Three-dimensional numerical modeling is performed to study intratidal and along-channel variability in stratification and mixing in the Hudson River estuary. The modeled fields show good agreement with observations, both qualitatively and quantitatively. Estuarine circulation dominates the mean fields, and intratidal variability is dominated by tidal straining that acts to strengthen the stratification during ebb and weaken it during flood. Mixing is mainly confined to a bottom layer during flood but occurs higher up in the water column during ebb. Mixing across the halocline shows marked along-channel variability due to bathymetric effects. During ebb, mixing occurs preferentially at an abrupt channel expansion seaward of a channel constriction at the George Washington Bridge, as predicted by Chant and Wilson <2000>. The salt flux across the halocline in this region, averaged over ebb, exceeds 5 ¿ 10-4 kg m-2 s-1, a factor of 3 greater than the along-channel average. Increased residence time of tracers should be expected in this region due to the strong mixing but also due to observed secondary circulation <Chant and Wilson, 1997>. Mixing across the halocline during flood is small, except for early flood, before the well-mixed bottom layer is developed. Mixing is then localized to the landward slope of sills.