Estuarine navigation channels have long been recognized as conduits for saltwater intrusion into coastal wetlands. Salt flux decomposition and time series measurements of velocity and salinity were used to examine salt flux components and drivers of baroclinic and barotropic exchange in the Houma Navigation Channel, an estuarine channel located in the Mississippi River delta plain that receives substantial freshwater inputs from the Mississippi-Atchafalaya River system at its inland extent. Two modes of vertical current structure were identified from the time series data. The first mode, accounting for 90% of the total flow field variability, strongly resembled a barotropic current structure and was coherent with alongshelf wind stress over the coastal Gulf of Mexico. The second mode was indicative of gravitational circulation and was linked to variability in tidal stirring and the horizontal salinity gradient along the channel’s length. Tidal oscillatory salt flux was more important than gravitational circulation in transporting salt upestuary, except over equatorial phases of the fortnightly tidal cycle during times when river inflows were minimal. During all tidal cycles sampled, the advective flux, driven by a combination of freshwater discharge and wind-driven changes in storage, was the dominant transport term, and net flux of salt was always out of the estuary. These findings indicate that although human-made channels can effectively facilitate inland intrusion of saline water, this intrusion can be minimized or even reversed when they are subject to significant freshwater inputs.