Date of Award

Spring 5-2025

Level of Access Assigned by Author

Open-Access Thesis

Language

English

Degree Name

Doctor of Philosophy (PhD)

Department

Civil Engineering

First Committee Advisor

Lauren Ross

Second Committee Member

Sean Smith

Third Committee Member

Gregory Gerbi

Additional Committee Members

Sean Birkel

Onur Apul

Abstract

As climate change and anthropogenic influences alter ecological conditions in interconnected watershed-estuary regions, there is an increasing need for science that supports decision-making related to shellfishing and aquaculture. To help water quality managers make more informed decisions affecting these industries, better understanding of how water-borne materials, like harmful algal blooms and bacterial pollution, are transported around coastlines is required. In this dissertation, the ways in which complex coastal features, like islands, channel constrictions, and bathymetric changes, alter circulation, the drivers of the resulting circulation patterns, and how these patterns are influenced by varying fortnightly tides and freshwater input are explored. Data collected in the field and from three-dimensional numerical simulations are used to investigate these topics. The study region for this work is Frenchman Bay, Maine, a coastal bay within the Gulf of Maine, USA, with a prolific, yet nascent, shellfish harvesting and aquaculture industry and a complex coastline partly formed by deglaciation ~15 kya.

The first chapter of this dissertation provides background and motivation for this study, defines the goal and research questions that guide it, and introduces the study region and the ongoing water quality issues there. In the second chapter, a field campaign was conducted to collect data including horizontal current velocities, turbulence, chlorophyll and Pseudo-nitzschia spp. cell abundance during a semidiurnal (~12.5 h) tidal cycle. Pseudo-nitzschia spp. are a genus of algae linked to recent harmful algal blooms in Frenchman Bay. The purpose of measuring of Pseudo-nitzschia spp. during the survey was therefore two-fold; to investigate their patterns as influenced by the circulation in the bay, and to serve as a proxy for material transport in general. The field data was coupled with a realistic numerical simulation to show that sub- mesoscale eddies (2−4 km diameter) influence the tidal circulation and dominate the residual circulation in the bay. Additional measurements of Pseudo-nitzschia spp. from two years of weekly sampling in the region reveal that algal cell abundance is highest where residual eddies form, indicating the potential for residual eddies to induce material accumulation “hot-spots” within the bay.

The identification of eddies in Frenchman Bay prompted further exploration into the driving mechanisms behind the circulation patterns in the third chapter of this dissertation. Idealized numerical simulations with forcing by tides and streamflow only are used to assess the relative influence of the fortnightly tidal phase and varying freshwater input on the formation of the eddies. The eddies are found to persist in the depth-averaged residual flow regardless of the freshwater forcing or tidal phase, leading to the conclusion that the eddies are “geomorphically-constrained” in the bay. Quantification of the terms in the horizontal momentum balance and a simulation performed without Coriolis forcing demonstrated that the tidal stresses (advection) predominantly balance the barotropic pressure gradient to give rise to the eddy patterns, while the Coriolis force acts to strengthen their vorticity. Freshwater input plays a larger role in modulating the residual circulation via the baroclinic pressure gradient when tidal forcing is weaker during neap tides.

To further investigate the impact of freshwater variability on the Frenchman Bay region, this work then zooms in to focus on the estuaries nearshore, where aquaculture farming and shellfishing activities are prevalent. The fourth chapter of this dissertation comprises a stakeholder-driven case study aimed to provide science-based evidence to inform closures and restrictions of shellfish harvesting regions within Frenchman Bay, implemented to avoid bacterial pollution exposure. Using hydrologic modeling coupled with idealized hydrodynamic modeling, this study explores a “worst-case scenario” for fecal coliform bacteria load concentrations in four of the region’s estuaries. Results suggest that the recovery of water quality in the days after the storm depends in part on the geometry of the estuary, which can alter the mechanisms driving the circulation. Narrow channel constrictions in the mid-reaches of an estuary act to separate the upper and lower portions of the system, resulting in two hydraulically disconnected systems. Estuaries with these features may have long recovery times upstream but be relatively unaffected by polluted freshwater downstream of the constriction.

Collectively, these studies illustrate potential impacts of coastline shape on water quality in complex regions like Frenchman Bay, which receive low freshwater input from numerous sources and have large tidal ranges. The findings of this work, including the location and persistence of the “geomorphically-constrained” eddies, their consequences for material transport, and the response of the Frenchman Bay region to anticipated increases in freshwater input due to climate change may be useful to those making decisions regarding aquaculture and shellfishing management in estuaries.

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