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Accumulation and remineralization of surface‐produced particulate organic matter (POM) in the water column and seabed link closely to hypoxia and the health of aquatic ecosystems. The POM retention time provides a key timescale to interpret biochemical reaction processes. In this study, we investigated the spatiotemporal variations in the vertical particulate age (VPA) of surface‐produced POM, which is the mean time elapsed since the particulates last contact the surface, by incorporating major physical processes including sinking, resuspension, and deposition in the Chesapeake Bay. It was found that the vertical transport time for the particulates (i.e., VPA) is much longer than the dissolved counterparts as the former consists of new material from the surface and the resuspended aged material that has elongated resting on the seabed after deposition. The VPA is sensitive to settling velocity, especially in low‐frequent resuspension environments, and varies over 2 orders of magnitude with settling velocity from 0 to 10 m/day. Slow‐sinking material can remain in suspension and seldom settle to the seabed, thus mainly contribute to pelagic processes, while the fast‐sinking material connects closely with benthic processes. The seasonality of VPA decreases as the settling velocity increases. No significant difference in VPA was found between wet and dry years, yet the episodic strong flood events entrain old materials from the depositional lateral shoals to increase VPA in the channel. The transport age bridges cross disciplinaries by providing the fourth‐dimensional age information as a common currency to compare the physical transport timescale with the timescales for biochemical reactions. The Chesapeake Bay is a highly productive estuary, characterized by spring phytoplankton blooms and subsequent accumulations of particulate organic matter (POM) in the bottom layer, which fuels summertime hypoxia. The retention time of POM provides an important timescale to interpret biochemical reactions in estuaries. In this study, we applied the vertical particulate age (VPA), the average time elapsed since the POM leaving the surface, to estimate the downward‐transport time. The VPA accounts for all possible trajectories, including direct sinking and interactions with the seabed via resuspension and deposition. It was found that the VPA is much longer than the vertical transport time for dissolved material due to the elongated resting of particulates on the seabed and contributions from the resuspended old material. The VPA is sensitive to the settling velocity and increases 2 orders of magnitude with the settling velocity from 0 to 10 m/day in less dynamic environments. The slow‐sinking material can remain in suspension while the fast‐sinking material mostly stays on the seabed. No significant difference in the VPA was found between wet and dry years except during the episodic freshwater pulse, which brought aged materials from the depositional shoals to increase the VPA in the channel. The vertical particulate age (VPA) explains the time lag between the springtime algae blooms and the summertime hypoxia in the bayLong resting of particulates on the seabed and resuspension of the aged seabed material largely elongate the VPA in the water columnThe VPA is sensitive to settling velocity and episodic freshwater pulse. The latter entrains old material from shoals to the deep channel The vertical particulate age (VPA) explains the time lag between the springtime algae blooms and the summertime hypoxia in the bay Long resting of particulates on the seabed and resuspension of the aged seabed material largely elongate the VPA in the water column The VPA is sensitive to settling velocity and episodic freshwater pulse. The latter entrains old material from shoals to the deep channel

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. 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. 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 Density‐driven exchange flow and river outflow dominate the salt and riverine dissolved material transport in Chesapeake Bay River outflow dominates the transport of riverine dissolved materials upstream, while exchange flow dominates the transport downstream Rapid seaward shoaling causes strong reflux that increases material retention in the middle of the bay