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Sediment Cycling Through Subtidal and Intertidal Habitats: Lissa J. MacVean

Project Title: Sediment Cycling Through Subtidal and Intertidal Habitats
Mendenhall Fellow: Lissa J. MacVean, (831) 427-4738,
Duty Station: Santa Cruz, CA
Start Date: November 8, 2010
Education: Ph.D. (2010), Civil and Environmental Engineering, University of California, Berkeley
Research Advisor:Jessica Lacy, (831) 427-4720,; Bruce Jaffe, (831) 427-4742,; David Schoellhamer, (916) 278-3126,; Mark Stacey, (510) 642-6776,

Project Description: Estuarine sediment transport is complex in any environment and especially so in San Francisco Bay, where salt marsh restoration projects ranging from a few to tens of thousands of acres are currently underway. Two of the most important questions faced by estuarine restoration projects are whether the marsh plain will accrete enough sediment to sustain a viable ecosystem and whether this accretion will come at the expense of other, existing, intertidal habitats. The answers to these questions lie in the dynamics that control sediment exchange between the subtidal and intertidal environments (fig. 1). The subtidal regions of an estuary often serve as the avenue by which sediment is imported and exported to the system, and it is the mechanisms that drive the redistribution of sediment into the intertidal mudflats and marshes that will determine the success or failure of an effort to restore perimeter estuarine habitat. This research utilizes field measurements and numerical modeling to answer the question of what controls sediment exchanges between subtidal and intertidal habitats.

Research Questions

  1. What mechanisms control the magnitude, direction, and variability of sediment fluxes between subtidal and intertidal habitats?

    Other researchers (Lacy and others, 1996; Schoellhamer, 1996) have studied the large-scale cycling of sediment through the San Francisco Bay, and the resulting framework is one in which the magnitude of the suspended sediment concentration is controlled by the amount of available sediment provided by freshwater flows and resuspended by wind-waves. Fluxes between subtidal and intertidal habitats are expected to vary tidally as the daily and spring-neap tides rework the available sediment, as well as in response to wind and rain events.

  2. What controls resuspension of sediment from subtidal and intertidal habitats, and how does it differ for these two environments?

    Resuspension is a function of the erodability of the bed (for example, grain size, compaction, cohesion) and the energy available in the flow from tides, wind-waves, and turbulence. This question addresses the complex comparison of subtidal habitats, which are not exposed to air, and intertidal habitats, which periodically are. Drying, re-wetting, heating, and cooling of the intertidal bed may affect compaction and cohesion, which will impact rates of resuspension. These habitat-specific factors are then layered on top of the variability in resuspension due to tides, winds, and sediment supplies.

  3. What are the implications for salt marsh restoration?

    Once the underlying physics of sediment exchange are better understood, what can be concluded about the success of marsh restoration in estuaries?

Figure 1: Schematic of a shoal-channel system, with subtidal and intertidal regions.   Acoustic Doppler Velocimeters (Left) and an Acoustic Doppler Current Profiler (Right) mounted in aluminum frames for deployment.


Figure 1. Schematic of a shoal-channel system, with subtidal and intertidal regions.

Figure 2. Acoustic Doppler Velocimeters (left) and an Acoustic Doppler Current Profiler (right) mounted in aluminum frames for deployment.

Research Approach

A combination of field measurements and idealized numerical modeling are being used to answer the research questions.  Oceanographic instruments will be deployed to measure velocities, suspended sediment concentrations, and water properties, such as salinity and temperature. Wind waves are measured using high-frequency pressure sensors. The Acoustic Doppler Velocimeter (ADV) (fig. 2) measures both velocity and acoustic backscatter, which is then calibrated to mass concentration of suspended sediment. Because these measurements are collocated, the ADV is uniquely capable of capturing fluxes of suspended sediment (Brand and others, 2010; Voulgaris and Meyers, 2004). Turbulence timescales, as well as the daily tidal and spring-neap tidal timescales, will be resolved during these experiments.

A numerical modeling component will augment the insights gained through observation.  The model will utilize idealized shoal-channel bathymetry (fig. 3), and will be constructed using the open-source Regional Ocean Modeling System (ROMS) with the Community Sediment Transport Model (CSTM) and the Simulating Waves Nearshore (SWAN) module.  ROMS is a hydrostatic, three-dimensional, primitive equation code using modern turbulence closures, and it has been used widely for estuarine environments, including other idealized studies (for example, Chen and Sanford, 2009). 

Sample of idealized bathymetry used for numerical modeling
Figure 3. Sample of idealized bathymetry used for numerical modeling.

The idealized bathymetry allows an exploration of the subtidal/intertidal exchange without the confounding effects of complex terrain.  The domain will be uniform in the along-channel direction, and the effects of pertinent parameters–such as tides, freshwater inflow with varying sediment loads, winds and wind-waves, lateral bottom slope and shape, as well as sediment grain size, and changing bed characteristics and morphology–on exchange and resuspension will be investigated.


Brand, A., Lacy, J.R., Hsu, K., Hoover, D., Gladding, S., and Stacey, M.T., 2010, Wind-enhanced resuspension in the shallow waters of South San Francisco Bay: Mechanisms and potential implications for cohesive sediment transport: Journal of Geophysical Research, v. 115, no. C11024, 15 p. doi:10.1029/2010JC006172

Chen, S.-N., and Sanford, L.P., 2009, Lateral circulation driven by boundary mixing and the associated transport of sediments in idealized partially mixed estuaries: Continental Shelf Research, v. 29, no. 1), p.101–118.

Lacy, J., Schoellhamer, D., and Burau, J., 1996, Suspended-solids flux at a shallow-water site in South San Francisco Bay, California, in Proceedings of the North American Water and Environment Congress: Anaheim, Calif,: American Society of Civil Engineers.

Schoellhamer, D., 1996, Factors affecting suspended-solids concentrations in South San Francisco Bay, California: Journal of Geophysical Research, v. 101, no. C5,p. 12,087–12,095. Available at [last accessed May 3, 2011].

Voulgaris, G., and Meyers, S.T., 2004, Temporal variability of hydrodynamics, sediment concentration and sediment settling velocity in a tidal creek: Continental Shelf Research, v. 24, no. 15, p.1659–1683.

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