Thesis advisor: Gail Kineke / The Penobscot River Estuary is heavily contaminated with mercury; previous studies indicate maximum mercury concentrations of 4.6 ppm within the Frankfort Flats reach. The transport and trapping of this contaminant is linked to the transport and trapping of fine sediment within the estuary. Hydrographic and flow measurements, coupled with a spatial and temporal characterization of the bottom sediments, were performed during and following the freshet in 2010 to determine the mechanisms driving sediment transport and trapping within the estuary. The Penobscot River likely has a turbidity maximum associated with the landward extent of the salinity intrusion that is positioned over the Frankfort Flats reach during average discharge and tidal conditions. This turbidity maximum may be responsible for a patch of fine sediments in the Frankfort Flats reach in an otherwise coarse-grained bed. Additional transport and trapping of fine sediments within this reach is the result of secondary circulation driven by centripetal acceleration around meanders in the channel. Close proximity of meanders at Frankfort Flats, within ~5 km, creates opposite secondary circulation of magnitude ~0.2 m/s during flood and ebb conditions. / Thesis (BS) — Boston College, 2011. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Geology & Geophysics Honors Program. / Discipline: Earth and Environmental Sciences.