By the USGS Pacific Coastal and Marine Science Center
The erodibility of bed sediment in estuaries can shape everything from water clarity to habitat quality, and influences the magnitude of sediment transport. While scientists largely understand how bed sediments in sandy environments erode, less attention has focused on muddy sediments in estuaries. New research from USGS shows that waves matter—but so do the animals living in the mud.
In a study conducted in the shallow waters of San Pablo Bay and Grizzly Bay in northern San Francisco Bay, scientists investigated what controls the erodibility of muddy sediments—how readily they are mobilized from the bayfloor and stirred up into the water column. The team collected detailed measurements during both summer 2019 and winter 2020, capturing seasonal contrasts in physical conditions and biological activity.
Using instruments deployed directly on the bayfloor, researchers tracked waves, currents, and suspended sediment concentrations over time. From these data, they calculated an erosion-rate parameter that quantifies how easily sediments are resuspended. In addition, samples of the seabed were collected to analyze sediment properties—such as grain size, density, and organic content—and to catalog the type and abundance of benthic animals living in the mud.
Across both bays, one physical driver stood out: waves. Stronger wave-driven shear stress consistently increased sediment erodibility, confirming that even in relatively sheltered estuaries, wave action plays a key role in mobilizing muddy bottoms.
However, in San Pablo Bay, sediments were about 50 percent less erodible in winter than in summer—a seasonal shift that could not be explained by waves or sediment properties alone. Instead, changes in the type and abundance of benthic animals, such as crustaceans, clams, and other invertebrates that live in or on the sediment, appeared to significantly alter how easily mud could be eroded. The lower erodibility in winter was attributed to increased abundance of the amphipod Ampelisca abdita, which creates small tubes in the sediment that can form dense mats, reducing the mobilization of bed sediment. In contrast, Grizzly Bay showed no strong seasonal change in erodibility, highlighting how local ecological differences can shape sediment behavior.
These findings underscore that muddy bay sediments are not just passive materials shaped by physics. They are living systems, where animals—both native and introduced—can stabilize or loosen sediments in ways that influence water clarity, nutrient transport, and habitat conditions. The results present a challenge to numerical models of sediment transport, which require specification of an erosion rate parameter.
RESEARCH PAPER: Biophysical Controls on Sediment Erodibility in Shallow Estuarine Embayments
By Jessica R. Lacy, Samantha C. McGill, Janet K. Thompson, Rachel M. Allen, Francis Parchaso, David Hart, Lukas T. WinklerPrins, Joseph Fackrell, Andrew W. Stevens
The erodibility of cohesive sediment is known to vary both spatially and temporally but the factors governing its variation are not well understood. We conducted a field investigation of the influence of hydrodynamic forcing, sediment properties, and benthic infauna on erodibility in the muddy shallows of San Pablo and Grizzly Bays in northern San Francisco Bay in summer 2019 and winter 2020. An erosion rate parameter was determined from regressions between near-bed vertical turbulent sediment flux, as a proxy for erosion, and bed shear stress due to currents. During each 2-month study period, we measured benthic infauna abundance and dry bulk density, particle size distribution, percent organic carbon, chlorophyll a, pheophytin a, and carbohydrates carbon concentrations of surficial bed sediments five or six times. increased with bed shear stress due to waves in both embayments. In San Pablo Bay, erodibility was approximately 50% lower during the winter than the summer deployment, whereas in Grizzly Bay, there was no significant difference. The factor most strongly related to the decrease in in San Pablo Bay was increased abundance of the amphipod Ampelisca abdita. The observed reduction in erodibility may occur in many muddy estuaries because A. abdita is broadly distributed in the coastal waters of North America. Erodibility was also directly related to biomass of the invasive clam Potamocorbula amurensis. Erodibility did not depend on dry bulk density: bulk density did not vary seasonally in San Pablo Bay and was lower in winter than summer in Grizzly Bay.
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