The transport of salt along the channel of an estuary determines the length of the saline intrusion and provides bounds on the transfer of other substances. Observations of salt transport have been hampered by a lack of long time series measurements and complexities of the sampling situation (e.g., local topography and simultaneous variations of tides, freshwater, and winds). Here we estimate salt transport at a relatively uniform section of the Hudson Estuary over a 70-day period during drought conditions. The salt balance of the estuary is also assessed by comparing salt transport at the section with surveys of total salt content in the estuary. Most salt enters the estuary in monthly pulses of estuarine salt transport (i.e., spatial variations of tidally-averaged velocity and salinity) during apogean neap tides when vertical stratification is greatest. Oscillatory salt transport (i.e., the covariance of tidally-varying velocity and salinity) is a more minor player in the salt balance and shows a surprising lack of spring-neap variation. Integrated salt transport at the section is consistent with estimates of total salt content of the estuary; however, the mismatch in magnitude of the variations indicates that the salinity intrusion is not in equilibrium within the spring-neap cycle. In contrast, the salt balance adjusts rapidly to an increase in freshwater flow at the end of the deployment. A scaling argument is derived to illustrate the adjustment of the salinity intrusion to the tides and freshwater flow. The results suggest that time dependence is an intrinsic part of the estuarine salt balance.