Research Oceanographer with the USGS Pacific Coastal and Marine Science Center
My research interests include: Hydrodynamics of the coastal ocean, estuaries, and lakes; Lateral dynamics in estuaries with complex topography, and their influence on mixing; The dynamics of stratification and baroclinic transport; Estimation of bottom roughness, bottom shear stress, and sediment resuspension in wave-dominated environments; Interaction between aquatic vegetation and hydrodynamics
Science and Products
Sediment Transport in Coastal Environments
Sediment transport between estuarine habitats in San Francisco Bay
Drag and sediment transport: conditions at the bottom boundary
Ecosystem Engineers: Impacts of Invasive Aquatic Vegetation on the Delta’s Critical Ecosystems
Grain size, bulk density, and carbon content of sediment collected from Whale's Tail South marsh and adjacent bay floor, South San Francisco Bay, California, 2021-2022
Structure-from-motion derived orthomosaic imagery and digital surface models (DSMs) from the intertidal region at Whale's Tail Marsh, South San Francisco Bay, CA
Hydrodynamic and sediment transport data from Whale's Tail marsh and adjacent waters in South San Francisco Bay, California 2021-2022
Hydrodynamic, sediment transport, and sediment flocculation data from south San Francisco Bay, California, summer 2020
Hydrodynamic and sediment transport data from San Pablo Bay and Grizzly Bay, California, 2020
Hydrodynamic and sediment transport data from San Pablo Bay and Grizzly Bay, California, 2019
Near-bed velocity measurements in Monterey Bay during arrival of the 2010 Chile Tsunami
Aerial imagery and structure-from-motion derived data products from UAS survey of the Liberty Island Conservation Bank Wildlands restoration site, Sacramento-San Joaquin Delta, California, October 2018
Bed sediment properties in Little Holland Tract and Liberty Island, Sacramento-San Joaquin Delta, California, 2014 to 2019 (ver. 3.0, April 2023)
Sediment transport and aquatic vegetation data from three locations in the Sacramento-San Joaquin Delta, California, 2017 to 2018
Bathymetry, topography, and acoustic backscatter data, and a digital elevation model (DEM) of the Cache Slough Complex and Sacramento River Deep Water Ship Channel, Sacramento-San Joaquin Delta, California
Wind-wave and suspended-sediment data from Liberty Island and Little Holland Tract, Sacramento-San Joaquin Delta, California (ver. 2.0, September 2019)
The influence of vegetated marshes on wave transformation in sheltered estuaries
What controls suspended-sediment concentration and export in flooded agricultural tracts in the Sacramento-San Joaquin Delta?
Numerical simulation of the boundary layer flow generated in Monterey Bay, California by the 2010 Chilean tsunami: Case study
Cohesive sediment modeling in a shallow estuary: Model and environmental implications of sediment parameter variation
Numerical models of sediment transport in estuarine systems rely on parameter values that are often poorly constrained and can vary on timescales relevant to model processes. The selection of parameter values can affect the accuracy of model predictions, while environmental variation of these parameters can impact the temporal and spatial ranges of sediment fluxes, erosion, and deposition in the r
Influence of invasive submerged aquatic vegetation (E. densa) on currents and sediment transport in a freshwater tidal system
We present a field study combining measurements of vegetation density, vegetative drag, and reduction of suspended-sediment concentration (SSC) within patches of the invasive submerged aquatic plant Egeria densa. Our study was motivated by concern that sediment trapping by E. densa, which has proliferated in the Sacramento–San Joaquin Delta, is impacting marsh accretion and reducing turbidity. In
The role of surges during periods of very shallow water on sediment transport over tidal flats
Carbon storage and sediment trapping by Egeria densa Planch., a globally invasive, freshwater macrophyte
Seasonal variation in sediment delivery across the bay-marsh interface of an estuarine salt marsh
Seasonal, spring-neap, and tidal variation in cohesive sediment transport parameters in estuarine shallows
Numerical models for predicting sediment concentrations and transport rely on parameters such as settling velocity and bed erodibility that describe sediment characteristics, yet these parameters are rarely probed directly. We investigated temporal and spatial variation in sediment parameters in the shallows of San Pablo Bay, CA. Flow, turbulence, and suspended sediment data were measured at sites
Measuring settling velocity in a strongly tidal estuary
Predicting sediment transport in estuarine systems requires understanding sediment settling velocity, its range of fluctuations, and the shortcomings of the tools to measure it. Previous studies have used Laser In-Situ Scattering and Transmissometry (LISST) instruments to measure particle size and Acoustic Doppler Velocimeters (ADV) to return estimates of settling velocity. We deployed both instru
Bed shear stress estimation under wave conditions using near-bottom measurements: Comparison of methods
The influence of neap-spring tidal variation and wave energy on sediment flux in salt marsh tidal creeks
Science and Products
- Science
Sediment Transport in Coastal Environments
Our research goals are to provide the scientific information, knowledge, and tools required to ensure that decisions about land and resource use, management practices, and future development in the coastal zone and adjacent watersheds can be evaluated with a complete understanding of the probable effects on coastal ecosystems and communities, and a full assessment of their vulnerability to natural...Sediment transport between estuarine habitats in San Francisco Bay
We investigate mechanisms of sediment transport, resuspension dynamics in shoals, wave evolution in the shallows, wave attenuation in marshes, and transport of sediment between mudflats and marshes. We produce data sets for calibration of and comparison with sediment transport models, including wave parameters, suspended sediment concentration, and sediment flux.Drag and sediment transport: conditions at the bottom boundary
Research on bed sediment grain size, bedform morphology, vegetation characteristics, and sediment resuspension and transport.Ecosystem Engineers: Impacts of Invasive Aquatic Vegetation on the Delta’s Critical Ecosystems
The Sacramento-San Joaquin Delta (Delta) is home to a diverse community of plants and animals and is the hub of California’s freshwater delivery system. The Delta supplies water for over 25 million Californians and supports millions of acres of farming, commercial and sport fishing, shipping and ports, and recreational boating. - Data
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Grain size, bulk density, and carbon content of sediment collected from Whale's Tail South marsh and adjacent bay floor, South San Francisco Bay, California, 2021-2022
Sediment samples were collected on and adjacent to the Whale's Tail South marsh. Short push-cores of bed sediment were collected in South San Francisco Bay adjacent to Whales Tail South marsh on five days from June through August 2021 and 3 days from November 2021 to January 2022. Additional samples were taken from ceramic tiles placed on the marsh to measure sediment deposition and from rip-up clStructure-from-motion derived orthomosaic imagery and digital surface models (DSMs) from the intertidal region at Whale's Tail Marsh, South San Francisco Bay, CA
This data release presents digital surface models (DSMs) and orthomosaic images of the Whale's Tail Marsh region of South San Francisco Bay, CA. The data were created using structure-from-motion (SfM) processing of repeat aerial imagery collected from fixed-wing aircraft. The raw images were acquired from an approximate altitude of 427 meters (1,400 feet) above ground level (AGL), using a HasselblHydrodynamic and sediment transport data from Whale's Tail marsh and adjacent waters in South San Francisco Bay, California 2021-2022
The U.S. Geological Survey Pacific Coastal and Marine Science Center collected hydrodynamic and sediment-transport data at shallow water sites in South San Francisco Bay and in the Whale's Tail South marsh in Eden Landing Ecological Reserve in Alameda County, CA in 2021 and 2022. This data release includes hydrodynamic and sediment transport time-series data spanning from June 2021 to January 2022Hydrodynamic, sediment transport, and sediment flocculation data from south San Francisco Bay, California, summer 2020
The U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center collected hydrodynamic and suspended sediment flocculation data at channel and shallow water sites in south San Francisco Bay in July 2020. The data were used to determine water column stratification, turbulence profiles, and floc size evolution. The goal of this project was to bound the controls on floc size and floc settHydrodynamic and sediment transport data from San Pablo Bay and Grizzly Bay, California, 2020
The U.S. Geological Survey Pacific Coastal and Marine Science Center collected hydrodynamic and sediment-transport data at shallow water sites in San Pablo Bay and Grizzly Bay, in northern San Francisco Bay between January and September 2020. The data were collected to determine hydrodynamic forcing, bed roughness, suspended-sediment concentration, and physical properties of the sediment bed. ThisHydrodynamic and sediment transport data from San Pablo Bay and Grizzly Bay, California, 2019
The U.S. Geological Survey Pacific Coastal and Marine Science Center collected hydrodynamic and sediment-transport data at shallow water sites in San Pablo Bay and Grizzly Bay, in northern San Francisco Bay between June and November 2019. The data were collected to determine hydrodynamic forcing, bed roughness, suspended-sediment concentration, and physical properties of the sediment bed. This datNear-bed velocity measurements in Monterey Bay during arrival of the 2010 Chile Tsunami
On February 27, 2010, a tsunami originating near Chile arrived in Monterey Bay, California. This data release comprises two hours of pressure and near-bed velocity data spanning the largest tsunami waves. At the time, the U.S. Geological Survey Pacific Coastal and Marine Science Center had a remotely-controlled instrumented platform deployed adjacent to the Santa Cruz Municipal Wharf (mean depth 9Aerial imagery and structure-from-motion derived data products from UAS survey of the Liberty Island Conservation Bank Wildlands restoration site, Sacramento-San Joaquin Delta, California, October 2018
Unmanned aerial systems (UAS) were used to acquire high-resolution imagery of the Liberty Island Conservation Bank Wildlands restoration site in the Sacramento-San Joaquin Delta in California, with the goal of using structure-from-motion (SfM) photogrammetric techniques to derive a digital surface model, orthomosaic imagery, and a topographic point cloud. The survey was conducted using two DepartBed sediment properties in Little Holland Tract and Liberty Island, Sacramento-San Joaquin Delta, California, 2014 to 2019 (ver. 3.0, April 2023)
Bed sediments were collected by the USGS Pacific Coastal and Marine Science Center (PCMSC) in two submerged agricultural tracts, Liberty Island and Little Holland Tract, in the northern Sacramento-San Joaquin Delta, California. Samples were analyzed for grain size distribution, bulk density, or both. Analyses were conducted using PCMSC sediment lab standard techniques (see Process Step in metadataSediment transport and aquatic vegetation data from three locations in the Sacramento-San Joaquin Delta, California, 2017 to 2018
We measured currents, suspended-sediment concentration (SSC), bed sediment characteristics, and vegetation biomass density in the Sacramento-San Joaquin Delta in 2017-2018, as part of a project investigating the influence of invasive aquatic vegetation (IAV) on flow and sediment flux. This data release includes data from three sites: Lindsey Slough (April 2017), Middle River (March 2018) and the lBathymetry, topography, and acoustic backscatter data, and a digital elevation model (DEM) of the Cache Slough Complex and Sacramento River Deep Water Ship Channel, Sacramento-San Joaquin Delta, California
This data release presents bathymetric and topographic data from surveys performed between 2017 and 2018 in the Cache Slough Complex and the Sacramento River Deep Water Ship Channel (DWSC), northern Sacramento-San Joaquin Delta, California. The shallow, highly vegetated aquatic habitats of this region necessitated a variety of survey platforms and techniques. In the deeper channels, swath bathymetWind-wave and suspended-sediment data from Liberty Island and Little Holland Tract, Sacramento-San Joaquin Delta, California (ver. 2.0, September 2019)
Data were collected by the U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center to investigate the influence of wind waves on sediment dynamics in two flooded agricultural tracts in the northern Sacramento-San Joaquin Delta: Little Holland Tract and Liberty Island. This effort is part of a large interdisciplinary study led by the USGS California Water Science Center and funded b - Multimedia
- Publications
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The influence of vegetated marshes on wave transformation in sheltered estuaries
Assessing the influence of marshes on mitigating flooding along estuarine shorelines under the pressures of sea level rise requires understanding wave transformation across the marsh. A numerical model was applied to investigate how vegetated marshes influence wave transformation. XBeach non-hydrostatic (XB-NH) was calibrated and validated with high frequency pressure data from the marsh at ChinaAuthorsRae M. Taylor-Burns, Kees Nederhoff, Jessica R. Lacy, Patrick L. BarnardWhat controls suspended-sediment concentration and export in flooded agricultural tracts in the Sacramento-San Joaquin Delta?
We investigated wind-wave and suspended-sediment dynamics in Little Holland Tract and Liberty Island, two subsided former agricultural tracts in the Cache Slough complex in the northern Sacramento-San Joaquin Delta which were restored to tidal shallows to improve habitat. Turbidity, and thus suspended-sediment concentration (SSC), is important to habitat quality because some species of native fishAuthorsJessica R. Lacy, Evan Dailey, Tara L. Morgan-KingNumerical simulation of the boundary layer flow generated in Monterey Bay, California by the 2010 Chilean tsunami: Case study
This work presents a case study involving the numerical simulation of the unsteady boundary layer generated by the 2010 Chilean tsunami, as measured by field equipment in Monterey Bay, California, USA. A one-dimensional vertical (1DV) boundary layer model is utilized, solving Reynolds-averaged Navier–Stokes equations, coupled with two-equation k–ω turbulence closure. Local effects of convective acAuthorsAthanasios Makris, Jessica R. Lacy, David R. FuhrmanCohesive sediment modeling in a shallow estuary: Model and environmental implications of sediment parameter variation
Numerical models of sediment transport in estuarine systems rely on parameter values that are often poorly constrained and can vary on timescales relevant to model processes. The selection of parameter values can affect the accuracy of model predictions, while environmental variation of these parameters can impact the temporal and spatial ranges of sediment fluxes, erosion, and deposition in the r
AuthorsRachel Allen, Jessica R. Lacy, Andrew W. StevensInfluence of invasive submerged aquatic vegetation (E. densa) on currents and sediment transport in a freshwater tidal system
We present a field study combining measurements of vegetation density, vegetative drag, and reduction of suspended-sediment concentration (SSC) within patches of the invasive submerged aquatic plant Egeria densa. Our study was motivated by concern that sediment trapping by E. densa, which has proliferated in the Sacramento–San Joaquin Delta, is impacting marsh accretion and reducing turbidity. In
AuthorsJessica R. Lacy, Madeline R. Foster-Martinez, Rachel M. Allen, Judith Z. DrexlerThe role of surges during periods of very shallow water on sediment transport over tidal flats
Periods of very shallow water (water depth in the order of 10 cm) occur daily on tidal flats because of the propagation of tides over very gently sloping beds, leading to distinct morphodynamical phenomena. To improve the understanding of the characteristics of velocity and suspended sediment concentration (SSC) surges and their contribution to sediment transport and local bed changes during perioAuthorsQian Zhang, Zheng Gong, Changkuan Zhang, Jessica R. Lacy, Bruce E. Jaffe, Beibei Xu, Xindi ChenCarbon storage and sediment trapping by Egeria densa Planch., a globally invasive, freshwater macrophyte
Invasive plants have long been recognized for altering ecosystem properties, but their long-term impacts on ecosystem processes remain largely unknown. In this study, we determined the impact of Egeria densa Planch, a globally invasive freshwater macrophyte, on sedimentation processes in a large tidal freshwater region. We measured carbon accumulation (CARs) and inorganic sedimentation rates in suAuthorsJudith Z. Drexler, Shruti Khanna, Jessica R. LacySeasonal variation in sediment delivery across the bay-marsh interface of an estuarine salt marsh
Sediment transport across bay–marsh interfaces depends on wave energy, vegetation, and marsh-edge morphology, and varies over a range of timescales. We investigated these dynamics in a tidal salt marsh with a gently-sloped, vegetated edge adjacent to northern San Francisco Bay. Spartina foliosa (cordgrass) inhabits the lower marsh and Salicornia pacifica (pickleweed) predominates on the marsh plainAuthorsJessica R. Lacy, Madeline R. Foster-Martinez, Rachel (Contractor) Allen, Matthew C. Ferner, John C. CallawaySeasonal, spring-neap, and tidal variation in cohesive sediment transport parameters in estuarine shallows
Numerical models for predicting sediment concentrations and transport rely on parameters such as settling velocity and bed erodibility that describe sediment characteristics, yet these parameters are rarely probed directly. We investigated temporal and spatial variation in sediment parameters in the shallows of San Pablo Bay, CA. Flow, turbulence, and suspended sediment data were measured at sites
AuthorsRachel Allen, Jessica R. Lacy, Mark T. Stacey, Evan A VarianoMeasuring settling velocity in a strongly tidal estuary
Predicting sediment transport in estuarine systems requires understanding sediment settling velocity, its range of fluctuations, and the shortcomings of the tools to measure it. Previous studies have used Laser In-Situ Scattering and Transmissometry (LISST) instruments to measure particle size and Acoustic Doppler Velocimeters (ADV) to return estimates of settling velocity. We deployed both instru
AuthorsRachel Allen, Jessica R. Lacy, Evan A VarianoBed shear stress estimation under wave conditions using near-bottom measurements: Comparison of methods
Understanding the influence of waves on bed shear stress is critical for predicting morphodynamical behaviours in coastal areas. Near-bed flow was measured on the middle and lower intertidal mudflats along the Jiangsu coast, China, using a three-dimensional acoustic velocimeter that collected a 3.5-cm vertical profile at 1mm resolution and sample rate of 25 Hz. On the lower and middle tidal flats,AuthorsQian Zhang, Zheng Gong, Changkuan Zhang, Jessica R. Lacy, Bruce E. Jaffe, Beibei XuThe influence of neap-spring tidal variation and wave energy on sediment flux in salt marsh tidal creeks
Sediment flux in marsh tidal creeks is commonly used to gage sediment supply to marshes. We conducted a field investigation of temporal variability in sediment flux in tidal creeks in the accreting tidal marsh at China Camp State Park adjacent to northern San Francisco Bay. Suspended-sediment concentration (SSC), velocity, and depth were measured near the mouths of two tidal creeks during threeAuthorsJessica R. Lacy, Matthew C. Ferner, John C. Callaway - News