A tidally averaged model of estuarine dynamics is used to estimate sediment transport in the Hudson River estuary over the period 1918 to 2005. In long-term and seasonal means, along-channel gradients in sediment flux depend on the estuarine salinity gradient and along-channel depth profile. Lateral depth variation across the estuary affects the near-bottom baroclinic circulation and consequently the direction of net sediment flux, with generally up-estuary transport in the channel and down-estuary transport on the shoals. Sediment transport capacity in the lower estuary depends largely on river discharge, but is modified by the timing of discharge events with respect to the spring–neap cycle and subtidal fluctuations in sea level. Sediment transport capacity also depends on the duration of high-discharge events relative to the estuarine response time, a factor that varies seasonally with discharge and estuarine length. Sediment fluxes are calculated with the assumption that over long periods, the system approaches morphological equilibrium and sediment accumulation equals sea level rise. The inferred across- and along-channel distributions of sediment erodibility correspond with observations of bed properties. Equilibrium is assumed at long time scales, but at annual to decadal time scales the estuary can develop an excess or deficit of sediment relative to equilibrium. On average, sediment accumulates in the estuary during low- and high-discharge periods and is exported during moderate discharge. During high-discharge periods, maximum export coincides with maximum sediment supply from the watershed, but the nearly cubic discharge dependence of fluvial sediment supply overwhelms the roughly linear increase in estuarine transport capacity. Consequently, sediment accumulates in the estuary during the highest flow conditions. Uncertainty remains in the model, particularly with sediment properties and boundary conditions, but the results clearly indicate variability in the sediment mass balance over long time scales due to discharge events.