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Particle tracking is widely utilized to study transport features in a range of physical, chemical, and biological processes in oceanography. In this study, a new offline particle-tracking package, Tracker v1.1, is introduced, and its performance is evaluated in comparison to an online Eulerian dye, one online particle-tracking software package, and three offline particle-tracking software packages in a small, high-resolution model domain and a large coarser model domain. It was found that both particle and dye approaches give similar results across different model resolutions and domains when they were tracking the same water mass, as indicated by similar mean advection pathways and spatial distributions of dye and particles. The flexibility of offline particle tracking and its similarity against online dye and online particle tracking make it a useful tool to complement existing ocean circulation models. The new Tracker was shown to be a reliable particle-tracking package to complement the Regional Ocean Modeling System (ROMS) with the advantages of platform independence and speed improvements, especially in large model domains achieved by the nearest-neighbor search algorithm. Lastly, trade-offs of computational efficiency, modifiability, and ease of use that can influence the choice of which package to use are explored. The main value of the present study is that the different particle and dye tracking codes were all run on the same model output or within the model that generated the output. This allows some measure of intercomparison between the different tracking schemes, and we conclude that all choices that make each tracking package unique do not necessarily lead to very different results. [ABSTRACT FROM AUTHOR]

Most estuaries are characterized by non‐uniform axial topography with shallow shoals near the mouth. Previous studies have addressed the impacts of the axial topographic variations on mixing and estuarine circulations yet seldom on material transport and retention. This study investigates the longitudinal structure and mechanisms of exchange flow and material transport of Chesapeake Bay (CB), featuring a shallow sill in the lower bay, by applying total exchange flow (TEF) algorithm, tracer experiments, and partial residence time (PRT) using a validated 32‐years numerical model simulation. A retention coefficient was adopted to quantify the material retention rate using two characteristic PRTs: with and without incorporating water parcels returning to a concerned region. It is found that shoaling from the Rappahannock Shoal to the mouth causes persistent downwelling, strong reflux, and the highest material retention rate in the middle of the bay. The gravitational circulation and the river outflow dominate the transport of salt and riverine dissolved materials (RDMs), whereas the contribution of the tidal oscillatory process is localized near the mouth. The dominance of river outflow over the gravitational circulation for transporting RDMs is confined within the upper bay, where PRTs exhibit distinct seasonality. PRTs show small seasonality in the middle to the lower bay controlled by the exchange flow. The present analysis combining TEF, efflux/reflux theory, and PRT is applicable to other coastal aquatic ecosystems to characterize the water exchange and renewal efficiency along the salinity gradient and understand the contributions of transport to biogeochemical processes. Plain Language Summary: Chesapeake Bay (CB) is the largest estuary in the United States, with a major deep channel indented by a shallow sill in the lower bay. The longitudinal topography of CB can be characterized as "Shallow‐Deep‐Shallow." Previous studies in other estuaries addressed the impact of the axial topographic variations on estuarine hydrodynamics yet seldom on material transport and retention, such as the retention time of organic matter, an important indicator for hypoxia issue. This study examines how the particular longitudinal topography affects the transport of salt (from the coastal ocean) and riverine dissolved materials (RDMs, from the river) by using a 32‐years numerical model simulation. We find that the shallow sill will obviously increase the retention time of RDMs upstream of the shoal, mainly because the abrupt shoaling near the shoal results in strong mixing and reflux of the surface outflow, associated with the surface velocity convergence and resultant downwelling. Exchange flow (i.e., surface outflow and bottom inflow) and river outflow dominate the transports of salt and RDMs in CB, whereas the contribution from the tidal process is localized near the mouth. It is also found the shallow sill will not block the exchange flow, which increases monotonically toward downstream. Key Points: Density‐driven exchange flow and river outflow dominate the salt and riverine dissolved material transport in Chesapeake BayRiver outflow dominates the transport of riverine dissolved materials upstream, while exchange flow dominates the transport downstreamRapid seaward shoaling causes strong reflux that increases material retention in the middle of the bay [ABSTRACT FROM AUTHOR]