The mechanisms driving the salt flux in the Modaomen estuary were investigated using measurements from along-channel shipboard surveys over a spring-neap tide cycle. During the investigation, river discharge was controlled to increase sharply and then decrease gently. The measurement data were analyzed with composition method. The results show that exchange flow varied significantly over the spring–neap cycle, being weakest during middle tides and strongest during neap tides. It could be concluded that sub-tidal vertical shear dispersion, resulting from the estuarine exchange flow, is the dominant mechanism driving the salt flux since the salt flux resulting from vertical shear dispersion varies in amplitude by over an order of magnitude, which is close to two times as large as the variation of advective salt flux.