysis, suggests that sand movement is easterly from the west-central part of the bay. A second pattern of sand movement is to the south from the southwestern extremity of San Pablo Bay (boundary approximated by the location of the Richmond-San Rafael Bridge). Age dates for central bay sediment samples were obtained by carbon-14 radiometric age dating. Age dates were determined from shell material that was interpreted to be largely in-place (not transported). Age dates subsequently were reservoir corrected and then converted to calendar years. Sediments sampled from central bay cores range in age from 330 to 4,155 years before present. Foraminiferal distribution in the San Francisco Bay estuary is fairly well

Open-File Report↗
USGS2008

Sediment deposition, erosion, and bathymetric change in central San Francisco Bay: 1855-1979

Central San Francisco Bay is the hub of a dynamic estuarine system connecting the San Joaquin and Sacramento River Deltas, Suisun Bay, and San Pablo Bay to the Pacific Ocean and South San Francisco Bay. To understand the role that Central San Francisco Bay plays in sediment transport throughout the system, it is necessary to first determine historical changes in patterns of sediment deposition and erosion from both natural and anthropogenic forces. The first extensive hydrographic survey of Central San Francisco Bay was conducted in 1853 by the National Ocean Service (NOS) (formerly the United States Coast and Geodetic Survey (USCGS)). From 1894 to 1979, four additional surveys, composed of a total of approximately 700,000 bathymetric soundings, were collected within Central San Francisco Bay. Converting these soundings into accurate bathymetric models involved many steps. The soundings were either hand digitized directly from the original USCGS and NOS hydrographic sheets (H-sheets) or obtained digitally from the National Geophysical Data Center's (NGDC) Geophysical Data System (GEODAS) (National Geophysical Data Center, 1996). Soundings were supplemented with contours that were either taken directly from the H-sheets or added in by hand. Shorelines and marsh areas were obtained from topographic sheets. The digitized soundings, depth contours, shorelines, and marsh areas were entered into a geographic information system (GIS) and georeferenced to a common horizontal datum. Using surface modeling software, bathymetric grids with a horizontal resolution of 25 m were developed for each of the five hydrographic surveys. Before analyses of sediment deposition and erosion were conducted, interpolation bias was removed and all of the grids were converted to a common vertical datum. These bathymetric grids were then used to develop bathymetric change maps for subsequent survey periods and to determine long-term changes in deposition and erosion by calculating volumes and rates of net sediment change. Central San Francisco Bay experienced periods of both deposition and erosion, but overall experienced a net gain in sediment from 1855 to 1979 of approximately 42x10 6 m 3 (0.33x10 6 m 3 / yr). Over this same time period, 92 percent of the tidal marsh and 69 percent of the intertidal mudflats were lost as human activity increased and the shorefront was developed. During the first time period, from 1855 to 1895, Central San Francisco Bay was erosional, losing roughly 2x10 6 m 3 / yr of sediment. The next time period was depositional, with a net gain of approximately 3x10 6 m 3 / yr of sediment from 1895 to 1947. The last time period, from 1947 to 1979, was erosional again, losing roughly 2x10 6 m 3 / yr of sediment. Sedimentation patterns also varied spatially. The northern part of Central San Francisco Bay was depositional during all change periods while the eastern region alternated between erosional and depositional. Central San Francisco Bay sedimentation patterns have also been strongly impacted by anthropogenic activities, such as dredging and dredge disposal, borrow pits, and sand mining. For example, bathymetric change at a borrow pit created near Bay Farm Island sometime between the 1947 and 1979 surveys indicates roughly 25x10 6 m 3 of sediment was removed from the system

California↗
USGS2006

Mapping South San Francisco Bay's seabed diversity for use in wetland restoration planning

In an effort to understand the role of sediment of South San Francisco Bay (South Bay) salt ponds, an acoustic seabed classification was performed with the condition of over two hundred sediment samples. The success of the large-scale tidal wetland restoration of up to 15,000 acres of South Bay partly depends on the ability of the converted ponds to acquire and retain enough sediment to support marsh growth. Determining the distribution of South Bay's seabed sediment types and understanding their potential erosive properties helps answer critical planning questions about sediment budgets and sediment transportation. Acoustic seabed classification is the organization of the seafloor into discrete units based on the characteristics of the acoustic response generated by an echosounder. Acoustic diversity is considered a proxy for geoacoustical parameters including acoustic impedance contrast, scatter and volume reverberation which all vary with sediment type. In addition, biological and anthropogenic features can influence the acoustic response. Data for an acoustic seabed classification were collected as a part of a California Coastal Conservancy funded bathymetric survey of South Bay in early 2005. A QTC VIEW seabed classification system recorded echoes from a sungle bean 50 kHz echosounder. Approximately 450,000 seabed classification records were generated from an are of of about 30 sq. miles. Ten district acoustic classes were identified through an unsupervised classification system using principle component and cluster analyses. One hundred and sixty-one grab samples and forty-five benthic community composition data samples collected in the study area shortly before and after the seabed classification survey, further refined the ten classes into groups based on grain size. A preliminary map of surficial grain size of South Bay was developed from the combination of the seabed classification and the grab and benthic samples. The initial seabed classification map, the grain size map, and locations of sediment samples will be displayed along with the methods of acousitc seabed classification.

Conference Paper↗