Date Awarded


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Virginia Institute of Marine Science


Jian JS Shen

Committee Member

Mark Brush

Committee Member

Kimberly Reece

Committee Member

Joseph Zhang

Committee Member

Kyeong Park


Estuaries are highly productive and characterized by complex shoreline geometry and topography. Multiple materials produced within or transported into estuaries include non-living dissolved/particulate materials and living organisms. Estuarine circulation determines material transport and distributions, which further impact estuarine ecosystem to support abundant fauna/flora and their vulnerability to escalated anthropogenic inputs. Short-term material transport process in Chesapeake Bay (CB) has been studied for years, yet its long-term characteristics and the transport of materials with settling and biological behaviors that interact with physical transport have not been fully studied. This study aims to understand the transport of non-living and non-motile dissolved/particulate materials, and motile algae in the bay under different timescales, via hydrodynamic model, transport timescale, remote sensing, and an improved particle tracking model with algal bloom dynamics and vertical migrations.Freshwater discharge and northwesterly wind together contribute more than 90% of the spatiotemporal variations in water exchange (inflow and outflow) in CB at seasonal to annual scales. The outflow responds positively to river discharge, while the inflow increases with river discharge due to enhanced gravitational circulation, then levels, and gradually declines due to overwhelming seaward barotropic currents. A time lag should be considered when computing the mean residence time (RT) of an embayment via its volume and its outflow since RT depends on the forward hydrodynamics whereas outflow was determined by previous hydrodynamics. The geometry and topography of CB impact greatly on material transport. The shallow region near bay mouth, i.e., Rappahannock Shoal, increases water recirculation of surface outflow back into the middle to upper bay, thus, increases material (e.g., dissolved nutrients and organic matter) retention inside the bay. Besides topographic effects, gravitational circulation and river outflow dominate the transport of dissolved materials, whereas tidal contributions are localized near the mouth. For particulate materials, specifically the surface-produced particulates, settling, resuspension, and interactions with bottom sediments dominate their downward transport and vertical distributions. The contribution of freshwater discharge on vertical transport time is weak. The overall “shallow-deep-shallow” topography also prolongs the resting of particulates in the deep-channel sediments. For particulates with biological behaviors, such as the motile harmful algal species Margalefidinum polykrikoide, its vertical migration behaviors alter the transport pathways and bloom concentrations as the latter varies with surrounding environmental conditions. Like estuary is a diverse environment, material transport in CB is subject to different drivers, whose contributions to material transport are not easy to quantify and compare. Transport timescale can help compare the importance of different drivers under a common scale and understand complex aquatic ecosystems, e.g., quantifying retention efficiency associated with topography; quantifying material retention time in water column and sediments to compare transport time with biochemical processes; revealing that the near-mouth shallow region increasing the retention of dissolved and particulate materials inside the bay and regulating the ecosystem of CB. For harmful algal bloom that is highly regulated by shore-term transport and vertical migrations of algae, particle tracking technique with embedded algal bloom dynamics and behaviors could simulate multiple biophysical scales and form the basis for a bloom forecast system in CB.




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